diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 56fcf548e6..b20118794f 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -22,33 +22,33 @@ src/MESSAGE/* @sjplimp src/MLIAP/* @athomps src/SNAP/* @athomps src/SPIN/* @julient31 -src/USER-BROWNIAN/* @samueljmcameron -src/USER-CGDNA/* @ohenrich -src/USER-CGSDK/* @akohlmey -src/USER-COLVARS/* @giacomofiorin -src/USER-DIELECTRIC/* @ndtrung81 -src/USER-FEP/* @agiliopadua -src/USER-HDNNP/* @singraber -src/USER-INTEL/* @wmbrownintel -src/USER-MANIFOLD/* @Pakketeretet2 -src/USER-MDI/* @taylor-a-barnes -src/USER-MEAMC/* @martok -src/USER-MESONT/* @iafoss -src/USER-MOFFF/* @hheenen -src/USER-MOLFILE/* @akohlmey -src/USER-NETCDF/* @pastewka -src/USER-PACE/* @yury-lysogorskiy -src/USER-PLUMED/* @gtribello -src/USER-PHONON/* @lingtikong -src/USER-PTM/* @pmla -src/USER-OMP/* @akohlmey -src/USER-QMMM/* @akohlmey -src/USER-REAXC/* @hasanmetin -src/USER-REACTION/* @jrgissing -src/USER-SCAFACOS/* @rhalver -src/USER-TALLY/* @akohlmey -src/USER-UEF/* @danicholson -src/USER-VTK/* @rbberger +src/BROWNIAN/* @samueljmcameron +src/CG-DNA/* @ohenrich +src/CG-SDK/* @akohlmey +src/COLVARS/* @giacomofiorin +src/DIELECTRIC/* @ndtrung81 +src/FEP/* @agiliopadua +src/ML-HDNNP/* @singraber +src/INTEL/* @wmbrownintel +src/MANIFOLD/* @Pakketeretet2 +src/MDI/* @taylor-a-barnes +src/MEAM/* @martok +src/MESONT/* @iafoss +src/MOFFF/* @hheenen +src/MOLFILE/* @akohlmey +src/NETCDF/* @pastewka +src/ML-PACE/* @yury-lysogorskiy +src/PLUMED/* @gtribello +src/PHONON/* @lingtikong +src/PTM/* @pmla +src/OPENMP/* @akohlmey +src/QMMM/* @akohlmey +src/REAXFF/* @hasanmetin +src/REACTION/* @jrgissing +src/SCAFACOS/* @rhalver +src/TALLY/* @akohlmey +src/UEF/* @danicholson +src/VTK/* @rbberger # individual files in packages @@ -138,7 +138,7 @@ unittest/* @akohlmey @rbberger # cmake cmake/* @junghans @rbberger -cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin +cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167 cmake/presets/*.cmake @akohlmey diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 31b9becc0c..54cb975723 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -74,13 +74,13 @@ Here is a checklist of steps you need to follow to submit a single file or user * For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included ( instead of , or instead of ). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages. * Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'. * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `.cpp` and `.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features. -* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory. +* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this FOO directory. * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code. -* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`. -* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind +* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file. For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`. +* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/PACKAGES for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind * For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree. * When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.). -* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the .cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide. +* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the .cpp source file. See src/EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide. Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature. diff --git a/.gitignore b/.gitignore index 0f1b01775d..14d9dbebc9 100644 --- a/.gitignore +++ b/.gitignore @@ -12,6 +12,7 @@ *.sif *.dll *.pyc +a.out __pycache__ Obj_* diff --git a/bench/POTENTIALS/in.meamc b/bench/POTENTIALS/in.meam similarity index 94% rename from bench/POTENTIALS/in.meamc rename to bench/POTENTIALS/in.meam index 0739b49411..9c6e06cd4d 100644 --- a/bench/POTENTIALS/in.meamc +++ b/bench/POTENTIALS/in.meam @@ -8,7 +8,7 @@ region box block 0 20 0 20 0 20 create_box 1 box create_atoms 1 box -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 velocity all create 1600.0 376847 loop geom diff --git a/bench/POTENTIALS/log.9Oct20.meamc.1 b/bench/POTENTIALS/log.9Oct20.meam.1 similarity index 96% rename from bench/POTENTIALS/log.9Oct20.meamc.1 rename to bench/POTENTIALS/log.9Oct20.meam.1 index d6bebcd664..03e027674f 100644 --- a/bench/POTENTIALS/log.9Oct20.meamc.1 +++ b/bench/POTENTIALS/log.9Oct20.meam.1 @@ -15,7 +15,7 @@ create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.002 seconds -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -38,12 +38,12 @@ Neighbor list info ... ghost atom cutoff = 5 binsize = 2.5, bins = 29 29 29 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/bench/POTENTIALS/log.9Oct20.meamc.4 b/bench/POTENTIALS/log.9Oct20.meam.4 similarity index 96% rename from bench/POTENTIALS/log.9Oct20.meamc.4 rename to bench/POTENTIALS/log.9Oct20.meam.4 index 4ccae5ddce..fa343e33b5 100644 --- a/bench/POTENTIALS/log.9Oct20.meamc.4 +++ b/bench/POTENTIALS/log.9Oct20.meam.4 @@ -15,7 +15,7 @@ create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.001 seconds -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -38,12 +38,12 @@ Neighbor list info ... ghost atom cutoff = 5 binsize = 2.5, bins = 29 29 29 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/bench/POTENTIALS/log.9Oct20.reaxc.1 b/bench/POTENTIALS/log.9Oct20.reaxc.1 index fc89a32c85..86e35aa664 100644 --- a/bench/POTENTIALS/log.9Oct20.reaxc.1 +++ b/bench/POTENTIALS/log.9Oct20.reaxc.1 @@ -24,7 +24,7 @@ velocity all create 300.0 9999 pair_style reax/c NULL pair_coeff * * ffield.reax C H O N -WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315) +WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxc_ffield.cpp:315) timestep 0.1 fix 1 all nve diff --git a/bench/POTENTIALS/log.9Oct20.reaxc.4 b/bench/POTENTIALS/log.9Oct20.reaxc.4 index c72cc9185d..f83ad2a05a 100644 --- a/bench/POTENTIALS/log.9Oct20.reaxc.4 +++ b/bench/POTENTIALS/log.9Oct20.reaxc.4 @@ -24,7 +24,7 @@ velocity all create 300.0 9999 pair_style reax/c NULL pair_coeff * * ffield.reax C H O N -WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315) +WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxc_ffield.cpp:315) timestep 0.1 fix 1 all nve diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index ab1fd6bba6..a64d18a6da 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -138,17 +138,86 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR}) option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) -set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE - GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS - PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK - USER-COLVARS USER-DIELECTRIC USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-H5MD USER-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT - USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB - USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN) +set(STANDARD_PACKAGES + ADIOS + ASPHERE + ATC + AWPMD + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + FEP + GRANULAR + H5MD + KIM + KSPACE + LATBOLTZ + LATTE + MACHDYN + MANIFOLD + MANYBODY + MC + MDI + MEAM + MESONT + MESSAGE + MGPT + MISC + ML-HDNNP + ML-IAP + ML-PACE + ML-QUIP + ML-RANN + ML-SNAP + MOFFF + MOLECULE + MOLFILE + MPIIO + MSCG + NETCDF + PERI + PHONON + PLUGIN + PLUMED + POEMS + PTM + PYTHON + QEQ + QMMM + QTB + REACTION + REAXFF + REPLICA + RIGID + SCAFACOS + SHOCK + SMTBQ + SPH + SPIN + SRD + TALLY + UEF + USER-MISC + VORONOI + VTK + YAFF) -set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP) +set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP) foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) @@ -159,7 +228,7 @@ endforeach() ###################################################### target_include_directories(lammps PUBLIC $) -if(PKG_USER-ADIOS) +if(PKG_ADIOS) # The search for ADIOS2 must come before MPI because # it includes its own MPI search with the latest FindMPI.cmake # script that defines the MPI::MPI_C target @@ -229,13 +298,13 @@ endif() # "hard" dependencies between packages resulting # in an error instead of skipping over files -pkg_depends(MLIAP SNAP) +pkg_depends(ML-IAP ML-SNAP) pkg_depends(MPIIO MPI) -pkg_depends(USER-ATC MANYBODY) -pkg_depends(USER-LB MPI) -pkg_depends(USER-PHONON KSPACE) -pkg_depends(USER-SCAFACOS MPI) -pkg_depends(USER-DIELECTRIC KSPACE) +pkg_depends(ATC MANYBODY) +pkg_depends(LATBOLTZ MPI) +pkg_depends(PHONON KSPACE) +pkg_depends(SCAFACOS MPI) +pkg_depends(DIELECTRIC KSPACE) # detect if we may enable OpenMP support by default set(BUILD_OMP_DEFAULT OFF) @@ -271,7 +340,7 @@ if(BUILD_OMP) target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX) endif() -if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) +if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE) enable_language(C) find_package(LAPACK) find_package(BLAS) @@ -350,8 +419,8 @@ else() set(CUDA_REQUEST_PIC) endif() -foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-HDNNP USER-MDI USER-MOLFILE USER-NETCDF - USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE) +foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF + PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() @@ -444,9 +513,8 @@ endforeach() ############################################## # add lib sources of (simple) enabled packages ############################################ -foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT) - if(PKG_${SIMPLE_LIB}) - string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") +foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT) + if(PKG_${PKG_LIB}) string(TOLOWER "${PKG_LIB}" PKG_LIB) if(PKG_LIB STREQUAL "mesont") enable_language(Fortran) @@ -470,13 +538,13 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT) endif() endforeach() -if(PKG_USER-AWPMD) +if(PKG_AWPMD) target_link_libraries(awpmd PRIVATE ${LAPACK_LIBRARIES}) endif() -if(PKG_USER-ATC) +if(PKG_ATC) if(LAMMPS_SIZES STREQUAL "BIGBIG") - message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG") + message(FATAL_ERROR "The ATC Package is not compatible with -DLAMMPS_BIGBIG") endif() target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES}) if(BUILD_MPI) @@ -488,15 +556,15 @@ if(PKG_USER-ATC) target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES}) endif() -if(PKG_USER-H5MD) - include(Packages/USER-H5MD) +if(PKG_H5MD) + include(Packages/H5MD) endif() ###################################################################### # packages which selectively include variants based on enabled styles # e.g. accelerator packages ###################################################################### -foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU) +foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() diff --git a/cmake/Modules/FindN2P2.cmake b/cmake/Modules/FindN2P2.cmake index 8a97b7dd81..597e3e4609 100644 --- a/cmake/Modules/FindN2P2.cmake +++ b/cmake/Modules/FindN2P2.cmake @@ -22,7 +22,7 @@ find_library(N2P2_LIBNNPIF NAMES nnpif HINTS "${N2P2_DIR}/lib") # # target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS) # -# to "lib/lammps-extra.cmake" which is then included by USER-HDNNP.cmake. +# to "lib/lammps-extra.cmake" which is then included by ML-HDNNP.cmake. find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake HINTS "${N2P2_DIR}/lib") find_package_handle_standard_args(N2P2 DEFAULT_MSG diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake index 6cb23db12a..74102ab244 100644 --- a/cmake/Modules/LAMMPSUtils.cmake +++ b/cmake/Modules/LAMMPSUtils.cmake @@ -67,7 +67,7 @@ endfunction() macro(pkg_depends PKG1 PKG2) if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2})) - message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}") + message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be build with the ${PKG2} package") endif() endmacro() diff --git a/cmake/Modules/Packages/USER-COLVARS.cmake b/cmake/Modules/Packages/COLVARS.cmake similarity index 100% rename from cmake/Modules/Packages/USER-COLVARS.cmake rename to cmake/Modules/Packages/COLVARS.cmake diff --git a/cmake/Modules/Packages/USER-SDPD.cmake b/cmake/Modules/Packages/DPD-SMOOTH.cmake similarity index 50% rename from cmake/Modules/Packages/USER-SDPD.cmake rename to cmake/Modules/Packages/DPD-SMOOTH.cmake index c9f419d918..c5271d9091 100644 --- a/cmake/Modules/Packages/USER-SDPD.cmake +++ b/cmake/Modules/Packages/DPD-SMOOTH.cmake @@ -1,13 +1,13 @@ # Fix rigid/meso requires RIGID to be installed -set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD) +set(DPD-SMOOTH_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/DPD-SMOOTH) get_property(hlist GLOBAL PROPERTY FIX) if(NOT PKG_RIGID) - list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h) + list(REMOVE_ITEM hlist ${DPD-SMOOTH_SOURCES_DIR}/fix_rigid_meso.h) get_target_property(LAMMPS_SOURCES lammps SOURCES) - list(REMOVE_ITEM LAMMPS_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp) + list(REMOVE_ITEM LAMMPS_SOURCES ${DPD-SMOOTH_SOURCES_DIR}/fix_rigid_meso.cpp) set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES}) endif() set_property(GLOBAL PROPERTY FIX "${hlist}") -target_include_directories(lammps PRIVATE ${USER-SDPD_SOURCES_DIR}) +target_include_directories(lammps PRIVATE ${DPD-SMOOTH_SOURCES_DIR}) diff --git a/cmake/Modules/Packages/USER-H5MD.cmake b/cmake/Modules/Packages/H5MD.cmake similarity index 100% rename from cmake/Modules/Packages/USER-H5MD.cmake rename to cmake/Modules/Packages/H5MD.cmake diff --git a/cmake/Modules/Packages/USER-INTEL.cmake b/cmake/Modules/Packages/INTEL.cmake similarity index 67% rename from cmake/Modules/Packages/USER-INTEL.cmake rename to cmake/Modules/Packages/INTEL.cmake index ecad135b70..fee86dc870 100644 --- a/cmake/Modules/Packages/USER-INTEL.cmake +++ b/cmake/Modules/Packages/INTEL.cmake @@ -5,7 +5,7 @@ endif() target_compile_definitions(lammps PRIVATE -DLMP_USER_INTEL) -set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)") +set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by INTEL (cpu or knl)") set(INTEL_ARCH_VALUES cpu knl) set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES}) validate_option(INTEL_ARCH INTEL_ARCH_VALUES) @@ -40,10 +40,10 @@ endif() if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16) - message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") + message(FATAL_ERROR "INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") endif() else() - message(WARNING "USER-INTEL gives best performance with Intel compilers") + message(WARNING "INTEL gives best performance with Intel compilers") endif() find_package(TBB_MALLOC QUIET) @@ -52,7 +52,7 @@ if(TBB_MALLOC_FOUND) else() target_compile_definitions(lammps PRIVATE -DLMP_INTEL_NO_TBB) if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") - message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries") + message(WARNING "INTEL with Intel compilers should use TBB malloc libraries") endif() endif() @@ -65,12 +65,12 @@ else() endif() if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256")) - message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform") + message(FATAL_ERROR "INTEL only supports memory alignment of 64, 128 or 256 on this platform") endif() if(INTEL_ARCH STREQUAL "KNL") if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel") - message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture") + message(FATAL_ERROR "Must use Intel compiler with INTEL for KNL architecture") endif() set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload") set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"") @@ -91,26 +91,26 @@ else() endif() # collect sources -set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL) -set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp - ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp - ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp - ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp - ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp) +set(INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/INTEL) +set(INTEL_SOURCES ${INTEL_SOURCES_DIR}/fix_intel.cpp + ${INTEL_SOURCES_DIR}/fix_nh_intel.cpp + ${INTEL_SOURCES_DIR}/intel_buffers.cpp + ${INTEL_SOURCES_DIR}/nbin_intel.cpp + ${INTEL_SOURCES_DIR}/npair_intel.cpp) -set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}") +set_property(GLOBAL PROPERTY "INTEL_SOURCES" "${INTEL_SOURCES}") -# detect styles which have a USER-INTEL version -RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES) -RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h) -RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h) -RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h) +# detect styles which have a INTEL version +RegisterStylesExt(${INTEL_SOURCES_DIR} intel INTEL_SOURCES) +RegisterNBinStyle(${INTEL_SOURCES_DIR}/nbin_intel.h) +RegisterNPairStyle(${INTEL_SOURCES_DIR}/npair_intel.h) +RegisterFixStyle(${INTEL_SOURCES_DIR}/fix_intel.h) -get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES) +get_property(INTEL_SOURCES GLOBAL PROPERTY INTEL_SOURCES) if(PKG_KSPACE) - list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp) - RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h) + list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp) + RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h) endif() -target_sources(lammps PRIVATE ${USER-INTEL_SOURCES}) -target_include_directories(lammps PRIVATE ${USER-INTEL_SOURCES_DIR}) +target_sources(lammps PRIVATE ${INTEL_SOURCES}) +target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR}) diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index 234c1f140d..e97f5546cd 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -116,7 +116,7 @@ RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h) RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h) RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h) -if(PKG_USER-DPD) +if(PKG_DPD-REACT) get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES) list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp) RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h) diff --git a/cmake/Modules/Packages/USER-SMD.cmake b/cmake/Modules/Packages/MACHDYN.cmake similarity index 100% rename from cmake/Modules/Packages/USER-SMD.cmake rename to cmake/Modules/Packages/MACHDYN.cmake diff --git a/cmake/Modules/Packages/USER-MDI.cmake b/cmake/Modules/Packages/MDI.cmake similarity index 100% rename from cmake/Modules/Packages/USER-MDI.cmake rename to cmake/Modules/Packages/MDI.cmake diff --git a/cmake/Modules/Packages/USER-HDNNP.cmake b/cmake/Modules/Packages/ML-HDNNP.cmake similarity index 100% rename from cmake/Modules/Packages/USER-HDNNP.cmake rename to cmake/Modules/Packages/ML-HDNNP.cmake diff --git a/cmake/Modules/Packages/MLIAP.cmake b/cmake/Modules/Packages/ML-IAP.cmake similarity index 78% rename from cmake/Modules/Packages/MLIAP.cmake rename to cmake/Modules/Packages/ML-IAP.cmake index 81bb10cb8f..63f91ba8d3 100644 --- a/cmake/Modules/Packages/MLIAP.cmake +++ b/cmake/Modules/Packages/ML-IAP.cmake @@ -1,4 +1,4 @@ -# if PYTHON package is included we may also include Python support in MLIAP +# if PYTHON package is included we may also include Python support in ML-IAP set(MLIAP_ENABLE_PYTHON_DEFAULT OFF) if(PKG_PYTHON) find_package(Cythonize QUIET) @@ -7,25 +7,25 @@ if(PKG_PYTHON) endif() endif() -option(MLIAP_ENABLE_PYTHON "Build MLIAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT}) +option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT}) if(MLIAP_ENABLE_PYTHON) find_package(Cythonize REQUIRED) if(NOT PKG_PYTHON) - message(FATAL_ERROR "Must enable PYTHON package for including Python support in MLIAP") + message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP") endif() if(CMAKE_VERSION VERSION_LESS 3.12) if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6) - message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later") + message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later") endif() else() if(Python_VERSION VERSION_LESS 3.6) - message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later") + message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later") endif() endif() set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython) - set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx) + set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx) get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE) file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR}) add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/ML-PACE.cmake similarity index 100% rename from cmake/Modules/Packages/USER-PACE.cmake rename to cmake/Modules/Packages/ML-PACE.cmake diff --git a/cmake/Modules/Packages/USER-QUIP.cmake b/cmake/Modules/Packages/ML-QUIP.cmake similarity index 100% rename from cmake/Modules/Packages/USER-QUIP.cmake rename to cmake/Modules/Packages/ML-QUIP.cmake diff --git a/cmake/Modules/Packages/USER-MOLFILE.cmake b/cmake/Modules/Packages/MOLFILE.cmake similarity index 100% rename from cmake/Modules/Packages/USER-MOLFILE.cmake rename to cmake/Modules/Packages/MOLFILE.cmake diff --git a/cmake/Modules/Packages/USER-NETCDF.cmake b/cmake/Modules/Packages/NETCDF.cmake similarity index 89% rename from cmake/Modules/Packages/USER-NETCDF.cmake rename to cmake/Modules/Packages/NETCDF.cmake index d63e9773c3..2e521b81b0 100644 --- a/cmake/Modules/Packages/USER-NETCDF.cmake +++ b/cmake/Modules/Packages/NETCDF.cmake @@ -1,4 +1,4 @@ -# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary. +# NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary. # NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio" # may use NetCDF or PNetCDF with MPI, but must have NetCDF without diff --git a/cmake/Modules/Packages/OPENMP.cmake b/cmake/Modules/Packages/OPENMP.cmake new file mode 100644 index 0000000000..922df86ef6 --- /dev/null +++ b/cmake/Modules/Packages/OPENMP.cmake @@ -0,0 +1,40 @@ + set(OPENMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPENMP) + set(OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/thr_data.cpp + ${OPENMP_SOURCES_DIR}/thr_omp.cpp + ${OPENMP_SOURCES_DIR}/fix_omp.cpp + ${OPENMP_SOURCES_DIR}/fix_nh_omp.cpp + ${OPENMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp + ${OPENMP_SOURCES_DIR}/domain_omp.cpp) + target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP) + set_property(GLOBAL PROPERTY "OMP_SOURCES" "${OPENMP_SOURCES}") + + # detects styles which have OPENMP version + RegisterStylesExt(${OPENMP_SOURCES_DIR} omp OMP_SOURCES) + RegisterFixStyle(${OPENMP_SOURCES_DIR}/fix_omp.h) + + get_property(OPENMP_SOURCES GLOBAL PROPERTY OMP_SOURCES) + + # manually add package dependent source files from OPENMP that do not provide styles + + if(PKG_ASPHERE) + list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp) + endif() + + if(PKG_RIGID) + list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp) + endif() + + if(PKG_REAXFF) + list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxc_bonds_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxc_init_md_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxc_forces_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp + ${OPENMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp) + endif() + + target_sources(lammps PRIVATE ${OPENMP_SOURCES}) + target_include_directories(lammps PRIVATE ${OPENMP_SOURCES_DIR}) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/PLUMED.cmake similarity index 100% rename from cmake/Modules/Packages/USER-PLUMED.cmake rename to cmake/Modules/Packages/PLUMED.cmake diff --git a/cmake/Modules/Packages/USER-QMMM.cmake b/cmake/Modules/Packages/QMMM.cmake similarity index 100% rename from cmake/Modules/Packages/USER-QMMM.cmake rename to cmake/Modules/Packages/QMMM.cmake diff --git a/cmake/Modules/Packages/USER-SCAFACOS.cmake b/cmake/Modules/Packages/SCAFACOS.cmake similarity index 100% rename from cmake/Modules/Packages/USER-SCAFACOS.cmake rename to cmake/Modules/Packages/SCAFACOS.cmake diff --git a/cmake/Modules/Packages/USER-OMP.cmake b/cmake/Modules/Packages/USER-OMP.cmake deleted file mode 100644 index a1053ad355..0000000000 --- a/cmake/Modules/Packages/USER-OMP.cmake +++ /dev/null @@ -1,40 +0,0 @@ - set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP) - set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp - ${USER-OMP_SOURCES_DIR}/thr_omp.cpp - ${USER-OMP_SOURCES_DIR}/fix_omp.cpp - ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp - ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp - ${USER-OMP_SOURCES_DIR}/domain_omp.cpp) - target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP) - set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}") - - # detects styles which have USER-OMP version - RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES) - RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h) - - get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES) - - # manually add package dependent source files from USER-OMP that do not provide styles - - if(PKG_ASPHERE) - list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp) - endif() - - if(PKG_RIGID) - list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp) - endif() - - if(PKG_USER-REAXC) - list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp - ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp) - endif() - - target_sources(lammps PRIVATE ${USER-OMP_SOURCES}) - target_include_directories(lammps PRIVATE ${USER-OMP_SOURCES_DIR}) diff --git a/cmake/Modules/Packages/USER-VTK.cmake b/cmake/Modules/Packages/VTK.cmake similarity index 100% rename from cmake/Modules/Packages/USER-VTK.cmake rename to cmake/Modules/Packages/VTK.cmake diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 457750c690..c95d3e8463 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -1,17 +1,90 @@ -# preset that turns on all existing packages off. can be used to reset +# Preset that turns on all existing packages off. Can be used to reset # an existing package selection without losing any other settings -set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE - MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN - SRD VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC) +set(ALL_PACKAGES + ADIOS + ASPHERE + ATC + AWPMD + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + CORESHELL + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + FEP + GPU + GRANULAR + H5MD + INTEL + KIM + KOKKOS + KSPACE + LATBOLTZ + LATTE + MACHDYN + MANIFOLD + MANYBODY + MC + MDI + MEAM + MESONT + MESSAGE + MGPT + MISC + ML-HDNNP + ML-IAP + ML-PACE + ML-QUIP + ML-RANN + ML-SNAP + MOFFF + MOLECULE + MOLFILE + MPIIO + MSCG + NETCDF + OPENMP + OPT + PERI + PHONON + PLUGIN + PLUMED + POEMS + PTM + PYTHON + QEQ + QMMM + QTB + REACTION + REAXFF + REPLICA + RIGID + SCAFACOS + SHOCK + SMTBQ + SPH + SPIN + SRD + TALLY + UEF + USER-MISC + VORONOI + VTK + YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index ae40bb0809..bc7ae553db 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -1,19 +1,92 @@ -# preset that turns on all existing packages. using the combination -# this preset followed by the nolib.cmake preset should configure a -# LAMMPS binary, with as many packages included, that can be compiled +# Preset that turns on all existing packages. Using the combination +# of this preset followed by the nolib.cmake preset should configure +# a LAMMPS binary, with as many packages included, that can be compiled # with just a working C++ compiler and an MPI library. -set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE - MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN - SRD VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP - USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN - USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC) +set(ALL_PACKAGES + ADIOS + ASPHERE + ATC + AWPMD + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + CORESHELL + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + FEP + GPU + GRANULAR + H5MD + INTEL + KIM + KOKKOS + KSPACE + LATBOLTZ + LATTE + MACHDYN + MANIFOLD + MANYBODY + MC + MDI + MEAM + MESONT + MESSAGE + MGPT + MISC + ML-HDNNP + ML-IAP + ML-PACE + ML-QUIP + ML-RANN + ML-SNAP + MOFFF + MOLECULE + MOLFILE + MPIIO + MSCG + NETCDF + OPENMP + OPT + PERI + PHONON + PLUGIN + PLUMED + POEMS + PTM + PYTHON + QEQ + QMMM + QTB + REACTION + REAXFF + REPLICA + RIGID + SCAFACOS + SHOCK + SMTBQ + SPH + SPIN + SRD + TALLY + UEF + USER-MISC + VORONOI + VTK + YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/minimal.cmake b/cmake/presets/basic.cmake similarity index 100% rename from cmake/presets/minimal.cmake rename to cmake/presets/basic.cmake diff --git a/cmake/presets/download.cmake b/cmake/presets/download.cmake index ebab6ab658..2030a97dbb 100644 --- a/cmake/presets/download.cmake +++ b/cmake/presets/download.cmake @@ -1,7 +1,7 @@ # Preset that turns on packages with automatic downloads of sources or potentials. # Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time. -set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI USER-PACE) +set(ALL_PACKAGES KIM LATTE MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index e1a6c5cf79..b07d1a707b 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -1,13 +1,69 @@ -set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT - PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI - USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK - USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP - USER-HDNNP USER-INTEL USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD - USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP - USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC - USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF - USER-YAFF USER-DIELECTRIC) +set(WIN_PACKAGES + ASPHERE + ATC + AWPMD + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + CORESHELL + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + FEP + GPU + GRANULAR + INTEL + KSPACE + LATTE + MACHDYN + MANIFOLD + MANYBODY + MC + MDI + MEAM + MESONT + MGPT + MISC + ML-HDNNP + ML-IAP + ML-SNAP + MOFFF + MOLECULE + MOLFILE + OPENMP + OPT + PERI + PHONON + POEMS + PTM + QEQ + QTB + REACTION + REAXFF + REPLICA + RIGID + SHOCK + SMTBQ + SPH + SPIN + SRD + TALLY + UEF + USER-MISC + VORONOI + YAFF) foreach(PKG ${WIN_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) @@ -16,7 +72,7 @@ endforeach() # these two packages require a full MPI implementation if(BUILD_MPI) set(PKG_MPIIO ON CACHE BOOL "" FORCE) - set(PKG_USER-LB ON CACHE BOOL "" FORCE) + set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE) endif() set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index e124b25d2b..ae65cc75bb 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -2,13 +2,59 @@ # external libraries. Compared to all_on.cmake some more unusual packages # are removed. The resulting binary should be able to run most inputs. -set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE - GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI - PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI - USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC - USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION - USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF USER-DIELECTRIC) +set(ALL_PACKAGES + ASPHERE + BOCS + BODY + BROWNIAN + CG-DNA + CG-SDK + CLASS2 + COLLOID + COLVARS + COMPRESS + CORESHELL + DIELECTRIC + DIFFRACTION + DIPOLE + DPD-BASIC + DPD-MESO + DPD-REACT + DPD-SMOOTH + DRUDE + EFF + FEP + GRANULAR + KSPACE + MACHDYN + MANYBODY + MC + MEAM + MISC + ML-IAP + ML-SNAP + MOFFF + MOLECULE + OPENMP + OPT + PERI + PHONON + PLUGIN + POEMS + PYTHON + QEQ + REACTION + REAXFF + REPLICA + RIGID + SHOCK + SPH + SPIN + SRD + UEF + USER-MISC + VORONOI + YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 08a3a531a1..fd9c2ed1ac 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -1,11 +1,34 @@ # preset that turns off all packages that require some form of external # library or special compiler (fortran or cuda) or equivalent. -set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG - PYTHON VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB USER-MOLFILE - USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP - USER-SCAFACOS USER-SMD USER-VTK) +set(PACKAGES_WITH_LIB + ADIOS + ATC + AWPMD + COMPRESS + GPU + H5MD + KIM + KOKKOS + LATBOLTZ + LATTE + MACHDYN + MDI + MESONT + MESSAGE + ML-HDNNP + ML-PACE + ML-QUIP + MOLFILE + MPIIO + MSCG + NETCDF + PLUMED + PYTHON + QMMM + SCAFACOS + VORONOI + VTK) foreach(PKG ${PACKAGES_WITH_LIB}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index 87b9eba8df..454964f0a9 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -122,7 +122,7 @@ recorded compilation commands information when typing `make iwyu`. A lot of code predates the application of the rules in this document and the rules themselves are a moving target. So there are going to be significant chunks of code that do not fully comply. This applies -for example to the USER-REAXC, or the USER-ATC package. The LAMMPS +for example to the REAXFF, or the ATC package. The LAMMPS developers are dedicated to make an effort to improve the compliance and welcome volunteers wanting to help with the process. diff --git a/doc/lammps.1 b/doc/lammps.1 index f18a9a118d..1c83bd9aae 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -135,7 +135,7 @@ For example "-pk gpu 2" is the same as "package gpu 2" in the input script. The possible styles and options are discussed in the .B LAMMPS manual for the "package" command. This switch can be used multiple -times, e.g. to set options for the USER-INTEL and USER-OMP packages +times, e.g. to set options for the INTEL and OPENMP packages when used together. Along with the "-sf" or "-suffix" switch, this is a convenient mechanism for invoking accelerator packages and their options without having to edit an input script. diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index 30e668a283..9ef209b3b3 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -90,7 +90,7 @@ standard. A more detailed discussion of that is below. directory, or ``make`` from the ``src/STUBS`` dir. If the build fails, you may need to edit the ``STUBS/Makefile`` for your platform. The stubs library does not provide MPI/IO functions - required by some LAMMPS packages, e.g. ``MPIIO`` or ``USER-LB``, + required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``, and thus is not compatible with those packages. .. note:: @@ -120,19 +120,19 @@ self-installed MPICH or OpenMPI, so you should study the provided documentation to find out how to build and link with it. The majority of OpenMP (threading) support in LAMMPS is provided by the -``USER-OMP`` package; see the :doc:`Speed_omp` -page for details. The ``USER-INTEL`` package also includes OpenMP -threading (it is compatible with ``USER-OMP`` and will usually fall -back on styles from that package, if a ``USER-INTEL`` does not exist) +``OPENMP`` package; see the :doc:`Speed_omp` +page for details. The ``INTEL`` package also includes OpenMP +threading (it is compatible with ``OPENMP`` and will usually fall +back on styles from that package, if a ``INTEL`` does not exist) and adds vectorization support when compiled with compatible compilers, in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS`` package can be compiled to include OpenMP threading. In addition, there are a few commands in LAMMPS that have native OpenMP support included as well. These are commands in the ``MPIIO``, -``SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages. In addition +``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages. In addition some packages support OpenMP threading indirectly through the libraries -they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``. +they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``. See the :doc:`Packages details ` page for more info on these packages and the pages for their respective commands for OpenMP threading info. @@ -176,7 +176,7 @@ performance. Vendor provided compilers for a specific hardware can produce faster code than open-source compilers like the GNU compilers. On the most common x86 hardware most popular C++ compilers are quite similar in performance of C/C++ code at high optimization levels. When -using the ``USER-INTEL`` package, there is a distinct advantage in using +using the ``INTEL`` package, there is a distinct advantage in using the `Intel C++ compiler `_ due to much improved vectorization through SSE and AVX instructions on compatible hardware as the source code includes changes and Intel compiler specific directives to enable @@ -325,9 +325,9 @@ LAMMPS. .. code-block:: bash Makefile.opt # OPT package - Makefile.omp # USER-OMP package - Makefile.intel_cpu # USER-INTEL package for CPUs - Makefile.intel_coprocessor # USER-INTEL package for KNLs + Makefile.omp # OPENMP package + Makefile.intel_cpu # INTEL package for CPUs + Makefile.intel_coprocessor # INTEL package for KNLs Makefile.gpu # GPU package Makefile.kokkos_cuda_mpi # KOKKOS package for GPUs Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP) diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst index 73268af0ce..2a64bc3240 100644 --- a/doc/src/Build_cmake.rst +++ b/doc/src/Build_cmake.rst @@ -140,7 +140,7 @@ can be used several times in one command. For your convenience we provide :ref:`CMake presets ` that combine multiple settings to enable optional LAMMPS packages or use a different compiler tool chain. Those are loaded with the *-C* flag -(``-C ../cmake/presets/minimal.cmake``). This step would only be needed +(``-C ../cmake/presets/basic.cmake``). This step would only be needed once, as the settings from the preset files are stored in the ``CMakeCache.txt`` file. It is also possible to customize the build by adding one or more *-D* flags to the CMake command line. diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index ea5c969056..a15d91c629 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -310,7 +310,7 @@ and working. parameter needs to be adjusted. Typically a value around 1.0e-13 can be used, but it may need to be as large as 1.0e-8 in some cases. - - The tests for pair styles from OPT, USER-OMP and USER-INTEL are + - The tests for pair styles from OPT, OPENMP and INTEL are performed with automatically rescaled epsilon to account for additional loss of precision from code optimizations and different summation orders. @@ -345,7 +345,7 @@ and compared. If the fix is a thermostat and thus the internal property ``t_target`` can be extracted, then this is compared to the reference data. The tests are repeated with the respa run style. -If the fix has a multi-threaded version in the USER-OMP package, then +If the fix has a multi-threaded version in the OPENMP package, then the entire set of tests is repeated for that version as well. For this to work, some additional conditions have to be met by the diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 423897fd7a..a78b798636 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -37,31 +37,31 @@ This is the list of packages that may require additional steps. * :ref:`KOKKOS ` * :ref:`LATTE ` * :ref:`MESSAGE ` - * :ref:`MLIAP ` + * :ref:`ML-IAP ` * :ref:`MSCG ` * :ref:`OPT ` * :ref:`POEMS ` * :ref:`PYTHON ` * :ref:`VORONOI ` - * :ref:`USER-ADIOS ` - * :ref:`USER-ATC ` - * :ref:`USER-AWPMD ` - * :ref:`USER-COLVARS ` - * :ref:`USER-H5MD ` - * :ref:`USER-HDNNP ` - * :ref:`USER-INTEL ` - * :ref:`USER-MDI ` - * :ref:`USER-MESONT ` - * :ref:`USER-MOLFILE ` - * :ref:`USER-NETCDF ` - * :ref:`USER-PACE ` - * :ref:`USER-PLUMED ` - * :ref:`USER-OMP ` - * :ref:`USER-QMMM ` - * :ref:`USER-QUIP ` - * :ref:`USER-SCAFACOS ` - * :ref:`USER-SMD ` - * :ref:`USER-VTK ` + * :ref:`ADIOS ` + * :ref:`ATC ` + * :ref:`AWPMD ` + * :ref:`COLVARS ` + * :ref:`H5MD ` + * :ref:`ML-HDNNP ` + * :ref:`INTEL ` + * :ref:`MDI ` + * :ref:`MESONT ` + * :ref:`MOLFILE ` + * :ref:`NETCDF ` + * :ref:`ML-PACE ` + * :ref:`PLUMED ` + * :ref:`OPENMP ` + * :ref:`QMMM ` + * :ref:`ML-QUIP ` + * :ref:`SCAFACOS ` + * :ref:`MACHDYN ` + * :ref:`VTK ` ---------- @@ -622,7 +622,7 @@ This list was last updated for version 3.4.1 of the Kokkos library. mkdir build-kokkos-cuda cd build-kokkos-cuda - cmake -C ../cmake/presets/minimal.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake + cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake cmake --build . .. tab:: Basic traditional make settings: @@ -811,16 +811,17 @@ be installed on your system. .. _mliap: -MLIAP package +ML-IAP package --------------------------- -Building the MLIAP package requires including the :ref:`SNAP ` -package. There will be an error message if this requirement is not satisfied. -Using the *mliappy* model also requires enabling Python support, which -in turn requires the :ref:`PYTHON ` -package **and** requires you have the `cython `_ software -installed and with it a working ``cythonize`` command. This feature requires -compiling LAMMPS with Python version 3.6 or later. +Building the ML-IAP package requires including the :ref:`ML-SNAP +` package. There will be an error message if this requirement +is not satisfied. Using the *mliappy* model also requires enabling +Python support, which in turn requires to include the :ref:`PYTHON +` package **and** requires to have the `cython +`_ software installed and with it a working +``cythonize`` command. This feature requires compiling LAMMPS with +Python version 3.6 or later. .. tabs:: @@ -834,9 +835,9 @@ compiling LAMMPS with Python version 3.6 or later. suitable Python version and the ``cythonize`` command and choose the default accordingly. During the build procedure the provided .pyx file(s) will be automatically translated to C++ code and compiled. - Please do **not** run ``cythonize`` manually in the ``src/MLIAP`` folder, + Please do **not** run ``cythonize`` manually in the ``src/ML-IAP`` folder, as that can lead to compilation errors if Python support is not enabled. - If you did by accident, please remove the generated .cpp and .h files. + If you did it by accident, please remove the generated .cpp and .h files. .. tab:: Traditional make @@ -845,15 +846,16 @@ compiling LAMMPS with Python version 3.6 or later. the ``cythonize`` command in case the corresponding .pyx file(s) were modified. You may need to modify ``lib/python/Makefile.lammps`` if the LAMMPS build fails. - To manually enforce building MLIAP with Python support enabled, - you can add - ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in your machine makefile. - You may have to manually run the ``cythonize`` command on .pyx file(s) - in the ``src`` folder, if this is not automatically done during - installing the MLIAP package. Please do **not** run ``cythonize`` - in the ``src/MLIAP`` folder, as that can lead to compilation errors - if Python support is not enabled. - If you did by accident, please remove the generated .cpp and .h files. + + To enable building the ML-IAP package with Python support enabled, + you need to add ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in + your machine makefile. You may have to manually run the + ``cythonize`` command on .pyx file(s) in the ``src`` folder, if + this is not automatically done during installing the ML-IAP + package. Please do **not** run ``cythonize`` in the ``src/ML-IAP`` + folder, as that can lead to compilation errors if Python support + is not enabled. If you did this by accident, please remove the + generated .cpp and .h files. ---------- @@ -1054,12 +1056,12 @@ binary package provided by your operating system. ---------- -.. _user-adios: +.. _adios: -USER-ADIOS package +ADIOS package ----------------------------------- -The USER-ADIOS package requires the `ADIOS I/O library +The ADIOS package requires the `ADIOS I/O library `_, version 2.3.1 or newer. Make sure that you have ADIOS built either with or without MPI to match if you build LAMMPS with or without MPI. ADIOS compilation settings for @@ -1075,38 +1077,38 @@ systems. .. code-block:: bash -D ADIOS2_DIR=path # path is where ADIOS 2.x is installed - -D PKG_USER-ADIOS=yes + -D PKG_ADIOS=yes .. tab:: Traditional make - Turn on the USER-ADIOS package before building LAMMPS. If the + Turn on the ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do: .. code-block:: bash - $ make yes-user-adios + $ make yes-adios otherwise, set ADIOS2_DIR environment variable when turning on the package: .. code-block:: bash - $ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed + $ ADIOS2_DIR=path make yes-adios # path is where ADIOS 2.x is installed ---------- -.. _user-atc: +.. _atc: -USER-ATC package +ATC package ------------------------------- -The USER-ATC package requires the MANYBODY package also be installed. +The ATC package requires the MANYBODY package also be installed. .. tabs:: .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-ATC=yes`` + No additional settings are needed besides ``-D PKG_ATC=yes`` and ``-D PKG_MANYBODY=yes``. .. tab:: Traditional make @@ -1149,16 +1151,16 @@ The USER-ATC package requires the MANYBODY package also be installed. ---------- -.. _user-awpmd: +.. _awpmd: -USER-AWPMD package +AWPMD package ------------------ .. tabs:: .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``. + No additional settings are needed besides ``-D PKG_AQPMD=yes``. .. tab:: Traditional make @@ -1200,9 +1202,9 @@ USER-AWPMD package ---------- -.. _user-colvars: +.. _colvars: -USER-COLVARS package +COLVARS package --------------------------------------- This package includes the `Colvars library @@ -1216,7 +1218,7 @@ be built for the most part with all major versions of the C++ language. This is the recommended build procedure for using Colvars in LAMMPS. No additional settings are normally needed besides - ``-D PKG_USER-COLVARS=yes``. + ``-D PKG_COLVARS=yes``. .. tab:: Traditional make @@ -1259,9 +1261,9 @@ be built for the most part with all major versions of the C++ language. ---------- -.. _user-pace: +.. _ml-pace: -USER-PACE package +ML-PACE package ----------------------------- This package requires a library that can be downloaded and built @@ -1274,8 +1276,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ `_. -The USER-PLUMED package has been tested to work with Plumed versions +The PLUMED package has been tested to work with Plumed versions 2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations with a different version of the Plumed kernel. @@ -1345,7 +1347,7 @@ LAMMPS build. .. tab:: CMake build - When the ``-D PKG_USER-PLUMED=yes`` flag is included in the cmake + When the ``-D PKG_PLUMED=yes`` flag is included in the cmake command you must ensure that GSL is installed in locations that are specified in your environment. There are then two additional variables that control the manner in which PLUMED is obtained and @@ -1378,7 +1380,7 @@ LAMMPS build. .. tab:: Traditional make - PLUMED needs to be installed before the USER-PLUMED package is + PLUMED needs to be installed before the PLUMED package is installed so that LAMMPS can find the right settings when compiling and linking the LAMMPS executable. You can either download and build PLUMED inside the LAMMPS plumed library folder @@ -1403,12 +1405,12 @@ LAMMPS build. build to use. A new file ``lib/plumed/Makefile.lammps`` is also created with settings suitable for LAMMPS to compile and link PLUMED using the desired linkage mode. After this step is - completed, you can install the USER-PLUMED package and compile + completed, you can install the PLUMED package and compile LAMMPS in the usual manner: .. code-block:: bash - $ make yes-user-plumed + $ make yes-plumed $ make machine Once this compilation completes you should be able to run LAMMPS @@ -1423,15 +1425,15 @@ LAMMPS build. If you want to change the linkage mode, you have to re-run "make lib-plumed" with the desired settings **and** do a re-install if - the USER-PLUMED package with "make yes-user-plumed" to update the + the PLUMED package with "make yes-plumed" to update the required makefile settings with the changes in the lib/plumed folder. ---------- -.. _user-h5md: +.. _h5md: -USER-H5MD package +H5MD package --------------------------------- To build with this package you must have the HDF5 software package @@ -1442,7 +1444,7 @@ the HDF5 library. .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-H5MD=yes``. + No additional settings are needed besides ``-D PKG_H5MD=yes``. This should auto-detect the H5MD library on your system. Several advanced CMake H5MD options exist if you need to specify where it @@ -1474,13 +1476,13 @@ the HDF5 library. ---------- -.. _user-hdnnp: +.. _ml-hdnnp: -USER-HDNNP package ---------------------------------- +ML-HDNNP package +---------------- -To build with the USER-HDNNP package it is required to download and build the -external `n2p2 `__ library ``v2.1.4`` +To build with the ML-HDNNP package it is required to download and build the +external `n2p2 `_ library ``v2.1.4`` (or higher). The LAMMPS build process offers an automatic download and compilation of *n2p2* or allows you to choose the installation directory of *n2p2* manually. Please see the boxes below for the CMake and traditional build @@ -1490,7 +1492,7 @@ In case of a manual installation of *n2p2* you only need to build the *n2p2* cor library ``libnnp`` and interface library ``libnnpif``. When using GCC it should suffice to execute ``make libnnpif`` in the *n2p2* ``src`` directory. For more details please see ``lib/hdnnp/README`` and the `n2p2 build documentation -`__. +`_. .. tabs:: @@ -1528,24 +1530,24 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation ---------- -.. _user-intel: +.. _intel: -USER-INTEL package +INTEL package ----------------------------------- To build with this package, you must choose which hardware you want to build for, either x86 CPUs or Intel KNLs in offload mode. You should -also typically :ref:`install the USER-OMP package `, as it can be -used in tandem with the USER-INTEL package to good effect, as explained +also typically :ref:`install the OPENMP package `, as it can be +used in tandem with the INTEL package to good effect, as explained on the :doc:`Speed_intel` page. When using Intel compilers version 16.0 or later is required. You can also use the GNU or Clang compilers and they will provide performance -improvements over regular styles and USER-OMP styles, but less so than +improvements over regular styles and OPENMP styles, but less so than with the Intel compilers. Please also note, that some compilers have been found to apply memory alignment constraints incompletely or incorrectly and thus can cause segmentation faults in otherwise correct -code when using features from the USER-INTEL package. +code when using features from the INTEL package. .. tabs:: @@ -1562,7 +1564,7 @@ code when using features from the USER-INTEL package. Choose which hardware to compile for in Makefile.machine via the following settings. See ``src/MAKE/OPTIONS/Makefile.intel_cpu*`` and ``Makefile.knl`` files for examples. and - ``src/USER-INTEL/README`` for additional information. + ``src/INTEL/README`` for additional information. For CPUs: @@ -1598,9 +1600,9 @@ TBB and MKL. ---------- -.. _user-mdi: +.. _mdi: -USER-MDI package +MDI package ----------------------------- .. tabs:: @@ -1627,9 +1629,9 @@ USER-MDI package ---------- -.. _user-mesont: +.. _mesont: -USER-MESONT package +MESONT package ------------------------- This package includes a library written in Fortran 90 in the @@ -1642,7 +1644,7 @@ they will be downloaded the first time this package is installed. .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-MESONT=yes`` + No additional settings are needed besides ``-D PKG_MESONT=yes`` .. tab:: Traditional make @@ -1669,9 +1671,9 @@ they will be downloaded the first time this package is installed. ---------- -.. _user-molfile: +.. _molfile: -USER-MOLFILE package +MOLFILE package --------------------------------------- .. tabs:: @@ -1681,9 +1683,9 @@ USER-MOLFILE package .. code-block:: bash -D MOLFILE_INCLUDE_DIR=path # (optional) path where VMD molfile plugin headers are installed - -D PKG_USER-MOLFILE=yes + -D PKG_MOLFILE=yes - Using ``-D PKG_USER-MOLFILE=yes`` enables the package, and setting + Using ``-D PKG_MOLFILE=yes`` enables the package, and setting ``-D MOLFILE_INCLUDE_DIR`` allows to provide a custom location for the molfile plugin header files. These should match the ABI of the plugin files used, and thus one typically sets them to include @@ -1707,9 +1709,9 @@ USER-MOLFILE package ---------- -.. _user-netcdf: +.. _netcdf: -USER-NETCDF package +NETCDF package ------------------------------------- To build with this package you must have the NetCDF library installed @@ -1719,7 +1721,7 @@ on your system. .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``. + No additional settings are needed besides ``-D PKG_NETCDF=yes``. This should auto-detect the NETCDF library if it is installed on your system at standard locations. Several advanced CMake NETCDF @@ -1738,9 +1740,9 @@ on your system. ---------- -.. _user-omp: +.. _openmp: -USER-OMP package +OPENMP package ------------------------------- .. tabs:: @@ -1748,13 +1750,13 @@ USER-OMP package .. tab:: CMake build No additional settings are required besides ``-D - PKG_USER-OMP=yes``. If CMake detects OpenMP compiler support, the - USER-OMP code will be compiled with multi-threading support + PKG_OPENMP=yes``. If CMake detects OpenMP compiler support, the + OPENMP code will be compiled with multi-threading support enabled, otherwise as optimized serial code. .. tab:: Traditional make - To enable multi-threading support in the USER-OMP package (and + To enable multi-threading support in the OPENMP package (and other styles supporting OpenMP) the following compile and link flags must be added to your Makefile.machine file. See ``src/MAKE/OPTIONS/Makefile.omp`` for an example. @@ -1771,12 +1773,12 @@ USER-OMP package ---------- -.. _user-qmmm: +.. _qmmm: -USER-QMMM package +QMMM package --------------------------------- -For using LAMMPS to do QM/MM simulations via the USER-QMMM package you +For using LAMMPS to do QM/MM simulations via the QMMM package you need to build LAMMPS as a library. A LAMMPS executable with :doc:`fix qmmm ` included can be built, but will not be able to do a QM/MM simulation on as such. You must also build a QM code - currently @@ -1799,11 +1801,11 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to libqmmm.a) are not included in the static LAMMPS library and (currently) not installed, while their code is included in the shared LAMMPS library. Thus a typical command line to configure - building LAMMPS for USER-QMMM would be: + building LAMMPS for QMMM would be: .. code-block:: bash - cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \ + cmake -C ../cmake/presets/basic.cmake -D PKG_QMMM=yes \ -D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake After completing the LAMMPS build and also configuring and @@ -1846,9 +1848,9 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to ---------- -.. _user-quip: +.. _ml-quip: -USER-QUIP package +ML-QUIP package --------------------------------- To build with this package, you must download and build the QUIP @@ -1866,7 +1868,7 @@ to be downloaded and configured. See step 1 and step 1.1 in the -D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) CMake will **not** download and build the QUIP library. But once you have - done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should + done that, a CMake build of LAMMPS with ``-D PKG_ML-QUIP=yes`` should work. Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library. .. tab:: Traditional make @@ -1881,9 +1883,9 @@ to be downloaded and configured. See step 1 and step 1.1 in the ---------- -.. _user-scafacos: +.. _scafacos: -USER-SCAFACOS package +SCAFACOS package ----------------------------------------- To build with this package, you must download and build the @@ -1928,9 +1930,9 @@ To build with this package, you must download and build the ---------- -.. _user-smd: +.. _machdyn: -USER-SMD package +MACHDYN package ------------------------------- To build with this package, you must download the Eigen3 library. @@ -1972,9 +1974,9 @@ Eigen3 is a template library, so you do not need to build it. ---------- -.. _user-vtk: +.. _vtk: -USER-VTK package +VTK package ------------------------------- To build with this package you must have the VTK library installed on @@ -1984,7 +1986,7 @@ your system. .. tab:: CMake build - No additional settings are needed besides ``-D PKG_USER-VTK=yes``. + No additional settings are needed besides ``-D PKG_VTK=yes``. This should auto-detect the VTK library if it is installed on your system at standard locations. Several advanced VTK options exist diff --git a/doc/src/Build_make.rst b/doc/src/Build_make.rst index 06f87fe904..c7b063e8a9 100644 --- a/doc/src/Build_make.rst +++ b/doc/src/Build_make.rst @@ -117,10 +117,10 @@ settings may become outdated: make mac # build serial LAMMPS on a Mac make mac_mpi # build parallel LAMMPS on a Mac - make intel_cpu # build with the USER-INTEL package optimized for CPUs - make knl # build with the USER-INTEL package optimized for KNLs + make intel_cpu # build with the INTEL package optimized for CPUs + make knl # build with the INTEL package optimized for KNLs make opt # build with the OPT package optimized for CPUs - make omp # build with the USER-OMP package optimized for OpenMP + make omp # build with the OPENMP package optimized for OpenMP make kokkos_omp # build with the KOKKOS package for OpenMP make kokkos_cuda_mpi # build with the KOKKOS package for GPUs make kokkos_phi # build with the KOKKOS package for KNLs diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst index e379153e6f..a2683e773b 100644 --- a/doc/src/Build_manual.rst +++ b/doc/src/Build_manual.rst @@ -204,7 +204,7 @@ be multiple tests run automatically: .. parsed-literal:: - Found 33 standard and 41 user packages + Found 74 packages Standard package NEWPACKAGE missing in Packages_standard.rst Standard package NEWPACKAGE missing in Packages_details.rst diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index 2b2993de50..a7dda52b41 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -30,17 +30,37 @@ steps, as explained on the :doc:`Build extras ` page. These links take you to the extra instructions for those select packages: -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-HDNNP ` | :ref:`USER-INTEL ` | -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`USER-MOLFILE ` | :ref:`USER-NETCDF ` | :ref:`USER-PACE ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`USER-QUIP ` | :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | -+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ +.. table_from_list:: + :columns: 6 + + * :ref:`ADIOS ` + * :ref:`ATC ` + * :ref:`AWPMD ` + * :ref:`COLVARS ` + * :ref:`COMPRESS ` + * :ref:`GPU ` + * :ref:`H5MD ` + * :ref:`INTEL ` + * :ref:`KIM ` + * :ref:`KOKKOS ` + * :ref:`LATTE ` + * :ref:`MACHDYN ` + * :ref:`MESSAGE ` + * :ref:`ML-HDNNP ` + * :ref:`ML-PACE ` + * :ref:`ML-QUIP ` + * :ref:`MOLFILE ` + * :ref:`MSCG ` + * :ref:`NETCDF ` + * :ref:`OPENMP ` + * :ref:`OPT ` + * :ref:`PLUMED ` + * :ref:`POEMS ` + * :ref:`PYTHON ` + * :ref:`QMMM ` + * :ref:`SCAFACOS ` + * :ref:`VORONOI ` + * :ref:`VTK ` The mechanism for including packages is simple but different for CMake versus make. @@ -58,14 +78,10 @@ versus make. .. code-block:: csh -D PKG_MANYBODY=yes - -D PKG_USER-INTEL=yes + -D PKG_INTEL=yes - All standard and user packages are included the same way. Note - that USER packages have a hyphen between USER and the rest of the - package name, not an underscore. - - See the shortcut section below for how to install many packages at - once with CMake. + All packages are included the same way. See the shortcut section + below for how to install many packages at once with CMake. .. note:: @@ -89,12 +105,10 @@ versus make. .. code-block:: bash make no-rigid - make yes-user-intel + make yes-intel - All standard and user packages are included the same way. - - See the shortcut section below for how to install many packages at - once with make. + All packages are included the same way. See the shortcut section + below for how to install many packages at once with make. .. note:: @@ -126,7 +140,7 @@ other files dependent on that package are also excluded. .. note:: - By default no package is installed. Prior to August 2018, however, + By default no packages are installed. Prior to August 2018, however, if you downloaded a tarball, 3 packages (KSPACE, MANYBODY, MOLECULE) were pre-installed via the traditional make procedure in the ``src`` directory. That is no longer the case, so that CMake will build @@ -153,7 +167,7 @@ one of them as a starting point and customize it to your needs. .. code-block:: bash - cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake # enable just a few core packages + cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake # enable just a few core packages cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools @@ -208,10 +222,10 @@ These commands install/un-install sets of packages: make yes-all # install all packages make no-all # uninstall all packages - make yes-standard or make yes-std # install standard packages - make no-standard or make no-std # uninstall standard packages - make yes-user # install user packages - make no-user # uninstall user packages + make yes-basic # install a few commonly used packages' + make no-basic # remove a few commonly used packages' + make yes-most # install most packages w/o libs' + make no-most # remove most packages w/o libs' make yes-lib # install packages that require extra libraries make no-lib # uninstall packages that require extra libraries make yes-ext # install packages that require external libraries @@ -225,15 +239,14 @@ package`` will list all the these commands. Installing or un-installing a package for the make based build process works by simply copying files back and forth between the main source directory src and the sub-directories with the package name (e.g. - src/KSPACE, src/USER-ATC), so that the files are included or excluded + src/KSPACE, src/ATC), so that the files are included or excluded when LAMMPS is built. Only source files in the src folder will be compiled. The following make commands help manage files that exist in both the src directory and in package sub-directories. You do not normally need to use these commands unless you are editing LAMMPS files or are -:doc:`installing a patch ` downloaded from the LAMMPS web -site. +updating LAMMPS via git. Type ``make package-status`` or ``make ps`` to show which packages are currently installed. For those that are installed, it will list any @@ -245,10 +258,10 @@ currently installed, without listing the status of packages that are not installed. Type ``make package-update`` or ``make pu`` to overwrite src files with -files from the package sub-directories if the package is installed. -It should be used after a :doc:`patch has been applied `, -since patches only update the files in the package sub-directory, but -not the src files. +files from the package sub-directories if the package is installed. It +should be used after the checkout has been :doc:`updated or changed +withy git `, this will only update the files in the package +sub-directories, but not the copies in the src folder. Type ``make package-overwrite`` to overwrite files in the package sub-directories with src files. diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index caa6042a51..074a6349e6 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -64,7 +64,7 @@ LAMMPS can use them if they are available on your system. selected, then CMake will try to detect, if threaded FFTW libraries are available and enable them by default. This setting is independent of whether OpenMP threads are enabled and a - packages like KOKKOS or USER-OMP is used. If CMake cannot detect + packages like KOKKOS or OPENMP is used. If CMake cannot detect the FFT library, you can set these variables to assist: .. code-block:: bash @@ -242,8 +242,8 @@ does not support 64-bit integers or incurs performance penalties when using them. These are limits for the core of the LAMMPS code, specific features or -some styles may impose additional limits. The :ref:`USER-ATC -` package cannot be compiled with the "bigbig" setting. +some styles may impose additional limits. The :ref:`ATC +` package cannot be compiled with the "bigbig" setting. Also, there are limitations when using the library interface where some functions with known issues have been replaced by dummy calls printing a corresponding error message rather than crashing randomly or corrupting diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index 70a021849d..1a0876e88f 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -18,7 +18,7 @@ Bond_style potentials All LAMMPS :doc:`bond_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: @@ -57,7 +57,7 @@ Angle_style potentials All LAMMPS :doc:`angle_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: @@ -99,7 +99,7 @@ Dihedral_style potentials All LAMMPS :doc:`dihedral_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: @@ -135,7 +135,7 @@ Improper_style potentials All LAMMPS :doc:`improper_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index 080e964558..0169826751 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -16,8 +16,8 @@ Compute commands An alphabetic list of all LAMMPS :doc:`compute ` commands. Some styles have accelerated versions. This is indicated by -additional letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. +additional letters in parenthesis: g = GPU, i = INTEL, k = +KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: :columns: 5 diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index c9c55277b2..bae7c5920a 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -16,7 +16,7 @@ Fix commands An alphabetic list of all LAMMPS :doc:`fix ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst index 2f7cd35f15..47188d1172 100644 --- a/doc/src/Commands_kspace.rst +++ b/doc/src/Commands_kspace.rst @@ -16,7 +16,7 @@ KSpace solvers All LAMMPS :doc:`kspace_style ` solvers. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 192c40b27a..bccb17224a 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -16,7 +16,7 @@ Pair_style potentials All LAMMPS :doc:`pair_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in -parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: @@ -190,7 +190,7 @@ OPT. * :doc:`lubricateU/poly ` * :doc:`mdpd ` * :doc:`mdpd/rhosum ` - * :doc:`meam/c ` + * :doc:`meam ` * :doc:`meam/spline (o) ` * :doc:`meam/sw/spline ` * :doc:`mesocnt ` diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index 1f6da57945..1000d11e29 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -25,23 +25,20 @@ The reset_ids command has been renamed to :doc:`reset_atom_ids ` MEAM package ------------ -The MEAM package has been removed since it was superseded by the -:ref:`USER-MEAMC package `. The code in -the USER-MEAMC package is a translation of the Fortran code of MEAM into C++, -which removes several restrictions (e.g. there can be multiple instances -in hybrid pair styles) and allows for some optimizations leading -to better performance. The new pair style :doc:`meam/c ` has -the exact same syntax as the old "meam" pair style and thus pair style -meam is an alias to the new style and backward -compatibility of old inputs is preserved. +The MEAM package in Fortran has been replaced by a C++ implementation. +The code in the :ref:`MEAM package ` is a translation of the +Fortran code of MEAM into C++, which removes several restrictions +(e.g. there can be multiple instances in hybrid pair styles) and allows +for some optimizations leading to better performance. The pair style +:doc:`meam ` has the exact same syntax. REAX package ------------ The REAX package has been removed since it was superseded by the -:ref:`USER-REAXC package `. The USER-REAXC +:ref:`REAXFF package `. The REAXFF package has been tested to yield equivalent results to the REAX package, -offers better performance, supports OpenMP multi-threading via USER-OMP, +offers better performance, supports OpenMP multi-threading via OPENMP, and GPU and threading parallelization through KOKKOS. The new pair styles are not syntax compatible with the removed reax pair style, so input files will have to be adapted. diff --git a/doc/src/Developer_unittest.rst b/doc/src/Developer_unittest.rst index 52753ee1b4..820e911a8f 100644 --- a/doc/src/Developer_unittest.rst +++ b/doc/src/Developer_unittest.rst @@ -404,8 +404,8 @@ noise). Then it will restart from the previously generated restart and compare with the reference and also start from the data file. A final check will use multi-cutoff r-RESPA (if supported by the pair style) at a 1:1 split and compare to the Verlet results. These sets of tests are -run with multiple test fixtures for accelerated styles (OPT, USER-OMP, -USER-INTEL) and for the latter two with 4 OpenMP threads enabled. For +run with multiple test fixtures for accelerated styles (OPT, OPENMP, +INTEL) and for the latter two with 4 OpenMP threads enabled. For these tests the relative error (epsilon) is lowered by a common factor due to the additional numerical noise, but the tests are still comparing to the same reference data. diff --git a/doc/src/Errors.rst b/doc/src/Errors.rst index 48db5f6472..5975c22c41 100644 --- a/doc/src/Errors.rst +++ b/doc/src/Errors.rst @@ -1,11 +1,11 @@ Errors ****** -These doc pages describe the errors you can encounter when using -LAMMPS. The common problems include conceptual issues. The messages -and warnings doc pages give complete lists of all the messages the -code may generate (except those generated by USER packages), with -additional details for many of them. +These doc pages describe many of the error and warning message you can +encounter when using LAMMPS. The common problems include conceptual +issues. The messages and warnings doc pages give complete lists of all +the messages the code may generate, with additional details for many of +them. .. toctree:: :maxdepth: 1 diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index d532ce7a31..3bbee1dc36 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -14,10 +14,6 @@ For example, a message like this: means that line #78 in the file src/velocity.cpp generated the error. Looking in the source code may help you figure out what went wrong. -Note that error messages from :doc:`user-contributed packages ` are not listed here. If such an error -occurs and is not self-explanatory, you will need to look in the source -code or contact the author of the package. - Doc page with :doc:`WARNING messages ` ---------- @@ -5899,7 +5895,7 @@ Doc page with :doc:`WARNING messages ` other. *Must set number of threads via package omp command* - Because you are using the USER-OMP package, set the number of threads + Because you are using the OPENMP package, set the number of threads via its settings, not by the pair_style snap nthreads setting. *Must shrink-wrap piston boundary* @@ -6344,16 +6340,16 @@ keyword to allow for additional bonds to be formed The GPU package must be installed via "make yes-gpu" before LAMMPS is built. -*Package intel command without USER-INTEL package installed* - The USER-INTEL package must be installed via "make yes-user-intel" +*Package intel command without INTEL package installed* + The INTEL package must be installed via "make yes-intel" before LAMMPS is built. *Package kokkos command without KOKKOS package enabled* The KOKKOS package must be installed via "make yes-kokkos" before LAMMPS is built, and the "-k on" must be used to enable the package. -*Package omp command without USER-OMP package installed* - The USER-OMP package must be installed via "make yes-user-omp" before +*Package omp command without OPENMP package installed* + The OPENMP package must be installed via "make yes-openmp" before LAMMPS is built. *Pair body requires atom style body* @@ -8064,13 +8060,13 @@ keyword to allow for additional bonds to be formed *Using suffix gpu without GPU package installed* Self-explanatory. -*Using suffix intel without USER-INTEL package installed* +*Using suffix intel without INTEL package installed* Self-explanatory. *Using suffix kk without KOKKOS package enabled* Self-explanatory. -*Using suffix omp without USER-OMP package installed* +*Using suffix omp without OPENMP package installed* Self-explanatory. *Using update dipole flag requires atom attribute mu* diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index 4f29fad9dd..68d6b0451a 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -14,10 +14,6 @@ generated. For example, a message like this: means that line #187 in the file src/domain.cpp generated the error. Looking in the source code may help you figure out what went wrong. -Note that warning messages from :doc:`user-contributed packages ` are not listed here. If such a warning -occurs and is not self-explanatory, you will need to look in the source -code or contact the author of the package. - Doc page with :doc:`ERROR messages ` ---------- @@ -529,7 +525,7 @@ This will most likely cause errors in kinetic fluctuations. *OMP_NUM_THREADS environment is not set.* This environment variable must be set appropriately to use the - USER-OMP package. + OPENMP package. *One or more atoms are time integrated more than once* This is probably an error since you typically do not want to diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 3eb25d5b30..0f1ab2626d 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -205,11 +205,13 @@ Uppercase directories +------------+--------------------------------------------------------------------------------------------------+ | MC | using LAMMPS in a Monte Carlo mode to relax the energy of a system | +------------+--------------------------------------------------------------------------------------------------+ +| PACKAGES | examples for specific packages and contributed commands in USER-MISC | ++------------+--------------------------------------------------------------------------------------------------+ | SPIN | examples for features of the SPIN package | +------------+--------------------------------------------------------------------------------------------------+ | UNITS | examples that run the same simulation in lj, real, metal units | +------------+--------------------------------------------------------------------------------------------------+ -| USER | examples for USER packages and USER-contributed commands | +| USER-MISC | examples for commands in the USER-MISC packages | +------------+--------------------------------------------------------------------------------------------------+ | VISCOSITY | compute viscosity via several methods | +------------+--------------------------------------------------------------------------------------------------+ @@ -217,11 +219,14 @@ Uppercase directories Nearly all of these directories have README files which give more details on how to understand and use their contents. -The USER directory has a large number of sub-directories which -correspond by name to a USER package. They contain scripts that -illustrate how to use the command(s) provided in that package. Many +The PACKAGES directory has a large number of sub-directories which +correspond by name to specific packages. They contain scripts that +illustrate how to use the command(s) provided in those packages. Many of the sub-directories have their own README files which give further instructions. See the :doc:`Packages_details ` doc -page for more info on specific USER packages. +page for more info on specific packages. + +Similarly the USER-MISC directory has sub-directories for examples +corresponding to individual commands or styles in the USER-MISC package. .. _openkim: https://openkim.org diff --git a/doc/src/Howto_cmake.rst b/doc/src/Howto_cmake.rst index 655c90bfd9..244bcf6323 100644 --- a/doc/src/Howto_cmake.rst +++ b/doc/src/Howto_cmake.rst @@ -382,9 +382,9 @@ change some variables later with additional *-D* flags. A few examples: .. code-block:: bash - cmake -C ../cmake/presets/minimal.cmake -D PKG_MISC=on ../cmake + cmake -C ../cmake/presets/basic.cmake -D PKG_MISC=on ../cmake cmake -C ../cmake/presets/clang.cmake -C ../cmake/presets/most.cmake ../cmake - cmake -C ../cmake/presets/minimal.cmake -D BUILD_MPI=off ../cmake + cmake -C ../cmake/presets/basic.cmake -D BUILD_MPI=off ../cmake The first command will install the packages ``KSPACE``, ``MANYBODY``, ``MOLECULE``, ``RIGID`` and ``MISC``; the first four from the preset @@ -400,7 +400,7 @@ It is also possible to do this incrementally. .. code-block:: bash - cmake -C ../cmake/presets/minimal.cmake ../cmake + cmake -C ../cmake/presets/basic.cmake ../cmake cmake -D PKG_MISC=on . will achieve the same final configuration as in the first example above. diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index 24c21f27b1..46d400c9e8 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -2,14 +2,14 @@ Tutorial for Thermalized Drude oscillators in LAMMPS ==================================================== This tutorial explains how to use Drude oscillators in LAMMPS to -simulate polarizable systems using the USER-DRUDE package. As an +simulate polarizable systems using the DRUDE package. As an illustration, the input files for a simulation of 250 phenol molecules are documented. First of all, LAMMPS has to be compiled with the -USER-DRUDE package activated. Then, the data file and input scripts +DRUDE package activated. Then, the data file and input scripts have to be modified to include the Drude dipoles and how to handle them. -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude ---------- @@ -82,7 +82,7 @@ The data file is similar to a standard LAMMPS data file for to their DC should appear in the data file as normal atoms and bonds. You can use the *polarizer* tool (Python script distributed with the -USER-DRUDE package) to convert a non-polarizable data file (here +DRUDE package) to convert a non-polarizable data file (here *data.102494.lmp*\ ) to a polarizable data file (\ *data-p.lmp*\ ) .. code-block:: bash diff --git a/doc/src/Howto_manifold.rst b/doc/src/Howto_manifold.rst index 41e1fb6a4c..f09e3017be 100644 --- a/doc/src/Howto_manifold.rst +++ b/doc/src/Howto_manifold.rst @@ -5,11 +5,11 @@ Manifolds (surfaces) This doc page is not about a LAMMPS input script command, but about manifolds, which are generalized surfaces, as defined and used by the -USER-MANIFOLD package, to track particle motion on the manifolds. See -the src/USER-MANIFOLD/README file for more details about the package +MANIFOLD package, to track particle motion on the manifolds. See +the src/MANIFOLD/README file for more details about the package and its commands. -Below is a list of currently supported manifolds by the USER-MANIFOLD +Below is a list of currently supported manifolds by the MANIFOLD package, their parameters and a short description of them. The parameters listed here are in the same order as they should be passed to the relevant fixes. diff --git a/doc/src/Howto_polarizable.rst b/doc/src/Howto_polarizable.rst index c1c6e1fc76..6361f8ad88 100644 --- a/doc/src/Howto_polarizable.rst +++ b/doc/src/Howto_polarizable.rst @@ -10,7 +10,7 @@ systems can be simulated in LAMMPS using three methods: * the adiabatic core-shell method, implemented in the :doc:`CORESHELL ` package, * the thermalized Drude dipole method, implemented in the - :doc:`USER-DRUDE ` package. + :doc:`DRUDE ` package. The fluctuating charge method calculates instantaneous charges on interacting atoms based on the electronegativity equalization diff --git a/doc/src/Howto_wsl.rst b/doc/src/Howto_wsl.rst index 28251ba5ee..df5644451f 100644 --- a/doc/src/Howto_wsl.rst +++ b/doc/src/Howto_wsl.rst @@ -208,7 +208,7 @@ Presets are a way to specify a collection of CMake options using a file. .. code-block:: bash - cmake ../cmake/presets/minimal.cmake ../cmake + cmake ../cmake/presets/basic.cmake ../cmake This command configures the build and generates the necessary Makefiles. To compile the binary, run the make command. diff --git a/doc/src/Install.rst b/doc/src/Install.rst index e0204c0bbd..157bd32208 100644 --- a/doc/src/Install.rst +++ b/doc/src/Install.rst @@ -18,7 +18,6 @@ need the source code. Install_tarball Install_git - Install_patch These are the files and sub-directories in the LAMMPS distribution: @@ -27,6 +26,8 @@ These are the files and sub-directories in the LAMMPS distribution: +------------+-------------------------------------------+ | LICENSE | GNU General Public License (GPL) | +------------+-------------------------------------------+ +| SECURITY.md| Security Policy for the LAMMPS package | ++------------+-------------------------------------------+ | bench | benchmark problems | +------------+-------------------------------------------+ | cmake | CMake build files | diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index 1a07b7f917..f62bad6847 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -120,8 +120,11 @@ changed. How to do this depends on the build system you are using. $ make package-update # sync package files with src files $ make foo # re-build for your machine (mpi, serial, etc) - Just as described on the :doc:`Apply patch ` page, - after a patch has been installed. + to enforce consistency of the source between the src folder + and package directories. This is OK to do even if you don't + use any packages. The "make purge" command removes any deprecated + src files if they were removed by the patch from a package + sub-directory. .. warning:: diff --git a/doc/src/Install_patch.rst b/doc/src/Install_patch.rst deleted file mode 100644 index f1f37f86c2..0000000000 --- a/doc/src/Install_patch.rst +++ /dev/null @@ -1,96 +0,0 @@ -Applying patches ----------------- - -It is easy to stay current with the most recent LAMMPS patch releases -if you use git to track the LAMMPS development. Instructions for -how to stay current are on the -:doc:`Download the LAMMPS source with git ` page. - -If you prefer to download a tarball, as described on the -:doc:`tarball download ` page, you can stay current by -downloading "patch files" when new patch releases are made. A link to -a patch file is posted on the -`bug fixes and new feature page `_ -of the LAMMPS website, along -with a list of changed files and details about what is in the new patch -release. This page explains how to apply the patch file to your local -LAMMPS directory. - -.. note:: - - You should not apply patch files to a local git checkout of - LAMMPS, only to an unpacked tarball. Use git commands to - update such a version of the LAMMPS source code. - -Here are the steps to apply a patch file. Note that if your version -of LAMMPS is several patch releases behind, you need to apply all the -intervening patch files in succession to bring your version of LAMMPS -up to date. - -* Download the patch file. You may have to shift-click in your browser - to download the file instead of display it. Patch files have names - like patch.12Dec16. -* Put the patch file in your top-level LAMMPS directory, where the - LICENSE and README files are. -* Apply the patch by typing the following command from your top-level - LAMMPS directory, where the redirected file is the name of the patch - file. - - .. code-block:: bash - - $ patch -bp1 < patch.12Dec16 - -* A list of updated files print out to the screen. The -b switch - creates backup files of your originals (e.g. src/force.cpp.orig), so - you can manually undo the patch if something goes wrong. - -* Once you have updated your local files you need to re-build LAMMPS. - If you are applying several patches successively, you only need to - do the rebuild once at the end. How to do it depends on the build - system you are using. - - .. tabs:: - - .. tab:: CMake build - - Change to your build folder and type: - - .. code-block:: bash - - cmake . --build - - CMake should auto-detect whether it needs to re-run the CMake - configuration step and otherwise redo the build for all files - that have been changed or files that depend on changed files. - In case some build options have been changed or renamed, you - may have to update those by running: - - .. code-block:: bash - - cmake . - - and then rebuild. - - .. tab:: Traditional make - - Switch to the src directory and type: - - .. code-block:: bash - - $ make purge # remove any deprecated src files - $ make package-update # sync package files with src files - $ make foo # re-build for your machine (mpi, serial, etc) - - to enforce consistency of the source between the src folder - and package directories. This is OK to do even if you don't - use any packages. The "make purge" command removes any deprecated - src files if they were removed by the patch from a package - sub-directory. - - .. warning:: - - If you wish to edit/change a src file that is from a package, - you should edit the version of the file inside the package - sub-directory with src, then re-install the package. The - version in the source directory is merely a copy and will be - wiped out if you type "make package-update". diff --git a/doc/src/Install_tarball.rst b/doc/src/Install_tarball.rst index 921ce8785a..caa8f700a9 100644 --- a/doc/src/Install_tarball.rst +++ b/doc/src/Install_tarball.rst @@ -47,15 +47,3 @@ release. .. _git: https://github.com/lammps/lammps/releases ----------- - -If you download a current LAMMPS tarball, one way to stay current as -new patch tarballs are released, is to download a patch file which you -can apply to your local directory to update it for each new patch -release. (Or of course you could just download the newest tarball -periodically.) - -The patch files are posted on the `bug and feature page `_ of the -website, along with a list of changed files and details about what is -in the new patch release. Instructions for applying a patch file are -on the :doc:`Install patch ` page. diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index 1df7ae7f3f..1e5c9684ac 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -18,9 +18,9 @@ needed to run in parallel with MPI. The LAMMPS binaries contain *all* :doc:`optional packages ` included in the source distribution except: KIM, KOKKOS, MSCG, PYTHON, -USER-ADIOS, USER-H5MD, USER-NETCDF, USER-QMMM, USER-QUIP, and USER-VTK. +ADIOS, H5MD, NETCDF, QMMM, ML-QUIP, and VTK. The serial version also does not include the MPIIO and -USER-LB packages. The GPU package is compiled for OpenCL with +LATBOLTZ packages. The GPU package is compiled for OpenCL with mixed precision kernels. The LAMMPS library is compiled as a shared library and the diff --git a/doc/src/Intro_authors.rst b/doc/src/Intro_authors.rst index 6af3996d1e..720221d4b7 100644 --- a/doc/src/Intro_authors.rst +++ b/doc/src/Intro_authors.rst @@ -29,19 +29,19 @@ The following folks deserve special recognition. Many of the packages they have written are unique for an MD code and LAMMPS would not be as general-purpose as it is without their expertise and efforts. -* Metin Aktulga (MSU), USER-REAXC package for C version of ReaxFF -* Mike Brown (Intel), GPU and USER-INTEL packages -* Colin Denniston (U Western Ontario), USER-LB package -* Georg Ganzenmuller (EMI), USER-SMD and USER-SPH packages -* Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field -* Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling +* Metin Aktulga (MSU), REAXFF package for C version of ReaxFF +* Mike Brown (Intel), GPU and INTEL packages +* Colin Denniston (U Western Ontario), LATBOLTZ package +* Georg Ganzenmuller (EMI), MACHDYN and SPH packages +* Andres Jaramillo-Botero (Caltech), EFF package for electron force field +* Reese Jones (Sandia) and colleagues, ATC package for atom/continuum coupling * Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS * Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion * Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages * Mike Parks (Sandia), PERI package for Peridynamics * Roy Pollock (LLNL), Ewald and PPPM solvers -* Christian Trott (Sandia), USER-CUDA and KOKKOS packages -* Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD +* Christian Trott (Sandia), CUDA and KOKKOS packages +* Ilya Valuev (JIHT), AWPMD package for wave packet MD * Greg Wagner (Northwestern U), MEAM package for MEAM potential ---------- diff --git a/doc/src/Library.rst b/doc/src/Library.rst index 0eddc5afb3..05b652f7a7 100644 --- a/doc/src/Library.rst +++ b/doc/src/Library.rst @@ -31,7 +31,7 @@ that are not possible with existing input script commands. applies to the core LAMMPS code and less so on add-on packages, especially when those packages require additional code in the *lib* folder, interface LAMMPS to Fortran libraries, or the code uses - static variables (like the USER-COLVARS package). + static variables (like the COLVARS package). Another major issue to deal with is to correctly handle MPI. Creating a LAMMPS instance requires passing an MPI communicator, or diff --git a/doc/src/Modify_compute.rst b/doc/src/Modify_compute.rst index e910d6f8e2..bf580a6561 100644 --- a/doc/src/Modify_compute.rst +++ b/doc/src/Modify_compute.rst @@ -53,5 +53,5 @@ in two stages: the callback function is registered with the pair style and then called from the Pair::ev_tally() function, which is called for each pair after force and energy has been computed for this pair. Then the tallied values are retrieved with the standard compute_scalar or -compute_vector or compute_peratom methods. The :doc:`compute styles in the USER-TALLY package ` +compute_vector or compute_peratom methods. The :doc:`compute styles in the TALLY package ` provide *examples* for utilizing this mechanism. diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index 4382753c42..42ce8d2498 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -49,13 +49,11 @@ with gzip. Please only use gzip compression, as this works well and is available on all platforms. If the new features/files are broadly useful we may add them as core -files to LAMMPS or as part of a :doc:`standard package `. Else we will add them as a -user-contributed file or :doc:`user package `. Examples -of user packages are in src sub-directories that start with USER. The +files to LAMMPS or as part of a :doc:`package `. The USER-MISC package is simply a collection of (mostly) unrelated single -files, which is the simplest way to have your contribution quickly -added to the LAMMPS distribution. All the standard and user packages -are listed and described on the :doc:`Packages details ` doc page. +files, which is the simplest way to have your contribution quickly added +to the LAMMPS distribution. All packages are listed and described +on the :doc:`Packages details ` doc page. Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL @@ -65,27 +63,19 @@ on request only and with files that are authorized for that kind of distribution removed (e.g. interface to FFTW). See the :doc:`LAMMPS license ` doc page for details. -With user packages and files, all we are really providing (aside from -the fame and fortune that accompanies having your name in the source -code and on the `Authors page `_ -of the `LAMMPS WWW site `_), is a means for you to distribute your -work to the LAMMPS user community, and a mechanism for others to -easily try out your new feature. This may help you find bugs or make -contact with new collaborators. Note that you're also implicitly -agreeing to support your code which means answer questions, fix bugs, -and maintain it if LAMMPS changes in some way that breaks it (an -unusual event). - .. note:: - If you prefer to actively develop and support your add-on - feature yourself, then you may wish to make it available for download - from your own website, as a user package that LAMMPS users can add to - their copy of LAMMPS. See the `Offsite LAMMPS packages and tools `_ page of the LAMMPS web - site for examples of groups that do this. We are happy to advertise - your package and web site from that page. Simply email the - `developers `_ with info about - your package and we will post it there. + If you prefer to actively develop and support your add-on feature + yourself, then you may wish to make it available for download from + your own website, as a user package that LAMMPS users can add to + their copy of LAMMPS. See the `Offsite LAMMPS packages and tools + `_ page of the LAMMPS web site + for examples of groups that do this. We are happy to advertise your + package and web site from that page. Simply email the `developers + `_ with info about your package + and we will post it there. We recommend to name external packages + USER-\ so they can be easily distinguished from bundled packages + that do not have the USER- prefix. .. _lws: https://www.lammps.org @@ -167,17 +157,20 @@ packages in the src directory for examples. If you are uncertain, please ask. 2 source files. You can do this multiple times if you wish to contribute several individual features. -* If you want your contribution to be added as a user-contribution and - it is several related features, it is probably best to make it a user - package directory with a name like USER-FOO. In addition to your new - files, the directory should contain a README text file. The README - should contain your name and contact information and a brief +* If you want your contribution to be added and it has several related + features or is dependent on an external or bundled library, it is best + to make it a package directory with a name like FOO. In addition to + your new files, the directory should contain a README text file. The + README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README - and Install.sh files in other USER directories as examples. Send us a - tarball of this USER-FOO directory. + and Install.sh files in other directories as examples. Submit a pull + request on GitHub or send us a tarball of this FOO directory. Pull + requests are strongly encouraged since the greatly reduce the effort + to integrate a contribution and simplify the process of adjusting the + contributed code to cleanly integrate into the LAMMPS distribution. * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other @@ -190,21 +183,21 @@ packages in the src directory for examples. If you are uncertain, please ask. code. * You **must** also create a **documentation** file for each new command - or style you are adding to LAMMPS. For simplicity and convenience, the - documentation of groups of closely related commands or styles may be - combined into a single file. This will be one file for a single-file - feature. For a package, it might be several files. These are text - files with a .rst extension using the `reStructuredText `_ - markup language, that are then converted to HTML and PDF using the - `Sphinx `_ documentation generator tool. Running Sphinx with - the included configuration requires Python 3.x. Configuration - settings and custom extensions for this conversion are included in the - source distribution, and missing python packages will be transparently - downloaded into a virtual environment via pip. Thus, if your local - system is missing required packages, you need access to the - internet. The translation can be as simple as doing "make html pdf" in - the doc folder. As appropriate, the text files can include inline - mathematical expression or figures (see doc/JPG for examples). + or style you are adding to LAMMPS. For simplicity and convenience, + the documentation of groups of closely related commands or styles may + be combined into a single file. This will be one file for a + single-file feature. For a package, it might be several files. These + are text files with a .rst extension using the `reStructuredText + `_ markup language, that are then converted to HTML and PDF + using the `Sphinx `_ documentation generator tool. Running + Sphinx with the included configuration requires Python 3.x. + Configuration settings and custom extensions for this conversion are + included in the source distribution, and missing python packages will + be transparently downloaded into a virtual environment via pip. Thus, + if your local system is missing required packages, you need access to + the internet. The translation can be as simple as doing "make html + pdf" in the doc folder. As appropriate, the text files can include + inline mathematical expression or figures (see doc/JPG for examples). Additional PDF files with further details (see doc/PDF for examples) may also be included. The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for @@ -212,21 +205,21 @@ packages in the src directory for examples. If you are uncertain, please ask. cite itself. Citation labels must be unique across all .rst files. The "Restrictions" section of the doc page should indicate if your command is only available if LAMMPS is built with the appropriate - USER-MISC or USER-FOO package. See other user package doc files for - examples of how to do this. Please run at least "make html" and "make - spelling" and carefully inspect and proofread the resulting HTML - format doc page before submitting your code. Upon submission of a - pull request, checks for error free completion of the HTML and PDF - build will be performed and also a spell check, a check for correct - anchors and labels, and a check for completeness of references all - styles in their corresponding tables and lists is run. In case the - spell check reports false positives they can be added to the file + USER-MISC or FOO package. See other package doc files for examples of + how to do this. Please run at least "make html" and "make spelling" + and carefully inspect and proofread the resulting HTML format doc page + before submitting your code. Upon submission of a pull request, + checks for error free completion of the HTML and PDF build will be + performed and also a spell check, a check for correct anchors and + labels, and a check for completeness of references all styles in their + corresponding tables and lists is run. In case the spell check + reports false positives they can be added to the file doc/utils/sphinx-config/false_positives.txt * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require - large data files as input. See directories under examples/USER for + large data files as input. See directories under examples/PACKAGES for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind @@ -234,7 +227,7 @@ packages in the src directory for examples. If you are uncertain, please ask. * If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the \*.cpp - source file. See src/USER-EFF/atom_vec_electron.cpp for an example. + source file. See src/EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code registering this variable is added to the constructor of the class. If there is additional functionality (which diff --git a/doc/src/PDF/USER-CGDNA.pdf b/doc/src/PDF/CG-DNA.pdf similarity index 100% rename from doc/src/PDF/USER-CGDNA.pdf rename to doc/src/PDF/CG-DNA.pdf diff --git a/doc/src/PDF/SMD_LAMMPS_userguide.pdf b/doc/src/PDF/MACHDYN_LAMMPS_userguide.pdf similarity index 100% rename from doc/src/PDF/SMD_LAMMPS_userguide.pdf rename to doc/src/PDF/MACHDYN_LAMMPS_userguide.pdf diff --git a/doc/src/Packages.rst b/doc/src/Packages.rst index 042485eb4b..31ac02df3c 100644 --- a/doc/src/Packages.rst +++ b/doc/src/Packages.rst @@ -14,6 +14,5 @@ LAMMPS build process. .. toctree:: :maxdepth: 1 - Packages_standard - Packages_user + Packages_list Packages_details diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index e4a371571b..cf70be0d4b 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1,13 +1,12 @@ Package details =============== -Here is a brief description of all the standard and user packages in -LAMMPS. It lists authors (if applicable) and summarizes the package -contents. It has specific instructions on how to install the package, -including, if necessary, info on how to download or build any extra -library it requires. It also gives links to documentation, example -scripts, and pictures/movies (if available) that illustrate use of the -package. +Here is a brief description of all packages in LAMMPS. It lists authors +(if applicable) and summarizes the package contents. It has specific +instructions on how to install the package, including, if necessary, +info on how to download or build any extra library it requires. It also +gives links to documentation, example scripts, and pictures/movies (if +available) that illustrate use of the package. The majority of packages can be included in a LAMMPS build with a single setting (``-D PGK_=on`` for CMake) or command @@ -27,92 +26,119 @@ page gives those details. .. table_from_list:: :columns: 6 + * :ref:`ADIOS ` * :ref:`ASPHERE ` + * :ref:`ATC ` + * :ref:`AWPMD ` + * :ref:`BOCS ` * :ref:`BODY ` + * :ref:`BROWNIAN ` + * :ref:`CG-DNA ` + * :ref:`CG-SDK ` * :ref:`CLASS2 ` * :ref:`COLLOID ` + * :ref:`COLVARS ` * :ref:`COMPRESS ` * :ref:`CORESHELL ` + * :ref:`DIELECTRIC ` + * :ref:`DIFFRACTION ` * :ref:`DIPOLE ` + * :ref:`DPD-BASIC ` + * :ref:`DPD-MESO ` + * :ref:`DPD-REACT ` + * :ref:`DPD-SMOOTH ` + * :ref:`DRUDE ` + * :ref:`EFF ` + * :ref:`FEP ` * :ref:`GPU ` * :ref:`GRANULAR ` + * :ref:`H5MD ` + * :ref:`INTEL ` * :ref:`KIM ` * :ref:`KOKKOS ` * :ref:`KSPACE ` + * :ref:`LATBOLTZ ` * :ref:`LATTE ` + * :ref:`MACHDYN ` + * :ref:`MANIFOLD ` * :ref:`MANYBODY ` * :ref:`MC ` + * :ref:`MDI ` + * :ref:`MEAM ` + * :ref:`MESONT ` * :ref:`MESSAGE ` + * :ref:`MGPT ` * :ref:`MISC ` - * :ref:`MLIAP ` + * :ref:`ML-HDNNP ` + * :ref:`ML-IAP ` + * :ref:`ML-PACE ` + * :ref:`ML-QUIP ` + * :ref:`ML-RANN ` + * :ref:`ML-SNAP ` + * :ref:`MOFFF ` * :ref:`MOLECULE ` + * :ref:`MOLFILE ` * :ref:`MPIIO ` * :ref:`MSCG ` + * :ref:`NETCDF ` + * :ref:`OPENMP ` * :ref:`OPT ` * :ref:`PERI ` + * :ref:`PHONON ` * :ref:`PLUGIN ` + * :ref:`PLUMED ` * :ref:`POEMS ` + * :ref:`PTM ` * :ref:`PYTHON ` * :ref:`QEQ ` + * :ref:`QMMM ` + * :ref:`QTB ` + * :ref:`REACTION ` + * :ref:`REAXFF ` * :ref:`REPLICA ` * :ref:`RIGID ` + * :ref:`SCAFACOS ` * :ref:`SHOCK ` - * :ref:`SNAP ` + * :ref:`SMTBQ ` + * :ref:`SPH ` * :ref:`SPIN ` * :ref:`SRD ` + * :ref:`TALLY ` + * :ref:`UEF ` * :ref:`VORONOI ` - -.. table_from_list:: - :columns: 6 - - * :ref:`USER-ADIOS ` - * :ref:`USER-ATC ` - * :ref:`USER-AWPMD ` - * :ref:`USER-BOCS ` - * :ref:`USER-BROWNIAN ` - * :ref:`USER-CGDNA ` - * :ref:`USER-CGSDK ` - * :ref:`USER-COLVARS ` - * :ref:`USER-DIELECTRIC ` - * :ref:`USER-DIFFRACTION ` - * :ref:`USER-DPD ` - * :ref:`USER-DRUDE ` - * :ref:`USER-EFF ` - * :ref:`USER-FEP ` - * :ref:`USER-H5MD ` - * :ref:`USER-HDNNP ` - * :ref:`USER-INTEL ` - * :ref:`USER-LB ` - * :ref:`USER-MANIFOLD ` - * :ref:`USER-MDI ` - * :ref:`USER-MEAMC ` - * :ref:`USER-MESODPD ` - * :ref:`USER-MESONT ` - * :ref:`USER-MGPT ` + * :ref:`VTK ` + * :ref:`YAFF ` * :ref:`USER-MISC ` - * :ref:`USER-MOFFF ` - * :ref:`USER-MOLFILE ` - * :ref:`USER-NETCDF ` - * :ref:`USER-OMP ` - * :ref:`USER-PACE ` - * :ref:`USER-PHONON ` - * :ref:`USER-PLUMED ` - * :ref:`USER-PTM ` - * :ref:`USER-QMMM ` - * :ref:`USER-QTB ` - * :ref:`USER-QUIP ` - * :ref:`USER-RANN ` - * :ref:`USER-REACTION ` - * :ref:`USER-REAXC ` - * :ref:`USER-SCAFACOS ` - * :ref:`USER-SDPD ` - * :ref:`USER-SMD ` - * :ref:`USER-SMTBQ ` - * :ref:`USER-SPH ` - * :ref:`USER-TALLY ` - * :ref:`USER-UEF ` - * :ref:`USER-VTK ` - * :ref:`USER-YAFF ` + +---------- + +.. _PKG-ADIOS: + +ADIOS package +------------------ + +**Contents:** + +ADIOS is a high-performance I/O library. This package implements the +:doc:`dump atom/adios `, :doc:`dump custom/adios ` and +:doc:`read_dump ... format adios ` +commands to write and read data using the ADIOS library. + +**Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/ADIOS: filenames -> commands +* src/ADIOS/README +* examples/PACKAGES/adios +* https://github.com/ornladios/ADIOS2 +* :doc:`dump atom/adios ` +* :doc:`dump custom/adios ` +* :doc:`read_dump ` ---------- @@ -141,6 +167,93 @@ particle models including ellipsoids, 2d lines, and 3d triangles. ---------- +.. _PKG-ATC: + +ATC package +---------------- + +**Contents:** + +ATC stands for atoms-to-continuum. This package implements a :doc:`fix atc ` command to either couple molecular dynamics with +continuum finite element equations or perform on-the-fly conversion of +atomic information to continuum fields. + +**Authors:** Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/ATC: filenames -> commands +* src/ATC/README +* :doc:`fix atc ` +* examples/PACKAGES/atc +* https://www.lammps.org/pictures.html#atc + +---------- + +.. _PKG-AWPMD: + +AWPMD package +------------------ + +**Contents:** + +AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This +package implements an atom, pair, and fix style which allows electrons +to be treated as explicit particles in a classical molecular dynamics +model. + +**Author:** Ilya Valuev (JIHT, Russia). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/AWPMD: filenames -> commands +* src/AWPMD/README +* :doc:`pair_style awpmd/cut ` +* examples/PACKAGES/awpmd + +---------- + +.. _PKG-BOCS: + +BOCS package +----------------- + +**Contents:** + +This package provides :doc:`fix bocs `, a modified version +of :doc:`fix npt ` which includes the pressure correction to +the barostat as outlined in: + +N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that +accurately describe the structure, pressure, and compressibility of +molecular liquids," J. Chem. Phys. 143, 243148 (2015). + +**Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The +Pennsylvania State University) + +**Supporting info:** + +The BOCS package for LAMMPS is part of the BOCS software package: +`https://github.com/noid-group/BOCS `_ + +See the following reference for information about the entire package: + +Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. +"BOCS: Bottom-Up Open-Source Coarse-Graining Software." +J. Phys. Chem. B. 122, 13, 3363-3377 (2018). + +Example inputs are in the examples/PACKAGES/bocs folder. + +---------- + .. _PKG-BODY: BODY package @@ -164,6 +277,79 @@ overview. ---------- +.. _PKG-BROWNIAN: + +BROWNIAN package +--------------------- + +**Contents:** + +This package provides :doc:`fix brownian, fix brownian/sphere, and +fix brownian/asphere ` as well as +:doc:`fix propel/self ` which allow to do Brownian +Dynamics time integration of point, spherical and aspherical particles +and also support self-propelled particles. + +**Authors:** Sam Cameron (University of Bristol), +Stefan Paquay (while at Brandeis University) (initial version of fix propel/self) + +Example inputs are in the examples/PACKAGES/brownian folder. + +---------- + +.. _PKG-CG-DNA: + +CG-DNA package +------------------ + +**Contents:** + +Several pair styles, bond styles, and integration fixes for coarse-grained +modelling of single- and double-stranded DNA and RNA based on the oxDNA and +oxRNA model of Doye, Louis and Ouldridge. The package includes Langevin-type +rigid-body integrators with improved stability. + +**Author:** Oliver Henrich (University of Strathclyde, Glasgow). + +**Supporting info:** + +* src/CG-DNA: filenames -> commands +* /src/CG-DNA/README +* :doc:`pair_style oxdna/\* ` +* :doc:`pair_style oxdna2/\* ` +* :doc:`pair_style oxrna2/\* ` +* :doc:`bond_style oxdna/\* ` +* :doc:`bond_style oxdna2/\* ` +* :doc:`bond_style oxrna2/\* ` +* :doc:`fix nve/dotc/langevin ` + +---------- + +.. _PKG-CG-SDK: + +CG-SDK package +------------------ + +**Contents:** + +Several pair styles and an angle style which implement the +coarse-grained SDK model of Shinoda, DeVane, and Klein which enables +simulation of ionic liquids, electrolytes, lipids and charged amino +acids. + +**Author:** Axel Kohlmeyer (Temple U). + +**Supporting info:** + +* src/CG-SDK: filenames -> commands +* src/CG-SDK/README +* :doc:`pair_style lj/sdk/\* ` +* :doc:`angle_style sdk ` +* examples/PACKAGES/cgsdk +* https://www.lammps.org/pictures.html#cg + +---------- + .. _PKG-CLASS2: CLASS2 package @@ -215,6 +401,41 @@ Higdon's group at UIUC. ---------- +.. _PKG-COLVARS: + +COLVARS package +-------------------- + +**Contents:** + +COLVARS stands for collective variables, which can be used to +implement various enhanced sampling methods, including Adaptive +Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and +Restraints. A :doc:`fix colvars ` command is implemented +which wraps a COLVARS library, which implements these methods. +simulations. + +**Authors:** The COLVARS library is written and maintained by +Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) +and Jerome Henin (LISM, CNRS, Marseille, France), originally for +the NAMD MD code, but with portability in mind. Axel Kohlmeyer +(Temple U) provided the interface to LAMMPS. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/COLVARS: filenames -> commands +* `doc/PDF/colvars-refman-lammps.pdf `_ +* src/COLVARS/README +* lib/colvars/README +* :doc:`fix colvars ` +* examples/PACKAGES/colvars + +---------- + .. _PKG-COMPRESS: COMPRESS package @@ -274,6 +495,51 @@ this package. ---------- +.. _PKG-DIELECTRIC: + +DIELECTRIC package +------------------------ + +**Contents:** + +An atom style, multiple pair styles, several fixes, Kspace styles and a +compute for simulating systems using boundary element solvers for +computing the induced charges at the interface between two media with +different dielectric constants. + +**Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U) + +**Supporting info:** + +* src/DIELECTRIC: filenames -> commands +* :doc:`compute efield/atom ` +* TODO: add all styles +* examples/PACKAGES/dielectric + +---------- + +.. _PKG-DIFFRACTION: + +DIFFRACTION package +------------------------ + +**Contents:** + +Two computes and a fix for calculating x-ray and electron diffraction +intensities based on kinematic diffraction theory. + +**Author:** Shawn Coleman while at the U Arkansas. + +**Supporting info:** + +* src/DIFFRACTION: filenames -> commands +* :doc:`compute saed ` +* :doc:`compute xrd ` +* :doc:`fix saed/vtk ` +* examples/PACKAGES/diffraction + +---------- + .. _PKG-DIPOLE: DIPOLE package @@ -295,6 +561,224 @@ short-range or long-range interactions. ---------- +.. _PKG-DPD-BASIC: + +DPD-BASIC package +-------------------- + +**Contents:** + +Pair styles for the basic dissipative particle dynamics (DPD) method +and DPD thermostatting. + +**Author:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP) + +**Supporting info:** + +* src/DPD-BASIC: filenames -> commands +* :doc:`pair_style dpd ` +* :doc:`pair_style dpd/tstat ` +* :doc:`pair_style dpd/ext ` +* :doc:`pair_style dpd/ext/tstat ` +* examples/PACKAGES/dpd-basic + +---------- + +.. _PKG-DPD-MESO: + +DPD-MESO package +-------------------- + +**Contents:** + +Several extensions of the dissipative particle dynamics (DPD) +method. Specifically, energy-conserving DPD (eDPD) that can model +non-isothermal processes, many-body DPD (mDPD) for simulating +vapor-liquid coexistence, and transport DPD (tDPD) for modeling +advection-diffusion-reaction systems. The equations of motion of these +DPD extensions are integrated through a modified velocity-Verlet (MVV) +algorithm. + +**Author:** Zhen Li (Division of Applied Mathematics, Brown University) + +**Supporting info:** + +* src/DPD-MESO: filenames -> commands +* src/DPD-MESO/README +* :doc:`atom_style edpd ` +* :doc:`pair_style edpd ` +* :doc:`pair_style mdpd ` +* :doc:`pair_style tdpd ` +* :doc:`fix mvv/dpd ` +* examples/PACKAGES/mesodpd +* https://www.lammps.org/movies.html#mesodpd + +---------- + +.. _PKG-DPD-REACT: + +DPD-REACT package +----------------- + +**Contents:** + +DPD stands for dissipative particle dynamics. This package implements +coarse-grained DPD-based models for energetic, reactive molecular +crystalline materials. It includes many pair styles specific to these +systems, including for reactive DPD, where each particle has internal +state for multiple species and a coupled set of chemical reaction ODEs +are integrated each timestep. Highly accurate time integrators for +isothermal, isoenergetic, isobaric and isenthalpic conditions are +included. These enable long timesteps via the Shardlow splitting +algorithm. + +**Authors:** Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John +Brennan (ARL). + +**Supporting info:** + +* src/DPD-REACT: filenames -> commands +* /src/DPD-REACT/README +* :doc:`compute dpd ` +* :doc:`compute dpd/atom ` +* :doc:`fix eos/cv ` +* :doc:`fix eos/table ` +* :doc:`fix eos/table/rx ` +* :doc:`fix shardlow ` +* :doc:`fix rx ` +* :doc:`pair_style table/rx ` +* :doc:`pair_style dpd/fdt ` +* :doc:`pair_style dpd/fdt/energy ` +* :doc:`pair_style exp6/rx ` +* :doc:`pair_style multi/lucy ` +* :doc:`pair_style multi/lucy/rx ` +* examples/PACKAGES/dpd-react + +---------- + +.. _PKG-DPD-SMOOTH: + +DPD-SMOOTH package +------------------ + +**Contents:** + +A pair style for smoothed dissipative particle dynamics (SDPD), which +is an extension of smoothed particle hydrodynamics (SPH) to mesoscale +where thermal fluctuations are important (see the +:ref:`SPH package `). +Also two fixes for moving and rigid body integration of SPH/SDPD particles +(particles of atom_style meso). + +**Author:** Morteza Jalalvand (Institute for Advanced Studies in Basic +Sciences, Iran). + +**Supporting info:** + +* src/DPD-SMOOTH: filenames -> commands +* src/DPD-SMOOTH/README +* :doc:`pair_style sdpd/taitwater/isothermal ` +* :doc:`fix meso/move ` +* :doc:`fix rigid/meso ` +* examples/PACKAGES/dpd-smooth + +---------- + +.. _PKG-DRUDE: + +DRUDE package +------------------ + +**Contents:** + +Fixes, pair styles, and a compute to simulate thermalized Drude +oscillators as a model of polarization. See the :doc:`Howto drude ` and :doc:`Howto drude2 ` pages +for an overview of how to use the package. There are auxiliary tools +for using this package in tools/drude. + +**Authors:** Alain Dequidt (U Clermont Auvergne), Julien +Devemy (CNRS), and Agilio Padua (ENS de Lyon). + +**Supporting info:** + +* src/DRUDE: filenames -> commands +* :doc:`Howto drude ` +* :doc:`Howto drude2 ` +* :doc:`Howto polarizable ` +* src/DRUDE/README +* :doc:`fix drude ` +* :doc:`fix drude/transform/\* ` +* :doc:`compute temp/drude ` +* :doc:`pair_style thole ` +* :doc:`pair_style lj/cut/thole/long ` +* examples/PACKAGES/drude +* tools/drude + +---------- + +.. _PKG-EFF: + +EFF package +---------------- + +**Contents:** + +EFF stands for electron force field which allows a classical MD code +to model electrons as particles of variable radius. This package +contains atom, pair, fix and compute styles which implement the eFF as +described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, +JCC, 2010. The eFF potential was first introduced by Su and Goddard, +in 2007. There are auxiliary tools for using this package in +tools/eff; see its README file. + +**Author:** Andres Jaramillo-Botero (CalTech). + +**Supporting info:** + +* src/EFF: filenames -> commands +* src/EFF/README +* :doc:`atom_style electron ` +* :doc:`fix nve/eff ` +* :doc:`fix nvt/eff ` +* :doc:`fix npt/eff ` +* :doc:`fix langevin/eff ` +* :doc:`compute temp/eff ` +* :doc:`pair_style eff/cut ` +* :doc:`pair_style eff/inline ` +* examples/PACKAGES/eff +* tools/eff/README +* tools/eff +* https://www.lammps.org/movies.html#eff + +---------- + +.. _PKG-FEP: + +FEP package +---------------- + +**Contents:** + +FEP stands for free energy perturbation. This package provides +methods for performing FEP simulations by using a :doc:`fix adapt/fep ` command with soft-core pair potentials, +which have a "soft" in their style name. There are auxiliary tools +for using this package in tools/fep; see its README file. + +**Author:** Agilio Padua (ENS de Lyon) + +**Supporting info:** + +* src/FEP: filenames -> commands +* src/FEP/README +* :doc:`fix adapt/fep ` +* :doc:`compute fep ` +* :doc:`pair_style \*/soft ` +* examples/PACKAGES/fep +* tools/fep/README +* tools/fep + +---------- + .. _PKG-GPU: GPU package @@ -352,7 +836,6 @@ potentials. * src/GRANULAR: filenames -> commands * :doc:`Howto granular ` -* :doc:`compute fabric ` * :doc:`fix pour ` * :doc:`fix wall/gran ` * :doc:`pair_style gran/hooke ` @@ -368,6 +851,88 @@ potentials. ---------- +.. _PKG-H5MD: + +H5MD package +----------------- + +**Contents:** + +H5MD stands for HDF5 for MD. `HDF5 `_ is a portable, binary, +self-describing file format, used by many scientific simulations. +H5MD is a format for molecular simulations, built on top of HDF5. +This package implements a :doc:`dump h5md ` command to output +LAMMPS snapshots in this format. + +.. _HDF5: http://www.hdfgroup.org/HDF5 + +To use this package you must have the HDF5 library available on your +system. + +**Author:** Pierre de Buyl (KU Leuven) created both the package and the +H5MD format. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/H5MD: filenames -> commands +* src/H5MD/README +* lib/h5md/README +* :doc:`dump h5md ` + +---------- + +.. _PKG-INTEL: + +INTEL package +------------------ + +**Contents:** + +Dozens of pair, fix, bond, angle, dihedral, improper, and kspace +styles which are optimized for Intel CPUs and KNLs (Knights Landing). +All of them have an "intel" in their style name. The +:doc:`INTEL package ` page gives details of what hardware and +compilers are required on your system, and how to build and use this +package. Its styles can be invoked at run time via the "-sf intel" or +"-suffix intel" :doc:`command-line switches `. Also see +the :ref:`KOKKOS `, :ref:`OPT `, and :ref:`OPENMP ` packages, +which have styles optimized for CPUs and KNLs. + +You need to have an Intel compiler, version 14 or higher to take full +advantage of this package. While compilation with GNU compilers is +supported, performance will be sub-optimal. + +.. note:: + + the INTEL package contains styles that require using the + -restrict flag, when compiling with Intel compilers. + +**Author:** Mike Brown (Intel). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/INTEL: filenames -> commands +* src/INTEL/README +* :doc:`Accelerator packages ` +* :doc:`INTEL package ` +* :doc:`Section 2.6 -sf intel ` +* :doc:`Section 2.6 -pk intel ` +* :doc:`package intel ` +* Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, + :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (i) +* src/INTEL/TEST +* `Benchmarks page `_ of web site + +---------- + .. _PKG-KIM: KIM package @@ -448,7 +1013,7 @@ style name. The :doc:`KOKKOS package ` page gives details of what hardware and software is required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf kk" or "-suffix kk" :doc:`command-line switches `. Also see the :ref:`GPU `, :ref:`OPT `, -:ref:`USER-INTEL `, and :ref:`USER-OMP ` packages, which +:ref:`INTEL `, and :ref:`OPENMP ` packages, which have styles optimized for CPUs, KNLs, and GPUs. You must have a C++14 compatible compiler to use this package. @@ -522,6 +1087,30 @@ different FFT options for your LAMPMS build. ---------- +.. _PKG-LATBOLTZ: + +LATBOLTZ package +---------------- + +**Contents:** + +Fixes which implement a background Lattice-Boltzmann (LB) fluid, which +can be used to model MD particles influenced by hydrodynamic forces. + +**Authors:** Frances Mackay and Colin Denniston (University of Western +Ontario). + +**Supporting info:** + +* src/LATBOLTZ: filenames -> commands +* src/LATBOLTZ/README +* :doc:`fix lb/fluid ` +* :doc:`fix lb/momentum ` +* :doc:`fix lb/viscous ` +* examples/PACKAGES/latboltz + +---------- + .. _PKG-LATTE: LATTE package @@ -558,6 +1147,75 @@ This package has :ref:`specific installation instructions ` on the :doc:` ---------- +.. _PKG-MACHDYN: + +MACHDYN package +---------------- + +**Contents:** + +An atom style, fixes, computes, and several pair styles which +implements smoothed Mach dynamics (SMD) for solids, which is a model +related to smoothed particle hydrodynamics (SPH) for liquids (see the +:ref:`SPH package `). + +This package solves solids mechanics problems via a state of the art +stabilized meshless method with hourglass control. It can specify +hydrostatic interactions independently from material strength models, +i.e. pressure and deviatoric stresses are separated. It provides many +material models (Johnson-Cook, plasticity with hardening, +Mie-Grueneisen, Polynomial EOS) and allows new material models to be +added. It implements rigid boundary conditions (walls) which can be +specified as surface geometries from \*.STL files. + +**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed +Dynamics, Ernst Mach Institute, Germany). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/MACHDYN: filenames -> commands +* src/MACHDYN/README +* doc/PDF/MACHDYN_LAMMPS_userguide.pdf +* examples/PACKAGES/machdyn +* https://www.lammps.org/movies.html#smd + +---------- + +.. _PKG-MANIFOLD: + +MANIFOLD package +--------------------- + +**Contents:** + +Several fixes and a "manifold" class which enable simulations of +particles constrained to a manifold (a 2D surface within the 3D +simulation box). This is done by applying the RATTLE constraint +algorithm to formulate single-particle constraint functions +g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) +n = grad(g). + +**Author:** Stefan Paquay (until 2017: Eindhoven University of +Technology (TU/e), The Netherlands; since 2017: Brandeis University, +Waltham, MA, USA) + +**Supporting info:** + +* src/MANIFOLD: filenames -> commands +* src/MANIFOLD/README +* :doc:`Howto manifold ` +* :doc:`fix manifoldforce ` +* :doc:`fix nve/manifold/rattle ` +* :doc:`fix nvt/manifold/rattle ` +* examples/PACKAGES/manifold +* https://www.lammps.org/movies.html#manifold + +---------- + .. _PKG-MANYBODY: MANYBODY package @@ -611,6 +1269,100 @@ bonds, for performing atomic swaps, and performing grand-canonical MC ---------- +.. _PKG-MDI: + +MDI package +---------------- + +**Contents:** + +A LAMMPS command and fix to allow client-server coupling of LAMMPS to +other atomic or molecular simulation codes via the `MolSSI Driver Interface +(MDI) library `_. + +**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com + +**Supporting info:** + +* src/MDI/README +* :doc:`mdi/engine ` +* :doc:`fix mdi/engine ` +* examples/PACKAGES/mdi + +---------- + +.. _PKG-MEAM: + +MEAM package +------------------ + +**Contents:** + +A pair style for the modified embedded atom (MEAM) potential +translated from the Fortran version in the (obsolete) MEAM package +to plain C++. The MEAM fully replaces the MEAM package, which +has been removed from LAMMPS after the 12 December 2018 version. + +**Author:** Sebastian Huetter, (Otto-von-Guericke University Magdeburg) +based on the Fortran version of Greg Wagner (Northwestern U) while at +Sandia. + +**Supporting info:** + +* src/MEAM: filenames -> commands +* src/MEAM/README +* :doc:`pair_style meam ` +* examples/meam + +---------- + +.. _PKG-MESONT: + +MESONT package +------------------- + +**Contents:** + +MESONT is a LAMMPS package for simulation of nanomechanics of +nanotubes (NTs). The model is based on a coarse-grained representation +of NTs as "flexible cylinders" consisting of a variable number of +segments. Internal interactions within a NT and the van der Waals +interaction between the tubes are described by a mesoscopic force field +designed and parameterized based on the results of atomic-level +molecular dynamics simulations. The description of the force field is +provided in the papers listed below. This package contains two +independent implementations of this model: :doc:`pair_style mesocnt +` is a (minimal) C++ implementation, and :doc:`pair_style +mesont/tpm ` is a more general and feature rich +implementation based on a Fortran library in the ``lib/mesont`` folder. + +**Download of potential files:** + +The potential files for these pair styles are *very* large and thus +are not included in the regular downloaded packages of LAMMPS or the +git repositories. Instead, they will be automatically downloaded +from a web server when the package is installed for the first time. + +**Authors of the *mesont* styles:** + +Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia) + +**Author of the *mesocnt* pair style:** +Philipp Kloza (U Cambridge) + +**Supporting info:** + +* src/MESONT: filenames -> commands +* src/MESONT/README +* :doc:`atom_style mesont ` +* :doc:`pair_style mesont/tpm ` +* :doc:`compute mesont ` +* :doc:`pair_style mesocnt ` +* examples/PACKAGES/mesont +* tools/mesont + +---------- + .. _PKG-MESSAGE: MESSAGE package @@ -637,6 +1389,33 @@ This package has :ref:`specific installation instructions ` on the :doc ---------- +.. _PKG-MGPT: + +MGPT package +----------------- + +**Contents:** + +A pair style which provides a fast implementation of the quantum-based +MGPT multi-ion potentials. The MGPT or model GPT method derives from +first-principles DFT-based generalized pseudopotential theory (GPT) +through a series of systematic approximations valid for mid-period +transition metals with nearly half-filled d bands. The MGPT method +was originally developed by John Moriarty at LLNL. The pair style in +this package calculates forces and energies using an optimized +matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. + +**Authors:** Tomas Oppelstrup and John Moriarty (LLNL). + +**Supporting info:** + +* src/MGPT: filenames -> commands +* src/MGPT/README +* :doc:`pair_style mgpt ` +* examples/PACKAGES/mgpt + +---------- + .. _PKG-MISC: MISC package @@ -658,6 +1437,8 @@ listing, "ls src/MISC", to see the list of commands. * src/MISC: filenames -> commands * :doc:`compute ti ` * :doc:`fix evaporate ` +* :doc:`fix imd ` +* :doc:`fix oneway ` * :doc:`fix orient/fcc ` * :doc:`fix ttm ` * :doc:`fix thermal/conductivity ` @@ -669,10 +1450,44 @@ listing, "ls src/MISC", to see the list of commands. ---------- -.. _PKG-MLIAP: +.. _PKG-ML-HDNNP: -MLIAP package -------------- +ML-HDNNP package +------------------ + +**Contents:** + +A :doc:`pair_style hdnnp ` command which allows to use +high-dimensional neural network potentials (HDNNPs), a form of machine learning +potentials. HDNNPs must be carefully trained prior to their application in a +molecular dynamics simulation. + +.. _n2p2: https://github.com/CompPhysVienna/n2p2 + +To use this package you must have the `n2p2 `_ library installed and +compiled on your system. + +**Author:** Andreas Singraber + +**Install:** + +This package has :ref:`specific installation instructions ` on the +:doc:`Build extras ` page. + +**Supporting info:** + +* src/ML-HDNNP: filenames -> commands +* src/ML-HDNNP/README +* lib/hdnnp/README +* :doc:`pair_style hdnnp ` +* examples/PACKAGES/hdnnp + +---------- + +.. _PKG-ML-IAP: + +ML-IAP package +-------------- **Contents:** @@ -680,7 +1495,7 @@ A general interface for machine-learning interatomic potentials, including PyTor **Install:** -To use this package, also the :ref:`SNAP package ` package needs +To use this package, also the :ref:`ML-SNAP package ` package needs to be installed. To make the *mliappy* model available, also the :ref:`PYTHON package ` package needs to be installed, the version of Python must be 3.6 or later, and the `cython `_ software @@ -690,8 +1505,8 @@ must be installed. **Supporting info:** -* src/MLIAP: filenames -> commands -* src/MLIAP/README +* src/ML-IAP: filenames -> commands +* src/ML-IAP/README.md * :doc:`pair_style mliap ` * :doc:`compute_style mliap ` * examples/mliap (see README) @@ -704,6 +1519,163 @@ therefore also needs to be installed to run those examples. ---------- +.. _PKG-ML-PACE: + +ML-PACE package +------------------- + +**Contents:** + +A pair style for the Atomic Cluster Expansion potential (ACE). +ACE is a methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. The ML-PACE +package provides an efficient implementation for running simulations +with ACE potentials. + +**Authors:** + +This package was written by Yury Lysogorskiy^1, +Cas van der Oord^2, Anton Bochkarev^1, +Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, +Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. + + ^1: Ruhr-University Bochum, Bochum, Germany + + ^2: University of Cambridge, Cambridge, United Kingdom + + ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + + ^4: University of British Columbia, Vancouver, BC, Canada + +**Install:** + +This package has :ref:`specific installation instructions ` on the +:doc:`Build extras ` page. + +**Supporting info:** + +* src/ML-PACE: filenames -> commands +* :doc:`pair_style pace ` +* examples/PACKAGES/pace + +---------- + +.. _PKG-ML-QUIP: + +ML-QUIP package +----------------- + +**Contents:** + +A :doc:`pair_style quip ` command which wraps the `QUIP +libAtoms library `_, which includes a variety of interatomic +potentials, including Gaussian Approximation Potential (GAP) models +developed by the Cambridge University group. + +.. _quip: https://github.com/libAtoms/QUIP + +To use this package you must have the QUIP libAtoms library available +on your system. + +**Author:** Albert Bartok (Cambridge University) + +**Install:** + +This package has :ref:`specific installation instructions ` on the +:doc:`Build extras ` page. + +**Supporting info:** + +* src/ML-QUIP: filenames -> commands +* src/ML-QUIP/README +* :doc:`pair_style quip ` +* examples/PACKAGES/quip + +---------- + +.. _PKG-ML-RANN: + +ML-RANN package +----------------- + +**Contents:** + +A pair style for using rapid atomistic neural network (RANN) potentials. +These neural network potentials work by first generating a series of symmetry +functions from the neighbor list and then using these values as the input layer +of a neural network. + +**Authors:** + +This package was written by Christopher Barrett +with contributions by Doyl Dickel, Mississippi State University. + +**Supporting info:** + +* src/ML-RANN: filenames -> commands +* :doc:`pair_style rann ` +* examples/PACKAGES/rann + +---------- + +.. _PKG-ML-SNAP: + +ML-SNAP package +--------------- + +**Contents:** + +A pair style for the spectral neighbor analysis potential (SNAP). +SNAP is methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. Also several +computes which analyze attributes of the potential. + +**Author:** Aidan Thompson (Sandia). + +**Supporting info:** + +* src/ML-SNAP: filenames -> commands +* :doc:`pair_style snap ` +* :doc:`compute sna/atom ` +* :doc:`compute snad/atom ` +* :doc:`compute snav/atom ` +* examples/snap + +---------- + +.. _PKG-MOFFF: + +MOFFF package +------------------ + +**Contents:** + +Pair, angle and improper styles needed to employ the MOF-FF +force field by Schmid and coworkers with LAMMPS. +MOF-FF is a first principles derived force field with the primary aim +to simulate MOFs and related porous framework materials, using spherical +Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B +2013, 250, 1128-1141. +For the usage of MOF-FF see the example in the example directory as +well as the `MOF+ `_ website. + +.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF + +**Author:** Hendrik Heenen (Technical U of Munich), +Rochus Schmid (Ruhr-University Bochum). + +**Supporting info:** + +* src/MOFFF: filenames -> commands +* src/MOFFF/README +* :doc:`pair_style buck6d/coul/gauss ` +* :doc:`angle_style class2 ` +* :doc:`angle_style cosine/buck6d ` +* :doc:`improper_style inversion/harmonic ` +* examples/PACKAGES/mofff + +---------- + .. _PKG-MOLECULE: MOLECULE package @@ -736,6 +1708,48 @@ force fields, and a TIP4P water model. ---------- +.. _PKG-MOLFILE: + +MOLFILE package +-------------------- + +**Contents:** + +A :doc:`dump molfile ` command which uses molfile plugins +that are bundled with the `VMD `_ +molecular visualization and analysis program, to enable LAMMPS to dump +snapshots in formats compatible with various molecular simulation +tools. + +To use this package you must have the desired VMD plugins available on +your system. + +Note that this package only provides the interface code, not the +plugins themselves, which will be accessed when requesting a specific +plugin via the :doc:`dump molfile ` command. Plugins can +be obtained from a VMD installation which has to match the platform +that you are using to compile LAMMPS for. By adding plugins to VMD, +support for new file formats can be added to LAMMPS (or VMD or other +programs that use them) without having to re-compile the application +itself. More information about the VMD molfile plugins can be found +at +`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile `_. + +**Author:** Axel Kohlmeyer (Temple U). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/MOLFILE: filenames -> commands +* src/MOLFILE/README +* lib/molfile/README +* :doc:`dump molfile ` + +---------- + .. _PKG-MPIIO: MPIIO package @@ -758,7 +1772,7 @@ written and read in parallel. ---------- -.. _PKG-mscg: +.. _PKG-MSCG: MSCG package ------------ @@ -790,6 +1804,101 @@ This package has :ref:`specific installation instructions ` on the :doc:`B ---------- +.. _PKG-NETCDF: + +NETCDF package +------------------- + +**Contents:** + +Dump styles for writing NetCDF formatted dump files. NetCDF is a +portable, binary, self-describing file format developed on top of +HDF5. The file contents follow the AMBER NetCDF trajectory conventions +(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions. + +To use this package you must have the NetCDF library available on your +system. + +Note that NetCDF files can be directly visualized with the following +tools: + +* `Ovito `_ (Ovito supports the AMBER convention and the extensions mentioned above) +* `VMD `_ + +.. _ovito: http://www.ovito.org + +.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/ + +**Author:** Lars Pastewka (Karlsruhe Institute of Technology). + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/NETCDF: filenames -> commands +* src/NETCDF/README +* lib/netcdf/README +* :doc:`dump netcdf ` + +---------- + +.. _PKG-OPENMP: + +OPENMP package +---------------- + +**Contents:** + +Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and +kspace styles which are altered to enable threading on many-core CPUs +via OpenMP directives. All of them have an "omp" in their style name. +The :doc:`OPENMP package ` page gives details of what hardware +and compilers are required on your system, and how to build and use +this package. Its styles can be invoked at run time via the "-sf omp" +or "-suffix omp" :doc:`command-line switches `. Also see +the :ref:`KOKKOS `, :ref:`OPT `, and :ref:`INTEL ` +packages, which have styles optimized for CPUs. + +**Author:** Axel Kohlmeyer (Temple U). + +.. note:: + + To enable multi-threading support the compile flag "-fopenmp" + and the link flag "-fopenmp" (for GNU compilers, you have to look up + the equivalent flags for other compilers) must be used to build LAMMPS. + When using Intel compilers, also the "-restrict" flag is required. + The OPENMP package can be compiled without enabling OpenMP; then + all code will be compiled as serial and the only improvement over the + regular styles are some data access optimization. These flags should + be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine. + See src/MAKE/OPTIONS/Makefile.omp for an example. + +Once you have an appropriate Makefile.machine, you can +install/un-install the package and build LAMMPS in the usual manner: + +**Install:** + +This package has :ref:`specific installation instructions ` on +the :doc:`Build extras ` page. + +**Supporting info:** + +* src/OPENMP: filenames -> commands +* src/OPENMP/README +* :doc:`Accelerator packages ` +* :doc:`OPENMP package ` +* :doc:`Command line option -suffix/-sf omp ` +* :doc:`Command line option -package/-pk omp ` +* :doc:`package omp ` +* Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, + :doc:`pair `, :doc:`bond, angle, dihedral, improper `, + :doc:`kspace `) for styles followed by (o) +* `Benchmarks page `_ of web site + +---------- + .. _PKG-OPT: OPT package @@ -803,7 +1912,7 @@ CHARMM, and Morse potentials. The styles have an "opt" suffix in their style name. The :doc:`OPT package ` page gives details of how to build and use this package. Its styles can be invoked at run time via the "-sf opt" or "-suffix opt" :doc:`command-line switches `. See also the :ref:`KOKKOS `, -:ref:`USER-INTEL `, and :ref:`USER-OMP ` packages, which +:ref:`INTEL `, and :ref:`OPENMP ` packages, which have styles optimized for CPU performance. **Authors:** James Fischer (High Performance Technologies), David Richie, @@ -855,6 +1964,34 @@ Foster (UTSA). ---------- +.. _PKG-PHONON: + +PHONON package +------------------- + +**Contents:** + +A :doc:`fix phonon ` command that calculates dynamical +matrices, which can then be used to compute phonon dispersion +relations, directly from molecular dynamics simulations. +And a :doc:`dynamical_matrix ` as well as a +:doc:`third_order ` command to compute the dynamical matrix +and third order tensor from finite differences. + +**Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" +and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" + +**Supporting info:** + +* src/PHONON: filenames -> commands +* src/PHONON/README +* :doc:`fix phonon ` +* :doc:`dynamical_matrix ` +* :doc:`third_order ` +* examples/PACKAGES/phonon + +---------- + .. _PKG-PLUGIN: PLUGIN package @@ -877,6 +2014,35 @@ having to recompile and relink LAMMPS. ---------- +.. _PKG-PLUMED: + +PLUMED package +------------------- + +**Contents:** + +The fix plumed command allows you to use the PLUMED free energy plugin +for molecular dynamics to analyze and bias your LAMMPS trajectory on +the fly. The PLUMED library is called from within the LAMMPS input +script by using the :doc:`fix plumed ` command. + +**Authors:** The `PLUMED library `_ is written +and maintained by Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni, +and Gareth Tribello. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/PLUMED/README +* lib/plumed/README +* :doc:`fix plumed ` +* examples/PACKAGES/plumed + +---------- + .. _PKG-POEMS: POEMS package @@ -906,6 +2072,28 @@ This package has :ref:`specific installation instructions ` on the :doc:` ---------- +.. _PKG-PTM: + +PTM package +---------------- + +**Contents:** + +A :doc:`compute ptm/atom ` command that calculates +local structure characterization using the Polyhedral Template +Matching methodology. + +**Author:** Peter Mahler Larsen (MIT). + +**Supporting info:** + +* src/PTM: filenames not starting with ptm\_ -> commands +* src/PTM: filenames starting with ptm\_ -> supporting code +* src/PTM/LICENSE +* :doc:`compute ptm/atom ` + +---------- + .. _PKG-PYTHON: PYTHON package @@ -959,6 +2147,135 @@ part of their formulation. ---------- +.. _PKG-QMMM: + +QMMM package +----------------- + +**Contents:** + +A :doc:`fix qmmm ` command which allows LAMMPS to be used as +the MM code in a QM/MM simulation. This is currently only available +in combination with the `Quantum ESPRESSO `_ package. + +.. _espresso: http://www.quantum-espresso.org + +To use this package you must have Quantum ESPRESSO (QE) available on +your system and include its coupling library in the compilation and +then compile LAMMPS as a library. For QM/MM calculations you then +build a custom binary with MPI support, that sets up 3 partitions with +MPI sub-communicators (for inter- and intra-partition communication) +and then calls the corresponding library interfaces on each partition +(2x LAMMPS and 1x QE). + +The current implementation supports an ONIOM style mechanical coupling +and a multi-pole based electrostatic coupling to the Quantum ESPRESSO +plane wave DFT package. The QM/MM interface has been written in a +manner that coupling to other QM codes should be possible without +changes to LAMMPS itself. + +**Authors:** Axel Kohlmeyer (Temple U). Mariella Ippolito and Carlo Cavazzoni (CINECA, Italy) + +**Install:** + +This package has :ref:`specific installation instructions ` +on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/QMMM: filenames -> commands +* src/QMMM/README +* lib/qmmm/README +* :doc:`fix phonon ` +* lib/qmmm/example-ec/README +* lib/qmmm/example-mc/README + +---------- + +.. _PKG-QTB: + +QTB package +---------------- + +**Contents:** + +Two fixes which provide a self-consistent quantum treatment of +vibrational modes in a classical molecular dynamics simulation. By +coupling the MD simulation to a colored thermostat, it introduces zero +point energy into the system, altering the energy power spectrum and +the heat capacity to account for their quantum nature. This is useful +when modeling systems at temperatures lower than their classical +limits or when temperatures ramp across the classical limits in a +simulation. + +**Author:** Yuan Shen (Stanford U). + +**Supporting info:** + +* src/QTB: filenames -> commands +* src/QTB/README +* :doc:`fix qtb ` +* :doc:`fix qbmsst ` +* examples/PACKAGES/qtb + +---------- + +.. _PKG-REACTION: + +REACTION package +--------------------- + +**Contents:** + +This package allows for complex bond topology changes (reactions) +during a running MD simulation, when using classical force fields. +Topology changes are defined in pre- and post-reaction molecule +templates and can include creation and deletion of bonds, angles, +dihedrals, impropers, atom types, bond types, angle types, dihedral +types, improper types, and/or atomic charges. Other options currently +available include reaction constraints (e.g. angle and Arrhenius +constraints), deletion of reaction byproducts or other small +molecules, and chiral-sensitive reactions. + +**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center. + +**Supporting info:** + +* src/REACTION: filenames -> commands +* src/REACTION/README +* :doc:`fix bond/react ` +* examples/PACKAGES/reaction +* `2017 LAMMPS Workshop `_ +* `2019 LAMMPS Workshop `_ +* reacter.org + +---------- + +.. _PKG-REAXFF: + +REAXFF package +------------------ + +**Contents:** + +A pair style which implements the ReaxFF potential in C/C++. ReaxFF +is a universal reactive force field. See the src/REAXFF/README file +for more info on differences between the two packages. Also two fixes +for monitoring molecules as bonds are created and destroyed. + +**Author:** Hasan Metin Aktulga (MSU) while at Purdue University. + +**Supporting info:** + +* src/REAXFF: filenames -> commands +* src/REAXFF/README +* :doc:`pair_style reax/c ` +* :doc:`fix reax/c/bonds ` +* :doc:`fix reax/c/species ` +* examples/reax + +---------- + .. _PKG-REPLICA: REPLICA package @@ -1017,6 +2334,41 @@ Also several computes which calculate properties of rigid bodies. ---------- +.. _PKG-SCAFACOS: + +SCAFACOS package +--------------------- + +**Contents:** + +A KSpace style which wraps the `ScaFaCoS Coulomb solver library `_ to compute long-range Coulombic +interactions. + +To use this package you must have the ScaFaCoS library available on +your system. + +**Author:** Rene Halver (JSC) wrote the scafacos LAMMPS command. + +ScaFaCoS itself was developed by a consortium of German research +facilities with a BMBF (German Ministry of Science and Education) +funded project in 2009-2012. Participants of the consortium were the +Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as +the Forschungszentrum Juelich. + +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + +**Supporting info:** + +* src/SCAFACOS: filenames -> commands +* src/SCAFACOS/README +* :doc:`kspace_style scafacos ` +* :doc:`kspace_modify ` +* examples/PACKAGES/scafacos + +---------- + .. _PKG-SHOCK: SHOCK package @@ -1039,28 +2391,60 @@ a material. ---------- -.. _PKG-SNAP: +.. _PKG-SMTBQ: -SNAP package ------------- +SMTBQ package +------------------ **Contents:** -A pair style for the spectral neighbor analysis potential (SNAP). -SNAP is methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. Also several -computes which analyze attributes of the potential. +A pair style which implements a Second Moment Tight Binding model with +QEq charge equilibration (SMTBQ) potential for the description of +ionocovalent bonds in oxides. -**Author:** Aidan Thompson (Sandia). +**Authors:** Nicolas Salles, Emile Maras, Olivier Politano, and Robert +Tetot (LAAS-CNRS, France). **Supporting info:** -* src/SNAP: filenames -> commands -* :doc:`pair_style snap ` -* :doc:`compute sna/atom ` -* :doc:`compute snad/atom ` -* :doc:`compute snav/atom ` -* examples/snap +* src/SMTBQ: filenames -> commands +* src/SMTBQ/README +* :doc:`pair_style smtbq ` +* examples/PACKAGES/smtbq + +---------- + +.. _PKG-SPH: + +SPH package +---------------- + +**Contents:** + +An atom style, fixes, computes, and several pair styles which +implements smoothed particle hydrodynamics (SPH) for liquids. See the +related :ref:`MACHDYN package ` package for smooth Mach dynamics +(SMD) for solids. + +This package contains ideal gas, Lennard-Jones equation of states, +Tait, and full support for complete (i.e. internal-energy dependent) +equations of state. It allows for plain or Monaghans XSPH integration +of the equations of motion. It has options for density continuity or +density summation to propagate the density field. It has +:doc:`set ` command options to set the internal energy and density +of particles from the input script and allows the same quantities to +be output with thermodynamic output or to dump files via the :doc:`compute property/atom ` command. + +**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed +Dynamics, Ernst Mach Institute, Germany). + +**Supporting info:** + +* src/SPH: filenames -> commands +* src/SPH/README +* doc/PDF/SPH_LAMMPS_userguide.pdf +* examples/PACKAGES/sph +* https://www.lammps.org/movies.html#sph ---------- @@ -1120,6 +2504,54 @@ colloidal particles. ---------- +.. _PKG-TALLY: + +TALLY package +------------------ + +**Contents:** + +Several compute styles that can be called when pairwise interactions +are calculated to tally information (forces, heat flux, energy, +stress, etc) about individual interactions. + +**Author:** Axel Kohlmeyer (Temple U). + +**Supporting info:** + +* src/TALLY: filenames -> commands +* src/TALLY/README +* :doc:`compute \*/tally ` +* examples/PACKAGES/tally + +---------- + +.. _PKG-UEF: + +UEF package +---------------- + +**Contents:** + +A fix style for the integration of the equations of motion under +extensional flow with proper boundary conditions, as well as several +supporting compute styles and an output option. + +**Author:** David Nicholson (MIT). + +**Supporting info:** + +* src/UEF: filenames -> commands +* src/UEF/README +* :doc:`fix nvt/uef ` +* :doc:`fix npt/uef ` +* :doc:`compute pressure/uef ` +* :doc:`compute temp/uef ` +* :doc:`dump cfg/uef ` +* examples/uef + +---------- + .. _PKG-VORONOI: VORONOI package @@ -1155,575 +2587,72 @@ This package has :ref:`specific installation instructions ` on the :doc ---------- -.. _PKG-USER-ADIOS: +.. _PKG-VTK: -USER-ADIOS package ------------------- - -**Contents:** - -ADIOS is a high-performance I/O library. This package implements the -:doc:`dump atom/adios `, :doc:`dump custom/adios ` and -:doc:`read_dump ... format adios ` -commands to write and read data using the ADIOS library. - -**Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team. - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-ADIOS: filenames -> commands -* src/USER-ADIOS/README -* examples/USER/adios -* https://github.com/ornladios/ADIOS2 -* :doc:`dump atom/adios ` -* :doc:`dump custom/adios ` -* :doc:`read_dump ` - ----------- - -.. _PKG-USER-ATC: - -USER-ATC package +VTK package ---------------- **Contents:** -ATC stands for atoms-to-continuum. This package implements a :doc:`fix atc ` command to either couple molecular dynamics with -continuum finite element equations or perform on-the-fly conversion of -atomic information to continuum fields. +A :doc:`dump vtk ` command which outputs snapshot info in the +`VTK format `_, enabling visualization by `Paraview `_ or +other visualization packages. -**Authors:** Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). +.. _vtk: http://www.vtk.org -**Install:** +.. _paraview: http://www.paraview.org -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-ATC: filenames -> commands -* src/USER-ATC/README -* :doc:`fix atc ` -* examples/USER/atc -* https://www.lammps.org/pictures.html#atc - ----------- - -.. _PKG-USER-AWPMD: - -USER-AWPMD package ------------------- - -**Contents:** - -AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This -package implements an atom, pair, and fix style which allows electrons -to be treated as explicit particles in a classical molecular dynamics -model. - -**Author:** Ilya Valuev (JIHT, Russia). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-AWPMD: filenames -> commands -* src/USER-AWPMD/README -* :doc:`pair_style awpmd/cut ` -* examples/USER/awpmd - ----------- - -.. _PKG-USER-BOCS: - -USER-BOCS package ------------------ - -**Contents:** - -This package provides :doc:`fix bocs `, a modified version -of :doc:`fix npt ` which includes the pressure correction to -the barostat as outlined in: - -N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that -accurately describe the structure, pressure, and compressibility of -molecular liquids," J. Chem. Phys. 143, 243148 (2015). - -**Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The -Pennsylvania State University) - -**Supporting info:** - -The USER-BOCS user package for LAMMPS is part of the BOCS software package: -`https://github.com/noid-group/BOCS `_ - -See the following reference for information about the entire package: - -Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. -"BOCS: Bottom-Up Open-Source Coarse-Graining Software." -J. Phys. Chem. B. 122, 13, 3363-3377 (2018). - -Example inputs are in the examples/USER/bocs folder. - ----------- - -.. _PKG-USER-BROWNIAN: - -USER-BROWNIAN package ---------------------- - -**Contents:** - -This package provides :doc:`fix brownian, fix brownian/sphere, and -fix brownian/asphere ` as well as -:doc:`fix propel/self ` which allow to do Brownian -Dynamics time integration of point, spherical and aspherical particles -and also support self-propelled particles. - -**Authors:** Sam Cameron (University of Bristol), -Stefan Paquay (while at Brandeis University) (initial version of fix propel/self) - -Example inputs are in the examples/USER/brownian folder. - ----------- - -.. _PKG-USER-CGDNA: - -USER-CGDNA package ------------------- - -**Contents:** - -Several pair styles, bond styles, and integration fixes for coarse-grained -modelling of single- and double-stranded DNA and RNA based on the oxDNA and -oxRNA model of Doye, Louis and Ouldridge. The package includes Langevin-type -rigid-body integrators with improved stability. - -**Author:** Oliver Henrich (University of Strathclyde, Glasgow). - -**Supporting info:** - -* src/USER-CGDNA: filenames -> commands -* /src/USER-CGDNA/README -* :doc:`pair_style oxdna/\* ` -* :doc:`pair_style oxdna2/\* ` -* :doc:`pair_style oxrna2/\* ` -* :doc:`bond_style oxdna/\* ` -* :doc:`bond_style oxdna2/\* ` -* :doc:`bond_style oxrna2/\* ` -* :doc:`fix nve/dotc/langevin ` - ----------- - -.. _PKG-USER-CGSDK: - -USER-CGSDK package ------------------- - -**Contents:** - -Several pair styles and an angle style which implement the -coarse-grained SDK model of Shinoda, DeVane, and Klein which enables -simulation of ionic liquids, electrolytes, lipids and charged amino -acids. - -**Author:** Axel Kohlmeyer (Temple U). - -**Supporting info:** - -* src/USER-CGSDK: filenames -> commands -* src/USER-CGSDK/README -* :doc:`pair_style lj/sdk/\* ` -* :doc:`angle_style sdk ` -* examples/USER/cgsdk -* https://www.lammps.org/pictures.html#cg - ----------- - -.. _PKG-USER-COLVARS: - -USER-COLVARS package --------------------- - -**Contents:** - -COLVARS stands for collective variables, which can be used to -implement various enhanced sampling methods, including Adaptive -Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and -Restraints. A :doc:`fix colvars ` command is implemented -which wraps a COLVARS library, which implements these methods. -simulations. - -**Authors:** The COLVARS library is written and maintained by -Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) -and Jerome Henin (LISM, CNRS, Marseille, France), originally for -the NAMD MD code, but with portability in mind. Axel Kohlmeyer -(Temple U) provided the interface to LAMMPS. - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-COLVARS: filenames -> commands -* `doc/PDF/colvars-refman-lammps.pdf `_ -* src/USER-COLVARS/README -* lib/colvars/README -* :doc:`fix colvars ` -* examples/USER/colvars - ----------- - -.. _PKG-USER-DIELECTRIC: - -USER-DIELECTRIC package ------------------------- - -**Contents:** - -An atom style, multiple pair styles, several fixes, Kspace styles and a -compute for simulating systems using boundary element solvers for -computing the induced charges at the interface between two media with -different dielectric constants. - -**Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U) - -**Supporting info:** - -* src/USER-DIELECTRIC: filenames -> commands -* :doc:`compute efield/atom ` -* TODO: add all styles -* examples/USER/dielectric - ----------- - -.. _PKG-USER-DIFFRACTION: - -USER-DIFFRACTION package ------------------------- - -**Contents:** - -Two computes and a fix for calculating x-ray and electron diffraction -intensities based on kinematic diffraction theory. - -**Author:** Shawn Coleman while at the U Arkansas. - -**Supporting info:** - -* src/USER-DIFFRACTION: filenames -> commands -* :doc:`compute saed ` -* :doc:`compute xrd ` -* :doc:`fix saed/vtk ` -* examples/USER/diffraction - ----------- - -.. _PKG-USER-DPD: - -USER-DPD package ----------------- - -**Contents:** - -DPD stands for dissipative particle dynamics. This package implements -coarse-grained DPD-based models for energetic, reactive molecular -crystalline materials. It includes many pair styles specific to these -systems, including for reactive DPD, where each particle has internal -state for multiple species and a coupled set of chemical reaction ODEs -are integrated each timestep. Highly accurate time integrators for -isothermal, isoenergetic, isobaric and isenthalpic conditions are -included. These enable long timesteps via the Shardlow splitting -algorithm. - -**Authors:** Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John -Brennan (ARL). - -**Supporting info:** - -* src/USER-DPD: filenames -> commands -* /src/USER-DPD/README -* :doc:`compute dpd ` -* :doc:`compute dpd/atom ` -* :doc:`fix eos/cv ` -* :doc:`fix eos/table ` -* :doc:`fix eos/table/rx ` -* :doc:`fix shardlow ` -* :doc:`fix rx ` -* :doc:`pair_style table/rx ` -* :doc:`pair_style dpd/fdt ` -* :doc:`pair_style dpd/fdt/energy ` -* :doc:`pair_style exp6/rx ` -* :doc:`pair_style multi/lucy ` -* :doc:`pair_style multi/lucy/rx ` -* examples/USER/dpd - ----------- - -.. _PKG-USER-DRUDE: - -USER-DRUDE package ------------------- - -**Contents:** - -Fixes, pair styles, and a compute to simulate thermalized Drude -oscillators as a model of polarization. See the :doc:`Howto drude ` and :doc:`Howto drude2 ` pages -for an overview of how to use the package. There are auxiliary tools -for using this package in tools/drude. - -**Authors:** Alain Dequidt (U Clermont Auvergne), Julien -Devemy (CNRS), and Agilio Padua (ENS de Lyon). - -**Supporting info:** - -* src/USER-DRUDE: filenames -> commands -* :doc:`Howto drude ` -* :doc:`Howto drude2 ` -* :doc:`Howto polarizable ` -* src/USER-DRUDE/README -* :doc:`fix drude ` -* :doc:`fix drude/transform/\* ` -* :doc:`compute temp/drude ` -* :doc:`pair_style thole ` -* :doc:`pair_style lj/cut/thole/long ` -* examples/USER/drude -* tools/drude - ----------- - -.. _PKG-USER-EFF: - -USER-EFF package ----------------- - -**Contents:** - -EFF stands for electron force field which allows a classical MD code -to model electrons as particles of variable radius. This package -contains atom, pair, fix and compute styles which implement the eFF as -described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, -JCC, 2010. The eFF potential was first introduced by Su and Goddard, -in 2007. There are auxiliary tools for using this package in -tools/eff; see its README file. - -**Author:** Andres Jaramillo-Botero (CalTech). - -**Supporting info:** - -* src/USER-EFF: filenames -> commands -* src/USER-EFF/README -* :doc:`atom_style electron ` -* :doc:`fix nve/eff ` -* :doc:`fix nvt/eff ` -* :doc:`fix npt/eff ` -* :doc:`fix langevin/eff ` -* :doc:`compute temp/eff ` -* :doc:`pair_style eff/cut ` -* :doc:`pair_style eff/inline ` -* examples/USER/eff -* tools/eff/README -* tools/eff -* https://www.lammps.org/movies.html#eff - ----------- - -.. _PKG-USER-FEP: - -USER-FEP package ----------------- - -**Contents:** - -FEP stands for free energy perturbation. This package provides -methods for performing FEP simulations by using a :doc:`fix adapt/fep ` command with soft-core pair potentials, -which have a "soft" in their style name. There are auxiliary tools -for using this package in tools/fep; see its README file. - -**Author:** Agilio Padua (ENS de Lyon) - -**Supporting info:** - -* src/USER-FEP: filenames -> commands -* src/USER-FEP/README -* :doc:`fix adapt/fep ` -* :doc:`compute fep ` -* :doc:`pair_style \*/soft ` -* examples/USER/fep -* tools/fep/README -* tools/fep - ----------- - -.. _PKG-USER-H5MD: - -USER-H5MD package ------------------ - -**Contents:** - -H5MD stands for HDF5 for MD. `HDF5 `_ is a portable, binary, -self-describing file format, used by many scientific simulations. -H5MD is a format for molecular simulations, built on top of HDF5. -This package implements a :doc:`dump h5md ` command to output -LAMMPS snapshots in this format. - -.. _HDF5: http://www.hdfgroup.org/HDF5 - -To use this package you must have the HDF5 library available on your +To use this package you must have VTK library available on your system. -**Author:** Pierre de Buyl (KU Leuven) created both the package and the -H5MD format. +**Authors:** Richard Berger (JKU) and Daniel Queteschiner (DCS Computing). **Install:** -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. **Supporting info:** -* src/USER-H5MD: filenames -> commands -* src/USER-H5MD/README -* lib/h5md/README -* :doc:`dump h5md ` +* src/VTK: filenames -> commands +* src/VTK/README +* lib/vtk/README +* :doc:`dump vtk ` ---------- -.. _PKG-USER-HDNNP: +.. _PKG-YAFF: -USER-HDNNP package ------------------- - -**Contents:** - -A :doc:`pair_style hdnnp ` command which allows to use -high-dimensional neural network potentials (HDNNPs), a form of machine learning -potentials. HDNNPs must be carefully trained prior to their application in a -molecular dynamics simulation. - -.. _n2p2: https://github.com/CompPhysVienna/n2p2 - -To use this package you must have the `n2p2 `_ library installed and -compiled on your system. - -**Author:** Andreas Singraber - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-HDNNP: filenames -> commands -* src/USER-HDNNP/README -* lib/hdnnp/README -* :doc:`pair_style hdnnp ` -* examples/USER/hdnnp - ----------- - -.. _PKG-USER-INTEL: - -USER-INTEL package ------------------- - -**Contents:** - -Dozens of pair, fix, bond, angle, dihedral, improper, and kspace -styles which are optimized for Intel CPUs and KNLs (Knights Landing). -All of them have an "intel" in their style name. The -:doc:`USER-INTEL package ` page gives details of what hardware and -compilers are required on your system, and how to build and use this -package. Its styles can be invoked at run time via the "-sf intel" or -"-suffix intel" :doc:`command-line switches `. Also see -the :ref:`KOKKOS `, :ref:`OPT `, and :ref:`USER-OMP ` packages, -which have styles optimized for CPUs and KNLs. - -You need to have an Intel compiler, version 14 or higher to take full -advantage of this package. While compilation with GNU compilers is -supported, performance will be sub-optimal. - -.. note:: - - the USER-INTEL package contains styles that require using the - -restrict flag, when compiling with Intel compilers. - -**Author:** Mike Brown (Intel). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-INTEL: filenames -> commands -* src/USER-INTEL/README -* :doc:`Accelerator packages ` -* :doc:`USER-INTEL package ` -* :doc:`Section 2.6 -sf intel ` -* :doc:`Section 2.6 -pk intel ` -* :doc:`package intel ` -* Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, - :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (i) -* src/USER-INTEL/TEST -* `Benchmarks page `_ of web site - ----------- - -.. _PKG-USER-LB: - -USER-LB package ---------------- - -**Contents:** - -Fixes which implement a background Lattice-Boltzmann (LB) fluid, which -can be used to model MD particles influenced by hydrodynamic forces. - -**Authors:** Frances Mackay and Colin Denniston (University of Western -Ontario). - -**Supporting info:** - -* src/USER-LB: filenames -> commands -* src/USER-LB/README -* :doc:`fix lb/fluid ` -* :doc:`fix lb/momentum ` -* :doc:`fix lb/viscous ` -* examples/USER/lb - ----------- - -.. _PKG-USER-MGPT: - -USER-MGPT package +YAFF package ----------------- **Contents:** -A pair style which provides a fast implementation of the quantum-based -MGPT multi-ion potentials. The MGPT or model GPT method derives from -first-principles DFT-based generalized pseudopotential theory (GPT) -through a series of systematic approximations valid for mid-period -transition metals with nearly half-filled d bands. The MGPT method -was originally developed by John Moriarty at LLNL. The pair style in -this package calculates forces and energies using an optimized -matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. +Some potentials that are also implemented in the Yet Another Force Field (`YAFF `_) code. +The expressions and their use are discussed in the following papers -**Authors:** Tomas Oppelstrup and John Moriarty (LLNL). +* Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) `link `_ +* Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) `link `_ + +which discuss the `QuickFF `_ methodology. + +.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877 +.. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173 +.. _quickff: http://molmod.github.io/QuickFF +.. _yaff: https://github.com/molmod/yaff + +**Author:** Steven Vandenbrande. **Supporting info:** -* src/USER-MGPT: filenames -> commands -* src/USER-MGPT/README -* :doc:`pair_style mgpt ` -* examples/USER/mgpt +* src/YAFF/README +* :doc:`angle_style cross ` +* :doc:`angle_style mm3 ` +* :doc:`bond_style mm3 ` +* :doc:`improper_style distharm ` +* :doc:`improper_style sqdistharm ` +* :doc:`pair_style mm3/switch3/coulgauss/long ` +* :doc:`pair_style lj/switch3/coulgauss/long ` +* examples/PACKAGES/yaff ---------- @@ -1746,908 +2675,4 @@ src/USER-MISC/README file. * src/USER-MISC: filenames -> commands * src/USER-MISC/README * one page per individual command listed in src/USER-MISC/README -* examples/USER/misc - ----------- - -.. _PKG-USER-MANIFOLD: - -USER-MANIFOLD package ---------------------- - -**Contents:** - -Several fixes and a "manifold" class which enable simulations of -particles constrained to a manifold (a 2D surface within the 3D -simulation box). This is done by applying the RATTLE constraint -algorithm to formulate single-particle constraint functions -g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) -n = grad(g). - -**Author:** Stefan Paquay (until 2017: Eindhoven University of -Technology (TU/e), The Netherlands; since 2017: Brandeis University, -Waltham, MA, USA) - -**Supporting info:** - -* src/USER-MANIFOLD: filenames -> commands -* src/USER-MANIFOLD/README -* :doc:`Howto manifold ` -* :doc:`fix manifoldforce ` -* :doc:`fix nve/manifold/rattle ` -* :doc:`fix nvt/manifold/rattle ` -* examples/USER/manifold -* https://www.lammps.org/movies.html#manifold - ----------- - -.. _PKG-USER-MDI: - -USER-MDI package ----------------- - -**Contents:** - -A LAMMPS command and fix to allow client-server coupling of LAMMPS to -other atomic or molecular simulation codes via the `MolSSI Driver Interface -(MDI) library `_. - -**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com - -**Supporting info:** - -* src/USER-MDI/README -* :doc:`mdi/engine ` -* :doc:`fix mdi/engine ` -* examples/USER/mdi - ----------- - -.. _PKG-USER-MEAMC: - -USER-MEAMC package ------------------- - -**Contents:** - -A pair style for the modified embedded atom (MEAM) potential -translated from the Fortran version in the (obsolete) MEAM package -to plain C++. The USER-MEAMC fully replaces the MEAM package, which -has been removed from LAMMPS after the 12 December 2018 version. - -**Author:** Sebastian Huetter, (Otto-von-Guericke University Magdeburg) -based on the Fortran version of Greg Wagner (Northwestern U) while at -Sandia. - -**Supporting info:** - -* src/USER-MEAMC: filenames -> commands -* src/USER-MEAMC/README -* :doc:`pair_style meam/c ` -* examples/meamc - ----------- - -.. _PKG-USER-MESODPD: - -USER-MESODPD package --------------------- - -**Contents:** - -Several extensions of the dissipative particle dynamics (DPD) -method. Specifically, energy-conserving DPD (eDPD) that can model -non-isothermal processes, many-body DPD (mDPD) for simulating -vapor-liquid coexistence, and transport DPD (tDPD) for modeling -advection-diffusion-reaction systems. The equations of motion of these -DPD extensions are integrated through a modified velocity-Verlet (MVV) -algorithm. - -**Author:** Zhen Li (Division of Applied Mathematics, Brown University) - -**Supporting info:** - -* src/USER-MESODPD: filenames -> commands -* src/USER-MESODPD/README -* :doc:`atom_style edpd ` -* :doc:`pair_style edpd ` -* :doc:`pair_style mdpd ` -* :doc:`pair_style tdpd ` -* :doc:`fix mvv/dpd ` -* examples/USER/mesodpd -* https://www.lammps.org/movies.html#mesodpd - ----------- - -.. _PKG-USER-MESONT: - -USER-MESONT package -------------------- - -**Contents:** - -USER-MESONT is a LAMMPS package for simulation of nanomechanics of -nanotubes (NTs). The model is based on a coarse-grained representation -of NTs as "flexible cylinders" consisting of a variable number of -segments. Internal interactions within a NT and the van der Waals -interaction between the tubes are described by a mesoscopic force field -designed and parameterized based on the results of atomic-level -molecular dynamics simulations. The description of the force field is -provided in the papers listed below. This package contains two -independent implementations of this model: :doc:`pair_style mesocnt -` is a (minimal) C++ implementation, and :doc:`pair_style -mesont/tpm ` is a more general and feature rich -implementation based on a Fortran library in the ``lib/mesont`` folder. - -**Download of potential files:** - -The potential files for these pair styles are *very* large and thus -are not included in the regular downloaded packages of LAMMPS or the -git repositories. Instead, they will be automatically downloaded -from a web server when the package is installed for the first time. - -**Authors of the *mesont* styles:** - -Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia) - -**Author of the *mesocnt* pair style:** -Philipp Kloza (U Cambridge) - -**Supporting info:** - -* src/USER-MESONT: filenames -> commands -* src/USER-MESONT/README -* :doc:`atom_style mesont ` -* :doc:`pair_style mesont/tpm ` -* :doc:`compute mesont ` -* :doc:`pair_style mesocnt ` -* examples/USER/mesont -* tools/mesont - ----------- - -.. _PKG-USER-MOFFF: - -USER-MOFFF package ------------------- - -**Contents:** - -Pair, angle and improper styles needed to employ the MOF-FF -force field by Schmid and coworkers with LAMMPS. -MOF-FF is a first principles derived force field with the primary aim -to simulate MOFs and related porous framework materials, using spherical -Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B -2013, 250, 1128-1141. -For the usage of MOF-FF see the example in the example directory as -well as the `MOF+ `_ website. - -.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF - -**Author:** Hendrik Heenen (Technical U of Munich), -Rochus Schmid (Ruhr-University Bochum). - -**Supporting info:** - -* src/USER-MOFFF: filenames -> commands -* src/USER-MOFFF/README -* :doc:`pair_style buck6d/coul/gauss ` -* :doc:`angle_style class2 ` -* :doc:`angle_style cosine/buck6d ` -* :doc:`improper_style inversion/harmonic ` -* examples/USER/mofff - ----------- - -.. _PKG-USER-MOLFILE: - -USER-MOLFILE package --------------------- - -**Contents:** - -A :doc:`dump molfile ` command which uses molfile plugins -that are bundled with the `VMD `_ -molecular visualization and analysis program, to enable LAMMPS to dump -snapshots in formats compatible with various molecular simulation -tools. - -To use this package you must have the desired VMD plugins available on -your system. - -Note that this package only provides the interface code, not the -plugins themselves, which will be accessed when requesting a specific -plugin via the :doc:`dump molfile ` command. Plugins can -be obtained from a VMD installation which has to match the platform -that you are using to compile LAMMPS for. By adding plugins to VMD, -support for new file formats can be added to LAMMPS (or VMD or other -programs that use them) without having to re-compile the application -itself. More information about the VMD molfile plugins can be found -at -`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile `_. - -**Author:** Axel Kohlmeyer (Temple U). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-MOLFILE: filenames -> commands -* src/USER-MOLFILE/README -* lib/molfile/README -* :doc:`dump molfile ` - ----------- - -.. _PKG-USER-NETCDF: - -USER-NETCDF package -------------------- - -**Contents:** - -Dump styles for writing NetCDF formatted dump files. NetCDF is a -portable, binary, self-describing file format developed on top of -HDF5. The file contents follow the AMBER NetCDF trajectory conventions -(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions. - -To use this package you must have the NetCDF library available on your -system. - -Note that NetCDF files can be directly visualized with the following -tools: - -* `Ovito `_ (Ovito supports the AMBER convention and the extensions mentioned above) -* `VMD `_ - -.. _ovito: http://www.ovito.org - -.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/ - -**Author:** Lars Pastewka (Karlsruhe Institute of Technology). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-NETCDF: filenames -> commands -* src/USER-NETCDF/README -* lib/netcdf/README -* :doc:`dump netcdf ` - ----------- - -.. _PKG-USER-OMP: - -USER-OMP package ----------------- - -**Contents:** - -Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and -kspace styles which are altered to enable threading on many-core CPUs -via OpenMP directives. All of them have an "omp" in their style name. -The :doc:`USER-OMP package ` page gives details of what hardware -and compilers are required on your system, and how to build and use -this package. Its styles can be invoked at run time via the "-sf omp" -or "-suffix omp" :doc:`command-line switches `. Also see -the :ref:`KOKKOS `, :ref:`OPT `, and :ref:`USER-INTEL ` -packages, which have styles optimized for CPUs. - -**Author:** Axel Kohlmeyer (Temple U). - -.. note:: - - To enable multi-threading support the compile flag "-fopenmp" - and the link flag "-fopenmp" (for GNU compilers, you have to look up - the equivalent flags for other compilers) must be used to build LAMMPS. - When using Intel compilers, also the "-restrict" flag is required. - The USER-OMP package can be compiled without enabling OpenMP; then - all code will be compiled as serial and the only improvement over the - regular styles are some data access optimization. These flags should - be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine. - See src/MAKE/OPTIONS/Makefile.omp for an example. - -Once you have an appropriate Makefile.machine, you can -install/un-install the package and build LAMMPS in the usual manner: - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-OMP: filenames -> commands -* src/USER-OMP/README -* :doc:`Accelerator packages ` -* :doc:`USER-OMP package ` -* :doc:`Section 2.6 -sf omp ` -* :doc:`Section 2.6 -pk omp ` -* :doc:`package omp ` -* Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, - :doc:`pair `, :doc:`bond, angle, dihedral, improper `, - :doc:`kspace `) for styles followed by (o) -* `Benchmarks page `_ of web site - ----------- - -.. _PKG-USER-PACE: - -USER-PACE package -------------------- - -**Contents:** - -A pair style for the Atomic Cluster Expansion potential (ACE). -ACE is a methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. The USER-PACE -package provides an efficient implementation for running simulations -with ACE potentials. - -**Authors:** - -This package was written by Yury Lysogorskiy^1, -Cas van der Oord^2, Anton Bochkarev^1, -Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, -Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. - - ^1: Ruhr-University Bochum, Bochum, Germany - - ^2: University of Cambridge, Cambridge, United Kingdom - - ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - - ^4: University of British Columbia, Vancouver, BC, Canada - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-PACE: filenames -> commands -* :doc:`pair_style pace ` -* examples/USER/pace - ----------- - -.. _PKG-USER-PHONON: - -USER-PHONON package -------------------- - -**Contents:** - -A :doc:`fix phonon ` command that calculates dynamical -matrices, which can then be used to compute phonon dispersion -relations, directly from molecular dynamics simulations. -And a :doc:`dynamical_matrix ` as well as a -:doc:`third_order ` command to compute the dynamical matrix -and third order tensor from finite differences. - -**Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" -and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" - -**Supporting info:** - -* src/USER-PHONON: filenames -> commands -* src/USER-PHONON/README -* :doc:`fix phonon ` -* :doc:`dynamical_matrix ` -* :doc:`third_order ` -* examples/USER/phonon - ----------- - -.. _PKG-USER-PLUMED: - -USER-PLUMED package -------------------- - -**Contents:** - -The fix plumed command allows you to use the PLUMED free energy plugin -for molecular dynamics to analyze and bias your LAMMPS trajectory on -the fly. The PLUMED library is called from within the LAMMPS input -script by using the :doc:`fix plumed ` command. - -**Authors:** The `PLUMED library `_ is written -and maintained by Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni, -and Gareth Tribello. - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-PLUMED/README -* lib/plumed/README -* :doc:`fix plumed ` -* examples/USER/plumed - ----------- - -.. _PKG-USER-PTM: - -USER-PTM package ----------------- - -**Contents:** - -A :doc:`compute ptm/atom ` command that calculates -local structure characterization using the Polyhedral Template -Matching methodology. - -**Author:** Peter Mahler Larsen (MIT). - -**Supporting info:** - -* src/USER-PTM: filenames not starting with ptm\_ -> commands -* src/USER-PTM: filenames starting with ptm\_ -> supporting code -* src/USER-PTM/LICENSE -* :doc:`compute ptm/atom ` - ----------- - -.. _PKG-USER-QMMM: - -USER-QMMM package ------------------ - -**Contents:** - -A :doc:`fix qmmm ` command which allows LAMMPS to be used as -the MM code in a QM/MM simulation. This is currently only available -in combination with the `Quantum ESPRESSO `_ package. - -.. _espresso: http://www.quantum-espresso.org - -To use this package you must have Quantum ESPRESSO (QE) available on -your system and include its coupling library in the compilation and -then compile LAMMPS as a library. For QM/MM calculations you then -build a custom binary with MPI support, that sets up 3 partitions with -MPI sub-communicators (for inter- and intra-partition communication) -and then calls the corresponding library interfaces on each partition -(2x LAMMPS and 1x QE). - -The current implementation supports an ONIOM style mechanical coupling -and a multi-pole based electrostatic coupling to the Quantum ESPRESSO -plane wave DFT package. The QM/MM interface has been written in a -manner that coupling to other QM codes should be possible without -changes to LAMMPS itself. - -**Authors:** Axel Kohlmeyer (Temple U). Mariella Ippolito and Carlo Cavazzoni (CINECA, Italy) - -**Install:** - -This package has :ref:`specific installation instructions ` -on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-QMMM: filenames -> commands -* src/USER-QMMM/README -* lib/qmmm/README -* :doc:`fix phonon ` -* lib/qmmm/example-ec/README -* lib/qmmm/example-mc/README - ----------- - -.. _PKG-USER-QTB: - -USER-QTB package ----------------- - -**Contents:** - -Two fixes which provide a self-consistent quantum treatment of -vibrational modes in a classical molecular dynamics simulation. By -coupling the MD simulation to a colored thermostat, it introduces zero -point energy into the system, altering the energy power spectrum and -the heat capacity to account for their quantum nature. This is useful -when modeling systems at temperatures lower than their classical -limits or when temperatures ramp across the classical limits in a -simulation. - -**Author:** Yuan Shen (Stanford U). - -**Supporting info:** - -* src/USER-QTB: filenames -> commands -* src/USER-QTB/README -* :doc:`fix qtb ` -* :doc:`fix qbmsst ` -* examples/USER/qtb - ----------- - -.. _PKG-USER-QUIP: - -USER-QUIP package ------------------ - -**Contents:** - -A :doc:`pair_style quip ` command which wraps the `QUIP libAtoms library `_, which includes a variety of interatomic -potentials, including Gaussian Approximation Potential (GAP) models -developed by the Cambridge University group. - -.. _quip: https://github.com/libAtoms/QUIP - -To use this package you must have the QUIP libAtoms library available -on your system. - -**Author:** Albert Bartok (Cambridge University) - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-QUIP: filenames -> commands -* src/USER-QUIP/README -* :doc:`pair_style quip ` -* examples/USER/quip - ----------- - -.. _PKG-USER-RANN: - -USER-RANN package ------------------ - -**Contents:** - -A pair style for using rapid atomistic neural network (RANN) potentials. -These neural network potentials work by first generating a series of symmetry -functions from the neighbor list and then using these values as the input layer -of a neural network. - -**Authors:** - -This package was written by Christopher Barrett -with contributions by Doyl Dickel, Mississippi State University. - -**Supporting info:** - -* src/USER-RANN: filenames -> commands -* :doc:`pair_style rann ` -* examples/USER/rann - ----------- - -.. _PKG-USER-REACTION: - -USER-REACTION package ---------------------- - -**Contents:** - -This package allows for complex bond topology changes (reactions) -during a running MD simulation, when using classical force fields. -Topology changes are defined in pre- and post-reaction molecule -templates and can include creation and deletion of bonds, angles, -dihedrals, impropers, atom types, bond types, angle types, dihedral -types, improper types, and/or atomic charges. Other options currently -available include reaction constraints (e.g. angle and Arrhenius -constraints), deletion of reaction byproducts or other small -molecules, and chiral-sensitive reactions. - -**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center. - -**Supporting info:** - -* src/USER-REACTION: filenames -> commands -* src/USER-REACTION/README -* :doc:`fix bond/react ` -* examples/USER/reaction -* `2017 LAMMPS Workshop `_ -* `2019 LAMMPS Workshop `_ -* reacter.org - ----------- - -.. _PKG-USER-REAXC: - -USER-REAXC package ------------------- - -**Contents:** - -A pair style which implements the ReaxFF potential in C/C++. ReaxFF -is a universal reactive force field. See the src/USER-REAXC/README file -for more info on differences between the two packages. Also two fixes -for monitoring molecules as bonds are created and destroyed. - -**Author:** Hasan Metin Aktulga (MSU) while at Purdue University. - -**Supporting info:** - -* src/USER-REAXC: filenames -> commands -* src/USER-REAXC/README -* :doc:`pair_style reax/c ` -* :doc:`fix reax/c/bonds ` -* :doc:`fix reax/c/species ` -* examples/reax - ----------- - -.. _PKG-USER-SCAFACOS: - -USER-SCAFACOS package ---------------------- - -**Contents:** - -A KSpace style which wraps the `ScaFaCoS Coulomb solver library `_ to compute long-range Coulombic -interactions. - -To use this package you must have the ScaFaCoS library available on -your system. - -**Author:** Rene Halver (JSC) wrote the scafacos LAMMPS command. - -ScaFaCoS itself was developed by a consortium of German research -facilities with a BMBF (German Ministry of Science and Education) -funded project in 2009-2012. Participants of the consortium were the -Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as -the Forschungszentrum Juelich. - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-SCAFACOS: filenames -> commands -* src/USER-SCAFACOS/README -* :doc:`kspace_style scafacos ` -* :doc:`kspace_modify ` -* examples/USER/scafacos - ----------- - -.. _PKG-USER-SDPD: - -USER-SDPD package ------------------ - -**Contents:** - -A pair style for smoothed dissipative particle dynamics (SDPD), which -is an extension of smoothed particle hydrodynamics (SPH) to mesoscale -where thermal fluctuations are important (see the -:ref:`USER-SPH package `). -Also two fixes for moving and rigid body integration of SPH/SDPD particles -(particles of atom_style meso). - -**Author:** Morteza Jalalvand (Institute for Advanced Studies in Basic -Sciences, Iran). - -**Supporting info:** - -* src/USER-SDPD: filenames -> commands -* src/USER-SDPD/README -* :doc:`pair_style sdpd/taitwater/isothermal ` -* :doc:`fix meso/move ` -* :doc:`fix rigid/meso ` -* examples/USER/sdpd - ----------- - -.. _PKG-USER-SMD: - -USER-SMD package ----------------- - -**Contents:** - -An atom style, fixes, computes, and several pair styles which -implements smoothed Mach dynamics (SMD) for solids, which is a model -related to smoothed particle hydrodynamics (SPH) for liquids (see the -:ref:`USER-SPH package `). - -This package solves solids mechanics problems via a state of the art -stabilized meshless method with hourglass control. It can specify -hydrostatic interactions independently from material strength models, -i.e. pressure and deviatoric stresses are separated. It provides many -material models (Johnson-Cook, plasticity with hardening, -Mie-Grueneisen, Polynomial EOS) and allows new material models to be -added. It implements rigid boundary conditions (walls) which can be -specified as surface geometries from \*.STL files. - -**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed -Dynamics, Ernst Mach Institute, Germany). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-SMD: filenames -> commands -* src/USER-SMD/README -* doc/PDF/SMD_LAMMPS_userguide.pdf -* examples/USER/smd -* https://www.lammps.org/movies.html#smd - ----------- - -.. _PKG-USER-SMTBQ: - -USER-SMTBQ package ------------------- - -**Contents:** - -A pair style which implements a Second Moment Tight Binding model with -QEq charge equilibration (SMTBQ) potential for the description of -ionocovalent bonds in oxides. - -**Authors:** Nicolas Salles, Emile Maras, Olivier Politano, and Robert -Tetot (LAAS-CNRS, France). - -**Supporting info:** - -* src/USER-SMTBQ: filenames -> commands -* src/USER-SMTBQ/README -* :doc:`pair_style smtbq ` -* examples/USER/smtbq - ----------- - -.. _PKG-USER-SPH: - -USER-SPH package ----------------- - -**Contents:** - -An atom style, fixes, computes, and several pair styles which -implements smoothed particle hydrodynamics (SPH) for liquids. See the -related :ref:`USER-SMD package ` package for smooth Mach dynamics -(SMD) for solids. - -This package contains ideal gas, Lennard-Jones equation of states, -Tait, and full support for complete (i.e. internal-energy dependent) -equations of state. It allows for plain or Monaghans XSPH integration -of the equations of motion. It has options for density continuity or -density summation to propagate the density field. It has -:doc:`set ` command options to set the internal energy and density -of particles from the input script and allows the same quantities to -be output with thermodynamic output or to dump files via the :doc:`compute property/atom ` command. - -**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed -Dynamics, Ernst Mach Institute, Germany). - -**Supporting info:** - -* src/USER-SPH: filenames -> commands -* src/USER-SPH/README -* doc/PDF/SPH_LAMMPS_userguide.pdf -* examples/USER/sph -* https://www.lammps.org/movies.html#sph - ----------- - -.. _PKG-USER-TALLY: - -USER-TALLY package ------------------- - -**Contents:** - -Several compute styles that can be called when pairwise interactions -are calculated to tally information (forces, heat flux, energy, -stress, etc) about individual interactions. - -**Author:** Axel Kohlmeyer (Temple U). - -**Supporting info:** - -* src/USER-TALLY: filenames -> commands -* src/USER-TALLY/README -* :doc:`compute \*/tally ` -* examples/USER/tally - ----------- - -.. _PKG-USER-UEF: - -USER-UEF package ----------------- - -**Contents:** - -A fix style for the integration of the equations of motion under -extensional flow with proper boundary conditions, as well as several -supporting compute styles and an output option. - -**Author:** David Nicholson (MIT). - -**Supporting info:** - -* src/USER-UEF: filenames -> commands -* src/USER-UEF/README -* :doc:`fix nvt/uef ` -* :doc:`fix npt/uef ` -* :doc:`compute pressure/uef ` -* :doc:`compute temp/uef ` -* :doc:`dump cfg/uef ` -* examples/uef - ----------- - -.. _PKG-USER-VTK: - -USER-VTK package ----------------- - -**Contents:** - -A :doc:`dump vtk ` command which outputs snapshot info in the -`VTK format `_, enabling visualization by `Paraview `_ or -other visualization packages. - -.. _vtk: http://www.vtk.org - -.. _paraview: http://www.paraview.org - -To use this package you must have VTK library available on your -system. - -**Authors:** Richard Berger (JKU) and Daniel Queteschiner (DCS Computing). - -**Install:** - -This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. - -**Supporting info:** - -* src/USER-VTK: filenames -> commands -* src/USER-VTK/README -* lib/vtk/README -* :doc:`dump vtk ` - ----------- - -.. _PKG-USER-YAFF: - -USER-YAFF package ------------------ - -**Contents:** - -Some potentials that are also implemented in the Yet Another Force Field (`YAFF `_) code. -The expressions and their use are discussed in the following papers - -* Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) `link `_ -* Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) `link `_ - -which discuss the `QuickFF `_ methodology. - -.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877 -.. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173 -.. _quickff: http://molmod.github.io/QuickFF -.. _yaff: https://github.com/molmod/yaff - -**Author:** Steven Vandenbrande. - -**Supporting info:** - -* src/USER-YAFF/README -* :doc:`angle_style cross ` -* :doc:`angle_style mm3 ` -* :doc:`bond_style mm3 ` -* :doc:`improper_style distharm ` -* :doc:`improper_style sqdistharm ` -* :doc:`pair_style mm3/switch3/coulgauss/long ` -* :doc:`pair_style lj/switch3/coulgauss/long ` -* examples/USER/yaff +* examples/USER-MISC diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst new file mode 100644 index 0000000000..44c05f8a39 --- /dev/null +++ b/doc/src/Packages_list.rst @@ -0,0 +1,449 @@ +Available Packages +================== + +This is the list of packages included in LAMMPS. The link for each +package name gives more details. + +Packages are supported by either the LAMMPS developers or the +contributing authors and written in a syntax and style consistent with +the rest of LAMMPS. + +The "Example" column is a sub-directory in the examples directory of the +distribution which has an input script that uses the package. +E.g. "peptide" refers to the examples/peptide directory; PACKAGES/atc refers +to the examples/PACKAGES/atc directory. The "Library" column indicates +whether an extra library is needed to build and use the package: + +* no = no library +* sys = system library: you likely have it on your machine +* int = internal library: provided with LAMMPS, but you may need to build it +* ext = external library: you will need to download and install it on your machine + +.. list-table:: + :header-rows: 1 + :widths: auto + + * - Package + - Description + - Doc page + - Example + - Library + * - :ref:`ADIOS ` + - dump output via ADIOS + - :doc:`dump adios ` + - PACKAGES/adios + - ext + * - :ref:`ASPHERE ` + - aspherical particle models + - :doc:`Howto spherical ` + - ellipse + - no + * - :ref:`ATC ` + - Atom-to-Continuum coupling + - :doc:`fix atc ` + - PACKAGES/atc + - int + * - :ref:`AWPMD ` + - wave packet MD + - :doc:`pair_style awpmd/cut ` + - PACKAGES/awpmd + - int + * - :ref:`BOCS ` + - BOCS bottom up coarse graining + - :doc:`fix bocs ` + - PACKAGES/bocs + - no + * - :ref:`BODY ` + - body-style particles + - :doc:`Howto body ` + - body + - no + * - :ref:`BROWNIAN ` + - Brownian dynamics, self-propelled particles + - :doc:`fix brownian `, :doc:`fix propel/self ` + - PACKAGES/brownian + - no + * - :ref:`CG-DNA ` + - coarse-grained DNA force fields + - src/CG-DNA/README + - PACKAGES/cgdna + - no + * - :ref:`CG-SDK ` + - SDK coarse-graining model + - :doc:`pair_style lj/sdk ` + - PACKAGES/cgsdk + - no + * - :ref:`CLASS2 ` + - class 2 force fields + - :doc:`pair_style lj/class2 ` + - n/a + - no + * - :ref:`COLLOID ` + - colloidal particles + - :doc:`atom_style colloid ` + - colloid + - no + * - :ref:`COLVARS ` + - collective variables library + - :doc:`fix colvars ` + - PACKAGES/colvars + - int + * - :ref:`COMPRESS ` + - I/O compression + - :doc:`dump \*/gz ` + - n/a + - sys + * - :ref:`CORESHELL ` + - adiabatic core/shell model + - :doc:`Howto coreshell ` + - coreshell + - no + * - :ref:`DIELECTRIC ` + - dielectric boundary solvers and force styles + - :doc:`compute efield/atom ` + - PACKAGES/dielectric + - no + * - :ref:`DIFFRACTION ` + - virtual x-ray and electron diffraction + - :doc:`compute xrd ` + - PACKAGES/diffraction + - no + * - :ref:`DIPOLE ` + - point dipole particles + - :doc:`pair_style lj/.../dipole ` + - dipole + - no + * - :ref:`DPD-BASIC ` + - basic DPD models + - :doc:`pair_styles dpd dpd/tstat ` :doc:`dpd/ext dpd/ext/tstat ` + - PACKAGES/dpd-basic + - no + * - :ref:`DPD-MESO ` + - mesoscale DPD models + - :doc:`pair_style edpd ` + - PACKAGES/dpd-meso + - no + * - :ref:`DPD-REACT ` + - reactive dissipative particle dynamics + - src/DPD-REACT/README + - PACKAGES/dpd-react + - no + * - :ref:`DPD-SMOOTH ` + - smoothed dissipative particle dynamics + - src/DPD-SMOOTH/README + - PACKAGES/dpd-smooth + - no + * - :ref:`DRUDE ` + - Drude oscillators + - :doc:`Howto drude ` + - PACKAGES/drude + - no + * - :ref:`EFF ` + - electron force field + - :doc:`pair_style eff/cut ` + - PACKAGES/eff + - no + * - :ref:`FEP ` + - free energy perturbation + - :doc:`compute fep ` + - PACKAGES/fep + - no + * - :ref:`GPU ` + - GPU-enabled styles + - :doc:`Section gpu ` + - `Benchmarks `_ + - int + * - :ref:`GRANULAR ` + - granular systems + - :doc:`Howto granular ` + - pour + - no + * - :ref:`H5MD ` + - dump output via HDF5 + - :doc:`dump h5md ` + - n/a + - ext + * - :ref:`INTEL ` + - optimized Intel CPU and KNL styles + - :doc:`Speed intel ` + - `Benchmarks `_ + - no + * - :ref:`KIM ` + - OpenKIM wrapper + - :doc:`pair_style kim ` + - kim + - ext + * - :ref:`KOKKOS ` + - Kokkos-enabled styles + - :doc:`Speed kokkos ` + - `Benchmarks `_ + - no + * - :ref:`KSPACE ` + - long-range Coulombic solvers + - :doc:`kspace_style ` + - peptide + - no + * - :ref:`LATBOLTZ ` + - Lattice Boltzmann fluid + - :doc:`fix lb/fluid ` + - PACKAGES/latboltz + - no + * - :ref:`LATTE ` + - quantum DFTB forces via LATTE + - :doc:`fix latte ` + - latte + - ext + * - :ref:`MACHDYN ` + - smoothed Mach dynamics + - `SMD User Guide `_ + - PACKAGES/machdyn + - ext + * - :ref:`MANIFOLD ` + - motion on 2d surfaces + - :doc:`fix manifoldforce ` + - PACKAGES/manifold + - no + * - :ref:`MANYBODY ` + - many-body potentials + - :doc:`pair_style tersoff ` + - shear + - no + * - :ref:`MC ` + - Monte Carlo options + - :doc:`fix gcmc ` + - n/a + - no + * - :ref:`MDI ` + - client-server coupling + - :doc:`MDI Howto ` + - PACKAGES/mdi + - ext + * - :ref:`MEAM ` + - modified EAM potential (C++) + - :doc:`pair_style meam ` + - meam + - no + * - :ref:`MESONT ` + - mesoscopic tubular potential model + - pair styles :doc:`mesont/tpm `, :doc:`mesocnt ` + - PACKAGES/mesont + - int + * - :ref:`MESSAGE ` + - client/server messaging + - :doc:`message ` + - message + - int + * - :ref:`MGPT ` + - fast MGPT multi-ion potentials + - :doc:`pair_style mgpt ` + - PACKAGES/mgpt + - no + * - :ref:`MISC ` + - miscellaneous single-file commands + - n/a + - no + - no + * - :ref:`ML-HDNNP ` + - High-dimensional neural network potentials + - :doc:`pair_style hdnnp ` + - PACKAGES/hdnnp + - ext + * - :ref:`ML-IAP ` + - multiple machine learning potentials + - :doc:`pair_style mliap ` + - mliap + - no + * - :ref:`ML-PACE ` + - Atomic Cluster Expansion potential + - :doc:`pair pace ` + - PACKAGES/pace + - ext + * - :ref:`ML-QUIP ` + - QUIP/libatoms interface + - :doc:`pair_style quip ` + - PACKAGES/quip + - ext + * - :ref:`ML-RANN ` + - Pair style for RANN potentials + - :doc:`pair rann ` + - PACKAGES/rann + - no + * - :ref:`ML-SNAP ` + - quantum-fitted potential + - :doc:`pair_style snap ` + - snap + - no + * - :ref:`MOFFF ` + - styles for `MOF-FF `_ force field + - :doc:`pair_style buck6d/coul/gauss ` + - PACKAGES/mofff + - no + * - :ref:`MOLECULE ` + - molecular system force fields + - :doc:`Howto bioFF ` + - peptide + - no + * - :ref:`MOLFILE ` + - `VMD `_ molfile plug-ins + - :doc:`dump molfile ` + - n/a + - ext + * - :ref:`MPIIO ` + - MPI parallel I/O dump and restart + - :doc:`dump ` + - n/a + - no + * - :ref:`MSCG ` + - multi-scale coarse-graining wrapper + - :doc:`fix mscg ` + - mscg + - ext + * - :ref:`NETCDF ` + - dump output via NetCDF + - :doc:`dump netcdf ` + - n/a + - ext + * - :ref:`OPENMP ` + - OpenMP-enabled styles + - :doc:`Speed omp ` + - `Benchmarks `_ + - no + * - :ref:`OPT ` + - optimized pair styles + - :doc:`Speed opt ` + - `Benchmarks `_ + - no + * - :ref:`PERI ` + - Peridynamics models + - :doc:`pair_style peri ` + - peri + - no + * - :ref:`PHONON ` + - phonon dynamical matrix + - :doc:`fix phonon ` + - PACKAGES/phonon + - no + * - :ref:`PLUGIN ` + - Plugin loader command + - :doc:`plugin ` + - plugins + - no + * - :ref:`PLUMED ` + - :ref:`PLUMED ` free energy library + - :doc:`fix plumed ` + - PACKAGES/plumed + - ext + * - :ref:`POEMS ` + - coupled rigid body motion + - :doc:`fix poems ` + - rigid + - int + * - :ref:`PTM ` + - Polyhedral Template Matching + - :doc:`compute ptm/atom ` + - n/a + - no + * - :ref:`PYTHON ` + - embed Python code in an input script + - :doc:`python ` + - python + - sys + * - :ref:`QEQ ` + - QEq charge equilibration + - :doc:`fix qeq ` + - qeq + - no + * - :ref:`QMMM ` + - QM/MM coupling + - :doc:`fix qmmm ` + - PACKAGES/qmmm + - ext + * - :ref:`QTB ` + - quantum nuclear effects + - :doc:`fix qtb ` :doc:`fix qbmsst ` + - qtb + - no + * - :ref:`REACTION ` + - chemical reactions in classical MD + - :doc:`fix bond/react ` + - PACKAGES/reaction + - no + * - :ref:`REAXFF ` + - ReaxFF potential (C/C++) + - :doc:`pair_style reaxc ` + - reax + - no + * - :ref:`REPLICA ` + - multi-replica methods + - :doc:`Howto replica ` + - tad + - no + * - :ref:`RIGID ` + - rigid bodies and constraints + - :doc:`fix rigid ` + - rigid + - no + * - :ref:`SCAFACOS ` + - wrapper for ScaFaCoS Kspace solver + - :doc:`kspace_style scafacos ` + - PACKAGES/scafacos + - ext + * - :ref:`SHOCK ` + - shock loading methods + - :doc:`fix msst ` + - n/a + - no + * - :ref:`SMTBQ ` + - second moment tight binding potential + - :doc:`pair_style smtbq ` + - PACKAGES/smtbq + - no + * - :ref:`SPH ` + - smoothed particle hydrodynamics + - `SPH User Guide `_ + - PACKAGES/sph + - no + * - :ref:`SPIN ` + - magnetic atomic spin dynamics + - :doc:`Howto spins ` + - SPIN + - no + * - :ref:`SRD ` + - stochastic rotation dynamics + - :doc:`fix srd ` + - srd + - no + * - :ref:`TALLY ` + - pairwise tally computes + - :doc:`compute XXX/tally ` + - PACKAGES/tally + - no + * - :ref:`UEF ` + - extensional flow + - :doc:`fix nvt/uef ` + - PACKAGES/uef + - no + * - :ref:`USER-MISC ` + - single-file contributions + - USER-MISC/README + - USER-MISC + - no + * - :ref:`VORONOI ` + - Voronoi tesselation + - :doc:`compute voronoi/atom ` + - n/a + - ext + * - :ref:`VTK ` + - dump output via VTK + - :doc:`compute vtk ` + - n/a + - ext + * - :ref:`YAFF ` + - additional styles implemented in YAFF + - :doc:`angle_style cross ` + - PACKAGES/yaff + - no + +.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF +.. _PLUMED: https://www.plumed.org +.. _VMD: https://www.ks.uiuc.edu/Research/vmd/ diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst deleted file mode 100644 index 8fc1e7df7a..0000000000 --- a/doc/src/Packages_standard.rst +++ /dev/null @@ -1,95 +0,0 @@ -Standard packages -================= - -This is the list of standard packages in LAMMPS. The link for each -package name gives more details. - -Standard packages are supported by the LAMMPS developers and are -written in a syntax and style consistent with the rest of LAMMPS. -This means the developers will answer questions about them, debug and -fix them if necessary, and keep them compatible with future changes to -LAMMPS. - -The "Example" column is a sub-directory in the examples directory of -the distribution which has an input script that uses the package. -E.g. "peptide" refers to the examples/peptide directory; USER/atc -refers to the examples/USER/atc directory. The "Library" column -indicates whether an extra library is needed to build and use the -package: - -* no = no library -* sys = system library: you likely have it on your machine -* int = internal library: provided with LAMMPS, but you may need to build it -* ext = external library: you will need to download and install it on your machine - -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| Package | Description | Doc page | Example | Library | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`ASPHERE ` | aspherical particle models | :doc:`Howto spherical ` | ellipse | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`BODY ` | body-style particles | :doc:`Howto body ` | body | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`CLASS2 ` | class 2 force fields | :doc:`pair_style lj/class2 ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`COLLOID ` | colloidal particles | :doc:`atom_style colloid ` | colloid | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`COMPRESS ` | I/O compression | :doc:`dump \*/gz ` | n/a | sys | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`CORESHELL ` | adiabatic core/shell model | :doc:`Howto coreshell ` | coreshell | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style lj/.../dipole ` | dipole | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`GPU ` | GPU-enabled styles | :doc:`Section gpu ` | `Benchmarks `_ | int | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`GRANULAR ` | granular systems | :doc:`Howto granular ` | pour | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`KIM ` | OpenKIM wrapper | :doc:`pair_style kim ` | kim | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`KOKKOS ` | Kokkos-enabled styles | :doc:`Speed kokkos ` | `Benchmarks `_ | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`KSPACE ` | long-range Coulombic solvers | :doc:`kspace_style ` | peptide | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`LATTE ` | quantum DFTB forces via LATTE | :doc:`fix latte ` | latte | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MANYBODY ` | many-body potentials | :doc:`pair_style tersoff ` | shear | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MC ` | Monte Carlo options | :doc:`fix gcmc ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MESSAGE ` | client/server messaging | :doc:`message ` | message | int | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MISC ` | miscellaneous single-file commands | n/a | no | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MLIAP ` | multiple machine learning potentials | :doc:`pair_style mliap ` | mliap | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MOLECULE ` | molecular system force fields | :doc:`Howto bioFF ` | peptide | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MPIIO ` | MPI parallel I/O dump and restart | :doc:`dump ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`MSCG ` | multi-scale coarse-graining wrapper | :doc:`fix mscg ` | mscg | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`OPT ` | optimized pair styles | :doc:`Speed opt ` | `Benchmarks `_ | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`PERI ` | Peridynamics models | :doc:`pair_style peri ` | peri | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`PLUGIN ` | Plugin loader command | :doc:`plugin ` | plugins | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`POEMS ` | coupled rigid body motion | :doc:`fix poems ` | rigid | int | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`PYTHON ` | embed Python code in an input script | :doc:`python ` | python | sys | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`QEQ ` | QEq charge equilibration | :doc:`fix qeq ` | qeq | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`REPLICA ` | multi-replica methods | :doc:`Howto replica ` | tad | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`RIGID ` | rigid bodies and constraints | :doc:`fix rigid ` | rigid | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`SHOCK ` | shock loading methods | :doc:`fix msst ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`SNAP ` | quantum-fitted potential | :doc:`pair_style snap ` | snap | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`SPIN ` | magnetic atomic spin dynamics | :doc:`Howto spins ` | SPIN | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`SRD ` | stochastic rotation dynamics | :doc:`fix srd ` | srd | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`VORONOI ` | Voronoi tesselation | :doc:`compute voronoi/atom ` | n/a | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst deleted file mode 100644 index 89d740939e..0000000000 --- a/doc/src/Packages_user.rst +++ /dev/null @@ -1,132 +0,0 @@ -User packages -============= - -This is a list of user packages in LAMMPS. The link for each package -name gives more details. - -User packages have been contributed by users, and begin with the -"user" prefix. If a contribution is a single command (single file), -it is typically in the USER-MISC package. User packages don't -necessarily meet the requirements of the :doc:`standard packages `. This means the developers will try -to keep things working and usually can answer technical questions -about compiling the package. If you have problems using a specific -feature provided in a user package, you may need to contact the -contributor directly to get help. Information on how to submit -additions you make to LAMMPS as single files or as a standard or user -package is explained on the :doc:`Modify contribute ` -doc page. - -The "Example" column is a sub-directory in the examples directory of -the distribution which has an input script that uses the package. -E.g. "peptide" refers to the examples/peptide directory; USER/atc -refers to the examples/USER/atc directory. The "Library" column -indicates whether an extra library is needed to build and use the -package: - -* no = no library -* sys = system library: you likely have it on your machine -* int = internal library: provided with LAMMPS, but you may need to build it -* ext = external library: you will need to download and install it on your machine - -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| Package | Description | Doc page | Example | Library | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-ADIOS ` | dump output via ADIOS | :doc:`dump adios ` | USER/adios | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-ATC ` | Atom-to-Continuum coupling | :doc:`fix atc ` | USER/atc | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-AWPMD ` | wave packet MD | :doc:`pair_style awpmd/cut ` | USER/awpmd | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-BOCS ` | BOCS bottom up coarse graining | :doc:`fix bocs ` | USER/bocs | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-BROWNIAN ` | Brownian dynamics and self-propelled particles | :doc:`fix brownian `, :doc:`fix propel/self ` | USER/brownian | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-CGDNA ` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-COLVARS ` | collective variables library | :doc:`fix colvars ` | USER/colvars | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-DIELECTRIC ` | dielectric boundary solvers and force styles | :doc:`compute efield/atom ` | USER/dielectric | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-DIFFRACTION ` | virtual x-ray and electron diffraction | :doc:`compute xrd ` | USER/diffraction | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-DPD ` | reactive dissipative particle dynamics | src/USER-DPD/README | USER/dpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-DRUDE ` | Drude oscillators | :doc:`Howto drude ` | USER/drude | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-EFF ` | electron force field | :doc:`pair_style eff/cut ` | USER/eff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-FEP ` | free energy perturbation | :doc:`compute fep ` | USER/fep | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-HDNNP ` | High-dimensional neural network potentials | :doc:`pair_style hdnnp ` | USER/hdnnp | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-LB ` | Lattice Boltzmann fluid | :doc:`fix lb/fluid ` | USER/lb | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MDI ` | client-server coupling | :doc:`MDI Howto ` | USER/mdi | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MESODPD ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/mesodpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MESONT ` | mesoscopic tubular potential model for nanotubes | pair style :doc:`mesont/tpm `, :doc:`mesocnt ` | USER/mesont | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MISC ` | single-file contributions | USER-MISC/README | USER/misc | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MOFFF ` | styles for `MOF-FF `_ force field | :doc:`pair_style buck6d/coul/gauss ` | USER/mofff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MOLFILE ` | `VMD `_ molfile plug-ins | :doc:`dump molfile ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-PACE ` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace ` | USER/pace | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-PLUMED ` | :ref:`PLUMED ` free energy library | :doc:`fix plumed ` | USER/plumed | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-PTM ` | Polyhedral Template Matching | :doc:`compute ptm/atom ` | n/a | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-QMMM ` | QM/MM coupling | :doc:`fix qmmm ` | USER/qmmm | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-QTB ` | quantum nuclear effects | :doc:`fix qtb ` :doc:`fix qbmsst ` | qtb | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-RANN ` | rapid atomistic neural network (RANN) potentials | :doc:`pair rann ` | USER/rann | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-REACTION ` | chemical reactions in classical MD | :doc:`fix bond/react ` | USER/reaction | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc ` | reax | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos ` | USER/scafacos | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-SDPD ` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal ` | USER/sdpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-SMD ` | smoothed Mach dynamics | `SMD User Guide `_ | USER/smd | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-SMTBQ ` | second moment tight binding QEq potential | :doc:`pair_style smtbq ` | USER/smtbq | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-SPH ` | smoothed particle hydrodynamics | `SPH User Guide `_ | USER/sph | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-TALLY ` | pairwise tally computes | :doc:`compute XXX/tally ` | USER/tally | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-UEF ` | extensional flow | :doc:`fix nvt/uef ` | USER/uef | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-VTK ` | dump output via VTK | :doc:`compute vtk ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-YAFF ` | additional styles implemented in YAFF | :doc:`angle_style cross ` | USER/yaff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ - -.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF -.. _PLUMED: https://www.plumed.org diff --git a/doc/src/Python_install.rst b/doc/src/Python_install.rst index 6b224bbf40..abf96accbf 100644 --- a/doc/src/Python_install.rst +++ b/doc/src/Python_install.rst @@ -69,7 +69,7 @@ this. cd build # configure LAMMPS compilation - cmake -C ../cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \ + cmake -C ../cmake/presets/basic.cmake -D BUILD_SHARED_LIBS=on \ -D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake # compile LAMMPS diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index d8adfcc5be..f8c6925dba 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -10,7 +10,7 @@ letter abbreviation can be used: * :ref:`-i or -in ` * :ref:`-k or -kokkos ` * :ref:`-l or -log ` -* :ref:`-mdi ` +* :ref:`-mdi ` * :ref:`-m or -mpicolor ` * :ref:`-c or -cite ` * :ref:`-nc or -nocite ` @@ -89,7 +89,7 @@ in the :doc:`the KOKKOS package page `, this switch must be set to running with KOKKOS-enabled styles the package provides. If the switch is not set (the default), LAMMPS will operate as if the KOKKOS package were not installed; i.e. you can run standard LAMMPS or with -the GPU or USER-OMP packages, for testing or benchmarking purposes. +the GPU or OPENMP packages, for testing or benchmarking purposes. Additional optional keyword/value pairs can be specified which determine how Kokkos will use the underlying hardware on your @@ -197,12 +197,12 @@ Option -plog will override the name of the partition log files file.N. ---------- -.. _mdi: +.. _mdi_flags: **-mdi 'multiple flags'** This flag is only recognized and used when LAMMPS has support for the MolSSI -Driver Interface (MDI) included as part of the :ref:`USER-MDI ` +Driver Interface (MDI) included as part of the :ref:`MDI ` package. This flag is specific to the MDI library and controls how LAMMPS interacts with MDI. There are usually multiple flags that have to follow it and those have to be placed in quotation marks. For more information about @@ -274,7 +274,7 @@ script. For example "-package gpu 2" or "-pk gpu 2" is the same as :doc:`package gpu 2 ` in the input script. The possible styles and args are documented on the :doc:`package ` doc page. This switch can be used multiple times, e.g. to set options for the -USER-INTEL and USER-OMP packages which can be used together. +INTEL and OPENMP packages which can be used together. Along with the "-suffix" command-line switch, this is a convenient mechanism for invoking accelerator packages and their options without @@ -540,16 +540,16 @@ Use variants of various styles if they exist. The specified style can be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt*\ , or *hybrid*\ . These refer to optional packages that LAMMPS can be built with, as described in :doc:`Accelerate performance `. The "gpu" style corresponds to the -GPU package, the "intel" style to the USER-INTEL package, the "kk" +GPU package, the "intel" style to the INTEL package, the "kk" style to the KOKKOS package, the "opt" style to the OPT package, and -the "omp" style to the USER-OMP package. The hybrid style is the only +the "omp" style to the OPENMP package. The hybrid style is the only style that accepts arguments. It allows for two packages to be specified. The first package specified is the default and will be used if it is available. If no style is available for the first package, the style for the second package will be used if available. For example, "-suffix hybrid intel omp" will use styles from the -USER-INTEL package if they are installed and available, but styles for -the USER-OMP package otherwise. +INTEL package if they are installed and available, but styles for +the OPENMP package otherwise. Along with the "-package" command-line switch, this is a convenient mechanism for invoking accelerator packages and their options without @@ -570,15 +570,15 @@ default GPU settings, as if the command "package gpu 1" were used at the top of your input script. These settings can be changed by using the "-package gpu" command-line switch or the :doc:`package gpu ` command in your script. -For the USER-INTEL package, using this command-line switch also -invokes the default USER-INTEL settings, as if the command "package +For the INTEL package, using this command-line switch also +invokes the default INTEL settings, as if the command "package intel 1" were used at the top of your input script. These settings can be changed by using the "-package intel" command-line switch or the :doc:`package intel ` command in your script. If the -USER-OMP package is also installed, the hybrid style with "intel omp" +OPENMP package is also installed, the hybrid style with "intel omp" arguments can be used to make the omp suffix a second choice, if a -requested style is not available in the USER-INTEL package. It will -also invoke the default USER-OMP settings, as if the command "package +requested style is not available in the INTEL package. It will +also invoke the default OPENMP settings, as if the command "package omp 0" were used at the top of your input script. These settings can be changed by using the "-package omp" command-line switch or the :doc:`package omp ` command in your script. diff --git a/doc/src/Run_windows.rst b/doc/src/Run_windows.rst index 8813d6d59e..f29155a839 100644 --- a/doc/src/Run_windows.rst +++ b/doc/src/Run_windows.rst @@ -11,7 +11,7 @@ To run a serial (non-MPI) executable, follow these steps: in.file is the name of your LAMMPS input script. Note that the serial executable includes support for multi-threading -parallelization from the styles in the USER-OMP packages. To run with +parallelization from the styles in the OPENMP packages. To run with 4 threads, you can type this: .. code-block:: bash diff --git a/doc/src/Speed_compare.rst b/doc/src/Speed_compare.rst index 4ab616a5da..7821214c83 100644 --- a/doc/src/Speed_compare.rst +++ b/doc/src/Speed_compare.rst @@ -67,12 +67,12 @@ section below for examples where this has been done. pair style - on the CPU. This can often be easily achieved with placing a *suffix off* command before and a *suffix on* command after the *kspace_style pppm* command. -* The KOKKOS/OpenMP and USER-OMP package have different thread management - strategies, which should result in USER-OMP being more efficient for a +* The KOKKOS/OpenMP and OPENMP package have different thread management + strategies, which should result in OPENMP being more efficient for a small number of threads with increasing overhead as the number of threads per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that case, but have lower performance with few threads. -* The USER-INTEL package contains many options and settings for achieving +* The INTEL package contains many options and settings for achieving additional performance on Intel hardware (CPU and accelerator cards), but to unlock this potential, an Intel compiler is required. The package code will compile with GNU gcc, but it will not be as efficient. @@ -90,5 +90,5 @@ section below for examples where this has been done. both, NVIDIA and AMD GPUs well. On NVIDIA hardware, using CUDA is typically resulting in equal or better performance over OpenCL. * OpenCL in the GPU package does theoretically also support Intel CPUs or - Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL) + Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL) is superior. diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index 2cb8c08fd5..3b6bb8845b 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -150,7 +150,7 @@ hardware, which pair style is used, the number of atoms/GPU, and the precision used on the GPU (double, single, mixed). Using the GPU package in OpenCL mode on CPUs (which uses vectorization and multithreading) is usually resulting in inferior performance compared to using LAMMPS' native -threading and vectorization support in the USER-OMP and USER-INTEL packages. +threading and vectorization support in the OPENMP and INTEL packages. See the `Benchmark page `_ of the LAMMPS web site for performance of the GPU package on various diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index 0d0551c008..20371b4256 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -1,7 +1,7 @@ -USER-INTEL package +INTEL package ================== -The USER-INTEL package is maintained by Mike Brown at Intel +The INTEL package is maintained by Mike Brown at Intel Corporation. It provides two methods for accelerating simulations, depending on the hardware you have. The first is acceleration on Intel CPUs by running in single, mixed, or double precision with @@ -12,7 +12,7 @@ When offloading to a co-processor from a CPU, the same routine is run twice, once on the CPU and once with an offload flag. This allows LAMMPS to run on the CPU cores and co-processor cores simultaneously. -Currently Available USER-INTEL Styles +Currently Available INTEL Styles """"""""""""""""""""""""""""""""""""" * Angle Styles: charmm, harmonic @@ -28,7 +28,7 @@ Currently Available USER-INTEL Styles .. warning:: - None of the styles in the USER-INTEL package currently + None of the styles in the INTEL package currently support computing per-atom stress. If any compute or fix in your input requires it, LAMMPS will abort with an error message. @@ -41,7 +41,7 @@ precision mode. Performance improvements are shown compared to LAMMPS *without using other acceleration packages* as these are under active development (and subject to performance changes). The measurements were performed using the input files available in -the src/USER-INTEL/TEST directory with the provided run script. +the src/INTEL/TEST directory with the provided run script. These are scalable in size; the results given are with 512K particles (524K for Liquid Crystal). Most of the simulations are standard LAMMPS benchmarks (indicated by the filename extension in @@ -56,7 +56,7 @@ Results are speedups obtained on Intel Xeon E5-2697v4 processors Knights Landing), and Intel Xeon Gold 6148 processors (code-named Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio 2017 update 2. Results are with 1 MPI task per physical core. See -*src/USER-INTEL/TEST/README* for the raw simulation rates and +*src/INTEL/TEST/README* for the raw simulation rates and instructions to reproduce. ---------- @@ -67,11 +67,11 @@ Accuracy and order of operations In most molecular dynamics software, parallelization parameters (# of MPI, OpenMP, and vectorization) can change the results due to changing the order of operations with finite-precision -calculations. The USER-INTEL package is deterministic. This means +calculations. The INTEL package is deterministic. This means that the results should be reproducible from run to run with the *same* parallel configurations and when using deterministic libraries or library settings (MPI, OpenMP, FFT). However, there -are differences in the USER-INTEL package that can change the +are differences in the INTEL package that can change the order of operations compared to LAMMPS without acceleration: * Neighbor lists can be created in a different order @@ -88,7 +88,7 @@ order of operations compared to LAMMPS without acceleration: Twister generator included in the Intel MKL library (that should be more robust than the default Masaglia random number generator) -The precision mode (described below) used with the USER-INTEL +The precision mode (described below) used with the INTEL package can change the *accuracy* of the calculations. For the default *mixed* precision option, calculations between pairs or triplets of atoms are performed in single precision, intended to @@ -102,7 +102,7 @@ mode should not be used without appropriate validation. Quick Start for Experienced Users """"""""""""""""""""""""""""""""" -LAMMPS should be built with the USER-INTEL package installed. +LAMMPS should be built with the INTEL package installed. Simulations should be run with 1 MPI task per physical *core*\ , not *hardware thread*\ . @@ -148,7 +148,7 @@ When using Intel compilers version 16.0 or later is required. In order to use offload to co-processors, an Intel Xeon Phi co-processor and an Intel compiler are required. -Although any compiler can be used with the USER-INTEL package, +Although any compiler can be used with the INTEL package, currently, vectorization directives are disabled by default when not using Intel compilers due to lack of standard support and observations of decreased performance. The OpenMP standard now @@ -185,7 +185,7 @@ can start running so that the CPU pipeline is still being used efficiently. Although benefits can be seen by launching a MPI task for every hardware thread, for multinode simulations, we recommend that OpenMP threads are used for SMT instead, either with the -USER-INTEL package, :doc:`USER-OMP package `, or +INTEL package, :doc:`OPENMP package `, or :doc:`KOKKOS package `. In the example above, up to 36X speedups can be observed by using all 36 physical cores with LAMMPS. By using all 72 hardware threads, an additional 10-30% @@ -202,10 +202,10 @@ this information can normally be obtained with: cat /proc/cpuinfo -Building LAMMPS with the USER-INTEL package +Building LAMMPS with the INTEL package """"""""""""""""""""""""""""""""""""""""""" -See the :ref:`Build extras ` doc page for +See the :ref:`Build extras ` doc page for instructions. Some additional details are covered here. For building with make, several example Makefiles for building with @@ -228,7 +228,7 @@ simple as: .. code-block:: bash - make yes-user-intel + make yes-intel source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh # or psxevars.csh for C-shell make intel_cpu_intelmpi @@ -238,7 +238,7 @@ binary can be used on nodes with or without co-processors installed. However, if you do not have co-processors on your system, building without offload support will produce a smaller binary. -The general requirements for Makefiles with the USER-INTEL package +The general requirements for Makefiles with the INTEL package are as follows. When using Intel compilers, "-restrict" is required and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads @@ -253,7 +253,7 @@ recommended CCFLAG options for best performance are "-O2 -fno-alias .. note:: - See the src/USER-INTEL/README file for additional flags that + See the src/INTEL/README file for additional flags that might be needed for best performance on Intel server processors code-named "Skylake". @@ -270,14 +270,14 @@ recommended CCFLAG options for best performance are "-O2 -fno-alias in most of the example Makefiles is to use "-xHost", however this should not be used when cross-compiling. -Running LAMMPS with the USER-INTEL package +Running LAMMPS with the INTEL package """""""""""""""""""""""""""""""""""""""""" -Running LAMMPS with the USER-INTEL package is similar to normal use +Running LAMMPS with the INTEL package is similar to normal use with the exceptions that one should 1) specify that LAMMPS should use -the USER-INTEL package, 2) specify the number of OpenMP threads, and +the INTEL package, 2) specify the number of OpenMP threads, and 3) optionally specify the specific LAMMPS styles that should use the -USER-INTEL package. 1) and 2) can be performed from the command-line +INTEL package. 1) and 2) can be performed from the command-line or by editing the input script. 3) requires editing the input script. Advanced performance tuning options are also described below to get the best performance. @@ -312,27 +312,27 @@ almost all cases. recommended, especially when running on a machine with Intel Hyper-Threading technology disabled. -Run with the USER-INTEL package from the command line +Run with the INTEL package from the command line """"""""""""""""""""""""""""""""""""""""""""""""""""" -To enable USER-INTEL optimizations for all available styles used in +To enable INTEL optimizations for all available styles used in the input script, the "-sf intel" :doc:`command-line switch ` can be used without any requirement for editing the input script. This switch will automatically append "intel" to styles that support it. It also invokes a default command: :doc:`package intel 1 `. This package command is used to set -options for the USER-INTEL package. The default package command will -specify that USER-INTEL calculations are performed in mixed precision, +options for the INTEL package. The default package command will +specify that INTEL calculations are performed in mixed precision, that the number of OpenMP threads is specified by the OMP_NUM_THREADS environment variable, and that if co-processors are present and the binary was built with offload support, that 1 co-processor per node will be used with automatic balancing of work between the CPU and the co-processor. -You can specify different options for the USER-INTEL package by using +You can specify different options for the INTEL package by using the "-pk intel Nphi" :doc:`command-line switch ` with keyword/value pairs as specified in the documentation. Here, Nphi = # of Xeon Phi co-processors/node (ignored without offload -support). Common options to the USER-INTEL package include *omp* to +support). Common options to the INTEL package include *omp* to override any OMP_NUM_THREADS setting and specify the number of OpenMP threads, *mode* to set the floating-point precision mode, and *lrt* to enable Long-Range Thread mode as described below. See the :doc:`package intel ` command for details, including the default values @@ -348,11 +348,11 @@ launching MPI applications): mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision -Or run with the USER-INTEL package by editing an input script +Or run with the INTEL package by editing an input script """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" As an alternative to adding command-line arguments, the input script -can be edited to enable the USER-INTEL package. This requires adding +can be edited to enable the INTEL package. This requires adding the :doc:`package intel ` command to the top of the input script. For the second example above, this would be: @@ -360,7 +360,7 @@ script. For the second example above, this would be: package intel 0 omp 2 mode double -To enable the USER-INTEL package only for individual styles, you can +To enable the INTEL package only for individual styles, you can add an "intel" suffix to the individual style, e.g.: .. code-block:: LAMMPS @@ -368,7 +368,7 @@ add an "intel" suffix to the individual style, e.g.: pair_style lj/cut/intel 2.5 Alternatively, the :doc:`suffix intel ` command can be added to -the input script to enable USER-INTEL styles for the commands that +the input script to enable INTEL styles for the commands that follow in the input script. Tuning for Performance @@ -376,7 +376,7 @@ Tuning for Performance .. note:: - The USER-INTEL package will perform better with modifications + The INTEL package will perform better with modifications to the input script when :doc:`PPPM ` is used: :doc:`kspace_modify diff ad ` should be added to the input script. @@ -388,7 +388,7 @@ is dedicated to performing some of the PPPM calculations and MPI communications. This feature requires setting the pre-processor flag -DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset in the default makefiles (\ *Makefile.mpi* and *Makefile.serial*\ ) but -it is set in all makefiles tuned for the USER-INTEL package. On Intel +it is set in all makefiles tuned for the INTEL package. On Intel Xeon Phi x200 series CPUs, the LRT feature will likely improve performance, even on a single node. On Intel Xeon processors, using this mode might result in better performance when using multiple nodes, @@ -407,9 +407,9 @@ when using offload. performance and/or scalability for simple 2-body potentials such as lj/cut or when using LRT mode on processors supporting AVX-512. -Not all styles are supported in the USER-INTEL package. You can mix -the USER-INTEL package with styles from the :doc:`OPT ` -package or the :doc:`USER-OMP package `. Of course, this +Not all styles are supported in the INTEL package. You can mix +the INTEL package with styles from the :doc:`OPT ` +package or the :doc:`OPENMP package `. Of course, this requires that these packages were installed at build time. This can performed automatically by using "-sf hybrid intel opt" or "-sf hybrid intel omp" command-line options. Alternatively, the "opt" and "omp" @@ -420,7 +420,7 @@ where Nt is the number of OpenMP threads. The number of OpenMP threads should not be set differently for the different packages. Note that the :doc:`suffix hybrid intel omp ` command can also be used within the input script to automatically append the "omp" suffix to -styles when USER-INTEL styles are not available. +styles when INTEL styles are not available. .. note:: @@ -492,7 +492,7 @@ tuning of the number of threads to use per MPI task or the number of threads to use per core can be accomplished with keyword settings of the :doc:`package intel ` command. -The USER-INTEL package has two modes for deciding which atoms will be +The INTEL package has two modes for deciding which atoms will be handled by the co-processor. This choice is controlled with the *ghost* keyword of the :doc:`package intel ` command. When set to 0, ghost atoms (atoms at the borders between MPI tasks) are not offloaded @@ -528,7 +528,7 @@ accelerated style may be used with hybrid styles when offloading. :doc:`Special_bonds ` exclusion lists are not currently supported with offload, however, the same effect can often be accomplished by setting cutoffs for excluded atom types to 0. None of -the pair styles in the USER-INTEL package currently support the +the pair styles in the INTEL package currently support the "inner", "middle", "outer" options for rRESPA integration via the :doc:`run_style respa ` command; only the "pair" option is supported. diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index c3f8945c62..c24c22e926 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -235,7 +235,7 @@ threads/task as Nt. The product of these two values should be N, i.e. To build with Kokkos support for Intel Xeon Phi co-processors such as Knight's Corner (KNC), your system must be configured to use - them in "native" mode, not "offload" mode like the USER-INTEL package + them in "native" mode, not "offload" mode like the INTEL package supports. Running on GPUs @@ -390,10 +390,10 @@ Generally speaking, the following rules of thumb apply: * When running on CPUs only, with a single thread per MPI task, performance of a KOKKOS style is somewhere between the standard (un-accelerated) styles (MPI-only mode), and those provided by the - USER-OMP package. However the difference between all 3 is small (less + OPENMP package. However the difference between all 3 is small (less than 20%). * When running on CPUs only, with multiple threads per MPI task, - performance of a KOKKOS style is a bit slower than the USER-OMP + performance of a KOKKOS style is a bit slower than the OPENMP package. * When running large number of atoms per GPU, KOKKOS is typically faster than the GPU package when compiled for double precision. The benefit @@ -401,8 +401,8 @@ Generally speaking, the following rules of thumb apply: significantly on the hardware in use and the simulated system and pair style. * When running on Intel hardware, KOKKOS is not as fast as - the USER-INTEL package, which is optimized for x86 hardware (not just - from Intel) and compilation with the Intel compilers. The USER-INTEL + the INTEL package, which is optimized for x86 hardware (not just + from Intel) and compilation with the Intel compilers. The INTEL package also can increase the vector length of vector instructions by switching to single or mixed precision mode. diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index f29e3743b4..060944e81b 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -1,7 +1,7 @@ -USER-OMP package +OPENMP package ================ -The USER-OMP package was developed by Axel Kohlmeyer at Temple +The OPENMP package was developed by Axel Kohlmeyer at Temple University. It provides optimized and multi-threaded versions of many pair styles, nearly all bonded styles (bond, angle, dihedral, improper), several Kspace styles, and a few fix styles. It uses @@ -15,13 +15,13 @@ To enable multi-threading, your compiler must support the OpenMP interface. You should have one or more multi-core CPUs, as multiple threads can only be launched by each MPI task on the local node (using shared memory). -Building LAMMPS with the USER-OMP package +Building LAMMPS with the OPENMP package """"""""""""""""""""""""""""""""""""""""" -See the :ref:`Build extras ` doc page for +See the :ref:`Build extras ` doc page for instructions. -Run with the USER-OMP package from the command line +Run with the OPENMP package from the command line """"""""""""""""""""""""""""""""""""""""""""""""""" These examples assume one or more 16-core nodes. @@ -39,7 +39,7 @@ tasks used per node. E.g. the mpirun command in MPICH does this via its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. You need to choose how many OpenMP threads per MPI task will be used -by the USER-OMP package. Note that the product of MPI tasks \* +by the OPENMP package. Note that the product of MPI tasks \* threads/task should not exceed the physical number of cores (on a node), otherwise performance will suffer. @@ -55,7 +55,7 @@ details, including the default values used if it is not specified. It also gives more details on how to set the number of threads via the OMP_NUM_THREADS environment variable. -Or run with the USER-OMP package by editing an input script +Or run with the OPENMP package by editing an input script """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" The discussion above for the mpirun/mpiexec command, MPI tasks/node, @@ -69,7 +69,7 @@ Use the :doc:`suffix omp ` command, or you can explicitly add an pair_style lj/cut/omp 2.5 You must also use the :doc:`package omp ` command to enable the -USER-OMP package. When you do this you also specify how many threads +OPENMP package. When you do this you also specify how many threads per MPI task to use. The command doc page explains other options and how to set the number of threads via the OMP_NUM_THREADS environment variable. @@ -82,10 +82,10 @@ reduction in the "Pair time", "Bond time", "KSpace time", and "Loop time" values printed at the end of a run. You may see a small performance advantage (5 to 20%) when running a -USER-OMP style (in serial or parallel) with a single thread per MPI +OPENMP style (in serial or parallel) with a single thread per MPI task, versus running standard LAMMPS with its standard un-accelerated styles (in serial or all-MPI parallelization with 1 task/core). This -is because many of the USER-OMP styles contain similar optimizations +is because many of the OPENMP styles contain similar optimizations to those used in the OPT package, described in :doc:`the OPT package ` doc page. @@ -95,19 +95,19 @@ tested via benchmark runs for a specific simulation running on a specific machine, paying attention to guidelines discussed in the next sub-section. -A description of the multi-threading strategy used in the USER-OMP +A description of the multi-threading strategy used in the OPENMP package and some performance examples are `presented here `_. Guidelines for best performance """"""""""""""""""""""""""""""" -For many problems on current generation CPUs, running the USER-OMP +For many problems on current generation CPUs, running the OPENMP package with a single thread/task is faster than running with multiple threads/task. This is because the MPI parallelization in LAMMPS is often more efficient than multi-threading as implemented in the -USER-OMP package. The parallel efficiency (in a threaded sense) also -varies for different USER-OMP styles. +OPENMP package. The parallel efficiency (in a threaded sense) also +varies for different OPENMP styles. Using multiple threads/task can be more effective under the following circumstances: @@ -143,7 +143,7 @@ circumstances: sometimes be achieved by increasing the length of the Coulombic cutoff and thus reducing the work done by the long-range solver. Using the :doc:`run_style verlet/split ` command, which is compatible - with the USER-OMP package, is an alternative way to reduce the number + with the OPENMP package, is an alternative way to reduce the number of MPI tasks assigned to the KSpace calculation. Additional performance tips are as follows: diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index f5da991f0b..be3f205f4b 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -12,17 +12,16 @@ All of these commands are in packages provided with LAMMPS. An overview of packages is give on the :doc:`Packages ` doc pages. -These are the accelerator packages currently in LAMMPS, either as -standard or user packages: +These are the accelerator packages currently in LAMMPS: +-----------------------------------------+-------------------------------------------------------+ | :doc:`GPU Package ` | for GPUs via CUDA, OpenCL, or ROCm HIP | +-----------------------------------------+-------------------------------------------------------+ -| :doc:`USER-INTEL Package ` | for Intel CPUs and Intel Xeon Phi | +| :doc:`INTEL Package ` | for Intel CPUs and Intel Xeon Phi | +-----------------------------------------+-------------------------------------------------------+ | :doc:`KOKKOS Package ` | for NVIDIA GPUs, Intel Xeon Phi, and OpenMP threading | +-----------------------------------------+-------------------------------------------------------+ -| :doc:`USER-OMP Package ` | for OpenMP threading and generic CPU optimizations | +| :doc:`OPENMP Package ` | for OpenMP threading and generic CPU optimizations | +-----------------------------------------+-------------------------------------------------------+ | :doc:`OPT Package ` | generic CPU optimizations | +-----------------------------------------+-------------------------------------------------------+ @@ -41,11 +40,11 @@ Inverting this list, LAMMPS currently has acceleration support for three kinds of hardware, via the listed packages: +-----------------+-----------------------------------------------------------------------------------------------------------------------------+ -| Many-core CPUs | :doc:`USER-INTEL `, :doc:`KOKKOS `, :doc:`USER-OMP `, :doc:`OPT ` packages | +| Many-core CPUs | :doc:`INTEL `, :doc:`KOKKOS `, :doc:`OPENMP `, :doc:`OPT ` packages | +-----------------+-----------------------------------------------------------------------------------------------------------------------------+ | GPUs | :doc:`GPU `, :doc:`KOKKOS ` packages | +-----------------+-----------------------------------------------------------------------------------------------------------------------------+ -| Intel Phi/AVX | :doc:`USER-INTEL `, :doc:`KOKKOS ` packages | +| Intel Phi/AVX | :doc:`INTEL `, :doc:`KOKKOS ` packages | +-----------------+-----------------------------------------------------------------------------------------------------------------------------+ Which package is fastest for your hardware may depend on the size @@ -84,9 +83,9 @@ listed above: +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | build the accelerator library | only for GPU package | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ -| install the accelerator package | make yes-opt, make yes-user-intel, etc | +| install the accelerator package | make yes-opt, make yes-intel, etc | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ -| add compile/link flags to Makefile.machine in src/MAKE | only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | +| add compile/link flags to Makefile.machine in src/MAKE | only for INTEL, KOKKOS, OPENMP, OPT packages | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | re-build LAMMPS | make machine | +--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ @@ -116,15 +115,15 @@ script. With a few exceptions, you can build a single LAMMPS executable with all its accelerator packages installed. Note however that the - USER-INTEL and KOKKOS packages require you to choose one of their + INTEL and KOKKOS packages require you to choose one of their hardware options when building for a specific platform. I.e. CPU or - Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi + Phi option for the INTEL package. Or the OpenMP, Cuda, or Phi option for the KOKKOS package. These are the exceptions. You cannot build a single executable with: -* both the USER-INTEL Phi and KOKKOS Phi options -* the USER-INTEL Phi or Kokkos Phi option, and the GPU package +* both the INTEL Phi and KOKKOS Phi options +* the INTEL Phi or Kokkos Phi option, and the GPU package See the examples/accelerate/README and make.list files for sample Make.py commands that build LAMMPS with any or all of the accelerator @@ -156,7 +155,7 @@ are in the individual accelerator sections. * Styles with a "gpu" suffix are part of the GPU package and can be run on Intel, NVIDIA, or AMD GPUs. The speed-up on a GPU depends on a variety of factors, discussed in the accelerator sections. -* Styles with an "intel" suffix are part of the USER-INTEL +* Styles with an "intel" suffix are part of the INTEL package. These styles support vectorized single and mixed precision calculations, in addition to full double precision. In extreme cases, this can provide speedups over 3.5x on CPUs. The package also @@ -167,7 +166,7 @@ are in the individual accelerator sections. run using OpenMP on multicore CPUs, on an NVIDIA or AMD GPU, or on an Intel Xeon Phi in "native" mode. The speed-up depends on a variety of factors, as discussed on the KOKKOS accelerator page. -* Styles with an "omp" suffix are part of the USER-OMP package and allow +* Styles with an "omp" suffix are part of the OPENMP package and allow a pair-style to be run in multi-threaded mode using OpenMP. This can be useful on nodes with high-core counts when using less MPI processes than cores is advantageous, e.g. when running with PPPM so that FFTs diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 4d46d32037..65a96ce44a 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -67,7 +67,7 @@ Post-processing tools * :ref:`amber2lmp ` * :ref:`binary2txt ` * :ref:`ch2lmp ` - * :ref:`colvars ` + * :ref:`colvars ` * :ref:`eff ` * :ref:`fep ` * :ref:`lmp2arc ` @@ -214,7 +214,7 @@ tool and the specific name of the program used (e.g. ``ninja-v1.10`` or ---------- -.. _colvars: +.. _colvars_tools: colvars tools --------------------------- @@ -341,7 +341,7 @@ fep tool The tools/fep directory contains Python scripts useful for post-processing results from performing free-energy perturbation -simulations using the USER-FEP package. +simulations using the FEP package. The scripts were contributed by Agilio Padua (ENS de Lyon), agilio.padua at ens-lyon.fr. @@ -861,10 +861,10 @@ phonon tool The phonon sub-directory contains a post-processing tool useful for analyzing the output of the :doc:`fix phonon ` command in -the USER-PHONON package. +the PHONON package. See the README file for instruction on building the tool and what -library it needs. And see the examples/USER/phonon directory +library it needs. And see the examples/PACKAGES/phonon directory for example problems that can be post-processed with this tool. This tool was written by Ling-Ti Kong at Shanghai Jiao Tong @@ -968,13 +968,13 @@ smd tool The smd sub-directory contains a C++ file dump2vtk_tris.cpp and Makefile which can be compiled and used to convert triangle output -files created by the Smooth-Mach Dynamics (USER-SMD) package into a +files created by the Smooth-Mach Dynamics (MACHDYN) package into a VTK-compatible unstructured grid file. It could then be read in and visualized by VTK. See the header of dump2vtk.cpp for more details. -This tool was written by the USER-SMD package author, Georg +This tool was written by the MACHDYN package author, Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). diff --git a/doc/src/accel_styles.rst b/doc/src/accel_styles.rst index b5ef400f12..bd7d88f9d7 100644 --- a/doc/src/accel_styles.rst +++ b/doc/src/accel_styles.rst @@ -5,8 +5,8 @@ hardware, as discussed on the :doc:`Speed packages ` doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. You can specify the accelerated styles explicitly in your input script diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index e557648d9f..d411599eaf 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -63,8 +63,8 @@ hardware, as discussed on the :doc:`Speed packages ` doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. You can specify the accelerated styles explicitly in your input script diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index bf0305055a..f257d96dc3 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -126,7 +126,7 @@ Restrictions This angle style can only be used if LAMMPS was built with the CLASS2 package. For the *class2/p6* style LAMMPS needs to be built with the -USER-MOFFF package. See the :doc:`Build package ` doc +MOFFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_cosine_buck6d.rst b/doc/src/angle_cosine_buck6d.rst index 4b8497d743..5061bc7b87 100644 --- a/doc/src/angle_cosine_buck6d.rst +++ b/doc/src/angle_cosine_buck6d.rst @@ -60,7 +60,7 @@ Restrictions :doc:`special_bonds ` 0.0 weighting of 1-3 interactions. This angle style can only be used if LAMMPS was built with the -USER-MOFFF package. See the :doc:`Build package ` doc +MOFFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index 340a3e4de7..fe0cd3968b 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -64,7 +64,7 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -USER-CGSDK package. See the :doc:`Build package ` doc +CG-SDK package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index 1b5aaccb9a..a54971cf3b 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -194,7 +194,7 @@ For the *peri* style, the particles are spherical and each stores a per-particle mass and volume. The *dpd* style is for dissipative particle dynamics (DPD) particles. -Note that it is part of the USER-DPD package, and is not for use with +Note that it is part of the DPD-REACT package, and is not for use with the :doc:`pair_style dpd or dpd/stat ` commands, which can simply use atom_style atomic. Atom_style dpd extends DPD particle properties with internal temperature (dpdTheta), internal conductive @@ -319,7 +319,7 @@ styles take the same arguments and should produce the same results, except for round-off and precision issues. Note that other acceleration packages in LAMMPS, specifically the GPU, -USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom +INTEL, OPENMP, and OPT packages do not use accelerated atom styles. The accelerated styles are part of the KOKKOS package. They are only @@ -352,24 +352,24 @@ The *dipole* style is part of the DIPOLE package. The *peri* style is part of the PERI package for Peridynamics. -The *electron* style is part of the USER-EFF package for :doc:`electronic force fields `. +The *electron* style is part of the EFF package for :doc:`electronic force fields `. -The *dpd* style is part of the USER-DPD package for dissipative +The *dpd* style is part of the DPD-REACT package for dissipative particle dynamics (DPD). -The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the USER-MESODPD package +The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the DPD-MESO package for energy-conserving dissipative particle dynamics (eDPD), many-body dissipative particle dynamics (mDPD), and transport dissipative particle dynamics (tDPD), respectively. -The *sph* style is part of the USER-SPH package for smoothed particle +The *sph* style is part of the SPH package for smoothed particle hydrodynamics (SPH). See `this PDF guide `_ to using SPH in LAMMPS. -The *mesont* style is part of the USER-MESONT package. +The *mesont* style is part of the MESONT package. The *spin* style is part of the SPIN package. -The *wavepacket* style is part of the USER-AWPMD package for the +The *wavepacket* style is part of the AWPMD package for the :doc:`antisymmetrized wave packet MD method `. Related commands diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 3f52424d49..b2cc68fa22 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -77,16 +77,16 @@ commands: be changed without reparameterizing the entire model. Example input and data files for DNA and RNA duplexes can be found in -examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python +examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA/RNA duplexes or arrays of DNA/RNA duplexes can be found in -examples/USER/cgdna/util/. +examples/PACKAGES/cgdna/util/. Please cite :ref:`(Henrich) ` in any publication that uses this implementation. The article contains general information on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found -`here `_. +`here `_. Please cite also the relevant oxDNA/oxRNA publications. These are :ref:`(Ouldridge) ` and :ref:`(Ouldridge-DPhil) ` for oxDNA, @@ -101,7 +101,7 @@ Restrictions """""""""""" This bond style can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the +CG-DNA package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_basal_atom.rst b/doc/src/compute_basal_atom.rst index a5558e6232..8d8037e54e 100644 --- a/doc/src/compute_basal_atom.rst +++ b/doc/src/compute_basal_atom.rst @@ -42,7 +42,7 @@ too frequently or to have multiple compute/dump commands, each of which computes this quantity. An example input script that uses this compute is provided -in examples/USER/misc/basal. +in examples/USER-MISC/basal. Output info """"""""""" diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst index a3b68451db..72cae28c22 100644 --- a/doc/src/compute_dpd.rst +++ b/doc/src/compute_dpd.rst @@ -60,7 +60,7 @@ The vector values will be in energy and temperature :doc:`units `. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This command also requires use of the :doc:`atom_style dpd ` diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst index 85dc977c52..6abbce10f0 100644 --- a/doc/src/compute_dpd_atom.rst +++ b/doc/src/compute_dpd_atom.rst @@ -50,7 +50,7 @@ and temperature (:math:`theta`) :doc:`units `. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This command also requires use of the :doc:`atom_style dpd ` diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index e31974f98a..920bda1a87 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -44,7 +44,7 @@ The per-atom vector values will be in temperature :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-MESODPD package. It is only enabled if +This compute is part of the DPD-MESO package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_efield_atom.rst b/doc/src/compute_efield_atom.rst index 1e87ad2556..27c4eea4f6 100644 --- a/doc/src/compute_efield_atom.rst +++ b/doc/src/compute_efield_atom.rst @@ -26,7 +26,7 @@ Description Define a computation that calculates the electric field at each atom in a group. The compute should only enabled with pair and kspace styles that are provided -by the USER-DIELECTRIC package because only these styles compute the per-atom +by the DIELECTRIC package because only these styles compute the per-atom electric field at every time step. The electric field is a 3-component vector. The value of the electric field @@ -52,7 +52,7 @@ The per-atom vector values will be in electric field :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-DIELECTRIC package. It is only enabled if +This compute is part of the DIELECTRIC package. It is only enabled if LAMMPS was built with that package. Related commands diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index ef908acfc0..5427538a73 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -48,7 +48,7 @@ Examples compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes compute 1 all fep 300 atom charge 2 v_delta -Example input scripts available: examples/USER/fep +Example input scripts available: examples/PACKAGES/fep Description """"""""""" @@ -303,7 +303,7 @@ The values calculated by this compute are "extensive". Restrictions """""""""""" -This compute is distributed as the USER-FEP package. It is only +This compute is distributed as the FEP package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index 5efb133bea..0f5b32b8d1 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -152,7 +152,7 @@ The following example illustrates the placement of this command in the input scr The :doc:`fix_modify energy yes ` command must also be specified if a fix is to contribute potential energy to this command. An example input script that uses this compute is included in -examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA +examples/PACKAGES/hma/ along with corresponding LAMMPS output showing that the HMA properties fluctuate less than the corresponding conventional properties. Output info diff --git a/doc/src/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst index 3ff9ce0c1f..e364b20f31 100644 --- a/doc/src/compute_ke_atom_eff.rst +++ b/doc/src/compute_ke_atom_eff.rst @@ -73,7 +73,7 @@ The per-atom vector values will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-EFF package. It is only enabled if +This compute is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst index 874ae8d629..6028099d07 100644 --- a/doc/src/compute_ke_eff.rst +++ b/doc/src/compute_ke_eff.rst @@ -78,7 +78,7 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-EFF package. It is only enabled if +This compute is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_mesont.rst b/doc/src/compute_mesont.rst index 44d6054e22..c449a0a175 100644 --- a/doc/src/compute_mesont.rst +++ b/doc/src/compute_mesont.rst @@ -43,7 +43,7 @@ The computed values are provided in energy :doc:`units `. Restrictions """""""""""" -These computes are part of the USER-MESONT package. They are only enabled if +These computes are part of the MESONT package. They are only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more info. In addition, :doc:`mesont pair_style ` must be used. diff --git a/doc/src/compute_mliap.rst b/doc/src/compute_mliap.rst index 579086ad4a..86dfe5a856 100644 --- a/doc/src/compute_mliap.rst +++ b/doc/src/compute_mliap.rst @@ -56,21 +56,22 @@ and it is also straightforward to add new descriptor styles. The compute *mliap* command must be followed by two keywords *model* and *descriptor* in either order. -The *model* keyword is followed by the model style (*linear*, *quadratic* or *mliappy*). -The *mliappy* model is only available -if lammps is built with MLIAPPY package. +The *model* keyword is followed by the model style (*linear*, +*quadratic* or *mliappy*). The *mliappy* model is only available if +LAMMPS is built with the *mliappy* python module. There are +:ref:`specific installation instructions ` for that. -The *descriptor* keyword is followed by a descriptor style, and additional arguments. -The compute currently supports just one descriptor style, but it is -is straightforward to add new descriptor styles. -The SNAP descriptor style *sna* is the same as that used by :doc:`pair_style snap `, -including the linear, quadratic, and chem variants. -A single additional argument specifies the descriptor filename -containing the parameters and setting used by the SNAP descriptor. -The descriptor filename usually ends in the *.mliap.descriptor* extension. -The format of this file is identical to the descriptor file in the -:doc:`pair_style mliap `, and is described in detail -there. +The *descriptor* keyword is followed by a descriptor style, and +additional arguments. The compute currently supports two descriptor +styles *sna* and *so3*, but it is is straightforward to add additional +descriptor styles. The SNAP descriptor style *sna* is the same as that +used by :doc:`pair_style snap `, including the linear, +quadratic, and chem variants. A single additional argument specifies +the descriptor filename containing the parameters and setting used by +the SNAP descriptor. The descriptor filename usually ends in the +*.mliap.descriptor* extension. The format of this file is identical to +the descriptor file in the :doc:`pair_style mliap `, and is +described in detail there. .. note:: @@ -164,11 +165,12 @@ potentials, see the examples in `FitSNAP `_. Restrictions """""""""""" -This compute is part of the MLIAP package. It is only enabled if LAMMPS -was built with that package. In addition, building LAMMPS with the MLIAP package -requires building LAMMPS with the SNAP package. -The *mliappy* model requires building LAMMPS with the PYTHON package. -See the :doc:`Build package ` doc page for more info. +This compute is part of the ML-IAP package. It is only enabled if +LAMMPS was built with that package. In addition, building LAMMPS with +the ML-IAP package requires building LAMMPS with the ML-SNAP package. +The *mliappy* model also requires building LAMMPS with the PYTHON +package. See the :doc:`Build package ` doc page for more +info. Related commands """""""""""""""" diff --git a/doc/src/compute_pressure_uef.rst b/doc/src/compute_pressure_uef.rst index bdd212cf5c..1e32c4d9b4 100644 --- a/doc/src/compute_pressure_uef.rst +++ b/doc/src/compute_pressure_uef.rst @@ -41,7 +41,7 @@ The keywords and output information are documented in Restrictions """""""""""" -This fix is part of the USER-UEF package. It is only enabled if LAMMPS +This fix is part of the UEF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This command can only be used when :doc:`fix nvt/uef ` diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index ec9322bb7b..32cda56659 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -74,7 +74,7 @@ Syntax .. parsed-literal:: - USER-EFF and USER-AWPMD package per-atom properties: + EFF and AWPMD package per-atom properties: spin = electron spin eradius = electron radius ervel = electron radial velocity @@ -82,7 +82,7 @@ Syntax .. parsed-literal:: - USER-SPH package per-atom properties: + SPH package per-atom properties: rho = density of SPH particles drho = change in density e = energy diff --git a/doc/src/compute_ptm_atom.rst b/doc/src/compute_ptm_atom.rst index fb590f6e4c..e271131987 100644 --- a/doc/src/compute_ptm_atom.rst +++ b/doc/src/compute_ptm_atom.rst @@ -112,7 +112,7 @@ For atoms that are not within the compute group-ID, all values are set to zero. Restrictions """""""""""" -This fix is part of the USER-PTM package. It is only enabled if +This fix is part of the PTM package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index 1057208900..989fe63d3d 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -245,7 +245,7 @@ All array values calculated by this compute are "intensive". Restrictions """""""""""" -This compute is part of the USER-DIFFRACTION package. It is only +This compute is part of the DIFFRACTION package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The compute_saed command does not work for triclinic cells. diff --git a/doc/src/compute_smd_contact_radius.rst b/doc/src/compute_smd_contact_radius.rst index 71630b827d..d310de826a 100644 --- a/doc/src/compute_smd_contact_radius.rst +++ b/doc/src/compute_smd_contact_radius.rst @@ -48,7 +48,7 @@ The per-particle vector values will be in distance :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_smd_damage.rst b/doc/src/compute_smd_damage.rst index ee3671e20c..e11fce1e9e 100644 --- a/doc/src/compute_smd_damage.rst +++ b/doc/src/compute_smd_damage.rst @@ -40,7 +40,7 @@ The per-particle values are dimensionless an in the range of zero to one. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the "Build Related commands diff --git a/doc/src/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst index 980d31454e..c3664997f9 100644 --- a/doc/src/compute_smd_hourglass_error.rst +++ b/doc/src/compute_smd_hourglass_error.rst @@ -50,7 +50,7 @@ The per-particle vector values will are dimensionless. See Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This quantity will be computed only for particles which interact with diff --git a/doc/src/compute_smd_internal_energy.rst b/doc/src/compute_smd_internal_energy.rst index c4df459d5f..f596b0ce54 100644 --- a/doc/src/compute_smd_internal_energy.rst +++ b/doc/src/compute_smd_internal_energy.rst @@ -42,7 +42,7 @@ The per-particle vector values will be given in :doc:`units ` of energy. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact via the updated Lagrangian or total Lagrangian SPH pair styles. diff --git a/doc/src/compute_smd_plastic_strain.rst b/doc/src/compute_smd_plastic_strain.rst index 81bacdc4bb..018b999716 100644 --- a/doc/src/compute_smd_plastic_strain.rst +++ b/doc/src/compute_smd_plastic_strain.rst @@ -42,7 +42,7 @@ The per-particle values will be given dimensionless. See :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact via the updated Lagrangian or total Lagrangian SPH pair styles. diff --git a/doc/src/compute_smd_plastic_strain_rate.rst b/doc/src/compute_smd_plastic_strain_rate.rst index cdcd377b41..4edb7c2ae5 100644 --- a/doc/src/compute_smd_plastic_strain_rate.rst +++ b/doc/src/compute_smd_plastic_strain_rate.rst @@ -42,7 +42,7 @@ The per-particle values will be given in :doc:`units ` of one over time. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact via the updated Lagrangian or total Lagrangian SPH pair styles. diff --git a/doc/src/compute_smd_rho.rst b/doc/src/compute_smd_rho.rst index e7cdb8a9d3..672fe225f0 100644 --- a/doc/src/compute_smd_rho.rst +++ b/doc/src/compute_smd_rho.rst @@ -44,7 +44,7 @@ The per-particle values will be in :doc:`units ` of mass over volume. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_smd_tlsph_defgrad.rst b/doc/src/compute_smd_tlsph_defgrad.rst index d74b684c5d..a8c2e80a12 100644 --- a/doc/src/compute_smd_tlsph_defgrad.rst +++ b/doc/src/compute_smd_tlsph_defgrad.rst @@ -47,7 +47,7 @@ entry is the determinant of the deformation gradient. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. TThis compute can only be used for particles which interact via the total Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_dt.rst b/doc/src/compute_smd_tlsph_dt.rst index 888140c534..6c6ad54187 100644 --- a/doc/src/compute_smd_tlsph_dt.rst +++ b/doc/src/compute_smd_tlsph_dt.rst @@ -48,7 +48,7 @@ The per-particle values will be given in :doc:`units ` of time. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles interacting with the diff --git a/doc/src/compute_smd_tlsph_num_neighs.rst b/doc/src/compute_smd_tlsph_num_neighs.rst index 5d34f1acef..1a42373717 100644 --- a/doc/src/compute_smd_tlsph_num_neighs.rst +++ b/doc/src/compute_smd_tlsph_num_neighs.rst @@ -43,7 +43,7 @@ The per-particle values are dimensionless. See :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This quantity will be computed only for particles which interact with diff --git a/doc/src/compute_smd_tlsph_shape.rst b/doc/src/compute_smd_tlsph_shape.rst index d9ce1e3d9a..33bd02d894 100644 --- a/doc/src/compute_smd_tlsph_shape.rst +++ b/doc/src/compute_smd_tlsph_shape.rst @@ -50,7 +50,7 @@ particle relative to its initial state. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This quantity will be computed only for particles which interact with diff --git a/doc/src/compute_smd_tlsph_strain.rst b/doc/src/compute_smd_tlsph_strain.rst index b89311eb4b..a05dbab8d7 100644 --- a/doc/src/compute_smd_tlsph_strain.rst +++ b/doc/src/compute_smd_tlsph_strain.rst @@ -46,7 +46,7 @@ zz, xy, xz, yz components of the symmetric strain tensor. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This quantity will be computed only for particles which interact with diff --git a/doc/src/compute_smd_tlsph_strain_rate.rst b/doc/src/compute_smd_tlsph_strain_rate.rst index d1fc399b42..f75db80d94 100644 --- a/doc/src/compute_smd_tlsph_strain_rate.rst +++ b/doc/src/compute_smd_tlsph_strain_rate.rst @@ -45,7 +45,7 @@ zz, xy, xz, yz components of the symmetric strain rate tensor. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This quantity will be computed only for particles which interact with diff --git a/doc/src/compute_smd_tlsph_stress.rst b/doc/src/compute_smd_tlsph_stress.rst index d3711954c5..0a194bea3d 100644 --- a/doc/src/compute_smd_tlsph_stress.rst +++ b/doc/src/compute_smd_tlsph_stress.rst @@ -47,7 +47,7 @@ invariant of the stress tensor, i.e., the von Mises equivalent stress. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This quantity will be computed only for particles which interact with diff --git a/doc/src/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst index d797891618..0f2f1cdd45 100644 --- a/doc/src/compute_smd_triangle_vertices.rst +++ b/doc/src/compute_smd_triangle_vertices.rst @@ -53,7 +53,7 @@ The values will be given in :doc:`units ` of distance. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_smd_ulsph_effm.rst b/doc/src/compute_smd_ulsph_effm.rst index ff12f9cdac..388969f4ae 100644 --- a/doc/src/compute_smd_ulsph_effm.rst +++ b/doc/src/compute_smd_ulsph_effm.rst @@ -44,7 +44,7 @@ style. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_num_neighs.rst b/doc/src/compute_smd_ulsph_num_neighs.rst index 3579a88079..b356b8adaa 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.rst +++ b/doc/src/compute_smd_ulsph_num_neighs.rst @@ -43,7 +43,7 @@ The per-particle values will be given dimensionless, see :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_strain.rst b/doc/src/compute_smd_ulsph_strain.rst index 09f06b084b..5a3617fd24 100644 --- a/doc/src/compute_smd_ulsph_strain.rst +++ b/doc/src/compute_smd_ulsph_strain.rst @@ -46,7 +46,7 @@ The per-particle tensor values will be given dimensionless, see Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_ulsph_strain_rate.rst b/doc/src/compute_smd_ulsph_strain_rate.rst index 391367321a..4fe5d53936 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.rst +++ b/doc/src/compute_smd_ulsph_strain_rate.rst @@ -46,7 +46,7 @@ zz, xy, xz, yz components of the symmetric strain rate tensor. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact with the diff --git a/doc/src/compute_smd_ulsph_stress.rst b/doc/src/compute_smd_ulsph_stress.rst index e1db7640a6..392b72e0fd 100644 --- a/doc/src/compute_smd_ulsph_stress.rst +++ b/doc/src/compute_smd_ulsph_stress.rst @@ -46,7 +46,7 @@ stress tensor, i.e., the von Mises equivalent stress. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_vol.rst b/doc/src/compute_smd_vol.rst index 4f9314ac32..862ed15a3e 100644 --- a/doc/src/compute_smd_vol.rst +++ b/doc/src/compute_smd_vol.rst @@ -46,7 +46,7 @@ per-particle volumes of the group for which the fix is defined. Restrictions """""""""""" -This compute is part of the USER-SMD package. It is only enabled if +This compute is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 08b06a32ec..4165c4e47a 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -72,64 +72,66 @@ Description """"""""""" Define a computation that calculates a set of quantities related to the -bispectrum components of the atoms in a group. These computes are -used primarily for calculating the dependence of energy, force, and -stress components on the linear coefficients in the -:doc:`snap pair_style `, which is useful when training a -SNAP potential to match target data. +bispectrum components of the atoms in a group. These computes are used +primarily for calculating the dependence of energy, force, and stress +components on the linear coefficients in the :doc:`snap pair_style +`, which is useful when training a SNAP potential to match +target data. -Bispectrum components of an atom are order parameters characterizing -the radial and angular distribution of neighbor atoms. The detailed +Bispectrum components of an atom are order parameters characterizing the +radial and angular distribution of neighbor atoms. The detailed mathematical definition is given in the paper by Thompson et al. :ref:`(Thompson) ` -The position of a neighbor atom *i'* relative to a central atom *i* is -a point within the 3D ball of radius :math:`R_{ii'}` = *rcutfac* :math:`(R_i + R_i')` +The position of a neighbor atom *i'* relative to a central atom *i* is a +point within the 3D ball of radius :math:`R_{ii'}` = *rcutfac* +:math:`(R_i + R_i')` -Bartok et al. :ref:`(Bartok) `, proposed mapping this 3D ball -onto the 3-sphere, the surface of the unit ball in a four-dimensional -space. The radial distance *r* within *R_ii'* is mapped on to a third -polar angle :math:`\theta_0` defined by, +Bartok et al. :ref:`(Bartok) `, proposed mapping this 3D +ball onto the 3-sphere, the surface of the unit ball in a +four-dimensional space. The radial distance *r* within *R_ii'* is +mapped on to a third polar angle :math:`\theta_0` defined by, .. math:: \theta_0 = {\sf rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi In this way, all possible neighbor positions are mapped on to a subset -of the 3-sphere. Points south of the latitude :math:`\theta_0` = *rfac0* :math:`\pi` -are excluded. +of the 3-sphere. Points south of the latitude :math:`\theta_0` = +*rfac0* :math:`\pi` are excluded. The natural basis for functions on the 3-sphere is formed by the -representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi, \theta_0)`. -These functions are better known as :math:`D^j_{m,m'}`, the elements of the Wigner -*D*\ -matrices :ref:`(Meremianin `, -:ref:`Varshalovich `, :ref:`Mason) ` -The density of neighbors on the 3-sphere can be written as a sum of -Dirac-delta functions, one for each neighbor, weighted by species and -radial distance. Expanding this density function as a generalized -Fourier series in the basis functions, we can write each Fourier -coefficient as +representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi, +\theta_0)`. These functions are better known as :math:`D^j_{m,m'}`, the +elements of the Wigner *D*\ -matrices :ref:`(Meremianin +`, :ref:`Varshalovich `, :ref:`Mason) +` The density of neighbors on the 3-sphere can be written as +a sum of Dirac-delta functions, one for each neighbor, weighted by +species and radial distance. Expanding this density function as a +generalized Fourier series in the basis functions, we can write each +Fourier coefficient as .. math:: u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{\mu_{i'}} U^j_{m,m'}(\theta_0,\theta,\phi)} -The :math:`w_{\mu_{i'}}` neighbor weights are dimensionless numbers that depend on -:math:`\mu_{i'}`, the SNAP element of atom *i'*, while the central atom is -arbitrarily assigned a unit weight. The function :math:`f_c(r)` ensures that -the contribution of each neighbor atom goes smoothly to zero at -:math:`R_{ii'}`: +The :math:`w_{\mu_{i'}}` neighbor weights are dimensionless numbers that +depend on :math:`\mu_{i'}`, the SNAP element of atom *i'*, while the +central atom is arbitrarily assigned a unit weight. The function +:math:`f_c(r)` ensures that the contribution of each neighbor atom goes +smoothly to zero at :math:`R_{ii'}`: .. math:: f_c(r) = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\ = & 0, r > R_{ii'} -The expansion coefficients :math:`u^j_{m,m'}` are complex-valued and they are -not directly useful as descriptors, because they are not invariant -under rotation of the polar coordinate frame. However, the following -scalar triple products of expansion coefficients can be shown to be -real-valued and invariant under rotation :ref:`(Bartok) `. +The expansion coefficients :math:`u^j_{m,m'}` are complex-valued and +they are not directly useful as descriptors, because they are not +invariant under rotation of the polar coordinate frame. However, the +following scalar triple products of expansion coefficients can be shown +to be real-valued and invariant under rotation :ref:`(Bartok) +`. .. math:: @@ -140,21 +142,20 @@ real-valued and invariant under rotation :ref:`(Bartok) `. {j_2} {m_2} {m'_2} \end{array}} u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2} -The constants :math:`H^{jmm'}_{j_1 m_1 m_{1'},j_2 m_ 2m_{2'}}` -are coupling coefficients, -analogous to Clebsch-Gordan coefficients for rotations on the -2-sphere. These invariants are the components of the bispectrum and -these are the quantities calculated by the compute *sna/atom*\ . They -characterize the strength of density correlations at three points on -the 3-sphere. The j2=0 subset form the power spectrum, which -characterizes the correlations of two points. The lowest-order -components describe the coarsest features of the density function, -while higher-order components reflect finer detail. Each bispectrum -component contains terms that depend on the positions of up to 4 -atoms (3 neighbors and the central atom). +The constants :math:`H^{jmm'}_{j_1 m_1 m_{1'},j_2 m_ 2m_{2'}}` are +coupling coefficients, analogous to Clebsch-Gordan coefficients for +rotations on the 2-sphere. These invariants are the components of the +bispectrum and these are the quantities calculated by the compute +*sna/atom*\ . They characterize the strength of density correlations at +three points on the 3-sphere. The j2=0 subset form the power spectrum, +which characterizes the correlations of two points. The lowest-order +components describe the coarsest features of the density function, while +higher-order components reflect finer detail. Each bispectrum component +contains terms that depend on the positions of up to 4 atoms (3 +neighbors and the central atom). -Compute *snad/atom* calculates the derivative of the bispectrum components -summed separately for each LAMMPS atom type: +Compute *snad/atom* calculates the derivative of the bispectrum +components summed separately for each LAMMPS atom type: .. math:: @@ -180,16 +181,16 @@ section below on output for a detailed explanation. Compute *snap* calculates a global array containing information related to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ , and *snav/atom*\ . The first row of the array contains the summation of -*sna/atom* over all atoms, but broken out by type. The last six rows -of the array contain the summation of *snav/atom* over all atoms, broken -out by type. In between these are 3\*\ *N* rows containing the same values -computed by *snad/atom* (these are already summed over all atoms and -broken out by type). The element in the last column of each row contains -the potential energy, force, or stress, according to the row. +*sna/atom* over all atoms, but broken out by type. The last six rows of +the array contain the summation of *snav/atom* over all atoms, broken +out by type. In between these are 3\*\ *N* rows containing the same +values computed by *snad/atom* (these are already summed over all atoms +and broken out by type). The element in the last column of each row +contains the potential energy, force, or stress, according to the row. These quantities correspond to the user-specified reference potential -that must be subtracted from the target data when fitting SNAP. -The potential energy calculation uses the built in compute *thermo_pe*. -The stress calculation uses a compute called *snap_press* that is +that must be subtracted from the target data when fitting SNAP. The +potential energy calculation uses the built in compute *thermo_pe*. The +stress calculation uses a compute called *snap_press* that is automatically created behind the scenes, according to the following command: @@ -225,36 +226,32 @@ The keyword *switchflag* can be used to turn off the switching function :math:`f_c(r)`. The keyword *bzeroflag* determines whether or not *B0*\ , the bispectrum -components of an atom with no neighbors, are subtracted from -the calculated bispectrum components. This optional keyword -normally only affects compute *sna/atom*\ . However, when -*quadraticflag* is on, it also affects *snad/atom* and *snav/atom*\ . +components of an atom with no neighbors, are subtracted from the +calculated bispectrum components. This optional keyword normally only +affects compute *sna/atom*\ . However, when *quadraticflag* is on, it +also affects *snad/atom* and *snav/atom*\ . -The keyword *quadraticflag* determines whether or not the -quadratic combinations of bispectrum quantities are generated. -These are formed by taking the outer product of the vector -of bispectrum components with itself. -See section below on output for a -detailed explanation of the number of quadratic terms and the -ordered in which they are listed. +The keyword *quadraticflag* determines whether or not the quadratic +combinations of bispectrum quantities are generated. These are formed +by taking the outer product of the vector of bispectrum components with +itself. See section below on output for a detailed explanation of the +number of quadratic terms and the ordered in which they are listed. -The keyword *chem* activates the explicit multi-element variant -of the SNAP bispectrum components. The argument *nelements* -specifies the number of SNAP elements that will be handled. -This is followed by *elementlist*, a list of integers of -length *ntypes*, with values in the range [0, *nelements* ), -which maps each LAMMPS type to one of the SNAP elements. -Note that multiple LAMMPS types can be mapped to the same element, -and some elements may be mapped by no LAMMPS type. However, in typical -use cases (training SNAP potentials) the mapping from LAMMPS types -to elements is one-to-one. +The keyword *chem* activates the explicit multi-element variant of the +SNAP bispectrum components. The argument *nelements* specifies the +number of SNAP elements that will be handled. This is followed by +*elementlist*, a list of integers of length *ntypes*, with values in the +range [0, *nelements* ), which maps each LAMMPS type to one of the SNAP +elements. Note that multiple LAMMPS types can be mapped to the same +element, and some elements may be mapped by no LAMMPS type. However, in +typical use cases (training SNAP potentials) the mapping from LAMMPS +types to elements is one-to-one. The explicit multi-element variant invoked by the *chem* keyword -partitions the density of neighbors into partial densities -for each chemical element. This is described in detail in the -paper by :ref:`Cusentino et al. ` -The bispectrum components are indexed on -ordered triplets of elements: +partitions the density of neighbors into partial densities for each +chemical element. This is described in detail in the paper by +:ref:`Cusentino et al. ` The bispectrum components are +indexed on ordered triplets of elements: .. math:: @@ -272,17 +269,19 @@ of element :math:`\mu` u^{\mu}_{j,m,m'} = w^{self}_{\mu_{i}\mu} U^{j,m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{\delta_{\mu\mu_{i'}}f_c(r_{ii'}) w_{\mu_{i'}} U^{j,m,m'}(\theta_0,\theta,\phi)} -where :math:`w^{self}_{\mu_{i}\mu}` is the self-contribution, which is either 1 or 0 -(see keyword *wselfallflag* below), :math:`\delta_{\mu\mu_{i'}}` indicates -that the sum is only over neighbor atoms of element :math:`\mu`, -and all other quantities are the same as those appearing in the -original equation for :math:`u^j_{m,m'}` given above. +where :math:`w^{self}_{\mu_{i}\mu}` is the self-contribution, which is +either 1 or 0 (see keyword *wselfallflag* below), +:math:`\delta_{\mu\mu_{i'}}` indicates that the sum is only over +neighbor atoms of element :math:`\mu`, and all other quantities are the +same as those appearing in the original equation for :math:`u^j_{m,m'}` +given above. -The keyword *wselfallflag* defines the rule used for the self-contribution. -If *wselfallflag* is on, then :math:`w^{self}_{\mu_{i}\mu}` = 1. If it is -off then :math:`w^{self}_{\mu_{i}\mu}` = 0, except in the case -of :math:`{\mu_{i}=\mu}`, when :math:`w^{self}_{\mu_{i}\mu}` = 1. -When the *chem* keyword is not used, this keyword has no effect. +The keyword *wselfallflag* defines the rule used for the +self-contribution. If *wselfallflag* is on, then +:math:`w^{self}_{\mu_{i}\mu}` = 1. If it is off then +:math:`w^{self}_{\mu_{i}\mu}` = 0, except in the case of +:math:`{\mu_{i}=\mu}`, when :math:`w^{self}_{\mu_{i}\mu}` = 1. When the +*chem* keyword is not used, this keyword has no effect. The keyword *bnormflag* determines whether or not the bispectrum component :math:`B_{j_1,j_2,j}` is divided by a factor of :math:`2j+1`. @@ -299,16 +298,16 @@ are not both set or not both unset. .. note:: - If you have a bonded system, then the settings of - :doc:`special_bonds ` command can remove pairwise - interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special_bonds ` - command, and means those pairwise interactions do not appear in the - neighbor list. Because this fix uses the neighbor list, it also means - those pairs will not be included in the calculation. One way to get - around this, is to write a dump file, and use the :doc:`rerun ` - command to compute the bispectrum components for snapshots in the dump - file. The rerun script can use a :doc:`special_bonds ` + If you have a bonded system, then the settings of :doc:`special_bonds + ` command can remove pairwise interactions between + atoms in the same bond, angle, or dihedral. This is the default + setting for the :doc:`special_bonds ` command, and + means those pairwise interactions do not appear in the neighbor list. + Because this fix uses the neighbor list, it also means those pairs + will not be included in the calculation. One way to get around this, + is to write a dump file, and use the :doc:`rerun ` command to + compute the bispectrum components for snapshots in the dump file. + The rerun script can use a :doc:`special_bonds ` command that includes all pairs in the neighbor list. ---------- @@ -317,10 +316,10 @@ Output info """"""""""" Compute *sna/atom* calculates a per-atom array, each column -corresponding to a particular bispectrum component. The total number -of columns and the identity of the bispectrum component contained in -each column depend of the value of *twojmax*\ , as -described by the following piece of python code: +corresponding to a particular bispectrum component. The total number of +columns and the identity of the bispectrum component contained in each +column depend of the value of *twojmax*\ , as described by the following +piece of python code: .. parsed-literal:: @@ -338,73 +337,72 @@ For even twojmax = 2(*m*\ -1), :math:`K = m(m+1)(2m+1)/6`, the *m*\ -th pyramida since all potentials use the value of 3, corresponding to the above set of bispectrum components. -Compute *snad/atom* evaluates a per-atom array. The columns are -arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each -block contains three sub-blocks corresponding to the *x*\ , *y*\ , and *z* +Compute *snad/atom* evaluates a per-atom array. The columns are arranged +into *ntypes* blocks, listed in order of atom type *I*\ . Each block +contains three sub-blocks corresponding to the *x*\ , *y*\ , and *z* components of the atom position. Each of these sub-blocks contains *K* -columns for the *K* bispectrum components, the same as for compute *sna/atom* +columns for the *K* bispectrum components, the same as for compute +*sna/atom* -Compute *snav/atom* evaluates a per-atom array. The columns are -arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each -block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ , +Compute *snav/atom* evaluates a per-atom array. The columns are arranged +into *ntypes* blocks, listed in order of atom type *I*\ . Each block +contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ , *yz*\ , *xz*\ , and *xy* components of the virial tensor in Voigt -notation. Each of these sub-blocks contains *K* -columns for the *K* bispectrum components, the same as for compute *sna/atom* +notation. Each of these sub-blocks contains *K* columns for the *K* +bispectrum components, the same as for compute *sna/atom* -Compute *snap* evaluates a global array. -The columns are arranged into -*ntypes* blocks, listed in order of atom type *I*\ . Each block -contains one column for each bispectrum component, the same as for compute -*sna/atom*\ . A final column contains the corresponding energy, force component -on an atom, or virial stress component. The rows of the array appear -in the following order: +Compute *snap* evaluates a global array. The columns are arranged into +*ntypes* blocks, listed in order of atom type *I*\ . Each block contains +one column for each bispectrum component, the same as for compute +*sna/atom*\ . A final column contains the corresponding energy, force +component on an atom, or virial stress component. The rows of the array +appear in the following order: * 1 row: *sna/atom* quantities summed for all atoms of type *I* * 3\*\ *N* rows: *snad/atom* quantities, with derivatives w.r.t. x, y, and z coordinate of atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID. * 6 rows: *snav/atom* quantities summed for all atoms of type *I* -For example, if *K* =30 and ntypes=1, the number of columns in the per-atom -arrays generated by *sna/atom*\ , *snad/atom*\ , and *snav/atom* -are 30, 90, and 180, respectively. With *quadratic* value=1, -the numbers of columns are 930, 2790, and 5580, respectively. -The number of columns in the global array generated by *snap* -are 31, and 931, respectively, while the number of rows is -1+3\*\ *N*\ +6, where *N* is the total number of atoms. +For example, if *K* =30 and ntypes=1, the number of columns in the +per-atom arrays generated by *sna/atom*\ , *snad/atom*\ , and +*snav/atom* are 30, 90, and 180, respectively. With *quadratic* value=1, +the numbers of columns are 930, 2790, and 5580, respectively. The +number of columns in the global array generated by *snap* are 31, and +931, respectively, while the number of rows is 1+3\*\ *N*\ +6, where *N* +is the total number of atoms. -If the *quadratic* keyword value is set to 1, then additional -columns are generated, corresponding to -the products of all distinct pairs of bispectrum components. If the -number of bispectrum components is *K*\ , then the number of distinct pairs -is *K*\ (\ *K*\ +1)/2. -For compute *sna/atom* these columns are appended to existing *K* columns. -The ordering of quadratic terms is upper-triangular, -(1,1),(1,2)...(1,\ *K*\ ),(2,1)...(\ *K*\ -1,\ *K*\ -1),(\ *K*\ -1,\ *K*\ ),(\ *K*\ ,\ *K*\ ). +If the *quadratic* keyword value is set to 1, then additional columns +are generated, corresponding to the products of all distinct pairs of +bispectrum components. If the number of bispectrum components is *K*\ , +then the number of distinct pairs is *K*\ (\ *K*\ +1)/2. For compute +*sna/atom* these columns are appended to existing *K* columns. The +ordering of quadratic terms is upper-triangular, (1,1),(1,2)...(1,\ *K*\ +),(2,1)...(\ *K*\ -1,\ *K*\ -1),(\ *K*\ -1,\ *K*\ ),(\ *K*\ ,\ *K*\ ). For computes *snad/atom* and *snav/atom* each set of *K*\ (\ *K*\ +1)/2 -additional columns is inserted directly after each of sub-block -of linear terms i.e. linear and quadratic terms are contiguous. -So the nesting order from inside to outside is bispectrum component, -linear then quadratic, vector/tensor component, type. +additional columns is inserted directly after each of sub-block of +linear terms i.e. linear and quadratic terms are contiguous. So the +nesting order from inside to outside is bispectrum component, linear +then quadratic, vector/tensor component, type. -If the *chem* keyword is used, then the data is arranged into :math:`N_{elem}^3` -sub-blocks, each sub-block corresponding to a particular chemical labeling -:math:`\kappa\lambda\mu` with the last label changing fastest. -Each sub-block contains *K* bispectrum components. For the purposes -of handling contributions to force, virial, and quadratic combinations, -these :math:`N_{elem}^3` sub-blocks are treated as a single block -of :math:`K N_{elem}^3` columns. +If the *chem* keyword is used, then the data is arranged into +:math:`N_{elem}^3` sub-blocks, each sub-block corresponding to a +particular chemical labeling :math:`\kappa\lambda\mu` with the last +label changing fastest. Each sub-block contains *K* bispectrum +components. For the purposes of handling contributions to force, virial, +and quadratic combinations, these :math:`N_{elem}^3` sub-blocks are +treated as a single block of :math:`K N_{elem}^3` columns. These values can be accessed by any command that uses per-atom values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. To see how this command -can be used within a Python workflow to train SNAP potentials, -see the examples in `FitSNAP `_. +can be used within a Python workflow to train SNAP potentials, see the +examples in `FitSNAP `_. Restrictions """""""""""" -These computes are part of the SNAP package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` -doc page for more info. +These computes are part of the ML-SNAP package. They are only enabled +if LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_sph_e_atom.rst b/doc/src/compute_sph_e_atom.rst index 17591257f2..b1eca85853 100644 --- a/doc/src/compute_sph_e_atom.rst +++ b/doc/src/compute_sph_e_atom.rst @@ -49,7 +49,7 @@ The per-atom vector values will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SPH package. It is only enabled if +This compute is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_sph_rho_atom.rst b/doc/src/compute_sph_rho_atom.rst index c422a5ecbb..34096df0ee 100644 --- a/doc/src/compute_sph_rho_atom.rst +++ b/doc/src/compute_sph_rho_atom.rst @@ -48,7 +48,7 @@ The per-atom vector values will be in mass/volume :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SPH package. It is only enabled if +This compute is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_sph_t_atom.rst b/doc/src/compute_sph_t_atom.rst index 922adfff58..7c4c126c6c 100644 --- a/doc/src/compute_sph_t_atom.rst +++ b/doc/src/compute_sph_t_atom.rst @@ -53,7 +53,7 @@ The per-atom vector values will be in temperature :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-SPH package. It is only enabled if +This compute is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index 393d3b2ffb..0f90f9bafe 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -233,7 +233,7 @@ since its computations are performed pairwise), nor granular pair styles with pairwise forces which are not aligned with the vector between the pair of particles. All bond styles are supported. All angle, dihedral, improper styles are supported with the exception of -USER-INTEL and KOKKOS variants of specific styles. It also does not +INTEL and KOKKOS variants of specific styles. It also does not support models with long-range Coulombic or dispersion forces, i.e. the kspace_style command in LAMMPS. It also does not support the following fixes which add rigid-body constraints: :doc:`fix shake diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index d68bafa48b..feda7ee193 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -87,7 +87,7 @@ and stress_dir,z. The values are in pressure :doc:`units `. -The values produced by this compute can be accessed by various :doc:`output commands `. For instance, the results can be written to a file using the :doc:`fix ave/time ` command. Please see the example in the examples/USER/mop folder. +The values produced by this compute can be accessed by various :doc:`output commands `. For instance, the results can be written to a file using the :doc:`fix ave/time ` command. Please see the example in the examples/PACKAGES/mop folder. Restrictions """""""""""" diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index 0e2856ea5e..32e3e31030 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -91,7 +91,7 @@ Both the scalar and vector values calculated by this compute are Restrictions """""""""""" -This compute is part of the USER-TALLY package. It is only enabled if +This compute is part of the TALLY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Not all pair styles can be evaluated in a pairwise mode as required by diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index dc18145e72..4c32fc448c 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -46,7 +46,7 @@ per unit mass. Restrictions """""""""""" -This compute is part of the USER-MESODPD package. It is only enabled if +This compute is part of the DPD-MESO package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index 03be4a89fd..bff5fb3bfb 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -61,7 +61,7 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-EFF package. It is only enabled if +This compute is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index 7e0f5f6555..7b92198cb9 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -20,7 +20,7 @@ Examples compute TDRUDE all temp/drude -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index 6bbad345e2..7bd0559090 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -89,7 +89,7 @@ the simulation. Restrictions """""""""""" -This compute is part of the USER-EFF package. It is only enabled if +This compute is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index 622b3eb203..84baf00aaa 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -53,7 +53,7 @@ vector values will be in energy :doc:`units `. Restrictions """""""""""" -This compute is part of the USER-EFF package. It is only enabled if +This compute is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/compute_temp_uef.rst b/doc/src/compute_temp_uef.rst index 11bfca48e9..18fc4a9fdf 100644 --- a/doc/src/compute_temp_uef.rst +++ b/doc/src/compute_temp_uef.rst @@ -38,7 +38,7 @@ documentation for :doc:`compute temp `. Restrictions """""""""""" -This fix is part of the USER-UEF package. It is only enabled if LAMMPS +This fix is part of the UEF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This command can only be used when :doc:`fix nvt/uef ` diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index d927b6599f..a0684109ea 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -223,7 +223,7 @@ All array values calculated by this compute are "intensive". Restrictions """""""""""" -This compute is part of the USER-DIFFRACTION package. It is only +This compute is part of the DIFFRACTION package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The compute_xrd command does not work for triclinic cells. diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst index e1b0fe000a..74c8dae189 100644 --- a/doc/src/dump_adios.rst +++ b/doc/src/dump_adios.rst @@ -64,7 +64,7 @@ When using the ADIOS tool 'bpls' to list the content of a .bp file, bpls will print *__* for the size of the output table indicating that its size is changing every step. -The *atom/adios* and *custom/adios* dump styles are part of the USER-ADIOS +The *atom/adios* and *custom/adios* dump styles are part of the ADIOS package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dump_cfg_uef.rst b/doc/src/dump_cfg_uef.rst index ee027e9347..9e33291880 100644 --- a/doc/src/dump_cfg_uef.rst +++ b/doc/src/dump_cfg_uef.rst @@ -42,7 +42,7 @@ reference frame as the atomic positions. Restrictions """""""""""" -This fix is part of the USER-UEF package. It is only enabled if LAMMPS +This fix is part of the UEF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This command can only be used when :doc:`fix nvt/uef ` diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst index de44572307..2f66e2863b 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -106,7 +106,7 @@ The position data is stored wrapped (box boundaries not enforced, see note above). Only orthogonal domains are currently supported. This is a limitation of the present dump h5md command and not of H5MD itself. -The *h5md* dump style is part of the USER-H5MD package. It is only +The *h5md* dump style is part of the H5MD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. It also requires (i) building the ch5md library provided with LAMMPS (See the :doc:`Build package ` doc page for more info.) and (ii) having the `HDF5 `_ library installed (C bindings are sufficient) on diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst index 69bd8aa8c2..aa8e04b22c 100644 --- a/doc/src/dump_molfile.rst +++ b/doc/src/dump_molfile.rst @@ -92,12 +92,12 @@ determine the sequence of timesteps on which dump files are written. Restrictions """""""""""" -The *molfile* dump style is part of the USER-MOLFILE package. It is +The *molfile* dump style is part of the MOLFILE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Molfile plugins provide a consistent programming interface to read and write file formats commonly used in molecular simulations. The -USER-MOLFILE package only provides the interface code, not the plugins. +MOLFILE package only provides the interface code, not the plugins. These can be obtained from a VMD installation which has to match the platform that you are using to compile LAMMPS for. By adding plugins to VMD, support for new file formats can be added to LAMMPS (or VMD diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst index 5627060452..9fac10dc99 100644 --- a/doc/src/dump_netcdf.rst +++ b/doc/src/dump_netcdf.rst @@ -69,7 +69,7 @@ Restrictions """""""""""" The *netcdf* and *netcdf/mpiio* dump styles are part of the -USER-NETCDF package. They are only enabled if LAMMPS was built with +NETCDF package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index 4f607c4fdd..8eea1def94 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -162,7 +162,7 @@ Restrictions The *vtk* style does not support writing of gzipped dump files. -The *vtk* dump style is part of the USER-VTK package. It is only +The *vtk* dump style is part of the VTK package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. To use this dump style, you also must link to the VTK library. See diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst index 9c4530eade..8d17f0aa1e 100644 --- a/doc/src/dynamical_matrix.rst +++ b/doc/src/dynamical_matrix.rst @@ -63,7 +63,7 @@ The command collects an array of nine times the number of atoms in a group on every single MPI rank, so the memory requirements can be very significant for large systems. -This command is part of the USER-PHONON package. It is only enabled if +This command is part of the PHONON package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 81a34ab75e..10a1faf202 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -57,7 +57,7 @@ Examples fix 1 all adapt/fep 10 atom diameter 1 v_size -Example input scripts available: examples/USER/fep +Example input scripts available: examples/PACKAGES/fep Description """"""""""" diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index 25f85f6f6c..06bdc9a69e 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -253,7 +253,7 @@ miscellaneous *fix_modify* commands: * :doc:`fix_modify AtC remove_molecule ` Note: a set of example input files with the attendant material files -are included in the ``examples/USER/atc`` folders. +are included in the ``examples/PACKAGES/atc`` folders. Default """"""" diff --git a/doc/src/fix_bocs.rst b/doc/src/fix_bocs.rst index f4b3080cc0..c6c7ed41aa 100644 --- a/doc/src/fix_bocs.rst +++ b/doc/src/fix_bocs.rst @@ -124,7 +124,7 @@ the examples. For the last argument in the command, you should put XXXX_press, where XXXX is the ID given to the fix bocs command (in the example, the ID of the fix bocs command is 1 ). -This fix is part of the USER-BOCS package. It is only enabled if +This fix is part of the BOCS package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Further information diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index c421185d87..baf7985ef5 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -69,7 +69,7 @@ Syntax Examples """""""" -For unabridged example scripts and files, see examples/USER/reaction. +For unabridged example scripts and files, see examples/PACKAGES/reaction. .. code-block:: LAMMPS @@ -159,7 +159,7 @@ constant-topology parts of your system separately. The dynamic group contains only atoms not involved in a reaction at a given timestep, and therefore should be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example -above (full examples can be found at examples/USER/reaction). The time +above (full examples can be found at examples/PACKAGES/reaction). The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. @@ -667,7 +667,7 @@ all other fixes that use any group created by fix bond/react. Restrictions """""""""""" -This fix is part of the USER-REACTION package. It is only enabled if +This fix is part of the REACTION package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_brownian.rst b/doc/src/fix_brownian.rst index d032346617..c274c394f3 100644 --- a/doc/src/fix_brownian.rst +++ b/doc/src/fix_brownian.rst @@ -185,7 +185,7 @@ as defined by the :doc:`atom_style ellipsoid ` command. If the *dipole* keyword is used, they must also store a dipole moment as defined by the :doc:`atom_style dipole ` command. -This fix is part of the USER-BROWNIAN package. It is only enabled if +This fix is part of the BROWNIAN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index 3f503410d3..6de30a3d84 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -50,7 +50,7 @@ The Colvars library is developed at `https://github.com/colvars/colvars `. There are some example scripts for using this package with LAMMPS in the -examples/USER/colvars directory. +examples/PACKAGES/colvars directory. ---------- @@ -122,7 +122,7 @@ energy mentioned above. The scalar value calculated by this fix is Restrictions """""""""""" -This fix is part of the USER-COLVARS package. It is only enabled if +This fix is part of the COLVARS package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 999a88c4e7..90192c6c00 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -100,7 +100,7 @@ adjusted independently and simultaneously by this command. This fix can be used to perform non-equilibrium MD (NEMD) simulations of a continuously strained system. See the :doc:`fix nvt/sllod ` and :doc:`compute temp/deform ` commands for more details. Note that simulation of a continuously extended system (extensional flow) -can be modeled using the :ref:`USER-UEF package ` and its :doc:`fix commands `. +can be modeled using the :ref:`UEF package ` and its :doc:`fix commands `. For the *x*\ , *y*\ , *z* parameters, the associated dimension cannot be shrink-wrapped. For the *xy*\ , *yz*\ , *xz* parameters, the associated diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index 732f99b516..a1e8ef2faf 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -45,7 +45,7 @@ can be specified by using fix *dpd/energy*\ , fix *nve* and pair_style *dpd/fdt/energy*\ . DPD under isoenthalpic conditions can be specified by using fix *dpd/energy*\ , fix *nph* and pair_style *dpd/fdt/energy*\ . Examples of each DPD variant are provided in the -examples/USER/dpd directory. +examples/PACKAGES/dpd-react directory. ---------- @@ -56,7 +56,7 @@ examples/USER/dpd directory. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix must be used with an additional fix that specifies time diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 29bbc92f78..5e1b92ae66 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -77,7 +77,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-MESODPD package. It is only enabled if +This fix is part of the DPD-MESO package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Fix *edpd/source* must be used with the :doc:`pair_style edpd ` command. Fix *tdpd/source* must be used with the diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst index a879f1594b..5300d1f490 100644 --- a/doc/src/fix_drude.rst +++ b/doc/src/fix_drude.rst @@ -22,7 +22,7 @@ Examples fix 1 all drude 1 1 0 1 0 2 2 2 fix 1 all drude C C N C N D D D -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 28d57306ea..9943ea0710 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -25,7 +25,7 @@ Examples fix 3 all drude/transform/direct fix 1 all drude/transform/inverse -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index 4533e0bbe9..62037e66c7 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -153,7 +153,7 @@ atoms moving above some minimum cutoff velocity (i.e., kinetic energy). These coefficients can be determined by fitting a quadratic polynomial to electronic stopping data predicted by, for example, SRIM or TD-DFT. Multiple 'Ecut c1 c2' values can be provided for multi-species simulations in the order -of the atom types. There is an examples/USER/misc/electron_stopping/ directory, +of the atom types. There is an examples/USER-MISC/electron_stopping/ directory, which illustrates uses of this command. Details of this implementation are further described in :ref:`Stewart2018 ` and :ref:`Lee2020 `. diff --git a/doc/src/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst index 5cbe0053ff..57f8c914ab 100644 --- a/doc/src/fix_eos_cv.rst +++ b/doc/src/fix_eos_cv.rst @@ -43,7 +43,7 @@ equation of state are possible. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This command also requires use of the :doc:`atom_style dpd ` diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst index ad734c391a..06310e9685 100644 --- a/doc/src/fix_eos_table.rst +++ b/doc/src/fix_eos_table.rst @@ -102,7 +102,7 @@ one that matches the specified keyword. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This command also requires use of the :doc:`atom_style dpd ` diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index 56bde44d98..eadac5d56c 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -177,7 +177,7 @@ coefficient. In this case, the format of the file is as follows: Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This command also requires use of the :doc:`atom_style dpd ` diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index 67a0218c9b..343bf083ae 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -73,7 +73,7 @@ pressure correction is discussed and described in :ref:`(Strong) `. For a complete example including the considerations discussed -above, see the examples/USER/flow_gauss directory. +above, see the examples/PACKAGES/flow_gauss directory. .. note:: diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst index 85702b909f..0dedda1e2e 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -66,7 +66,7 @@ processors be on the order of the number of desired replicas. A 100-replica simulation would require at least 100 processors (1 per world at minimum). If many replicas are needed on a small number of processors, multi-replica runs can be run outside of LAMMPS. An -example of this can be found in examples/USER/misc/grem and has no +example of this can be found in examples/USER-MISC/grem and has no limit on the number of replicas per processor. However, this is very inefficient and error prone and should be avoided if possible. diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index 3b84ec6f72..5bb4075873 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -52,7 +52,7 @@ latencies for slow communication links. This feature has only been tested under linux. There are example scripts for using this package with LAMMPS in -examples/USER/imd. Additional examples and a driver for use with the +examples/PACKAGES/imd. Additional examples and a driver for use with the Novint Falcon game controller as haptic device can be found at: http://sites.google.com/site/akohlmey/software/vrpn-icms. @@ -149,7 +149,7 @@ fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if +This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. When used in combination with VMD, a topology or coordinate file has diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index 1d1ed795cd..ccd1c9f58c 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -36,7 +36,7 @@ following publication :ref:`(IPI-CPC) `. A version of the i-PI package, containing only files needed for use with LAMMPS, is provided in the tools/i-pi directory. See the tools/i-pi/manual.pdf for an introduction to i-PI. The -examples/USER/i-pi directory contains example scripts for using i-PI +examples/PACKAGES/i-pi directory contains example scripts for using i-PI with LAMMPS. In brief, the path integral molecular dynamics is performed by the diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index c075a56549..77e59a0848 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -35,7 +35,7 @@ Examples fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451 fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index c6fd1b0b40..383980b232 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -104,7 +104,7 @@ Restrictions """""""""""" none -This fix is part of the USER-EFF package. It is only enabled if +This fix is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index b2b85b8f5f..127e846589 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -341,7 +341,7 @@ of this fix can be used with the *start/stop* keywords of the Restrictions """""""""""" -This fix is part of the USER-LB package. It is only enabled if LAMMPS +This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix can only be used with an orthogonal simulation domain. diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst index 479f480e50..5a01e1916e 100644 --- a/doc/src/fix_lb_momentum.rst +++ b/doc/src/fix_lb_momentum.rst @@ -66,7 +66,7 @@ Can only be used if a lattice-Boltzmann fluid has been created via the :doc:`fix lb/fluid ` command, and must come after this command. -This fix is part of the USER-LB package. It is only enabled if LAMMPS +This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst index c6f5048126..6ba28ec309 100644 --- a/doc/src/fix_lb_pc.rst +++ b/doc/src/fix_lb_pc.rst @@ -41,7 +41,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-LB package. It is only enabled if LAMMPS +This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the diff --git a/doc/src/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst index b6a19c98d5..5ee32c29f0 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.rst +++ b/doc/src/fix_lb_rigid_pc_sphere.rst @@ -139,7 +139,7 @@ of the :doc:`run ` command. These fixes are not invoked during Restrictions """""""""""" -This fix is part of the USER-LB package. It is only enabled if LAMMPS +This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst index da8922c92f..5bd6889808 100644 --- a/doc/src/fix_lb_viscous.rst +++ b/doc/src/fix_lb_viscous.rst @@ -71,7 +71,7 @@ for details." Restrictions """""""""""" -This fix is part of the USER-LB package. It is only enabled if LAMMPS +This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst index 6d13fab7b8..964fc1ad1f 100644 --- a/doc/src/fix_manifoldforce.rst +++ b/doc/src/fix_manifoldforce.rst @@ -48,7 +48,7 @@ the :doc:`run ` command. This fix is invoked during :doc:`energy minimizat Restrictions """""""""""" -This fix is part of the USER-MANIFOLD package. It is only enabled if +This fix is part of the MANIFOLD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Only use this with *min_style hftn* or *min_style quickmin*. If not, diff --git a/doc/src/fix_mdi_engine.rst b/doc/src/fix_mdi_engine.rst index 76506f3e19..ca667bfe3b 100644 --- a/doc/src/fix_mdi_engine.rst +++ b/doc/src/fix_mdi_engine.rst @@ -44,7 +44,7 @@ For more information about running LAMMPS as an MDI engine, see the Restrictions """""""""""" -This command is part of the USER-MDI package. It is only enabled if +This command is part of the MDI package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst index 06b0d16686..6b290382a3 100644 --- a/doc/src/fix_meso_move.rst +++ b/doc/src/fix_meso_move.rst @@ -238,7 +238,7 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-SDPD package. It is only enabled if +This fix is part of the DPD-SMOOTH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index d0df1bd0f9..429c1c3bb7 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -90,7 +90,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-MESODPD package. It is only enabled if +This fix is part of the DPD-MESO package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index 3e54ed9765..2dbd5aa85e 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -116,7 +116,7 @@ for details. Restrictions """""""""""" -This fix is part of the USER-EFF package. It is only enabled if +This fix is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Other restriction discussed on the doc page for the :doc:`fix nvt, npt, and nph ` commands also apply. diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 74e61472c6..e33b2a639d 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -199,7 +199,7 @@ The fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-UEF package. It is only enabled if LAMMPS +This fix is part of the UEF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Due to requirements of the boundary conditions, when the *strain* diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst index b112aacd60..a294cebd73 100644 --- a/doc/src/fix_nve_awpmd.rst +++ b/doc/src/fix_nve_awpmd.rst @@ -45,7 +45,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-AWPMD package. It is only enabled if +This fix is part of the AWPMD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst index ac60b40f47..26af6efb4b 100644 --- a/doc/src/fix_nve_dot.rst +++ b/doc/src/fix_nve_dot.rst @@ -36,9 +36,9 @@ in a NVE ensemble prior to using the Langevin-type DOTC-integrator The command is equivalent to the :doc:`fix nve `. The particles are always considered to have a finite size. -An example input file can be found in /examples/USER/cgdna/examples/duplex1/. +An example input file can be found in /examples/PACKAGES/cgdna/examples/duplex1/. Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) `. -The preprint version of the article can be found `here `_. +The preprint version of the article can be found `here `_. ---------- @@ -46,7 +46,7 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -:ref:`USER-CGDNA ` package and the MOLECULE and ASPHERE package. +:ref:`CG-DNA ` package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index 4ffead3f25..944767ff51 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/doc/src/fix_nve_dotc_langevin.rst @@ -120,9 +120,9 @@ freedom in addition to the usual translational degrees of freedom. The scale factor after the *angmom* keyword gives the ratio of the rotational to the translational friction coefficient. -An example input file can be found in examples/USER/cgdna/examples/duplex2/. +An example input file can be found in examples/PACKAGES/cgdna/examples/duplex2/. Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) `. -The preprint version of the article can be found `here `_. +The preprint version of the article can be found `here `_. ---------- @@ -130,7 +130,7 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -:ref:`USER-CGDNA ` package and the MOLECULE and ASPHERE package. +:ref:`CG-DNA ` package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst index 2c14bb07a9..87e64a9661 100644 --- a/doc/src/fix_nve_eff.rst +++ b/doc/src/fix_nve_eff.rst @@ -42,7 +42,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-EFF package. It is only enabled if +This fix is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index b24277a8c7..e0c0c10b4a 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -83,7 +83,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-MANIFOLD package. It is only enabled if +This fix is part of the MANIFOLD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. ---------- diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index f822df5b8d..3815138064 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -63,7 +63,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-MANIFOLD package. It is only enabled if +This fix is part of the MANIFOLD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. ---------- diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst index e07e990d4b..328ff7d4e5 100644 --- a/doc/src/fix_nvt_sllod_eff.rst +++ b/doc/src/fix_nvt_sllod_eff.rst @@ -69,7 +69,7 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-EFF package. It is only enabled if +This fix is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix works best without Nose-Hoover chain thermostats, i.e. using diff --git a/doc/src/fix_pafi.rst b/doc/src/fix_pafi.rst index 8f1d02ac49..f50dc1dc0e 100644 --- a/doc/src/fix_pafi.rst +++ b/doc/src/fix_pafi.rst @@ -45,7 +45,7 @@ projection is also calculated, whose time integral can be shown to be equal to the true free energy gradient along the minimum free energy path local to the reference pathway. A detailed discussion of the projection technique can be found in :ref:`(Swinburne) `. -This fix can be used with LAMMPS as demonstrated in examples/USER/misc/pafi, +This fix can be used with LAMMPS as demonstrated in examples/USER-MISC/pafi, though it is primarily intended to be coupled with the PAFI C++ code, developed at `https://github.com/tomswinburne/pafi `_, which distributes multiple LAMMPS workers in parallel to compute and collate diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index b30037ade7..e151d8a671 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -181,7 +181,7 @@ This fix assumes a crystalline system with periodical lattice. The temperature of the system should not exceed the melting temperature to keep the system in its solid state. -This fix is part of the USER-PHONON package. It is only enabled if +This fix is part of the PHONON package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires LAMMPS be built with an FFT library. See the :doc:`Build settings ` doc page for details. diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index bd2c05adfe..5c32ccee99 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -44,7 +44,7 @@ in the PLUMED source code. The PLUMED library development is hosted at A detailed discussion of the code can be found in :ref:`(PLUMED) `. There is an example input for using this package with LAMMPS in the -examples/USER/plumed directory. +examples/PACKAGES/plumed directory. ---------- @@ -113,7 +113,7 @@ are native to PLUMED. Restrictions """""""""""" -This fix is part of the USER-PLUMED package. It is only enabled if +This fix is part of the PLUMED package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_polarize.rst b/doc/src/fix_polarize.rst index 2c499fce3c..2667cb5eeb 100644 --- a/doc/src/fix_polarize.rst +++ b/doc/src/fix_polarize.rst @@ -40,7 +40,7 @@ These fixes compute induced charges at the interface between two impermeable media with different dielectric constants. There are some example scripts for using this fix -with LAMMPS in the examples/USER/dielectric directory. +with LAMMPS in the examples/PACKAGES/dielectric directory. ---------- @@ -77,7 +77,7 @@ Restart, fix_modify, output, run start/stop, minimize info Restrictions """""""""""" -These fixes are part of the USER-DIELECTRIC package. It is only enabled +These fixes are part of the DIELECTRIC package. It is only enabled if LAMMPS was built with that package, which requires that also the KSPACE package is installed. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index ddc96817f9..a086cb442b 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -148,7 +148,7 @@ Restrictions With keyword *dipole*, this fix only works when the DIPOLE package is enabled. See the :doc:`Build package ` doc page for more info. -This fix is part of the USER-BROWNIAN package. It is only enabled if +This fix is part of the BROWNIAN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst index ef820a68d6..abf8ed1aae 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -208,7 +208,7 @@ It is worth noting that the temp keyword for the :doc:`thermo_style Restrictions """""""""""" -This fix style is part of the USER-QTB package. It is only enabled if +This fix style is part of the QTB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst index 8752888c4c..1b0f4c37e5 100644 --- a/doc/src/fix_qeq_reax.rst +++ b/doc/src/fix_qeq_reax.rst @@ -97,7 +97,7 @@ This fix is invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-REAXC package. It is only enabled if +This fix is part of the REAXFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix does not correctly handle interactions diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst index 81bb315e23..acbafccded 100644 --- a/doc/src/fix_qmmm.rst +++ b/doc/src/fix_qmmm.rst @@ -54,7 +54,7 @@ fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-QMMM package. It is only enabled if +This fix is part of the QMMM package. It is only enabled if LAMMPS was built with that package. It also requires building a library provided with LAMMPS. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst index 594b8b78a7..6ea3e97f9a 100644 --- a/doc/src/fix_qtb.rst +++ b/doc/src/fix_qtb.rst @@ -161,7 +161,7 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix style is part of the USER-QTB package. It is only enabled if +This fix style is part of the QTB package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst index 2d0d2d18db..9207ee7a63 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxc_bonds.rst @@ -77,7 +77,7 @@ Restrictions """""""""""" The fix reax/c/bonds command requires that the :doc:`pair_style reax/c ` is invoked. This fix is part of the -USER-REAXC package. It is only enabled if LAMMPS was built with that +REAXFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index 9935ecaa3a..bce140a9af 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -146,7 +146,7 @@ Restrictions """""""""""" The "fix reax/c/species" currently only works with :doc:`pair_style reax/c ` and it requires that the :doc:`pair_style reax/c ` be invoked. This fix is part of the -USER-REAXC package. It is only enabled if LAMMPS was built with that +REAXFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst index cffba5bafa..71a575810c 100644 --- a/doc/src/fix_rhok.rst +++ b/doc/src/fix_rhok.rst @@ -43,7 +43,7 @@ used to study crystal-liquid interfaces and determine melting temperatures :ref:`(Pedersen) `. An example of using the interface pinning method is located in the -*examples/USER/misc/rhok* directory. +*examples/USER-MISC/rhok* directory. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index dea2354bad..32ad4aa6c6 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -344,7 +344,7 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-SDPD package and also depends on the RIGID +This fix is part of the DPD-SMOOTH package and also depends on the RIGID package. It is only enabled if LAMMPS was built with both packages. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index 9eab06ffad..c3406df5d0 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -206,7 +206,7 @@ read_data data.dpd fix foo_SPECIES NULL Species Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This command also requires use of the :doc:`atom_style dpd ` diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index f928044db7..9f60df7e75 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -49,7 +49,7 @@ under isobaric conditions can be specified by using fix shardlow, fix *nph* and pair_style *dpd/fdt*\ . DPD under isoenthalpic conditions can be specified by using fix shardlow, fix *nph* and pair_style *dpd/fdt/energy*\ . Examples of each DPD variant are provided in the -examples/USER/dpd directory. +examples/PACKAGES/dpd-react directory. ---------- @@ -60,7 +60,7 @@ examples/USER/dpd directory. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix is currently limited to orthogonal simulation cell diff --git a/doc/src/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst index fb19c07b15..c1dc008c55 100644 --- a/doc/src/fix_smd_adjust_dt.rst +++ b/doc/src/fix_smd_adjust_dt.rst @@ -49,12 +49,12 @@ Dynamics in LAMMPS. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor minimization. +Currently, no part of MACHDYN supports restarting nor minimization. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if +This fix is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_smd_integrate_tlsph.rst b/doc/src/fix_smd_integrate_tlsph.rst index 867141bd6f..4f19b98c49 100644 --- a/doc/src/fix_smd_integrate_tlsph.rst +++ b/doc/src/fix_smd_integrate_tlsph.rst @@ -44,13 +44,13 @@ velocity limit. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor +Currently, no part of MACHDYN supports restarting nor minimization. This fix has no outputs. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if +This fix is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index 5b4c117452..d6bcdd68a5 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -52,13 +52,13 @@ the velocity vector to max_vel in case it exceeds this velocity limit. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor +Currently, no part of MACHDYN supports restarting nor minimization. This fix has no outputs. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if +This fix is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst index 293f5401a2..2da904400a 100644 --- a/doc/src/fix_smd_move_triangulated_surface.rst +++ b/doc/src/fix_smd_move_triangulated_surface.rst @@ -66,13 +66,13 @@ Dynamics in LAMMPS. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor +Currently, no part of MACHDYN supports restarting nor minimization. This fix has no outputs. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if +This fix is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst index 53aa5f649c..bc475914df 100644 --- a/doc/src/fix_smd_setvel.rst +++ b/doc/src/fix_smd_setvel.rst @@ -66,7 +66,7 @@ specified geometric :doc:`region ` in order to have its velocity set by Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor minimization +Currently, no part of MACHDYN supports restarting nor minimization None of the :doc:`fix_modify ` options are relevant to this fix. @@ -81,7 +81,7 @@ the :doc:`run ` command. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if +This fix is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst index 38efee0977..040cfa7483 100644 --- a/doc/src/fix_smd_wall_surface.rst +++ b/doc/src/fix_smd_wall_surface.rst @@ -44,7 +44,7 @@ is possible to move the triangulated surface via the Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles -in the system. See the "funnel_flow" example in the USER-SMD examples +in the system. See the "funnel_flow" example in the MACHDYN examples directory. See `this PDF guide `_ to use Smooth Mach @@ -53,13 +53,13 @@ Dynamics in LAMMPS. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -Currently, no part of USER-SMD supports restarting nor +Currently, no part of MACHDYN supports restarting nor minimization. This fix has no outputs. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if +This fix is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The molecule ID given to the particles created by this fix have to be diff --git a/doc/src/fix_sph.rst b/doc/src/fix_sph.rst index 5ba752debb..1866893b93 100644 --- a/doc/src/fix_sph.rst +++ b/doc/src/fix_sph.rst @@ -44,7 +44,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-SPH package. It is only enabled if +This fix is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_sph_stationary.rst b/doc/src/fix_sph_stationary.rst index c86a30b542..34db080121 100644 --- a/doc/src/fix_sph_stationary.rst +++ b/doc/src/fix_sph_stationary.rst @@ -44,7 +44,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" -This fix is part of the USER-SPH package. It is only enabled if +This fix is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst index 01017c0267..1eaa8cf360 100644 --- a/doc/src/fix_temp_rescale_eff.rst +++ b/doc/src/fix_temp_rescale_eff.rst @@ -66,7 +66,7 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the USER-EFF package. It is only enabled if +This fix is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_tgnh_drude.rst b/doc/src/fix_tgnh_drude.rst index a6e9832833..744c7e75f3 100644 --- a/doc/src/fix_tgnh_drude.rst +++ b/doc/src/fix_tgnh_drude.rst @@ -62,7 +62,7 @@ Examples fix 2 jello tgnpt/drude temp 300.0 300.0 100.0 1.0 20.0 tri 5.0 5.0 1000.0 fix 2 ice tgnpt/drude temp 250.0 250.0 100.0 1.0 20.0 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" @@ -271,7 +271,7 @@ Restrictions """""""""""" These fixes are only available when LAMMPS was built with the -USER-DRUDE package. These fixes cannot be used with dynamic groups as +DRUDE package. These fixes cannot be used with dynamic groups as defined by the :doc:`group ` command. These fixes cannot be used in 2D simulations. diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index cf689f3a77..1b1e904126 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -117,7 +117,7 @@ ellipsoidal particles according to the EES potential introduced above. Other details of this command are the same as for the :doc:`fix wall/region ` command. One may also find an example -of using this fix in the examples/USER/misc/ees/ directory. +of using this fix in the examples/USER-MISC/ees/ directory. ---------- diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst index 8c265db197..31b46ce2ce 100644 --- a/doc/src/group2ndx.rst +++ b/doc/src/group2ndx.rst @@ -57,7 +57,7 @@ Restrictions This command requires that atoms have atom IDs, since this is the information that is written to the index file. -These commands are part of the USER-COLVARS package. They are only +These commands are part of the COLVARS package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/improper_distharm.rst b/doc/src/improper_distharm.rst index e29ae95ac5..0399a5c6e2 100644 --- a/doc/src/improper_distharm.rst +++ b/doc/src/improper_distharm.rst @@ -48,7 +48,7 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -USER-YAFF package. See the :doc:`Build package ` doc +YAFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index 4f21e48fa9..41d533eebe 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -71,8 +71,8 @@ hardware, as discussed on the :doc:`Speed packages ` doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/improper_inversion_harmonic.rst b/doc/src/improper_inversion_harmonic.rst index 1c57b5daf1..9826ab6218 100644 --- a/doc/src/improper_inversion_harmonic.rst +++ b/doc/src/improper_inversion_harmonic.rst @@ -58,7 +58,7 @@ Restrictions """""""""""" This improper style can only be used if LAMMPS was built with the -USER-MOFFF package. See the :doc:`Build package ` doc +MOFFF package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/info.rst b/doc/src/info.rst index 395bc2c1f4..b3eb6d7000 100644 --- a/doc/src/info.rst +++ b/doc/src/info.rst @@ -89,8 +89,8 @@ corresponding coefficients have been set. This can be very helpful to debug error messages like "All pair coeffs are not set". The *accelerator* category prints out information about compile time -settings of included accelerator support for the GPU, KOKKOS, USER-INTEL, -and USER-OMP packages. +settings of included accelerator support for the GPU, KOKKOS, INTEL, +and OPENMP packages. The *styles* category prints the list of styles available in the current LAMMPS binary. It supports one of the following options diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 01ad15a08e..c184b5b006 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -298,9 +298,9 @@ be cloned from the git-repository "git://github.com/scafacos/scafacos.git". In order to use this KSpace style, you must download and build the -ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package +ScaFaCoS library, then build LAMMPS with the SCAFACOS package installed package which links LAMMPS to the ScaFaCoS library. -See details on :ref:`this page `. +See details on :ref:`this page `. .. note:: @@ -420,8 +420,8 @@ The *pppm/kk* style performs charge assignment and force interpolation calculations, along with the FFTs themselves, on the GPU or (optionally) threaded on the CPU when using OpenMP and FFTW3. -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP, and OPT packages respectively. They are only enabled if +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP, and OPT packages respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. See the :doc:`Speed packages ` doc page for more @@ -446,7 +446,7 @@ only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The *msm/dielectric* and *pppm/dielectric* kspace styles are part of the -USER-DIELECTRIC package. They are only enabled if LAMMPS was built with +DIELECTRIC package. They are only enabled if LAMMPS was built with that package **and** the KSPACE package. See the :doc:`Build package ` doc page for more info. @@ -460,7 +460,7 @@ dimensions. The only exception is if the slab option is set with must be periodic and the z dimension must be non-periodic. The scafacos KSpace style will only be enabled if LAMMPS is built with -the USER-SCAFACOS package. See the :doc:`Build package ` +the SCAFACOS package. See the :doc:`Build package ` doc page for more info. The use of ScaFaCos in LAMMPS does not yet support molecular charged diff --git a/doc/src/mdi_engine.rst b/doc/src/mdi_engine.rst index b39999606d..d26a1f8cd3 100644 --- a/doc/src/mdi_engine.rst +++ b/doc/src/mdi_engine.rst @@ -67,13 +67,13 @@ about these commands in the `MDI library documentation If these commands are not sufficient to support what a driver which you write needs, additional commands can be defined by simply using a new command name not in this list. Code to support the new command -needs to be added to the USER-MDI package within LAMMPS; see its -src/USER-MDI/mdi_engine.cpp and fix_mdi_engine.cpp files. +needs to be added to the MDI package within LAMMPS; see its +src/MDI/mdi_engine.cpp and fix_mdi_engine.cpp files. Restrictions """""""""""" -This command is part of the USER-MDI package. It is only enabled if +This command is part of the MDI package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/package.rst b/doc/src/package.rst index 1613ff2fae..e997dc6147 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -130,8 +130,8 @@ Description This command invokes package-specific settings for the various accelerator packages available in LAMMPS. Currently the following -packages use settings from this command: GPU, USER-INTEL, KOKKOS, and -USER-OMP. +packages use settings from this command: GPU, INTEL, KOKKOS, and +OPENMP. If this command is specified in an input script, it must be near the top of the script, before the simulation box has been defined. This @@ -152,7 +152,7 @@ accelerator settings. The KOKKOS package requires a "-k on" :doc:`command-line switch ` respectively, which invokes a "package kokkos" command with default settings. -For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf +For the GPU, INTEL, and OPENMP packages, if a "-sf gpu" or "-sf intel" or "-sf omp" :doc:`command-line switch ` is used to auto-append accelerator suffixes to various styles in the input script, then those switches also invoke a "package gpu", "package @@ -289,7 +289,7 @@ threads allocated for each MPI task. This setting controls OpenMP parallelism only for routines run on the CPUs. For more details on setting the number of OpenMP threads, see the discussion of the *Nthreads* setting on this doc page for the "package omp" command. -The meaning of *Nthreads* is exactly the same for the GPU, USER-INTEL, +The meaning of *Nthreads* is exactly the same for the GPU, INTEL, and GPU packages. The *platform* keyword is only used with OpenCL to specify the ID for @@ -333,7 +333,7 @@ specify additional flags for the runtime build. ---------- The *intel* style invokes settings associated with the use of the -USER-INTEL package. All of its settings, except the *omp* and *mode* +INTEL package. All of its settings, except the *omp* and *mode* keywords, are ignored if LAMMPS was not built with Xeon Phi co-processor support. All of its settings, including the *omp* and *mode* keyword are applicable if LAMMPS was built with co-processor @@ -351,12 +351,12 @@ threads allocated for each MPI task. This setting controls OpenMP parallelism only for routines run on the CPUs. For more details on setting the number of OpenMP threads, see the discussion of the *Nthreads* setting on this doc page for the "package omp" command. -The meaning of *Nthreads* is exactly the same for the GPU, USER-INTEL, +The meaning of *Nthreads* is exactly the same for the GPU, INTEL, and GPU packages. The *mode* keyword determines the precision mode to use for computing pair style forces, either on the CPU or on the co-processor, -when using a USER-INTEL supported :doc:`pair style `. It +when using a INTEL supported :doc:`pair style `. It can take a value of *single*\ , *mixed* which is the default, or *double*\ . *Single* means single precision is used for the entire force calculation. *Mixed* means forces between a pair of atoms are @@ -376,7 +376,7 @@ Simultaneous Multithreading (SMT) such as Hyper-Threading (HT) on Intel processors. In this mode, one additional thread is generated per MPI process. LAMMPS will generate a warning in the case that more threads are used than available in SMT hardware on a node. If the PPPM solver -from the USER-INTEL package is not used, then the LRT setting is +from the INTEL package is not used, then the LRT setting is ignored and no extra threads are generated. Enabling LRT will replace the :doc:`run_style ` with the *verlet/lrt/intel* style that is identical to the default *verlet* style aside from supporting the @@ -556,7 +556,7 @@ result in better performance for certain configurations and system sizes. ---------- The *omp* style invokes settings associated with the use of the -USER-OMP package. +OPENMP package. The *Nthreads* argument sets the number of OpenMP threads allocated for each MPI task. For example, if your system has nodes with dual @@ -595,12 +595,12 @@ for OpenMPI. Check your MPI documentation for additional details. What combination of threads and MPI tasks gives the best performance is difficult to predict and can depend on many components of your input. Not all features of LAMMPS support OpenMP threading via the -USER-OMP package and the parallel efficiency can be very different, +OPENMP package and the parallel efficiency can be very different, too. .. note:: - If you build LAMMPS with the GPU, USER-INTEL, and / or USER-OMP + If you build LAMMPS with the GPU, INTEL, and / or OPENMP packages, be aware these packages all allow setting of the *Nthreads* value via their package commands, but there is only a single global *Nthreads* value used by OpenMP. Thus if multiple package commands are @@ -642,14 +642,14 @@ with the GPU package. See the :doc:`Build package ` doc page for more info. The intel style of this command can only be invoked if LAMMPS was -built with the USER-INTEL package. See the :doc:`Build package ` doc page for more info. +built with the INTEL package. See the :doc:`Build package ` doc page for more info. The kk style of this command can only be invoked if LAMMPS was built with the KOKKOS package. See the :doc:`Build package ` doc page for more info. The omp style of this command can only be invoked if LAMMPS was built -with the USER-OMP package. See the :doc:`Build package ` +with the OPENMP package. See the :doc:`Build package ` doc page for more info. Related commands @@ -667,7 +667,7 @@ automatically if the "-sf gpu" :doc:`command-line switch ` is used. If it is not used, you must invoke the package gpu command in your input script or via the "-pk gpu" :doc:`command-line switch `. -For the USER-INTEL package, the default is Nphi = 1 and the option +For the INTEL package, the default is Nphi = 1 and the option defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4, tptask = 240. The default ghost option is determined by the pair style being used. This value is output to the screen in the offload diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index 087c39e8f9..cfbcfb0c05 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -63,7 +63,7 @@ to specify the path for the force field file. An AGNI force field is fully specified by the filename which contains the parameters of the force field, i.e., the reference training environments used to construct the machine learning force field. Example force field -and input files are provided in the examples/USER/misc/agni directory. +and input files are provided in the examples/USER-MISC/agni directory. ---------- @@ -73,7 +73,7 @@ depending on your available hardware, as discussed on the :doc:`Speed packages < the same arguments and should produce the same results, except for round-off and precision issues. -The accelerated style is part of the USER-OMP. They are only enabled +The accelerated style is part of the OPENMP. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. You can specify the accelerated style explicitly in your input script diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index 5f96a93fee..740ed0292f 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -135,7 +135,7 @@ to be specified in an input script that reads a restart file. Restrictions """""""""""" -These styles are part of the USER-MOFFF package. They are only +These styles are part of the MOFFF package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index cfa085cc28..f88663d36b 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -121,7 +121,7 @@ for mixing the cutoff distance. ---------- A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in -free energy calculations, is part of the USER-FEP package and is documented with +free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_coul_tt.rst b/doc/src/pair_coul_tt.rst index b01d46d7ae..d1465ef147 100644 --- a/doc/src/pair_coul_tt.rst +++ b/doc/src/pair_coul_tt.rst @@ -29,7 +29,7 @@ Examples pair_coeff 1 2 coul/tt 4.0 1.0 4 12.0 pair_coeff 1 3* coul/tt 4.5 1.0 4 -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" @@ -95,7 +95,7 @@ for all I,J pairs must be specified explicitly. Restrictions """""""""""" -These pair styles are part of the USER-DRUDE package. They are only +These pair styles are part of the DRUDE package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 62cf94786d..aa8323379a 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -154,14 +154,14 @@ These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -These pair styles writes their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. Note -that the user-specified random number seed is stored in the restart -file, so when a simulation is restarted, each processor will -re-initialize its random number generator the same way it did -initially. This means the random forces will be random, but will not -be the same as they would have been if the original simulation had -continued past the restart time. +These pair styles write their information to :doc:`binary restart files +`, so pair_style and pair_coeff commands do not need to be +specified in an input script that reads a restart file. Note that the +user-specified random number seed is stored in the restart file, so when +a simulation is restarted, each processor will re-initialize its random +number generator the same way it did initially. This means the random +forces will be random, but will not be the same as they would have been +if the original simulation had continued past the restart time. These pair styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the @@ -177,22 +177,26 @@ this. Restrictions """""""""""" +These styles are part of the DPD-BASIC package. They are only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. + The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too -infrequent for style *dpd* simulations since particles move rapidly -and can overlap by large amounts. If this setting yields a non-zero -number of "dangerous" reneighborings (printed at the end of a -simulation), you should experiment with forcing reneighboring more -often and see if system energies/trajectories change. +infrequent for style *dpd* simulations since particles move rapidly and +can overlap by large amounts. If this setting yields a non-zero number +of "dangerous" reneighborings (printed at the end of a simulation), you +should experiment with forcing reneighboring more often and see if +system energies/trajectories change. -These pair styles requires you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost -atoms. +These pair styles requires you to use the :doc:`comm_modify vel yes +` command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the :doc:`read_restart ` command, though they should provide -statistically similar results. This is because the forces they -compute depend on atom velocities. See the -:doc:`read_restart ` command for more details. +statistically similar results. This is because the forces they compute +depend on atom velocities. See the :doc:`read_restart ` +command for more details. Related commands """""""""""""""" diff --git a/doc/src/pair_dpd_ext.rst b/doc/src/pair_dpd_ext.rst index cfc72fe84c..0523a19e0b 100644 --- a/doc/src/pair_dpd_ext.rst +++ b/doc/src/pair_dpd_ext.rst @@ -38,12 +38,19 @@ Examples Description """"""""""" -The style *dpd/ext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) `, :ref:`(Junghans) `. +The style *dpd/ext* computes an extended force field for dissipative +particle dynamics (DPD) following the exposition in :ref:`(Groot) +`, :ref:`(Junghans) `. -Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise interactions, equivalent to the non-conservative portion of the extended DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. +Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise +interactions, equivalent to the non-conservative portion of the extended +DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair +style, use the :doc:`pair_style hybrid/overlay ` command to +compute both the desired pair interaction and the thermostat for each +pair of particles. -For the style *dpd/ext*\ , the force on atom I due to atom J is given as a sum -of 3 terms +For the style *dpd/ext*\ , the force on atom I due to atom J is given as +a sum of 3 terms .. math:: @@ -53,17 +60,51 @@ of 3 terms f^R = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij} + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\ w(r) = & 1 - r/r_c \\ -where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command. +where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` +is a dissipative force, and :math:`\mathbf{f}^R` is a random +force. :math:`A_{ij}` is the maximum repulsion between the two atoms, +:math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction +:math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = +\mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of +the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian +random numbers with zero mean and unit variance, :math:`\Delta t` is the +timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the +conservative interactions that varies between 0 and 1, :math:`r_c` is +the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c +)^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight +functions with coefficients :math:`s_\alpha` that vary between 0 and 1, +:math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the +unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, +where :math:`k` is the Boltzmann constant and :math:`T` is the +temperature in the pair\_style command. -For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. +For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is +the same as the above equation, except that the conservative +:math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set +each timestep to a ramped value from Tstart to Tstop. -For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. +For the style *dpd/ext*\ , the pairwise energy associated with style +*dpd/ext* is only due to the conservative force term +:math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance +:math:`r_c`. The pairwise virial is calculated using all three +terms. There is no pairwise energy for style *dpd/ext/tstat*, but the +last two terms of the formula contribute the virial. -For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop. +For the style *dpd/ext/tstat*, the force on atom I due to atom J is the +same as the above equation, except that the conservative +:math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set +each timestep to a ramped value from Tstart to Tstop. -For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial. +For the style *dpd/ext*\ , the pairwise energy associated with style +*dpd/ext* is only due to the conservative force term +:math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance +:math:`r_c`. The pairwise virial is calculated using all three +terms. There is no pairwise energy for style *dpd/ext/tstat*, but the +last two terms of the formula contribute the virial. -For the style *dpd/ext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above: +For the style *dpd/ext*, the following coefficients must be defined for +each pair of atoms types via the :doc:`pair_coeff ` command +as in the examples above: * A (force units) * :math:`\gamma_{\perp}` (force/velocity units) @@ -72,35 +113,55 @@ For the style *dpd/ext*, the following coefficients must be defined for each pai * :math:`s_{\parallel}` (unitless) * :math:`r_c` (distance units) -The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. +The last coefficient is optional. If not specified, the global DPD +cutoff is used. Note that :math:`\sigma`'s are set equal to +:math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by +the :doc:`pair_style ` command so it does not need to be +specified. - -For the style *dpd/ext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. +For the style *dpd/ext/tstat*, the coefficients defined for each pair of +atoms types via the :doc:`pair_coeff ` command is the same, +except that A is not included. .. note:: - If you are modeling DPD polymer chains, you may want to use the :doc:`pair_style srp ` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other. + If you are modeling DPD polymer chains, you may want to use the + :doc:`pair_style srp ` command in conjunction with these pair + styles. It is a soft segmental repulsive potential (SRP) that can + prevent DPD polymer chains from crossing each other. .. note:: - The virial calculation for pressure when using this pair style includes all the components of force listed above, including the random force. + The virial calculation for pressure when using this pair style includes + all the components of force listed above, including the random force. ---------- **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The style *dpd/ext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. +The style *dpd/ext* does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. -The pair styles do not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`. +The pair styles do not support the :doc:`pair_modify ` +shift option for the energy of the pair interaction. Note that as +discussed above, the energy due to the conservative :math:`\mathbf{f}^C` +term is already shifted to be zero at the cutoff distance :math:`r_c`. -The :doc:`pair_modify ` table option is not relevant for the style *dpd/ext*. +The :doc:`pair_modify ` table option is not relevant for +the style *dpd/ext*. -The style *dpd/ext* does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. +The style *dpd/ext* does not support the :doc:`pair_modify +` tail option for adding long-range tail corrections to +energy and pressure. -The pair styles can only be used via the pair keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , and *outer*\ keywords. +The pair styles can only be used via the pair keyword of the +:doc:`run_style respa ` command. They do not support the +*inner*\ , *middle*\ , and *outer*\ keywords. -The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. +The style *dpd/ext/tstat* can ramp its target temperature over multiple +runs, using the start and stop keywords of the :doc:`run ` +command. See the :doc:`run ` command for details of how to do this. ---------- @@ -108,31 +169,42 @@ The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, us Restrictions """""""""""" -The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpd/ext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. +These styles are part of the DPD-BASIC package. They are only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. -The pair styles require to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. +The default frequency for rebuilding neighbor lists is every 10 steps +(see the :doc:`neigh_modify ` command). This may be too +infrequent for style *dpd/ext* simulations since particles move rapidly +and can overlap by large amounts. If this setting yields a non-zero +number of \say{dangerous} reneighborings (printed at the end of a +simulation), you should experiment with forcing reneighboring more often +and see if system energies/trajectories change. -The pair styles will not restart exactly when using the :doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the :doc:`read_restart ` command for more details. +The pair styles require to use the :doc:`comm_modify vel yes +` command so that velocities are stored by ghost atoms. + +The pair styles will not restart exactly when using the +:doc:`read_restart ` command, though they should provide +statistically similar results. This is because the forces they compute +depend on atom velocities. See the :doc:`read_restart ` +command for more details. Related commands """""""""""""""" -:doc:`pair_style dpd `, :doc:`pair_coeff `, :doc:`fix nvt `, :doc:`fix langevin `, :doc:`pair_style srp ` +:doc:`pair_style dpd `, :doc:`pair_coeff `, +:doc:`fix nvt `, :doc:`fix langevin `, +:doc:`pair_style srp ` **Default:** none - ---------- - .. _Groot: - - **(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997). .. _Junghans: - - **(Junghans)** Junghans, Praprotnik and Kremer, Soft Matter 4, 156, 1119-1128 (2008). diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index bb810b0fe6..8767c5b99e 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -162,7 +162,7 @@ significantly larger timesteps to be taken. Restrictions """""""""""" -These commands are part of the USER-DPD package. They are only +These commands are part of the DPD-REACT package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Pair styles *dpd/fdt* and *dpd/fdt/energy* require use of the diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index f031bf193d..2083e61119 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -111,7 +111,7 @@ If the neigh setting is too large, the pair style will use more memory than nece This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the :doc:`compute pair ` command as a vector of values of length 4. The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term. -See the examples/USER/misc/e3b directory for a complete example script. +See the examples/USER-MISC/e3b directory for a complete example script. ---------- diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index b5462aab01..ceb571a58d 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -232,7 +232,7 @@ complexity in higher Z elements (up to Z<18). A fixed-core should be defined with a mass that includes the corresponding nuclear mass plus the 2 s electrons in atomic mass units (2x5.4857990943e-4), and a radius equivalent to that of minimized 1s electrons (see examples -under /examples/USER/eff/fixed-core). An pseudo-core should be +under /examples/PACKAGES/eff/fixed-core). An pseudo-core should be described with a mass that includes the corresponding nuclear mass, plus all the core electrons (i.e no outer shell electrons), and a radius equivalent to that of a corresponding minimized full-electron @@ -291,7 +291,7 @@ Restrictions """""""""""" These pair styles will only be enabled if LAMMPS is built with the -USER-EFF package. It will only be enabled if LAMMPS was built with +EFF package. It will only be enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index 49a4c5436f..e9550c2152 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -178,7 +178,7 @@ pair interaction. Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index ce8227abeb..6f8954a0a7 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -182,7 +182,7 @@ Examples pair_coeff * * 100.0 2.0 1.5 1.0 pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 -Example input scripts available: examples/USER/fep +Example input scripts available: examples/PACKAGES/fep Description """"""""""" @@ -313,7 +313,7 @@ the second coefficient. electrostatic terms (kspace) are correct. It is not necessary to use soft-core Coulomb potentials if the van der Waals site is present during the free-energy route, thus avoiding overlap of the charges. Examples are - provided in the LAMMPS source directory tree, under examples/USER/fep. + provided in the LAMMPS source directory tree, under examples/PACKAGES/fep. .. note:: @@ -414,7 +414,7 @@ Restrictions """""""""""" The pair styles with soft core are only enabled if LAMMPS was built with the -USER-FEP package. The *long* versions also require the KSPACE package to be +FEP package. The *long* versions also require the KSPACE package to be installed. The soft *tip4p* versions also require the MOLECULE package to be installed. These styles are only enabled if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more diff --git a/doc/src/pair_hdnnp.rst b/doc/src/pair_hdnnp.rst index 77a87642c4..ff1739aa9a 100644 --- a/doc/src/pair_hdnnp.rst +++ b/doc/src/pair_hdnnp.rst @@ -188,7 +188,7 @@ keywords. Restrictions """""""""""" -This pair style is part of the USER-HDNNP package. It is only enabled if LAMMPS +This pair style is part of the ML-HDNNP package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index f7de713c94..b9b51e04c0 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -389,7 +389,7 @@ corresponding suffix to all sub-styles, if those versions exist. Otherwise the non-accelerated version will be used. The individual accelerated sub-styles are part of the GPU, KOKKOS, -USER-INTEL, USER-OMP, and OPT packages, respectively. They are only +INTEL, OPENMP, and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index 22f0d0dd37..c42f3ffbb8 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -73,7 +73,7 @@ LJ cutoff specified in the pair_style command are used. ---------- A version of these styles with a soft core, *lj/cut/soft*\ , suitable -for use in free energy calculations, is part of the USER-FEP package and +for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. diff --git a/doc/src/pair_lj_cut_coul.rst b/doc/src/pair_lj_cut_coul.rst index f729c2016e..30ea469071 100644 --- a/doc/src/pair_lj_cut_coul.rst +++ b/doc/src/pair_lj_cut_coul.rst @@ -245,7 +245,7 @@ the pair_style command. A version of these styles with a soft core, *lj/cut/coul/soft*\ and *lj/cut/coul/long/soft*\ , suitable for use in free energy calculations, is -part of the USER-FEP package and is documented with the :doc:`pair_style */soft ` styles. +part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. ---------- diff --git a/doc/src/pair_lj_cut_tip4p.rst b/doc/src/pair_lj_cut_tip4p.rst index 5f3b4e48e7..273483c941 100644 --- a/doc/src/pair_lj_cut_tip4p.rst +++ b/doc/src/pair_lj_cut_tip4p.rst @@ -164,7 +164,7 @@ the pair_style command. ---------- A version of these styles with a soft core, *lj/cut/tip4p/long/soft*\ , suitable -for use in free energy calculations, is part of the USER-FEP package and +for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index 3609d093d9..f190d7b502 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -177,7 +177,7 @@ specified in the pair_style command. ---------- A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in -free energy calculations, is part of the USER-FEP package and is documented with +free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index 6b918c1071..631addeb57 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -135,7 +135,7 @@ These pair styles can only be used via the *pair* keyword of the Restrictions """""""""""" -These styles are part of the USER-YAFF package. They are only enabled +These styles are part of the YAFF package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meam.rst similarity index 98% rename from doc/src/pair_meamc.rst rename to doc/src/pair_meam.rst index 757c4c6712..c55967a756 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meam.rst @@ -1,6 +1,6 @@ -.. index:: pair_style meam/c +.. index:: pair_style meam -pair_style meam/c command +pair_style meam command ========================= Syntax @@ -8,14 +8,14 @@ Syntax .. code-block:: LAMMPS - pair_style meam/c + pair_style meam Examples """""""" .. code-block:: LAMMPS - pair_style meam/c + pair_style meam pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni @@ -28,13 +28,13 @@ Description as of November 2010; see description below of the mixture_ref_t parameter -Style *meam/c* computes pairwise interactions for a variety of materials +Style *meam* computes pairwise interactions for a variety of materials using modified embedded-atom method (MEAM) potentials :ref:`(Baskes) `. Conceptually, it is an extension to the original :doc:`EAM potentials ` which adds angular forces. It is thus suitable for modeling metals and alloys with fcc, bcc, hcp and diamond cubic structures, as well as covalently bonded materials like -silicon and carbon. Style *meam/c* is a translation of the (now obsolete) +silicon and carbon. Style *meam* is a translation of the (now obsolete) *meam* code from Fortran to C++. It is functionally equivalent to *meam* but more efficient, and thus *meam* has been removed from LAMMPS after the 12 December 2018 release. @@ -383,7 +383,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -The *meam/c* style is provided in the USER-MEAMC package. It is +The *meam* style is provided in the MEAM package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -391,7 +391,7 @@ The maximum number of elements, that can be read from the MEAM library file, is determined at compile time. The default is 5. If you need support for more elements, you have to change the define for the constant 'maxelt' at the beginning of the file -src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no +src/MEAM/meam.h and update/recompile LAMMPS. There is no limit on the number of atoms types. Related commands diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index 6bedb9b4fb..a24b74bc7f 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -151,7 +151,7 @@ info. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair_style meam/c ` +:doc:`pair_coeff `, :doc:`pair_style meam ` Default """"""" diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index 70567d9ffa..b57d122774 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -94,7 +94,7 @@ potentials. systems in the future. Example input scripts that use this pair style are provided -in the examples/USER/misc/meam_sw_spline directory. +in the examples/USER-MISC/meam_sw_spline directory. ---------- @@ -131,7 +131,7 @@ info. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair_style meam/c `, +:doc:`pair_coeff `, :doc:`pair_style meam `, :doc:`pair_style meam/spline ` Default diff --git a/doc/src/pair_mesocnt.rst b/doc/src/pair_mesocnt.rst index 90b6644fd9..ca461aee7a 100644 --- a/doc/src/pair_mesocnt.rst +++ b/doc/src/pair_mesocnt.rst @@ -122,7 +122,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This style is part of the USER-MESONT package. It is only +This style is part of the MESONT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This pair potential requires the :doc:`newton ` setting to be diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index 6bb259a10d..567c14f0ea 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -238,7 +238,7 @@ Example scripts """"""""""""""" There are example scripts for using all these pair styles in -examples/USER/mesodpd. The example for an eDPD simulation models heat +examples/PACKAGES/mesodpd. The example for an eDPD simulation models heat conduction with source terms analog of periodic Poiseuille flow problem. The setup follows Fig.12 in :ref:`(Li2014_JCP) `. The output of the short eDPD simulation (about 2 minutes on a single core) @@ -299,7 +299,7 @@ Restrictions """""""""""" The pair styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* are part of -the USER-MESODPD package. It is only enabled if LAMMPS was built with +the DPD-MESO package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_mesont_tpm.rst b/doc/src/pair_mesont_tpm.rst index d698dddd92..efdb70baf0 100644 --- a/doc/src/pair_mesont_tpm.rst +++ b/doc/src/pair_mesont_tpm.rst @@ -132,7 +132,7 @@ Restrictions """""""""""" -This pair style is a part of the USER-MSEONT package, and it is only enabled if +This pair style is a part of the MSEONT package, and it is only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more information. diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 673c5f5160..ea6621a3fd 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -132,7 +132,7 @@ range for each potential and give appropriate references for the potentials. It is expected that MGPT potentials for additional materials will be added over time. -Useful example MGPT scripts are given in the examples/USER/mgpt +Useful example MGPT scripts are given in the examples/PACKAGES/mgpt directory. These scripts show the necessary steps to perform constant-volume calculations and simulations. It is strongly recommended that the user work through and understand these examples @@ -168,7 +168,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This pair style is part of the USER-MGPT package and is only enabled +This pair style is part of the MGPT package and is only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more info. The MGPT potentials require the :doc:`newtion ` setting to be diff --git a/doc/src/pair_mliap.rst b/doc/src/pair_mliap.rst index 73ebe48856..199f23e1b2 100644 --- a/doc/src/pair_mliap.rst +++ b/doc/src/pair_mliap.rst @@ -192,11 +192,11 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This pair style is part of the MLIAP package. It is only enabled if +This pair style is part of the ML-IAP package. It is only enabled if LAMMPS was built with that package. In addition, building LAMMPS with -the MLIAP package requires building LAMMPS with the SNAP package. The -*mliappy* model requires building LAMMPS with the PYTHON package. See -the :doc:`Build package ` doc page for more info. +the ML-IAP package requires building LAMMPS with the ML-SNAP package. +The *mliappy* model requires building LAMMPS with the PYTHON package. +See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index b8969c0131..9c021e60a4 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -256,7 +256,7 @@ and *coul* settings to different values. .. note:: The *special* keyword is not compatible with pair styles from the - GPU or the USER-INTEL package and attempting to use it will cause + GPU or the INTEL package and attempting to use it will cause an error. .. note:: @@ -289,7 +289,7 @@ Restrictions You cannot use *shift* yes with *tail* yes, since those are conflicting options. You cannot use *tail* yes with 2d simulations. You cannot use *special* with pair styles from the GPU or -USER-INTEL package. +INTEL package. Related commands """""""""""""""" diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 5ede37a916..87638e16f4 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -86,7 +86,7 @@ the *morse* and *morse/smooth/linear* styles. ---------- A version of the *morse* style with a soft core, *morse/soft*\ , -suitable for use in free energy calculations, is part of the USER-FEP +suitable for use in free energy calculations, is part of the FEP package and is documented with the :doc:`pair_style */soft ` styles. The version with soft core is only available if LAMMPS was built with that package. See the :doc:`Build package diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index 111660c2bb..8f65d8f438 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -193,7 +193,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index f6e6652271..b39bd02b6d 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -225,7 +225,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index 4cc57868b4..b6b55a503b 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -91,15 +91,15 @@ for a detailed description of the oxDNA force field. or :doc:`fix nve/dotc/langevin ` the temperature coefficients have to be matched to the one used in the fix. -Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. +Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. +DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. Please cite :ref:`(Henrich) ` in any publication that uses this implementation. The article contains general information on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found -`here `_. +`here `_. Please cite also the relevant oxDNA publications :ref:`(Ouldridge) `, :ref:`(Ouldridge-DPhil) ` @@ -111,7 +111,7 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the +CG-DNA package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index ee01f2f488..37739c3813 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -100,15 +100,15 @@ and :ref:`(Ouldridge) ` for a detailed description of the oxDNA2 fo e.g. through :doc:`fix langevin ` or :doc:`fix nve/dotc/langevin ` the temperature coefficients have to be matched to the one used in the fix. -Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. +Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. +DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. Please cite :ref:`(Henrich) ` in any publication that uses this implementation. The article contains general information on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found -`here `_. +`here `_. Please cite also the relevant oxDNA2 publications :ref:`(Snodin) ` and :ref:`(Sulc) `. @@ -118,7 +118,7 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the +CG-DNA package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 831e4d9c4e..bd89f1fec0 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -101,15 +101,15 @@ and :ref:`(Ouldridge) ` for a detailed description of the oxRNA2 fo e.g. through :doc:`fix langevin ` or :doc:`fix nve/dotc/langevin ` the temperature coefficients have to be matched to the one used in the fix. -Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. +Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. +DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/. Please cite :ref:`(Henrich) ` in any publication that uses this implementation. The article contains general information on the model, its implementation and performance as well as the structure of the data and input file. The preprint version of the article can be found -`here `_. +`here `_. Please cite also the relevant oxRNA2 publications :ref:`(Sulc1) ` and :ref:`(Sulc2) `. @@ -119,7 +119,7 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the +CG-DNA package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst index 56ae0f32dc..e737072e7b 100644 --- a/doc/src/pair_pace.rst +++ b/doc/src/pair_pace.rst @@ -91,7 +91,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This pair style is part of the USER-PACE package. It is only enabled if LAMMPS +This pair style is part of the ML-PACE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index 43aa2eef62..5f520f3d03 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -55,7 +55,7 @@ appropriate initialization strings are also advised. The list of atomic numbers must be matched to the LAMMPS atom types specified in the LAMMPS data file or elsewhere. -Two examples input scripts are provided in the examples/USER/quip +Two examples input scripts are provided in the examples/PACKAGES/quip directory. Mixing, shift, table, tail correction, restart, rRESPA info @@ -75,7 +75,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This pair style is part of the USER-QUIP package. It is only enabled +This pair style is part of the ML-QUIP package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. QUIP potentials are parameterized in electron-volts and Angstroms and diff --git a/doc/src/pair_rann.rst b/doc/src/pair_rann.rst index 4177bae0c7..b02a81e4b8 100644 --- a/doc/src/pair_rann.rst +++ b/doc/src/pair_rann.rst @@ -378,7 +378,7 @@ The activation functions are computed as follows: Restrictions """""""""""" -Pair style *rann* is part of the USER-RANN package. It is only enabled if LAMMPS was built with that +Pair style *rann* is part of the ML-RANN package. It is only enabled if LAMMPS was built with that package. Additionally, if any spin fingerprint styles are used LAMMPS must be built with the SPIN package as well. diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index b28b387e0b..352bcb4847 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -332,7 +332,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This pair style is part of the USER-REAXC package. It is only enabled +This pair style is part of the REAXFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The ReaxFF potential files provided with LAMMPS in the potentials diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 541c53d37e..a89a833998 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -148,7 +148,7 @@ the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_styl Restrictions """""""""""" -All of the lj/sdk pair styles are part of the USER-CGSDK package. The +All of the lj/sdk pair styles are part of the CG-SDK package. The *lj/sdk/coul/long* style also requires the KSPACE package to be built (which is enabled by default). They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` diff --git a/doc/src/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst index b45ac31f63..15a4eb5374 100644 --- a/doc/src/pair_sdpd_taitwater_isothermal.rst +++ b/doc/src/pair_sdpd_taitwater_isothermal.rst @@ -97,7 +97,7 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" -This pair style is part of the USER-SDPD package. It is only enabled +This pair style is part of the DPD-SMOOTH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_smd_hertz.rst b/doc/src/pair_smd_hertz.rst index c15a8d26dc..a10edde6b0 100644 --- a/doc/src/pair_smd_hertz.rst +++ b/doc/src/pair_smd_hertz.rst @@ -41,7 +41,7 @@ approach each other. Usually, *scale_factor* =1.0. Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No mixing is performed automatically. Currently, no part of USER-SMD +No mixing is performed automatically. Currently, no part of MACHDYN supports restarting nor minimization. rRESPA does not apply to this pair style. @@ -50,7 +50,7 @@ pair style. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if +This fix is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_smd_tlsph.rst b/doc/src/pair_smd_tlsph.rst index bd46209cdc..cab156167e 100644 --- a/doc/src/pair_smd_tlsph.rst +++ b/doc/src/pair_smd_tlsph.rst @@ -56,7 +56,7 @@ complete listing of the possible keywords and material models. Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No mixing is performed automatically. Currently, no part of USER-SMD +No mixing is performed automatically. Currently, no part of MACHDYN supports restarting nor minimization. rRESPA does not apply to this pair style. @@ -65,7 +65,7 @@ pair style. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if +This fix is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 1e33254865..957ff1ca19 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -43,7 +43,7 @@ Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" No mixing is performed automatically. -Currently, no part of USER-SMD supports restarting nor minimization. +Currently, no part of MACHDYN supports restarting nor minimization. rRESPA does not apply to this pair style. ---------- @@ -51,7 +51,7 @@ rRESPA does not apply to this pair style. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if +This fix is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index 33946d4649..c69fbf2a43 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -67,7 +67,7 @@ complete listing of the possible keywords and material models. Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No mixing is performed automatically. Currently, no part of USER-SMD +No mixing is performed automatically. Currently, no part of MACHDYN supports restarting nor minimization. rRESPA does not apply to this pair style. @@ -76,7 +76,7 @@ pair style. Restrictions """""""""""" -This fix is part of the USER-SMD package. It is only enabled if +This fix is part of the MACHDYN package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst index 0f309869f0..96ccc5c4c7 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -284,7 +284,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This pair style is part of the USER-SMTBQ package and is only enabled +This pair style is part of the SMTBQ package and is only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more info. This potential requires using atom type 1 for oxygen and atom type diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 2de1b59dd4..5638087d78 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -24,32 +24,28 @@ Examples Description """"""""""" -Pair style *snap* defines the spectral -neighbor analysis potential (SNAP), a machine-learning -interatomic potential :ref:`(Thompson) `. -Like the GAP framework of Bartok et al. :ref:`(Bartok2010) `, -SNAP uses bispectrum components -to characterize the local neighborhood of each atom -in a very general way. The mathematical definition of the -bispectrum calculation and its derivatives w.r.t. atom positions -is identical to that used by :doc:`compute snap `, -which is used to fit SNAP potentials to *ab initio* energy, force, -and stress data. -In SNAP, the total energy is decomposed into a sum over -atom energies. The energy of atom *i* is -expressed as a weighted sum over bispectrum components. +Pair style *snap* defines the spectral neighbor analysis potential +(SNAP), a machine-learning interatomic potential :ref:`(Thompson) +`. Like the GAP framework of Bartok et +al. :ref:`(Bartok2010) `, SNAP uses bispectrum components +to characterize the local neighborhood of each atom in a very general +way. The mathematical definition of the bispectrum calculation and its +derivatives w.r.t. atom positions is identical to that used by +:doc:`compute snap `, which is used to fit SNAP +potentials to *ab initio* energy, force, and stress data. In SNAP, the +total energy is decomposed into a sum over atom energies. The energy of +atom *i* is expressed as a weighted sum over bispectrum components. .. math:: E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\mu_i}_0 + \sum_{k=1}^K \beta_k^{\mu_i} B_k^i where :math:`B_k^i` is the *k*\ -th bispectrum component of atom *i*\ , -and :math:`\beta_k^{\mu_i}` is the corresponding linear coefficient -that depends on :math:`\mu_i`, the SNAP element of atom *i*\ . The -number of bispectrum components used and their definitions -depend on the value of *twojmax* and other parameters -defined in the SNAP parameter file described below. -The bispectrum calculation is described in more detail +and :math:`\beta_k^{\mu_i}` is the corresponding linear coefficient that +depends on :math:`\mu_i`, the SNAP element of atom *i*\ . The number of +bispectrum components used and their definitions depend on the value of +*twojmax* and other parameters defined in the SNAP parameter file +described below. The bispectrum calculation is described in more detail in :doc:`compute sna/atom `. Note that unlike for other potentials, cutoffs for SNAP potentials are @@ -80,32 +76,28 @@ The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types 3 and 4 to the SNAP 'P' element. -If a SNAP mapping value is -specified as NULL, the mapping is not performed. -This can be used when a *snap* potential is used as part of the -*hybrid* pair style. The NULL values are placeholders for atom types -that will be used with other potentials. +If a SNAP mapping value is specified as NULL, the mapping is not +performed. This can be used when a *snap* potential is used as part of +the *hybrid* pair style. The NULL values are placeholders for atom +types that will be used with other potentials. -The name of the SNAP coefficient file usually ends in the -".snapcoeff" extension. It may contain coefficients -for many SNAP elements. The only requirement is that -each of the unique element names appearing in the -LAMMPS pair_coeff command appear exactly once in -the SNAP coefficient file. It is okay if the SNAP coefficient file -contains additional elements not in the pair_coeff command, -except when using *chemflag* (see below). -The name of the SNAP parameter file usually ends in the ".snapparam" -extension. It contains a small number -of parameters that define the overall form of the SNAP potential. -See the :doc:`pair_coeff ` doc page for alternate ways -to specify the path for these files. +The name of the SNAP coefficient file usually ends in the ".snapcoeff" +extension. It may contain coefficients for many SNAP elements. The only +requirement is that each of the unique element names appearing in the +LAMMPS pair_coeff command appear exactly once in the SNAP coefficient +file. It is okay if the SNAP coefficient file contains additional +elements not in the pair_coeff command, except when using *chemflag* +(see below). The name of the SNAP parameter file usually ends in the +".snapparam" extension. It contains a small number of parameters that +define the overall form of the SNAP potential. See the :doc:`pair_coeff +` doc page for alternate ways to specify the path for these +files. -Quite commonly, -SNAP potentials are combined with one or more other LAMMPS pair styles -using the *hybrid/overlay* pair style. As an example, the SNAP -tantalum potential provided in the LAMMPS potentials directory -combines the *snap* and *zbl* pair styles. It is invoked -by the following commands: +SNAP potentials are quite commonly combined with one or more other +LAMMPS pair styles using the *hybrid/overlay* pair style. As an +example, the SNAP tantalum potential provided in the LAMMPS potentials +directory combines the *snap* and *zbl* pair styles. It is invoked by +the following commands: .. code-block:: LAMMPS @@ -118,13 +110,13 @@ by the following commands: pair_coeff 1 1 zbl ${zblz} pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta -It is convenient to keep these commands in a separate file that can -be inserted in any LAMMPS input script using the :doc:`include ` +It is convenient to keep these commands in a separate file that can be +inserted in any LAMMPS input script using the :doc:`include ` command. -The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict -format after that. The first non-blank non-comment -line must contain two integers: +The top of the SNAP coefficient file can contain any number of blank and +comment lines (start with #), but follows a strict format after +that. The first non-blank non-comment line must contain two integers: * nelem = Number of elements * ncoeff = Number of coefficients @@ -157,39 +149,44 @@ The default values for these keywords are * *wselfallflag* = 0 * *chunksize* = 4096 -If *quadraticflag* is set to 1, then the SNAP energy expression includes additional quadratic terms -that have been shown to increase the overall accuracy of the potential without much increase -in computational cost :ref:`(Wood) `. +If *quadraticflag* is set to 1, then the SNAP energy expression includes +additional quadratic terms that have been shown to increase the overall +accuracy of the potential without much increase in computational cost +:ref:`(Wood) `. .. math:: E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \boldsymbol{\beta}^{\mu_i} \cdot \mathbf{B}_i + \frac{1}{2}\mathbf{B}^t_i \cdot \boldsymbol{\alpha}^{\mu_i} \cdot \mathbf{B}_i where :math:`\mathbf{B}_i` is the *K*-vector of bispectrum components, -:math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear coefficients -for element :math:`\mu_i`, and :math:`\boldsymbol{\alpha}^{\mu_i}` -is the symmetric *K* by *K* matrix of quadratic coefficients. -The SNAP coefficient file should contain *K*\ (\ *K*\ +1)/2 additional coefficients -in each element block, the upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`. +:math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear +coefficients for element :math:`\mu_i`, and +:math:`\boldsymbol{\alpha}^{\mu_i}` is the symmetric *K* by *K* matrix +of quadratic coefficients. The SNAP coefficient file should contain +*K*\ (\ *K*\ +1)/2 additional coefficients in each element block, the +upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`. -If *chemflag* is set to 1, then the energy expression is written in terms of explicit multi-element bispectrum -components indexed on ordered triplets of elements, which has been shown to increase the ability of the SNAP -potential to capture energy differences in chemically complex systems, -at the expense of a significant increase in computational cost :ref:`(Cusentino) `. +If *chemflag* is set to 1, then the energy expression is written in +terms of explicit multi-element bispectrum components indexed on ordered +triplets of elements, which has been shown to increase the ability of +the SNAP potential to capture energy differences in chemically complex +systems, at the expense of a significant increase in computational cost +:ref:`(Cusentino) `. .. math:: E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \sum_{\kappa,\lambda,\mu} \boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i} \cdot \mathbf{B}^{\kappa\lambda\mu}_i -where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of bispectrum components -for neighbors of elements :math:`\kappa`, :math:`\lambda`, and :math:`\mu` and -:math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the corresponding *K*-vector -of linear coefficients for element :math:`\mu_i`. The SNAP coefficient file should contain -a total of :math:`K N_{elem}^3` coefficients in each element block, -where :math:`N_{elem}` is the number of elements in the SNAP coefficient file, -which must equal the number of unique elements appearing in the -LAMMPS pair_coeff command, to avoid ambiguity in the -number of coefficients. +where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of +bispectrum components for neighbors of elements :math:`\kappa`, +:math:`\lambda`, and :math:`\mu` and +:math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the +corresponding *K*-vector of linear coefficients for element +:math:`\mu_i`. The SNAP coefficient file should contain a total of +:math:`K N_{elem}^3` coefficients in each element block, where +:math:`N_{elem}` is the number of elements in the SNAP coefficient file, +which must equal the number of unique elements appearing in the LAMMPS +pair_coeff command, to avoid ambiguity in the number of coefficients. The keyword *chunksize* is only applicable when using the pair style *snap* with the KOKKOS package and is ignored otherwise. @@ -221,9 +218,10 @@ specify a pair_coeff command with I != J arguments for this style. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. -This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. +This pair style does not write its information to :doc:`binary restart +files `, since it is stored in potential files. Thus, you need +to re-specify the pair_style and pair_coeff commands in an input script +that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the @@ -238,8 +236,9 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This style is part of the SNAP package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +This style is part of the ML-SNAP package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst index 404a99e785..6568fbe5f0 100644 --- a/doc/src/pair_sph_heatconduction.rst +++ b/doc/src/pair_sph_heatconduction.rst @@ -54,7 +54,7 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" -This pair style is part of the USER-SPH package. It is only enabled +This pair style is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst index 74bc2d4f7e..84de28fdfd 100644 --- a/doc/src/pair_sph_idealgas.rst +++ b/doc/src/pair_sph_idealgas.rst @@ -63,7 +63,7 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" -This pair style is part of the USER-SPH package. It is only enabled +This pair style is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst index b678f3c149..3239dca507 100644 --- a/doc/src/pair_sph_lj.rst +++ b/doc/src/pair_sph_lj.rst @@ -61,7 +61,7 @@ Restrictions As noted above, the Lennard-Jones parameters epsilon and sigma are set to unity. -This pair style is part of the USER-SPH package. It is only enabled +This pair style is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst index 6d0cbeb133..4db3b1efa2 100644 --- a/doc/src/pair_sph_rhosum.rst +++ b/doc/src/pair_sph_rhosum.rst @@ -55,7 +55,7 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" -This pair style is part of the USER-SPH package. It is only enabled +This pair style is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst index b06d15579a..77739e09fa 100644 --- a/doc/src/pair_sph_taitwater.rst +++ b/doc/src/pair_sph_taitwater.rst @@ -67,7 +67,7 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" -This pair style is part of the USER-SPH package. It is only enabled +This pair style is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst index f26a5db356..f21b8d2b9d 100644 --- a/doc/src/pair_sph_taitwater_morris.rst +++ b/doc/src/pair_sph_taitwater_morris.rst @@ -66,7 +66,7 @@ This style can only be used via the *pair* keyword of the :doc:`run_style respa Restrictions """""""""""" -This pair style is part of the USER-SPH package. It is only enabled +This pair style is part of the SPH package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index 59df8be1e2..05168ce1ba 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -49,7 +49,7 @@ acts between pairs of bonds. This potential is useful for preventing bonds from passing through one another when a soft non-bonded potential acts between beads in, for example, DPD polymer chains. An example input script that uses this command is provided in -examples/USER/srp. +examples/PACKAGES/srp. Bonds of specified type *btype* interact with one another through a bond-pairwise potential, such that the force on bond *i* due to bond diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 1f023a7312..99ed142af6 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -255,7 +255,7 @@ accelerated styles exist. * :doc:`lubricateU/poly ` - hydrodynamic lubrication forces for Fast Lubrication with polydispersity * :doc:`mdpd ` - mDPD particle interactions * :doc:`mdpd/rhosum ` - mDPD particle interactions for mass density -* :doc:`meam/c ` - modified embedded atom method (MEAM) in C +* :doc:`meam ` - modified embedded atom method (MEAM) in C * :doc:`meam/spline ` - splined version of MEAM * :doc:`meam/sw/spline ` - splined version of MEAM with a Stillinger-Weber term * :doc:`mesocnt ` - mesoscale model for (carbon) nanotubes diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index bea417ed3d..a4b39be3c9 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -166,15 +166,15 @@ hardware, as discussed on the :doc:`Speed packages ` doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if +These accelerated styles are part of the GPU, INTEL, KOKKOS, +OPENMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the :doc:`suffix ` command in your input script. -When using the USER-INTEL package with this style, there is an +When using the INTEL package with this style, there is an additional 5 to 10 percent performance improvement when the Stillinger-Weber parameters p and q are set to 4 and 0 respectively. These parameters are common for modeling silicon and water. diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index 9d23a479a3..1c860b90ad 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -232,7 +232,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This command is part of the USER-DPD package. It is only enabled if +This command is part of the DPD-REACT package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index 183bab48c9..68966a3d9b 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -42,7 +42,7 @@ Examples pair_style lj/cut/thole/long 2.6 12.0 -Example input scripts available: examples/USER/drude +Example input scripts available: examples/PACKAGES/drude Description """"""""""" @@ -155,7 +155,7 @@ are defined using Restrictions """""""""""" -These pair styles are part of the USER-DRUDE package. They are only +These pair styles are part of the DRUDE package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This pair_style should currently not be used with the :doc:`charmm dihedral style ` if the latter has non-zero 1-4 weighting diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index f9a8c87c86..5a51e9ad7a 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -121,7 +121,7 @@ formatted dump files. These formats take no additional values. The *molfile* format supports reading data through using the `VMD `_ molfile plugin interface. This dump reader format is only available, -if the USER-MOLFILE package has been installed when compiling +if the MOLFILE package has been installed when compiling LAMMPS. The *molfile* format takes one or two additional values. The *style* @@ -188,7 +188,7 @@ you must set the *box* flag to *no*\ . See details below. For the *molfile* format, reading simulation box information is typically supported, but the location of the simulation box origin is lost and no explicit information about periodicity or -orthogonal/triclinic box shape is available. The USER-MOLFILE package +orthogonal/triclinic box shape is available. The MOLFILE package makes a best effort to guess based on heuristics, but this may not always work perfectly. @@ -376,12 +376,12 @@ To read gzipped dump files, you must compile LAMMPS with the -DLAMMPS_GZIP option. See the :doc:`Build settings ` doc page for details. -The *molfile* dump file formats are part of the USER-MOLFILE package. +The *molfile* dump file formats are part of the MOLFILE package. They are only enabled if LAMMPS was built with that packages. See the :doc:`Build package ` doc page for more info. To write and read adios .bp files, you must compile LAMMPS with the -:ref:`USER-ADIOS ` package. +:ref:`ADIOS ` package. Related commands """""""""""""""" diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index 713fedae70..3cb5e28597 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -308,7 +308,7 @@ Restrictions The *verlet/split* style can only be used if LAMMPS was built with the REPLICA package. Correspondingly the *respa/omp* style is available -only if the USER-OMP package was included. See the :doc:`Build package ` doc page for more info. +only if the OPENMP package was included. See the :doc:`Build package ` doc page for more info. Whenever using rRESPA, the user should experiment with trade-offs in speed and accuracy for their system, and verify that they are diff --git a/doc/src/set.rst b/doc/src/set.rst index 420190f0fd..28ab2d6d0b 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -446,12 +446,12 @@ to using SPH in LAMMPS. Keyword *smd/mass/density* sets the mass of all selected particles, but it is only applicable to the Smooth Mach Dynamics package -USER-SMD. It assumes that the particle volume has already been +MACHDYN. It assumes that the particle volume has already been correctly set and calculates particle mass from the provided mass density value. Keyword *smd/contact/radius* only applies to simulations with the -Smooth Mach Dynamics package USER-SMD. Itsets an interaction radius +Smooth Mach Dynamics package MACHDYN. Itsets an interaction radius for computing short-range interactions, e.g. repulsive forces to prevent different individual physical bodies from penetrating each other. Note that the SPH smoothing kernel diameter used for computing @@ -459,7 +459,7 @@ long range, nonlocal interactions, is set using the *diameter* keyword. Keyword *dpd/theta* sets the internal temperature of a DPD particle as -defined by the USER-DPD package. If the specified value is a number +defined by the DPD-REACT package. If the specified value is a number it must be >= 0.0. If the specified value is NULL, then the kinetic temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 m v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz). Each particle's internal @@ -470,13 +470,13 @@ value >= 0.0, the internal temperature is set to that value. If it is temperature is set to that value. Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric -heat capacity of an eDPD particle as defined by the USER-MESODPD package. +heat capacity of an eDPD particle as defined by the DPD-MESO package. Currently, only :doc:`atom_style edpd ` defines particles with these attributes. The values for the temperature and heat capacity must be positive. Keyword *cc* sets the chemical concentration of a tDPD particle for a -specified species as defined by the USER-MESODPD package. Currently, only +specified species as defined by the DPD-MESO package. Currently, only :doc:`atom_style tdpd ` defines particles with this attribute. An integer for "index" selects a chemical species (1 to Nspecies) where Nspecies is set by the atom_style command. The value diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst index 9df3ce1658..1ece739f55 100644 --- a/doc/src/suffix.rst +++ b/doc/src/suffix.rst @@ -36,21 +36,21 @@ The specified style can be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt* or *hybrid*\ . These refer to optional packages that LAMMPS can be built with, as described on the :doc:`Build package ` doc page. The "gpu" style corresponds to the GPU package, the "intel" style to -the USER-INTEL package, the "kk" style to the KOKKOS package, the -"omp" style to the USER-OMP package, and the "opt" style to the OPT +the INTEL package, the "kk" style to the KOKKOS package, the +"omp" style to the OPENMP package, and the "opt" style to the OPT package. These are the variants these packages provide: * GPU = a handful of pair styles and the PPPM kspace_style, optimized to run on one or more GPUs or multicore CPU/GPU nodes -* USER-INTEL = a collection of pair styles and neighbor routines +* INTEL = a collection of pair styles and neighbor routines optimized to run in single, mixed, or double precision on CPUs and Intel(R) Xeon Phi(TM) co-processors. * KOKKOS = a collection of atom, pair, and fix styles optimized to run using the Kokkos library on various kinds of hardware, including GPUs via CUDA and many-core chips via OpenMP or threading. -* USER-OMP = a collection of pair, bond, angle, dihedral, improper, +* OPENMP = a collection of pair, bond, angle, dihedral, improper, kspace, compute, and fix styles with support for OpenMP multi-threading * OPT = a handful of pair styles, cache-optimized for faster CPU @@ -74,9 +74,9 @@ created. For "hybrid", two packages are specified. The first is used whenever available. If a style with the first suffix is not available, the style with the suffix for the second package will be used if available. For -example, "hybrid intel omp" will use styles from the USER-INTEL package -as a first choice and styles from the USER-OMP package as a second choice -if no USER-INTEL variant is available. +example, "hybrid intel omp" will use styles from the INTEL package +as a first choice and styles from the OPENMP package as a second choice +if no INTEL variant is available. If the specified style is *off*\ , then any previously specified suffix is temporarily disabled, whether it was specified by a command-line diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst index 2a6de933e0..513d96b9e8 100644 --- a/doc/src/third_order.rst +++ b/doc/src/third_order.rst @@ -55,7 +55,7 @@ Restrictions The command collects a 9 times the number of atoms in the group on every single MPI rank, so the memory requirements can be very significant for large systems. -This command is part of the USER-PHONON package. It is only enabled if +This command is part of the PHONON package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/variable.rst b/doc/src/variable.rst index ef876847d6..f24c262e58 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -943,7 +943,7 @@ features or LAMMPS, *respa* allows to check whether the inner/middle/outer mode of r-RESPA is supported. In the various style categories, the checking is also done using suffix flags, if available and enabled. -Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP). +Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with OPENMP). .. code-block:: LAMMPS diff --git a/doc/utils/check-packages.py b/doc/utils/check-packages.py index 339d584c59..cb64259f15 100755 --- a/doc/utils/check-packages.py +++ b/doc/utils/check-packages.py @@ -41,12 +41,10 @@ if not os.path.isdir(doc_dir): pkgdirs = glob(os.path.join(src_dir, '[A-Z][A-Z]*')) dirs = re.compile(".*/([0-9A-Z-]+)$") -user = re.compile("USER-.*") -stdpkg = [] -usrpkg = [] +pkgs = [] -# find package names and add to standard and user package lists. +# find package names and add package list. # anything starting with at least two upper case characters, is a # folder, and is not called 'MAKE' is a package @@ -54,47 +52,29 @@ for d in pkgdirs: pkg = dirs.match(d).group(1) if not os.path.isdir(os.path.join(src_dir, pkg)): continue if pkg in ['DEPEND','MAKE','STUBS']: continue - if user.match(pkg): - usrpkg.append(pkg) - else: - stdpkg.append(pkg) + pkgs.append(pkg) -print(f"Found {len(stdpkg)} standard and {len(usrpkg)} user packages") +print(f"Found {len(pkgs)} packages") counter = 0 -with open(os.path.join(doc_dir, 'Packages_standard.rst')) as fp: +with open(os.path.join(doc_dir, 'Packages_list.rst')) as fp: text = fp.read() matches = set(re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`', text, re.MULTILINE)) -for p in stdpkg: +for p in pkgs: if not p in matches: counter += 1 - print(f"Standard package {p} missing in Packages_standard.rst") - -with open(os.path.join(doc_dir, 'Packages_user.rst')) as fp: - text = fp.read() - -matches = set(re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`', text, re.MULTILINE)) -for p in usrpkg: - if not p in matches: - counter += 1 - print(f"User package {p} missing in Packages_user.rst") + print(f"Package {p} missing in Packages_list.rst") with open(os.path.join(doc_dir, 'Packages_details.rst')) as fp: text = fp.read() -matches = set(re.findall(':ref:`([A-Z0-9]+) `', text, re.MULTILINE)) -for p in stdpkg: +matches = set(re.findall(':ref:`([A-Z0-9-]+) `', text, re.MULTILINE)) +for p in pkgs: if not p in matches: counter += 1 - print(f"Standard package {p} missing in Packages_details.rst") - -matches = set(re.findall(':ref:`(USER-[A-Z0-9]+) `', text, re.MULTILINE)) -for p in usrpkg: - if not p in matches: - counter +=1 - print(f"User package {p} missing in Packages_details.rst") + print(f"Package {p} missing in Packages_details.rst") if counter: print(f"Found {counter} issue(s) with package lists") diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index f9a7d3e39a..16a7cf2a5c 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -267,9 +267,9 @@ counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) `", counter += check_style('fix.rst', doc_dir, ":doc:`(.+) ` -", fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=False) counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) `", - pair,'Pair',skip=('meam','lj/sf'),suffix=True) + pair,'Pair',skip=('meam/c','lj/sf'),suffix=True) counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) ` -", - pair,'Pair',skip=('meam','lj/sf'),suffix=False) + pair,'Pair',skip=('meam/c','lj/sf'),suffix=False) counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `", bond,'Bond',suffix=True) counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) ` -", @@ -301,7 +301,7 @@ counter += check_style_index("bond_style", bond, index["bond_style"]) counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"]) counter += check_style_index("improper_style", improper, index["improper_style"]) counter += check_style_index("kspace_style", kspace, index["kspace_style"]) -counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam', 'lj/sf']) +counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf']) if counter: print(f"Found {counter} issue(s) with style index") diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 99538ff8ee..e57f81dbc8 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1325,6 +1325,7 @@ hyperradius hyperspherical hysteretic hz +IAP Ibanez iatom ibar @@ -1647,6 +1648,8 @@ larentzos Larentzos Laroche lars +LATBOLTZ +latboltz latencies Latour latourr @@ -1797,6 +1800,8 @@ Lysogorskiy Lyulin lz Maaravi +MACHDYN +machdyn Mackay Mackrodt Macromolecules @@ -1891,8 +1896,7 @@ mdi mdpd mDPD meam -meamc -MEAMC +MEAM meamf meanDist mech @@ -2736,7 +2740,7 @@ README realtime reamin reax -REAXC +REAXFF ReaxFF rebo recursing diff --git a/examples/USER/adios/balance/adios2_config.xml b/examples/PACKAGES/adios/balance/adios2_config.xml similarity index 100% rename from examples/USER/adios/balance/adios2_config.xml rename to examples/PACKAGES/adios/balance/adios2_config.xml diff --git a/examples/USER/adios/balance/in.adios_balance b/examples/PACKAGES/adios/balance/in.adios_balance similarity index 100% rename from examples/USER/adios/balance/in.adios_balance rename to examples/PACKAGES/adios/balance/in.adios_balance diff --git a/examples/USER/adios/balance/in.adios_balance2 b/examples/PACKAGES/adios/balance/in.adios_balance2 similarity index 100% rename from examples/USER/adios/balance/in.adios_balance2 rename to examples/PACKAGES/adios/balance/in.adios_balance2 diff --git a/examples/USER/adios/balance/log.balance b/examples/PACKAGES/adios/balance/log.balance similarity index 100% rename from examples/USER/adios/balance/log.balance rename to examples/PACKAGES/adios/balance/log.balance diff --git a/examples/USER/adios/rerun/README b/examples/PACKAGES/adios/rerun/README similarity index 100% rename from examples/USER/adios/rerun/README rename to examples/PACKAGES/adios/rerun/README diff --git a/examples/USER/adios/rerun/adios2_config.xml b/examples/PACKAGES/adios/rerun/adios2_config.xml similarity index 100% rename from examples/USER/adios/rerun/adios2_config.xml rename to examples/PACKAGES/adios/rerun/adios2_config.xml diff --git a/examples/USER/adios/rerun/in.first b/examples/PACKAGES/adios/rerun/in.first similarity index 100% rename from examples/USER/adios/rerun/in.first rename to examples/PACKAGES/adios/rerun/in.first diff --git a/examples/USER/adios/rerun/in.read_dump b/examples/PACKAGES/adios/rerun/in.read_dump similarity index 100% rename from examples/USER/adios/rerun/in.read_dump rename to examples/PACKAGES/adios/rerun/in.read_dump diff --git a/examples/USER/adios/rerun/in.rerun b/examples/PACKAGES/adios/rerun/in.rerun similarity index 100% rename from examples/USER/adios/rerun/in.rerun rename to examples/PACKAGES/adios/rerun/in.rerun diff --git a/examples/USER/adios/rerun/log.20Jan20.first.g++.7.4 b/examples/PACKAGES/adios/rerun/log.20Jan20.first.g++.7.4 similarity index 100% rename from examples/USER/adios/rerun/log.20Jan20.first.g++.7.4 rename to examples/PACKAGES/adios/rerun/log.20Jan20.first.g++.7.4 diff --git a/examples/USER/adios/rerun/log.20Jan20.read_dump.g++.7.4 b/examples/PACKAGES/adios/rerun/log.20Jan20.read_dump.g++.7.4 similarity index 100% rename from examples/USER/adios/rerun/log.20Jan20.read_dump.g++.7.4 rename to examples/PACKAGES/adios/rerun/log.20Jan20.read_dump.g++.7.4 diff --git a/examples/USER/adios/rerun/log.20Jan20.rerun.g++.7.4 b/examples/PACKAGES/adios/rerun/log.20Jan20.rerun.g++.7.4 similarity index 100% rename from examples/USER/adios/rerun/log.20Jan20.rerun.g++.7.4 rename to examples/PACKAGES/adios/rerun/log.20Jan20.rerun.g++.7.4 diff --git a/examples/USER/atc/README b/examples/PACKAGES/atc/README similarity index 100% rename from examples/USER/atc/README rename to examples/PACKAGES/atc/README diff --git a/examples/USER/atc/cauchy_born/Ar_CauchyBorn.mat b/examples/PACKAGES/atc/cauchy_born/Ar_CauchyBorn.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Ar_CauchyBorn.mat rename to examples/PACKAGES/atc/cauchy_born/Ar_CauchyBorn.mat diff --git a/examples/USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat b/examples/PACKAGES/atc/cauchy_born/Ar_CauchyBorn_linear.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat rename to examples/PACKAGES/atc/cauchy_born/Ar_CauchyBorn_linear.mat diff --git a/examples/USER/atc/cauchy_born/Au_CauchyBorn.mat b/examples/PACKAGES/atc/cauchy_born/Au_CauchyBorn.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Au_CauchyBorn.mat rename to examples/PACKAGES/atc/cauchy_born/Au_CauchyBorn.mat diff --git a/examples/USER/atc/cauchy_born/Au_CauchyBorn_linear.mat b/examples/PACKAGES/atc/cauchy_born/Au_CauchyBorn_linear.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Au_CauchyBorn_linear.mat rename to examples/PACKAGES/atc/cauchy_born/Au_CauchyBorn_linear.mat diff --git a/examples/USER/atc/cauchy_born/Au_eam.mat b/examples/PACKAGES/atc/cauchy_born/Au_eam.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Au_eam.mat rename to examples/PACKAGES/atc/cauchy_born/Au_eam.mat diff --git a/examples/USER/atc/cauchy_born/Au_eam_linear.mat b/examples/PACKAGES/atc/cauchy_born/Au_eam_linear.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Au_eam_linear.mat rename to examples/PACKAGES/atc/cauchy_born/Au_eam_linear.mat diff --git a/examples/USER/atc/cauchy_born/Au_u3.eam b/examples/PACKAGES/atc/cauchy_born/Au_u3.eam similarity index 100% rename from examples/USER/atc/cauchy_born/Au_u3.eam rename to examples/PACKAGES/atc/cauchy_born/Au_u3.eam diff --git a/examples/USER/atc/cauchy_born/Cu_CauchyBorn.mat b/examples/PACKAGES/atc/cauchy_born/Cu_CauchyBorn.mat similarity index 100% rename from examples/USER/atc/cauchy_born/Cu_CauchyBorn.mat rename to examples/PACKAGES/atc/cauchy_born/Cu_CauchyBorn.mat diff --git a/examples/USER/atc/cauchy_born/cb_biaxial.screen b/examples/PACKAGES/atc/cauchy_born/cb_biaxial.screen similarity index 100% rename from examples/USER/atc/cauchy_born/cb_biaxial.screen rename to examples/PACKAGES/atc/cauchy_born/cb_biaxial.screen diff --git a/examples/USER/atc/cauchy_born/cb_shear.screen b/examples/PACKAGES/atc/cauchy_born/cb_shear.screen similarity index 100% rename from examples/USER/atc/cauchy_born/cb_shear.screen rename to examples/PACKAGES/atc/cauchy_born/cb_shear.screen diff --git a/examples/USER/atc/cauchy_born/cb_unistrain.screen b/examples/PACKAGES/atc/cauchy_born/cb_unistrain.screen similarity index 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a/examples/USER/atc/elastic/in.bar1d_flux b/examples/PACKAGES/atc/elastic/in.bar1d_flux similarity index 100% rename from examples/USER/atc/elastic/in.bar1d_flux rename to examples/PACKAGES/atc/elastic/in.bar1d_flux diff --git a/examples/USER/atc/elastic/in.bar1d_frac_step b/examples/PACKAGES/atc/elastic/in.bar1d_frac_step similarity index 100% rename from examples/USER/atc/elastic/in.bar1d_frac_step rename to examples/PACKAGES/atc/elastic/in.bar1d_frac_step diff --git a/examples/USER/atc/elastic/in.bar1d_ghost_flux b/examples/PACKAGES/atc/elastic/in.bar1d_ghost_flux similarity index 100% rename from examples/USER/atc/elastic/in.bar1d_ghost_flux rename to examples/PACKAGES/atc/elastic/in.bar1d_ghost_flux diff --git a/examples/USER/atc/elastic/in.bar1d_thermo_elastic b/examples/PACKAGES/atc/elastic/in.bar1d_thermo_elastic similarity index 100% rename from examples/USER/atc/elastic/in.bar1d_thermo_elastic rename to examples/PACKAGES/atc/elastic/in.bar1d_thermo_elastic diff --git a/examples/USER/atc/elastic/in.eam_energy b/examples/PACKAGES/atc/elastic/in.eam_energy similarity index 100% rename from examples/USER/atc/elastic/in.eam_energy rename to examples/PACKAGES/atc/elastic/in.eam_energy diff --git a/examples/USER/atc/elastic/in.electron_density b/examples/PACKAGES/atc/elastic/in.electron_density similarity index 100% rename from examples/USER/atc/elastic/in.electron_density rename to examples/PACKAGES/atc/elastic/in.electron_density diff --git a/examples/USER/atc/elastic/in.no_atoms b/examples/PACKAGES/atc/elastic/in.no_atoms similarity index 100% rename from examples/USER/atc/elastic/in.no_atoms rename to examples/PACKAGES/atc/elastic/in.no_atoms diff --git a/examples/USER/atc/elastic/in.no_atoms_cb b/examples/PACKAGES/atc/elastic/in.no_atoms_cb similarity index 100% rename from examples/USER/atc/elastic/in.no_atoms_cb rename to examples/PACKAGES/atc/elastic/in.no_atoms_cb diff --git a/examples/USER/atc/elastic/in.no_atoms_cb_linear 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a/examples/USER/atc/elastic/temp.init b/examples/PACKAGES/atc/elastic/temp.init similarity index 100% rename from examples/USER/atc/elastic/temp.init rename to examples/PACKAGES/atc/elastic/temp.init diff --git a/examples/USER/atc/fluids/Ar_elastic.mat b/examples/PACKAGES/atc/fluids/Ar_elastic.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_elastic.mat rename to examples/PACKAGES/atc/fluids/Ar_elastic.mat diff --git a/examples/USER/atc/fluids/Ar_electrostatic.mat b/examples/PACKAGES/atc/fluids/Ar_electrostatic.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_electrostatic.mat rename to examples/PACKAGES/atc/fluids/Ar_electrostatic.mat diff --git a/examples/USER/atc/fluids/Ar_liquid.mat b/examples/PACKAGES/atc/fluids/Ar_liquid.mat similarity index 100% rename from examples/USER/atc/fluids/Ar_liquid.mat rename to examples/PACKAGES/atc/fluids/Ar_liquid.mat diff --git a/examples/USER/atc/fluids/Ar_species.mat b/examples/PACKAGES/atc/fluids/Ar_species.mat 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similarity index 100% rename from examples/USER/atc/fluids/in.bar1d_fluids rename to examples/PACKAGES/atc/fluids/in.bar1d_fluids diff --git a/examples/USER/atc/fluids/in.concentration b/examples/PACKAGES/atc/fluids/in.concentration similarity index 100% rename from examples/USER/atc/fluids/in.concentration rename to examples/PACKAGES/atc/fluids/in.concentration diff --git a/examples/USER/atc/fluids/in.conducting_interface b/examples/PACKAGES/atc/fluids/in.conducting_interface similarity index 100% rename from examples/USER/atc/fluids/in.conducting_interface rename to examples/PACKAGES/atc/fluids/in.conducting_interface diff --git a/examples/USER/atc/fluids/in.dielectric_interface b/examples/PACKAGES/atc/fluids/in.dielectric_interface similarity index 100% rename from examples/USER/atc/fluids/in.dielectric_interface rename to examples/PACKAGES/atc/fluids/in.dielectric_interface diff --git a/examples/USER/atc/fluids/in.double_layer b/examples/PACKAGES/atc/fluids/in.double_layer similarity index 100% rename from examples/USER/atc/fluids/in.double_layer rename to examples/PACKAGES/atc/fluids/in.double_layer diff --git a/examples/USER/atc/fluids/in.liquid_electrostatic b/examples/PACKAGES/atc/fluids/in.liquid_electrostatic similarity index 100% rename from examples/USER/atc/fluids/in.liquid_electrostatic rename to examples/PACKAGES/atc/fluids/in.liquid_electrostatic diff --git a/examples/USER/atc/fluids/in.opp_force b/examples/PACKAGES/atc/fluids/in.opp_force similarity index 100% rename from examples/USER/atc/fluids/in.opp_force rename to examples/PACKAGES/atc/fluids/in.opp_force diff --git a/examples/USER/atc/fluids/in.poisson b/examples/PACKAGES/atc/fluids/in.poisson similarity index 100% rename from examples/USER/atc/fluids/in.poisson rename to examples/PACKAGES/atc/fluids/in.poisson diff --git a/examples/USER/atc/fluids/in.shear_flow b/examples/PACKAGES/atc/fluids/in.shear_flow similarity index 100% rename from examples/USER/atc/fluids/in.shear_flow rename to examples/PACKAGES/atc/fluids/in.shear_flow diff --git a/examples/USER/atc/fluids/in.shear_no_atoms b/examples/PACKAGES/atc/fluids/in.shear_no_atoms similarity index 100% rename from examples/USER/atc/fluids/in.shear_no_atoms rename to examples/PACKAGES/atc/fluids/in.shear_no_atoms diff --git a/examples/USER/atc/fluids/interface_init.data b/examples/PACKAGES/atc/fluids/interface_init.data similarity index 100% rename from examples/USER/atc/fluids/interface_init.data rename to examples/PACKAGES/atc/fluids/interface_init.data diff --git a/examples/USER/atc/fluids/liquid_electrostatic.screen b/examples/PACKAGES/atc/fluids/liquid_electrostatic.screen similarity index 100% rename from examples/USER/atc/fluids/liquid_electrostatic.screen rename to examples/PACKAGES/atc/fluids/liquid_electrostatic.screen diff --git a/examples/USER/atc/fluids/opp_force.screen b/examples/PACKAGES/atc/fluids/opp_force.screen similarity index 100% rename from examples/USER/atc/fluids/opp_force.screen rename to examples/PACKAGES/atc/fluids/opp_force.screen diff --git a/examples/USER/atc/fluids/poisson.screen b/examples/PACKAGES/atc/fluids/poisson.screen similarity index 100% rename from examples/USER/atc/fluids/poisson.screen rename to examples/PACKAGES/atc/fluids/poisson.screen diff --git a/examples/USER/atc/fluids/post_eq.init b/examples/PACKAGES/atc/fluids/post_eq.init similarity index 100% rename from examples/USER/atc/fluids/post_eq.init rename to examples/PACKAGES/atc/fluids/post_eq.init diff --git a/examples/USER/atc/fluids/shear_flow.screen b/examples/PACKAGES/atc/fluids/shear_flow.screen similarity index 100% rename from examples/USER/atc/fluids/shear_flow.screen rename to examples/PACKAGES/atc/fluids/shear_flow.screen diff --git a/examples/USER/atc/fluids/shear_no_atoms.screen b/examples/PACKAGES/atc/fluids/shear_no_atoms.screen similarity index 100% rename from examples/USER/atc/fluids/shear_no_atoms.screen rename to examples/PACKAGES/atc/fluids/shear_no_atoms.screen diff --git a/examples/USER/atc/fluids/temp.init b/examples/PACKAGES/atc/fluids/temp.init similarity index 100% rename from examples/USER/atc/fluids/temp.init rename to examples/PACKAGES/atc/fluids/temp.init diff --git a/examples/USER/atc/fluids/velocities.init b/examples/PACKAGES/atc/fluids/velocities.init similarity index 100% rename from examples/USER/atc/fluids/velocities.init rename to examples/PACKAGES/atc/fluids/velocities.init diff --git a/examples/USER/atc/fluids/waternve.atm b/examples/PACKAGES/atc/fluids/waternve.atm similarity index 100% rename from examples/USER/atc/fluids/waternve.atm rename to examples/PACKAGES/atc/fluids/waternve.atm diff --git a/examples/USER/atc/hardy/consistency.screen b/examples/PACKAGES/atc/hardy/consistency.screen similarity index 100% rename from examples/USER/atc/hardy/consistency.screen rename to examples/PACKAGES/atc/hardy/consistency.screen diff --git a/examples/USER/atc/hardy/eam_kernel_convergence.screen 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examples/PACKAGES/atc/hardy/eam_unistrain_qcylinder.screen diff --git a/examples/USER/atc/hardy/eam_unistrain_qsphere.screen b/examples/PACKAGES/atc/hardy/eam_unistrain_qsphere.screen similarity index 100% rename from examples/USER/atc/hardy/eam_unistrain_qsphere.screen rename to examples/PACKAGES/atc/hardy/eam_unistrain_qsphere.screen diff --git a/examples/USER/atc/hardy/eam_unistrain_step.screen b/examples/PACKAGES/atc/hardy/eam_unistrain_step.screen similarity index 100% rename from examples/USER/atc/hardy/eam_unistrain_step.screen rename to examples/PACKAGES/atc/hardy/eam_unistrain_step.screen diff --git a/examples/USER/atc/hardy/eam_volume_stretch.screen b/examples/PACKAGES/atc/hardy/eam_volume_stretch.screen similarity index 100% rename from examples/USER/atc/hardy/eam_volume_stretch.screen rename to examples/PACKAGES/atc/hardy/eam_volume_stretch.screen diff --git a/examples/USER/atc/hardy/eshelby_static.screen b/examples/PACKAGES/atc/hardy/eshelby_static.screen similarity index 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b/examples/PACKAGES/atc/hardy/in.eam_volume_stretch similarity index 100% rename from examples/USER/atc/hardy/in.eam_volume_stretch rename to examples/PACKAGES/atc/hardy/in.eam_volume_stretch diff --git a/examples/USER/atc/hardy/in.eshelby_static b/examples/PACKAGES/atc/hardy/in.eshelby_static similarity index 100% rename from examples/USER/atc/hardy/in.eshelby_static rename to examples/PACKAGES/atc/hardy/in.eshelby_static diff --git a/examples/USER/atc/hardy/in.nvt b/examples/PACKAGES/atc/hardy/in.nvt similarity index 100% rename from examples/USER/atc/hardy/in.nvt rename to examples/PACKAGES/atc/hardy/in.nvt diff --git a/examples/USER/atc/hardy/nvt.data b/examples/PACKAGES/atc/hardy/nvt.data similarity index 100% rename from examples/USER/atc/hardy/nvt.data rename to examples/PACKAGES/atc/hardy/nvt.data diff --git a/examples/USER/atc/hardy/nvt.init b/examples/PACKAGES/atc/hardy/nvt.init similarity index 100% rename from examples/USER/atc/hardy/nvt.init rename to 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a/examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_hex_uniform.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_hex_uniform.screen diff --git a/examples/USER/atc/mesh/gaussianIC2d_tet.screen b/examples/PACKAGES/atc/mesh/gaussianIC2d_tet.screen similarity index 100% rename from examples/USER/atc/mesh/gaussianIC2d_tet.screen rename to examples/PACKAGES/atc/mesh/gaussianIC2d_tet.screen diff --git a/examples/USER/atc/mesh/in.gaussianIC1d_hex b/examples/PACKAGES/atc/mesh/in.gaussianIC1d_hex similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC1d_hex rename to examples/PACKAGES/atc/mesh/in.gaussianIC1d_hex diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex b/examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC2d_hex rename to examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex20_uniform b/examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex20_uniform similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC2d_hex20_uniform rename to examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex20_uniform diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_hex27_uniform b/examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex27_uniform similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC2d_hex27_uniform rename to examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex27_uniform diff --git a/examples/USER/atc/mesh/in.gaussianIC2d_tet b/examples/PACKAGES/atc/mesh/in.gaussianIC2d_tet similarity index 100% rename from examples/USER/atc/mesh/in.gaussianIC2d_tet rename to examples/PACKAGES/atc/mesh/in.gaussianIC2d_tet diff --git a/examples/USER/atc/mesh/in.kernel2d_hex b/examples/PACKAGES/atc/mesh/in.kernel2d_hex similarity index 100% rename from examples/USER/atc/mesh/in.kernel2d_hex rename to examples/PACKAGES/atc/mesh/in.kernel2d_hex diff --git a/examples/USER/atc/mesh/in.kernel2d_tet b/examples/PACKAGES/atc/mesh/in.kernel2d_tet similarity index 100% rename from examples/USER/atc/mesh/in.kernel2d_tet rename to examples/PACKAGES/atc/mesh/in.kernel2d_tet diff --git a/examples/USER/atc/mesh/in.mesh2d_tet b/examples/PACKAGES/atc/mesh/in.mesh2d_tet similarity index 100% rename from examples/USER/atc/mesh/in.mesh2d_tet rename to examples/PACKAGES/atc/mesh/in.mesh2d_tet diff --git a/examples/USER/atc/mesh/in.semicircle b/examples/PACKAGES/atc/mesh/in.semicircle similarity index 100% rename from examples/USER/atc/mesh/in.semicircle rename to examples/PACKAGES/atc/mesh/in.semicircle diff --git a/examples/USER/atc/mesh/kernel2d_hex.screen b/examples/PACKAGES/atc/mesh/kernel2d_hex.screen similarity index 100% rename from examples/USER/atc/mesh/kernel2d_hex.screen rename to examples/PACKAGES/atc/mesh/kernel2d_hex.screen diff --git a/examples/USER/atc/mesh/kernel2d_tet.screen b/examples/PACKAGES/atc/mesh/kernel2d_tet.screen similarity index 100% rename from examples/USER/atc/mesh/kernel2d_tet.screen rename to examples/PACKAGES/atc/mesh/kernel2d_tet.screen diff --git a/examples/USER/atc/mesh/mesh2d_tet.screen b/examples/PACKAGES/atc/mesh/mesh2d_tet.screen similarity index 100% rename from examples/USER/atc/mesh/mesh2d_tet.screen rename to examples/PACKAGES/atc/mesh/mesh2d_tet.screen diff --git a/examples/USER/atc/mesh/semicircle.init b/examples/PACKAGES/atc/mesh/semicircle.init similarity index 100% rename from examples/USER/atc/mesh/semicircle.init rename to examples/PACKAGES/atc/mesh/semicircle.init diff --git a/examples/USER/atc/mesh/semicircle.screen b/examples/PACKAGES/atc/mesh/semicircle.screen similarity index 100% rename from examples/USER/atc/mesh/semicircle.screen rename to examples/PACKAGES/atc/mesh/semicircle.screen diff --git a/examples/USER/atc/mesh/si_semicircle.init 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a/examples/USER/atc/thermal/bar1d.screen b/examples/PACKAGES/atc/thermal/bar1d.screen similarity index 100% rename from examples/USER/atc/thermal/bar1d.screen rename to examples/PACKAGES/atc/thermal/bar1d.screen diff --git a/examples/USER/atc/thermal/bar1d_all_atoms.screen b/examples/PACKAGES/atc/thermal/bar1d_all_atoms.screen similarity index 100% rename from examples/USER/atc/thermal/bar1d_all_atoms.screen rename to examples/PACKAGES/atc/thermal/bar1d_all_atoms.screen diff --git a/examples/USER/atc/thermal/bar1d_combined.screen b/examples/PACKAGES/atc/thermal/bar1d_combined.screen similarity index 100% rename from examples/USER/atc/thermal/bar1d_combined.screen rename to examples/PACKAGES/atc/thermal/bar1d_combined.screen diff --git a/examples/USER/atc/thermal/bar1d_flux.screen b/examples/PACKAGES/atc/thermal/bar1d_flux.screen similarity index 100% rename from examples/USER/atc/thermal/bar1d_flux.screen rename to examples/PACKAGES/atc/thermal/bar1d_flux.screen diff --git a/examples/USER/atc/thermal/bar1d_frac_step.screen b/examples/PACKAGES/atc/thermal/bar1d_frac_step.screen similarity index 100% rename from examples/USER/atc/thermal/bar1d_frac_step.screen rename to examples/PACKAGES/atc/thermal/bar1d_frac_step.screen diff --git a/examples/USER/atc/thermal/bar1d_hoover.screen b/examples/PACKAGES/atc/thermal/bar1d_hoover.screen similarity index 100% rename from examples/USER/atc/thermal/bar1d_hoover.screen rename to examples/PACKAGES/atc/thermal/bar1d_hoover.screen diff --git a/examples/USER/atc/thermal/bar1d_interpolate.screen b/examples/PACKAGES/atc/thermal/bar1d_interpolate.screen similarity index 100% rename from examples/USER/atc/thermal/bar1d_interpolate.screen rename to examples/PACKAGES/atc/thermal/bar1d_interpolate.screen diff --git a/examples/USER/atc/thermal/bar1d_lumped.screen b/examples/PACKAGES/atc/thermal/bar1d_lumped.screen similarity index 100% rename from examples/USER/atc/thermal/bar1d_lumped.screen rename to 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a/examples/USER/atc/thermal/in.bar1d_frac_step b/examples/PACKAGES/atc/thermal/in.bar1d_frac_step similarity index 100% rename from examples/USER/atc/thermal/in.bar1d_frac_step rename to examples/PACKAGES/atc/thermal/in.bar1d_frac_step diff --git a/examples/USER/atc/thermal/in.bar1d_hoover b/examples/PACKAGES/atc/thermal/in.bar1d_hoover similarity index 100% rename from examples/USER/atc/thermal/in.bar1d_hoover rename to examples/PACKAGES/atc/thermal/in.bar1d_hoover diff --git a/examples/USER/atc/thermal/in.bar1d_interpolate b/examples/PACKAGES/atc/thermal/in.bar1d_interpolate similarity index 100% rename from examples/USER/atc/thermal/in.bar1d_interpolate rename to examples/PACKAGES/atc/thermal/in.bar1d_interpolate diff --git a/examples/USER/atc/thermal/in.bar1d_lumped b/examples/PACKAGES/atc/thermal/in.bar1d_lumped similarity index 100% rename from examples/USER/atc/thermal/in.bar1d_lumped rename to examples/PACKAGES/atc/thermal/in.bar1d_lumped diff --git a/examples/USER/atc/thermal/in.no_atoms b/examples/PACKAGES/atc/thermal/in.no_atoms similarity index 100% rename from examples/USER/atc/thermal/in.no_atoms rename to examples/PACKAGES/atc/thermal/in.no_atoms diff --git a/examples/USER/atc/thermal/no_atoms.screen b/examples/PACKAGES/atc/thermal/no_atoms.screen similarity index 100% rename from examples/USER/atc/thermal/no_atoms.screen rename to examples/PACKAGES/atc/thermal/no_atoms.screen diff --git a/examples/USER/atc/thermal/temp.init b/examples/PACKAGES/atc/thermal/temp.init similarity index 100% rename from examples/USER/atc/thermal/temp.init rename to examples/PACKAGES/atc/thermal/temp.init diff --git a/examples/USER/atc/two_temperature/Ar_ttm.mat b/examples/PACKAGES/atc/two_temperature/Ar_ttm.mat similarity index 100% rename from examples/USER/atc/two_temperature/Ar_ttm.mat rename to examples/PACKAGES/atc/two_temperature/Ar_ttm.mat diff --git a/examples/USER/atc/two_temperature/Cu_ttm.mat 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a/examples/USER/atc/two_temperature/gaussianIC_ttm.screen b/examples/PACKAGES/atc/two_temperature/gaussianIC_ttm.screen similarity index 100% rename from examples/USER/atc/two_temperature/gaussianIC_ttm.screen rename to examples/PACKAGES/atc/two_temperature/gaussianIC_ttm.screen diff --git a/examples/USER/atc/two_temperature/in.bar1d_ttm b/examples/PACKAGES/atc/two_temperature/in.bar1d_ttm similarity index 100% rename from examples/USER/atc/two_temperature/in.bar1d_ttm rename to examples/PACKAGES/atc/two_temperature/in.bar1d_ttm diff --git a/examples/USER/atc/two_temperature/in.cutout b/examples/PACKAGES/atc/two_temperature/in.cutout similarity index 100% rename from examples/USER/atc/two_temperature/in.cutout rename to examples/PACKAGES/atc/two_temperature/in.cutout diff --git a/examples/USER/atc/two_temperature/in.gaussianIC_ttm b/examples/PACKAGES/atc/two_temperature/in.gaussianIC_ttm similarity index 100% rename from examples/USER/atc/two_temperature/in.gaussianIC_ttm rename to 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examples/PACKAGES/brownian/point/log.11May2021.in2d.point.g++.1 diff --git a/examples/USER/brownian/point/log.11May2021.in2d.point.g++.4 b/examples/PACKAGES/brownian/point/log.11May2021.in2d.point.g++.4 similarity index 100% rename from examples/USER/brownian/point/log.11May2021.in2d.point.g++.4 rename to examples/PACKAGES/brownian/point/log.11May2021.in2d.point.g++.4 diff --git a/examples/USER/brownian/point/log.11May2021.in3d.point.g++.1 b/examples/PACKAGES/brownian/point/log.11May2021.in3d.point.g++.1 similarity index 100% rename from examples/USER/brownian/point/log.11May2021.in3d.point.g++.1 rename to examples/PACKAGES/brownian/point/log.11May2021.in3d.point.g++.1 diff --git a/examples/USER/brownian/point/log.11May2021.in3d.point.g++.4 b/examples/PACKAGES/brownian/point/log.11May2021.in3d.point.g++.4 similarity index 100% rename from examples/USER/brownian/point/log.11May2021.in3d.point.g++.4 rename to examples/PACKAGES/brownian/point/log.11May2021.in3d.point.g++.4 diff --git a/examples/USER/brownian/sphere/in2d.sphere b/examples/PACKAGES/brownian/sphere/in2d.sphere similarity index 100% rename from examples/USER/brownian/sphere/in2d.sphere rename to examples/PACKAGES/brownian/sphere/in2d.sphere diff --git a/examples/USER/brownian/sphere/in3d.sphere b/examples/PACKAGES/brownian/sphere/in3d.sphere similarity index 100% rename from examples/USER/brownian/sphere/in3d.sphere rename to examples/PACKAGES/brownian/sphere/in3d.sphere diff --git a/examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1 b/examples/PACKAGES/brownian/sphere/log.11May2021.in2d.sphere.g++.1 similarity index 100% rename from examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1 rename to examples/PACKAGES/brownian/sphere/log.11May2021.in2d.sphere.g++.1 diff --git a/examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4 b/examples/PACKAGES/brownian/sphere/log.11May2021.in2d.sphere.g++.4 similarity index 100% rename from examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4 rename to examples/PACKAGES/brownian/sphere/log.11May2021.in2d.sphere.g++.4 diff --git a/examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1 b/examples/PACKAGES/brownian/sphere/log.11May2021.in3d.sphere.g++.1 similarity index 100% rename from examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1 rename to examples/PACKAGES/brownian/sphere/log.11May2021.in3d.sphere.g++.1 diff --git a/examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4 b/examples/PACKAGES/brownian/sphere/log.11May2021.in3d.sphere.g++.4 similarity index 100% rename from examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4 rename to examples/PACKAGES/brownian/sphere/log.11May2021.in3d.sphere.g++.4 diff --git a/examples/USER/brownian/spherical_ABP/in2d.abp b/examples/PACKAGES/brownian/spherical_ABP/in2d.abp similarity index 100% rename from examples/USER/brownian/spherical_ABP/in2d.abp rename to examples/PACKAGES/brownian/spherical_ABP/in2d.abp diff --git a/examples/USER/brownian/spherical_ABP/in3d.ideal_abp b/examples/PACKAGES/brownian/spherical_ABP/in3d.ideal_abp similarity index 100% rename from examples/USER/brownian/spherical_ABP/in3d.ideal_abp rename to examples/PACKAGES/brownian/spherical_ABP/in3d.ideal_abp diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 b/examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 similarity index 100% rename from examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 rename to examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.1 diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 b/examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 similarity index 100% rename from examples/USER/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 rename to examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in2d.apb.g++.4 diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 b/examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 similarity index 100% rename from examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 rename to examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.1 diff --git a/examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 b/examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 similarity index 100% rename from examples/USER/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 rename to examples/PACKAGES/brownian/spherical_ABP/log.11May2021.in3d.ideal_apb.g++.4 diff --git a/examples/USER/cgdna/README b/examples/PACKAGES/cgdna/README similarity index 100% rename from examples/USER/cgdna/README rename to examples/PACKAGES/cgdna/README diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1 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similarity index 100% rename from examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.1 rename to examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.1 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.4 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.4 rename to examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.30Jun20.duplex2.g++.4 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/data.duplex1 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/data.duplex1 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/in.duplex1 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/in.duplex1 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.1 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.1 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.1 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.4 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.4 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.4 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/data.duplex2 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/data.duplex2 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/in.duplex2 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/in.duplex2 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.1 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.1 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.1 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.4 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.4 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.30Jun20.duplex2.g++.4 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/data.duplex3 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/data.duplex3 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/in.duplex3 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/in.duplex3 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.1 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.1 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.1 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.4 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.4 rename to examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.4 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++1 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++1 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++1 rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++1 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++4 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++4 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++4 rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++4 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++1 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++1 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++1 rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++1 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++4 b/examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++4 similarity index 100% rename from examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++4 rename to examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++4 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4 b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex4/data.duplex4 similarity index 100% rename from examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4 rename to examples/PACKAGES/cgdna/examples/oxRNA2/duplex4/data.duplex4 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4 b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex4/in.duplex4 similarity index 100% rename from examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4 rename to examples/PACKAGES/cgdna/examples/oxRNA2/duplex4/in.duplex4 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.1 b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.1 similarity index 100% rename from examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.1 rename to examples/PACKAGES/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.1 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.4 b/examples/PACKAGES/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.4 similarity index 100% rename from examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.4 rename to examples/PACKAGES/cgdna/examples/oxRNA2/duplex4/log.30Jun20.duplex4.g++.4 diff --git a/examples/USER/cgdna/util/generate.py b/examples/PACKAGES/cgdna/util/generate.py similarity index 100% rename from examples/USER/cgdna/util/generate.py rename to examples/PACKAGES/cgdna/util/generate.py diff --git a/examples/USER/cgdna/util/generate_simple.py b/examples/PACKAGES/cgdna/util/generate_simple.py similarity index 100% rename from examples/USER/cgdna/util/generate_simple.py rename to examples/PACKAGES/cgdna/util/generate_simple.py diff --git a/examples/USER/cgdna/util/input.ref b/examples/PACKAGES/cgdna/util/input.ref similarity index 100% rename from examples/USER/cgdna/util/input.ref rename to examples/PACKAGES/cgdna/util/input.ref diff --git a/examples/USER/cgdna/util/sequence.txt b/examples/PACKAGES/cgdna/util/sequence.txt similarity index 100% rename from examples/USER/cgdna/util/sequence.txt rename to examples/PACKAGES/cgdna/util/sequence.txt diff --git a/examples/USER/cgdna/util/sequence_simple.txt b/examples/PACKAGES/cgdna/util/sequence_simple.txt similarity index 100% rename from examples/USER/cgdna/util/sequence_simple.txt rename to examples/PACKAGES/cgdna/util/sequence_simple.txt diff --git a/examples/USER/cgsdk/README b/examples/PACKAGES/cgsdk/README similarity index 95% rename from examples/USER/cgsdk/README rename to examples/PACKAGES/cgsdk/README index 5d3a493779..09b9b0a8ea 100644 --- a/examples/USER/cgsdk/README +++ b/examples/PACKAGES/cgsdk/README @@ -1,4 +1,4 @@ -LAMMPS USER-CGSDK example problems +LAMMPS CG-SDK example problems Each of these sub-directories contains a sample problem for the SDK coarse grained MD potentials that you can run with LAMMPS. diff --git a/examples/USER/cgsdk/peg-verlet/data.pegc12e8.gz b/examples/PACKAGES/cgsdk/peg-verlet/data.pegc12e8.gz similarity index 100% rename from examples/USER/cgsdk/peg-verlet/data.pegc12e8.gz rename to examples/PACKAGES/cgsdk/peg-verlet/data.pegc12e8.gz diff --git a/examples/USER/cgsdk/peg-verlet/in.pegc12e8 b/examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8 similarity index 100% rename from examples/USER/cgsdk/peg-verlet/in.pegc12e8 rename to examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8 diff --git a/examples/USER/cgsdk/peg-verlet/in.pegc12e8-angle b/examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8-angle similarity index 100% rename from examples/USER/cgsdk/peg-verlet/in.pegc12e8-angle rename to examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8-angle diff --git a/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 b/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 similarity index 100% rename from examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 rename to examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 diff --git a/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 b/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 similarity index 100% rename from examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 rename to examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 diff --git a/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 b/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 similarity index 100% rename from examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 rename to examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 diff --git a/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 b/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 similarity index 100% rename from examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 rename to examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 diff --git a/examples/USER/cgsdk/sds-monolayer/data.sds.gz b/examples/PACKAGES/cgsdk/sds-monolayer/data.sds.gz similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/data.sds.gz rename to examples/PACKAGES/cgsdk/sds-monolayer/data.sds.gz diff --git a/examples/USER/cgsdk/sds-monolayer/in.sds-hybrid b/examples/PACKAGES/cgsdk/sds-monolayer/in.sds-hybrid similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/in.sds-hybrid rename to examples/PACKAGES/cgsdk/sds-monolayer/in.sds-hybrid diff --git a/examples/USER/cgsdk/sds-monolayer/in.sds-regular b/examples/PACKAGES/cgsdk/sds-monolayer/in.sds-regular similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/in.sds-regular rename to examples/PACKAGES/cgsdk/sds-monolayer/in.sds-regular diff --git a/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 b/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 rename to examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 diff --git a/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 b/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 rename to examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 diff --git a/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 b/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 rename to examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 diff --git a/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 b/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 similarity index 100% rename from examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 rename to examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 diff --git a/examples/USER/colvars/data.peptide b/examples/PACKAGES/colvars/data.peptide similarity index 100% rename from examples/USER/colvars/data.peptide rename to examples/PACKAGES/colvars/data.peptide diff --git a/examples/USER/colvars/in.peptide-colvars b/examples/PACKAGES/colvars/in.peptide-colvars similarity index 100% rename from examples/USER/colvars/in.peptide-colvars rename to examples/PACKAGES/colvars/in.peptide-colvars diff --git a/examples/USER/colvars/in.peptide-colvars2 b/examples/PACKAGES/colvars/in.peptide-colvars2 similarity index 100% rename from examples/USER/colvars/in.peptide-colvars2 rename to examples/PACKAGES/colvars/in.peptide-colvars2 diff --git a/examples/USER/colvars/in.peptide-spring b/examples/PACKAGES/colvars/in.peptide-spring similarity index 100% rename from examples/USER/colvars/in.peptide-spring rename to examples/PACKAGES/colvars/in.peptide-spring diff --git a/examples/USER/colvars/in.peptide-spring2 b/examples/PACKAGES/colvars/in.peptide-spring2 similarity index 100% rename from examples/USER/colvars/in.peptide-spring2 rename to examples/PACKAGES/colvars/in.peptide-spring2 diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.1 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.1 diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.4 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.4 diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.1 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.1 diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.4 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.4 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.1 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-spring.g++.1 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.1 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.4 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-spring.g++.4 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.4 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring2.g++.1 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.1 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-spring2.g++.1 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.1 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring2.g++.4 b/examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.4 similarity index 100% rename from examples/USER/colvars/log.27Nov18.peptide-spring2.g++.4 rename to examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.4 diff --git a/examples/USER/colvars/out.colvars.state b/examples/PACKAGES/colvars/out.colvars.state similarity index 100% rename from examples/USER/colvars/out.colvars.state rename to examples/PACKAGES/colvars/out.colvars.state diff --git a/examples/USER/colvars/out.colvars.state.old b/examples/PACKAGES/colvars/out.colvars.state.old similarity index 100% rename from examples/USER/colvars/out.colvars.state.old rename to examples/PACKAGES/colvars/out.colvars.state.old diff --git a/examples/USER/colvars/out.colvars.traj b/examples/PACKAGES/colvars/out.colvars.traj similarity index 100% rename from examples/USER/colvars/out.colvars.traj rename to examples/PACKAGES/colvars/out.colvars.traj diff --git a/examples/USER/colvars/out2.colvars.state b/examples/PACKAGES/colvars/out2.colvars.state similarity index 100% rename from examples/USER/colvars/out2.colvars.state rename to examples/PACKAGES/colvars/out2.colvars.state diff --git a/examples/USER/colvars/out2.colvars.traj b/examples/PACKAGES/colvars/out2.colvars.traj similarity index 100% rename from examples/USER/colvars/out2.colvars.traj rename to examples/PACKAGES/colvars/out2.colvars.traj diff --git a/examples/USER/colvars/peptide.colvars b/examples/PACKAGES/colvars/peptide.colvars similarity index 100% rename from examples/USER/colvars/peptide.colvars rename to examples/PACKAGES/colvars/peptide.colvars diff --git a/examples/USER/colvars/peptide.colvars2 b/examples/PACKAGES/colvars/peptide.colvars2 similarity index 100% rename from examples/USER/colvars/peptide.colvars2 rename to examples/PACKAGES/colvars/peptide.colvars2 diff --git a/examples/USER/colvars/peptide.psf b/examples/PACKAGES/colvars/peptide.psf similarity index 100% rename from examples/USER/colvars/peptide.psf rename to examples/PACKAGES/colvars/peptide.psf diff --git a/examples/USER/colvars/peptide2.colvars.state b/examples/PACKAGES/colvars/peptide2.colvars.state similarity index 100% rename from examples/USER/colvars/peptide2.colvars.state rename to examples/PACKAGES/colvars/peptide2.colvars.state diff --git a/examples/USER/colvars/peptide2.colvars.traj b/examples/PACKAGES/colvars/peptide2.colvars.traj similarity index 100% rename from examples/USER/colvars/peptide2.colvars.traj rename to examples/PACKAGES/colvars/peptide2.colvars.traj diff --git a/examples/USER/dielectric/README b/examples/PACKAGES/dielectric/README similarity index 96% rename from examples/USER/dielectric/README rename to examples/PACKAGES/dielectric/README index 6cbb1e204d..fa7ac28c97 100644 --- a/examples/USER/dielectric/README +++ b/examples/PACKAGES/dielectric/README @@ -1,4 +1,4 @@ -This folder contains some example data and input scripts for the USER-DIELECTRIC package. Please refer to the following reference for more details: +This folder contains some example data and input scripts for the DIELECTRIC package. Please refer to the following reference for more details: Nguyen TD, Li H, Bagchi D, Solis FJ, Olvera de la Cruz, Incorporating surface polarization effects into large-scale coarse-grained molecular dynamics simulation, Computer Physics Communications 2019, 241, 80--91. diff --git a/examples/USER/dielectric/data.confined b/examples/PACKAGES/dielectric/data.confined similarity index 100% rename from examples/USER/dielectric/data.confined rename to examples/PACKAGES/dielectric/data.confined diff --git a/examples/USER/dielectric/data.sphere b/examples/PACKAGES/dielectric/data.sphere similarity index 100% rename from examples/USER/dielectric/data.sphere rename to examples/PACKAGES/dielectric/data.sphere diff --git a/examples/USER/dielectric/in.confined b/examples/PACKAGES/dielectric/in.confined similarity index 100% rename from examples/USER/dielectric/in.confined rename to examples/PACKAGES/dielectric/in.confined diff --git a/examples/USER/dielectric/in.nopbc b/examples/PACKAGES/dielectric/in.nopbc similarity index 100% rename from examples/USER/dielectric/in.nopbc rename to examples/PACKAGES/dielectric/in.nopbc diff --git a/examples/USER/diffraction/Output/bulkNi.hist.xrd.correct b/examples/PACKAGES/diffraction/Output/bulkNi.hist.xrd.correct similarity index 100% rename from examples/USER/diffraction/Output/bulkNi.hist.xrd.correct rename to examples/PACKAGES/diffraction/Output/bulkNi.hist.xrd.correct diff --git a/examples/USER/diffraction/Output/bulkNi.log.correct b/examples/PACKAGES/diffraction/Output/bulkNi.log.correct similarity index 100% rename from examples/USER/diffraction/Output/bulkNi.log.correct rename to examples/PACKAGES/diffraction/Output/bulkNi.log.correct diff --git a/examples/USER/diffraction/Output/bulkNi_001.saed.0.vtk.correct b/examples/PACKAGES/diffraction/Output/bulkNi_001.saed.0.vtk.correct similarity index 100% rename from examples/USER/diffraction/Output/bulkNi_001.saed.0.vtk.correct rename to examples/PACKAGES/diffraction/Output/bulkNi_001.saed.0.vtk.correct diff --git a/examples/USER/diffraction/Output/bulkNi_001.saed.0_VisIt_Image.png b/examples/PACKAGES/diffraction/Output/bulkNi_001.saed.0_VisIt_Image.png similarity index 100% rename from examples/USER/diffraction/Output/bulkNi_001.saed.0_VisIt_Image.png rename to examples/PACKAGES/diffraction/Output/bulkNi_001.saed.0_VisIt_Image.png diff --git a/examples/USER/diffraction/Output/log.cite b/examples/PACKAGES/diffraction/Output/log.cite similarity index 100% rename from examples/USER/diffraction/Output/log.cite rename to examples/PACKAGES/diffraction/Output/log.cite diff --git a/examples/USER/diffraction/README b/examples/PACKAGES/diffraction/README similarity index 100% rename from examples/USER/diffraction/README rename to examples/PACKAGES/diffraction/README diff --git a/examples/USER/diffraction/in.BulkNi b/examples/PACKAGES/diffraction/in.BulkNi similarity index 100% rename from examples/USER/diffraction/in.BulkNi rename to examples/PACKAGES/diffraction/in.BulkNi diff --git a/examples/USER/diffraction/log.27Nov18.BulkNi.g++.1 b/examples/PACKAGES/diffraction/log.27Nov18.BulkNi.g++.1 similarity index 100% rename from examples/USER/diffraction/log.27Nov18.BulkNi.g++.1 rename to examples/PACKAGES/diffraction/log.27Nov18.BulkNi.g++.1 diff --git a/examples/USER/diffraction/log.27Nov18.BulkNi.g++.4 b/examples/PACKAGES/diffraction/log.27Nov18.BulkNi.g++.4 similarity index 100% rename from examples/USER/diffraction/log.27Nov18.BulkNi.g++.4 rename to examples/PACKAGES/diffraction/log.27Nov18.BulkNi.g++.4 diff --git a/examples/USER/misc/dpd_ext/README b/examples/PACKAGES/dpd-basic/README similarity index 100% rename from examples/USER/misc/dpd_ext/README rename to examples/PACKAGES/dpd-basic/README diff --git a/examples/USER/misc/dpd_ext/dpdext/dpdext.data b/examples/PACKAGES/dpd-basic/dpdext/dpdext.data similarity index 100% rename from examples/USER/misc/dpd_ext/dpdext/dpdext.data rename to examples/PACKAGES/dpd-basic/dpdext/dpdext.data diff --git a/examples/USER/misc/dpd_ext/dpdext/in.dpdext b/examples/PACKAGES/dpd-basic/dpdext/in.dpdext similarity index 100% rename from examples/USER/misc/dpd_ext/dpdext/in.dpdext rename to examples/PACKAGES/dpd-basic/dpdext/in.dpdext diff --git a/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 b/examples/PACKAGES/dpd-basic/dpdext/log.10Mar21.dpdext.g++.1 similarity index 100% rename from examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 rename to examples/PACKAGES/dpd-basic/dpdext/log.10Mar21.dpdext.g++.1 diff --git a/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 b/examples/PACKAGES/dpd-basic/dpdext/log.10Mar21.dpdext.g++.4 similarity index 100% rename from examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 rename to examples/PACKAGES/dpd-basic/dpdext/log.10Mar21.dpdext.g++.4 diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data b/examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce.data similarity index 100% rename from examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data rename to examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce.data diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot b/examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot similarity index 100% rename from examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot rename to examples/PACKAGES/dpd-basic/dpdext_tstat/cg_spce_table.pot diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce b/examples/PACKAGES/dpd-basic/dpdext_tstat/in.cg_spce similarity index 100% rename from examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce rename to examples/PACKAGES/dpd-basic/dpdext_tstat/in.cg_spce diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 b/examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.1 similarity index 100% rename from examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 rename to examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.1 diff --git a/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 b/examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.4 similarity index 100% rename from examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 rename to examples/PACKAGES/dpd-basic/dpdext_tstat/log.10Mar21.dpdext.g++.4 diff --git a/examples/USER/mesodpd/README b/examples/PACKAGES/dpd-meso/README similarity index 100% rename from examples/USER/mesodpd/README rename to examples/PACKAGES/dpd-meso/README diff --git a/examples/USER/mesodpd/edpd/in.edpd b/examples/PACKAGES/dpd-meso/edpd/in.edpd similarity index 100% rename from examples/USER/mesodpd/edpd/in.edpd rename to examples/PACKAGES/dpd-meso/edpd/in.edpd diff --git a/examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.1 b/examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.1 similarity index 100% rename from examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.1 rename to examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.1 diff --git a/examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.4 b/examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.4 similarity index 100% rename from examples/USER/mesodpd/edpd/log.16Aug17.edpd.g++.4 rename to examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.4 diff --git a/examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.1 b/examples/PACKAGES/dpd-meso/edpd/temp.profile.16Aug17.edpd.g++.1 similarity index 100% rename from examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.1 rename to examples/PACKAGES/dpd-meso/edpd/temp.profile.16Aug17.edpd.g++.1 diff --git a/examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.4 b/examples/PACKAGES/dpd-meso/edpd/temp.profile.16Aug17.edpd.g++.4 similarity index 100% rename from examples/USER/mesodpd/edpd/temp.profile.16Aug17.edpd.g++.4 rename to examples/PACKAGES/dpd-meso/edpd/temp.profile.16Aug17.edpd.g++.4 diff --git a/examples/USER/mesodpd/mdpd/in.mdpd b/examples/PACKAGES/dpd-meso/mdpd/in.mdpd similarity index 100% rename from examples/USER/mesodpd/mdpd/in.mdpd rename to examples/PACKAGES/dpd-meso/mdpd/in.mdpd diff --git a/examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.1 b/examples/PACKAGES/dpd-meso/mdpd/log.16Aug17.mdpd.g++.1 similarity index 100% rename from examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.1 rename to examples/PACKAGES/dpd-meso/mdpd/log.16Aug17.mdpd.g++.1 diff --git a/examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.4 b/examples/PACKAGES/dpd-meso/mdpd/log.16Aug17.mdpd.g++.4 similarity index 100% rename from examples/USER/mesodpd/mdpd/log.16Aug17.mdpd.g++.4 rename to examples/PACKAGES/dpd-meso/mdpd/log.16Aug17.mdpd.g++.4 diff --git a/examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.1 b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 similarity index 100% rename from examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.1 rename to examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 diff --git a/examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.4 b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 similarity index 100% rename from examples/USER/mesodpd/tdpd/cc.profile.16Aug17.tdpd.g++.4 rename to examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 diff --git a/examples/USER/mesodpd/tdpd/in.tdpd b/examples/PACKAGES/dpd-meso/tdpd/in.tdpd similarity index 100% rename from examples/USER/mesodpd/tdpd/in.tdpd rename to examples/PACKAGES/dpd-meso/tdpd/in.tdpd diff --git a/examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.1 b/examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.1 similarity index 100% rename from examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.1 rename to examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.1 diff --git a/examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.4 b/examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.4 similarity index 100% rename from examples/USER/mesodpd/tdpd/log.16Aug17.tdpd.g++.4 rename to examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.4 diff --git a/examples/USER/dpd/README b/examples/PACKAGES/dpd-react/README similarity index 100% rename from examples/USER/dpd/README rename to examples/PACKAGES/dpd-react/README diff --git a/examples/USER/dpd/dpd-shardlow/data.dpd b/examples/PACKAGES/dpd-react/dpd-shardlow/data.dpd similarity index 100% rename from examples/USER/dpd/dpd-shardlow/data.dpd rename to examples/PACKAGES/dpd-react/dpd-shardlow/data.dpd diff --git a/examples/USER/dpd/dpd-shardlow/in.dpd-shardlow b/examples/PACKAGES/dpd-react/dpd-shardlow/in.dpd-shardlow similarity index 100% rename from examples/USER/dpd/dpd-shardlow/in.dpd-shardlow rename to examples/PACKAGES/dpd-react/dpd-shardlow/in.dpd-shardlow diff --git a/examples/USER/dpd/dpd-shardlow/log.dpd-shardlow.reference b/examples/PACKAGES/dpd-react/dpd-shardlow/log.dpd-shardlow.reference similarity index 100% rename from examples/USER/dpd/dpd-shardlow/log.dpd-shardlow.reference rename to 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rename from examples/USER/manifold/energy/sphere.data rename to examples/PACKAGES/manifold/energy/sphere.data diff --git a/examples/USER/manifold/energy/sphere.setup b/examples/PACKAGES/manifold/energy/sphere.setup similarity index 100% rename from examples/USER/manifold/energy/sphere.setup rename to examples/PACKAGES/manifold/energy/sphere.setup diff --git a/examples/USER/manifold/energy/torus.data b/examples/PACKAGES/manifold/energy/torus.data similarity index 100% rename from examples/USER/manifold/energy/torus.data rename to examples/PACKAGES/manifold/energy/torus.data diff --git a/examples/USER/manifold/energy/torus.setup b/examples/PACKAGES/manifold/energy/torus.setup similarity index 100% rename from examples/USER/manifold/energy/torus.setup rename to examples/PACKAGES/manifold/energy/torus.setup diff --git a/examples/USER/manifold/thylakoid/README b/examples/PACKAGES/manifold/thylakoid/README similarity index 100% rename from examples/USER/manifold/thylakoid/README rename to examples/PACKAGES/manifold/thylakoid/README diff --git a/examples/USER/manifold/thylakoid/thylakoid.data b/examples/PACKAGES/manifold/thylakoid/thylakoid.data similarity index 100% rename from examples/USER/manifold/thylakoid/thylakoid.data rename to examples/PACKAGES/manifold/thylakoid/thylakoid.data diff --git a/examples/USER/manifold/thylakoid/thylakoid.in b/examples/PACKAGES/manifold/thylakoid/thylakoid.in similarity index 100% rename from examples/USER/manifold/thylakoid/thylakoid.in rename to examples/PACKAGES/manifold/thylakoid/thylakoid.in diff --git a/examples/USER/manifold/virus/README b/examples/PACKAGES/manifold/virus/README similarity index 100% rename from examples/USER/manifold/virus/README rename to examples/PACKAGES/manifold/virus/README diff --git a/examples/USER/manifold/virus/init.data b/examples/PACKAGES/manifold/virus/init.data similarity index 100% rename from examples/USER/manifold/virus/init.data rename to examples/PACKAGES/manifold/virus/init.data diff --git a/examples/USER/manifold/virus/vir.in b/examples/PACKAGES/manifold/virus/vir.in similarity index 100% rename from examples/USER/manifold/virus/vir.in rename to examples/PACKAGES/manifold/virus/vir.in diff --git a/examples/USER/mdi/README b/examples/PACKAGES/mdi/README similarity index 100% rename from examples/USER/mdi/README rename to examples/PACKAGES/mdi/README diff --git a/examples/USER/mdi/Script.sh b/examples/PACKAGES/mdi/Script.sh similarity index 100% rename from examples/USER/mdi/Script.sh rename to examples/PACKAGES/mdi/Script.sh diff --git a/examples/USER/mdi/driver.py b/examples/PACKAGES/mdi/driver.py similarity index 100% rename from examples/USER/mdi/driver.py rename to examples/PACKAGES/mdi/driver.py diff --git a/examples/USER/mdi/lammps.data b/examples/PACKAGES/mdi/lammps.data similarity index 100% rename from examples/USER/mdi/lammps.data rename to examples/PACKAGES/mdi/lammps.data diff --git a/examples/USER/mdi/lammps.in b/examples/PACKAGES/mdi/lammps.in similarity index 100% rename from examples/USER/mdi/lammps.in rename to examples/PACKAGES/mdi/lammps.in diff --git a/examples/USER/mesont/C_10_10.mesocnt b/examples/PACKAGES/mesont/C_10_10.mesocnt similarity index 100% rename from examples/USER/mesont/C_10_10.mesocnt rename to examples/PACKAGES/mesont/C_10_10.mesocnt diff --git a/examples/USER/mesont/README b/examples/PACKAGES/mesont/README similarity index 88% rename from examples/USER/mesont/README rename to examples/PACKAGES/mesont/README index ffbc667120..7d6be7993a 100644 --- a/examples/USER/mesont/README +++ b/examples/PACKAGES/mesont/README @@ -1,8 +1,8 @@ -=== USER-MESONT examples === +=== MESONT examples === =============================== The files in this folder provide examples of using the CNT -mesoscopic force field (USER-MESONT). +mesoscopic force field (MESONT). Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu diff --git a/examples/USER/mesont/TABTP_10_10.mesont b/examples/PACKAGES/mesont/TABTP_10_10.mesont similarity index 100% rename from examples/USER/mesont/TABTP_10_10.mesont rename to examples/PACKAGES/mesont/TABTP_10_10.mesont diff --git a/examples/USER/mesont/cnt.data b/examples/PACKAGES/mesont/cnt.data similarity index 100% rename from examples/USER/mesont/cnt.data rename to examples/PACKAGES/mesont/cnt.data diff --git a/examples/USER/mesont/data.bundle b/examples/PACKAGES/mesont/data.bundle similarity index 100% rename from examples/USER/mesont/data.bundle rename to examples/PACKAGES/mesont/data.bundle diff --git a/examples/USER/mesont/data.film b/examples/PACKAGES/mesont/data.film similarity index 100% rename from examples/USER/mesont/data.film rename to examples/PACKAGES/mesont/data.film diff --git a/examples/USER/mesont/in.bundle b/examples/PACKAGES/mesont/in.bundle similarity index 100% rename from examples/USER/mesont/in.bundle rename to examples/PACKAGES/mesont/in.bundle diff --git a/examples/USER/mesont/in.cnt b/examples/PACKAGES/mesont/in.cnt similarity index 100% rename from examples/USER/mesont/in.cnt rename to examples/PACKAGES/mesont/in.cnt diff --git a/examples/USER/mesont/in.film b/examples/PACKAGES/mesont/in.film similarity index 100% rename from examples/USER/mesont/in.film rename to examples/PACKAGES/mesont/in.film diff --git a/examples/USER/mesont/log.2Jun2020.bundle.g++.1 b/examples/PACKAGES/mesont/log.2Jun2020.bundle.g++.1 similarity index 100% rename from examples/USER/mesont/log.2Jun2020.bundle.g++.1 rename to examples/PACKAGES/mesont/log.2Jun2020.bundle.g++.1 diff --git a/examples/USER/mesont/log.2Jun2020.bundle.g++.4 b/examples/PACKAGES/mesont/log.2Jun2020.bundle.g++.4 similarity index 100% rename from examples/USER/mesont/log.2Jun2020.bundle.g++.4 rename to examples/PACKAGES/mesont/log.2Jun2020.bundle.g++.4 diff --git a/examples/USER/mesont/log.2Jun2020.film.g++.1 b/examples/PACKAGES/mesont/log.2Jun2020.film.g++.1 similarity index 100% rename from examples/USER/mesont/log.2Jun2020.film.g++.1 rename to examples/PACKAGES/mesont/log.2Jun2020.film.g++.1 diff --git a/examples/USER/mesont/log.2Jun2020.film.g++.4 b/examples/PACKAGES/mesont/log.2Jun2020.film.g++.4 similarity index 100% rename from examples/USER/mesont/log.2Jun2020.film.g++.4 rename to examples/PACKAGES/mesont/log.2Jun2020.film.g++.4 diff --git a/examples/USER/mesont/log.9Jan20.cnt.g++.1 b/examples/PACKAGES/mesont/log.9Jan20.cnt.g++.1 similarity index 100% rename from examples/USER/mesont/log.9Jan20.cnt.g++.1 rename to examples/PACKAGES/mesont/log.9Jan20.cnt.g++.1 diff --git a/examples/USER/mesont/log.9Jan20.cnt.g++.4 b/examples/PACKAGES/mesont/log.9Jan20.cnt.g++.4 similarity index 100% rename from examples/USER/mesont/log.9Jan20.cnt.g++.4 rename to examples/PACKAGES/mesont/log.9Jan20.cnt.g++.4 diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.README b/examples/PACKAGES/mgpt/Ta6.8x.mgpt.README similarity index 100% rename from examples/USER/mgpt/Ta6.8x.mgpt.README rename to examples/PACKAGES/mgpt/Ta6.8x.mgpt.README diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.parmin b/examples/PACKAGES/mgpt/Ta6.8x.mgpt.parmin similarity index 100% rename from examples/USER/mgpt/Ta6.8x.mgpt.parmin rename to examples/PACKAGES/mgpt/Ta6.8x.mgpt.parmin diff --git a/examples/USER/mgpt/Ta6.8x.mgpt.potin b/examples/PACKAGES/mgpt/Ta6.8x.mgpt.potin similarity index 100% rename from examples/USER/mgpt/Ta6.8x.mgpt.potin rename to examples/PACKAGES/mgpt/Ta6.8x.mgpt.potin diff --git a/examples/USER/mgpt/in.bcc0 b/examples/PACKAGES/mgpt/in.bcc0 similarity index 100% rename from examples/USER/mgpt/in.bcc0 rename to examples/PACKAGES/mgpt/in.bcc0 diff --git a/examples/USER/mgpt/in.vac0-bcc b/examples/PACKAGES/mgpt/in.vac0-bcc similarity index 100% rename from examples/USER/mgpt/in.vac0-bcc rename to examples/PACKAGES/mgpt/in.vac0-bcc diff --git a/examples/USER/mgpt/in.vacmin-bcc b/examples/PACKAGES/mgpt/in.vacmin-bcc similarity index 100% rename from examples/USER/mgpt/in.vacmin-bcc rename to examples/PACKAGES/mgpt/in.vacmin-bcc diff --git a/examples/USER/mgpt/log.bcc0 b/examples/PACKAGES/mgpt/log.bcc0 similarity index 100% rename from examples/USER/mgpt/log.bcc0 rename to examples/PACKAGES/mgpt/log.bcc0 diff --git a/examples/USER/mgpt/log.vac0-bcc b/examples/PACKAGES/mgpt/log.vac0-bcc similarity index 100% rename from examples/USER/mgpt/log.vac0-bcc rename to examples/PACKAGES/mgpt/log.vac0-bcc diff --git a/examples/USER/mgpt/log.vacmin-bcc b/examples/PACKAGES/mgpt/log.vacmin-bcc similarity index 100% rename from examples/USER/mgpt/log.vacmin-bcc rename to examples/PACKAGES/mgpt/log.vacmin-bcc diff --git a/examples/USER/mofff/hkust1.data b/examples/PACKAGES/mofff/hkust1.data similarity index 100% rename from examples/USER/mofff/hkust1.data rename to examples/PACKAGES/mofff/hkust1.data diff --git a/examples/USER/mofff/in.hkust1 b/examples/PACKAGES/mofff/in.hkust1 similarity index 100% rename from examples/USER/mofff/in.hkust1 rename to examples/PACKAGES/mofff/in.hkust1 diff --git a/examples/USER/mofff/in.hkust1_long b/examples/PACKAGES/mofff/in.hkust1_long similarity index 100% rename from examples/USER/mofff/in.hkust1_long rename to examples/PACKAGES/mofff/in.hkust1_long diff --git a/examples/USER/mofff/log.27Nov18.hkust1.g++.1 b/examples/PACKAGES/mofff/log.27Nov18.hkust1.g++.1 similarity index 100% rename from examples/USER/mofff/log.27Nov18.hkust1.g++.1 rename to examples/PACKAGES/mofff/log.27Nov18.hkust1.g++.1 diff --git a/examples/USER/mofff/log.27Nov18.hkust1.g++.4 b/examples/PACKAGES/mofff/log.27Nov18.hkust1.g++.4 similarity index 100% rename from examples/USER/mofff/log.27Nov18.hkust1.g++.4 rename to examples/PACKAGES/mofff/log.27Nov18.hkust1.g++.4 diff --git a/examples/USER/mofff/log.27Nov18.hkust1_long.g++.1 b/examples/PACKAGES/mofff/log.27Nov18.hkust1_long.g++.1 similarity index 100% rename from examples/USER/mofff/log.27Nov18.hkust1_long.g++.1 rename to examples/PACKAGES/mofff/log.27Nov18.hkust1_long.g++.1 diff --git a/examples/USER/mofff/log.27Nov18.hkust1_long.g++.4 b/examples/PACKAGES/mofff/log.27Nov18.hkust1_long.g++.4 similarity index 100% rename from examples/USER/mofff/log.27Nov18.hkust1_long.g++.4 rename to examples/PACKAGES/mofff/log.27Nov18.hkust1_long.g++.4 diff --git a/examples/USER/pace/Cu-PBE-core-rep.ace b/examples/PACKAGES/pace/Cu-PBE-core-rep.ace similarity index 100% rename from examples/USER/pace/Cu-PBE-core-rep.ace rename to examples/PACKAGES/pace/Cu-PBE-core-rep.ace diff --git a/examples/USER/pace/in.pace.product b/examples/PACKAGES/pace/in.pace.product similarity index 100% rename from examples/USER/pace/in.pace.product rename to examples/PACKAGES/pace/in.pace.product diff --git a/examples/USER/pace/in.pace.recursive b/examples/PACKAGES/pace/in.pace.recursive similarity index 100% rename from examples/USER/pace/in.pace.recursive rename to examples/PACKAGES/pace/in.pace.recursive diff --git a/examples/USER/pace/log.03Feb2021.pace.product.g++.1 b/examples/PACKAGES/pace/log.03Feb2021.pace.product.g++.1 similarity index 100% rename from examples/USER/pace/log.03Feb2021.pace.product.g++.1 rename to examples/PACKAGES/pace/log.03Feb2021.pace.product.g++.1 diff --git a/examples/USER/pace/log.03Feb2021.pace.product.g++.4 b/examples/PACKAGES/pace/log.03Feb2021.pace.product.g++.4 similarity index 100% rename from examples/USER/pace/log.03Feb2021.pace.product.g++.4 rename to examples/PACKAGES/pace/log.03Feb2021.pace.product.g++.4 diff --git a/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 b/examples/PACKAGES/pace/log.03Feb2021.pace.recursive.g++.1 similarity index 100% rename from examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 rename to examples/PACKAGES/pace/log.03Feb2021.pace.recursive.g++.1 diff --git a/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 b/examples/PACKAGES/pace/log.03Feb2021.pace.recursive.g++.4 similarity index 100% rename from examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 rename to examples/PACKAGES/pace/log.03Feb2021.pace.recursive.g++.4 diff --git a/examples/USER/phonon/1-1D-mono/README b/examples/PACKAGES/phonon/1-1D-mono/README similarity index 100% rename from examples/USER/phonon/1-1D-mono/README rename to examples/PACKAGES/phonon/1-1D-mono/README diff --git a/examples/USER/phonon/1-1D-mono/data.pos b/examples/PACKAGES/phonon/1-1D-mono/data.pos similarity index 100% rename from examples/USER/phonon/1-1D-mono/data.pos rename to examples/PACKAGES/phonon/1-1D-mono/data.pos diff --git a/examples/USER/phonon/1-1D-mono/disp.dat b/examples/PACKAGES/phonon/1-1D-mono/disp.dat similarity index 100% rename from examples/USER/phonon/1-1D-mono/disp.dat rename to examples/PACKAGES/phonon/1-1D-mono/disp.dat diff --git a/examples/USER/phonon/1-1D-mono/in.Ana b/examples/PACKAGES/phonon/1-1D-mono/in.Ana similarity index 100% rename from examples/USER/phonon/1-1D-mono/in.Ana rename to examples/PACKAGES/phonon/1-1D-mono/in.Ana diff --git a/examples/USER/phonon/1-1D-mono/in.disp b/examples/PACKAGES/phonon/1-1D-mono/in.disp similarity index 100% rename from examples/USER/phonon/1-1D-mono/in.disp rename to examples/PACKAGES/phonon/1-1D-mono/in.disp diff --git a/examples/USER/phonon/1-1D-mono/log.lammps b/examples/PACKAGES/phonon/1-1D-mono/log.lammps similarity index 100% rename from examples/USER/phonon/1-1D-mono/log.lammps rename to examples/PACKAGES/phonon/1-1D-mono/log.lammps diff --git a/examples/USER/phonon/1-1D-mono/map.in b/examples/PACKAGES/phonon/1-1D-mono/map.in similarity index 100% rename from examples/USER/phonon/1-1D-mono/map.in rename to examples/PACKAGES/phonon/1-1D-mono/map.in diff --git a/examples/USER/phonon/1-1D-mono/pdisp.eps b/examples/PACKAGES/phonon/1-1D-mono/pdisp.eps similarity index 100% rename from examples/USER/phonon/1-1D-mono/pdisp.eps rename to examples/PACKAGES/phonon/1-1D-mono/pdisp.eps diff --git a/examples/USER/phonon/1-1D-mono/pdisp.gnuplot b/examples/PACKAGES/phonon/1-1D-mono/pdisp.gnuplot similarity index 100% rename from examples/USER/phonon/1-1D-mono/pdisp.gnuplot rename to examples/PACKAGES/phonon/1-1D-mono/pdisp.gnuplot diff --git a/examples/USER/phonon/1-1D-mono/phonon.bin.2000000 b/examples/PACKAGES/phonon/1-1D-mono/phonon.bin.2000000 similarity index 100% rename from examples/USER/phonon/1-1D-mono/phonon.bin.2000000 rename to examples/PACKAGES/phonon/1-1D-mono/phonon.bin.2000000 diff --git a/examples/USER/phonon/1-1D-mono/phonon.log b/examples/PACKAGES/phonon/1-1D-mono/phonon.log similarity index 100% rename from examples/USER/phonon/1-1D-mono/phonon.log rename to examples/PACKAGES/phonon/1-1D-mono/phonon.log diff --git a/examples/USER/phonon/1-1D-mono/plot.disp b/examples/PACKAGES/phonon/1-1D-mono/plot.disp similarity index 100% rename from examples/USER/phonon/1-1D-mono/plot.disp rename to examples/PACKAGES/phonon/1-1D-mono/plot.disp diff --git a/examples/USER/phonon/2-1D-diatomic/README b/examples/PACKAGES/phonon/2-1D-diatomic/README similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/README rename to examples/PACKAGES/phonon/2-1D-diatomic/README diff --git a/examples/USER/phonon/2-1D-diatomic/data.pos b/examples/PACKAGES/phonon/2-1D-diatomic/data.pos similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/data.pos rename to examples/PACKAGES/phonon/2-1D-diatomic/data.pos diff --git a/examples/USER/phonon/2-1D-diatomic/disp.dat b/examples/PACKAGES/phonon/2-1D-diatomic/disp.dat similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/disp.dat rename to examples/PACKAGES/phonon/2-1D-diatomic/disp.dat diff --git a/examples/USER/phonon/2-1D-diatomic/in.Ana b/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/in.Ana rename to examples/PACKAGES/phonon/2-1D-diatomic/in.Ana diff --git a/examples/USER/phonon/2-1D-diatomic/in.disp b/examples/PACKAGES/phonon/2-1D-diatomic/in.disp similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/in.disp rename to examples/PACKAGES/phonon/2-1D-diatomic/in.disp diff --git a/examples/USER/phonon/2-1D-diatomic/log.lammps b/examples/PACKAGES/phonon/2-1D-diatomic/log.lammps similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/log.lammps rename to examples/PACKAGES/phonon/2-1D-diatomic/log.lammps diff --git a/examples/USER/phonon/2-1D-diatomic/map.in b/examples/PACKAGES/phonon/2-1D-diatomic/map.in similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/map.in rename to examples/PACKAGES/phonon/2-1D-diatomic/map.in diff --git a/examples/USER/phonon/2-1D-diatomic/pdisp.eps b/examples/PACKAGES/phonon/2-1D-diatomic/pdisp.eps similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/pdisp.eps rename to examples/PACKAGES/phonon/2-1D-diatomic/pdisp.eps diff --git a/examples/USER/phonon/2-1D-diatomic/pdisp.gnuplot b/examples/PACKAGES/phonon/2-1D-diatomic/pdisp.gnuplot similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/pdisp.gnuplot rename to examples/PACKAGES/phonon/2-1D-diatomic/pdisp.gnuplot diff --git a/examples/USER/phonon/2-1D-diatomic/phonon.bin.2000000 b/examples/PACKAGES/phonon/2-1D-diatomic/phonon.bin.2000000 similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/phonon.bin.2000000 rename to examples/PACKAGES/phonon/2-1D-diatomic/phonon.bin.2000000 diff --git a/examples/USER/phonon/2-1D-diatomic/phonon.log b/examples/PACKAGES/phonon/2-1D-diatomic/phonon.log similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/phonon.log rename to examples/PACKAGES/phonon/2-1D-diatomic/phonon.log diff --git a/examples/USER/phonon/2-1D-diatomic/plot.disp b/examples/PACKAGES/phonon/2-1D-diatomic/plot.disp similarity index 100% rename from examples/USER/phonon/2-1D-diatomic/plot.disp rename to examples/PACKAGES/phonon/2-1D-diatomic/plot.disp diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/README b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/README similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/README rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/README diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/cuu3.eam b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/cuu3.eam similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/cuu3.eam rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/cuu3.eam diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/data.pos b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/data.pos similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/data.pos rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/data.pos diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/disp.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/dos.dat b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos.dat similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/dos.dat rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/dos.dat diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/in.EAM3D b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.EAM3D similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/in.EAM3D rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.EAM3D diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.disp similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.disp diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp2 b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.disp2 similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp2 rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.disp2 diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/in.dos b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.dos similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/in.dos rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/in.dos diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/map.in b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/map.in similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/map.in rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/map.in diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.eps b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdisp.eps similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.eps rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdisp.eps diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.gnuplot b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdisp.gnuplot similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.gnuplot rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdisp.gnuplot diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/pdos.eps b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdos.eps similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/pdos.eps rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/pdos.eps diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.disp b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/plot.disp similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.disp rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/plot.disp diff --git a/examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.dos b/examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/plot.dos similarity index 100% rename from examples/USER/phonon/3-3D-FCC-Cu-EAM/plot.dos rename to examples/PACKAGES/phonon/3-3D-FCC-Cu-EAM/plot.dos diff --git a/examples/USER/phonon/4-Graphene/Graphene.bin.6000000 b/examples/PACKAGES/phonon/4-Graphene/Graphene.bin.6000000 similarity index 100% rename from examples/USER/phonon/4-Graphene/Graphene.bin.6000000 rename to examples/PACKAGES/phonon/4-Graphene/Graphene.bin.6000000 diff --git a/examples/USER/phonon/4-Graphene/Graphene.log b/examples/PACKAGES/phonon/4-Graphene/Graphene.log similarity index 100% rename from examples/USER/phonon/4-Graphene/Graphene.log rename to examples/PACKAGES/phonon/4-Graphene/Graphene.log diff --git a/examples/USER/phonon/4-Graphene/README b/examples/PACKAGES/phonon/4-Graphene/README similarity index 100% rename from examples/USER/phonon/4-Graphene/README rename to examples/PACKAGES/phonon/4-Graphene/README diff --git a/examples/USER/phonon/4-Graphene/SiC.tersoff b/examples/PACKAGES/phonon/4-Graphene/SiC.tersoff similarity index 100% rename from examples/USER/phonon/4-Graphene/SiC.tersoff rename to examples/PACKAGES/phonon/4-Graphene/SiC.tersoff diff --git a/examples/USER/phonon/4-Graphene/data.pos b/examples/PACKAGES/phonon/4-Graphene/data.pos similarity index 100% rename from examples/USER/phonon/4-Graphene/data.pos rename to examples/PACKAGES/phonon/4-Graphene/data.pos diff --git a/examples/USER/phonon/4-Graphene/in.disp b/examples/PACKAGES/phonon/4-Graphene/in.disp similarity index 100% rename from examples/USER/phonon/4-Graphene/in.disp rename to examples/PACKAGES/phonon/4-Graphene/in.disp diff --git a/examples/USER/phonon/4-Graphene/in.graphene b/examples/PACKAGES/phonon/4-Graphene/in.graphene similarity index 100% rename from examples/USER/phonon/4-Graphene/in.graphene rename to examples/PACKAGES/phonon/4-Graphene/in.graphene diff --git a/examples/USER/phonon/4-Graphene/map.in b/examples/PACKAGES/phonon/4-Graphene/map.in similarity index 100% rename from examples/USER/phonon/4-Graphene/map.in rename to examples/PACKAGES/phonon/4-Graphene/map.in diff --git a/examples/USER/phonon/4-Graphene/pdisp.dat b/examples/PACKAGES/phonon/4-Graphene/pdisp.dat similarity index 100% rename from examples/USER/phonon/4-Graphene/pdisp.dat rename to examples/PACKAGES/phonon/4-Graphene/pdisp.dat diff --git a/examples/USER/phonon/4-Graphene/pdisp.eps b/examples/PACKAGES/phonon/4-Graphene/pdisp.eps similarity index 100% rename from examples/USER/phonon/4-Graphene/pdisp.eps rename to examples/PACKAGES/phonon/4-Graphene/pdisp.eps diff --git a/examples/USER/phonon/4-Graphene/pdisp.gnuplot b/examples/PACKAGES/phonon/4-Graphene/pdisp.gnuplot similarity index 100% rename from examples/USER/phonon/4-Graphene/pdisp.gnuplot rename to examples/PACKAGES/phonon/4-Graphene/pdisp.gnuplot diff --git a/examples/USER/phonon/4-Graphene/plot.disp b/examples/PACKAGES/phonon/4-Graphene/plot.disp similarity index 100% rename from examples/USER/phonon/4-Graphene/plot.disp rename to examples/PACKAGES/phonon/4-Graphene/plot.disp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/README.md b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/README.md similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/README.md rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/README.md diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/SiCGe.tersoff b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/SiCGe.tersoff similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/SiCGe.tersoff rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/SiCGe.tersoff diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/in.silicon b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/in.silicon similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/in.silicon rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/in.silicon diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/out.silicon similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/results/out.silicon diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/python/README.md b/examples/PACKAGES/phonon/dynamical_matrix_command/python/README.md similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/README.md rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/README.md diff --git a/examples/USER/phonon/dynamical_matrix_command/python/SiCGe.tersoff b/examples/PACKAGES/phonon/dynamical_matrix_command/python/SiCGe.tersoff similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/SiCGe.tersoff rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/SiCGe.tersoff diff --git a/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py b/examples/PACKAGES/phonon/dynamical_matrix_command/python/dynmat.py similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/dynmat.py rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/dynmat.py diff --git a/examples/USER/phonon/dynamical_matrix_command/python/ff-silicon.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/python/ff-silicon.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/ff-silicon.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/ff-silicon.lmp diff --git a/examples/USER/phonon/dynamical_matrix_command/python/results/dynmat.dat b/examples/PACKAGES/phonon/dynamical_matrix_command/python/results/dynmat.dat similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/results/dynmat.dat rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/results/dynmat.dat diff --git a/examples/USER/phonon/dynamical_matrix_command/python/results/out.dynamt b/examples/PACKAGES/phonon/dynamical_matrix_command/python/results/out.dynamt similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/results/out.dynamt rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/results/out.dynamt diff --git a/examples/USER/phonon/dynamical_matrix_command/python/silicon_input_file.lmp b/examples/PACKAGES/phonon/dynamical_matrix_command/python/silicon_input_file.lmp similarity index 100% rename from examples/USER/phonon/dynamical_matrix_command/python/silicon_input_file.lmp rename to examples/PACKAGES/phonon/dynamical_matrix_command/python/silicon_input_file.lmp diff --git a/examples/USER/misc/filter_corotate/data.peptide b/examples/PACKAGES/plumed/data.peptide similarity index 100% rename from examples/USER/misc/filter_corotate/data.peptide rename to examples/PACKAGES/plumed/data.peptide diff --git a/examples/USER/plumed/in.peptide-plumed b/examples/PACKAGES/plumed/in.peptide-plumed similarity index 100% rename from examples/USER/plumed/in.peptide-plumed rename to examples/PACKAGES/plumed/in.peptide-plumed diff --git a/examples/USER/plumed/log.4Feb20.peptide-plumed.g++.1 b/examples/PACKAGES/plumed/log.4Feb20.peptide-plumed.g++.1 similarity index 100% rename from examples/USER/plumed/log.4Feb20.peptide-plumed.g++.1 rename to examples/PACKAGES/plumed/log.4Feb20.peptide-plumed.g++.1 diff --git a/examples/USER/plumed/log.4Feb20.peptide-plumed.g++.4 b/examples/PACKAGES/plumed/log.4Feb20.peptide-plumed.g++.4 similarity index 100% rename from examples/USER/plumed/log.4Feb20.peptide-plumed.g++.4 rename to examples/PACKAGES/plumed/log.4Feb20.peptide-plumed.g++.4 diff --git a/examples/USER/plumed/plumed.dat b/examples/PACKAGES/plumed/plumed.dat similarity index 100% rename from examples/USER/plumed/plumed.dat rename to examples/PACKAGES/plumed/plumed.dat diff --git a/examples/USER/plumed/reference/colvar b/examples/PACKAGES/plumed/reference/colvar similarity index 100% rename from examples/USER/plumed/reference/colvar rename to examples/PACKAGES/plumed/reference/colvar diff --git a/examples/USER/plumed/reference/p.log b/examples/PACKAGES/plumed/reference/p.log similarity index 100% rename from examples/USER/plumed/reference/p.log rename to examples/PACKAGES/plumed/reference/p.log diff --git a/examples/USER/ptm/ptm_example.in b/examples/PACKAGES/ptm/ptm_example.in similarity index 100% rename from examples/USER/ptm/ptm_example.in rename to examples/PACKAGES/ptm/ptm_example.in diff --git a/examples/USER/qtb/README b/examples/PACKAGES/qtb/README similarity index 71% rename from examples/USER/qtb/README rename to examples/PACKAGES/qtb/README index 41dec0dea3..80cde6395c 100644 --- a/examples/USER/qtb/README +++ b/examples/PACKAGES/qtb/README @@ -1,5 +1,5 @@ -There are example scripts for using the USER-QTB package. -See its src/USER-QTB/README file for more info on +There are example scripts for using the QTB package. +See its src/QTB/README file for more info on quantum nuclear effects and when they are important to include in your model. diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_potential.mod b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/alpha_quartz_potential.mod similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_potential.mod rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/alpha_quartz_potential.mod diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_qtb.mod b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/alpha_quartz_qtb.mod similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_qtb.mod rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/alpha_quartz_qtb.mod diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.1 b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.1 similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.1 rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.1 diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.4 b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.4 similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.4 rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/log.09Feb21.alpha_quartz_qbmsst.g++.4 diff --git a/examples/USER/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF b/examples/PACKAGES/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF similarity index 100% rename from examples/USER/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF rename to examples/PACKAGES/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF diff --git a/examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb b/examples/PACKAGES/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb similarity index 100% rename from examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb rename to examples/PACKAGES/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb diff --git a/examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 b/examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 similarity index 100% rename from examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 rename to examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1 diff --git a/examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 b/examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 similarity index 100% rename from examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 rename to examples/PACKAGES/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4 diff --git a/examples/USER/qtb/methane_qbmsst/ffield.reax b/examples/PACKAGES/qtb/methane_qbmsst/ffield.reax similarity index 100% rename from examples/USER/qtb/methane_qbmsst/ffield.reax rename to examples/PACKAGES/qtb/methane_qbmsst/ffield.reax diff --git a/examples/USER/qtb/methane_qbmsst/methane_qbmsst.in b/examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in similarity index 100% rename from examples/USER/qtb/methane_qbmsst/methane_qbmsst.in rename to examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in diff --git a/examples/USER/qtb/methane_qbmsst/methane_qtb.mod b/examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod similarity index 100% rename from examples/USER/qtb/methane_qbmsst/methane_qtb.mod rename to examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod diff --git a/examples/USER/qtb/methane_qtb/ffield.reax b/examples/PACKAGES/qtb/methane_qtb/ffield.reax similarity index 100% rename from examples/USER/qtb/methane_qtb/ffield.reax rename to examples/PACKAGES/qtb/methane_qtb/ffield.reax diff --git a/examples/USER/qtb/methane_qtb/methane_qtb.in b/examples/PACKAGES/qtb/methane_qtb/methane_qtb.in similarity index 100% rename from examples/USER/qtb/methane_qtb/methane_qtb.in rename to examples/PACKAGES/qtb/methane_qtb/methane_qtb.in diff --git a/examples/USER/quip/data_gap b/examples/PACKAGES/quip/data_gap similarity index 100% rename from examples/USER/quip/data_gap rename to examples/PACKAGES/quip/data_gap diff --git a/examples/USER/quip/data_sw b/examples/PACKAGES/quip/data_sw similarity index 100% rename from examples/USER/quip/data_sw rename to examples/PACKAGES/quip/data_sw diff --git a/examples/USER/quip/gap_example.xml b/examples/PACKAGES/quip/gap_example.xml similarity index 100% rename from examples/USER/quip/gap_example.xml rename to examples/PACKAGES/quip/gap_example.xml diff --git a/examples/USER/quip/gap_example_sparse.dat b/examples/PACKAGES/quip/gap_example_sparse.dat similarity index 100% rename from examples/USER/quip/gap_example_sparse.dat rename to examples/PACKAGES/quip/gap_example_sparse.dat diff --git a/examples/USER/quip/in.gap b/examples/PACKAGES/quip/in.gap similarity index 100% rename from examples/USER/quip/in.gap rename to examples/PACKAGES/quip/in.gap diff --git a/examples/USER/quip/in.molecular b/examples/PACKAGES/quip/in.molecular similarity index 100% rename from examples/USER/quip/in.molecular rename to examples/PACKAGES/quip/in.molecular diff --git a/examples/USER/quip/in.sw b/examples/PACKAGES/quip/in.sw similarity index 100% rename from examples/USER/quip/in.sw rename to examples/PACKAGES/quip/in.sw diff --git a/examples/USER/quip/log.24Jul17.gap.g++.1 b/examples/PACKAGES/quip/log.24Jul17.gap.g++.1 similarity index 100% rename from examples/USER/quip/log.24Jul17.gap.g++.1 rename to examples/PACKAGES/quip/log.24Jul17.gap.g++.1 diff --git a/examples/USER/quip/log.24Jul17.gap.g++.4 b/examples/PACKAGES/quip/log.24Jul17.gap.g++.4 similarity index 100% rename from examples/USER/quip/log.24Jul17.gap.g++.4 rename to examples/PACKAGES/quip/log.24Jul17.gap.g++.4 diff --git a/examples/USER/quip/log.24Jul17.molecular.g++.1 b/examples/PACKAGES/quip/log.24Jul17.molecular.g++.1 similarity index 100% rename from examples/USER/quip/log.24Jul17.molecular.g++.1 rename to examples/PACKAGES/quip/log.24Jul17.molecular.g++.1 diff --git a/examples/USER/quip/log.24Jul17.molecular.g++.4 b/examples/PACKAGES/quip/log.24Jul17.molecular.g++.4 similarity index 100% rename from examples/USER/quip/log.24Jul17.molecular.g++.4 rename to examples/PACKAGES/quip/log.24Jul17.molecular.g++.4 diff --git a/examples/USER/quip/log.24Jul17.sw.g++.1 b/examples/PACKAGES/quip/log.24Jul17.sw.g++.1 similarity index 100% rename from examples/USER/quip/log.24Jul17.sw.g++.1 rename to examples/PACKAGES/quip/log.24Jul17.sw.g++.1 diff --git a/examples/USER/quip/log.24Jul17.sw.g++.4 b/examples/PACKAGES/quip/log.24Jul17.sw.g++.4 similarity index 100% rename from examples/USER/quip/log.24Jul17.sw.g++.4 rename to examples/PACKAGES/quip/log.24Jul17.sw.g++.4 diff --git a/examples/USER/quip/methane-box-8.data b/examples/PACKAGES/quip/methane-box-8.data similarity index 100% rename from examples/USER/quip/methane-box-8.data rename to examples/PACKAGES/quip/methane-box-8.data diff --git a/examples/USER/quip/out.molecular b/examples/PACKAGES/quip/out.molecular similarity index 100% rename from examples/USER/quip/out.molecular rename to examples/PACKAGES/quip/out.molecular diff --git a/examples/USER/quip/sw_example.xml b/examples/PACKAGES/quip/sw_example.xml similarity index 100% rename from examples/USER/quip/sw_example.xml rename to examples/PACKAGES/quip/sw_example.xml diff --git a/examples/USER/rann/in.rann b/examples/PACKAGES/rann/in.rann similarity index 100% rename from examples/USER/rann/in.rann rename to examples/PACKAGES/rann/in.rann diff --git a/examples/USER/rann/log.22Jun21.rann.g++.1 b/examples/PACKAGES/rann/log.22Jun21.rann.g++.1 similarity index 100% rename from examples/USER/rann/log.22Jun21.rann.g++.1 rename to examples/PACKAGES/rann/log.22Jun21.rann.g++.1 diff --git a/examples/USER/rann/log.22Jun21.rann.g++.4 b/examples/PACKAGES/rann/log.22Jun21.rann.g++.4 similarity index 100% rename from examples/USER/rann/log.22Jun21.rann.g++.4 rename to examples/PACKAGES/rann/log.22Jun21.rann.g++.4 diff --git a/examples/USER/reaction/create_atoms_polystyrene/grow_styrene.map b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene.map similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/grow_styrene.map rename to examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene.map diff --git a/examples/USER/reaction/create_atoms_polystyrene/grow_styrene_post.data_template b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/grow_styrene_post.data_template rename to examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template diff --git a/examples/USER/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template rename to examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template diff --git a/examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene b/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene rename to examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene diff --git a/examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 b/examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 rename to examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 diff --git a/examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 b/examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 rename to examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 diff --git a/examples/USER/reaction/create_atoms_polystyrene/trimer.data b/examples/PACKAGES/reaction/create_atoms_polystyrene/trimer.data similarity index 100% rename from examples/USER/reaction/create_atoms_polystyrene/trimer.data rename to examples/PACKAGES/reaction/create_atoms_polystyrene/trimer.data diff --git a/examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt rename to examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt diff --git a/examples/USER/reaction/nylon,6-6_melt/large_nylon_melt.data.gz b/examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/large_nylon_melt.data.gz rename to examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz diff --git a/examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 rename to examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 diff --git a/examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 rename to examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_map b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_map similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_map rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_map diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_map b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_map similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_map rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_map diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template diff --git a/examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template similarity index 100% rename from examples/USER/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template rename to examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template diff --git a/examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized similarity index 100% rename from examples/USER/reaction/tiny_epoxy/in.tiny_epoxy.stabilized rename to examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized diff --git a/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 similarity index 100% rename from examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 rename to examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 diff --git a/examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 similarity index 100% rename from examples/USER/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1.map b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1.map similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp1.map rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1.map diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp1_post.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.data_template diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp1_pre.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_pre.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp1_pre.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_pre.data_template diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp2.map b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp2.map similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp2.map rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp2.map diff --git a/examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp2_post.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn1_stp2_post.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp2_post.data_template diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp1.map b/examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1.map similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn2_stp1.map rename to examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1.map diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp1_post.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_post.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn2_stp1_post.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_post.data_template diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp1_pre.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_pre.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn2_stp1_pre.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp1_pre.data_template diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp2.map b/examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp2.map similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn2_stp2.map rename to examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp2.map diff --git a/examples/USER/reaction/tiny_epoxy/rxn2_stp2_post.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp2_post.data_template similarity index 100% rename from examples/USER/reaction/tiny_epoxy/rxn2_stp2_post.data_template rename to examples/PACKAGES/reaction/tiny_epoxy/rxn2_stp2_post.data_template diff --git a/examples/USER/reaction/tiny_epoxy/tiny_epoxy.data b/examples/PACKAGES/reaction/tiny_epoxy/tiny_epoxy.data similarity index 100% rename from examples/USER/reaction/tiny_epoxy/tiny_epoxy.data rename to examples/PACKAGES/reaction/tiny_epoxy/tiny_epoxy.data diff --git a/examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized similarity index 100% rename from examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized rename to examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized diff --git a/examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability similarity index 100% rename from examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability rename to examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability diff --git a/examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized similarity index 100% rename from examples/USER/reaction/tiny_nylon/in.tiny_nylon.unstabilized rename to examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized diff --git a/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 similarity index 98% rename from examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 rename to examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 index 16e4deef51..57455b04f4 100644 --- a/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 +++ b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 @@ -96,8 +96,8 @@ thermo 50 # dump 1 all xyz 1 test_vis.xyz fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 -WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051) -WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051) +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined diff --git a/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 similarity index 98% rename from examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 rename to examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 index 527d71ce87..b6dcdafc54 100644 --- a/examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 +++ b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 @@ -96,8 +96,8 @@ thermo 50 # dump 1 all xyz 1 test_vis.xyz fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 -WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051) -WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051) +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined diff --git a/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 similarity index 100% rename from examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 rename to examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 diff --git a/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 similarity index 100% rename from examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 diff --git a/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 similarity index 100% rename from examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 rename to examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 diff --git a/examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 similarity index 100% rename from examples/USER/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp1_map b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_map similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp1_map rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_map diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp1_reacted.data_template rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp2_map b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_map similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp2_map rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_map diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp2_reacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp2_reacted.data_template rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.data_template diff --git a/examples/USER/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template diff --git a/examples/USER/reaction/tiny_nylon/tiny_nylon.data b/examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data similarity index 100% rename from examples/USER/reaction/tiny_nylon/tiny_nylon.data rename to examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_map b/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_map similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/2styrene_map rename to examples/PACKAGES/reaction/tiny_polystyrene/2styrene_map diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_reacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/2styrene_reacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/2styrene_reacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/2styrene_unreacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/2styrene_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_map b/examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_map similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_chain_map rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_map diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_reacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_chain_reacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_reacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/chain_chain_unreacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_chain_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_chain_unreacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_map b/examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_map similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_map rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_map diff --git a/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_reacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template rename to examples/PACKAGES/reaction/tiny_polystyrene/chain_plus_styrene_unreacted.data_template diff --git a/examples/USER/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized rename to examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized diff --git a/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 rename to examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 diff --git a/examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 rename to examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 diff --git a/examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data b/examples/PACKAGES/reaction/tiny_polystyrene/tiny_polystyrene.data similarity index 100% rename from examples/USER/reaction/tiny_polystyrene/tiny_polystyrene.data rename to examples/PACKAGES/reaction/tiny_polystyrene/tiny_polystyrene.data diff --git a/examples/USER/scafacos/data.NaCl b/examples/PACKAGES/scafacos/data.NaCl similarity index 100% rename from examples/USER/scafacos/data.NaCl rename to examples/PACKAGES/scafacos/data.NaCl diff --git a/examples/USER/scafacos/data.cloud_wall b/examples/PACKAGES/scafacos/data.cloud_wall similarity index 100% rename from examples/USER/scafacos/data.cloud_wall rename to examples/PACKAGES/scafacos/data.cloud_wall diff --git a/examples/USER/scafacos/data.hammersley_sphere b/examples/PACKAGES/scafacos/data.hammersley_sphere similarity index 100% rename from examples/USER/scafacos/data.hammersley_sphere rename to examples/PACKAGES/scafacos/data.hammersley_sphere diff --git a/examples/USER/scafacos/in.scafacos b/examples/PACKAGES/scafacos/in.scafacos similarity index 100% rename from examples/USER/scafacos/in.scafacos rename to examples/PACKAGES/scafacos/in.scafacos diff --git a/examples/USER/scafacos/in.scafacos.cw.ewald b/examples/PACKAGES/scafacos/in.scafacos.cw.ewald similarity index 100% rename from examples/USER/scafacos/in.scafacos.cw.ewald rename to examples/PACKAGES/scafacos/in.scafacos.cw.ewald diff --git a/examples/USER/scafacos/in.scafacos.cw.fmm b/examples/PACKAGES/scafacos/in.scafacos.cw.fmm similarity index 100% rename from examples/USER/scafacos/in.scafacos.cw.fmm rename to examples/PACKAGES/scafacos/in.scafacos.cw.fmm diff --git a/examples/USER/scafacos/in.scafacos.cw.p2nfft b/examples/PACKAGES/scafacos/in.scafacos.cw.p2nfft similarity index 100% rename from examples/USER/scafacos/in.scafacos.cw.p2nfft rename to examples/PACKAGES/scafacos/in.scafacos.cw.p2nfft diff --git a/examples/USER/scafacos/in.scafacos.cw.p3m b/examples/PACKAGES/scafacos/in.scafacos.cw.p3m similarity index 100% rename from examples/USER/scafacos/in.scafacos.cw.p3m rename to examples/PACKAGES/scafacos/in.scafacos.cw.p3m diff --git a/examples/USER/scafacos/in.scafacos.ewald b/examples/PACKAGES/scafacos/in.scafacos.ewald similarity index 100% rename from examples/USER/scafacos/in.scafacos.ewald rename to examples/PACKAGES/scafacos/in.scafacos.ewald diff --git a/examples/USER/scafacos/in.scafacos.fmm b/examples/PACKAGES/scafacos/in.scafacos.fmm similarity index 100% rename from examples/USER/scafacos/in.scafacos.fmm rename to examples/PACKAGES/scafacos/in.scafacos.fmm diff --git a/examples/USER/scafacos/in.scafacos.hsph.direct b/examples/PACKAGES/scafacos/in.scafacos.hsph.direct similarity index 100% rename from examples/USER/scafacos/in.scafacos.hsph.direct rename to examples/PACKAGES/scafacos/in.scafacos.hsph.direct diff --git a/examples/USER/scafacos/in.scafacos.hsph.fmm b/examples/PACKAGES/scafacos/in.scafacos.hsph.fmm similarity index 100% rename from examples/USER/scafacos/in.scafacos.hsph.fmm rename to examples/PACKAGES/scafacos/in.scafacos.hsph.fmm diff --git a/examples/USER/scafacos/in.scafacos.hsph.p2nfft b/examples/PACKAGES/scafacos/in.scafacos.hsph.p2nfft similarity index 100% rename from examples/USER/scafacos/in.scafacos.hsph.p2nfft rename to examples/PACKAGES/scafacos/in.scafacos.hsph.p2nfft diff --git a/examples/USER/scafacos/in.scafacos.p2nfft b/examples/PACKAGES/scafacos/in.scafacos.p2nfft similarity index 100% rename from examples/USER/scafacos/in.scafacos.p2nfft rename to examples/PACKAGES/scafacos/in.scafacos.p2nfft diff --git a/examples/USER/scafacos/in.scafacos.p3m b/examples/PACKAGES/scafacos/in.scafacos.p3m similarity index 100% rename from examples/USER/scafacos/in.scafacos.p3m rename to examples/PACKAGES/scafacos/in.scafacos.p3m diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 index e0b10de95e..179f3bfcb2 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 @@ -36,7 +36,7 @@ run_style verlet thermo 10 run 100 Setting up ScaFaCoS with solver ewald ... -WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) +WARNING: Virial computation for Ewald not available (src/SCAFACOS/scafacos.cpp:107) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 index f881ed003a..877cf778fa 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 @@ -36,7 +36,7 @@ run_style verlet thermo 10 run 100 Setting up ScaFaCoS with solver ewald ... -WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) +WARNING: Virial computation for Ewald not available (src/SCAFACOS/scafacos.cpp:107) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 index 9410529284..8b6cd7d81e 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 @@ -36,7 +36,7 @@ run_style verlet thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 index 2dc5c07b2b..2d44371649 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 @@ -36,7 +36,7 @@ run_style verlet thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.1 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.1 index e6cd7c506f..a4547054c2 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.1 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.1 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver ewald ... -WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) +WARNING: Virial computation for Ewald not available (src/SCAFACOS/scafacos.cpp:107) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.4 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.4 index 39e0387491..2036be9b24 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.4 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.4 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver ewald ... -WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) +WARNING: Virial computation for Ewald not available (src/SCAFACOS/scafacos.cpp:107) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.fmm.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.fmm.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.fmm.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.fmm.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.1 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.1 index 6b36f0ba91..417c8e9f84 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.g++.1 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.1 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.4 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.4 index 23f55fc5a6..9cad97aa6b 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.g++.4 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.4 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 similarity index 100% rename from examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.1 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.1 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.1 index 92e85e072e..3c5a48c251 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.1 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.1 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.4 similarity index 97% rename from examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.4 rename to examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.4 index 18199eca16..4e079da923 100644 --- a/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.4 +++ b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.4 @@ -46,7 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver p3m ... -WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +WARNING: Virial computation for P3M not available (src/SCAFACOS/scafacos.cpp:104) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 diff --git a/examples/USER/smtbq/data.Alpha b/examples/PACKAGES/smtbq/data.Alpha similarity index 100% rename from examples/USER/smtbq/data.Alpha rename to examples/PACKAGES/smtbq/data.Alpha diff --git a/examples/USER/smtbq/ffield.smtbq.Al b/examples/PACKAGES/smtbq/ffield.smtbq.Al similarity index 100% rename from examples/USER/smtbq/ffield.smtbq.Al rename to examples/PACKAGES/smtbq/ffield.smtbq.Al diff --git a/examples/USER/smtbq/ffield.smtbq.Al2O3 b/examples/PACKAGES/smtbq/ffield.smtbq.Al2O3 similarity index 100% rename from examples/USER/smtbq/ffield.smtbq.Al2O3 rename to examples/PACKAGES/smtbq/ffield.smtbq.Al2O3 diff --git a/examples/USER/smtbq/ffield.smtbq.TiO2 b/examples/PACKAGES/smtbq/ffield.smtbq.TiO2 similarity index 100% rename from examples/USER/smtbq/ffield.smtbq.TiO2 rename to examples/PACKAGES/smtbq/ffield.smtbq.TiO2 diff --git a/examples/USER/smtbq/in.smtbq.Al b/examples/PACKAGES/smtbq/in.smtbq.Al similarity index 100% rename from examples/USER/smtbq/in.smtbq.Al rename to examples/PACKAGES/smtbq/in.smtbq.Al diff --git a/examples/USER/smtbq/in.smtbq.Al2O3 b/examples/PACKAGES/smtbq/in.smtbq.Al2O3 similarity index 100% rename from examples/USER/smtbq/in.smtbq.Al2O3 rename to examples/PACKAGES/smtbq/in.smtbq.Al2O3 diff --git a/examples/USER/smtbq/in.smtbq.TiO2 b/examples/PACKAGES/smtbq/in.smtbq.TiO2 similarity index 100% rename from examples/USER/smtbq/in.smtbq.TiO2 rename to examples/PACKAGES/smtbq/in.smtbq.TiO2 diff --git a/examples/USER/smtbq/log.smtbq.Al.g++.1 b/examples/PACKAGES/smtbq/log.smtbq.Al.g++.1 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al.g++.1 rename to examples/PACKAGES/smtbq/log.smtbq.Al.g++.1 diff --git a/examples/USER/smtbq/log.smtbq.Al.g++.4 b/examples/PACKAGES/smtbq/log.smtbq.Al.g++.4 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al.g++.4 rename to examples/PACKAGES/smtbq/log.smtbq.Al.g++.4 diff --git a/examples/USER/smtbq/log.smtbq.Al2O3.g++.1 b/examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.1 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al2O3.g++.1 rename to examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.1 diff --git a/examples/USER/smtbq/log.smtbq.Al2O3.g++.4 b/examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.4 similarity index 100% rename from examples/USER/smtbq/log.smtbq.Al2O3.g++.4 rename to examples/PACKAGES/smtbq/log.smtbq.Al2O3.g++.4 diff --git a/examples/USER/smtbq/log.smtbq.TiO2.g++.1 b/examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.1 similarity index 100% rename from examples/USER/smtbq/log.smtbq.TiO2.g++.1 rename to examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.1 diff --git a/examples/USER/smtbq/log.smtbq.TiO2.g++.4 b/examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.4 similarity index 100% rename from examples/USER/smtbq/log.smtbq.TiO2.g++.4 rename to examples/PACKAGES/smtbq/log.smtbq.TiO2.g++.4 diff --git a/examples/PACKAGES/sph/README b/examples/PACKAGES/sph/README new file mode 100644 index 0000000000..9df07acab7 --- /dev/null +++ b/examples/PACKAGES/sph/README @@ -0,0 +1 @@ +see the SPH user's guide for a detailed explanation of these examples. diff --git a/examples/USER/sph/cavity_flow/cavity_flow.lmp b/examples/PACKAGES/sph/cavity_flow/cavity_flow.lmp similarity index 100% rename from examples/USER/sph/cavity_flow/cavity_flow.lmp rename to examples/PACKAGES/sph/cavity_flow/cavity_flow.lmp diff --git a/examples/USER/sph/heatconduction/compare_analytic.gpl b/examples/PACKAGES/sph/heatconduction/compare_analytic.gpl similarity index 100% rename from examples/USER/sph/heatconduction/compare_analytic.gpl rename to examples/PACKAGES/sph/heatconduction/compare_analytic.gpl diff --git a/examples/USER/sph/heatconduction/sph_heat_conduction_2d.lmp b/examples/PACKAGES/sph/heatconduction/sph_heat_conduction_2d.lmp similarity index 100% rename from examples/USER/sph/heatconduction/sph_heat_conduction_2d.lmp rename to examples/PACKAGES/sph/heatconduction/sph_heat_conduction_2d.lmp diff --git a/examples/USER/sph/heatconduction/sph_heat_conduction_3d.lmp b/examples/PACKAGES/sph/heatconduction/sph_heat_conduction_3d.lmp similarity index 100% rename from examples/USER/sph/heatconduction/sph_heat_conduction_3d.lmp rename to examples/PACKAGES/sph/heatconduction/sph_heat_conduction_3d.lmp diff --git a/examples/USER/sph/shock_tube/compare_exact.gpl b/examples/PACKAGES/sph/shock_tube/compare_exact.gpl similarity index 100% rename from examples/USER/sph/shock_tube/compare_exact.gpl rename to examples/PACKAGES/sph/shock_tube/compare_exact.gpl diff --git a/examples/USER/sph/shock_tube/exact_solution.dat b/examples/PACKAGES/sph/shock_tube/exact_solution.dat similarity index 100% rename from examples/USER/sph/shock_tube/exact_solution.dat rename to examples/PACKAGES/sph/shock_tube/exact_solution.dat diff --git a/examples/USER/sph/shock_tube/shock2d.lmp b/examples/PACKAGES/sph/shock_tube/shock2d.lmp similarity index 100% rename from examples/USER/sph/shock_tube/shock2d.lmp rename to examples/PACKAGES/sph/shock_tube/shock2d.lmp diff --git a/examples/USER/sph/shock_tube/shock3d.lmp b/examples/PACKAGES/sph/shock_tube/shock3d.lmp similarity index 100% rename from examples/USER/sph/shock_tube/shock3d.lmp rename to examples/PACKAGES/sph/shock_tube/shock3d.lmp diff --git a/examples/USER/sph/water_collapse/data.initial b/examples/PACKAGES/sph/water_collapse/data.initial similarity index 100% rename from examples/USER/sph/water_collapse/data.initial rename to examples/PACKAGES/sph/water_collapse/data.initial diff --git a/examples/USER/sph/water_collapse/water_collapse.lmp b/examples/PACKAGES/sph/water_collapse/water_collapse.lmp similarity index 100% rename from examples/USER/sph/water_collapse/water_collapse.lmp rename to examples/PACKAGES/sph/water_collapse/water_collapse.lmp diff --git a/examples/USER/tally/README b/examples/PACKAGES/tally/README similarity index 84% rename from examples/USER/tally/README rename to examples/PACKAGES/tally/README index fcc58e6e0d..074193b0f2 100644 --- a/examples/USER/tally/README +++ b/examples/PACKAGES/tally/README @@ -1,4 +1,4 @@ -Examples and tests for USER-TALLY compute styles. +Examples and tests for TALLY compute styles. The examples in this directory show where and how compute tally styles are equivalent to other facilities in LAMMPS and thus they can also be diff --git a/examples/USER/tally/data.spce b/examples/PACKAGES/tally/data.spce similarity index 100% rename from examples/USER/tally/data.spce rename to examples/PACKAGES/tally/data.spce diff --git a/examples/USER/tally/in.force b/examples/PACKAGES/tally/in.force similarity index 100% rename from examples/USER/tally/in.force rename to examples/PACKAGES/tally/in.force diff --git a/examples/USER/tally/in.pe b/examples/PACKAGES/tally/in.pe similarity index 100% rename from examples/USER/tally/in.pe rename to examples/PACKAGES/tally/in.pe diff --git a/examples/USER/tally/in.stress b/examples/PACKAGES/tally/in.stress similarity index 100% rename from examples/USER/tally/in.stress rename to examples/PACKAGES/tally/in.stress diff --git a/examples/USER/tally/log.12Jun17.force.1 b/examples/PACKAGES/tally/log.12Jun17.force.1 similarity index 100% rename from examples/USER/tally/log.12Jun17.force.1 rename to examples/PACKAGES/tally/log.12Jun17.force.1 diff --git a/examples/USER/tally/log.12Jun17.force.4 b/examples/PACKAGES/tally/log.12Jun17.force.4 similarity index 100% rename from examples/USER/tally/log.12Jun17.force.4 rename to examples/PACKAGES/tally/log.12Jun17.force.4 diff --git a/examples/USER/tally/log.12Jun17.pe.1 b/examples/PACKAGES/tally/log.12Jun17.pe.1 similarity index 100% rename from examples/USER/tally/log.12Jun17.pe.1 rename to examples/PACKAGES/tally/log.12Jun17.pe.1 diff --git a/examples/USER/tally/log.12Jun17.pe.4 b/examples/PACKAGES/tally/log.12Jun17.pe.4 similarity index 100% rename from examples/USER/tally/log.12Jun17.pe.4 rename to examples/PACKAGES/tally/log.12Jun17.pe.4 diff --git a/examples/USER/tally/log.12Jun17.stress.1 b/examples/PACKAGES/tally/log.12Jun17.stress.1 similarity index 100% rename from examples/USER/tally/log.12Jun17.stress.1 rename to examples/PACKAGES/tally/log.12Jun17.stress.1 diff --git a/examples/USER/tally/log.12Jun17.stress.4 b/examples/PACKAGES/tally/log.12Jun17.stress.4 similarity index 100% rename from examples/USER/tally/log.12Jun17.stress.4 rename to examples/PACKAGES/tally/log.12Jun17.stress.4 diff --git a/examples/USER/uef/README b/examples/PACKAGES/uef/README similarity index 92% rename from examples/USER/uef/README rename to examples/PACKAGES/uef/README index aaf53fa2a1..bedffbfb08 100644 --- a/examples/USER/uef/README +++ b/examples/PACKAGES/uef/README @@ -1,4 +1,4 @@ -This directory contains two short example scripts for the USER-UEF +This directory contains two short example scripts for the UEF package. diff --git a/examples/USER/uef/npt_biaxial/data.wca b/examples/PACKAGES/uef/npt_biaxial/data.wca similarity index 100% rename from examples/USER/uef/npt_biaxial/data.wca rename to examples/PACKAGES/uef/npt_biaxial/data.wca diff --git a/examples/USER/uef/npt_biaxial/in.npt_biaxial b/examples/PACKAGES/uef/npt_biaxial/in.npt_biaxial similarity index 100% rename from examples/USER/uef/npt_biaxial/in.npt_biaxial rename to examples/PACKAGES/uef/npt_biaxial/in.npt_biaxial diff --git a/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 b/examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 similarity index 100% rename from examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 rename to examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 diff --git a/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 b/examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 similarity index 100% rename from examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 rename to examples/PACKAGES/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 diff --git a/examples/USER/uef/nvt_uniaxial/data.wca b/examples/PACKAGES/uef/nvt_uniaxial/data.wca similarity index 100% rename from examples/USER/uef/nvt_uniaxial/data.wca rename to examples/PACKAGES/uef/nvt_uniaxial/data.wca diff --git a/examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial b/examples/PACKAGES/uef/nvt_uniaxial/in.nvt_uniaxial similarity index 100% rename from examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial rename to examples/PACKAGES/uef/nvt_uniaxial/in.nvt_uniaxial diff --git a/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 b/examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 similarity index 100% rename from examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 rename to examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 diff --git a/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 b/examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 similarity index 100% rename from examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 rename to examples/PACKAGES/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 diff --git a/examples/USER/vtk/.gitignore b/examples/PACKAGES/vtk/.gitignore similarity index 100% rename from examples/USER/vtk/.gitignore rename to examples/PACKAGES/vtk/.gitignore diff --git a/examples/USER/vtk/in.vtk b/examples/PACKAGES/vtk/in.vtk similarity index 100% rename from examples/USER/vtk/in.vtk rename to examples/PACKAGES/vtk/in.vtk diff --git a/examples/USER/vtk/in.vtp b/examples/PACKAGES/vtk/in.vtp similarity index 100% rename from examples/USER/vtk/in.vtp rename to examples/PACKAGES/vtk/in.vtp diff --git a/examples/USER/yaff/README b/examples/PACKAGES/yaff/README similarity index 100% rename from examples/USER/yaff/README rename to examples/PACKAGES/yaff/README diff --git a/examples/USER/yaff/mil53al/lammps.data b/examples/PACKAGES/yaff/mil53al/lammps.data similarity index 100% rename from examples/USER/yaff/mil53al/lammps.data rename to examples/PACKAGES/yaff/mil53al/lammps.data diff --git a/examples/USER/yaff/mil53al/lammps.in b/examples/PACKAGES/yaff/mil53al/lammps.in similarity index 100% rename from examples/USER/yaff/mil53al/lammps.in rename to examples/PACKAGES/yaff/mil53al/lammps.in diff --git a/examples/USER/yaff/mof5/lammps.data b/examples/PACKAGES/yaff/mof5/lammps.data similarity index 100% rename from examples/USER/yaff/mof5/lammps.data rename to examples/PACKAGES/yaff/mof5/lammps.data diff --git a/examples/USER/yaff/mof5/lammps.in b/examples/PACKAGES/yaff/mof5/lammps.in similarity index 100% rename from examples/USER/yaff/mof5/lammps.in rename to examples/PACKAGES/yaff/mof5/lammps.in diff --git a/examples/README b/examples/README index 9efac36a47..4f4f671a29 100644 --- a/examples/README +++ b/examples/README @@ -5,7 +5,8 @@ problems you can run with LAMMPS. lower-case directories = simple test problems for LAMMPS and its packages upper-case directories = more complex problems -USER directory with its own sub-directories = tests for USER packages +PACKAGES directory with its own sub-directories = tests for specific packages +USER-MISC directory with its own sub-directories = tests for commands in USER-MISC package Each is discussed below. @@ -170,6 +171,12 @@ The MC directory has an example script for using LAMMPS as an energy-evaluation engine in a iterative Monte Carlo energy-relaxation loop. +The PACKAGES directory contains subdirectories of example scripts for +individual packages. Most of those are contributed by the corresponding +package developers. See the README files in those directories +for more info. See the doc/html/Build_package.html file for more info +about installing and building packages. + The TIP4P directory has an example for testing forces computed on a GPU. @@ -179,10 +186,11 @@ lj, real, and metal. So that you can see how to scale/unscale input and output values read/written by LAMMPS to verify you are performing the same simulation in different unit systems. -The USER directory contains subdirectories of user-provided example -scripts for ser packages. See the README files in those directories +The USER-MISC directory contains subdirectories of example scripts for +individual commands in the USER-MISC package. Most of those are contributed +by the corresponding developers. See the README files in those directories for more info. See the doc/html/Build_package.html file for more info -about installing and building user packages. +about installing and building packages. The VISCOSITY directory has example scripts for computing the viscosity of a LJ liquid using 4 different methods. See the diff --git a/examples/TIP4P/gpu_dump/data.spce b/examples/TIP4P/gpu_dump/data.spce deleted file mode 120000 index 4c8051fdff..0000000000 --- a/examples/TIP4P/gpu_dump/data.spce +++ /dev/null @@ -1 +0,0 @@ -../../rdf-adf/data.spce \ No newline at end of file diff --git a/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1 b/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1 deleted file mode 100644 index faa6d3c117..0000000000 --- a/examples/TIP4P/gpu_dump/dump.force_cpu.19Dec19.tip4p.g++.1 +++ /dev/null @@ -1,9018 +0,0 @@ -ITEM: TIMESTEP -0 -ITEM: NUMBER OF ATOMS -4500 -ITEM: BOX BOUNDS pp pp pp -2.6450000000000001e-02 3.5532800000000002e+01 -2.6450000000000001e-02 3.5532800000000002e+01 -2.6409999999999999e-02 3.5473599999999998e+01 -ITEM: ATOMS id type x y z fx fy fz -1 1 12.1247 28.092 22.2745 44.3296 17.0725 48.5356 -2 2 12.4974 28.7565 22.854 -24.598 -41.7029 -32.885 -3 2 11.5314 28.5784 21.7021 -26.0334 10.24 -23.1056 -4 1 1.17081 29.3781 23.7307 -74.0189 -7.00332 56.5394 -5 2 1.86259 29.4619 23.0745 28.6874 -4.77355 -53.1747 -6 2 0.455888 28.9379 23.2709 28.8474 14.4006 -7.70694 -7 1 29.6824 14.7369 21.6275 -6.84135 -10.4682 -14.9806 -8 2 30.5192 14.9459 21.2125 -6.0991 2.52794 20.3786 -9 2 29.7669 15.072 22.5202 13.979 5.65532 2.32707 -10 1 10.8733 7.00191 35.1099 71.1535 29.5945 64.996 -11 2 11.0641 6.25389 34.5439 -29.2143 -6.46229 -20.2952 -12 2 9.99418 7.27965 34.8524 -52.7015 -16.0671 -37.9354 -13 1 9.46552 6.437 19.7997 85.2674 -39.8413 10.9994 -14 2 9.09748 6.31006 18.9252 -72.8621 17.4338 -56.4264 -15 2 10.2738 5.92429 19.7966 -6.89627 25.8832 52.2923 -16 1 3.17887 29.6978 22.1201 11.0669 36.9603 2.15921 -17 2 3.20092 30.5775 21.7434 1.96842 -53.5324 1.10468 -18 2 3.38088 29.1173 21.3863 -1.13041 18.9593 -2.63733 -19 1 23.3853 11.3001 30.7823 -23.52 11.4998 -1.78141 -20 2 23.7233 10.5129 31.2094 -10.6549 -69.8744 42.1205 -21 2 24.1635 11.7415 30.442 31.685 49.5553 -38.1127 -22 1 11.0372 10.4605 30.1467 -38.6093 -16.0236 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-84.4452 -1968 2 5.70739 11.1679 7.92785 -16.8375 -20.6972 23.7848 -1969 1 10.1308 13.458 3.45525 -19.289 -27.8108 18.398 -1970 2 9.47924 14.0224 3.03904 59.8681 9.66437 -14.5467 -1971 2 10.9686 13.7582 3.10271 -46.1431 27.4514 -18.5848 -1972 1 2.78627 23.982 22.6844 61.7668 -37.9237 -21.697 -1973 2 2.23775 23.3518 22.2172 -8.17893 -35.1455 -20.7984 -1974 2 2.17291 24.6441 23.0031 -46.5196 68.0647 37.1881 -1975 1 29.6763 34.0661 9.4221 -25.2085 -34.5053 76.7307 -1976 2 29.4116 33.869 10.3206 -13.3027 -22.4655 -41.4267 -1977 2 30.2063 34.8598 9.49668 49.5961 63.0099 -39.1917 -1978 1 17.3951 25.0142 9.24935 74.1256 -119.972 13.8699 -1979 2 18.0557 25.5131 8.76884 -7.409 57.2755 -19.7204 -1980 2 17.7887 24.1502 9.37149 -78.6001 67.4017 9.86198 -1981 1 11.139 14.0733 32.9523 31.4256 -0.03008 -5.2348 -1982 2 12.066 14.2725 33.0835 -15.5197 6.63618 -14.1202 -1983 2 10.9478 13.388 33.5926 -13.6636 8.48879 -3.5036 -1984 1 1.12572 32.0183 27.5356 24.6266 46.3494 2.8897 -1985 2 0.546692 31.3048 27.8037 -3.08121 -31.7776 -12.0256 -1986 2 1.55521 31.6943 26.7439 -12.2274 -17.2869 5.12609 -1987 1 16.7457 10.366 22.1454 -15.3164 -22.3958 -16.0252 -1988 2 17.6114 10.1816 22.5099 -14.3265 37.126 0.80158 -1989 2 16.5565 11.2637 22.4183 29.9704 0.0490406 16.3066 -1990 1 3.7604 22.8172 16.7231 -94.979 -46.3638 63.4302 -1991 2 3.80199 23.6592 16.2696 52.6252 2.42304 -21.4425 -1992 2 4.60092 22.4005 16.533 37.2062 36.1623 -37.5204 -1993 1 1.85858 2.74219 27.3787 -16.8615 -16.8421 15.8272 -1994 2 2.54214 2.17108 27.7292 -4.59146 35.0941 -40.6374 -1995 2 2.27945 3.20266 26.6527 25.2819 -23.6186 22.0617 -1996 1 20.9735 33.5714 23.8814 -106.803 36.5464 88.0259 -1997 2 21.6236 32.9171 24.1374 45.6079 -11.0665 -63.4639 -1998 2 21.2264 33.8268 22.9943 67.7875 -35.3184 -31.857 -1999 1 14.9346 6.66221 21.3527 -126.314 -3.88715 -82.8474 -2000 2 14.0911 6.81595 20.927 39.2653 62.6904 53.7569 -2001 2 15.1982 5.79131 21.0556 85.678 -53.7307 17.9606 -2002 1 22.2461 5.18918 17.8715 -69.145 -31.4218 -18.0837 -2003 2 21.9344 5.83223 17.2347 -27.7401 11.8107 -16.433 -2004 2 23.137 5.47038 18.0801 108.344 19.9553 34.4799 -2005 1 31.7359 29.9237 26.3736 -84.3482 -146.558 -73.4212 -2006 2 32.1627 30.6728 26.7895 111.481 40.2155 8.28834 -2007 2 32.4462 29.4563 25.9339 -20.9159 104.035 73.147 -2008 1 24.5541 23.2903 6.20562 34.8499 -73.6669 40.9676 -2009 2 25.3233 22.7463 6.0363 -54.9847 54.2625 4.3351 -2010 2 24.1245 22.8728 6.95223 10.9892 27.9336 -36.5991 -2011 1 25.8826 13.3692 31.6978 -39.5587 45.0721 109.942 -2012 2 26.0654 12.9392 30.8624 14.4928 -55.2593 -101.315 -2013 2 26.7459 13.5818 32.0524 34.4682 10.678 13.5079 -2014 1 31.9081 10.2232 30.8508 60.5777 139.069 -26.1959 -2015 2 32.2481 10.7082 31.6027 -21.552 -31.8062 -26.0603 -2016 2 31.6024 9.39393 31.2183 -39.6468 -107.76 57.4176 -2017 1 0.849757 3.66316 11.6882 -66.4227 -77.864 -86.3174 -2018 2 0.839326 4.56785 12.0007 9.47524 78.9317 34.8726 -2019 2 0.14017 3.62253 11.047 60.8788 -7.45935 55.9047 -2020 1 12.6493 6.4064 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48.6556 -2038 1 26.8593 19.3342 13.6851 30.7677 67.3413 -148.698 -2039 2 26.0004 19.2038 14.0871 -50.0945 -27.4421 67.323 -2040 2 27.4811 19.0115 14.3374 18.1351 -38.3726 82.2067 -2041 1 7.83885 28.1834 15.8334 16.5365 20.604 -8.56175 -2042 2 7.60386 27.3316 16.2014 -33.7069 20.3127 -2.25908 -2043 2 7.02096 28.6807 15.838 5.21927 -39.3621 14.9074 -2044 1 32.631 18.2249 29.7861 41.9215 38.3318 11.8543 -2045 2 32.1421 17.5039 29.3895 -39.2744 -31.6531 -17.1652 -2046 2 31.957 18.8189 30.1164 -14.576 -4.73824 -0.949144 -2047 1 3.25628 33.4796 7.39391 71.9746 30.5666 -22.4299 -2048 2 4.11434 33.8297 7.63344 -69.5572 -27.2519 -15.9057 -2049 2 3.24436 33.5071 6.43718 -2.52475 -1.44402 31.1707 -2050 1 0.842237 3.50013 3.05753 16.9517 -63.8559 -23.0072 -2051 2 1.37533 4.09985 3.57944 19.8724 20.4219 19.8016 -2052 2 1.42823 2.77011 2.85767 -26.1771 37.5505 12.1175 -2053 1 25.1227 15.9755 21.4703 2.5941 62.4248 -49.2139 -2054 2 25.4287 15.7265 22.3424 20.0835 -17.1737 50.8233 -2055 2 25.5184 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-1861 1 31.8145 4.72505 13.9315 3.51696 2.46284 -9.06312 -1862 2 32.7583 4.70545 14.09 -0.860689 -3.55617 -0.581682 -1863 2 31.7034 4.28385 13.0893 -0.970181 0.0843368 0.95089 -1864 1 24.2418 18.8281 7.32442 19.8697 2.2108 -6.54484 -1865 2 24.4226 18.4746 8.19539 2.81024 2.54724 -0.45717 -1866 2 25.0242 18.62 6.81378 0.970146 1.95667 -0.32899 -1867 1 30.0972 6.70621 9.34508 -7.11575 -10.6459 5.95087 -1868 2 30.6725 6.85653 10.0952 0.385181 0.328039 -2.98084 -1869 2 30.3149 5.82236 9.04901 -0.729241 -1.02843 1.76281 -1870 1 6.44717 22.2065 16.5255 -3.59057 -4.00173 16.1678 -1871 2 6.64259 21.3661 16.94 3.11856 0.683016 0.647408 -1872 2 6.76977 22.1127 15.6292 0.416604 1.37739 1.48251 -1873 1 26.5355 4.89359 31.4896 -7.52384 6.40183 3.48158 -1874 2 26.4108 4.09458 30.9775 1.28288 1.47802 -0.0815147 -1875 2 26.2333 5.59673 30.9148 0.174929 0.381041 0.467201 -1876 1 16.6203 30.9547 12.5759 2.29181 3.31892 0.336466 -1877 2 17.5257 31.2473 12.4718 -0.428516 1.14843 0.686943 -1878 2 16.5321 30.7758 13.5121 -0.928822 -0.936925 -0.848334 -1879 1 4.87322 34.619 34.4415 0.500801 -6.20716 0.421653 -1880 2 5.78673 34.74 34.7005 -1.1578 1.99203 1.93461 -1881 2 4.62688 35.45 34.0352 -2.67178 0.290957 3.74667 -1882 1 2.50149 12.2801 26.0877 -3.61028 1.8033 -1.8975 -1883 2 3.14626 12.3987 25.3903 -1.63452 1.76565 0.0939493 -1884 2 2.99924 11.9029 26.8131 -0.546173 -2.4228 -3.67059 -1885 1 11.0044 34.2914 8.17886 15.9126 -2.73607 2.69613 -1886 2 10.7906 34.3407 9.11057 -2.69506 0.109664 -0.892116 -1887 2 11.8744 33.8931 8.15305 0.922075 0.494336 3.88877 -1888 1 10.4642 16.7648 26.4147 2.80971 1.51282 -9.61072 -1889 2 10.4264 17.0779 27.3185 1.17471 -1.35509 -0.280756 -1890 2 11.3146 17.0636 26.0926 0.590472 -1.32977 -0.414974 -1891 1 17.2152 4.69462 34.6747 11.9213 0.65814 -4.69715 -1892 2 18.0195 4.45625 34.2137 1.04857 -0.57361 0.535519 -1893 2 16.8774 3.86516 35.0125 1.91423 1.04657 2.96864 -1894 1 6.97445 35.1353 32.2671 9.97328 -11.6302 -7.33462 -1895 2 7.55154 34.8288 32.9666 0.774769 -1.62199 -1.46055 -1896 2 6.63884 0.467797 32.5832 1.02155 -1.24749 0.362107 -1897 1 30.2645 4.69075 18.0422 0.694439 -2.46184 2.97624 -1898 2 29.6017 4.00886 17.9326 1.10342 -1.19819 0.759635 -1899 2 30.7589 4.42264 18.8167 -1.07894 2.27368 1.54311 -1900 1 14.1656 29.632 31.6787 5.05867 -0.355939 -0.980506 -1901 2 14.4451 30.4041 31.1867 -0.842964 -0.790639 -0.294246 -1902 2 13.5563 29.1821 31.0933 0.0725257 -1.19259 1.4708 -1903 1 22.4084 9.52165 9.7397 0.735332 -1.67091 -3.93305 -1904 2 22.7212 9.37225 10.6319 -1.09142 1.00002 -0.542777 -1905 2 23.025 9.04279 9.18587 1.34861 1.44662 0.230846 -1906 1 22.2367 0.136878 35.4162 2.39769 -1.00634 11.3877 -1907 2 23.1336 0.346647 0.22933 -0.416125 0.426818 1.11968 -1908 2 21.8755 35.1657 0.715801 -0.0814999 0.0454572 0.682247 -1909 1 30.8013 21.126 11.6255 -3.46793 -5.01909 1.70411 -1910 2 31.1601 21.6971 10.9462 -4.45423 -1.15624 -2.23432 -1911 2 31.4336 20.4108 11.6964 2.44046 2.26421 0.934019 -1912 1 27.4508 5.23152 21.4006 1.74025 1.89877 19.0993 -1913 2 27.8319 4.73772 22.1266 0.4018 0.947765 0.850108 -1914 2 26.5774 5.47438 21.7079 -0.634266 -2.0344 0.72118 -1915 1 34.2517 16.5309 18.5306 0.907524 -6.93269 -4.04601 -1916 2 34.8715 15.8322 18.7399 -0.501769 0.835994 1.04597 -1917 2 33.8909 16.2844 17.6789 -0.976215 1.5179 3.59303 -1918 1 32.115 35.0905 16.482 2.22898 -11.9743 -20.9485 -1919 2 32.966 34.6682 16.5991 -0.636814 -0.495605 0.383446 -1920 2 32.3008 0.353133 15.9431 0.148533 0.858467 3.15742 -1921 1 5.2813 31.5245 24.5891 -0.88265 3.56081 0.527901 -1922 2 5.6102 31.6063 25.4843 2.8911 0.897716 -1.16555 -1923 2 5.50826 32.3562 24.1732 0.0452461 -1.83796 -1.84019 -1924 1 25.7935 25.4126 18.2933 8.42974 5.04501 3.04403 -1925 2 25.4171 24.7186 17.752 -3.18932 0.154086 3.92798 -1926 2 25.7522 26.195 17.7434 -1.62301 -1.62428 -0.262324 -1927 1 4.94055 22.5134 12.7286 -9.04805 -9.98913 0.740441 -1928 2 4.66669 21.7387 13.2196 -2.25032 0.777095 0.693415 -1929 2 4.12797 22.9905 12.5602 2.55025 2.81834 1.88639 -1930 1 12.3705 3.40796 24.8702 -10.2718 -6.94273 4.16449 -1931 2 11.5354 3.79201 25.1374 1.11482 2.05237 1.26765 -1932 2 12.7415 4.04279 24.2574 1.31703 -1.09657 1.0894 -1933 1 17.2229 21.0728 32.2314 -8.179 -5.27121 -18.2871 -1934 2 16.3825 21.3411 31.86 1.15239 -1.37236 -2.54915 -1935 2 17.7485 20.8146 31.4742 0.636225 0.416061 0.167394 -1936 1 25.4211 13.6617 27.4256 -0.423575 1.5864 -14.144 -1937 2 25.9311 14.3939 27.0792 0.209498 -1.21813 2.94262 -1938 2 25.0385 13.2482 26.6517 -1.88498 1.40152 0.678356 -1939 1 31.3452 0.921707 6.09496 5.75289 0.0456399 -1.04313 -1940 2 31.5193 0.206077 5.48357 1.7599 -1.91271 2.66807 -1941 2 31.9558 1.61205 5.83652 -0.775733 -0.136291 -2.46929 -1942 1 14.5238 27.1426 0.855822 -0.28203 -13.8472 13.0001 -1943 2 15.0637 27.8615 0.527327 -2.90129 -0.385453 -1.8344 -1944 2 14.5862 27.2115 1.8085 -1.36301 3.80564 -1.12804 -1945 1 28.8746 13.8014 31.4027 -2.88672 6.47051 7.86952 -1946 2 29.2232 14.2517 32.1721 1.91816 0.252514 -1.72337 -1947 2 28.8041 14.4848 30.7362 -2.55312 0.206489 0.885327 -1948 1 32.2921 1.69364 30.0162 -5.24318 6.11719 0.10458 -1949 2 32.9509 1.85569 29.3409 -1.02656 -2.73336 -0.95222 -1950 2 31.7703 2.49576 30.0398 2.18736 -0.0064308 0.36284 -1951 1 12.6171 8.26014 20.3408 -0.40671 -8.63132 6.16379 -1952 2 12.7962 8.9555 20.9737 1.99194 1.08407 -2.86475 -1953 2 12.1389 8.69542 19.635 2.27749 -2.82959 -1.29442 -1954 1 12.5264 25.4516 7.87552 -4.00904 -0.543437 10.3565 -1955 2 12.9562 24.654 8.18449 -0.215524 -0.0928553 -1.74864 -1956 2 11.705 25.1474 7.48948 4.50811 -0.52052 -4.58555 -1957 1 1.10395 20.9772 6.76689 -12.4418 -4.87906 -17.0173 -1958 2 0.841381 21.0115 5.84704 0.961335 2.29109 -0.167377 -1959 2 1.91806 21.4794 6.80294 -0.662195 -1.08577 2.11991 -1960 1 4.82166 0.411135 13.4723 -6.95497 7.27665 -10.2603 -1961 2 4.31632 1.13144 13.0954 -1.71759 1.5163 4.71861 -1962 2 4.19868 35.4546 14.0325 3.34255 0.282635 2.02706 -1963 1 7.98045 14.3231 18.3954 3.08041 14.4496 -7.04888 -1964 2 7.47829 15.0927 18.6634 -2.22303 -2.54215 1.24386 -1965 2 7.75094 13.6513 19.0374 2.28408 -1.12721 -2.33416 -1966 1 6.57567 10.8403 7.6939 2.74017 2.33053 3.06743 -1967 2 6.87818 11.4306 7.00375 -0.816871 -0.135469 -0.424054 -1968 2 5.69956 11.1571 7.91368 0.353319 -2.48188 -0.273827 -1969 1 10.1296 13.4617 3.4523 -7.92991 7.36607 -13.5551 -1970 2 9.4814 14.0411 3.05172 2.81436 1.47522 -1.87702 -1971 2 10.9658 13.745 3.08241 -0.999119 -0.282534 1.18626 -1972 1 2.78873 23.9803 22.6823 7.39875 -2.15156 -6.43063 -1973 2 2.24341 23.3472 22.2153 1.0523 -1.39215 0.678747 -1974 2 2.17172 24.6381 23.0029 -0.309516 -1.48449 0.660469 -1975 1 29.681 34.0668 9.41834 9.5803 -0.140978 0.198088 -1976 2 29.4023 33.8738 10.3135 -0.39736 4.75337 0.09998 -1977 2 30.2232 34.8514 9.49973 0.132783 -0.224159 -2.50537 -1978 1 17.3964 25.0161 9.25437 -10.6964 6.49204 10.2875 -1979 2 18.0663 25.5133 8.78518 -2.57426 -0.200004 -1.71763 -1980 2 17.7826 24.1488 9.37642 -1.26016 -0.11254 -2.41078 -1981 1 11.1411 14.0768 32.9507 2.74692 8.93145 -23.0737 -1982 2 12.0674 14.2752 33.0877 0.326495 0.0181461 -2.13137 -1983 2 10.9448 13.3932 33.5914 -1.40918 5.092 2.7765 -1984 1 1.12682 32.0133 27.5402 4.517 -1.51145 -4.02069 -1985 2 0.552584 31.2959 27.8081 3.00058 -1.99467 0.131487 -1986 2 1.5621 31.6905 26.7511 1.52551 1.30495 -0.0263278 -1987 1 16.7481 10.3694 22.1507 0.264039 13.0692 4.69918 -1988 2 17.6248 10.1979 22.4946 -0.0377334 0.851346 -4.78636 -1989 2 16.5624 11.2729 22.4066 -1.46932 -0.377234 0.467584 -1990 1 3.76375 22.8172 16.7293 -4.0741 -10.5757 1.02761 -1991 2 3.80151 23.6586 16.2743 -0.690304 1.29329 3.69566 -1992 2 4.5994 22.3969 16.5262 -0.197813 0.973283 -0.721214 -1993 1 1.85399 2.73861 27.3822 3.20071 -7.68688 -3.72082 -1994 2 2.53752 2.17131 27.7389 0.0246343 -1.14856 -1.23911 -1995 2 2.27395 3.18876 26.6492 0.934788 1.93265 2.10385 -1996 1 20.9724 33.5726 23.8784 8.10433 -9.20518 -4.51155 -1997 2 21.6189 32.9194 24.1461 -2.046 -3.87957 -3.38316 -1998 2 21.2405 33.8276 22.9955 0.119388 1.30018 0.791288 -1999 1 14.9356 6.66547 21.3473 -4.32378 2.01425 -5.99167 -2000 2 14.0917 6.81509 20.921 0.850589 0.904261 -2.27949 -2001 2 15.2025 5.79487 21.0522 1.98877 1.97817 -3.72271 -2002 1 22.2485 5.18667 17.87 13.215 -1.9753 -1.37536 -2003 2 21.9401 5.84134 17.2434 -1.85661 0.524428 2.90348 -2004 2 23.1453 5.4526 18.0731 0.178716 1.34064 -2.4977 -2005 1 31.7392 29.9223 26.3752 4.76914 0.177865 5.41636 -2006 2 32.1647 30.6696 26.7955 0.903997 -0.87703 1.20137 -2007 2 32.4505 29.4583 25.9336 0.0227674 -0.433216 0.401033 -2008 1 24.5495 23.287 6.21014 -9.6064 5.24279 8.20718 -2009 2 25.3283 22.7624 6.02443 0.116339 4.39189 1.8768 -2010 2 24.1468 22.8595 6.966 0.2289 -0.0589481 -2.13137 -2011 1 25.8848 13.3641 31.6949 11.7976 1.283 28.4217 -2012 2 26.0644 12.9328 30.8595 -3.81135 -1.20515 1.50928 -2013 2 26.7491 13.586 32.0412 2.1747 1.23594 -3.73301 -2014 1 31.9059 10.2239 30.8521 3.15397 -0.693558 5.50864 -2015 2 32.2432 10.7005 31.6105 -2.64306 -0.474064 1.50947 -2016 2 31.6065 9.38729 31.2082 -1.91976 0.707005 -1.14165 -2017 1 0.84878 3.6625 11.6852 3.82778 -4.24681 3.04899 -2018 2 0.853073 4.56299 12.0097 1.00506 -0.863618 -0.913913 -2019 2 0.134074 3.64014 11.0488 -1.02679 -1.02985 3.07516 -2020 1 12.653 6.40924 27.2569 -10.896 -2.3651 4.67545 -2021 2 12.0107 5.88536 26.7781 -1.95087 -0.422561 2.90655 -2022 2 12.932 7.07765 26.6311 3.33215 -5.37792 -3.19321 -2023 1 15.9575 7.9951 15.8816 6.43964 -4.15323 6.61769 -2024 2 16.7831 7.8467 15.4206 0.588477 2.84349 1.20404 -2025 2 15.4803 8.61195 15.3266 -2.08725 -4.05933 -0.295667 -2026 1 20.0375 20.1391 12.665 -4.11025 1.52341 -3.10314 -2027 2 19.4274 20.3342 11.9537 2.89664 -0.270393 -1.94487 -2028 2 20.3292 19.244 12.4922 -2.13637 -0.289793 3.97752 -2029 1 21.356 6.30845 10.1293 11.8845 -7.32937 -8.40835 -2030 2 20.9041 5.54426 10.4872 -0.836302 1.13214 -0.345734 -2031 2 21.8894 6.63336 10.8547 0.11176 0.0745871 -0.490015 -2032 1 35.1526 30.9366 9.83286 7.59845 5.2547 -1.12957 -2033 2 0.311501 31.622 9.89575 0.964885 -1.25019 -0.233494 -2034 2 34.6019 31.0651 10.6052 0.344797 -0.803576 -0.904465 -2035 1 4.27525 27.2569 26.2869 4.28071 5.72746 7.8462 -2036 2 3.39987 27.3692 25.9163 0.165296 -0.828825 2.86229 -2037 2 4.39971 28.0244 26.8452 0.266735 0.0706906 -1.3371 -2038 1 26.8649 19.3391 13.6882 0.177125 1.61838 2.46927 -2039 2 26.0052 19.1944 14.0834 -0.103725 0.362381 -1.50792 -2040 2 27.4862 19.0117 14.3386 -0.695576 -0.902314 0.251747 -2041 1 7.83542 28.181 15.8382 -13.3943 -2.71551 5.4783 -2042 2 7.57758 27.3247 16.1794 -0.25335 2.11014 -2.48558 -2043 2 7.02351 28.6878 15.8233 1.95232 1.88776 0.576467 -2044 1 32.6262 18.2228 29.791 -14.1882 1.19327 -8.66236 -2045 2 32.1279 17.5186 29.3763 0.458993 0.618559 0.834874 -2046 2 31.9606 18.8321 30.1103 1.27184 -0.0824113 1.15038 -2047 1 3.26267 33.4782 7.39241 0.72256 1.05107 -6.58477 -2048 2 4.1177 33.8412 7.62335 -1.20198 1.46048 -0.601021 -2049 2 3.2457 33.4941 6.43549 0.071718 0.812761 -0.0287205 -2050 1 0.844894 3.50214 3.06141 10.9265 -6.46418 5.34726 -2051 2 1.3825 4.10673 3.57296 -1.34547 0.02462 1.3239 -2052 2 1.43348 2.7774 2.85035 0.956803 -0.0258241 1.47884 -2053 1 25.1225 15.9729 21.4727 1.26189 6.66637 7.55006 -2054 2 25.4376 15.7328 22.3441 1.99941 -1.50251 -1.18582 -2055 2 25.5145 16.8296 21.3033 0.649747 -0.161475 0.915999 -2056 1 7.27486 22.2101 14.0385 10.1815 -3.49421 -8.18063 -2057 2 7.84619 21.46 13.8737 1.50039 1.74304 -3.72093 -2058 2 6.53621 22.0846 13.4428 1.08182 3.6941 2.34564 -2059 1 14.2409 9.72949 11.5638 -2.21614 13.7167 -2.62635 -2060 2 13.6906 9.62021 10.7883 -0.22348 -2.43277 0.646692 -2061 2 14.9733 10.2682 11.2645 -0.353329 -0.504752 -2.50308 -2062 1 24.5604 34.1124 22.5076 2.81011 9.56643 12.8028 -2063 2 24.4651 33.192 22.2624 2.76066 3.39389 -3.794 -2064 2 24.909 34.0885 23.3987 -0.0660125 2.15758 -2.31326 -2065 1 28.1787 24.2138 14.4977 2.85163 13.2743 10.1108 -2066 2 28.1314 24.0884 15.4454 -1.95 -0.314329 0.254779 -2067 2 27.5593 23.5776 14.1402 4.78697 -1.19745 -1.90137 -2068 1 35.2086 9.78789 0.994199 1.76044 6.5307 -5.2317 -2069 2 0.557202 10.1754 0.806894 0.418955 -1.44608 0.928967 -2070 2 34.6067 10.532 1.01289 1.59781 1.15857 -0.38696 -2071 1 0.696525 26.2392 12.9981 6.15683 2.43528 1.97356 -2072 2 0.0853603 25.8774 12.3564 0.126465 3.40177 -1.1815 -2073 2 0.827069 27.1459 12.7205 1.01216 -0.0198955 3.9203 -2074 1 22.1927 29.1204 4.3329 10.0155 4.13346 -1.27455 -2075 2 21.5089 28.451 4.35461 1.49845 0.495267 -0.159421 -2076 2 22.908 28.7169 3.84119 -2.47796 1.10379 -2.16302 -2077 1 17.916 28.683 14.989 -2.36263 0.654597 -2.84745 -2078 2 18.4385 28.392 15.7363 -2.11473 0.465722 -0.120026 -2079 2 17.5044 27.8844 14.6585 2.66175 -0.386546 -1.02105 -2080 1 12.7952 25.7665 32.6497 13.9949 3.53752 8.37998 -2081 2 13.7341 25.6434 32.7898 0.325895 -1.85511 0.845326 -2082 2 12.4802 26.1577 33.4645 0.612139 -2.92432 1.79416 -2083 1 30.8742 23.167 13.459 1.42585 -4.1257 6.75052 -2084 2 30.4067 23.0024 14.2778 -1.88886 -0.614314 -1.43999 -2085 2 30.9172 22.3119 13.0311 -1.44327 1.00043 -2.06414 -2086 1 9.82816 23.5848 1.74826 4.09339 -9.25808 -17.9911 -2087 2 9.74381 23.4546 0.803719 0.485579 -1.71759 0.88707 -2088 2 10.3572 22.8448 2.04625 -1.70334 -0.335486 -1.80313 -2089 1 6.89263 12.5722 5.59003 -3.42428 7.18815 0.109591 -2090 2 7.81348 12.4179 5.37924 -0.409968 -0.134661 3.03095 -2091 2 6.43412 12.4627 4.75695 2.18255 -2.57536 -0.0517335 -2092 1 11.0294 29.5516 32.8106 9.33574 -3.0002 -9.362 -2093 2 11.6012 29.3802 33.5589 1.86495 1.52792 -1.29087 -2094 2 11.3895 29.014 32.1053 -0.11513 -1.05364 -0.15456 -2095 1 5.68421 15.1154 32.971 -6.10389 17.5032 9.81276 -2096 2 6.44786 15.1804 32.3976 -2.76176 -5.22659 1.4758 -2097 2 5.84755 15.7576 33.6618 -0.353412 4.33933 -2.88367 -2098 1 21.2619 27.2128 29.9745 13.6163 -5.96544 1.97752 -2099 2 21.1023 27.9709 30.5368 -0.179442 -1.82524 1.45305 -2100 2 20.5969 27.2782 29.2891 0.137903 -0.746035 1.06037 -2101 1 6.19181 8.13957 30.3451 -8.48727 -8.28994 6.01453 -2102 2 6.97701 7.67729 30.0519 -2.03856 -3.21695 4.93459 -2103 2 5.52559 7.45652 30.4214 -1.35773 1.55745 0.920755 -2104 1 32.4099 28.4116 3.86444 -4.18766 8.07464 1.54038 -2105 2 32.5147 27.4665 3.9742 3.5415 2.18598 0.381035 -2106 2 31.5078 28.5858 4.13297 -0.124238 -0.90634 -1.56255 -2107 1 23.9935 26.6237 31.2156 -1.77594 5.02662 -3.69764 -2108 2 23.2047 26.8918 30.7444 0.0659868 -0.69126 -0.258411 -2109 2 24.4759 27.438 31.3587 -2.36725 0.937325 2.90768 -2110 1 28.5047 29.5758 20.8717 -11.8816 10.0842 -0.798304 -2111 2 29.2407 29.9723 20.4054 -1.63534 -5.14698 -5.99675 -2112 2 28.9026 29.1526 21.6325 1.97682 0.775721 -2.26728 -2113 1 27.7507 21.2746 18.519 -2.5653 -10.6239 2.62546 -2114 2 27.4235 20.422 18.2324 0.481061 -0.629309 0.781079 -2115 2 28.2537 21.0848 19.311 -1.00646 0.362905 0.392864 -2116 1 25.2532 27.4363 16.553 -8.60012 2.32024 -6.4729 -2117 2 25.6623 28.3016 16.542 2.83422 -2.12619 2.30998 -2118 2 24.92 27.317 15.6636 5.31661 1.51202 -2.34852 -2119 1 5.61824 2.12637 21.503 -1.17612 0.715888 4.06576 -2120 2 4.8052 2.11258 22.008 1.06061 -0.364635 -2.05514 -2121 2 5.91777 1.21725 21.5055 -2.31637 0.137551 -1.97542 -2122 1 14.2045 17.3028 2.13313 13.8322 -9.9262 14.7443 -2123 2 13.4643 17.6404 1.62874 2.50063 -2.15093 -0.197974 -2124 2 13.9013 17.314 3.04098 -1.33233 -2.7535 0.223921 -2125 1 33.7781 2.9239 0.155769 0.178407 -4.43945 -0.37031 -2126 2 33.4616 3.50802 34.9138 0.119409 -0.168031 0.668625 -2127 2 33.6395 3.41265 0.967026 0.0418614 -0.671587 -0.0553616 -2128 1 0.227757 13.6891 9.35453 3.75917 4.51084 1.19032 -2129 2 0.64664 13.3875 10.1607 -2.554 -4.83332 -1.99438 -2130 2 0.820174 13.4088 8.65689 -2.36288 -2.906 2.52442 -2131 1 27.5718 24.3683 33.9227 11.8758 -14.0536 -0.652827 -2132 2 27.0285 24.2545 33.1429 -0.126379 2.90913 0.147778 -2133 2 28.103 23.573 33.9632 -2.25564 -2.06787 -1.68633 -2134 1 18.7547 23.4368 22.1148 1.76793 -3.43652 -5.89452 -2135 2 17.8334 23.3516 21.8695 0.21508 -0.204651 0.176003 -2136 2 19.1852 23.7587 21.3229 -0.448118 0.043474 -0.389491 -2137 1 2.29221 10.8734 1.51363 3.40588 -1.78065 -4.02462 -2138 2 2.50322 11.7417 1.85678 -0.631189 -1.51747 1.05411 -2139 2 2.85137 10.2765 2.01087 0.643156 1.05988 -1.16649 -2140 1 25.6214 25.899 25.2413 3.03123 -3.73655 12.5526 -2141 2 25.4794 26.589 25.8893 -0.15111 -0.362854 -0.719554 -2142 2 26.3846 25.42 25.5642 0.366269 1.78247 -0.942643 -2143 1 16.9269 16.3234 9.79661 -6.62239 -4.09948 11.2029 -2144 2 17.2235 17.0918 9.30892 4.24477 -4.29454 -0.846488 -2145 2 17.3507 16.4032 10.6511 0.535424 -3.08265 -0.22927 -2146 1 10.4746 17.2104 29.111 0.461956 5.13833 10.1707 -2147 2 10.9241 18.0338 29.3012 -0.703571 0.85844 -2.15095 -2148 2 10.1952 16.8862 29.9673 -1.05192 3.52498 1.46743 -2149 1 16.0666 22.3671 1.6953 -13.4076 -7.95118 -0.708657 -2150 2 15.3907 23.0043 1.46427 1.07175 1.7325 0.439819 -2151 2 16.8399 22.6498 1.20714 1.38044 0.287258 3.91095 -2152 1 16.3357 27.5846 32.8085 2.54571 4.88704 -14.3477 -2153 2 15.9474 26.7327 32.6096 4.10112 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-11.7913 -1926 2 25.758 26.186 17.7278 -5.43932 -10.731 -2.4049 -1927 1 4.9373 22.5181 12.7303 -6.4384 -109.105 57.2178 -1928 2 4.67073 21.7372 13.2154 46.7558 31.8331 -22.6463 -1929 2 4.1183 22.9792 12.549 -49.1964 70.1051 -30.4411 -1930 1 12.3715 3.4068 24.8685 96.9889 -105.459 -2.59257 -1931 2 11.5379 3.78717 25.1454 -78.5271 72.7012 7.46574 -1932 2 12.7376 4.04834 24.2597 -26.2048 27.0425 1.81415 -1933 1 17.2206 21.0678 32.2286 70.9033 -32.4857 -28.922 -1934 2 16.37 21.3218 31.8703 -31.2433 6.59635 -32.464 -1935 2 17.7395 20.8211 31.463 -47.0509 20.4749 43.9242 -1936 1 25.4169 13.6587 27.4317 -0.727949 9.42962 -145.923 -1937 2 25.9517 14.3734 27.0861 -3.23386 -8.44445 54.635 -1938 2 25.0518 13.2348 26.655 1.65215 1.37226 80.6823 -1939 1 31.3457 0.922103 6.09387 93.2805 93.8551 -38.7299 -1940 2 31.5155 0.207477 5.48008 -21.219 -72.6924 -14.0259 -1941 2 31.9625 1.6085 5.83961 -64.7524 -23.8625 51.719 -1942 1 14.5195 27.1466 0.851682 38.6886 37.2405 14.6579 -1943 2 15.053 27.8652 0.512027 -28.0679 -32.9887 -8.99741 -1944 2 14.6072 27.2114 1.80267 -15.0183 -14.128 4.77814 -1945 1 28.877 13.802 31.4018 -4.50288 23.8843 -13.5573 -1946 2 29.2081 14.2631 32.1725 -0.230544 2.07915 -12.4648 -1947 2 28.8087 14.4787 30.7282 1.77038 -19.7831 31.8497 -1948 1 32.2979 1.69743 30.0205 -28.8467 109.78 -38.9645 -1949 2 32.9555 1.84764 29.3413 24.5461 -47.0658 1.39339 -1950 2 31.7668 2.49381 30.0206 1.00965 -60.2251 37.5257 -1951 1 12.623 8.26205 20.3365 -51.0291 54.698 -56.076 -1952 2 12.8038 8.94712 20.98 7.54061 -8.85741 0.764622 -1953 2 12.1346 8.70659 19.6435 47.8511 -55.3633 57.2868 -1954 1 12.529 25.4483 7.87221 -48.9382 -101.6 1.11575 -1955 2 12.9572 24.6439 8.16517 48.6378 37.6284 17.52 -1956 2 11.6948 25.156 7.50493 -0.295674 62.8691 -15.443 -1957 1 1.10092 20.9789 6.76259 27.205 20.4467 -20.553 -1958 2 0.8209 21.0263 5.84848 -7.50941 -2.67192 -4.52081 -1959 2 1.91303 21.4847 6.79139 -30.6585 -22.163 10.0435 -1960 1 4.82409 0.410104 13.4746 -3.61871 -66.6275 45.8026 -1961 2 4.33159 1.13563 13.0908 -33.7684 83.5475 -47.5464 -1962 2 4.1925 35.4689 14.0377 32.5565 -8.9676 -2.20459 -1963 1 7.97943 14.3227 18.3991 -62.6546 39.1623 68.9072 -1964 2 7.48796 15.0929 18.6846 32.7298 -3.02693 -45.5565 -1965 2 7.74856 13.6426 19.0319 33.3077 -26.9346 -30.733 -1966 1 6.57492 10.8376 7.69432 -42.1835 -33.4879 61.6812 -1967 2 6.88034 11.43 7.00728 61.1077 54.5155 -84.4452 -1968 2 5.70739 11.1679 7.92785 -16.8375 -20.6972 23.7848 -1969 1 10.1308 13.458 3.45525 -19.289 -27.8108 18.398 -1970 2 9.47924 14.0224 3.03904 59.8681 9.66437 -14.5467 -1971 2 10.9686 13.7582 3.10271 -46.1431 27.4514 -18.5848 -1972 1 2.78627 23.982 22.6844 61.7668 -37.9237 -21.697 -1973 2 2.23775 23.3518 22.2172 -8.17893 -35.1455 -20.7984 -1974 2 2.17291 24.6441 23.0031 -46.5196 68.0647 37.1881 -1975 1 29.6763 34.0661 9.4221 -25.2085 -34.5053 76.7307 -1976 2 29.4116 33.869 10.3206 -13.3027 -22.4655 -41.4267 -1977 2 30.2063 34.8598 9.49668 49.5961 63.0099 -39.1917 -1978 1 17.3951 25.0142 9.24935 74.1256 -119.972 13.8699 -1979 2 18.0557 25.5131 8.76884 -7.409 57.2755 -19.7204 -1980 2 17.7887 24.1502 9.37149 -78.6001 67.4017 9.86198 -1981 1 11.139 14.0733 32.9523 31.4256 -0.03008 -5.2348 -1982 2 12.066 14.2725 33.0835 -15.5197 6.63618 -14.1202 -1983 2 10.9478 13.388 33.5926 -13.6636 8.48879 -3.5036 -1984 1 1.12572 32.0183 27.5356 24.6266 46.3494 2.8897 -1985 2 0.546692 31.3048 27.8037 -3.08121 -31.7776 -12.0256 -1986 2 1.55521 31.6943 26.7439 -12.2274 -17.2869 5.12609 -1987 1 16.7457 10.366 22.1454 -15.3164 -22.3958 -16.0252 -1988 2 17.6114 10.1816 22.5099 -14.3265 37.126 0.80158 -1989 2 16.5565 11.2637 22.4183 29.9704 0.0490406 16.3066 -1990 1 3.7604 22.8172 16.7231 -94.979 -46.3638 63.4302 -1991 2 3.80199 23.6592 16.2696 52.6252 2.42304 -21.4425 -1992 2 4.60092 22.4005 16.533 37.2062 36.1623 -37.5204 -1993 1 1.85858 2.74219 27.3787 -16.8615 -16.8421 15.8272 -1994 2 2.54214 2.17108 27.7292 -4.59146 35.0941 -40.6374 -1995 2 2.27945 3.20266 26.6527 25.2819 -23.6186 22.0617 -1996 1 20.9735 33.5714 23.8814 -106.803 36.5464 88.0259 -1997 2 21.6236 32.9171 24.1374 45.6079 -11.0665 -63.4639 -1998 2 21.2264 33.8268 22.9943 67.7875 -35.3184 -31.857 -1999 1 14.9346 6.66221 21.3527 -126.314 -3.88715 -82.8474 -2000 2 14.0911 6.81595 20.927 39.2653 62.6904 53.7569 -2001 2 15.1982 5.79131 21.0556 85.678 -53.7307 17.9606 -2002 1 22.2461 5.18918 17.8715 -69.145 -31.4218 -18.0837 -2003 2 21.9344 5.83223 17.2347 -27.7401 11.8107 -16.433 -2004 2 23.137 5.47038 18.0801 108.344 19.9553 34.4799 -2005 1 31.7359 29.9237 26.3736 -84.3482 -146.558 -73.4212 -2006 2 32.1627 30.6728 26.7895 111.481 40.2155 8.28834 -2007 2 32.4462 29.4563 25.9339 -20.9159 104.035 73.147 -2008 1 24.5541 23.2903 6.20562 34.8499 -73.6669 40.9676 -2009 2 25.3233 22.7463 6.0363 -54.9847 54.2625 4.3351 -2010 2 24.1245 22.8728 6.95223 10.9892 27.9336 -36.5991 -2011 1 25.8826 13.3692 31.6978 -39.5587 45.0721 109.942 -2012 2 26.0654 12.9392 30.8624 14.4928 -55.2593 -101.315 -2013 2 26.7459 13.5818 32.0524 34.4682 10.678 13.5079 -2014 1 31.9081 10.2232 30.8508 60.5777 139.069 -26.1959 -2015 2 32.2481 10.7082 31.6027 -21.552 -31.8062 -26.0603 -2016 2 31.6024 9.39393 31.2183 -39.6468 -107.76 57.4176 -2017 1 0.849757 3.66316 11.6882 -66.4227 -77.864 -86.3174 -2018 2 0.839326 4.56785 12.0007 9.47524 78.9317 34.8726 -2019 2 0.14017 3.62253 11.047 60.8788 -7.45935 55.9047 -2020 1 12.6493 6.4064 27.2531 -40.9759 17.8512 -96.8045 -2021 2 11.9988 5.88507 26.7827 30.2874 12.9967 48.5047 -2022 2 12.9203 7.07589 26.6249 2.54534 -39.1725 52.0268 -2023 1 15.9599 7.99333 15.8859 30.1406 -18.388 8.6192 -2024 2 16.7797 7.85417 15.4117 -4.79859 1.07516 10.1564 -2025 2 15.4667 8.60439 15.3385 -20.0761 12.8881 -12.5608 -2026 1 20.0344 20.1357 12.6654 -3.86966 -64.7249 -48.8174 -2027 2 19.4344 20.3202 11.9427 10.3543 13.9442 17.6237 -2028 2 20.3441 19.2454 12.4988 -10.1918 51.4785 29.9814 -2029 1 21.356 6.30633 10.131 -67.0198 -114.109 -5.58798 -2030 2 20.9103 5.53439 10.4799 -7.83167 25.8119 -63.3827 -2031 2 21.891 6.6238 10.8585 85.5245 81.2641 57.4267 -2032 1 35.1559 30.9332 9.83309 61.3262 -2.90007 -69.3354 -2033 2 0.303167 31.6302 9.88912 -24.8958 -15.4978 13.785 -2034 2 34.5934 31.0698 10.5955 -26.5859 21.8525 52.7843 -2035 1 4.27659 27.2552 26.2915 116.968 -151.738 -34.7454 -2036 2 3.39554 27.3768 25.9377 -83.718 52.8428 -4.72735 -2037 2 4.42257 28.0247 26.8419 -28.396 103.456 48.6556 -2038 1 26.8593 19.3342 13.6851 30.7677 67.3413 -148.698 -2039 2 26.0004 19.2038 14.0871 -50.0945 -27.4421 67.323 -2040 2 27.4811 19.0115 14.3374 18.1351 -38.3726 82.2067 -2041 1 7.83885 28.1834 15.8334 16.5365 20.604 -8.56175 -2042 2 7.60386 27.3316 16.2014 -33.7069 20.3127 -2.25908 -2043 2 7.02096 28.6807 15.838 5.21927 -39.3621 14.9074 -2044 1 32.631 18.2249 29.7861 41.9215 38.3318 11.8543 -2045 2 32.1421 17.5039 29.3895 -39.2744 -31.6531 -17.1652 -2046 2 31.957 18.8189 30.1164 -14.576 -4.73824 -0.949144 -2047 1 3.25628 33.4796 7.39391 71.9746 30.5666 -22.4299 -2048 2 4.11434 33.8297 7.63344 -69.5572 -27.2519 -15.9057 -2049 2 3.24436 33.5071 6.43718 -2.52475 -1.44402 31.1707 -2050 1 0.842237 3.50013 3.05753 16.9517 -63.8559 -23.0072 -2051 2 1.37533 4.09985 3.57944 19.8724 20.4219 19.8016 -2052 2 1.42823 2.77011 2.85767 -26.1771 37.5505 12.1175 -2053 1 25.1227 15.9755 21.4703 2.5941 62.4248 -49.2139 -2054 2 25.4287 15.7265 22.3424 20.0835 -17.1737 50.8233 -2055 2 25.5184 16.8328 21.3129 -18.0552 -40.9029 7.45317 -2056 1 7.27484 22.2113 14.035 48.561 60.0034 62.6588 -2057 2 7.83751 21.4533 13.8765 -38.0713 -11.7879 -38.4589 -2058 2 6.51927 22.0729 13.4638 0.293443 -44.8648 -32.9729 -2059 1 14.2406 9.72758 11.5631 116.878 81.801 14.5405 -2060 2 13.6867 9.60902 10.7914 -66.2487 -25.9071 -61.3884 -2061 2 14.9707 10.264 11.2543 -53.7978 -46.298 43.148 -2062 1 24.5661 34.1068 22.5037 -12.6784 75.01 -32.2381 -2063 2 24.4448 33.1898 22.2577 -6.71238 -64.4707 -26.8253 -2064 2 24.8834 34.0733 23.4061 24.4774 5.00072 65.3718 -2065 1 28.1828 24.2163 14.5011 36.8397 60.2005 -124.445 -2066 2 28.1283 24.0875 15.448 -42.2705 -47.9485 79.128 -2067 2 27.5548 23.5921 14.1374 10.284 -1.76503 54.6319 -2068 1 35.2069 9.7887 0.991304 -95.944 64.7317 5.27254 -2069 2 0.552607 10.1881 0.815879 115.488 -3.29094 -17.0999 -2070 2 34.5965 10.5257 1.01417 -16.4988 -53.7782 7.85015 -2071 1 0.691695 26.2382 12.9947 -9.41017 61.2975 -51.419 -2072 2 0.0768464 25.8717 12.3592 -28.0544 -73.2286 1.85962 -2073 2 0.833398 27.1379 12.7003 45.2238 18.3035 55.3252 -2074 1 22.1934 29.1186 4.33055 7.9951 12.5985 3.19312 -2075 2 21.5188 28.4403 4.36471 47.1765 5.49724 -20.3584 -2076 2 22.9008 28.7279 3.81759 -48.2839 -12.3785 13.5407 -2077 1 17.9152 28.6807 14.9942 -54.009 -38.437 -55.3386 -2078 2 18.4519 28.3813 15.7281 -12.5555 -30.3197 -4.96761 -2079 2 17.4906 27.8873 14.668 64.847 68.7897 58.1862 -2080 1 12.7944 25.7701 32.651 87.3127 -33.674 -49.9122 -2081 2 13.7325 25.6374 32.7874 -23.9657 -5.59064 -20.5018 -2082 2 12.4854 26.1582 33.4696 -48.9202 37.6441 80.1222 -2083 1 30.8723 23.1715 13.4622 -9.11844 -27.0426 17.3174 -2084 2 30.4177 23.0049 14.2879 -11.7763 32.8722 29.883 -2085 2 30.92 22.3151 13.0374 18.8176 -9.0042 -46.3578 -2086 1 9.82399 23.583 1.7494 3.91602 -23.2748 -58.3544 -2087 2 9.72916 23.4277 0.80965 -20.0403 27.4058 -4.72991 -2088 2 10.3677 22.8585 2.05872 18.1457 -16.7879 43.7545 -2089 1 6.8955 12.5745 5.5963 85.8424 -23.1235 -93.8407 -2090 2 7.81182 12.4154 5.36977 -59.0646 18.9114 61.7966 -2091 2 6.4222 12.4672 4.77122 -25.9937 7.60744 34.9584 -2092 1 11.0245 29.5546 32.8142 27.2343 -22.8279 -26.0862 -2093 2 11.5962 29.377 33.5611 -2.51259 4.69703 -3.95931 -2094 2 11.3841 29.0222 32.1047 -13.3466 16.0372 20.0845 -2095 1 5.68503 15.1158 32.9715 71.9243 84.7749 22.2842 -2096 2 6.43529 15.2072 32.3842 -29.722 -48.1256 -23.5074 -2097 2 5.83799 15.7643 33.6589 -49.7197 -21.4736 10.4848 -2098 1 21.2604 27.2124 29.976 9.35206 -13.3824 -10.3518 -2099 2 21.1086 27.9685 30.543 -0.00945565 9.47109 13.7934 -2100 2 20.5932 27.2863 29.2937 2.67135 -4.7572 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-1887 2 11.8744 33.8931 8.15305 0.922075 0.494336 3.88877 -1888 1 10.4642 16.7648 26.4147 2.80971 1.51282 -9.61072 -1889 2 10.4264 17.0779 27.3185 1.17471 -1.35509 -0.280756 -1890 2 11.3146 17.0636 26.0926 0.590472 -1.32977 -0.414974 -1891 1 17.2152 4.69462 34.6747 11.9213 0.65814 -4.69715 -1892 2 18.0195 4.45625 34.2137 1.04857 -0.57361 0.535519 -1893 2 16.8774 3.86516 35.0125 1.91423 1.04657 2.96864 -1894 1 6.97445 35.1353 32.2671 9.97328 -11.6302 -7.33462 -1895 2 7.55154 34.8288 32.9666 0.774769 -1.62199 -1.46055 -1896 2 6.63884 0.467797 32.5832 1.02155 -1.24749 0.362107 -1897 1 30.2645 4.69075 18.0422 0.694439 -2.46184 2.97624 -1898 2 29.6017 4.00886 17.9326 1.10342 -1.19819 0.759635 -1899 2 30.7589 4.42264 18.8167 -1.07894 2.27368 1.54311 -1900 1 14.1656 29.632 31.6787 5.05867 -0.355939 -0.980506 -1901 2 14.4451 30.4041 31.1867 -0.842964 -0.790639 -0.294246 -1902 2 13.5563 29.1821 31.0933 0.0725257 -1.19259 1.4708 -1903 1 22.4084 9.52165 9.7397 0.735332 -1.67091 -3.93305 -1904 2 22.7212 9.37225 10.6319 -1.09142 1.00002 -0.542777 -1905 2 23.025 9.04279 9.18587 1.34861 1.44662 0.230846 -1906 1 22.2367 0.136878 35.4162 2.39769 -1.00634 11.3877 -1907 2 23.1336 0.346647 0.22933 -0.416125 0.426818 1.11968 -1908 2 21.8755 35.1657 0.715801 -0.0814999 0.0454572 0.682247 -1909 1 30.8013 21.126 11.6255 -3.46793 -5.01909 1.70411 -1910 2 31.1601 21.6971 10.9462 -4.45423 -1.15624 -2.23432 -1911 2 31.4336 20.4108 11.6964 2.44046 2.26421 0.934019 -1912 1 27.4508 5.23152 21.4006 1.74025 1.89877 19.0993 -1913 2 27.8319 4.73772 22.1266 0.4018 0.947765 0.850108 -1914 2 26.5774 5.47438 21.7079 -0.634266 -2.0344 0.72118 -1915 1 34.2517 16.5309 18.5306 0.907524 -6.93269 -4.04601 -1916 2 34.8715 15.8322 18.7399 -0.501769 0.835994 1.04597 -1917 2 33.8909 16.2844 17.6789 -0.976215 1.5179 3.59303 -1918 1 32.115 35.0905 16.482 2.22898 -11.9743 -20.9485 -1919 2 32.966 34.6682 16.5991 -0.636814 -0.495605 0.383446 -1920 2 32.3008 0.353133 15.9431 0.148533 0.858467 3.15742 -1921 1 5.2813 31.5245 24.5891 -0.88265 3.56081 0.527901 -1922 2 5.6102 31.6063 25.4843 2.8911 0.897716 -1.16555 -1923 2 5.50826 32.3562 24.1732 0.0452461 -1.83796 -1.84019 -1924 1 25.7935 25.4126 18.2933 8.42974 5.04501 3.04403 -1925 2 25.4171 24.7186 17.752 -3.18932 0.154086 3.92798 -1926 2 25.7522 26.195 17.7434 -1.62301 -1.62428 -0.262324 -1927 1 4.94055 22.5134 12.7286 -9.04805 -9.98913 0.740441 -1928 2 4.66669 21.7387 13.2196 -2.25032 0.777095 0.693415 -1929 2 4.12797 22.9905 12.5602 2.55025 2.81834 1.88639 -1930 1 12.3705 3.40796 24.8702 -10.2718 -6.94273 4.16449 -1931 2 11.5354 3.79201 25.1374 1.11482 2.05237 1.26765 -1932 2 12.7415 4.04279 24.2574 1.31703 -1.09657 1.0894 -1933 1 17.2229 21.0728 32.2314 -8.179 -5.27121 -18.2871 -1934 2 16.3825 21.3411 31.86 1.15239 -1.37236 -2.54915 -1935 2 17.7485 20.8146 31.4742 0.636225 0.416061 0.167394 -1936 1 25.4211 13.6617 27.4256 -0.423575 1.5864 -14.144 -1937 2 25.9311 14.3939 27.0792 0.209498 -1.21813 2.94262 -1938 2 25.0385 13.2482 26.6517 -1.88498 1.40152 0.678356 -1939 1 31.3452 0.921707 6.09496 5.75289 0.0456399 -1.04313 -1940 2 31.5193 0.206077 5.48357 1.7599 -1.91271 2.66807 -1941 2 31.9558 1.61205 5.83652 -0.775733 -0.136291 -2.46929 -1942 1 14.5238 27.1426 0.855822 -0.28203 -13.8472 13.0001 -1943 2 15.0637 27.8615 0.527327 -2.90129 -0.385453 -1.8344 -1944 2 14.5862 27.2115 1.8085 -1.36301 3.80564 -1.12804 -1945 1 28.8746 13.8014 31.4027 -2.88672 6.47051 7.86952 -1946 2 29.2232 14.2517 32.1721 1.91816 0.252514 -1.72337 -1947 2 28.8041 14.4848 30.7362 -2.55312 0.206489 0.885327 -1948 1 32.2921 1.69364 30.0162 -5.24318 6.11719 0.10458 -1949 2 32.9509 1.85569 29.3409 -1.02656 -2.73336 -0.95222 -1950 2 31.7703 2.49576 30.0398 2.18736 -0.0064308 0.36284 -1951 1 12.6171 8.26014 20.3408 -0.40671 -8.63132 6.16379 -1952 2 12.7962 8.9555 20.9737 1.99194 1.08407 -2.86475 -1953 2 12.1389 8.69542 19.635 2.27749 -2.82959 -1.29442 -1954 1 12.5264 25.4516 7.87552 -4.00904 -0.543437 10.3565 -1955 2 12.9562 24.654 8.18449 -0.215524 -0.0928553 -1.74864 -1956 2 11.705 25.1474 7.48948 4.50811 -0.52052 -4.58555 -1957 1 1.10395 20.9772 6.76689 -12.4418 -4.87906 -17.0173 -1958 2 0.841381 21.0115 5.84704 0.961335 2.29109 -0.167377 -1959 2 1.91806 21.4794 6.80294 -0.662195 -1.08577 2.11991 -1960 1 4.82166 0.411135 13.4723 -6.95497 7.27665 -10.2603 -1961 2 4.31632 1.13144 13.0954 -1.71759 1.5163 4.71861 -1962 2 4.19868 35.4546 14.0325 3.34255 0.282635 2.02706 -1963 1 7.98045 14.3231 18.3954 3.08041 14.4496 -7.04888 -1964 2 7.47829 15.0927 18.6634 -2.22303 -2.54215 1.24386 -1965 2 7.75094 13.6513 19.0374 2.28408 -1.12721 -2.33416 -1966 1 6.57567 10.8403 7.6939 2.74017 2.33053 3.06743 -1967 2 6.87818 11.4306 7.00375 -0.816871 -0.135469 -0.424054 -1968 2 5.69956 11.1571 7.91368 0.353319 -2.48188 -0.273827 -1969 1 10.1296 13.4617 3.4523 -7.92991 7.36607 -13.5551 -1970 2 9.4814 14.0411 3.05172 2.81436 1.47522 -1.87702 -1971 2 10.9658 13.745 3.08241 -0.999119 -0.282534 1.18626 -1972 1 2.78873 23.9803 22.6823 7.39875 -2.15156 -6.43063 -1973 2 2.24341 23.3472 22.2153 1.0523 -1.39215 0.678747 -1974 2 2.17172 24.6381 23.0029 -0.309516 -1.48449 0.660469 -1975 1 29.681 34.0668 9.41834 9.5803 -0.140978 0.198088 -1976 2 29.4023 33.8738 10.3135 -0.39736 4.75337 0.09998 -1977 2 30.2232 34.8514 9.49973 0.132783 -0.224159 -2.50537 -1978 1 17.3964 25.0161 9.25437 -10.6964 6.49204 10.2875 -1979 2 18.0663 25.5133 8.78518 -2.57426 -0.200004 -1.71763 -1980 2 17.7826 24.1488 9.37642 -1.26016 -0.11254 -2.41078 -1981 1 11.1411 14.0768 32.9507 2.74692 8.93145 -23.0737 -1982 2 12.0674 14.2752 33.0877 0.326495 0.0181461 -2.13137 -1983 2 10.9448 13.3932 33.5914 -1.40918 5.092 2.7765 -1984 1 1.12682 32.0133 27.5402 4.517 -1.51145 -4.02069 -1985 2 0.552584 31.2959 27.8081 3.00058 -1.99467 0.131487 -1986 2 1.5621 31.6905 26.7511 1.52551 1.30495 -0.0263278 -1987 1 16.7481 10.3694 22.1507 0.264039 13.0692 4.69918 -1988 2 17.6248 10.1979 22.4946 -0.0377334 0.851346 -4.78636 -1989 2 16.5624 11.2729 22.4066 -1.46932 -0.377234 0.467584 -1990 1 3.76375 22.8172 16.7293 -4.0741 -10.5757 1.02761 -1991 2 3.80151 23.6586 16.2743 -0.690304 1.29329 3.69566 -1992 2 4.5994 22.3969 16.5262 -0.197813 0.973283 -0.721214 -1993 1 1.85399 2.73861 27.3822 3.20071 -7.68688 -3.72082 -1994 2 2.53752 2.17131 27.7389 0.0246343 -1.14856 -1.23911 -1995 2 2.27395 3.18876 26.6492 0.934788 1.93265 2.10385 -1996 1 20.9724 33.5726 23.8784 8.10433 -9.20518 -4.51155 -1997 2 21.6189 32.9194 24.1461 -2.046 -3.87957 -3.38316 -1998 2 21.2405 33.8276 22.9955 0.119388 1.30018 0.791288 -1999 1 14.9356 6.66547 21.3473 -4.32378 2.01425 -5.99167 -2000 2 14.0917 6.81509 20.921 0.850589 0.904261 -2.27949 -2001 2 15.2025 5.79487 21.0522 1.98877 1.97817 -3.72271 -2002 1 22.2485 5.18667 17.87 13.215 -1.9753 -1.37536 -2003 2 21.9401 5.84134 17.2434 -1.85661 0.524428 2.90348 -2004 2 23.1453 5.4526 18.0731 0.178716 1.34064 -2.4977 -2005 1 31.7392 29.9223 26.3752 4.76914 0.177865 5.41636 -2006 2 32.1647 30.6696 26.7955 0.903997 -0.87703 1.20137 -2007 2 32.4505 29.4583 25.9336 0.0227674 -0.433216 0.401033 -2008 1 24.5495 23.287 6.21014 -9.6064 5.24279 8.20718 -2009 2 25.3283 22.7624 6.02443 0.116339 4.39189 1.8768 -2010 2 24.1468 22.8595 6.966 0.2289 -0.0589481 -2.13137 -2011 1 25.8848 13.3641 31.6949 11.7976 1.283 28.4217 -2012 2 26.0644 12.9328 30.8595 -3.81135 -1.20515 1.50928 -2013 2 26.7491 13.586 32.0412 2.1747 1.23594 -3.73301 -2014 1 31.9059 10.2239 30.8521 3.15397 -0.693558 5.50864 -2015 2 32.2432 10.7005 31.6105 -2.64306 -0.474064 1.50947 -2016 2 31.6065 9.38729 31.2082 -1.91976 0.707005 -1.14165 -2017 1 0.84878 3.6625 11.6852 3.82778 -4.24681 3.04899 -2018 2 0.853073 4.56299 12.0097 1.00506 -0.863618 -0.913913 -2019 2 0.134074 3.64014 11.0488 -1.02679 -1.02985 3.07516 -2020 1 12.653 6.40924 27.2569 -10.896 -2.3651 4.67545 -2021 2 12.0107 5.88536 26.7781 -1.95087 -0.422561 2.90655 -2022 2 12.932 7.07765 26.6311 3.33215 -5.37792 -3.19321 -2023 1 15.9575 7.9951 15.8816 6.43964 -4.15323 6.61769 -2024 2 16.7831 7.8467 15.4206 0.588477 2.84349 1.20404 -2025 2 15.4803 8.61195 15.3266 -2.08725 -4.05933 -0.295667 -2026 1 20.0375 20.1391 12.665 -4.11025 1.52341 -3.10314 -2027 2 19.4274 20.3342 11.9537 2.89664 -0.270393 -1.94487 -2028 2 20.3292 19.244 12.4922 -2.13637 -0.289793 3.97752 -2029 1 21.356 6.30845 10.1293 11.8845 -7.32937 -8.40835 -2030 2 20.9041 5.54426 10.4872 -0.836302 1.13214 -0.345734 -2031 2 21.8894 6.63336 10.8547 0.11176 0.0745871 -0.490015 -2032 1 35.1526 30.9366 9.83286 7.59845 5.2547 -1.12957 -2033 2 0.311501 31.622 9.89575 0.964885 -1.25019 -0.233494 -2034 2 34.6019 31.0651 10.6052 0.344797 -0.803576 -0.904465 -2035 1 4.27525 27.2569 26.2869 4.28071 5.72746 7.8462 -2036 2 3.39987 27.3692 25.9163 0.165296 -0.828825 2.86229 -2037 2 4.39971 28.0244 26.8452 0.266735 0.0706906 -1.3371 -2038 1 26.8649 19.3391 13.6882 0.177125 1.61838 2.46927 -2039 2 26.0052 19.1944 14.0834 -0.103725 0.362381 -1.50792 -2040 2 27.4862 19.0117 14.3386 -0.695576 -0.902314 0.251747 -2041 1 7.83542 28.181 15.8382 -13.3943 -2.71551 5.4783 -2042 2 7.57758 27.3247 16.1794 -0.25335 2.11014 -2.48558 -2043 2 7.02351 28.6878 15.8233 1.95232 1.88776 0.576467 -2044 1 32.6262 18.2228 29.791 -14.1882 1.19327 -8.66236 -2045 2 32.1279 17.5186 29.3763 0.458993 0.618559 0.834874 -2046 2 31.9606 18.8321 30.1103 1.27184 -0.0824113 1.15038 -2047 1 3.26267 33.4782 7.39241 0.72256 1.05107 -6.58477 -2048 2 4.1177 33.8412 7.62335 -1.20198 1.46048 -0.601021 -2049 2 3.2457 33.4941 6.43549 0.071718 0.812761 -0.0287205 -2050 1 0.844894 3.50214 3.06141 10.9265 -6.46418 5.34726 -2051 2 1.3825 4.10673 3.57296 -1.34547 0.02462 1.3239 -2052 2 1.43348 2.7774 2.85035 0.956803 -0.0258241 1.47884 -2053 1 25.1225 15.9729 21.4727 1.26189 6.66637 7.55006 -2054 2 25.4376 15.7328 22.3441 1.99941 -1.50251 -1.18582 -2055 2 25.5145 16.8296 21.3033 0.649747 -0.161475 0.915999 -2056 1 7.27486 22.2101 14.0385 10.1815 -3.49421 -8.18063 -2057 2 7.84619 21.46 13.8737 1.50039 1.74304 -3.72093 -2058 2 6.53621 22.0846 13.4428 1.08182 3.6941 2.34564 -2059 1 14.2409 9.72949 11.5638 -2.21614 13.7167 -2.62635 -2060 2 13.6906 9.62021 10.7883 -0.22348 -2.43277 0.646692 -2061 2 14.9733 10.2682 11.2645 -0.353329 -0.504752 -2.50308 -2062 1 24.5604 34.1124 22.5076 2.81011 9.56643 12.8028 -2063 2 24.4651 33.192 22.2624 2.76066 3.39389 -3.794 -2064 2 24.909 34.0885 23.3987 -0.0660125 2.15758 -2.31326 -2065 1 28.1787 24.2138 14.4977 2.85163 13.2743 10.1108 -2066 2 28.1314 24.0884 15.4454 -1.95 -0.314329 0.254779 -2067 2 27.5593 23.5776 14.1402 4.78697 -1.19745 -1.90137 -2068 1 35.2086 9.78789 0.994199 1.76044 6.5307 -5.2317 -2069 2 0.557202 10.1754 0.806894 0.418955 -1.44608 0.928967 -2070 2 34.6067 10.532 1.01289 1.59781 1.15857 -0.38696 -2071 1 0.696525 26.2392 12.9981 6.15683 2.43528 1.97356 -2072 2 0.0853603 25.8774 12.3564 0.126465 3.40177 -1.1815 -2073 2 0.827069 27.1459 12.7205 1.01216 -0.0198955 3.9203 -2074 1 22.1927 29.1204 4.3329 10.0155 4.13346 -1.27455 -2075 2 21.5089 28.451 4.35461 1.49845 0.495267 -0.159421 -2076 2 22.908 28.7169 3.84119 -2.47796 1.10379 -2.16302 -2077 1 17.916 28.683 14.989 -2.36263 0.654597 -2.84745 -2078 2 18.4385 28.392 15.7363 -2.11473 0.465722 -0.120026 -2079 2 17.5044 27.8844 14.6585 2.66175 -0.386546 -1.02105 -2080 1 12.7952 25.7665 32.6497 13.9949 3.53752 8.37998 -2081 2 13.7341 25.6434 32.7898 0.325895 -1.85511 0.845326 -2082 2 12.4802 26.1577 33.4645 0.612139 -2.92432 1.79416 -2083 1 30.8742 23.167 13.459 1.42585 -4.1257 6.75052 -2084 2 30.4067 23.0024 14.2778 -1.88886 -0.614314 -1.43999 -2085 2 30.9172 22.3119 13.0311 -1.44327 1.00043 -2.06414 -2086 1 9.82816 23.5848 1.74826 4.09339 -9.25808 -17.9911 -2087 2 9.74381 23.4546 0.803719 0.485579 -1.71759 0.88707 -2088 2 10.3572 22.8448 2.04625 -1.70334 -0.335486 -1.80313 -2089 1 6.89263 12.5722 5.59003 -3.42428 7.18815 0.109591 -2090 2 7.81348 12.4179 5.37924 -0.409968 -0.134661 3.03095 -2091 2 6.43412 12.4627 4.75695 2.18255 -2.57536 -0.0517335 -2092 1 11.0294 29.5516 32.8106 9.33574 -3.0002 -9.362 -2093 2 11.6012 29.3802 33.5589 1.86495 1.52792 -1.29087 -2094 2 11.3895 29.014 32.1053 -0.11513 -1.05364 -0.15456 -2095 1 5.68421 15.1154 32.971 -6.10389 17.5032 9.81276 -2096 2 6.44786 15.1804 32.3976 -2.76176 -5.22659 1.4758 -2097 2 5.84755 15.7576 33.6618 -0.353412 4.33933 -2.88367 -2098 1 21.2619 27.2128 29.9745 13.6163 -5.96544 1.97752 -2099 2 21.1023 27.9709 30.5368 -0.179442 -1.82524 1.45305 -2100 2 20.5969 27.2782 29.2891 0.137903 -0.746035 1.06037 -2101 1 6.19181 8.13957 30.3451 -8.48727 -8.28994 6.01453 -2102 2 6.97701 7.67729 30.0519 -2.03856 -3.21695 4.93459 -2103 2 5.52559 7.45652 30.4214 -1.35773 1.55745 0.920755 -2104 1 32.4099 28.4116 3.86444 -4.18766 8.07464 1.54038 -2105 2 32.5147 27.4665 3.9742 3.5415 2.18598 0.381035 -2106 2 31.5078 28.5858 4.13297 -0.124238 -0.90634 -1.56255 -2107 1 23.9935 26.6237 31.2156 -1.77594 5.02662 -3.69764 -2108 2 23.2047 26.8918 30.7444 0.0659868 -0.69126 -0.258411 -2109 2 24.4759 27.438 31.3587 -2.36725 0.937325 2.90768 -2110 1 28.5047 29.5758 20.8717 -11.8816 10.0842 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-1.59847 -4379 2 21.9921 26.2272 17.7279 -0.0319833 -0.570092 0.694787 -4380 2 21.3181 25.1281 16.9343 1.91105 0.442844 0.0444748 -4381 1 30.9762 0.893719 8.90624 6.84658 4.89315 4.34164 -4382 2 31.2866 0.970928 8.00407 -1.30872 -1.28953 0.0387564 -4383 2 30.0457 1.11331 8.85952 1.85147 1.23716 1.21913 -4384 1 25.4566 22.8733 21.0012 8.46941 -6.2365 -4.41175 -4385 2 26.2934 22.4661 21.2251 -0.0869085 0.997113 -0.522472 -4386 2 25.6712 23.793 20.8454 -2.04348 -0.380031 3.58637 -4387 1 24.8743 30.4839 12.6069 5.18592 -5.90954 -3.66721 -4388 2 25.6363 30.6355 12.0478 -2.47753 -1.31299 -1.73489 -4389 2 25.0041 29.602 12.9557 1.098 0.771613 1.03075 -4390 1 13.8113 7.99004 5.29125 -6.25539 2.54191 5.22156 -4391 2 13.7892 8.73645 4.69241 1.40451 -0.877124 -0.322734 -4392 2 14.7345 7.89861 5.52688 -0.824712 -3.60413 -2.23204 -4393 1 33.9717 12.8445 16.8206 -5.08834 3.24579 2.32558 -4394 2 34.7638 12.3611 17.0557 -0.912544 -1.123 -1.64622 -4395 2 33.6042 13.1252 17.6586 -0.0818337 -2.83827 1.19082 -4396 1 26.5929 21.8369 5.4998 15.2188 -12.8758 -3.5611 -4397 2 27.193 22.4961 5.15108 1.54123 -0.472239 4.36294 -4398 2 27.1503 21.0829 5.69232 0.775207 0.532331 0.731822 -4399 1 5.16966 25.9262 12.3542 3.63388 -10.9707 -4.2268 -4400 2 4.39065 25.3778 12.4469 0.868663 0.512582 0.49162 -4401 2 5.73068 25.672 13.0869 1.15015 -1.40555 -2.02342 -4402 1 26.7931 35.4254 5.15069 -2.58439 4.8653 0.22666 -4403 2 26.5925 34.8211 5.86542 2.47532 -0.574882 -0.655596 -4404 2 27.2131 0.665389 5.57819 2.08955 -0.944702 -1.56575 -4405 1 1.20884 3.82973 0.244724 1.66138 -1.50883 -2.97877 -4406 2 2.01641 3.42102 0.556221 -0.565104 -0.453085 -0.98583 -4407 2 0.510904 3.36319 0.704569 -0.652139 1.89174 -3.14661 -4408 1 26.4335 3.26352 13.8621 2.94116 4.56618 2.38726 -4409 2 26.7833 4.04332 14.2931 1.33818 -0.0840263 -3.07679 -4410 2 25.7332 3.59406 13.2994 -3.10068 -2.3533 4.10846 -4411 1 33.2055 12.6395 8.23391 5.45516 1.9919 5.8193 -4412 2 32.6787 12.8131 9.01402 -0.345731 -1.59928 -1.24485 -4413 2 34.1053 12.8183 8.50726 -0.805487 1.53365 1.78742 -4414 1 29.9023 24.5626 20.7116 3.42295 -6.98403 -0.952027 -4415 2 29.4679 25.4132 20.6473 -0.48284 -2.69496 0.222901 -4416 2 30.2739 24.4166 19.8417 -0.244826 -2.35878 0.7128 -4417 1 15.2998 4.02453 16.4417 -2.15742 4.79241 6.05563 -4418 2 15.7057 4.6226 17.0692 0.191126 1.42105 -2.21766 -4419 2 14.9946 3.28953 16.9736 -0.120429 1.69431 2.26192 -4420 1 31.2753 25.1783 0.424078 -3.05861 -1.08728 17.9787 -4421 2 31.0586 24.4517 35.287 4.05906 -1.40755 1.82856 -4422 2 30.7422 25.0259 1.20438 -1.38424 0.164027 -0.204301 -4423 1 12.1221 3.02324 0.180171 5.54245 -1.23026 6.11818 -4424 2 11.8464 2.17458 35.281 1.14317 0.150516 -0.180026 -4425 2 11.3607 3.34415 0.66332 2.03454 -2.74467 1.9593 -4426 1 32.8431 11.557 14.38 0.147749 2.67556 -1.98289 -4427 2 31.9068 11.5678 14.1811 0.291943 -1.00905 2.75821 -4428 2 32.9664 12.2812 14.9936 1.19966 -2.12497 2.082 -4429 1 20.5645 17.4424 12.4515 6.55406 0.156517 0.559841 -4430 2 19.8459 16.8903 12.1433 -1.42603 2.83887 0.952488 -4431 2 20.6495 17.2292 13.3808 1.56555 -1.24922 -0.696423 -4432 1 15.2816 11.6269 18.8168 5.55975 3.4447 3.66971 -4433 2 14.386 11.8473 19.0727 -0.646747 -2.40537 -4.21442 -4434 2 15.3862 10.7109 19.0741 1.74861 1.0941 -0.195148 -4435 1 29.7377 20.372 3.36652 0.797329 -7.98301 -8.63454 -4436 2 30.4736 19.7997 3.5836 -1.83703 -0.890419 1.54523 -4437 2 29.86 20.5792 2.44008 0.781849 -1.5009 -0.273719 -4438 1 10.4638 28.1009 15.3794 8.14468 4.22684 -0.814723 -4439 2 9.53379 28.2306 15.5652 0.0260372 -2.67835 -1.69305 -4440 2 10.6322 28.642 14.608 -0.570693 -1.3859 -1.11001 -4441 1 16.7704 6.13101 17.944 -0.211983 -1.47772 3.31 -4442 2 17.2683 6.32159 18.7389 1.86764 1.15901 -3.46209 -4443 2 16.6681 6.98075 17.5153 -2.39931 -1.61441 -0.74807 -4444 1 21.5135 0.327334 25.1409 8.66564 11.1895 -11.7105 -4445 2 22.2279 0.15114 25.7531 -4.2921 0.404201 4.61487 -4446 2 21.4118 35.0184 24.6498 0.519456 -0.928846 2.19863 -4447 1 8.71062 23.6629 10.1362 3.05079 1.60887 0.77512 -4448 2 9.03714 24.1011 10.9221 0.259856 1.17771 -1.23482 -4449 2 9.41576 23.0672 9.88307 -1.85123 -1.62472 0.915088 -4450 1 20.2468 3.67222 10.3704 0.4777 5.10365 7.10224 -4451 2 20.359 3.07898 11.1132 -0.765711 0.100413 -2.14552 -4452 2 19.4836 3.33128 9.90403 2.85534 1.08452 -0.754728 -4453 1 5.99164 17.0864 14.8678 -5.37574 3.84131 -0.459775 -4454 2 6.63127 17.7689 14.6646 3.22934 -2.98012 2.44679 -4455 2 5.554 17.396 15.6608 -0.457156 0.512177 -0.289605 -4456 1 9.83882 21.0265 7.18035 5.95081 -1.40299 -8.14061 -4457 2 9.12061 21.5838 6.88056 -2.6067 -3.24929 2.7288 -4458 2 9.85976 21.1517 8.1291 3.24078 0.788148 -1.58199 -4459 1 14.2806 22.3479 30.4744 -5.28704 8.01428 14.3895 -4460 2 13.8253 23.128 30.1575 2.20354 -0.167513 -4.00018 -4461 2 14.4934 21.8556 29.6816 1.73645 -3.40489 3.93134 -4462 1 9.99574 22.3649 18.625 -1.24662 -2.70761 -10.6994 -4463 2 10.4595 21.9481 17.8987 0.183494 1.6516 0.642745 -4464 2 10.6595 22.4657 19.3072 -3.1201 -0.222712 1.57266 -4465 1 13.5444 23.3091 25.3305 6.03923 1.55312 0.42896 -4466 2 13.2633 22.9728 26.1815 -0.932337 -1.00851 -1.27722 -4467 2 14.4265 22.9566 25.2126 -1.02044 -2.61951 -0.48294 -4468 1 20.38 18.6937 28.3968 7.14119 -6.8925 -2.09374 -4469 2 20.0167 18.9886 27.5617 0.316244 -5.43562 -1.75257 -4470 2 21.3206 18.6184 28.2361 0.666353 0.344779 0.815735 -4471 1 31.9689 7.20731 11.1996 7.34708 3.16447 9.75319 -4472 2 31.6099 7.15114 12.0852 0.998483 0.911771 -1.0382 -4473 2 32.8409 6.81882 11.269 -0.906482 -0.425175 -2.58612 -4474 1 3.59826 34.1759 15.1126 -11.7123 -5.68349 5.97393 -4475 2 3.21043 33.454 14.6179 1.39026 0.0576551 1.52481 -4476 2 3.54331 33.8972 16.0267 0.654449 -1.39662 -0.127074 -4477 1 16.7556 18.4081 28.9987 8.31009 -1.52636 -3.73736 -4478 2 17.6307 18.6606 29.2931 -1.43242 0.172472 0.00350369 -4479 2 16.5433 17.6311 29.5158 -4.3853 4.025 1.85791 -4480 1 4.3102 29.9995 27.41 12.3163 -5.69934 9.04024 -4481 2 5.14895 30.4141 27.2079 -1.45489 3.42303 0.773461 -4482 2 3.71946 30.3049 26.7216 -0.489848 -3.13791 0.780952 -4483 1 6.15571 15.7166 24.0745 -10.4675 14.0348 8.09529 -4484 2 5.31022 15.8535 24.5019 -1.15491 -4.01696 -1.7966 -4485 2 6.50126 14.9194 24.4761 0.366863 0.626035 -2.42182 -4486 1 1.16849 28.775 19.8427 0.210476 14.8941 -2.95759 -4487 2 0.55835 28.0645 19.6452 -0.37833 1.16517 1.01041 -4488 2 2.02094 28.3459 19.9163 -1.22217 1.3797 3.29741 -4489 1 23.2346 29.7445 8.55319 -3.19073 0.0591217 -1.71373 -4490 2 24.177 29.8703 8.66448 -1.37464 0.315561 0.0894517 -4491 2 22.981 30.3965 7.89984 0.244518 -1.23007 0.476314 -4492 1 19.4825 19.1594 6.42054 2.91673 9.05689 -8.3853 -4493 2 19.0036 18.5381 5.87205 1.04646 3.76482 -1.27192 -4494 2 18.8796 19.8942 6.5334 2.07477 2.20963 -2.23813 -4495 1 33.0425 24.822 13.641 6.63183 6.2187 -2.78039 -4496 2 33.7809 24.3577 13.2468 -0.641414 -1.92179 0.68381 -4497 2 32.2751 24.3054 13.3949 -0.245517 -1.04267 4.99319 -4498 1 26.0476 6.03912 17.2588 1.74441 -5.97008 8.24573 -4499 2 26.4147 5.4419 17.9106 -0.885223 -2.61028 -1.33276 -4500 2 26.4184 5.74408 16.4271 1.8916 3.73175 0.920143 diff --git a/examples/TIP4P/gpu_dump/in.tip4p b/examples/TIP4P/gpu_dump/in.tip4p deleted file mode 100644 index b31960d203..0000000000 --- a/examples/TIP4P/gpu_dump/in.tip4p +++ /dev/null @@ -1,49 +0,0 @@ -# sample script to compare and debug GPU accelerated tip4p water -# use '-sf gpu' to enables the GPU accelerated pair style -# without it the original lj/cut/tip4p/long from module KSPACE will be used - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -atom_modify map array - -pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0 -pair_modify table 0 - -#long-range solver for TIP4P from module KSPACE works on CPU -suffix off -newton on -kspace_style pppm/tip4p 1.0e-5 -suffix on - -read_data data.spce - -pair_coeff * * 0.0 0.0 -pair_coeff 1 1 0.1852 3.1589 - -bond_coeff 1 0.0 0.9572 -angle_coeff 1 0.0 104.52 - -group water type 1 2 - -#maintain the water molecule rigid -fix 1 water shake 1.0e-4 200 0 b 1 a 1 -fix 2 water nve - -thermo 100 -thermo_style custom step etotal ke pe temp evdwl ecoul elong press -thermo_modify format float "%.15g" - -velocity water create 300 123 - -if $(is_active(package,gpu)) & - then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz"& - else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz" -dump_modify 11 sort id - -timestep 1 - -run 1 diff --git a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1 b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1 deleted file mode 100644 index 57b0db597c..0000000000 --- a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1 +++ /dev/null @@ -1,127 +0,0 @@ -LAMMPS (30 Oct 2019) -# - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -atom_modify map array - -pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0 -pair_modify table 0 - -#long-range solver for TIP4P from module KSPACE works on CPU -suffix off -newton on -kspace_style pppm/tip4p 1.0e-5 -suffix on - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.00143709 secs - read_data CPU = 0.0185545 secs - -pair_coeff * * 0.0 0.0 -pair_coeff 1 1 0.1852 3.1589 - -bond_coeff 1 0.0 0.9572 -angle_coeff 1 0.0 104.52 - -group water type 1 2 -4500 atoms in group water - -#maintain the water molecule rigid -fix 1 water shake 1.0e-4 200 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 water nve - -thermo 100 -thermo_style custom step etotal ke pe temp evdwl ecoul elong press -thermo_modify format float "%.15g" - -velocity water create 300 123 - -if $(is_active(package,gpu)) then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz" -if 0 then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz" -dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz -dump_modify 11 sort id - -timestep 1 - -run 1 -PPPM initialization ... - extracting TIP4P info from pair style - using polynomial approximation for long-range coulomb (../kspace.cpp:323) - G vector (1/distance) = 0.342797 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.00261362 - estimated relative force accuracy = 7.87083e-06 - using double precision KISS FFT - 3d grid and FFT values/proc = 79507 46656 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 11.3092 - ghost atom cutoff = 11.3092 - binsize = 5.6546, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/tip4p/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 30.18 | 30.18 | 30.18 Mbytes -Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press - 0 -6581.1098053463 2681.834801985 -9262.9446073313 300 3652.16918734499 90723.8782743546 -103638.992069031 20828.2770003273 - 1 -6293.09711304554 1787.55263217222 -8080.64974521776 199.96227554909 3652.66537554581 91910.2042281151 -103643.519348879 20986.2037813061 -Loop time of 0.0943946 on 1 procs for 1 steps with 4500 atoms - -Performance: 0.915 ns/day, 26.221 hours/ns, 10.594 timesteps/s -101.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.071838 | 0.071838 | 0.071838 | 0.0 | 76.10 -Bond | 1.974e-06 | 1.974e-06 | 1.974e-06 | 0.0 | 0.00 -Kspace | 0.012686 | 0.012686 | 0.012686 | 0.0 | 13.44 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00012462 | 0.00012462 | 0.00012462 | 0.0 | 0.13 -Output | 0.0093175 | 0.0093175 | 0.0093175 | 0.0 | 9.87 -Modify | 0.00038138 | 0.00038138 | 0.00038138 | 0.0 | 0.40 -Other | | 4.484e-05 | | | 0.05 - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 15219 ave 15219 max 15219 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.37151e+06 ave 1.37151e+06 max 1.37151e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1371514 -Ave neighs/atom = 304.781 -Ave special neighs/atom = 2 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp b/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp deleted file mode 100644 index 4441a448da..0000000000 --- a/examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1.gtx1070.dp +++ /dev/null @@ -1,120 +0,0 @@ -LAMMPS (30 Oct 2019) -package gpu 1 -# - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -atom_modify map array - -pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0 -pair_modify table 0 - -#long-range solver for TIP4P from module KSPACE works on CPU -suffix off -newton on -kspace_style pppm/tip4p 1.0e-5 -suffix on - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000921346 secs - read_data CPU = 0.0115216 secs - -pair_coeff * * 0.0 0.0 -pair_coeff 1 1 0.1852 3.1589 - -bond_coeff 1 0.0 0.9572 -angle_coeff 1 0.0 104.52 - -group water type 1 2 -4500 atoms in group water - -#maintain the water molecule rigid -fix 1 water shake 1.0e-4 200 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 water nve - -thermo 100 -thermo_style custom step etotal ke pe temp evdwl ecoul elong press -thermo_modify format float "%.15g" - -velocity water create 300 123 - -if $(is_active(package,gpu)) then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz" -if 1 then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz" -dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz -dump_modify 11 sort id - -timestep 1 - -run 1 -PPPM initialization ... - extracting TIP4P info from pair style - using polynomial approximation for long-range coulomb (../kspace.cpp:323) - G vector (1/distance) = 0.342797 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.00261362 - estimated relative force accuracy = 7.87083e-06 - using double precision KISS FFT - 3d grid and FFT values/proc = 79507 46656 -WARNING: Increasing communication cutoff for TIP4P GPU style (../pair_lj_cut_tip4p_long_gpu.cpp:220) -Per MPI rank memory allocation (min/avg/max) = 25.12 | 25.12 | 25.12 Mbytes -Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press - 0 -6581.10980534572 2681.834801985 -9262.94460733072 300 3652.169187345 90723.8782743551 -103638.992069031 20828.2770003278 - 1 -6293.09711304691 1787.55263217221 -8080.64974521913 199.96227554909 3652.6653755458 91910.2042281137 -103643.519348879 20986.203781307 -Loop time of 0.0230916 on 1 procs for 1 steps with 4500 atoms - -Performance: 3.742 ns/day, 6.414 hours/ns, 43.306 timesteps/s -103.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.000606 | 0.000606 | 0.000606 | 0.0 | 2.62 -Bond | 1.682e-06 | 1.682e-06 | 1.682e-06 | 0.0 | 0.01 -Kspace | 0.012588 | 0.012588 | 0.012588 | 0.0 | 54.51 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00015025 | 0.00015025 | 0.00015025 | 0.0 | 0.65 -Output | 0.0093124 | 0.0093124 | 0.0093124 | 0.0 | 40.33 -Modify | 0.00039674 | 0.00039674 | 0.00039674 | 0.0 | 1.72 -Other | | 3.623e-05 | | | 0.16 - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 16834 ave 16834 max 16834 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 2 -Neighbor list builds = 0 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/USER/misc/addtorque/in.addtorque b/examples/USER-MISC/addtorque/in.addtorque similarity index 100% rename from examples/USER/misc/addtorque/in.addtorque rename to examples/USER-MISC/addtorque/in.addtorque diff --git a/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.1 b/examples/USER-MISC/addtorque/log.9Nov16.addtorque.g++.1 similarity index 100% rename from examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.1 rename to examples/USER-MISC/addtorque/log.9Nov16.addtorque.g++.1 diff --git a/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.4 b/examples/USER-MISC/addtorque/log.9Nov16.addtorque.g++.4 similarity index 100% rename from examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.4 rename to examples/USER-MISC/addtorque/log.9Nov16.addtorque.g++.4 diff --git a/examples/USER/misc/agni/Al_jpc.agni b/examples/USER-MISC/agni/Al_jpc.agni similarity index 100% rename from examples/USER/misc/agni/Al_jpc.agni rename to examples/USER-MISC/agni/Al_jpc.agni diff --git a/examples/USER/misc/agni/adatom.data b/examples/USER-MISC/agni/adatom.data similarity index 100% rename from examples/USER/misc/agni/adatom.data rename to examples/USER-MISC/agni/adatom.data diff --git a/examples/USER/misc/agni/in.adatom b/examples/USER-MISC/agni/in.adatom similarity index 100% rename from examples/USER/misc/agni/in.adatom rename to examples/USER-MISC/agni/in.adatom diff --git a/examples/USER/misc/agni/in.vacancy b/examples/USER-MISC/agni/in.vacancy similarity index 100% rename from examples/USER/misc/agni/in.vacancy rename to examples/USER-MISC/agni/in.vacancy diff --git a/examples/USER/misc/agni/log.20Jan21.adatom.g++.1 b/examples/USER-MISC/agni/log.20Jan21.adatom.g++.1 similarity index 100% rename from examples/USER/misc/agni/log.20Jan21.adatom.g++.1 rename to examples/USER-MISC/agni/log.20Jan21.adatom.g++.1 diff --git a/examples/USER/misc/agni/log.20Jan21.adatom.g++.4 b/examples/USER-MISC/agni/log.20Jan21.adatom.g++.4 similarity index 100% rename from examples/USER/misc/agni/log.20Jan21.adatom.g++.4 rename to examples/USER-MISC/agni/log.20Jan21.adatom.g++.4 diff --git a/examples/USER/misc/agni/log.20Jan21.vacancy.g++.1 b/examples/USER-MISC/agni/log.20Jan21.vacancy.g++.1 similarity index 100% rename from examples/USER/misc/agni/log.20Jan21.vacancy.g++.1 rename to examples/USER-MISC/agni/log.20Jan21.vacancy.g++.1 diff --git a/examples/USER/misc/agni/log.20Jan21.vacancy.g++.4 b/examples/USER-MISC/agni/log.20Jan21.vacancy.g++.4 similarity index 100% rename from examples/USER/misc/agni/log.20Jan21.vacancy.g++.4 rename to examples/USER-MISC/agni/log.20Jan21.vacancy.g++.4 diff --git a/examples/USER/misc/agni/vacancy.data b/examples/USER-MISC/agni/vacancy.data similarity index 100% rename from examples/USER/misc/agni/vacancy.data rename to examples/USER-MISC/agni/vacancy.data diff --git a/examples/USER/misc/basal/almg.liu b/examples/USER-MISC/basal/almg.liu similarity index 100% rename from examples/USER/misc/basal/almg.liu rename to examples/USER-MISC/basal/almg.liu diff --git a/examples/USER/misc/basal/in.basal b/examples/USER-MISC/basal/in.basal similarity index 100% rename from examples/USER/misc/basal/in.basal rename to examples/USER-MISC/basal/in.basal diff --git a/examples/USER/misc/cauchy/NiAlH_jea.eam.alloy b/examples/USER-MISC/cauchy/NiAlH_jea.eam.alloy similarity index 100% rename from examples/USER/misc/cauchy/NiAlH_jea.eam.alloy rename to examples/USER-MISC/cauchy/NiAlH_jea.eam.alloy diff --git a/examples/USER/misc/cauchy/README b/examples/USER-MISC/cauchy/README similarity index 100% rename from examples/USER/misc/cauchy/README rename to examples/USER-MISC/cauchy/README diff --git a/examples/USER/misc/cauchy/in.cauchystat b/examples/USER-MISC/cauchy/in.cauchystat similarity index 100% rename from examples/USER/misc/cauchy/in.cauchystat rename to examples/USER-MISC/cauchy/in.cauchystat diff --git a/examples/USER/misc/cauchy/log.2Jun2020.cauchystat.g++.1 b/examples/USER-MISC/cauchy/log.2Jun2020.cauchystat.g++.1 similarity index 100% rename from examples/USER/misc/cauchy/log.2Jun2020.cauchystat.g++.1 rename to examples/USER-MISC/cauchy/log.2Jun2020.cauchystat.g++.1 diff --git a/examples/USER/misc/charge_regulation/README b/examples/USER-MISC/charge_regulation/README similarity index 100% rename from examples/USER/misc/charge_regulation/README rename to examples/USER-MISC/charge_regulation/README diff --git a/examples/USER/misc/charge_regulation/data.chreg-acid b/examples/USER-MISC/charge_regulation/data.chreg-acid similarity index 100% rename from examples/USER/misc/charge_regulation/data.chreg-acid rename to examples/USER-MISC/charge_regulation/data.chreg-acid diff --git a/examples/USER/misc/charge_regulation/data.chreg-acid-real b/examples/USER-MISC/charge_regulation/data.chreg-acid-real similarity index 100% rename from examples/USER/misc/charge_regulation/data.chreg-acid-real rename to examples/USER-MISC/charge_regulation/data.chreg-acid-real diff --git a/examples/USER/misc/charge_regulation/data.chreg-polymer b/examples/USER-MISC/charge_regulation/data.chreg-polymer similarity index 100% rename from examples/USER/misc/charge_regulation/data.chreg-polymer rename to examples/USER-MISC/charge_regulation/data.chreg-polymer diff --git a/examples/USER/misc/charge_regulation/in.chreg-acid b/examples/USER-MISC/charge_regulation/in.chreg-acid similarity index 100% rename from examples/USER/misc/charge_regulation/in.chreg-acid rename to examples/USER-MISC/charge_regulation/in.chreg-acid diff --git a/examples/USER/misc/charge_regulation/in.chreg-acid-real b/examples/USER-MISC/charge_regulation/in.chreg-acid-real similarity index 100% rename from examples/USER/misc/charge_regulation/in.chreg-acid-real rename to examples/USER-MISC/charge_regulation/in.chreg-acid-real diff --git a/examples/USER/misc/charge_regulation/in.chreg-polymer b/examples/USER-MISC/charge_regulation/in.chreg-polymer similarity index 100% rename from examples/USER/misc/charge_regulation/in.chreg-polymer rename to examples/USER-MISC/charge_regulation/in.chreg-polymer diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 b/examples/USER-MISC/charge_regulation/log.10Feb21.chreg-acid.g++.1 similarity index 100% rename from examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 rename to examples/USER-MISC/charge_regulation/log.10Feb21.chreg-acid.g++.1 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 b/examples/USER-MISC/charge_regulation/log.10Feb21.chreg-acid.g++.4 similarity index 100% rename from examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 rename to examples/USER-MISC/charge_regulation/log.10Feb21.chreg-acid.g++.4 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 b/examples/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.1 similarity index 100% rename from examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 rename to examples/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.1 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 b/examples/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.4 similarity index 100% rename from examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 rename to examples/USER-MISC/charge_regulation/log.10Feb21.chreg-polymer.g++.4 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 b/examples/USER-MISC/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 similarity index 100% rename from examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 rename to examples/USER-MISC/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 b/examples/USER-MISC/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 similarity index 100% rename from examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 rename to examples/USER-MISC/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 diff --git a/examples/USER/misc/cnp/Cu_Mishin1.eam b/examples/USER-MISC/cnp/Cu_Mishin1.eam similarity index 100% rename from examples/USER/misc/cnp/Cu_Mishin1.eam rename to examples/USER-MISC/cnp/Cu_Mishin1.eam diff --git a/examples/USER/misc/cnp/in.cnp b/examples/USER-MISC/cnp/in.cnp similarity index 100% rename from examples/USER/misc/cnp/in.cnp rename to examples/USER-MISC/cnp/in.cnp diff --git a/examples/USER/misc/cnp/log.31May17.cnp.g++.4 b/examples/USER-MISC/cnp/log.31May17.cnp.g++.4 similarity index 100% rename from examples/USER/misc/cnp/log.31May17.cnp.g++.4 rename to examples/USER-MISC/cnp/log.31May17.cnp.g++.4 diff --git a/examples/USER/misc/drip/C.drip b/examples/USER-MISC/drip/C.drip similarity index 100% rename from examples/USER/misc/drip/C.drip rename to examples/USER-MISC/drip/C.drip diff --git a/examples/USER/misc/drip/CH.rebo b/examples/USER-MISC/drip/CH.rebo similarity index 100% rename from examples/USER/misc/drip/CH.rebo rename to examples/USER-MISC/drip/CH.rebo diff --git a/examples/USER/misc/drip/README.txt b/examples/USER-MISC/drip/README.txt similarity index 100% rename from examples/USER/misc/drip/README.txt rename to examples/USER-MISC/drip/README.txt diff --git a/examples/USER/misc/drip/data.C b/examples/USER-MISC/drip/data.C similarity index 100% rename from examples/USER/misc/drip/data.C rename to examples/USER-MISC/drip/data.C diff --git a/examples/USER/misc/drip/data.CH b/examples/USER-MISC/drip/data.CH similarity index 100% rename from examples/USER/misc/drip/data.CH rename to examples/USER-MISC/drip/data.CH diff --git a/examples/USER/misc/drip/in.CH_drip b/examples/USER-MISC/drip/in.CH_drip similarity index 100% rename from examples/USER/misc/drip/in.CH_drip rename to examples/USER-MISC/drip/in.CH_drip diff --git a/examples/USER/misc/drip/in.C_drip b/examples/USER-MISC/drip/in.C_drip similarity index 100% rename from examples/USER/misc/drip/in.C_drip rename to examples/USER-MISC/drip/in.C_drip diff --git a/examples/USER/misc/drip/log.30Apr19.CH_drip.g++.1 b/examples/USER-MISC/drip/log.30Apr19.CH_drip.g++.1 similarity index 100% rename from examples/USER/misc/drip/log.30Apr19.CH_drip.g++.1 rename to examples/USER-MISC/drip/log.30Apr19.CH_drip.g++.1 diff --git a/examples/USER/misc/drip/log.30Apr19.CH_drip.g++.4 b/examples/USER-MISC/drip/log.30Apr19.CH_drip.g++.4 similarity index 100% rename from examples/USER/misc/drip/log.30Apr19.CH_drip.g++.4 rename to examples/USER-MISC/drip/log.30Apr19.CH_drip.g++.4 diff --git a/examples/USER/misc/drip/log.30Apr19.C_drip.g++.1 b/examples/USER-MISC/drip/log.30Apr19.C_drip.g++.1 similarity index 100% rename from examples/USER/misc/drip/log.30Apr19.C_drip.g++.1 rename to examples/USER-MISC/drip/log.30Apr19.C_drip.g++.1 diff --git a/examples/USER/misc/drip/log.30Apr19.C_drip.g++.4 b/examples/USER-MISC/drip/log.30Apr19.C_drip.g++.4 similarity index 100% rename from examples/USER/misc/drip/log.30Apr19.C_drip.g++.4 rename to examples/USER-MISC/drip/log.30Apr19.C_drip.g++.4 diff --git a/examples/USER/misc/e3b/README b/examples/USER-MISC/e3b/README similarity index 100% rename from examples/USER/misc/e3b/README rename to examples/USER-MISC/e3b/README diff --git a/examples/USER/misc/e3b/e3b_box.data b/examples/USER-MISC/e3b/e3b_box.data similarity index 100% rename from examples/USER/misc/e3b/e3b_box.data rename to examples/USER-MISC/e3b/e3b_box.data diff --git a/examples/USER/misc/e3b/in.e3b-tip4p2005 b/examples/USER-MISC/e3b/in.e3b-tip4p2005 similarity index 100% rename from examples/USER/misc/e3b/in.e3b-tip4p2005 rename to examples/USER-MISC/e3b/in.e3b-tip4p2005 diff --git a/examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 b/examples/USER-MISC/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 similarity index 100% rename from examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 rename to examples/USER-MISC/e3b/log.29Mar2019.e3b-tip4p2005.g++.1 diff --git a/examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 b/examples/USER-MISC/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 similarity index 100% rename from examples/USER/misc/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 rename to examples/USER-MISC/e3b/log.29Mar2019.e3b-tip4p2005.g++.4 diff --git a/examples/USER/misc/edip/Si.edip b/examples/USER-MISC/edip/Si.edip similarity index 100% rename from examples/USER/misc/edip/Si.edip rename to examples/USER-MISC/edip/Si.edip diff --git a/examples/USER/misc/edip/SiC.edip b/examples/USER-MISC/edip/SiC.edip similarity index 100% rename from examples/USER/misc/edip/SiC.edip rename to examples/USER-MISC/edip/SiC.edip diff --git a/examples/USER/misc/edip/data.SiC b/examples/USER-MISC/edip/data.SiC similarity index 100% rename from examples/USER/misc/edip/data.SiC rename to examples/USER-MISC/edip/data.SiC diff --git a/examples/USER/misc/edip/in.edip-Si b/examples/USER-MISC/edip/in.edip-Si similarity index 100% rename from examples/USER/misc/edip/in.edip-Si rename to examples/USER-MISC/edip/in.edip-Si diff --git a/examples/USER/misc/edip/in.edip-Si-multi b/examples/USER-MISC/edip/in.edip-Si-multi similarity index 100% rename from examples/USER/misc/edip/in.edip-Si-multi rename to examples/USER-MISC/edip/in.edip-Si-multi diff --git a/examples/USER/misc/edip/in.edip-SiC b/examples/USER-MISC/edip/in.edip-SiC similarity index 100% rename from examples/USER/misc/edip/in.edip-SiC rename to examples/USER-MISC/edip/in.edip-SiC diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1 b/examples/USER-MISC/edip/log.4May2017.g++.edip-Si-multi.1 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1 rename to examples/USER-MISC/edip/log.4May2017.g++.edip-Si-multi.1 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4 b/examples/USER-MISC/edip/log.4May2017.g++.edip-Si-multi.4 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4 rename to examples/USER-MISC/edip/log.4May2017.g++.edip-Si-multi.4 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si.1 b/examples/USER-MISC/edip/log.4May2017.g++.edip-Si.1 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si.1 rename to examples/USER-MISC/edip/log.4May2017.g++.edip-Si.1 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si.4 b/examples/USER-MISC/edip/log.4May2017.g++.edip-Si.4 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-Si.4 rename to examples/USER-MISC/edip/log.4May2017.g++.edip-Si.4 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1 b/examples/USER-MISC/edip/log.4May2017.g++.edip-SiC.1 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1 rename to examples/USER-MISC/edip/log.4May2017.g++.edip-SiC.1 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4 b/examples/USER-MISC/edip/log.4May2017.g++.edip-SiC.4 similarity index 100% rename from examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4 rename to examples/USER-MISC/edip/log.4May2017.g++.edip-SiC.4 diff --git a/examples/USER/misc/ees/Data_region b/examples/USER-MISC/ees/Data_region similarity index 100% rename from examples/USER/misc/ees/Data_region rename to examples/USER-MISC/ees/Data_region diff --git a/examples/USER/misc/ees/Data_wall b/examples/USER-MISC/ees/Data_wall similarity index 100% rename from examples/USER/misc/ees/Data_wall rename to examples/USER-MISC/ees/Data_wall diff --git a/examples/USER/misc/ees/README b/examples/USER-MISC/ees/README similarity index 100% rename from examples/USER/misc/ees/README rename to examples/USER-MISC/ees/README diff --git a/examples/USER/misc/ees/in.fix_wall b/examples/USER-MISC/ees/in.fix_wall similarity index 100% rename from examples/USER/misc/ees/in.fix_wall rename to examples/USER-MISC/ees/in.fix_wall diff --git a/examples/USER/misc/ees/in.fix_wall_region b/examples/USER-MISC/ees/in.fix_wall_region similarity index 100% rename from examples/USER/misc/ees/in.fix_wall_region rename to examples/USER-MISC/ees/in.fix_wall_region diff --git a/examples/USER/misc/ees/log.23Jun17.fix_wall.g++.1 b/examples/USER-MISC/ees/log.23Jun17.fix_wall.g++.1 similarity index 100% rename from examples/USER/misc/ees/log.23Jun17.fix_wall.g++.1 rename to examples/USER-MISC/ees/log.23Jun17.fix_wall.g++.1 diff --git a/examples/USER/misc/ees/log.23Jun17.fix_wall.g++.4 b/examples/USER-MISC/ees/log.23Jun17.fix_wall.g++.4 similarity index 100% rename from examples/USER/misc/ees/log.23Jun17.fix_wall.g++.4 rename to examples/USER-MISC/ees/log.23Jun17.fix_wall.g++.4 diff --git a/examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.1 b/examples/USER-MISC/ees/log.23Jun17.fix_wall_region.g++.1 similarity index 100% rename from examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.1 rename to examples/USER-MISC/ees/log.23Jun17.fix_wall_region.g++.1 diff --git a/examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.4 b/examples/USER-MISC/ees/log.23Jun17.fix_wall_region.g++.4 similarity index 100% rename from examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.4 rename to examples/USER-MISC/ees/log.23Jun17.fix_wall_region.g++.4 diff --git a/examples/USER/misc/electron_stopping/Si.Si.elstop b/examples/USER-MISC/electron_stopping/Si.Si.elstop similarity index 100% rename from examples/USER/misc/electron_stopping/Si.Si.elstop rename to examples/USER-MISC/electron_stopping/Si.Si.elstop diff --git a/examples/USER/misc/electron_stopping/Si.sw b/examples/USER-MISC/electron_stopping/Si.sw similarity index 100% rename from examples/USER/misc/electron_stopping/Si.sw rename to examples/USER-MISC/electron_stopping/Si.sw diff --git a/examples/USER/misc/electron_stopping/in.cascade_AlCu b/examples/USER-MISC/electron_stopping/in.cascade_AlCu similarity index 100% rename from examples/USER/misc/electron_stopping/in.cascade_AlCu rename to examples/USER-MISC/electron_stopping/in.cascade_AlCu diff --git a/examples/USER/misc/electron_stopping/in.cascade_SiSi b/examples/USER-MISC/electron_stopping/in.cascade_SiSi similarity index 100% rename from examples/USER/misc/electron_stopping/in.cascade_SiSi rename to examples/USER-MISC/electron_stopping/in.cascade_SiSi diff --git a/examples/USER/misc/electron_stopping/in.elstop b/examples/USER-MISC/electron_stopping/in.elstop similarity index 100% rename from examples/USER/misc/electron_stopping/in.elstop rename to examples/USER-MISC/electron_stopping/in.elstop diff --git a/examples/USER/misc/electron_stopping/in.elstop.only b/examples/USER-MISC/electron_stopping/in.elstop.only similarity index 100% rename from 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rename from examples/USER/misc/kolmogorov_crespi_z/data.bilayer-graphene rename to examples/USER-MISC/kolmogorov_crespi_z/data.bilayer-graphene diff --git a/examples/USER/misc/kolmogorov_crespi_z/data.graphene-adsorbant b/examples/USER-MISC/kolmogorov_crespi_z/data.graphene-adsorbant similarity index 100% rename from examples/USER/misc/kolmogorov_crespi_z/data.graphene-adsorbant rename to examples/USER-MISC/kolmogorov_crespi_z/data.graphene-adsorbant diff --git a/examples/USER/misc/kolmogorov_crespi_z/in.atom-diffusion b/examples/USER-MISC/kolmogorov_crespi_z/in.atom-diffusion similarity index 100% rename from examples/USER/misc/kolmogorov_crespi_z/in.atom-diffusion rename to examples/USER-MISC/kolmogorov_crespi_z/in.atom-diffusion diff --git a/examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene b/examples/USER-MISC/kolmogorov_crespi_z/in.bilayer-graphene similarity index 100% rename from examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene rename to examples/USER-MISC/kolmogorov_crespi_z/in.bilayer-graphene diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.1 b/examples/USER-MISC/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.1 similarity index 100% rename from examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.1 rename to examples/USER-MISC/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.1 diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.4 b/examples/USER-MISC/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.4 similarity index 100% rename from examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.4 rename to examples/USER-MISC/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.4 diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 b/examples/USER-MISC/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 similarity index 100% rename from examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 rename to examples/USER-MISC/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 b/examples/USER-MISC/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 similarity index 100% rename from examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 rename to examples/USER-MISC/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 diff --git a/examples/USER/misc/lebedeva/2particles.dat b/examples/USER-MISC/lebedeva/2particles.dat similarity index 100% rename from examples/USER/misc/lebedeva/2particles.dat rename to examples/USER-MISC/lebedeva/2particles.dat diff --git a/examples/USER/misc/lebedeva/2particles.in b/examples/USER-MISC/lebedeva/2particles.in similarity index 100% rename from examples/USER/misc/lebedeva/2particles.in rename to examples/USER-MISC/lebedeva/2particles.in diff --git a/examples/USER/misc/lebedeva/CC.Lebedeva b/examples/USER-MISC/lebedeva/CC.Lebedeva similarity index 100% rename from examples/USER/misc/lebedeva/CC.Lebedeva rename to examples/USER-MISC/lebedeva/CC.Lebedeva diff --git a/examples/USER/misc/lebedeva/LammpsResult.dat b/examples/USER-MISC/lebedeva/LammpsResult.dat similarity index 100% rename from examples/USER/misc/lebedeva/LammpsResult.dat rename to examples/USER-MISC/lebedeva/LammpsResult.dat diff --git a/examples/USER/misc/lebedeva/LebDer.pl b/examples/USER-MISC/lebedeva/LebDer.pl similarity index 100% rename from examples/USER/misc/lebedeva/LebDer.pl rename to examples/USER-MISC/lebedeva/LebDer.pl diff --git a/examples/USER/misc/lebedeva/lebedeva00.plot b/examples/USER-MISC/lebedeva/lebedeva00.plot similarity index 100% rename from examples/USER/misc/lebedeva/lebedeva00.plot rename to examples/USER-MISC/lebedeva/lebedeva00.plot diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.data b/examples/USER-MISC/local_density/benzene_water/benzene_water.data similarity index 100% rename from examples/USER/misc/local_density/benzene_water/benzene_water.data rename to examples/USER-MISC/local_density/benzene_water/benzene_water.data diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.in b/examples/USER-MISC/local_density/benzene_water/benzene_water.in similarity index 100% rename from examples/USER/misc/local_density/benzene_water/benzene_water.in rename to examples/USER-MISC/local_density/benzene_water/benzene_water.in diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.localdensity.table b/examples/USER-MISC/local_density/benzene_water/benzene_water.localdensity.table similarity index 100% rename from examples/USER/misc/local_density/benzene_water/benzene_water.localdensity.table rename to examples/USER-MISC/local_density/benzene_water/benzene_water.localdensity.table diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.pair.table b/examples/USER-MISC/local_density/benzene_water/benzene_water.pair.table similarity index 100% rename from examples/USER/misc/local_density/benzene_water/benzene_water.pair.table rename to examples/USER-MISC/local_density/benzene_water/benzene_water.pair.table diff --git a/examples/USER/misc/local_density/benzene_water/log.04Sep19.g++.1 b/examples/USER-MISC/local_density/benzene_water/log.04Sep19.g++.1 similarity index 100% rename from examples/USER/misc/local_density/benzene_water/log.04Sep19.g++.1 rename to examples/USER-MISC/local_density/benzene_water/log.04Sep19.g++.1 diff --git a/examples/USER/misc/local_density/methanol_implicit_water/log.04Sep19.g++.1 b/examples/USER-MISC/local_density/methanol_implicit_water/log.04Sep19.g++.1 similarity index 100% rename from examples/USER/misc/local_density/methanol_implicit_water/log.04Sep19.g++.1 rename to examples/USER-MISC/local_density/methanol_implicit_water/log.04Sep19.g++.1 diff --git a/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.data b/examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.data similarity index 100% rename from examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.data rename to examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.data diff --git a/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.in b/examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.in similarity index 100% rename from examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.in rename to examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.in diff --git a/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table b/examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table similarity index 100% rename from examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table rename to examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table diff --git a/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.pair.table b/examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.pair.table similarity index 100% rename from examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.pair.table rename to examples/USER-MISC/local_density/methanol_implicit_water/methanol_implicit_water.pair.table diff --git a/examples/USER/misc/meam_spline/Si_1.meam.spline b/examples/USER-MISC/meam_spline/Si_1.meam.spline similarity index 100% rename from examples/USER/misc/meam_spline/Si_1.meam.spline rename to examples/USER-MISC/meam_spline/Si_1.meam.spline diff --git a/examples/USER/misc/meam_spline/TiO.meam.spline b/examples/USER-MISC/meam_spline/TiO.meam.spline similarity index 100% rename from examples/USER/misc/meam_spline/TiO.meam.spline rename to examples/USER-MISC/meam_spline/TiO.meam.spline diff --git a/examples/USER/misc/meam_spline/in.meam-spline.Si b/examples/USER-MISC/meam_spline/in.meam-spline.Si similarity index 100% rename from examples/USER/misc/meam_spline/in.meam-spline.Si rename to examples/USER-MISC/meam_spline/in.meam-spline.Si diff --git a/examples/USER/misc/meam_spline/in.meam-spline.TiO2 b/examples/USER-MISC/meam_spline/in.meam-spline.TiO2 similarity index 100% rename from examples/USER/misc/meam_spline/in.meam-spline.TiO2 rename to examples/USER-MISC/meam_spline/in.meam-spline.TiO2 diff --git a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.1 b/examples/USER-MISC/meam_spline/log.4May2017.meam-spline.Si.g++.1 similarity index 100% rename from examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.1 rename to examples/USER-MISC/meam_spline/log.4May2017.meam-spline.Si.g++.1 diff --git a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.4 b/examples/USER-MISC/meam_spline/log.4May2017.meam-spline.Si.g++.4 similarity index 100% rename from examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.4 rename to examples/USER-MISC/meam_spline/log.4May2017.meam-spline.Si.g++.4 diff --git a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 b/examples/USER-MISC/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 similarity index 100% rename from examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 rename to examples/USER-MISC/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 diff --git a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 b/examples/USER-MISC/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 similarity index 100% rename from examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 rename to examples/USER-MISC/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 diff --git a/examples/USER/misc/meam_sw_spline/Si/bcc.in b/examples/USER-MISC/meam_sw_spline/Si/bcc.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/bcc.in rename to examples/USER-MISC/meam_sw_spline/Si/bcc.in diff --git a/examples/USER/misc/meam_sw_spline/Si/bcc_relax.in b/examples/USER-MISC/meam_sw_spline/Si/bcc_relax.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/bcc_relax.in rename to examples/USER-MISC/meam_sw_spline/Si/bcc_relax.in diff --git a/examples/USER/misc/meam_sw_spline/Si/dc.in b/examples/USER-MISC/meam_sw_spline/Si/dc.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/dc.in rename to examples/USER-MISC/meam_sw_spline/Si/dc.in diff --git a/examples/USER/misc/meam_sw_spline/Si/dc_relax.in b/examples/USER-MISC/meam_sw_spline/Si/dc_relax.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/dc_relax.in rename to examples/USER-MISC/meam_sw_spline/Si/dc_relax.in diff --git a/examples/USER/misc/meam_sw_spline/Si/energy_conservation.meam.sw.in b/examples/USER-MISC/meam_sw_spline/Si/energy_conservation.meam.sw.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/energy_conservation.meam.sw.in rename to examples/USER-MISC/meam_sw_spline/Si/energy_conservation.meam.sw.in diff --git a/examples/USER/misc/meam_sw_spline/Si/fcc.in b/examples/USER-MISC/meam_sw_spline/Si/fcc.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/fcc.in rename to examples/USER-MISC/meam_sw_spline/Si/fcc.in diff --git a/examples/USER/misc/meam_sw_spline/Si/fcc_relax.in b/examples/USER-MISC/meam_sw_spline/Si/fcc_relax.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/fcc_relax.in rename to examples/USER-MISC/meam_sw_spline/Si/fcc_relax.in diff --git a/examples/USER/misc/meam_sw_spline/Si/hcp_relax.in b/examples/USER-MISC/meam_sw_spline/Si/hcp_relax.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/hcp_relax.in rename to examples/USER-MISC/meam_sw_spline/Si/hcp_relax.in diff --git a/examples/USER/misc/meam_sw_spline/Si/sc.in b/examples/USER-MISC/meam_sw_spline/Si/sc.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/sc.in rename to examples/USER-MISC/meam_sw_spline/Si/sc.in diff --git a/examples/USER/misc/meam_sw_spline/Si/sc_relax.in b/examples/USER-MISC/meam_sw_spline/Si/sc_relax.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/sc_relax.in rename to examples/USER-MISC/meam_sw_spline/Si/sc_relax.in diff --git a/examples/USER/misc/meam_sw_spline/Si/single_atom.in b/examples/USER-MISC/meam_sw_spline/Si/single_atom.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Si/single_atom.in rename to examples/USER-MISC/meam_sw_spline/Si/single_atom.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/alpha.in b/examples/USER-MISC/meam_sw_spline/Ti/alpha.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/alpha.in rename to examples/USER-MISC/meam_sw_spline/Ti/alpha.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/alpha_relaxation.in b/examples/USER-MISC/meam_sw_spline/Ti/alpha_relaxation.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/alpha_relaxation.in rename to examples/USER-MISC/meam_sw_spline/Ti/alpha_relaxation.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/beta.in b/examples/USER-MISC/meam_sw_spline/Ti/beta.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/beta.in rename to examples/USER-MISC/meam_sw_spline/Ti/beta.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/energy_conservation.meam.sw.in b/examples/USER-MISC/meam_sw_spline/Ti/energy_conservation.meam.sw.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/energy_conservation.meam.sw.in rename to examples/USER-MISC/meam_sw_spline/Ti/energy_conservation.meam.sw.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/fcc.in b/examples/USER-MISC/meam_sw_spline/Ti/fcc.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/fcc.in rename to examples/USER-MISC/meam_sw_spline/Ti/fcc.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/hexagonal.in b/examples/USER-MISC/meam_sw_spline/Ti/hexagonal.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/hexagonal.in rename to examples/USER-MISC/meam_sw_spline/Ti/hexagonal.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/omega.in b/examples/USER-MISC/meam_sw_spline/Ti/omega.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/omega.in rename to examples/USER-MISC/meam_sw_spline/Ti/omega.in diff --git a/examples/USER/misc/meam_sw_spline/Ti/single_atom.in b/examples/USER-MISC/meam_sw_spline/Ti/single_atom.in similarity index 100% rename from examples/USER/misc/meam_sw_spline/Ti/single_atom.in rename to examples/USER-MISC/meam_sw_spline/Ti/single_atom.in diff --git a/examples/USER/misc/momb/Ag_O1X5.5_O2X0.55.eam.fs b/examples/USER-MISC/momb/Ag_O1X5.5_O2X0.55.eam.fs similarity index 100% rename from examples/USER/misc/momb/Ag_O1X5.5_O2X0.55.eam.fs rename to examples/USER-MISC/momb/Ag_O1X5.5_O2X0.55.eam.fs diff --git a/examples/USER/misc/momb/README b/examples/USER-MISC/momb/README similarity index 100% rename from examples/USER/misc/momb/README rename to examples/USER-MISC/momb/README diff --git a/examples/USER/misc/momb/in.system b/examples/USER-MISC/momb/in.system similarity index 100% rename from examples/USER/misc/momb/in.system rename to examples/USER-MISC/momb/in.system diff --git a/examples/USER/misc/momb/log.17Mar2017.system.g++.1 b/examples/USER-MISC/momb/log.17Mar2017.system.g++.1 similarity index 100% rename from examples/USER/misc/momb/log.17Mar2017.system.g++.1 rename to examples/USER-MISC/momb/log.17Mar2017.system.g++.1 diff --git a/examples/USER/misc/momb/log.17Mar2017.system.g++.4 b/examples/USER-MISC/momb/log.17Mar2017.system.g++.4 similarity index 100% rename from examples/USER/misc/momb/log.17Mar2017.system.g++.4 rename to examples/USER-MISC/momb/log.17Mar2017.system.g++.4 diff --git a/examples/USER/misc/momb/system.data b/examples/USER-MISC/momb/system.data similarity index 100% rename from examples/USER/misc/momb/system.data rename to examples/USER-MISC/momb/system.data diff --git a/examples/USER/misc/momentum/in.momentum b/examples/USER-MISC/momentum/in.momentum similarity index 100% rename from examples/USER/misc/momentum/in.momentum rename to examples/USER-MISC/momentum/in.momentum diff --git a/examples/USER/misc/mop/data.mop b/examples/USER-MISC/mop/data.mop similarity index 100% rename from examples/USER/misc/mop/data.mop rename to examples/USER-MISC/mop/data.mop diff --git a/examples/USER/misc/mop/in.compute_stress_mop b/examples/USER-MISC/mop/in.compute_stress_mop similarity index 100% rename from examples/USER/misc/mop/in.compute_stress_mop rename to examples/USER-MISC/mop/in.compute_stress_mop diff --git a/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 b/examples/USER-MISC/mop/log.5Sep18.compute_stress_mop.g++.1 similarity index 100% rename from examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 rename to examples/USER-MISC/mop/log.5Sep18.compute_stress_mop.g++.1 diff --git a/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 b/examples/USER-MISC/mop/log.5Sep18.compute_stress_mop.g++.4 similarity index 100% rename from examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 rename to examples/USER-MISC/mop/log.5Sep18.compute_stress_mop.g++.4 diff --git a/examples/USER/misc/mop/moppz.time.reference b/examples/USER-MISC/mop/moppz.time.reference similarity index 100% rename from examples/USER/misc/mop/moppz.time.reference rename to examples/USER-MISC/mop/moppz.time.reference diff --git a/examples/USER/misc/mop/mopz0.time.reference b/examples/USER-MISC/mop/mopz0.time.reference similarity index 100% rename from examples/USER/misc/mop/mopz0.time.reference rename to examples/USER-MISC/mop/mopz0.time.reference diff --git a/examples/USER/misc/orient_eco/Ni_u3.eam b/examples/USER-MISC/orient_eco/Ni_u3.eam similarity index 100% rename from examples/USER/misc/orient_eco/Ni_u3.eam rename to examples/USER-MISC/orient_eco/Ni_u3.eam diff --git a/examples/USER/misc/orient_eco/data.sigma5 b/examples/USER-MISC/orient_eco/data.sigma5 similarity index 100% rename from examples/USER/misc/orient_eco/data.sigma5 rename to examples/USER-MISC/orient_eco/data.sigma5 diff --git a/examples/USER/misc/orient_eco/in.orient_eco b/examples/USER-MISC/orient_eco/in.orient_eco similarity index 100% rename from examples/USER/misc/orient_eco/in.orient_eco rename to examples/USER-MISC/orient_eco/in.orient_eco diff --git a/examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.1 b/examples/USER-MISC/orient_eco/log.2Jun2020.orent_eco.g++.1 similarity index 100% rename from examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.1 rename to examples/USER-MISC/orient_eco/log.2Jun2020.orent_eco.g++.1 diff --git a/examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.4 b/examples/USER-MISC/orient_eco/log.2Jun2020.orent_eco.g++.4 similarity index 100% rename from examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.4 rename to examples/USER-MISC/orient_eco/log.2Jun2020.orent_eco.g++.4 diff --git a/examples/USER/misc/orient_eco/sigma5.ori b/examples/USER-MISC/orient_eco/sigma5.ori similarity index 100% rename from examples/USER/misc/orient_eco/sigma5.ori rename to examples/USER-MISC/orient_eco/sigma5.ori diff --git a/examples/USER/misc/pafi/.gitignore b/examples/USER-MISC/pafi/.gitignore similarity index 100% rename from examples/USER/misc/pafi/.gitignore rename to examples/USER-MISC/pafi/.gitignore diff --git a/examples/USER/misc/pafi/README b/examples/USER-MISC/pafi/README similarity index 93% rename from examples/USER/misc/pafi/README rename to examples/USER-MISC/pafi/README index c35dff313c..675ce59de4 100644 --- a/examples/USER/misc/pafi/README +++ b/examples/USER-MISC/pafi/README @@ -1,4 +1,4 @@ -Run an example constrained sample for USER-PAFI calculation +Run an example constrained sample for PAFI calculation Author: Thomas Swinburne, CNRS / CINaM, Marseille @@ -21,7 +21,7 @@ allowing the calculation of free energy barriers and minimum free energy paths. To compile: -make yes-user-misc # for PAFI +make yes-misc # for PAFI make yes-manybody # for EAM potential make machine # for binary (machine= e.g. mpi) diff --git a/examples/USER/misc/pafi/in.pafi b/examples/USER-MISC/pafi/in.pafi similarity index 100% rename from examples/USER/misc/pafi/in.pafi rename to examples/USER-MISC/pafi/in.pafi diff --git a/examples/USER/misc/pafi/log.15Apr20.pafi.g++.1 b/examples/USER-MISC/pafi/log.15Apr20.pafi.g++.1 similarity index 100% rename from examples/USER/misc/pafi/log.15Apr20.pafi.g++.1 rename to examples/USER-MISC/pafi/log.15Apr20.pafi.g++.1 diff --git a/examples/USER/misc/pafi/log.15Apr20.pafi.g++.4 b/examples/USER-MISC/pafi/log.15Apr20.pafi.g++.4 similarity index 100% rename from examples/USER/misc/pafi/log.15Apr20.pafi.g++.4 rename to examples/USER-MISC/pafi/log.15Apr20.pafi.g++.4 diff --git a/examples/USER/misc/pafi/pafipath.4.data b/examples/USER-MISC/pafi/pafipath.4.data similarity index 100% rename from examples/USER/misc/pafi/pafipath.4.data rename to examples/USER-MISC/pafi/pafipath.4.data diff --git a/examples/USER/misc/pimd/para-h2/H2.data b/examples/USER-MISC/pimd/para-h2/H2.data similarity index 100% rename from examples/USER/misc/pimd/para-h2/H2.data rename to examples/USER-MISC/pimd/para-h2/H2.data diff --git a/examples/USER/misc/pimd/para-h2/H2.xyz b/examples/USER-MISC/pimd/para-h2/H2.xyz similarity index 100% rename from examples/USER/misc/pimd/para-h2/H2.xyz rename to examples/USER-MISC/pimd/para-h2/H2.xyz diff --git a/examples/USER/misc/pimd/para-h2/NM.info b/examples/USER-MISC/pimd/para-h2/NM.info similarity index 100% rename from examples/USER/misc/pimd/para-h2/NM.info rename to examples/USER-MISC/pimd/para-h2/NM.info diff --git a/examples/USER/misc/pimd/para-h2/in.scp b/examples/USER-MISC/pimd/para-h2/in.scp similarity index 100% rename from examples/USER/misc/pimd/para-h2/in.scp rename to examples/USER-MISC/pimd/para-h2/in.scp diff --git a/examples/USER/misc/pimd/para-h2/pair.table b/examples/USER-MISC/pimd/para-h2/pair.table similarity index 100% rename from examples/USER/misc/pimd/para-h2/pair.table rename to examples/USER-MISC/pimd/para-h2/pair.table diff --git a/examples/USER/misc/pimd/para-h2/run.sh b/examples/USER-MISC/pimd/para-h2/run.sh similarity index 100% rename from examples/USER/misc/pimd/para-h2/run.sh rename to examples/USER-MISC/pimd/para-h2/run.sh diff --git a/examples/USER/misc/pimd/para-h2/vmd.src b/examples/USER-MISC/pimd/para-h2/vmd.src similarity index 100% rename from examples/USER/misc/pimd/para-h2/vmd.src rename to examples/USER-MISC/pimd/para-h2/vmd.src diff --git a/examples/USER/misc/pimd/prot-hairpin/in.scp b/examples/USER-MISC/pimd/prot-hairpin/in.scp similarity index 100% rename from examples/USER/misc/pimd/prot-hairpin/in.scp rename to examples/USER-MISC/pimd/prot-hairpin/in.scp diff --git a/examples/USER/misc/pimd/prot-hairpin/run.sh b/examples/USER-MISC/pimd/prot-hairpin/run.sh similarity index 100% rename from examples/USER/misc/pimd/prot-hairpin/run.sh rename to examples/USER-MISC/pimd/prot-hairpin/run.sh diff --git a/examples/USER/misc/pimd/prot-hairpin/system.data b/examples/USER-MISC/pimd/prot-hairpin/system.data similarity index 100% rename from examples/USER/misc/pimd/prot-hairpin/system.data rename to examples/USER-MISC/pimd/prot-hairpin/system.data diff --git a/examples/USER/misc/rhok/README.md b/examples/USER-MISC/rhok/README.md similarity index 100% rename from examples/USER/misc/rhok/README.md rename to examples/USER-MISC/rhok/README.md diff --git a/examples/USER/misc/rhok/in.crystal b/examples/USER-MISC/rhok/in.crystal similarity index 100% rename from examples/USER/misc/rhok/in.crystal rename to examples/USER-MISC/rhok/in.crystal diff --git a/examples/USER/misc/rhok/in.pinning b/examples/USER-MISC/rhok/in.pinning similarity index 100% rename from examples/USER/misc/rhok/in.pinning rename to examples/USER-MISC/rhok/in.pinning diff --git a/examples/USER/misc/rhok/in.setup b/examples/USER-MISC/rhok/in.setup similarity index 100% rename from examples/USER/misc/rhok/in.setup rename to examples/USER-MISC/rhok/in.setup diff --git a/examples/USER/misc/rhok/log.22Sep2017.crystal.g++.1 b/examples/USER-MISC/rhok/log.22Sep2017.crystal.g++.1 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.crystal.g++.1 rename to examples/USER-MISC/rhok/log.22Sep2017.crystal.g++.1 diff --git a/examples/USER/misc/rhok/log.22Sep2017.crystal.g++.4 b/examples/USER-MISC/rhok/log.22Sep2017.crystal.g++.4 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.crystal.g++.4 rename to examples/USER-MISC/rhok/log.22Sep2017.crystal.g++.4 diff --git a/examples/USER/misc/rhok/log.22Sep2017.pinning.g++.1 b/examples/USER-MISC/rhok/log.22Sep2017.pinning.g++.1 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.pinning.g++.1 rename to examples/USER-MISC/rhok/log.22Sep2017.pinning.g++.1 diff --git a/examples/USER/misc/rhok/log.22Sep2017.pinning.g++.4 b/examples/USER-MISC/rhok/log.22Sep2017.pinning.g++.4 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.pinning.g++.4 rename to examples/USER-MISC/rhok/log.22Sep2017.pinning.g++.4 diff --git a/examples/USER/misc/rhok/log.22Sep2017.setup.g++.1 b/examples/USER-MISC/rhok/log.22Sep2017.setup.g++.1 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.setup.g++.1 rename to examples/USER-MISC/rhok/log.22Sep2017.setup.g++.1 diff --git a/examples/USER/misc/rhok/log.22Sep2017.setup.g++.4 b/examples/USER-MISC/rhok/log.22Sep2017.setup.g++.4 similarity index 100% rename from examples/USER/misc/rhok/log.22Sep2017.setup.g++.4 rename to examples/USER-MISC/rhok/log.22Sep2017.setup.g++.4 diff --git a/examples/USER/misc/slater/data.after_equilibration b/examples/USER-MISC/slater/data.after_equilibration similarity index 100% rename from examples/USER/misc/slater/data.after_equilibration rename to examples/USER-MISC/slater/data.after_equilibration diff --git a/examples/USER/misc/slater/data.after_production_run b/examples/USER-MISC/slater/data.after_production_run similarity index 100% rename from examples/USER/misc/slater/data.after_production_run rename to examples/USER-MISC/slater/data.after_production_run diff --git a/examples/USER/misc/slater/in.slater b/examples/USER-MISC/slater/in.slater similarity index 100% rename from examples/USER/misc/slater/in.slater rename to examples/USER-MISC/slater/in.slater diff --git a/examples/USER/misc/slater/log.lammps b/examples/USER-MISC/slater/log.lammps similarity index 100% rename from examples/USER/misc/slater/log.lammps rename to examples/USER-MISC/slater/log.lammps diff --git a/examples/USER/misc/slater/tmp_1_1.rdf b/examples/USER-MISC/slater/tmp_1_1.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_1_1.rdf rename to examples/USER-MISC/slater/tmp_1_1.rdf diff --git a/examples/USER/misc/slater/tmp_1_2.rdf b/examples/USER-MISC/slater/tmp_1_2.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_1_2.rdf rename to examples/USER-MISC/slater/tmp_1_2.rdf diff --git a/examples/USER/misc/slater/tmp_1_3.rdf b/examples/USER-MISC/slater/tmp_1_3.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_1_3.rdf rename to examples/USER-MISC/slater/tmp_1_3.rdf diff --git a/examples/USER/misc/slater/tmp_2_2.rdf b/examples/USER-MISC/slater/tmp_2_2.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_2_2.rdf rename to examples/USER-MISC/slater/tmp_2_2.rdf diff --git a/examples/USER/misc/slater/tmp_2_3.rdf b/examples/USER-MISC/slater/tmp_2_3.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_2_3.rdf rename to examples/USER-MISC/slater/tmp_2_3.rdf diff --git a/examples/USER/misc/slater/tmp_3_3.rdf b/examples/USER-MISC/slater/tmp_3_3.rdf similarity index 100% rename from examples/USER/misc/slater/tmp_3_3.rdf rename to examples/USER-MISC/slater/tmp_3_3.rdf diff --git a/examples/USER/misc/srp/data.chain b/examples/USER-MISC/srp/data.chain similarity index 100% rename from examples/USER/misc/srp/data.chain rename to examples/USER-MISC/srp/data.chain diff --git a/examples/USER/misc/srp/in.srp b/examples/USER-MISC/srp/in.srp similarity index 100% rename from examples/USER/misc/srp/in.srp rename to examples/USER-MISC/srp/in.srp diff --git a/examples/USER/plumed/data.peptide b/examples/USER-MISC/temper_npt/data.peptide similarity index 100% rename from examples/USER/plumed/data.peptide rename to examples/USER-MISC/temper_npt/data.peptide diff --git a/examples/USER/misc/temper_npt/in.temper_npt b/examples/USER-MISC/temper_npt/in.temper_npt similarity index 100% rename from examples/USER/misc/temper_npt/in.temper_npt rename to examples/USER-MISC/temper_npt/in.temper_npt diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.0 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.0 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.0 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.0 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.1 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.1 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.1 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.1 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.2 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.2 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.2 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.2 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.3 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.3 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.3 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.3 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.4 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.4 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.4 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.4 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.5 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.5 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.5 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.5 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.6 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.6 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.6 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.6 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.7 b/examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.7 similarity index 100% rename from examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.7 rename to examples/USER-MISC/temper_npt/log.temper_npt-17Aug17.g++.8.7 diff --git a/examples/USER/misc/ti/in.ti_spring b/examples/USER-MISC/ti/in.ti_spring similarity index 100% rename from examples/USER/misc/ti/in.ti_spring rename to examples/USER-MISC/ti/in.ti_spring diff --git a/examples/USER/sph/README b/examples/USER/sph/README deleted file mode 100644 index b5a1acc614..0000000000 --- a/examples/USER/sph/README +++ /dev/null @@ -1 +0,0 @@ -see the USER-SPH user's guide for a detailed explanation of these examples. diff --git a/examples/meam/in.meamc b/examples/meam/in.meam similarity index 96% rename from examples/meam/in.meamc rename to examples/meam/in.meam index f6815cd7d4..b4463be365 100644 --- a/examples/meam/in.meamc +++ b/examples/meam/in.meam @@ -7,7 +7,7 @@ atom_style atomic read_data data.meam -pair_style meam/c +pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C neighbor 0.3 bin diff --git a/examples/meam/in.meamc.shear b/examples/meam/in.meamc.shear deleted file mode 100644 index e4584d9744..0000000000 --- a/examples/meam/in.meamc.shear +++ /dev/null @@ -1,79 +0,0 @@ -# 3d metal shear simulation - -units metal -boundary s s p - -atom_style atomic -lattice fcc 3.52 -region box block 0 16.0 0 10.0 0 2.828427 -create_box 3 box - -lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 & - origin 0.5 0 0 -create_atoms 1 box - -pair_style meam/c -pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 - -neighbor 0.3 bin -neigh_modify delay 5 - -region lower block INF INF INF 0.9 INF INF -region upper block INF INF 6.1 INF INF INF -group lower region lower -group upper region upper -group boundary union lower upper -group mobile subtract all boundary - -set group lower type 2 -set group upper type 3 - -# void - -#region void cylinder z 8 5 2.5 INF INF -#delete_atoms region void - -# temp controllers - -compute new3d mobile temp -compute new2d mobile temp/partial 0 1 1 - -# equilibrate - -velocity mobile create 300.0 5812775 temp new3d -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 - -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new3d - -thermo 25 -thermo_modify temp new3d - -timestep 0.001 -run 100 - -# shear - -velocity upper set 1.0 0 0 -velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes - -unfix 3 -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new2d - -#dump 1 all atom 500 dump.meam.shear - -#dump 2 all image 100 image.*.jpg type type & -# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 -#dump_modify 2 pad 4 - -#dump 3 all movie 100 movie.mpg type type & -# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 -#dump_modify 3 pad 4 - -thermo 100 -thermo_modify temp new2d - -reset_timestep 0 -run 3000 diff --git a/examples/meam/log.27Nov18.meamc.g++.1 b/examples/meam/log.27Nov18.meam.g++.1 similarity index 97% rename from examples/meam/log.27Nov18.meamc.g++.1 rename to examples/meam/log.27Nov18.meam.g++.1 index 2fcd24077b..40f999c00a 100644 --- a/examples/meam/log.27Nov18.meamc.g++.1 +++ b/examples/meam/log.27Nov18.meam.g++.1 @@ -13,7 +13,7 @@ read_data data.meam reading atoms ... 128 atoms -pair_style meam/c +pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C Reading potential file library.meam with DATE: 2012-06-29 Reading potential file SiC.meam with DATE: 2007-06-11 @@ -41,12 +41,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/meam/log.27Nov18.meamc.g++.4 b/examples/meam/log.27Nov18.meam.g++.4 similarity index 97% rename from examples/meam/log.27Nov18.meamc.g++.4 rename to examples/meam/log.27Nov18.meam.g++.4 index b97f18b25c..8a8070b28a 100644 --- a/examples/meam/log.27Nov18.meamc.g++.4 +++ b/examples/meam/log.27Nov18.meam.g++.4 @@ -13,7 +13,7 @@ read_data data.meam reading atoms ... 128 atoms -pair_style meam/c +pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C Reading potential file library.meam with DATE: 2012-06-29 Reading potential file SiC.meam with DATE: 2007-06-11 @@ -41,12 +41,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/meam/log.27Nov18.meamc.shear.g++.1 b/examples/meam/log.27Nov18.meam.shear.g++.1 similarity index 98% rename from examples/meam/log.27Nov18.meamc.shear.g++.1 rename to examples/meam/log.27Nov18.meam.shear.g++.1 index 4aff7d2399..e183bc698a 100644 --- a/examples/meam/log.27Nov18.meamc.shear.g++.1 +++ b/examples/meam/log.27Nov18.meam.shear.g++.1 @@ -19,7 +19,7 @@ create_atoms 1 box Created 1912 atoms Time spent = 0.000667334 secs -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -75,12 +75,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 27 17 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/meam/log.27Nov18.meamc.shear.g++.4 b/examples/meam/log.27Nov18.meam.shear.g++.4 similarity index 98% rename from examples/meam/log.27Nov18.meamc.shear.g++.4 rename to examples/meam/log.27Nov18.meam.shear.g++.4 index 702e13f554..63f6adf8a1 100644 --- a/examples/meam/log.27Nov18.meamc.shear.g++.4 +++ b/examples/meam/log.27Nov18.meam.shear.g++.4 @@ -19,7 +19,7 @@ create_atoms 1 box Created 1912 atoms Time spent = 0.000405788 secs -pair_style meam/c +pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 @@ -75,12 +75,12 @@ Neighbor list info ... ghost atom cutoff = 4.3 binsize = 2.15, bins = 27 17 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam/c, perpetual + (1) pair meam, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (2) pair meam/c, perpetual, half/full from (1) + (2) pair meam, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none diff --git a/examples/plugins/CMakeLists.txt b/examples/plugins/CMakeLists.txt index 6e29676530..1169ab490a 100644 --- a/examples/plugins/CMakeLists.txt +++ b/examples/plugins/CMakeLists.txt @@ -44,7 +44,7 @@ include(LAMMPSInterfaceCXX) # building the plugins add_library(morse2plugin MODULE morse2plugin.cpp pair_morse2.cpp pair_morse2_omp.cpp) -target_include_directories(morse2plugin PRIVATE "${LAMMPS_HEADER_DIR}/USER-OMP") +target_include_directories(morse2plugin PRIVATE "${LAMMPS_HEADER_DIR}/OPENMP") target_link_libraries(morse2plugin PRIVATE lammps) add_library(nve2plugin MODULE nve2plugin.cpp fix_nve2.cpp) diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile index f4d8b41086..c342742740 100644 --- a/examples/plugins/Makefile +++ b/examples/plugins/Makefile @@ -1,5 +1,5 @@ CXX=mpicxx -CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp +CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/OPENMP -fopenmp LD=$(CXX) -shared -rdynamic -fopenmp DSOEXT=.so diff --git a/examples/plugins/Makefile.macos b/examples/plugins/Makefile.macos index a7c20ff90f..c890314cd4 100644 --- a/examples/plugins/Makefile.macos +++ b/examples/plugins/Makefile.macos @@ -1,5 +1,5 @@ CXX=mpicxx -CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP +CXXFLAGS=-I../../src -Wall -Wextra -O3 -fPIC -I../../src/OPENMP LD=$(CXX) -bundle -rdynamic -Wl,-undefined,dynamic_lookup DSOEXT=.dylib diff --git a/examples/plugins/Makefile.serial b/examples/plugins/Makefile.serial index ecc7631a05..fff7d99a2e 100644 --- a/examples/plugins/Makefile.serial +++ b/examples/plugins/Makefile.serial @@ -1,5 +1,5 @@ CXX=g++ -CXXFLAGS=-I../../src -I../../src/STUBS -Wall -Wextra -O3 -fPIC -I../../src/USER-OMP -fopenmp +CXXFLAGS=-I../../src -I../../src/STUBS -Wall -Wextra -O3 -fPIC -I../../src/OPENMP -fopenmp LD=$(CXX) -shared -rdynamic -fopenmp DSOEXT=.so diff --git a/lib/Install.py b/lib/Install.py index 284ef6888b..0a0979c2ee 100644 --- a/lib/Install.py +++ b/lib/Install.py @@ -26,7 +26,7 @@ specify -m and optionally -e, order does not matter Examples: make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src -make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as in the mpi Makefile in src +make lib-colvars args="-m mpi" # build COLVARS lib with same settings as in the mpi Makefile in src make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran) """ diff --git a/lib/README b/lib/README index 2b7a38f5db..75fca5c185 100644 --- a/lib/README +++ b/lib/README @@ -15,7 +15,7 @@ one of the provided Makefiles to make it suitable for your machine. The libraries in this directory are the following: -atc atomistic-to-continuum methods, USER-ATC package +atc atomistic-to-continuum methods, ATC package from Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia) awpmd antisymmetrized wave packet molecular dynamics, AWPMD package from Ilya Valuev (JIHT RAS) @@ -27,17 +27,17 @@ gpu general GPU routines, GPU package from Mike Brown (ORNL) h5md ch5md library for output of MD data in HDF5 format from Pierre de Buyl (KU Leuven) -hdnnp hooks to n2p2, neural network potential package, used by USER-HDNNP +hdnnp hooks to n2p2, neural network potential package, used by ML-HDNNP from Andreas Singraber kim hooks to the KIM library, used by KIM package from Ryan Elliott and Ellad Tadmor (U Minn) kokkos Kokkos package for GPU and many-core acceleration from Kokkos development team (Sandia) -linalg set of BLAS and LAPACK routines needed by USER-ATC package +linalg set of BLAS and LAPACK routines needed by ATC package from Axel Kohlmeyer (Temple U) message client/server communication library via MPI, sockets, files from Steve Plimpton (Sandia) -molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package +molfile hooks to VMD molfile plugins, used by the MOLFILE package from Axel Kohlmeyer (Temple U) and the VMD development team mscg hooks to the MSCG library, used by fix_mscg command from Jacob Wagner and Greg Voth group (U Chicago) @@ -51,9 +51,9 @@ python hooks to the system Python library, used by the PYTHON package from the LAMMPS development team qmmm quantum mechanics/molecular mechanics coupling interface from Axel Kohlmeyer (Temple U) -quip interface to QUIP/libAtoms framework, USER-QUIP package +quip interface to QUIP/libAtoms framework, ML-QUIP package from Albert Bartok-Partay and Gabor Csanyi (U Cambridge) -smd hooks to Eigen library, used by USER-SMD package +machdyn hooks to Eigen library, used by MACHDYN package from Georg Ganzenmueller (Ernst Mach Institute, Germany) voronoi hooks to the Voro++ library, used by compute voronoi/atom command from Daniel Schwen (LANL) diff --git a/lib/atc/Makefile.lammps.empty b/lib/atc/Makefile.lammps.empty index 49cab486a9..8624fdcadb 100644 --- a/lib/atc/Makefile.lammps.empty +++ b/lib/atc/Makefile.lammps.empty @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -user-atc_SYSINC = -user-atc_SYSLIB = -user-atc_SYSPATH = +atc_SYSINC = +atc_SYSLIB = +atc_SYSPATH = diff --git a/lib/atc/Makefile.lammps.installed b/lib/atc/Makefile.lammps.installed index c8cd66af26..223f41cd08 100644 --- a/lib/atc/Makefile.lammps.installed +++ b/lib/atc/Makefile.lammps.installed @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -user-atc_SYSINC = -user-atc_SYSLIB = -lblas -llapack -user-atc_SYSPATH = +atc_SYSINC = +atc_SYSLIB = -lblas -llapack +atc_SYSPATH = diff --git a/lib/atc/Makefile.lammps.linalg b/lib/atc/Makefile.lammps.linalg index 5d92fd8cfb..930ee6357b 100644 --- a/lib/atc/Makefile.lammps.linalg +++ b/lib/atc/Makefile.lammps.linalg @@ -1,6 +1,6 @@ # Settings that the LAMMPS build will import when this package library is used -user-atc_SYSINC = -user-atc_SYSLIB = -llinalg -lgfortran -user-atc_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) +atc_SYSINC = +atc_SYSLIB = -llinalg -lgfortran +atc_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) diff --git a/lib/atc/README b/lib/atc/README index d3adfdafe4..70a83e5c8f 100644 --- a/lib/atc/README +++ b/lib/atc/README @@ -10,7 +10,7 @@ estimation and molecular dynamics-finite element coupling methods. ------------------------------------------------- This directory has source files to build a library that LAMMPS -links against when using the USER-ATC package. +links against when using the ATC package. This library must be built with a C++ compiler, before LAMMPS is built, so LAMMPS can link against it. diff --git a/lib/awpmd/Makefile.lammps.empty b/lib/awpmd/Makefile.lammps.empty index d80c517f3d..551267720e 100644 --- a/lib/awpmd/Makefile.lammps.empty +++ b/lib/awpmd/Makefile.lammps.empty @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -user-awpmd_SYSINC = -user-awpmd_SYSLIB = -user-awpmd_SYSPATH = +awpmd_SYSINC = +awpmd_SYSLIB = +awpmd_SYSPATH = diff --git a/lib/awpmd/Makefile.lammps.installed b/lib/awpmd/Makefile.lammps.installed index 6b089784a0..975133e429 100644 --- a/lib/awpmd/Makefile.lammps.installed +++ b/lib/awpmd/Makefile.lammps.installed @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -user-awpmd_SYSINC = -user-awpmd_SYSLIB = -lblas -llapack -user-awpmd_SYSPATH = +awpmd_SYSINC = +awpmd_SYSLIB = -lblas -llapack +awpmd_SYSPATH = diff --git a/lib/awpmd/Makefile.lammps.linalg b/lib/awpmd/Makefile.lammps.linalg index a30f4a821d..1d986da5d7 100644 --- a/lib/awpmd/Makefile.lammps.linalg +++ b/lib/awpmd/Makefile.lammps.linalg @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -user-awpmd_SYSINC = -user-awpmd_SYSLIB = -llinalg -lgfortran -user-awpmd_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) +awpmd_SYSINC = +awpmd_SYSLIB = -llinalg -lgfortran +awpmd_SYSPATH = -L../../lib/linalg$(LIBOBJDIR) diff --git a/lib/awpmd/README b/lib/awpmd/README index 20e142f74c..d829361a1b 100644 --- a/lib/awpmd/README +++ b/lib/awpmd/README @@ -14,7 +14,7 @@ of wxWidgets Library License (see license directory for details). ------------------------------------------------- This directory has source files to build a library that LAMMPS -links against when using the USER-AWPMD package. +links against when using the AWPMD package. This library must be built with a C++ compiler, before LAMMPS is built, so LAMMPS can link against it. diff --git a/lib/awpmd/ivutils/include/pairhash.h b/lib/awpmd/ivutils/include/pairhash.h index 401b7b91e3..ea598e9f4d 100644 --- a/lib/awpmd/ivutils/include/pairhash.h +++ b/lib/awpmd/ivutils/include/pairhash.h @@ -11,7 +11,7 @@ /*e**************************************************************************** * $Log: pairhash.h,v $ * Revision 1.3 2011/06/11 18:18:50 morozov - * USER-AWPMD compiles on Linux now! + * AWPMD compiles on Linux now! * * Revision 1.2 2011/06/11 16:53:55 valuev * sync with LAMMPS diff --git a/lib/colvars/README b/lib/colvars/README index cd6e59511a..eeba557ce3 100644 --- a/lib/colvars/README +++ b/lib/colvars/README @@ -49,7 +49,7 @@ C++11-only features. ## How to build (CMake) This is the recommended build recipe: no additional settings are normally -needed besides "-D PKG_USER-COLVARS=yes". +needed besides "-D PKG_COLVARS=yes". Building and linking of Lepton (or other C++11-only features) is enabled automatically when compilation is carried out with C++11 support, and disabled diff --git a/lib/h5md/README b/lib/h5md/README index 4768b50697..a6d4d8206b 100644 --- a/lib/h5md/README +++ b/lib/h5md/README @@ -1,6 +1,6 @@ This directory contains the ch5md library, which is bundled with LAMMPS under its own BSD license; see below. This library is used -when the USER-H5MD package is included in a LAMMPS build and the dump +when the H5MD package is included in a LAMMPS build and the dump h5md command is invoked in a LAMMPS input script. You can type "make lib-h5md" from the src directory to see help on how @@ -25,7 +25,7 @@ license that can be found in the file LICENSE. To use the h5md dump style in lammps, execute make -f Makefile.h5cc in this directory then -make yes-user-h5md +make yes-h5md in the src directory of LAMMPS to rebuild LAMMPS. Note that you must have the h5cc compiler installed to use diff --git a/lib/hdnnp/README b/lib/hdnnp/README index ed61f211ea..708f36c179 100644 --- a/lib/hdnnp/README +++ b/lib/hdnnp/README @@ -1,4 +1,4 @@ -The USER-HDNNP package requires access to pre-compiled libraries of the n2p2 +The ML-HDNNP package requires access to pre-compiled libraries of the n2p2 package (https://github.com/CompPhysVienna/n2p2). More precisely, the n2p2 core library ("libnnp"), the interface library ("libnnpif"), some headers and extra build helper files are needed. These files will be created automatically during @@ -6,7 +6,7 @@ the n2p2 build process. This file gives some basic instructions on how to compile n2p2 manually. How to integrate it then in the LAMMPS build process or how to use the automatic -download and build option is described in detail on the USER-HDNNP build +download and build option is described in detail on the ML-HDNNP build instructions page of the LAMMPS documentation. IMPORTANT: The n2p2 version must be "v2.1.4" or higher. @@ -25,7 +25,7 @@ After downloading n2p2, change to the "src" directory and simply execute make libnnpif -which should create the following files needed by the USER-HDNNP package: +which should create the following files needed by the ML-HDNNP package: * "n2p2/lib/libnnp.a" * "n2p2/lib/libnnpif.a" @@ -48,7 +48,7 @@ also available (e.g. "makefile.intel") and can be activated by supplying the Please make sure that your compiler settings for n2p2 and LAMMPS are compatible (avoid mixing different compilers). -If you want to build a serial version of LAMMPS with USER-HDNNP package n2p2 must +If you want to build a serial version of LAMMPS with ML-HDNNP package n2p2 must also be built with MPI disabled. This can be achieved with a preprocessor flag (-DN2P2_NO_MPI) which is (among others) prepared, but commented out, in the provided compiler-specific settings makefiles. For example, if you use the GNU @@ -64,10 +64,10 @@ For more information about the n2p2 build process please visit https://compphysvienna.github.io/n2p2/topics/build.html or ask questions on the Github issue page (https://github.com/CompPhysVienna/n2p2/issues). -Testing a successful build of LAMMPS with USER-HDNNP +Testing a successful build of LAMMPS with ML-HDNNP ==================================================== -An example is provided in the LAMMPS directory "examples/USER/hdnnp" which runs +An example is provided in the LAMMPS directory "examples/PACKAGES/hdnnp" which runs 10 timesteps with 360 water molecules. The neural network potential is defined via files in the "hdnnp-data" subdirectory. Use the "in.hdnnp" LAMMPS script file to run the simulation. You should see a large output of the n2p2 library when diff --git a/lib/linalg/README b/lib/linalg/README index 725df86c4c..de2d83dcbd 100644 --- a/lib/linalg/README +++ b/lib/linalg/README @@ -1,10 +1,10 @@ -This directory has BLAS and LAPACK files needed by the USER-ATC and -USER-AWPMD packages, and possibly by other packages in the future. +This directory has BLAS and LAPACK files needed by the ATC and +AWPMD packages, and possibly by other packages in the future. Note that this is an *incomplete* subset of full BLAS/LAPACK. You should only need to build and use the library in this directory if -you want to build LAMMPS with the USER-ATC and/or USER-AWPMD packages +you want to build LAMMPS with the ATC and/or AWPMD packages AND you do not have any other suitable BLAS and LAPACK libraries installed on your system. E.g. ATLAS, GOTO-BLAS, OpenBLAS, ACML, or MKL. diff --git a/lib/smd/.gitignore b/lib/machdyn/.gitignore similarity index 100% rename from lib/smd/.gitignore rename to lib/machdyn/.gitignore diff --git a/lib/smd/Install.py b/lib/machdyn/Install.py similarity index 100% rename from lib/smd/Install.py rename to lib/machdyn/Install.py diff --git a/lib/machdyn/Makefile.lammps b/lib/machdyn/Makefile.lammps new file mode 100644 index 0000000000..6c914708dd --- /dev/null +++ b/lib/machdyn/Makefile.lammps @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +machdyn_SYSINC = -I../../lib/includelink/eigen3 +machdyn_SYSLIB = +machdyn_SYSPATH = diff --git a/lib/smd/README b/lib/machdyn/README similarity index 94% rename from lib/smd/README rename to lib/machdyn/README index 1bd5902a1f..38a2957648 100644 --- a/lib/smd/README +++ b/lib/machdyn/README @@ -1,5 +1,5 @@ This directory contains links to the Eigen library which is required -to use the USER-SMD package in a LAMMPS input script. +to use the MACHDYN package in a LAMMPS input script. The Eigen library is available at http://eigen.tuxfamily.org. It's a general C++ template library for linear algebra. @@ -26,10 +26,10 @@ Instructions: % ln -s /home/sjplimp/tools/eigen includelink When these steps are complete you can build LAMMPS -with the USER-SMD package installed: +with the MACHDYN package installed: % cd lammps/src -% make yes-user-smd +% make yes-machdyn % make g++ (or whatever target you wish) Note that if you download and unpack a new LAMMPS tarball, the diff --git a/lib/mdi/Install.py b/lib/mdi/Install.py index 1c411d349e..d67437d0ce 100644 --- a/lib/mdi/Install.py +++ b/lib/mdi/Install.py @@ -28,7 +28,7 @@ specify -m and optionally -e, order does not matter Examples: make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src -make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as in the mpi Makefile in src +make lib-colvars args="-m mpi" # build COLVARS lib with same settings as in the mpi Makefile in src make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran) """ diff --git a/lib/mesont/Install.py b/lib/mesont/Install.py index 284ef6888b..0a0979c2ee 100644 --- a/lib/mesont/Install.py +++ b/lib/mesont/Install.py @@ -26,7 +26,7 @@ specify -m and optionally -e, order does not matter Examples: make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src -make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as in the mpi Makefile in src +make lib-colvars args="-m mpi" # build COLVARS lib with same settings as in the mpi Makefile in src make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran) """ diff --git a/lib/mesont/README b/lib/mesont/README index 886263ddb3..3ed47bf218 100644 --- a/lib/mesont/README +++ b/lib/mesont/README @@ -1,4 +1,4 @@ -USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon +MESONT is a LAMMPS package for simulation of nanomechanics of carbon nanotubes (CNTs). The model is based on a coarse-grained representation of CNTs as "flexible cylinders" consisting of a variable number of segments. Internal interactions within a CNT and the van der Waals diff --git a/lib/molfile/Makefile.lammps b/lib/molfile/Makefile.lammps index a181f48aec..55a0487a9f 100644 --- a/lib/molfile/Makefile.lammps +++ b/lib/molfile/Makefile.lammps @@ -3,7 +3,7 @@ # # http://www.ks.uiuc.edu/Research/vmd/plugins/molfile # -# When you build LAMMPS with the USER-MOLFILE package installed, it will +# When you build LAMMPS with the MOLFILE package installed, it will # use the 3 settings in this file. They should be set as follows. # # The molfile_SYSINC setting is to point to the folder with the VMD diff --git a/lib/molfile/README b/lib/molfile/README index 9e8260c202..9960b5a836 100644 --- a/lib/molfile/README +++ b/lib/molfile/README @@ -1,6 +1,6 @@ This directory has a Makefile.lammps file with settings that allows LAMMPS to dynamically link to the VMD molfile library. This is -required to use the USER-MOLFILE package and its interface to the dump +required to use the MOLFILE package and its interface to the dump and write_dump commands in a LAMMPS input script. More information about the VMD molfile plugins can be found at diff --git a/lib/mscg/README b/lib/mscg/README index 329eebba96..5e3cfe4452 100755 --- a/lib/mscg/README +++ b/lib/mscg/README @@ -51,7 +51,7 @@ When these steps are complete you can build LAMMPS with the MS-CG package installed: % cd lammps/src -% make yes-USER-MSCG +% make yes-MSCG % make g++ (or whatever target you wish) Note that if you download and unpack a new LAMMPS tarball, the diff --git a/lib/netcdf/README b/lib/netcdf/README index b18ea1d276..c23b7fbb06 100644 --- a/lib/netcdf/README +++ b/lib/netcdf/README @@ -1,6 +1,6 @@ The Makefile.lammps file in this directory is used when building LAMMPS with packages that make use of the NetCDF library or its -parallel version. For example, the USER-NETCDF package which adds +parallel version. For example, the NETCDF package which adds dump netcdf and dump netcdf/mpiio commands. The file has several settings needed to compile diff --git a/lib/pace/Makefile b/lib/pace/Makefile index c2e1892ddd..ac9f3a3151 100644 --- a/lib/pace/Makefile +++ b/lib/pace/Makefile @@ -2,8 +2,8 @@ SHELL = /bin/sh # ------ FILES ------ -SRC_FILES = $(wildcard src/USER-PACE/*.cpp) -SRC = $(filter-out src/USER-PACE/pair_pace.cpp, $(SRC_FILES)) +SRC_FILES = $(wildcard src/ML-PACE/*.cpp) +SRC = $(filter-out src/ML-PACE/pair_pace.cpp, $(SRC_FILES)) # ------ DEFINITIONS ------ @@ -12,7 +12,7 @@ OBJ = $(SRC:.cpp=.o) # ------ SETTINGS ------ -CXXFLAGS = -O3 -fPIC -Isrc/USER-PACE +CXXFLAGS = -O3 -fPIC -Isrc/ML-PACE ARCHIVE = ar ARCHFLAG = -rc diff --git a/lib/pace/Makefile.lammps b/lib/pace/Makefile.lammps index 17820716df..89761c1b4b 100644 --- a/lib/pace/Makefile.lammps +++ b/lib/pace/Makefile.lammps @@ -1,3 +1,3 @@ -pace_SYSINC =-I../../lib/pace/src/USER-PACE +pace_SYSINC =-I../../lib/pace/src/ML-PACE pace_SYSLIB = -L../../lib/pace/ -lpace pace_SYSPATH = diff --git a/lib/pace/README b/lib/pace/README index ddc6f7f7a7..1cbc9fad68 100644 --- a/lib/pace/README +++ b/lib/pace/README @@ -1,18 +1,14 @@ -This directory contains files required to use the USER-PACE package, -which provides the pace pair style, an efficient implementation of -the Atomic Cluster Expansion potential (ACE). -ACE is a methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. -This package was written by Yury Lysogorskiy and others -at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, -Ruhr University Bochum, Germany, http://www.icams.de +This directory contains files required to use the ML-PACE package, which +provides the pace pair style, an efficient implementation of the Atomic +Cluster Expansion potential (ACE). ACE is a methodology for deriving a +highly accurate classical potential fit to a large archive of quantum +mechanical (DFT) data. This package was written by Yury Lysogorskiy and +others at ICAMS, the Interdisciplinary Centre for Advanced Materials +Simulation, Ruhr University Bochum, Germany, http://www.icams.de -You can type "make lib-pace" from the src directory to see help on -how to download and build this library via make commands, or you can -do the same thing by typing "python Install.py" from within this -directory. +You can type "make lib-pace" from the src directory to see help on how +to download and build this library via make commands, or you can do the +same thing by typing "python Install.py" from within this directory. -More information about the USER-PACE implementation of ACE -is available here: - -https://github.com/ICAMS/lammps-user-pace +More information about the ML-PACE implementation of ACE is available +here: https://github.com/ICAMS/lammps-user-pace diff --git a/lib/plumed/README b/lib/plumed/README index 6b9b22bbce..a21b40ced1 100644 --- a/lib/plumed/README +++ b/lib/plumed/README @@ -51,6 +51,6 @@ When these steps are complete you can build LAMMPS with the PLUMED package installed: % cd lammps/src -% make yes-user-plumed +% make yes-plumed % make mpi (or whatever target you wish) diff --git a/lib/qmmm/README b/lib/qmmm/README index 196aa4d7e0..7e9f30d692 100644 --- a/lib/qmmm/README +++ b/lib/qmmm/README @@ -21,7 +21,7 @@ and also an interface layer into the QM code similar to the one in QE. LAMMPS has support for two build systems, the traditional make based one and a newer one based on CMake. You have to build LAMMPS as a -library with the USER-QMMM package included and for that you need to +library with the QMMM package included and for that you need to also build the libqmmm.a library in this folder. Below you will find some description of the steps needed in either case. @@ -55,7 +55,7 @@ build configuration with CMake: mkdir build-qmmm cd build-qmmm - cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \ + cmake -C ../cmake/presets/basic.cmake -D PKG_QMMM=yes \ -D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake make make install @@ -139,7 +139,7 @@ this library exist. Step 2) Build a standalone LAMMPS executable as described in the LAMMPS -documentation and include the USER-QMMM package. This executable +documentation and include the QMMM package. This executable is not functional for QM/MM, but it will usually be needed to run all MM calculations for equilibration and testing and also to confirm that the classical part of the code is set up correctly. @@ -147,7 +147,7 @@ Also build a the LAMMPS library. This can be a static library or a shared library. For example for a static library with the minimum set of packages required for the examples here: - make yes-molecule yes-kspace yes-rigid yes-user-qmmm + make yes-molecule yes-kspace yes-rigid yes-qmmm make mpi make mode=lib mpi diff --git a/lib/quip/README b/lib/quip/README index 5e737db11d..7b74dc2d7e 100644 --- a/lib/quip/README +++ b/lib/quip/README @@ -76,15 +76,17 @@ and QUIP_ARCH should be autodetected, even without having to set the environment variables. Otherwise export the environment variables as shown above or edit Makefile.lammps -LAMMPS ships with a user package containing the interface necessary +LAMMPS ships with a package containing the interface necessary to use QUIP potentials, but it needs to be added to the compilation -first. To do that, enter the LAMMPS source directory and type: +first. To do that, either enter the LAMMPS source directory and type: -$ make yes-user-quip +$ make yes-ml-quip + +or use -DPKG_ML-QUIP=yes when configuring LAMMPS for compilation with CMake. 2.2) Build LAMMPS according to the instructions on the LAMMPS website. -3) There are three example sets in examples/USER/quip: +3) There are three example sets in examples/PACKAGES/quip: - a set of input files to compute the energy of an 8-atom cubic diamond cell of silicon with the Stillinger-Weber potential. Use diff --git a/lib/smd/Makefile.lammps b/lib/smd/Makefile.lammps deleted file mode 100644 index 6951a1394c..0000000000 --- a/lib/smd/Makefile.lammps +++ /dev/null @@ -1,5 +0,0 @@ -# Settings that the LAMMPS build will import when this package library is used - -user-smd_SYSINC = -I../../lib/includelink/eigen3 -user-smd_SYSLIB = -user-smd_SYSPATH = diff --git a/lib/vtk/README b/lib/vtk/README index 61e2a40c23..d0e2481f6f 100644 --- a/lib/vtk/README +++ b/lib/vtk/README @@ -1,5 +1,5 @@ The Makefile.lammps file in this directory is used when building -LAMMPS with its USER-VTK package installed. The file has several +LAMMPS with its VTK package installed. The file has several settings needed to compile and link LAMMPS with the VTK library. You should choose a Makefile.lammps.* file compatible with your system and your version of VTK, and copy it to Makefile.lammps before building @@ -23,7 +23,7 @@ vtk_SYSINC refers to the include directory of the installed VTK library vtk_SYSLIB refers to the libraries needed to link to from an application (LAMMPS in this case) to "embed" VTK in the application. VTK consists of multiple shared libraries which are -needed when using the USER-VTK package. +needed when using the VTK package. vtk_SYSPATH = refers to the path (e.g. -L/usr/local/lib) where the VTK library can be found. You may not need this setting if the path is diff --git a/potentials/README b/potentials/README index fbc49f8613..4df315a7f2 100644 --- a/potentials/README +++ b/potentials/README @@ -84,18 +84,18 @@ Au_u3 = Gold universal 3 The suffix of each file indicates the pair style it is used with: adp ADP angular dependent potential -airebo AI-REBO and REBO potentials +airebo AI-REBO and REBO potentials bop.table BOP potential, tabulated form cdeam concentration-dependent EAM comb COMB potential comb3 COMB3 potential -eam embedded atom method (EAM) single element, DYNAMO funcfl format +eam embedded atom method (EAM) single element, DYNAMO funcfl format eam.alloy EAM multi-element alloy, DYNAMO setfl format -eam.fs Finnis-Sinclair EAM format (single element or alloy) +eam.fs Finnis-Sinclair EAM format (single element or alloy) edip EDIP potential for silicon-based materials eim embedded-ion method (EIM) potential lcbop LCBOP long-range bond-order potential -meam modified EAM (MEAM) library and individual elements/alloys +meam modified EAM (MEAM) library and individual elements/alloys meam.spline modified EAM (MEAM) spline potential meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential mesocnt mesoscopic carbon nanotube (CNT) potential @@ -105,14 +105,14 @@ mliap.descriptor MLIAP potential descriptor mliap.model MLIAP potential model nb3b.harmonic nonbonded 3-body harmonic potential poly polymorphic 3-body potential -reax ReaxFF potential (see README.reax for more info) +reax ReaxFF potential (see README.reax for more info) smtbq second moment tight binding QEq (SMTBQ) potential snap SNAP potential snapcoeff SNAP potential snapparam SNAP potential streitz Coulombic portion of Streitz-Mintmire potential -sw Stillinger-Weber potential -tersoff Tersoff potential +sw Stillinger-Weber potential +tersoff Tersoff potential tersoff.mod modified Tersoff potential tersoff.zbl Tersoff with ZBL core vashishta Vashishta 2-body and 3-body potential diff --git a/python/examples/pylammps/README.md b/python/examples/pylammps/README.md index 7ee8c8ac90..e66f5a2a8e 100644 --- a/python/examples/pylammps/README.md +++ b/python/examples/pylammps/README.md @@ -51,7 +51,7 @@ which has both LAMMPS and its Python package installed: 6. Configure LAMMPS compilation (CMake) ```shell - (myenv)$ cmake -C ../cmake/presets/minimal.cmake \ + (myenv)$ cmake -C ../cmake/presets/basic.cmake \ -D BUILD_SHARED_LIBS=on \ -D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on \ -D CMAKE_INSTALL_PREFIX=$VIRTUAL_ENV \ diff --git a/python/lammps/core.py b/python/lammps/core.py index c7b51a6b54..2f101f4eab 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -1542,7 +1542,7 @@ class lammps(object): """ result = {} - for p in ['GPU', 'KOKKOS', 'USER-INTEL', 'USER-OMP']: + for p in ['GPU', 'KOKKOS', 'INTEL', 'OPENMP']: result[p] = {} c = 'api' result[p][c] = [] diff --git a/python/lammps/mliap/loader.py b/python/lammps/mliap/loader.py index 8588c2b4bf..dff791bfc1 100644 --- a/python/lammps/mliap/loader.py +++ b/python/lammps/mliap/loader.py @@ -39,13 +39,13 @@ def activate_mliappy(lmp): # End Importlib magic to find the embedded python module except Exception as ee: - raise ImportError("Could not load MLIAP python coupling module.") from ee + raise ImportError("Could not load ML-IAP python coupling module.") from ee def load_model(model): try: import mliap_model_python_couple except ImportError as ie: - raise ImportError("MLIAP python module must be activated before loading\n" + raise ImportError("ML-IAP python module must be activated before loading\n" "the pair style. Call lammps.mliap.activate_mliappy(lmp)." ) from ie mliap_model_python_couple.load_from_python(model) diff --git a/src/.gitignore b/src/.gitignore index b15707ed79..c562f89e61 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -70,8 +70,8 @@ /meam*.h /meam*.cpp -/pair_meamc.cpp -/pair_meamc.h +/pair_meam.cpp +/pair_meam.h /compute_mliap.cpp /compute_mliap.h @@ -1431,6 +1431,10 @@ /pair_thole.h /pair_buck_mdf.cpp /pair_buck_mdf.h +/pair_dpd.cpp +/pair_dpd.h +/pair_dpd_tstat.cpp +/pair_dpd_tstat.h /pair_dpd_ext.cpp /pair_dpd_ext.h /pair_dpd_ext_tstat.cpp diff --git a/src/USER-ADIOS/Install.sh b/src/ADIOS/Install.sh similarity index 98% rename from src/USER-ADIOS/Install.sh rename to src/ADIOS/Install.sh index b8a2f1f9a9..ddca8c6efe 100644 --- a/src/USER-ADIOS/Install.sh +++ b/src/ADIOS/Install.sh @@ -72,7 +72,7 @@ adios_SYSLIB=${ADIOS2_LIB} sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ -include ../USER-ADIOS/Makefile.lammps +include ../ADIOS/Makefile.lammps ' ../Makefile.package.settings fi fi diff --git a/src/USER-ADIOS/README b/src/ADIOS/README similarity index 95% rename from src/USER-ADIOS/README rename to src/ADIOS/README index 2b66f27f6b..18f4a8aed4 100644 --- a/src/USER-ADIOS/README +++ b/src/ADIOS/README @@ -8,7 +8,7 @@ Configure LAMMPS with CMake ADIOS2_DIR to the ADIOS 2.x installation path b. use the cmake option - -D PKG_USER-ADIOS=yes + -D PKG_ADIOS=yes The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory); If you need help, please submit a ticket at the OLCF ticket user support mentioning his name in the ticket. diff --git a/src/USER-ADIOS/dump_atom_adios.cpp b/src/ADIOS/dump_atom_adios.cpp similarity index 100% rename from src/USER-ADIOS/dump_atom_adios.cpp rename to src/ADIOS/dump_atom_adios.cpp diff --git a/src/USER-ADIOS/dump_atom_adios.h b/src/ADIOS/dump_atom_adios.h similarity index 100% rename from src/USER-ADIOS/dump_atom_adios.h rename to src/ADIOS/dump_atom_adios.h diff --git a/src/USER-ADIOS/dump_custom_adios.cpp b/src/ADIOS/dump_custom_adios.cpp similarity index 100% rename from src/USER-ADIOS/dump_custom_adios.cpp rename to src/ADIOS/dump_custom_adios.cpp diff --git a/src/USER-ADIOS/dump_custom_adios.h b/src/ADIOS/dump_custom_adios.h similarity index 100% rename from src/USER-ADIOS/dump_custom_adios.h rename to src/ADIOS/dump_custom_adios.h diff --git a/src/USER-ADIOS/reader_adios.cpp b/src/ADIOS/reader_adios.cpp similarity index 100% rename from src/USER-ADIOS/reader_adios.cpp rename to src/ADIOS/reader_adios.cpp diff --git a/src/USER-ADIOS/reader_adios.h b/src/ADIOS/reader_adios.h similarity index 100% rename from src/USER-ADIOS/reader_adios.h rename to src/ADIOS/reader_adios.h diff --git a/src/USER-ATC/Install.sh b/src/ATC/Install.sh similarity index 86% rename from src/USER-ATC/Install.sh rename to src/ATC/Install.sh index f241f92065..e1dacdd7d6 100755 --- a/src/USER-ATC/Install.sh +++ b/src/ATC/Install.sh @@ -31,7 +31,7 @@ action () { if (test $1 = 1) then if (test ! -e ../pair_eam.cpp) then - echo "Must install MANYBODY package with USER-ATC" + echo "Must install MANYBODY package with ATC" exit 1 fi fi @@ -54,9 +54,9 @@ if (test $1 = 1) then # sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/atc |' ../Makefile.package # sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/atc$(LIBSOBJDIR) |' ../Makefile.package sed -i -e 's|^PKG_LIB =[ \t]*|&-latc |' ../Makefile.package - sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(user-atc_SYSINC) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-atc_SYSLIB) |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-atc_SYSPATH) |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(atc_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(atc_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(atc_SYSPATH) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then diff --git a/src/USER-ATC/README b/src/ATC/README similarity index 93% rename from src/USER-ATC/README rename to src/ATC/README index 06ab91ed80..0a6475236e 100644 --- a/src/USER-ATC/README +++ b/src/ATC/README @@ -7,7 +7,7 @@ See the doc page for the fix atc command to get started. At the bottom of the doc page are many links to additional documentation contained in the doc/USER/atc directory. -There are example scripts for using this package in examples/USER/atc. +There are example scripts for using this package in examples/PACKAGES/atc. This package uses an external library in lib/atc which must be compiled before making LAMMPS. See the lib/atc/README file and the diff --git a/src/USER-ATC/fix_atc.cpp b/src/ATC/fix_atc.cpp similarity index 99% rename from src/USER-ATC/fix_atc.cpp rename to src/ATC/fix_atc.cpp index b4f5b1eade..d9770d86de 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/ATC/fix_atc.cpp @@ -37,7 +37,7 @@ using namespace FixConst; using std::string; #ifdef LAMMPS_BIGBIG -#error "The USER-ATC package is not compatible with -DLAMMPS_BIGBIG" +#error "The ATC package is not compatible with -DLAMMPS_BIGBIG" #endif // main page of doxygen documentation diff --git a/src/USER-ATC/fix_atc.h b/src/ATC/fix_atc.h similarity index 100% rename from src/USER-ATC/fix_atc.h rename to src/ATC/fix_atc.h diff --git a/src/USER-AWPMD/Install.sh b/src/AWPMD/Install.sh similarity index 90% rename from src/USER-AWPMD/Install.sh rename to src/AWPMD/Install.sh index 094e10c157..70e87c3fbc 100755 --- a/src/USER-AWPMD/Install.sh +++ b/src/AWPMD/Install.sh @@ -41,8 +41,8 @@ if (test $1 = 1) then sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/awpmd/ivutils/include -I../../lib/awpmd/systems/interact |' ../Makefile.package sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/awpmd |' ../Makefile.package sed -i -e 's|^PKG_LIB =[ \t]*|&-lawpmd |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-awpmd_SYSPATH) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-awpmd_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(awpmd_SYSPATH) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(awpmd_SYSLIB) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then diff --git a/src/USER-AWPMD/README b/src/AWPMD/README similarity index 97% rename from src/USER-AWPMD/README rename to src/AWPMD/README index 6d8e8d032d..82ce245ab1 100644 --- a/src/USER-AWPMD/README +++ b/src/AWPMD/README @@ -4,7 +4,7 @@ Wave Packet Molecular Dynamics (AWPMD) method. See the doc page for the pair_style awpmd/cut command to get started. There are example scripts for using this package in -examples/USER/awpmd. +examples/PACKAGES/awpmd. This package uses an external library in lib/awpmd which must be compiled before making LAMMPS. See the lib/awpmd/README file and the diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/AWPMD/atom_vec_wavepacket.cpp similarity index 100% rename from src/USER-AWPMD/atom_vec_wavepacket.cpp rename to src/AWPMD/atom_vec_wavepacket.cpp diff --git a/src/USER-AWPMD/atom_vec_wavepacket.h b/src/AWPMD/atom_vec_wavepacket.h similarity index 100% rename from src/USER-AWPMD/atom_vec_wavepacket.h rename to src/AWPMD/atom_vec_wavepacket.h diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/AWPMD/fix_nve_awpmd.cpp similarity index 100% rename from src/USER-AWPMD/fix_nve_awpmd.cpp rename to src/AWPMD/fix_nve_awpmd.cpp diff --git a/src/USER-AWPMD/fix_nve_awpmd.h b/src/AWPMD/fix_nve_awpmd.h similarity index 100% rename from src/USER-AWPMD/fix_nve_awpmd.h rename to src/AWPMD/fix_nve_awpmd.h diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/AWPMD/pair_awpmd_cut.cpp similarity index 100% rename from src/USER-AWPMD/pair_awpmd_cut.cpp rename to src/AWPMD/pair_awpmd_cut.cpp diff --git a/src/USER-AWPMD/pair_awpmd_cut.h b/src/AWPMD/pair_awpmd_cut.h similarity index 100% rename from src/USER-AWPMD/pair_awpmd_cut.h rename to src/AWPMD/pair_awpmd_cut.h diff --git a/src/USER-BOCS/README b/src/BOCS/README similarity index 81% rename from src/USER-BOCS/README rename to src/BOCS/README index 45aecc278c..b8cd001031 100644 --- a/src/USER-BOCS/README +++ b/src/BOCS/README @@ -7,7 +7,7 @@ molecular liquids," J. Chem. Phys. 143, 243148 (2015). doi: 10.1063/1.4937383 -The USER-BOCS user package for LAMMPS is part of the BOCS software package: +The BOCS user package for LAMMPS is part of the BOCS software package: https://github.com/noid-group/BOCS See the following reference for information about the entire package: @@ -16,4 +16,4 @@ Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. "BOCS: Bottom-Up Open-Source Coarse-Graining Software." J. Phys. Chem. B. 122, 13, 3363-3377 (2018). -Example inputs are in the examples/USER/bocs folder. +Example inputs are in the examples/PACKAGES/bocs folder. diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/BOCS/compute_pressure_bocs.cpp similarity index 99% rename from src/USER-BOCS/compute_pressure_bocs.cpp rename to src/BOCS/compute_pressure_bocs.cpp index b62d7cd1bf..8d891006b2 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/BOCS/compute_pressure_bocs.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- - USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser from The Pennsylvania State University ------------------------------------------------------------------------- */ diff --git a/src/USER-BOCS/compute_pressure_bocs.h b/src/BOCS/compute_pressure_bocs.h similarity index 98% rename from src/USER-BOCS/compute_pressure_bocs.h rename to src/BOCS/compute_pressure_bocs.h index d5d4b1a7b9..ccae6ce0e3 100644 --- a/src/USER-BOCS/compute_pressure_bocs.h +++ b/src/BOCS/compute_pressure_bocs.h @@ -10,7 +10,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- - USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser from The Pennsylvania State University ------------------------------------------------------------------------- */ diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/BOCS/fix_bocs.cpp similarity index 99% rename from src/USER-BOCS/fix_bocs.cpp rename to src/BOCS/fix_bocs.cpp index 4f773e7c65..d372d607e8 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/BOCS/fix_bocs.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- - USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser from The Pennsylvania State University ------------------------------------------------------------------------- */ @@ -43,7 +43,7 @@ using namespace LAMMPS_NS; using namespace FixConst; static const char cite_user_bocs_package[] = - "USER-BOCS package:\n\n" + "BOCS package:\n\n" "@Article{Dunn2018,\n" " author = {NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid},\n" " title = {BOCS: Bottom-Up Open-Source Coarse-Graining Software},\n" diff --git a/src/USER-BOCS/fix_bocs.h b/src/BOCS/fix_bocs.h similarity index 99% rename from src/USER-BOCS/fix_bocs.h rename to src/BOCS/fix_bocs.h index fd1e09115d..4edf670fa5 100644 --- a/src/USER-BOCS/fix_bocs.h +++ b/src/BOCS/fix_bocs.h @@ -10,7 +10,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- - USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser from The Pennsylvania State University ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian.cpp b/src/BROWNIAN/fix_brownian.cpp similarity index 98% rename from src/USER-BROWNIAN/fix_brownian.cpp rename to src/BROWNIAN/fix_brownian.cpp index fc6b434080..b811ede721 100644 --- a/src/USER-BROWNIAN/fix_brownian.cpp +++ b/src/BROWNIAN/fix_brownian.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp. Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian.h b/src/BROWNIAN/fix_brownian.h similarity index 100% rename from src/USER-BROWNIAN/fix_brownian.h rename to src/BROWNIAN/fix_brownian.h diff --git a/src/USER-BROWNIAN/fix_brownian_asphere.cpp b/src/BROWNIAN/fix_brownian_asphere.cpp similarity index 99% rename from src/USER-BROWNIAN/fix_brownian_asphere.cpp rename to src/BROWNIAN/fix_brownian_asphere.cpp index ef0c246508..fccc6b5040 100644 --- a/src/USER-BROWNIAN/fix_brownian_asphere.cpp +++ b/src/BROWNIAN/fix_brownian_asphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp. Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian_asphere.h b/src/BROWNIAN/fix_brownian_asphere.h similarity index 100% rename from src/USER-BROWNIAN/fix_brownian_asphere.h rename to src/BROWNIAN/fix_brownian_asphere.h diff --git a/src/USER-BROWNIAN/fix_brownian_base.cpp b/src/BROWNIAN/fix_brownian_base.cpp similarity index 99% rename from src/USER-BROWNIAN/fix_brownian_base.cpp rename to src/BROWNIAN/fix_brownian_base.cpp index fd5d1f5df7..0fa928bebf 100644 --- a/src/USER-BROWNIAN/fix_brownian_base.cpp +++ b/src/BROWNIAN/fix_brownian_base.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp. Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian_base.h b/src/BROWNIAN/fix_brownian_base.h similarity index 100% rename from src/USER-BROWNIAN/fix_brownian_base.h rename to src/BROWNIAN/fix_brownian_base.h diff --git a/src/USER-BROWNIAN/fix_brownian_sphere.cpp b/src/BROWNIAN/fix_brownian_sphere.cpp similarity index 98% rename from src/USER-BROWNIAN/fix_brownian_sphere.cpp rename to src/BROWNIAN/fix_brownian_sphere.cpp index 4621be595f..cf835dcdc1 100644 --- a/src/USER-BROWNIAN/fix_brownian_sphere.cpp +++ b/src/BROWNIAN/fix_brownian_sphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp. + Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp. Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian_sphere.h b/src/BROWNIAN/fix_brownian_sphere.h similarity index 100% rename from src/USER-BROWNIAN/fix_brownian_sphere.h rename to src/BROWNIAN/fix_brownian_sphere.h diff --git a/src/USER-BROWNIAN/fix_propel_self.cpp b/src/BROWNIAN/fix_propel_self.cpp similarity index 100% rename from src/USER-BROWNIAN/fix_propel_self.cpp rename to src/BROWNIAN/fix_propel_self.cpp diff --git a/src/USER-BROWNIAN/fix_propel_self.h b/src/BROWNIAN/fix_propel_self.h similarity index 100% rename from src/USER-BROWNIAN/fix_propel_self.h rename to src/BROWNIAN/fix_propel_self.h diff --git a/src/USER-CGDNA/Install.sh b/src/CG-DNA/Install.sh similarity index 100% rename from src/USER-CGDNA/Install.sh rename to src/CG-DNA/Install.sh diff --git a/src/USER-CGDNA/README.md b/src/CG-DNA/README.md similarity index 96% rename from src/USER-CGDNA/README.md rename to src/CG-DNA/README.md index 015c1db188..bd3799a060 100644 --- a/src/USER-CGDNA/README.md +++ b/src/CG-DNA/README.md @@ -40,13 +40,13 @@ gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, 144114 (2015). Example input and data files can be found in -/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/. +examples/PACKAGES/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/. Python setup tools which create single straight or helical DNA or RNA strands as well as DNA or RNA duplexes or arrays of duplexes can be -found in /examples/USER/cgdna/util/. A technical report with more +found in examples/PACKAGES/cgdna/util/. A technical report with more general information on the model, its implementation and performance as well as the structure of the data and input file can be found -in /doc/src/PDF/USER-CGDNA.pdf. +in doc/src/PDF/CG-DNA.pdf. IMPORTANT NOTE: This package can only be used if LAMMPS is compiled with the MOLECULE and ASPHERE packages. These should be included in diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/CG-DNA/bond_oxdna2_fene.cpp similarity index 100% rename from src/USER-CGDNA/bond_oxdna2_fene.cpp rename to src/CG-DNA/bond_oxdna2_fene.cpp diff --git a/src/USER-CGDNA/bond_oxdna2_fene.h b/src/CG-DNA/bond_oxdna2_fene.h similarity index 100% rename from src/USER-CGDNA/bond_oxdna2_fene.h rename to src/CG-DNA/bond_oxdna2_fene.h diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp similarity index 100% rename from src/USER-CGDNA/bond_oxdna_fene.cpp rename to src/CG-DNA/bond_oxdna_fene.cpp diff --git a/src/USER-CGDNA/bond_oxdna_fene.h b/src/CG-DNA/bond_oxdna_fene.h similarity index 100% rename from src/USER-CGDNA/bond_oxdna_fene.h rename to src/CG-DNA/bond_oxdna_fene.h diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/CG-DNA/bond_oxrna2_fene.cpp similarity index 100% rename from src/USER-CGDNA/bond_oxrna2_fene.cpp rename to src/CG-DNA/bond_oxrna2_fene.cpp diff --git a/src/USER-CGDNA/bond_oxrna2_fene.h b/src/CG-DNA/bond_oxrna2_fene.h similarity index 100% rename from src/USER-CGDNA/bond_oxrna2_fene.h rename to src/CG-DNA/bond_oxrna2_fene.h diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/CG-DNA/fix_nve_dot.cpp similarity index 100% rename from src/USER-CGDNA/fix_nve_dot.cpp rename to src/CG-DNA/fix_nve_dot.cpp diff --git a/src/USER-CGDNA/fix_nve_dot.h b/src/CG-DNA/fix_nve_dot.h similarity index 100% rename from src/USER-CGDNA/fix_nve_dot.h rename to src/CG-DNA/fix_nve_dot.h diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/CG-DNA/fix_nve_dotc_langevin.cpp similarity index 100% rename from src/USER-CGDNA/fix_nve_dotc_langevin.cpp rename to src/CG-DNA/fix_nve_dotc_langevin.cpp diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.h b/src/CG-DNA/fix_nve_dotc_langevin.h similarity index 100% rename from src/USER-CGDNA/fix_nve_dotc_langevin.h rename to src/CG-DNA/fix_nve_dotc_langevin.h diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/CG-DNA/mf_oxdna.h similarity index 100% rename from src/USER-CGDNA/mf_oxdna.h rename to src/CG-DNA/mf_oxdna.h diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/CG-DNA/pair_oxdna2_coaxstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_coaxstk.cpp rename to src/CG-DNA/pair_oxdna2_coaxstk.cpp diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.h b/src/CG-DNA/pair_oxdna2_coaxstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_coaxstk.h rename to src/CG-DNA/pair_oxdna2_coaxstk.h diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/CG-DNA/pair_oxdna2_dh.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_dh.cpp rename to src/CG-DNA/pair_oxdna2_dh.cpp diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/CG-DNA/pair_oxdna2_dh.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_dh.h rename to src/CG-DNA/pair_oxdna2_dh.h diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/CG-DNA/pair_oxdna2_excv.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_excv.cpp rename to src/CG-DNA/pair_oxdna2_excv.cpp diff --git a/src/USER-CGDNA/pair_oxdna2_excv.h b/src/CG-DNA/pair_oxdna2_excv.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_excv.h rename to src/CG-DNA/pair_oxdna2_excv.h diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/CG-DNA/pair_oxdna_coaxstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_coaxstk.cpp rename to src/CG-DNA/pair_oxdna_coaxstk.cpp diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.h b/src/CG-DNA/pair_oxdna_coaxstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_coaxstk.h rename to src/CG-DNA/pair_oxdna_coaxstk.h diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/CG-DNA/pair_oxdna_excv.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_excv.cpp rename to src/CG-DNA/pair_oxdna_excv.cpp diff --git a/src/USER-CGDNA/pair_oxdna_excv.h b/src/CG-DNA/pair_oxdna_excv.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_excv.h rename to src/CG-DNA/pair_oxdna_excv.h diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/CG-DNA/pair_oxdna_hbond.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_hbond.cpp rename to src/CG-DNA/pair_oxdna_hbond.cpp diff --git a/src/USER-CGDNA/pair_oxdna_hbond.h b/src/CG-DNA/pair_oxdna_hbond.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_hbond.h rename to src/CG-DNA/pair_oxdna_hbond.h diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/CG-DNA/pair_oxdna_stk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_stk.cpp rename to src/CG-DNA/pair_oxdna_stk.cpp diff --git a/src/USER-CGDNA/pair_oxdna_stk.h b/src/CG-DNA/pair_oxdna_stk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_stk.h rename to src/CG-DNA/pair_oxdna_stk.h diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/CG-DNA/pair_oxdna_xstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_xstk.cpp rename to src/CG-DNA/pair_oxdna_xstk.cpp diff --git a/src/USER-CGDNA/pair_oxdna_xstk.h b/src/CG-DNA/pair_oxdna_xstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_xstk.h rename to src/CG-DNA/pair_oxdna_xstk.h diff --git a/src/USER-CGDNA/pair_oxrna2_dh.cpp b/src/CG-DNA/pair_oxrna2_dh.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_dh.cpp rename to src/CG-DNA/pair_oxrna2_dh.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_dh.h b/src/CG-DNA/pair_oxrna2_dh.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_dh.h rename to src/CG-DNA/pair_oxrna2_dh.h diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/CG-DNA/pair_oxrna2_excv.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_excv.cpp rename to src/CG-DNA/pair_oxrna2_excv.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_excv.h b/src/CG-DNA/pair_oxrna2_excv.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_excv.h rename to src/CG-DNA/pair_oxrna2_excv.h diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.cpp b/src/CG-DNA/pair_oxrna2_hbond.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_hbond.cpp rename to src/CG-DNA/pair_oxrna2_hbond.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.h b/src/CG-DNA/pair_oxrna2_hbond.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_hbond.h rename to src/CG-DNA/pair_oxrna2_hbond.h diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/CG-DNA/pair_oxrna2_stk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_stk.cpp rename to src/CG-DNA/pair_oxrna2_stk.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_stk.h b/src/CG-DNA/pair_oxrna2_stk.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_stk.h rename to src/CG-DNA/pair_oxrna2_stk.h diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/CG-DNA/pair_oxrna2_xstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_xstk.cpp rename to src/CG-DNA/pair_oxrna2_xstk.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.h b/src/CG-DNA/pair_oxrna2_xstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_xstk.h rename to src/CG-DNA/pair_oxrna2_xstk.h diff --git a/src/USER-CGSDK/Install.sh b/src/CG-SDK/Install.sh similarity index 100% rename from src/USER-CGSDK/Install.sh rename to src/CG-SDK/Install.sh diff --git a/src/USER-CGSDK/README b/src/CG-SDK/README similarity index 91% rename from src/USER-CGSDK/README rename to src/CG-SDK/README index 3d5cae9b20..c6bd90531e 100644 --- a/src/USER-CGSDK/README +++ b/src/CG-SDK/README @@ -1,8 +1,9 @@ -This package implements 3 commands which can be used in a LAMMPS input +This package implements 4 commands which can be used in a LAMMPS input script: pair_style lj/sdk pair_style lj/sdk/coul/long +pair_style lj/sdk/coul/msm angle_style sdk These styles allow coarse grained MD simulations with the @@ -13,7 +14,7 @@ lipids and charged amino acids. See the doc pages for these commands for details. There are example scripts for using this package in -examples/USER/cgsdk +examples/PACKAGES/cgsdk This is the second generation implementation reducing the the clutter of the previous version. For many systems with long range diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/CG-SDK/angle_sdk.cpp similarity index 100% rename from src/USER-CGSDK/angle_sdk.cpp rename to src/CG-SDK/angle_sdk.cpp diff --git a/src/USER-CGSDK/angle_sdk.h b/src/CG-SDK/angle_sdk.h similarity index 100% rename from src/USER-CGSDK/angle_sdk.h rename to src/CG-SDK/angle_sdk.h diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/CG-SDK/lj_sdk_common.h similarity index 100% rename from src/USER-CGSDK/lj_sdk_common.h rename to src/CG-SDK/lj_sdk_common.h diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/CG-SDK/pair_lj_sdk.cpp similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk.cpp rename to src/CG-SDK/pair_lj_sdk.cpp diff --git a/src/USER-CGSDK/pair_lj_sdk.h b/src/CG-SDK/pair_lj_sdk.h similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk.h rename to src/CG-SDK/pair_lj_sdk.h diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/CG-SDK/pair_lj_sdk_coul_long.cpp similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_long.cpp rename to src/CG-SDK/pair_lj_sdk_coul_long.cpp diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.h b/src/CG-SDK/pair_lj_sdk_coul_long.h similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_long.h rename to src/CG-SDK/pair_lj_sdk_coul_long.h diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/CG-SDK/pair_lj_sdk_coul_msm.cpp similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp rename to src/CG-SDK/pair_lj_sdk_coul_msm.cpp diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.h b/src/CG-SDK/pair_lj_sdk_coul_msm.h similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_msm.h rename to src/CG-SDK/pair_lj_sdk_coul_msm.h diff --git a/src/USER-COLVARS/Install.sh b/src/COLVARS/Install.sh similarity index 100% rename from src/USER-COLVARS/Install.sh rename to src/COLVARS/Install.sh diff --git a/src/USER-COLVARS/README b/src/COLVARS/README similarity index 92% rename from src/USER-COLVARS/README rename to src/COLVARS/README index 6627bc9ec4..eebaecf4a8 100644 --- a/src/USER-COLVARS/README +++ b/src/COLVARS/README @@ -13,7 +13,7 @@ on building LAMMPS with external libraries. The settings in the Makefile.lammps file in that directory must be correct for LAMMPS to build correctly with this package installed. -The files in the USER-COLVARS package folder implement an interface +The files in the COLVARS package folder implement an interface between LAMMPS and Colvars, originally written by Axel Kohlmeyer (akohlmey@gmail.com) and maintained by Giacomo Fiorin (giacomo.fiorin@gmail.com). @@ -36,7 +36,7 @@ which also includes citations to the articles documenting the various methods that make use Colvars. There are also example scripts for using this package in the folder -examples/USER/colvars, as well as the GitHub page for Colvars. +examples/PACKAGES/colvars, as well as the GitHub page for Colvars. Please contact Giacomo Fiorin (giacomo.fiorin@gmail.com) for questions regarding this package. diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/COLVARS/colvarproxy_lammps.cpp similarity index 100% rename from src/USER-COLVARS/colvarproxy_lammps.cpp rename to src/COLVARS/colvarproxy_lammps.cpp diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/COLVARS/colvarproxy_lammps.h similarity index 100% rename from src/USER-COLVARS/colvarproxy_lammps.h rename to src/COLVARS/colvarproxy_lammps.h diff --git a/src/USER-COLVARS/colvarproxy_lammps_version.h b/src/COLVARS/colvarproxy_lammps_version.h similarity index 100% rename from src/USER-COLVARS/colvarproxy_lammps_version.h rename to src/COLVARS/colvarproxy_lammps_version.h diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/COLVARS/fix_colvars.cpp similarity index 100% rename from src/USER-COLVARS/fix_colvars.cpp rename to src/COLVARS/fix_colvars.cpp diff --git a/src/USER-COLVARS/fix_colvars.h b/src/COLVARS/fix_colvars.h similarity index 100% rename from src/USER-COLVARS/fix_colvars.h rename to src/COLVARS/fix_colvars.h diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/COLVARS/group_ndx.cpp similarity index 100% rename from src/USER-COLVARS/group_ndx.cpp rename to src/COLVARS/group_ndx.cpp diff --git a/src/USER-COLVARS/group_ndx.h b/src/COLVARS/group_ndx.h similarity index 100% rename from src/USER-COLVARS/group_ndx.h rename to src/COLVARS/group_ndx.h diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/COLVARS/ndx_group.cpp similarity index 100% rename from src/USER-COLVARS/ndx_group.cpp rename to src/COLVARS/ndx_group.cpp diff --git a/src/USER-COLVARS/ndx_group.h b/src/COLVARS/ndx_group.h similarity index 100% rename from src/USER-COLVARS/ndx_group.h rename to src/COLVARS/ndx_group.h diff --git a/src/USER-DIELECTRIC/Install.sh b/src/DIELECTRIC/Install.sh similarity index 88% rename from src/USER-DIELECTRIC/Install.sh rename to src/DIELECTRIC/Install.sh index fd540f3c7e..43285260ba 100644 --- a/src/USER-DIELECTRIC/Install.sh +++ b/src/DIELECTRIC/Install.sh @@ -30,8 +30,8 @@ action () { # are installed, which in turn requires KSPACE if (test $1 = 1) then - if (test ! -e ../ppp.cpp) then - echo "Must install KSPACE package with USER-DIELECTRIC" + if (test ! -e ../pppm.cpp) then + echo "Must install KSPACE package with DIELECTRIC" exit 1 fi fi diff --git a/src/USER-DIELECTRIC/README b/src/DIELECTRIC/README similarity index 85% rename from src/USER-DIELECTRIC/README rename to src/DIELECTRIC/README index 11e9bde03f..37a9d673bf 100644 --- a/src/USER-DIELECTRIC/README +++ b/src/DIELECTRIC/README @@ -1,4 +1,4 @@ -The USER-DIELECTRIC package provides several solvers for computing surface induced charges +The DIELECTRIC package provides several solvers for computing surface induced charges at the interface between two media with different dielectric constants: * the boundary element solver using the GMRES algorithm (fix polarize/bem/gmres), @@ -10,7 +10,7 @@ or mobile (for example, dielectric colloids in a solvent). See the header of the source files for more details on the references of the methods. -The USER-DIELECTRIC package was created by Trung Nguyen while at Northwestern. +The DIELECTRIC package was created by Trung Nguyen while at Northwestern. Questions can be addressed to Trung Nguyen (ndactrung@gmail.com). * Citation @@ -23,6 +23,6 @@ Molecular Dynamics simulation", Computer Physics Communications 241, 80--91 (201 * Examples -Example input scripts and data files can be found under examples/USER/dielectric: +Example input scripts and data files can be found under examples/PACKAGES/dielectric: mpirun -np 8 ../../../src/lmp_mpi -in in.confined diff --git a/src/USER-DIELECTRIC/atom_vec_dielectric.cpp b/src/DIELECTRIC/atom_vec_dielectric.cpp similarity index 99% rename from src/USER-DIELECTRIC/atom_vec_dielectric.cpp rename to src/DIELECTRIC/atom_vec_dielectric.cpp index b0e3487807..cc182251e9 100644 --- a/src/USER-DIELECTRIC/atom_vec_dielectric.cpp +++ b/src/DIELECTRIC/atom_vec_dielectric.cpp @@ -20,7 +20,7 @@ using namespace LAMMPS_NS; static const char cite_user_dielectric_package[] = - "USER-DIELECTRIC package:\n\n" + "DIELECTRIC package:\n\n" "@Article{TrungCPC19,\n" " author = {Trung Dac Nguyen, Honghao Li, Debarshee Bagchi," " Francisco J. Solis, Monica Olvera de la Cruz,\n" diff --git a/src/USER-DIELECTRIC/atom_vec_dielectric.h b/src/DIELECTRIC/atom_vec_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/atom_vec_dielectric.h rename to src/DIELECTRIC/atom_vec_dielectric.h diff --git a/src/USER-DIELECTRIC/compute_efield_atom.cpp b/src/DIELECTRIC/compute_efield_atom.cpp similarity index 100% rename from src/USER-DIELECTRIC/compute_efield_atom.cpp rename to src/DIELECTRIC/compute_efield_atom.cpp diff --git a/src/USER-DIELECTRIC/compute_efield_atom.h b/src/DIELECTRIC/compute_efield_atom.h similarity index 100% rename from src/USER-DIELECTRIC/compute_efield_atom.h rename to src/DIELECTRIC/compute_efield_atom.h diff --git a/src/USER-DIELECTRIC/fix_polarize_bem_gmres.cpp b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp similarity index 100% rename from src/USER-DIELECTRIC/fix_polarize_bem_gmres.cpp rename to src/DIELECTRIC/fix_polarize_bem_gmres.cpp diff --git a/src/USER-DIELECTRIC/fix_polarize_bem_gmres.h b/src/DIELECTRIC/fix_polarize_bem_gmres.h similarity index 100% rename from src/USER-DIELECTRIC/fix_polarize_bem_gmres.h rename to src/DIELECTRIC/fix_polarize_bem_gmres.h diff --git a/src/USER-DIELECTRIC/fix_polarize_bem_icc.cpp b/src/DIELECTRIC/fix_polarize_bem_icc.cpp similarity index 100% rename from src/USER-DIELECTRIC/fix_polarize_bem_icc.cpp rename to src/DIELECTRIC/fix_polarize_bem_icc.cpp diff --git a/src/USER-DIELECTRIC/fix_polarize_bem_icc.h b/src/DIELECTRIC/fix_polarize_bem_icc.h similarity index 100% rename from src/USER-DIELECTRIC/fix_polarize_bem_icc.h rename to src/DIELECTRIC/fix_polarize_bem_icc.h diff --git a/src/USER-DIELECTRIC/fix_polarize_functional.cpp b/src/DIELECTRIC/fix_polarize_functional.cpp similarity index 100% rename from src/USER-DIELECTRIC/fix_polarize_functional.cpp rename to src/DIELECTRIC/fix_polarize_functional.cpp diff --git a/src/USER-DIELECTRIC/fix_polarize_functional.h b/src/DIELECTRIC/fix_polarize_functional.h similarity index 100% rename from src/USER-DIELECTRIC/fix_polarize_functional.h rename to src/DIELECTRIC/fix_polarize_functional.h diff --git a/src/USER-DIELECTRIC/msm_dielectric.cpp b/src/DIELECTRIC/msm_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/msm_dielectric.cpp rename to src/DIELECTRIC/msm_dielectric.cpp diff --git a/src/USER-DIELECTRIC/msm_dielectric.h b/src/DIELECTRIC/msm_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/msm_dielectric.h rename to src/DIELECTRIC/msm_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_coul_cut_dielectric.cpp b/src/DIELECTRIC/pair_coul_cut_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_coul_cut_dielectric.cpp rename to src/DIELECTRIC/pair_coul_cut_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_coul_cut_dielectric.h b/src/DIELECTRIC/pair_coul_cut_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_coul_cut_dielectric.h rename to src/DIELECTRIC/pair_coul_cut_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_coul_long_dielectric.cpp b/src/DIELECTRIC/pair_coul_long_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_coul_long_dielectric.cpp rename to src/DIELECTRIC/pair_coul_long_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_coul_long_dielectric.h b/src/DIELECTRIC/pair_coul_long_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_coul_long_dielectric.h rename to src/DIELECTRIC/pair_coul_long_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp rename to src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h rename to src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp rename to src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h rename to src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp rename to src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_long_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_long_dielectric.h rename to src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp b/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp rename to src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h b/src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h rename to src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.h diff --git a/src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp b/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp rename to src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.h b/src/DIELECTRIC/pair_lj_long_coul_long_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.h rename to src/DIELECTRIC/pair_lj_long_coul_long_dielectric.h diff --git a/src/USER-DIELECTRIC/pppm_dielectric.cpp b/src/DIELECTRIC/pppm_dielectric.cpp similarity index 100% rename from src/USER-DIELECTRIC/pppm_dielectric.cpp rename to src/DIELECTRIC/pppm_dielectric.cpp diff --git a/src/USER-DIELECTRIC/pppm_dielectric.h b/src/DIELECTRIC/pppm_dielectric.h similarity index 100% rename from src/USER-DIELECTRIC/pppm_dielectric.h rename to src/DIELECTRIC/pppm_dielectric.h diff --git a/src/USER-DIFFRACTION/README b/src/DIFFRACTION/README similarity index 98% rename from src/USER-DIFFRACTION/README rename to src/DIFFRACTION/README index fb36011960..a9a8ad523e 100644 --- a/src/USER-DIFFRACTION/README +++ b/src/DIFFRACTION/README @@ -42,7 +42,7 @@ User-diffraction includes: See the doc pages for these commands for detailed usage instructions. There are example scripts for using this package in -examples/USER/diffraction. +examples/PACKAGES/diffraction. --------------------------------- diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/DIFFRACTION/compute_saed.cpp similarity index 100% rename from src/USER-DIFFRACTION/compute_saed.cpp rename to src/DIFFRACTION/compute_saed.cpp diff --git a/src/USER-DIFFRACTION/compute_saed.h b/src/DIFFRACTION/compute_saed.h similarity index 100% rename from src/USER-DIFFRACTION/compute_saed.h rename to src/DIFFRACTION/compute_saed.h diff --git a/src/USER-DIFFRACTION/compute_saed_consts.h b/src/DIFFRACTION/compute_saed_consts.h similarity index 100% rename from src/USER-DIFFRACTION/compute_saed_consts.h rename to src/DIFFRACTION/compute_saed_consts.h diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/DIFFRACTION/compute_xrd.cpp similarity index 100% rename from src/USER-DIFFRACTION/compute_xrd.cpp rename to src/DIFFRACTION/compute_xrd.cpp diff --git a/src/USER-DIFFRACTION/compute_xrd.h b/src/DIFFRACTION/compute_xrd.h similarity index 100% rename from src/USER-DIFFRACTION/compute_xrd.h rename to src/DIFFRACTION/compute_xrd.h diff --git a/src/USER-DIFFRACTION/compute_xrd_consts.h b/src/DIFFRACTION/compute_xrd_consts.h similarity index 100% rename from src/USER-DIFFRACTION/compute_xrd_consts.h rename to src/DIFFRACTION/compute_xrd_consts.h diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/DIFFRACTION/fix_saed_vtk.cpp similarity index 100% rename from src/USER-DIFFRACTION/fix_saed_vtk.cpp rename to src/DIFFRACTION/fix_saed_vtk.cpp diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/DIFFRACTION/fix_saed_vtk.h similarity index 100% rename from src/USER-DIFFRACTION/fix_saed_vtk.h rename to src/DIFFRACTION/fix_saed_vtk.h diff --git a/src/pair_dpd.cpp b/src/DPD-BASIC/pair_dpd.cpp similarity index 100% rename from src/pair_dpd.cpp rename to src/DPD-BASIC/pair_dpd.cpp diff --git a/src/pair_dpd.h b/src/DPD-BASIC/pair_dpd.h similarity index 100% rename from src/pair_dpd.h rename to src/DPD-BASIC/pair_dpd.h diff --git a/src/USER-MISC/pair_dpd_ext.cpp b/src/DPD-BASIC/pair_dpd_ext.cpp similarity index 100% rename from src/USER-MISC/pair_dpd_ext.cpp rename to src/DPD-BASIC/pair_dpd_ext.cpp diff --git a/src/USER-MISC/pair_dpd_ext.h b/src/DPD-BASIC/pair_dpd_ext.h similarity index 100% rename from src/USER-MISC/pair_dpd_ext.h rename to src/DPD-BASIC/pair_dpd_ext.h diff --git a/src/USER-MISC/pair_dpd_ext_tstat.cpp b/src/DPD-BASIC/pair_dpd_ext_tstat.cpp similarity index 100% rename from src/USER-MISC/pair_dpd_ext_tstat.cpp rename to src/DPD-BASIC/pair_dpd_ext_tstat.cpp diff --git a/src/USER-MISC/pair_dpd_ext_tstat.h b/src/DPD-BASIC/pair_dpd_ext_tstat.h similarity index 100% rename from src/USER-MISC/pair_dpd_ext_tstat.h rename to src/DPD-BASIC/pair_dpd_ext_tstat.h diff --git a/src/pair_dpd_tstat.cpp b/src/DPD-BASIC/pair_dpd_tstat.cpp similarity index 100% rename from src/pair_dpd_tstat.cpp rename to src/DPD-BASIC/pair_dpd_tstat.cpp diff --git a/src/pair_dpd_tstat.h b/src/DPD-BASIC/pair_dpd_tstat.h similarity index 100% rename from src/pair_dpd_tstat.h rename to src/DPD-BASIC/pair_dpd_tstat.h diff --git a/src/USER-MESODPD/README b/src/DPD-MESO/README similarity index 98% rename from src/USER-MESODPD/README rename to src/DPD-MESO/README index 0119fdb9f8..c2d4904808 100644 --- a/src/USER-MESODPD/README +++ b/src/DPD-MESO/README @@ -43,7 +43,7 @@ started. At the bottom of the doc pages are many links to additional documentation contained in the doc/USER/meso directory. There are example scripts for using this package in -examples/USER/meso. +examples/PACKAGES/meso. The person who created this package is Zhen Li (zhen_li at brown.edu) at Division of Applied Mathematics, Brown University, USA. Contact him diff --git a/src/USER-MESODPD/atom_vec_edpd.cpp b/src/DPD-MESO/atom_vec_edpd.cpp similarity index 100% rename from src/USER-MESODPD/atom_vec_edpd.cpp rename to src/DPD-MESO/atom_vec_edpd.cpp diff --git a/src/USER-MESODPD/atom_vec_edpd.h b/src/DPD-MESO/atom_vec_edpd.h similarity index 100% rename from src/USER-MESODPD/atom_vec_edpd.h rename to src/DPD-MESO/atom_vec_edpd.h diff --git a/src/USER-MESODPD/atom_vec_mdpd.cpp b/src/DPD-MESO/atom_vec_mdpd.cpp similarity index 100% rename from src/USER-MESODPD/atom_vec_mdpd.cpp rename to src/DPD-MESO/atom_vec_mdpd.cpp diff --git a/src/USER-MESODPD/atom_vec_mdpd.h b/src/DPD-MESO/atom_vec_mdpd.h similarity index 100% rename from src/USER-MESODPD/atom_vec_mdpd.h rename to src/DPD-MESO/atom_vec_mdpd.h diff --git a/src/USER-MESODPD/atom_vec_tdpd.cpp b/src/DPD-MESO/atom_vec_tdpd.cpp similarity index 100% rename from src/USER-MESODPD/atom_vec_tdpd.cpp rename to src/DPD-MESO/atom_vec_tdpd.cpp diff --git a/src/USER-MESODPD/atom_vec_tdpd.h b/src/DPD-MESO/atom_vec_tdpd.h similarity index 100% rename from src/USER-MESODPD/atom_vec_tdpd.h rename to src/DPD-MESO/atom_vec_tdpd.h diff --git a/src/USER-MESODPD/compute_edpd_temp_atom.cpp b/src/DPD-MESO/compute_edpd_temp_atom.cpp similarity index 100% rename from src/USER-MESODPD/compute_edpd_temp_atom.cpp rename to src/DPD-MESO/compute_edpd_temp_atom.cpp diff --git a/src/USER-MESODPD/compute_edpd_temp_atom.h b/src/DPD-MESO/compute_edpd_temp_atom.h similarity index 100% rename from src/USER-MESODPD/compute_edpd_temp_atom.h rename to src/DPD-MESO/compute_edpd_temp_atom.h diff --git a/src/USER-MESODPD/compute_tdpd_cc_atom.cpp b/src/DPD-MESO/compute_tdpd_cc_atom.cpp similarity index 100% rename from src/USER-MESODPD/compute_tdpd_cc_atom.cpp rename to src/DPD-MESO/compute_tdpd_cc_atom.cpp diff --git a/src/USER-MESODPD/compute_tdpd_cc_atom.h b/src/DPD-MESO/compute_tdpd_cc_atom.h similarity index 100% rename from src/USER-MESODPD/compute_tdpd_cc_atom.h rename to src/DPD-MESO/compute_tdpd_cc_atom.h diff --git a/src/USER-MESODPD/fix_edpd_source.cpp b/src/DPD-MESO/fix_edpd_source.cpp similarity index 100% rename from src/USER-MESODPD/fix_edpd_source.cpp rename to src/DPD-MESO/fix_edpd_source.cpp diff --git a/src/USER-MESODPD/fix_edpd_source.h b/src/DPD-MESO/fix_edpd_source.h similarity index 100% rename from src/USER-MESODPD/fix_edpd_source.h rename to src/DPD-MESO/fix_edpd_source.h diff --git a/src/USER-MESODPD/fix_mvv_dpd.cpp b/src/DPD-MESO/fix_mvv_dpd.cpp similarity index 100% rename from src/USER-MESODPD/fix_mvv_dpd.cpp rename to src/DPD-MESO/fix_mvv_dpd.cpp diff --git a/src/USER-MESODPD/fix_mvv_dpd.h b/src/DPD-MESO/fix_mvv_dpd.h similarity index 100% rename from src/USER-MESODPD/fix_mvv_dpd.h rename to src/DPD-MESO/fix_mvv_dpd.h diff --git a/src/USER-MESODPD/fix_mvv_edpd.cpp b/src/DPD-MESO/fix_mvv_edpd.cpp similarity index 100% rename from src/USER-MESODPD/fix_mvv_edpd.cpp rename to src/DPD-MESO/fix_mvv_edpd.cpp diff --git a/src/USER-MESODPD/fix_mvv_edpd.h b/src/DPD-MESO/fix_mvv_edpd.h similarity index 100% rename from src/USER-MESODPD/fix_mvv_edpd.h rename to src/DPD-MESO/fix_mvv_edpd.h diff --git a/src/USER-MESODPD/fix_mvv_tdpd.cpp b/src/DPD-MESO/fix_mvv_tdpd.cpp similarity index 100% rename from src/USER-MESODPD/fix_mvv_tdpd.cpp rename to src/DPD-MESO/fix_mvv_tdpd.cpp diff --git a/src/USER-MESODPD/fix_mvv_tdpd.h b/src/DPD-MESO/fix_mvv_tdpd.h similarity index 100% rename from src/USER-MESODPD/fix_mvv_tdpd.h rename to src/DPD-MESO/fix_mvv_tdpd.h diff --git a/src/USER-MESODPD/fix_tdpd_source.cpp b/src/DPD-MESO/fix_tdpd_source.cpp similarity index 100% rename from src/USER-MESODPD/fix_tdpd_source.cpp rename to src/DPD-MESO/fix_tdpd_source.cpp diff --git a/src/USER-MESODPD/fix_tdpd_source.h b/src/DPD-MESO/fix_tdpd_source.h similarity index 100% rename from src/USER-MESODPD/fix_tdpd_source.h rename to src/DPD-MESO/fix_tdpd_source.h diff --git a/src/USER-MESODPD/pair_edpd.cpp b/src/DPD-MESO/pair_edpd.cpp similarity index 100% rename from src/USER-MESODPD/pair_edpd.cpp rename to src/DPD-MESO/pair_edpd.cpp diff --git a/src/USER-MESODPD/pair_edpd.h b/src/DPD-MESO/pair_edpd.h similarity index 100% rename from src/USER-MESODPD/pair_edpd.h rename to src/DPD-MESO/pair_edpd.h diff --git a/src/USER-MESODPD/pair_mdpd.cpp b/src/DPD-MESO/pair_mdpd.cpp similarity index 100% rename from src/USER-MESODPD/pair_mdpd.cpp rename to src/DPD-MESO/pair_mdpd.cpp diff --git a/src/USER-MESODPD/pair_mdpd.h b/src/DPD-MESO/pair_mdpd.h similarity index 100% rename from src/USER-MESODPD/pair_mdpd.h rename to src/DPD-MESO/pair_mdpd.h diff --git a/src/USER-MESODPD/pair_mdpd_rhosum.cpp b/src/DPD-MESO/pair_mdpd_rhosum.cpp similarity index 100% rename from src/USER-MESODPD/pair_mdpd_rhosum.cpp rename to src/DPD-MESO/pair_mdpd_rhosum.cpp diff --git a/src/USER-MESODPD/pair_mdpd_rhosum.h b/src/DPD-MESO/pair_mdpd_rhosum.h similarity index 100% rename from src/USER-MESODPD/pair_mdpd_rhosum.h rename to src/DPD-MESO/pair_mdpd_rhosum.h diff --git a/src/USER-MESODPD/pair_tdpd.cpp b/src/DPD-MESO/pair_tdpd.cpp similarity index 100% rename from src/USER-MESODPD/pair_tdpd.cpp rename to src/DPD-MESO/pair_tdpd.cpp diff --git a/src/USER-MESODPD/pair_tdpd.h b/src/DPD-MESO/pair_tdpd.h similarity index 100% rename from src/USER-MESODPD/pair_tdpd.h rename to src/DPD-MESO/pair_tdpd.h diff --git a/src/USER-DPD/README b/src/DPD-REACT/README similarity index 94% rename from src/USER-DPD/README rename to src/DPD-REACT/README index ef895bef2a..c79a2455b0 100644 --- a/src/USER-DPD/README +++ b/src/DPD-REACT/README @@ -27,7 +27,7 @@ dpd/conservative" and "pair dpd/fdt" and "pair dpd/fdt/energy" commands to get started. At the bottom of the doc page are many links to additional documentation contained in the doc/USER/dpd directory. -There are example scripts for using this package in examples/USER/dpd. +There are example scripts for using this package in examples/PACKAGES/dpd-react. The primary people who created this package are James Larentzos (james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/DPD-REACT/atom_vec_dpd.cpp similarity index 100% rename from src/USER-DPD/atom_vec_dpd.cpp rename to src/DPD-REACT/atom_vec_dpd.cpp diff --git a/src/USER-DPD/atom_vec_dpd.h b/src/DPD-REACT/atom_vec_dpd.h similarity index 100% rename from src/USER-DPD/atom_vec_dpd.h rename to src/DPD-REACT/atom_vec_dpd.h diff --git a/src/USER-DPD/compute_dpd.cpp b/src/DPD-REACT/compute_dpd.cpp similarity index 100% rename from src/USER-DPD/compute_dpd.cpp rename to src/DPD-REACT/compute_dpd.cpp diff --git a/src/USER-DPD/compute_dpd.h b/src/DPD-REACT/compute_dpd.h similarity index 100% rename from src/USER-DPD/compute_dpd.h rename to src/DPD-REACT/compute_dpd.h diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/DPD-REACT/compute_dpd_atom.cpp similarity index 100% rename from src/USER-DPD/compute_dpd_atom.cpp rename to src/DPD-REACT/compute_dpd_atom.cpp diff --git a/src/USER-DPD/compute_dpd_atom.h b/src/DPD-REACT/compute_dpd_atom.h similarity index 100% rename from src/USER-DPD/compute_dpd_atom.h rename to src/DPD-REACT/compute_dpd_atom.h diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/DPD-REACT/fix_dpd_energy.cpp similarity index 100% rename from src/USER-DPD/fix_dpd_energy.cpp rename to src/DPD-REACT/fix_dpd_energy.cpp diff --git a/src/USER-DPD/fix_dpd_energy.h b/src/DPD-REACT/fix_dpd_energy.h similarity index 100% rename from src/USER-DPD/fix_dpd_energy.h rename to src/DPD-REACT/fix_dpd_energy.h diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/DPD-REACT/fix_eos_cv.cpp similarity index 100% rename from src/USER-DPD/fix_eos_cv.cpp rename to src/DPD-REACT/fix_eos_cv.cpp diff --git a/src/USER-DPD/fix_eos_cv.h b/src/DPD-REACT/fix_eos_cv.h similarity index 100% rename from src/USER-DPD/fix_eos_cv.h rename to src/DPD-REACT/fix_eos_cv.h diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/DPD-REACT/fix_eos_table.cpp similarity index 100% rename from src/USER-DPD/fix_eos_table.cpp rename to src/DPD-REACT/fix_eos_table.cpp diff --git a/src/USER-DPD/fix_eos_table.h b/src/DPD-REACT/fix_eos_table.h similarity index 100% rename from src/USER-DPD/fix_eos_table.h rename to src/DPD-REACT/fix_eos_table.h diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/DPD-REACT/fix_eos_table_rx.cpp similarity index 100% rename from src/USER-DPD/fix_eos_table_rx.cpp rename to src/DPD-REACT/fix_eos_table_rx.cpp diff --git a/src/USER-DPD/fix_eos_table_rx.h b/src/DPD-REACT/fix_eos_table_rx.h similarity index 100% rename from src/USER-DPD/fix_eos_table_rx.h rename to src/DPD-REACT/fix_eos_table_rx.h diff --git a/src/USER-DPD/fix_rx.cpp b/src/DPD-REACT/fix_rx.cpp similarity index 100% rename from src/USER-DPD/fix_rx.cpp rename to src/DPD-REACT/fix_rx.cpp diff --git a/src/USER-DPD/fix_rx.h b/src/DPD-REACT/fix_rx.h similarity index 100% rename from src/USER-DPD/fix_rx.h rename to src/DPD-REACT/fix_rx.h diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/DPD-REACT/fix_shardlow.cpp similarity index 99% rename from src/USER-DPD/fix_shardlow.cpp rename to src/DPD-REACT/fix_shardlow.cpp index 0881edd468..65fa14daeb 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/DPD-REACT/fix_shardlow.cpp @@ -158,7 +158,7 @@ void FixShardlow::setup(int /*vflag*/) for (int i = 0; i < modify->nfix; i++) if (strstr(modify->fix[i]->style,"nvt") || strstr(modify->fix[i]->style,"npt") || strstr(modify->fix[i]->style,"gle") || strstr(modify->fix[i]->style,"gld")) - error->all(FLERR,"Cannot use constant temperature integration routines with USER-DPD."); + error->all(FLERR,"Cannot use constant temperature integration routines with DPD-REACT."); for (int i = 0; i < modify->nfix; i++) { if (utils::strmatch(modify->fix[i]->style,"^shardlow")) fixShardlow = true; diff --git a/src/USER-DPD/fix_shardlow.h b/src/DPD-REACT/fix_shardlow.h similarity index 100% rename from src/USER-DPD/fix_shardlow.h rename to src/DPD-REACT/fix_shardlow.h diff --git a/src/USER-DPD/nbin_ssa.cpp b/src/DPD-REACT/nbin_ssa.cpp similarity index 100% rename from src/USER-DPD/nbin_ssa.cpp rename to src/DPD-REACT/nbin_ssa.cpp diff --git a/src/USER-DPD/nbin_ssa.h b/src/DPD-REACT/nbin_ssa.h similarity index 100% rename from src/USER-DPD/nbin_ssa.h rename to src/DPD-REACT/nbin_ssa.h diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/DPD-REACT/npair_half_bin_newton_ssa.cpp similarity index 100% rename from src/USER-DPD/npair_half_bin_newton_ssa.cpp rename to src/DPD-REACT/npair_half_bin_newton_ssa.cpp diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.h b/src/DPD-REACT/npair_half_bin_newton_ssa.h similarity index 100% rename from src/USER-DPD/npair_half_bin_newton_ssa.h rename to src/DPD-REACT/npair_half_bin_newton_ssa.h diff --git a/src/USER-DPD/nstencil_half_bin_2d_ssa.cpp b/src/DPD-REACT/nstencil_half_bin_2d_ssa.cpp similarity index 100% rename from src/USER-DPD/nstencil_half_bin_2d_ssa.cpp rename to src/DPD-REACT/nstencil_half_bin_2d_ssa.cpp diff --git a/src/USER-DPD/nstencil_half_bin_2d_ssa.h b/src/DPD-REACT/nstencil_half_bin_2d_ssa.h similarity index 100% rename from src/USER-DPD/nstencil_half_bin_2d_ssa.h rename to src/DPD-REACT/nstencil_half_bin_2d_ssa.h diff --git a/src/USER-DPD/nstencil_half_bin_3d_ssa.cpp b/src/DPD-REACT/nstencil_half_bin_3d_ssa.cpp similarity index 100% rename from src/USER-DPD/nstencil_half_bin_3d_ssa.cpp rename to src/DPD-REACT/nstencil_half_bin_3d_ssa.cpp diff --git a/src/USER-DPD/nstencil_half_bin_3d_ssa.h b/src/DPD-REACT/nstencil_half_bin_3d_ssa.h similarity index 100% rename from src/USER-DPD/nstencil_half_bin_3d_ssa.h rename to src/DPD-REACT/nstencil_half_bin_3d_ssa.h diff --git a/src/USER-DPD/nstencil_ssa.h b/src/DPD-REACT/nstencil_ssa.h similarity index 100% rename from src/USER-DPD/nstencil_ssa.h rename to src/DPD-REACT/nstencil_ssa.h diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/DPD-REACT/pair_dpd_fdt.cpp similarity index 100% rename from src/USER-DPD/pair_dpd_fdt.cpp rename to src/DPD-REACT/pair_dpd_fdt.cpp diff --git a/src/USER-DPD/pair_dpd_fdt.h b/src/DPD-REACT/pair_dpd_fdt.h similarity index 100% rename from src/USER-DPD/pair_dpd_fdt.h rename to src/DPD-REACT/pair_dpd_fdt.h diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/DPD-REACT/pair_dpd_fdt_energy.cpp similarity index 100% rename from src/USER-DPD/pair_dpd_fdt_energy.cpp rename to src/DPD-REACT/pair_dpd_fdt_energy.cpp diff --git a/src/USER-DPD/pair_dpd_fdt_energy.h b/src/DPD-REACT/pair_dpd_fdt_energy.h similarity index 100% rename from src/USER-DPD/pair_dpd_fdt_energy.h rename to src/DPD-REACT/pair_dpd_fdt_energy.h diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/DPD-REACT/pair_exp6_rx.cpp similarity index 100% rename from src/USER-DPD/pair_exp6_rx.cpp rename to src/DPD-REACT/pair_exp6_rx.cpp diff --git a/src/USER-DPD/pair_exp6_rx.h b/src/DPD-REACT/pair_exp6_rx.h similarity index 100% rename from src/USER-DPD/pair_exp6_rx.h rename to src/DPD-REACT/pair_exp6_rx.h diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/DPD-REACT/pair_multi_lucy.cpp similarity index 100% rename from src/USER-DPD/pair_multi_lucy.cpp rename to src/DPD-REACT/pair_multi_lucy.cpp diff --git a/src/USER-DPD/pair_multi_lucy.h b/src/DPD-REACT/pair_multi_lucy.h similarity index 100% rename from src/USER-DPD/pair_multi_lucy.h rename to src/DPD-REACT/pair_multi_lucy.h diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/DPD-REACT/pair_multi_lucy_rx.cpp similarity index 100% rename from src/USER-DPD/pair_multi_lucy_rx.cpp rename to src/DPD-REACT/pair_multi_lucy_rx.cpp diff --git a/src/USER-DPD/pair_multi_lucy_rx.h b/src/DPD-REACT/pair_multi_lucy_rx.h similarity index 100% rename from src/USER-DPD/pair_multi_lucy_rx.h rename to src/DPD-REACT/pair_multi_lucy_rx.h diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/DPD-REACT/pair_table_rx.cpp similarity index 100% rename from src/USER-DPD/pair_table_rx.cpp rename to src/DPD-REACT/pair_table_rx.cpp diff --git a/src/USER-DPD/pair_table_rx.h b/src/DPD-REACT/pair_table_rx.h similarity index 100% rename from src/USER-DPD/pair_table_rx.h rename to src/DPD-REACT/pair_table_rx.h diff --git a/src/USER-DPD/random_external_state.h b/src/DPD-REACT/random_external_state.h similarity index 100% rename from src/USER-DPD/random_external_state.h rename to src/DPD-REACT/random_external_state.h diff --git a/src/USER-SDPD/Install.sh b/src/DPD-SMOOTH/Install.sh similarity index 100% rename from src/USER-SDPD/Install.sh rename to src/DPD-SMOOTH/Install.sh diff --git a/src/USER-SDPD/README b/src/DPD-SMOOTH/README similarity index 100% rename from src/USER-SDPD/README rename to src/DPD-SMOOTH/README diff --git a/src/USER-SDPD/fix_meso_move.cpp b/src/DPD-SMOOTH/fix_meso_move.cpp similarity index 100% rename from src/USER-SDPD/fix_meso_move.cpp rename to src/DPD-SMOOTH/fix_meso_move.cpp diff --git a/src/USER-SDPD/fix_meso_move.h b/src/DPD-SMOOTH/fix_meso_move.h similarity index 100% rename from src/USER-SDPD/fix_meso_move.h rename to src/DPD-SMOOTH/fix_meso_move.h diff --git a/src/USER-SDPD/fix_rigid_meso.cpp b/src/DPD-SMOOTH/fix_rigid_meso.cpp similarity index 100% rename from src/USER-SDPD/fix_rigid_meso.cpp rename to src/DPD-SMOOTH/fix_rigid_meso.cpp diff --git a/src/USER-SDPD/fix_rigid_meso.h b/src/DPD-SMOOTH/fix_rigid_meso.h similarity index 100% rename from src/USER-SDPD/fix_rigid_meso.h rename to src/DPD-SMOOTH/fix_rigid_meso.h diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp similarity index 100% rename from src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp rename to src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.h b/src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.h similarity index 100% rename from src/USER-SDPD/pair_sdpd_taitwater_isothermal.h rename to src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.h diff --git a/src/USER-DRUDE/README b/src/DRUDE/README similarity index 92% rename from src/USER-DRUDE/README rename to src/DRUDE/README index 540e74279e..e6ee049a99 100644 --- a/src/USER-DRUDE/README +++ b/src/DRUDE/README @@ -13,7 +13,7 @@ See the file doc/drude_tutorial.html for getting started. There are auxiliary tools for using this package in tools/drude. -There are example scripts for using this package in examples/USER/drude. +There are example scripts for using this package in examples/PACKAGES/drude. The person who created this package is Alain Dequidt at the Chemistry Institute of Clermont-Ferrand, Clermont University, France diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/DRUDE/compute_temp_drude.cpp similarity index 100% rename from src/USER-DRUDE/compute_temp_drude.cpp rename to src/DRUDE/compute_temp_drude.cpp diff --git a/src/USER-DRUDE/compute_temp_drude.h b/src/DRUDE/compute_temp_drude.h similarity index 100% rename from src/USER-DRUDE/compute_temp_drude.h rename to src/DRUDE/compute_temp_drude.h diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/DRUDE/fix_drude.cpp similarity index 100% rename from src/USER-DRUDE/fix_drude.cpp rename to src/DRUDE/fix_drude.cpp diff --git a/src/USER-DRUDE/fix_drude.h b/src/DRUDE/fix_drude.h similarity index 100% rename from src/USER-DRUDE/fix_drude.h rename to src/DRUDE/fix_drude.h diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/DRUDE/fix_drude_transform.cpp similarity index 100% rename from src/USER-DRUDE/fix_drude_transform.cpp rename to src/DRUDE/fix_drude_transform.cpp diff --git a/src/USER-DRUDE/fix_drude_transform.h b/src/DRUDE/fix_drude_transform.h similarity index 100% rename from src/USER-DRUDE/fix_drude_transform.h rename to src/DRUDE/fix_drude_transform.h diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/DRUDE/fix_langevin_drude.cpp similarity index 100% rename from src/USER-DRUDE/fix_langevin_drude.cpp rename to src/DRUDE/fix_langevin_drude.cpp diff --git a/src/USER-DRUDE/fix_langevin_drude.h b/src/DRUDE/fix_langevin_drude.h similarity index 100% rename from src/USER-DRUDE/fix_langevin_drude.h rename to src/DRUDE/fix_langevin_drude.h diff --git a/src/USER-DRUDE/fix_tgnh_drude.cpp b/src/DRUDE/fix_tgnh_drude.cpp similarity index 100% rename from src/USER-DRUDE/fix_tgnh_drude.cpp rename to src/DRUDE/fix_tgnh_drude.cpp diff --git a/src/USER-DRUDE/fix_tgnh_drude.h b/src/DRUDE/fix_tgnh_drude.h similarity index 100% rename from src/USER-DRUDE/fix_tgnh_drude.h rename to src/DRUDE/fix_tgnh_drude.h diff --git a/src/USER-DRUDE/fix_tgnpt_drude.cpp b/src/DRUDE/fix_tgnpt_drude.cpp similarity index 100% rename from src/USER-DRUDE/fix_tgnpt_drude.cpp rename to src/DRUDE/fix_tgnpt_drude.cpp diff --git a/src/USER-DRUDE/fix_tgnpt_drude.h b/src/DRUDE/fix_tgnpt_drude.h similarity index 100% rename from src/USER-DRUDE/fix_tgnpt_drude.h rename to src/DRUDE/fix_tgnpt_drude.h diff --git a/src/USER-DRUDE/fix_tgnvt_drude.cpp b/src/DRUDE/fix_tgnvt_drude.cpp similarity index 100% rename from src/USER-DRUDE/fix_tgnvt_drude.cpp rename to src/DRUDE/fix_tgnvt_drude.cpp diff --git a/src/USER-DRUDE/fix_tgnvt_drude.h b/src/DRUDE/fix_tgnvt_drude.h similarity index 100% rename from src/USER-DRUDE/fix_tgnvt_drude.h rename to src/DRUDE/fix_tgnvt_drude.h diff --git a/src/USER-DRUDE/pair_coul_tt.cpp b/src/DRUDE/pair_coul_tt.cpp similarity index 100% rename from src/USER-DRUDE/pair_coul_tt.cpp rename to src/DRUDE/pair_coul_tt.cpp diff --git a/src/USER-DRUDE/pair_coul_tt.h b/src/DRUDE/pair_coul_tt.h similarity index 100% rename from src/USER-DRUDE/pair_coul_tt.h rename to src/DRUDE/pair_coul_tt.h diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/DRUDE/pair_lj_cut_thole_long.cpp similarity index 100% rename from src/USER-DRUDE/pair_lj_cut_thole_long.cpp rename to src/DRUDE/pair_lj_cut_thole_long.cpp diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.h b/src/DRUDE/pair_lj_cut_thole_long.h similarity index 100% rename from src/USER-DRUDE/pair_lj_cut_thole_long.h rename to src/DRUDE/pair_lj_cut_thole_long.h diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/DRUDE/pair_thole.cpp similarity index 100% rename from src/USER-DRUDE/pair_thole.cpp rename to src/DRUDE/pair_thole.cpp diff --git a/src/USER-DRUDE/pair_thole.h b/src/DRUDE/pair_thole.h similarity index 100% rename from src/USER-DRUDE/pair_thole.h rename to src/DRUDE/pair_thole.h diff --git a/src/Depend.sh b/src/Depend.sh index f77d435fc5..6dbfed903c 100755 --- a/src/Depend.sh +++ b/src/Depend.sh @@ -47,105 +47,111 @@ depend () { if (test $1 = "ASPHERE") then depend GPU - depend USER-OMP - depend USER-CGDNA - depend USER-INTEL + depend OPENMP + depend CG-DNA + depend INTEL fi if (test $1 = "CLASS2") then depend GPU depend KOKKOS - depend USER-OMP + depend OPENMP fi if (test $1 = "COLLOID") then depend GPU - depend USER-OMP + depend OPENMP fi if (test $1 = "DIPOLE") then depend USER-MISC - depend USER-OMP + depend OPENMP +fi + +if (test $1 = "DPD-BASIC") then + depend GPU fi if (test $1 = "GRANULAR") then depend KOKKOS - depend USER-OMP + depend OPENMP fi if (test $1 = "KSPACE") then depend CORESHELL + depend DIELECTRIC depend GPU depend KOKKOS depend OPT - depend USER-OMP - depend USER-INTEL - depend USER-PHONON - depend USER-FEP + depend OPENMP + depend INTEL + depend PHONON + depend FEP fi if (test $1 = "MANYBODY") then + depend ATC depend GPU depend KOKKOS depend OPT depend QEQ depend USER-MISC - depend USER-OMP + depend OPENMP fi if (test $1 = "MOLECULE") then depend GPU depend KOKKOS depend USER-MISC - depend USER-FEP - depend USER-OMP - depend USER-INTEL + depend FEP + depend OPENMP + depend INTEL fi if (test $1 = "PERI") then - depend USER-OMP + depend OPENMP fi if (test $1 = "PYTHON") then - depend MLIAP + depend ML-IAP fi if (test $1 = "RIGID") then depend KOKKOS - depend USER-OMP - depend USER-SDPD + depend OPENMP + depend DPD-SMOOTH fi -if (test $1 = "SNAP") then +if (test $1 = "ML-SNAP") then depend KOKKOS - depend MLIAP + depend ML-IAP fi -if (test $1 = "USER-CGSDK") then +if (test $1 = "CG-SDK") then depend GPU depend KOKKOS - depend USER-OMP + depend OPENMP fi -if (test $1 = "USER-DPD") then +if (test $1 = "DPD-REACT") then depend KOKKOS fi -if (test $1 = "USER-DRUDE") then - depend USER-OMP +if (test $1 = "DRUDE") then + depend OPENMP fi -if (test $1 = "USER-FEP") then - depend USER-OMP +if (test $1 = "FEP") then + depend OPENMP fi if (test $1 = "USER-MISC") then depend GPU - depend USER-OMP - depend USER-INTEL + depend OPENMP + depend INTEL fi -if (test $1 = "USER-REAXC") then +if (test $1 = "REAXFF") then depend KOKKOS - depend USER-OMP + depend OPENMP fi diff --git a/src/USER-EFF/README b/src/EFF/README similarity index 99% rename from src/USER-EFF/README rename to src/EFF/README index 5caa1cd7da..18c8516905 100644 --- a/src/USER-EFF/README +++ b/src/EFF/README @@ -27,7 +27,7 @@ minimization and dynamics. See the doc page for the pair_style eff/cut command to get started. There are example scripts for using this package in -examples/USER/eff. +examples/PACKAGES/eff. There are auxiliary tools for using this package in tools/eff. diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/EFF/atom_vec_electron.cpp similarity index 99% rename from src/USER-EFF/atom_vec_electron.cpp rename to src/EFF/atom_vec_electron.cpp index 87bec2ce9f..ca80f186a8 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/EFF/atom_vec_electron.cpp @@ -26,7 +26,7 @@ using namespace LAMMPS_NS; static const char cite_user_eff_package[] = - "USER-EFF package:\n\n" + "EFF package:\n\n" "@Article{Jaramillo-Botero11,\n" " author = {A. Jaramillo-Botero, J. Su, A. Qi, W. A. Goddard III},\n" " title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},\n" diff --git a/src/USER-EFF/atom_vec_electron.h b/src/EFF/atom_vec_electron.h similarity index 100% rename from src/USER-EFF/atom_vec_electron.h rename to src/EFF/atom_vec_electron.h diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/EFF/compute_ke_atom_eff.cpp similarity index 100% rename from src/USER-EFF/compute_ke_atom_eff.cpp rename to src/EFF/compute_ke_atom_eff.cpp diff --git a/src/USER-EFF/compute_ke_atom_eff.h b/src/EFF/compute_ke_atom_eff.h similarity index 100% rename from src/USER-EFF/compute_ke_atom_eff.h rename to src/EFF/compute_ke_atom_eff.h diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/EFF/compute_ke_eff.cpp similarity index 100% rename from src/USER-EFF/compute_ke_eff.cpp rename to src/EFF/compute_ke_eff.cpp diff --git a/src/USER-EFF/compute_ke_eff.h b/src/EFF/compute_ke_eff.h similarity index 100% rename from src/USER-EFF/compute_ke_eff.h rename to src/EFF/compute_ke_eff.h diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/EFF/compute_temp_deform_eff.cpp similarity index 100% rename from src/USER-EFF/compute_temp_deform_eff.cpp rename to src/EFF/compute_temp_deform_eff.cpp diff --git a/src/USER-EFF/compute_temp_deform_eff.h b/src/EFF/compute_temp_deform_eff.h similarity index 100% rename from src/USER-EFF/compute_temp_deform_eff.h rename to src/EFF/compute_temp_deform_eff.h diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/EFF/compute_temp_eff.cpp similarity index 100% rename from src/USER-EFF/compute_temp_eff.cpp rename to src/EFF/compute_temp_eff.cpp diff --git a/src/USER-EFF/compute_temp_eff.h b/src/EFF/compute_temp_eff.h similarity index 100% rename from src/USER-EFF/compute_temp_eff.h rename to src/EFF/compute_temp_eff.h diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/EFF/compute_temp_region_eff.cpp similarity index 100% rename from src/USER-EFF/compute_temp_region_eff.cpp rename to src/EFF/compute_temp_region_eff.cpp diff --git a/src/USER-EFF/compute_temp_region_eff.h b/src/EFF/compute_temp_region_eff.h similarity index 100% rename from src/USER-EFF/compute_temp_region_eff.h rename to src/EFF/compute_temp_region_eff.h diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/EFF/fix_langevin_eff.cpp similarity index 100% rename from src/USER-EFF/fix_langevin_eff.cpp rename to src/EFF/fix_langevin_eff.cpp diff --git a/src/USER-EFF/fix_langevin_eff.h b/src/EFF/fix_langevin_eff.h similarity index 100% rename from src/USER-EFF/fix_langevin_eff.h rename to src/EFF/fix_langevin_eff.h diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/EFF/fix_nh_eff.cpp similarity index 100% rename from src/USER-EFF/fix_nh_eff.cpp rename to src/EFF/fix_nh_eff.cpp diff --git a/src/USER-EFF/fix_nh_eff.h b/src/EFF/fix_nh_eff.h similarity index 100% rename from src/USER-EFF/fix_nh_eff.h rename to src/EFF/fix_nh_eff.h diff --git a/src/USER-EFF/fix_nph_eff.cpp b/src/EFF/fix_nph_eff.cpp similarity index 100% rename from src/USER-EFF/fix_nph_eff.cpp rename to src/EFF/fix_nph_eff.cpp diff --git a/src/USER-EFF/fix_nph_eff.h b/src/EFF/fix_nph_eff.h similarity index 100% rename from src/USER-EFF/fix_nph_eff.h rename to src/EFF/fix_nph_eff.h diff --git a/src/USER-EFF/fix_npt_eff.cpp b/src/EFF/fix_npt_eff.cpp similarity index 100% rename from src/USER-EFF/fix_npt_eff.cpp rename to src/EFF/fix_npt_eff.cpp diff --git a/src/USER-EFF/fix_npt_eff.h b/src/EFF/fix_npt_eff.h similarity index 100% rename from src/USER-EFF/fix_npt_eff.h rename to src/EFF/fix_npt_eff.h diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/EFF/fix_nve_eff.cpp similarity index 100% rename from src/USER-EFF/fix_nve_eff.cpp rename to src/EFF/fix_nve_eff.cpp diff --git a/src/USER-EFF/fix_nve_eff.h b/src/EFF/fix_nve_eff.h similarity index 100% rename from src/USER-EFF/fix_nve_eff.h rename to src/EFF/fix_nve_eff.h diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/EFF/fix_nvt_eff.cpp similarity index 100% rename from src/USER-EFF/fix_nvt_eff.cpp rename to src/EFF/fix_nvt_eff.cpp diff --git a/src/USER-EFF/fix_nvt_eff.h b/src/EFF/fix_nvt_eff.h similarity index 100% rename from src/USER-EFF/fix_nvt_eff.h rename to src/EFF/fix_nvt_eff.h diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/EFF/fix_nvt_sllod_eff.cpp similarity index 100% rename from src/USER-EFF/fix_nvt_sllod_eff.cpp rename to src/EFF/fix_nvt_sllod_eff.cpp diff --git a/src/USER-EFF/fix_nvt_sllod_eff.h b/src/EFF/fix_nvt_sllod_eff.h similarity index 100% rename from src/USER-EFF/fix_nvt_sllod_eff.h rename to src/EFF/fix_nvt_sllod_eff.h diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/EFF/fix_temp_rescale_eff.cpp similarity index 100% rename from src/USER-EFF/fix_temp_rescale_eff.cpp rename to src/EFF/fix_temp_rescale_eff.cpp diff --git a/src/USER-EFF/fix_temp_rescale_eff.h b/src/EFF/fix_temp_rescale_eff.h similarity index 100% rename from src/USER-EFF/fix_temp_rescale_eff.h rename to src/EFF/fix_temp_rescale_eff.h diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/EFF/pair_eff_cut.cpp similarity index 100% rename from src/USER-EFF/pair_eff_cut.cpp rename to src/EFF/pair_eff_cut.cpp diff --git a/src/USER-EFF/pair_eff_cut.h b/src/EFF/pair_eff_cut.h similarity index 100% rename from src/USER-EFF/pair_eff_cut.h rename to src/EFF/pair_eff_cut.h diff --git a/src/USER-EFF/pair_eff_inline.h b/src/EFF/pair_eff_inline.h similarity index 100% rename from src/USER-EFF/pair_eff_inline.h rename to src/EFF/pair_eff_inline.h diff --git a/src/USER-FEP/Install.sh b/src/FEP/Install.sh similarity index 100% rename from src/USER-FEP/Install.sh rename to src/FEP/Install.sh diff --git a/src/USER-FEP/README b/src/FEP/README similarity index 97% rename from src/USER-FEP/README rename to src/FEP/README index 3ed5a52b44..00b6ac518f 100644 --- a/src/USER-FEP/README +++ b/src/FEP/README @@ -4,7 +4,7 @@ simulations with soft-core pair potentials in LAMMPS. See the doc page for the fix adapt/fep command to get started. There are example scripts for using this package in -examples/USER/fep. +examples/PACKAGES/fep. There are auxiliary tools for using this package in tools/fep. diff --git a/src/USER-FEP/compute_fep.cpp b/src/FEP/compute_fep.cpp similarity index 100% rename from src/USER-FEP/compute_fep.cpp rename to src/FEP/compute_fep.cpp diff --git a/src/USER-FEP/compute_fep.h b/src/FEP/compute_fep.h similarity index 100% rename from src/USER-FEP/compute_fep.h rename to src/FEP/compute_fep.h diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/FEP/fix_adapt_fep.cpp similarity index 100% rename from src/USER-FEP/fix_adapt_fep.cpp rename to src/FEP/fix_adapt_fep.cpp diff --git a/src/USER-FEP/fix_adapt_fep.h b/src/FEP/fix_adapt_fep.h similarity index 100% rename from src/USER-FEP/fix_adapt_fep.h rename to src/FEP/fix_adapt_fep.h diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/FEP/pair_coul_cut_soft.cpp similarity index 100% rename from src/USER-FEP/pair_coul_cut_soft.cpp rename to src/FEP/pair_coul_cut_soft.cpp diff --git a/src/USER-FEP/pair_coul_cut_soft.h b/src/FEP/pair_coul_cut_soft.h similarity index 100% rename from src/USER-FEP/pair_coul_cut_soft.h rename to src/FEP/pair_coul_cut_soft.h diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/FEP/pair_coul_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_coul_long_soft.cpp rename to src/FEP/pair_coul_long_soft.cpp diff --git a/src/USER-FEP/pair_coul_long_soft.h b/src/FEP/pair_coul_long_soft.h similarity index 100% rename from src/USER-FEP/pair_coul_long_soft.h rename to src/FEP/pair_coul_long_soft.h diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/FEP/pair_lj_charmm_coul_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp rename to src/FEP/pair_lj_charmm_coul_long_soft.cpp diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.h b/src/FEP/pair_lj_charmm_coul_long_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_charmm_coul_long_soft.h rename to src/FEP/pair_lj_charmm_coul_long_soft.h diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/FEP/pair_lj_class2_coul_cut_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp rename to src/FEP/pair_lj_class2_coul_cut_soft.cpp diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.h b/src/FEP/pair_lj_class2_coul_cut_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_class2_coul_cut_soft.h rename to src/FEP/pair_lj_class2_coul_cut_soft.h diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/FEP/pair_lj_class2_coul_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_class2_coul_long_soft.cpp rename to src/FEP/pair_lj_class2_coul_long_soft.cpp diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.h b/src/FEP/pair_lj_class2_coul_long_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_class2_coul_long_soft.h rename to src/FEP/pair_lj_class2_coul_long_soft.h diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/FEP/pair_lj_class2_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_class2_soft.cpp rename to src/FEP/pair_lj_class2_soft.cpp diff --git a/src/USER-FEP/pair_lj_class2_soft.h b/src/FEP/pair_lj_class2_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_class2_soft.h rename to src/FEP/pair_lj_class2_soft.h diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/FEP/pair_lj_cut_coul_cut_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp rename to src/FEP/pair_lj_cut_coul_cut_soft.cpp diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.h b/src/FEP/pair_lj_cut_coul_cut_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_cut_coul_cut_soft.h rename to src/FEP/pair_lj_cut_coul_cut_soft.h diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/FEP/pair_lj_cut_coul_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_cut_coul_long_soft.cpp rename to src/FEP/pair_lj_cut_coul_long_soft.cpp diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.h b/src/FEP/pair_lj_cut_coul_long_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_cut_coul_long_soft.h rename to src/FEP/pair_lj_cut_coul_long_soft.h diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/FEP/pair_lj_cut_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_cut_soft.cpp rename to src/FEP/pair_lj_cut_soft.cpp diff --git a/src/USER-FEP/pair_lj_cut_soft.h b/src/FEP/pair_lj_cut_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_cut_soft.h rename to src/FEP/pair_lj_cut_soft.h diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/FEP/pair_lj_cut_tip4p_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp rename to src/FEP/pair_lj_cut_tip4p_long_soft.cpp diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.h b/src/FEP/pair_lj_cut_tip4p_long_soft.h similarity index 100% rename from src/USER-FEP/pair_lj_cut_tip4p_long_soft.h rename to src/FEP/pair_lj_cut_tip4p_long_soft.h diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/FEP/pair_morse_soft.cpp similarity index 100% rename from src/USER-FEP/pair_morse_soft.cpp rename to src/FEP/pair_morse_soft.cpp diff --git a/src/USER-FEP/pair_morse_soft.h b/src/FEP/pair_morse_soft.h similarity index 100% rename from src/USER-FEP/pair_morse_soft.h rename to src/FEP/pair_morse_soft.h diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/FEP/pair_tip4p_long_soft.cpp similarity index 100% rename from src/USER-FEP/pair_tip4p_long_soft.cpp rename to src/FEP/pair_tip4p_long_soft.cpp diff --git a/src/USER-FEP/pair_tip4p_long_soft.h b/src/FEP/pair_tip4p_long_soft.h similarity index 100% rename from src/USER-FEP/pair_tip4p_long_soft.h rename to src/FEP/pair_tip4p_long_soft.h diff --git a/src/USER-H5MD/Install.sh b/src/H5MD/Install.sh similarity index 100% rename from src/USER-H5MD/Install.sh rename to src/H5MD/Install.sh diff --git a/src/USER-H5MD/README b/src/H5MD/README similarity index 100% rename from src/USER-H5MD/README rename to src/H5MD/README diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/H5MD/dump_h5md.cpp similarity index 100% rename from src/USER-H5MD/dump_h5md.cpp rename to src/H5MD/dump_h5md.cpp diff --git a/src/USER-H5MD/dump_h5md.h b/src/H5MD/dump_h5md.h similarity index 100% rename from src/USER-H5MD/dump_h5md.h rename to src/H5MD/dump_h5md.h diff --git a/src/USER-INTEL/Install.sh b/src/INTEL/Install.sh similarity index 100% rename from src/USER-INTEL/Install.sh rename to src/INTEL/Install.sh diff --git a/src/USER-INTEL/README b/src/INTEL/README similarity index 98% rename from src/USER-INTEL/README rename to src/INTEL/README index 650e2c3a2d..b59b0619b3 100644 --- a/src/USER-INTEL/README +++ b/src/INTEL/README @@ -42,8 +42,8 @@ be added or changed in the Makefile depending on the version: ----------------------------------------------------------------------------- When using the suffix command with "intel", intel styles will be used if they -exist. If the suffix command is used with "hybrid intel omp" and the USER-OMP -is installed, USER-OMP styles will be used whenever USER-INTEL styles are not +exist. If the suffix command is used with "hybrid intel omp" and the OPENMP +is installed, OPENMP styles will be used whenever INTEL styles are not available. This allow for running most styles in LAMMPS with threading. ----------------------------------------------------------------------------- diff --git a/src/USER-INTEL/TEST/README b/src/INTEL/TEST/README similarity index 95% rename from src/USER-INTEL/TEST/README rename to src/INTEL/TEST/README index fdc92b363d..a3eee3f69c 100644 --- a/src/USER-INTEL/TEST/README +++ b/src/INTEL/TEST/README @@ -32,7 +32,7 @@ ############################################################################# ############################################################################# -# For Skylake server (Xeon) architectures, see notes in the USER-INTEL/README +# For Skylake server (Xeon) architectures, see notes in the INTEL/README # for build flags that should be used. ############################################################################# @@ -62,7 +62,7 @@ # -v N off # newton off # # The default is on for all of the benchmarks except for LJ where the off -# setting performs best with the USER-INTEL package +# setting performs best with the INTEL package ############################################################################# # Example for running benchmarks (see run_benchmarks.sh for script): @@ -106,17 +106,17 @@ export bench=in.intel.lj mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -v N on ############################################################################# -# To run with USER-OMP package +# To run with OPENMP package ############################################################################# mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk omp 0 -sf omp -v N on ############################################################################# -# To run with USER-INTEL package and no coprocessor +# To run with INTEL package and no coprocessor ############################################################################# mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk intel 0 -sf intel ############################################################################# -# To run with USER-INTEL and automatic load balancing to 1 coprocessor +# To run with INTEL and automatic load balancing to 1 coprocessor ############################################################################# mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk intel 1 -sf intel diff --git a/src/USER-INTEL/TEST/in.intel.airebo b/src/INTEL/TEST/in.intel.airebo similarity index 100% rename from src/USER-INTEL/TEST/in.intel.airebo rename to src/INTEL/TEST/in.intel.airebo diff --git a/src/USER-INTEL/TEST/in.intel.dpd b/src/INTEL/TEST/in.intel.dpd similarity index 100% rename from src/USER-INTEL/TEST/in.intel.dpd rename to src/INTEL/TEST/in.intel.dpd diff --git a/src/USER-INTEL/TEST/in.intel.eam b/src/INTEL/TEST/in.intel.eam similarity index 100% rename from src/USER-INTEL/TEST/in.intel.eam rename to src/INTEL/TEST/in.intel.eam diff --git a/src/USER-INTEL/TEST/in.intel.lc b/src/INTEL/TEST/in.intel.lc similarity index 100% rename from src/USER-INTEL/TEST/in.intel.lc rename to src/INTEL/TEST/in.intel.lc diff --git a/src/USER-INTEL/TEST/in.intel.lj b/src/INTEL/TEST/in.intel.lj similarity index 100% rename from src/USER-INTEL/TEST/in.intel.lj rename to src/INTEL/TEST/in.intel.lj diff --git a/src/USER-INTEL/TEST/in.intel.rhodo b/src/INTEL/TEST/in.intel.rhodo similarity index 100% rename from src/USER-INTEL/TEST/in.intel.rhodo rename to src/INTEL/TEST/in.intel.rhodo diff --git a/src/USER-INTEL/TEST/in.intel.sw b/src/INTEL/TEST/in.intel.sw similarity index 100% rename from src/USER-INTEL/TEST/in.intel.sw rename to src/INTEL/TEST/in.intel.sw diff --git a/src/USER-INTEL/TEST/in.intel.tersoff b/src/INTEL/TEST/in.intel.tersoff similarity index 100% rename from src/USER-INTEL/TEST/in.intel.tersoff rename to src/INTEL/TEST/in.intel.tersoff diff --git a/src/USER-INTEL/TEST/in.intel.water b/src/INTEL/TEST/in.intel.water similarity index 100% rename from src/USER-INTEL/TEST/in.intel.water rename to src/INTEL/TEST/in.intel.water diff --git a/src/USER-INTEL/TEST/in.lc_generate_restart b/src/INTEL/TEST/in.lc_generate_restart similarity index 100% rename from src/USER-INTEL/TEST/in.lc_generate_restart rename to src/INTEL/TEST/in.lc_generate_restart diff --git a/src/USER-INTEL/TEST/mW.sw b/src/INTEL/TEST/mW.sw similarity index 100% rename from src/USER-INTEL/TEST/mW.sw rename to src/INTEL/TEST/mW.sw diff --git a/src/USER-INTEL/TEST/mW_32k_cube.data b/src/INTEL/TEST/mW_32k_cube.data similarity index 100% rename from src/USER-INTEL/TEST/mW_32k_cube.data rename to src/INTEL/TEST/mW_32k_cube.data diff --git a/src/USER-INTEL/TEST/run_benchmarks.sh b/src/INTEL/TEST/run_benchmarks.sh similarity index 100% rename from src/USER-INTEL/TEST/run_benchmarks.sh rename to src/INTEL/TEST/run_benchmarks.sh diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/INTEL/angle_charmm_intel.cpp similarity index 99% rename from src/USER-INTEL/angle_charmm_intel.cpp rename to src/INTEL/angle_charmm_intel.cpp index 9284150522..29b7ec208b 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/INTEL/angle_charmm_intel.cpp @@ -83,7 +83,7 @@ void AngleCharmmIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/angle_charmm_intel.h b/src/INTEL/angle_charmm_intel.h similarity index 100% rename from src/USER-INTEL/angle_charmm_intel.h rename to src/INTEL/angle_charmm_intel.h diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/INTEL/angle_harmonic_intel.cpp similarity index 99% rename from src/USER-INTEL/angle_harmonic_intel.cpp rename to src/INTEL/angle_harmonic_intel.cpp index 6a7a5c2fe2..a2d8cc7d13 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/INTEL/angle_harmonic_intel.cpp @@ -83,7 +83,7 @@ void AngleHarmonicIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/angle_harmonic_intel.h b/src/INTEL/angle_harmonic_intel.h similarity index 100% rename from src/USER-INTEL/angle_harmonic_intel.h rename to src/INTEL/angle_harmonic_intel.h diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/INTEL/bond_fene_intel.cpp similarity index 99% rename from src/USER-INTEL/bond_fene_intel.cpp rename to src/INTEL/bond_fene_intel.cpp index 0efcdafaef..44a8c0d3cf 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/INTEL/bond_fene_intel.cpp @@ -82,7 +82,7 @@ void BondFENEIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/bond_fene_intel.h b/src/INTEL/bond_fene_intel.h similarity index 100% rename from src/USER-INTEL/bond_fene_intel.h rename to src/INTEL/bond_fene_intel.h diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/INTEL/bond_harmonic_intel.cpp similarity index 99% rename from src/USER-INTEL/bond_harmonic_intel.cpp rename to src/INTEL/bond_harmonic_intel.cpp index db531ee650..a37ae091a0 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/INTEL/bond_harmonic_intel.cpp @@ -79,7 +79,7 @@ void BondHarmonicIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/bond_harmonic_intel.h b/src/INTEL/bond_harmonic_intel.h similarity index 100% rename from src/USER-INTEL/bond_harmonic_intel.h rename to src/INTEL/bond_harmonic_intel.h diff --git a/src/USER-INTEL/dihedral_charmm_intel.cpp b/src/INTEL/dihedral_charmm_intel.cpp similarity index 99% rename from src/USER-INTEL/dihedral_charmm_intel.cpp rename to src/INTEL/dihedral_charmm_intel.cpp index c49768afe6..a317be00fb 100644 --- a/src/USER-INTEL/dihedral_charmm_intel.cpp +++ b/src/INTEL/dihedral_charmm_intel.cpp @@ -88,7 +88,7 @@ void DihedralCharmmIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); // insure pair->ev_tally() will use 1-4 virial contribution diff --git a/src/USER-INTEL/dihedral_charmm_intel.h b/src/INTEL/dihedral_charmm_intel.h similarity index 100% rename from src/USER-INTEL/dihedral_charmm_intel.h rename to src/INTEL/dihedral_charmm_intel.h diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/INTEL/dihedral_fourier_intel.cpp similarity index 99% rename from src/USER-INTEL/dihedral_fourier_intel.cpp rename to src/INTEL/dihedral_fourier_intel.cpp index d8a500b40e..4d44ea36d2 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/INTEL/dihedral_fourier_intel.cpp @@ -77,7 +77,7 @@ void DihedralFourierIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/dihedral_fourier_intel.h b/src/INTEL/dihedral_fourier_intel.h similarity index 100% rename from src/USER-INTEL/dihedral_fourier_intel.h rename to src/INTEL/dihedral_fourier_intel.h diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/INTEL/dihedral_harmonic_intel.cpp similarity index 99% rename from src/USER-INTEL/dihedral_harmonic_intel.cpp rename to src/INTEL/dihedral_harmonic_intel.cpp index 82eb87e90f..f7009689c7 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/INTEL/dihedral_harmonic_intel.cpp @@ -77,7 +77,7 @@ void DihedralHarmonicIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/dihedral_harmonic_intel.h b/src/INTEL/dihedral_harmonic_intel.h similarity index 100% rename from src/USER-INTEL/dihedral_harmonic_intel.h rename to src/INTEL/dihedral_harmonic_intel.h diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/INTEL/dihedral_opls_intel.cpp similarity index 99% rename from src/USER-INTEL/dihedral_opls_intel.cpp rename to src/INTEL/dihedral_opls_intel.cpp index a19482a2d8..ab007dad8c 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/INTEL/dihedral_opls_intel.cpp @@ -81,7 +81,7 @@ void DihedralOPLSIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/dihedral_opls_intel.h b/src/INTEL/dihedral_opls_intel.h similarity index 100% rename from src/USER-INTEL/dihedral_opls_intel.h rename to src/INTEL/dihedral_opls_intel.h diff --git a/src/USER-INTEL/fix_intel.cpp b/src/INTEL/fix_intel.cpp similarity index 99% rename from src/USER-INTEL/fix_intel.cpp rename to src/INTEL/fix_intel.cpp index edec1f0c42..59eea4961a 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/INTEL/fix_intel.cpp @@ -510,7 +510,7 @@ void FixIntel::bond_init_check() if ((_offload_balance != 0.0) && (atom->molecular != Atom::ATOMIC) && (force->newton_pair != force->newton_bond)) error->all(FLERR, - "USER-INTEL package requires same setting for newton bond and non-bond."); + "INTEL package requires same setting for newton bond and non-bond."); int intel_pair = 0; if (force->pair_match("/intel$", 0) != nullptr) @@ -557,12 +557,12 @@ void FixIntel::check_neighbor_intel() if (neighbor->requests[i]->skip && _offload_balance != 0.0) error->all(FLERR, "Cannot yet use hybrid styles with Intel offload."); - // avoid flagging a neighbor list as both USER-INTEL and USER-OMP + // avoid flagging a neighbor list as both INTEL and OPENMP if (neighbor->requests[i]->intel) neighbor->requests[i]->omp = 0; } #else - // avoid flagging a neighbor list as both USER-INTEL and USER-OMP + // avoid flagging a neighbor list as both INTEL and OPENMP const int nrequest = neighbor->nrequest; for (int i = 0; i < nrequest; ++i) if (neighbor->requests[i]->intel) diff --git a/src/USER-INTEL/fix_intel.h b/src/INTEL/fix_intel.h similarity index 98% rename from src/USER-INTEL/fix_intel.h rename to src/INTEL/fix_intel.h index 8bc3e80780..8e5d2b524d 100644 --- a/src/USER-INTEL/fix_intel.h +++ b/src/INTEL/fix_intel.h @@ -541,19 +541,19 @@ W: More MPI tasks/OpenMP threads than available cores Using more MPI tasks/OpenMP threads than available cores will typically decrease performance. -E: USER-INTEL package requires same setting for newton bond and non-bond. +E: INTEL package requires same setting for newton bond and non-bond. The newton setting must be the same for both pairwise and bonded forces. E: Intel styles for bond/angle/dihedral/improper require intel pair style." -You cannot use the USER-INTEL package for bond calculations without a -USER-INTEL supported pair style. +You cannot use the INTEL package for bond calculations without a +INTEL supported pair style. E: Intel styles for kspace require intel pair style. -You cannot use the USER-INTEL package for kspace calculations without a -USER-INTEL supported pair style. +You cannot use the INTEL package for kspace calculations without a +INTEL supported pair style. E: Cannot currently get per-atom virials with intel package. diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/INTEL/fix_nh_intel.cpp similarity index 100% rename from src/USER-INTEL/fix_nh_intel.cpp rename to src/INTEL/fix_nh_intel.cpp diff --git a/src/USER-INTEL/fix_nh_intel.h b/src/INTEL/fix_nh_intel.h similarity index 100% rename from src/USER-INTEL/fix_nh_intel.h rename to src/INTEL/fix_nh_intel.h diff --git a/src/USER-INTEL/fix_npt_intel.cpp b/src/INTEL/fix_npt_intel.cpp similarity index 100% rename from src/USER-INTEL/fix_npt_intel.cpp rename to src/INTEL/fix_npt_intel.cpp diff --git a/src/USER-INTEL/fix_npt_intel.h b/src/INTEL/fix_npt_intel.h similarity index 100% rename from src/USER-INTEL/fix_npt_intel.h rename to src/INTEL/fix_npt_intel.h diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/INTEL/fix_nve_asphere_intel.cpp similarity index 100% rename from src/USER-INTEL/fix_nve_asphere_intel.cpp rename to src/INTEL/fix_nve_asphere_intel.cpp diff --git a/src/USER-INTEL/fix_nve_asphere_intel.h b/src/INTEL/fix_nve_asphere_intel.h similarity index 100% rename from src/USER-INTEL/fix_nve_asphere_intel.h rename to src/INTEL/fix_nve_asphere_intel.h diff --git a/src/USER-INTEL/fix_nve_intel.cpp b/src/INTEL/fix_nve_intel.cpp similarity index 100% rename from src/USER-INTEL/fix_nve_intel.cpp rename to src/INTEL/fix_nve_intel.cpp diff --git a/src/USER-INTEL/fix_nve_intel.h b/src/INTEL/fix_nve_intel.h similarity index 100% rename from src/USER-INTEL/fix_nve_intel.h rename to src/INTEL/fix_nve_intel.h diff --git a/src/USER-INTEL/fix_nvt_intel.cpp b/src/INTEL/fix_nvt_intel.cpp similarity index 100% rename from src/USER-INTEL/fix_nvt_intel.cpp rename to src/INTEL/fix_nvt_intel.cpp diff --git a/src/USER-INTEL/fix_nvt_intel.h b/src/INTEL/fix_nvt_intel.h similarity index 100% rename from src/USER-INTEL/fix_nvt_intel.h rename to src/INTEL/fix_nvt_intel.h diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/INTEL/fix_nvt_sllod_intel.cpp similarity index 100% rename from src/USER-INTEL/fix_nvt_sllod_intel.cpp rename to src/INTEL/fix_nvt_sllod_intel.cpp diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.h b/src/INTEL/fix_nvt_sllod_intel.h similarity index 100% rename from src/USER-INTEL/fix_nvt_sllod_intel.h rename to src/INTEL/fix_nvt_sllod_intel.h diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/INTEL/improper_cvff_intel.cpp similarity index 99% rename from src/USER-INTEL/improper_cvff_intel.cpp rename to src/INTEL/improper_cvff_intel.cpp index 9fe1ad8eb1..62dcde36b9 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/INTEL/improper_cvff_intel.cpp @@ -87,7 +87,7 @@ void ImproperCvffIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/improper_cvff_intel.h b/src/INTEL/improper_cvff_intel.h similarity index 100% rename from src/USER-INTEL/improper_cvff_intel.h rename to src/INTEL/improper_cvff_intel.h diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/INTEL/improper_harmonic_intel.cpp similarity index 99% rename from src/USER-INTEL/improper_harmonic_intel.cpp rename to src/INTEL/improper_harmonic_intel.cpp index c5bf84b2d5..b3d4c342d9 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/INTEL/improper_harmonic_intel.cpp @@ -89,7 +89,7 @@ void ImproperHarmonicIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/improper_harmonic_intel.h b/src/INTEL/improper_harmonic_intel.h similarity index 100% rename from src/USER-INTEL/improper_harmonic_intel.h rename to src/INTEL/improper_harmonic_intel.h diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/INTEL/intel_buffers.cpp similarity index 100% rename from src/USER-INTEL/intel_buffers.cpp rename to src/INTEL/intel_buffers.cpp diff --git a/src/USER-INTEL/intel_buffers.h b/src/INTEL/intel_buffers.h similarity index 100% rename from src/USER-INTEL/intel_buffers.h rename to src/INTEL/intel_buffers.h diff --git a/src/USER-INTEL/intel_intrinsics.h b/src/INTEL/intel_intrinsics.h similarity index 100% rename from src/USER-INTEL/intel_intrinsics.h rename to src/INTEL/intel_intrinsics.h diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/INTEL/intel_intrinsics_airebo.h similarity index 100% rename from src/USER-INTEL/intel_intrinsics_airebo.h rename to src/INTEL/intel_intrinsics_airebo.h diff --git a/src/USER-INTEL/intel_preprocess.h b/src/INTEL/intel_preprocess.h similarity index 99% rename from src/USER-INTEL/intel_preprocess.h rename to src/INTEL/intel_preprocess.h index c082bb237f..6f9b37a700 100644 --- a/src/USER-INTEL/intel_preprocess.h +++ b/src/INTEL/intel_preprocess.h @@ -43,7 +43,7 @@ // LAMMPS_MEMALIGN is set to 64 by default for -DLMP_USER_INTEL // so we only need to error out in case of a different alignment #if LAMMPS_MEMALIGN && (LAMMPS_MEMALIGN != 64) -#error Please set -DLAMMPS_MEMALIGN=64 in CCFLAGS of your LAMMPS makefile for USER-INTEL package +#error Please set -DLAMMPS_MEMALIGN=64 in CCFLAGS of your LAMMPS makefile for INTEL package #endif #if defined(_OPENMP) diff --git a/src/USER-INTEL/intel_simd.h b/src/INTEL/intel_simd.h similarity index 100% rename from src/USER-INTEL/intel_simd.h rename to src/INTEL/intel_simd.h diff --git a/src/USER-INTEL/math_extra_intel.h b/src/INTEL/math_extra_intel.h similarity index 100% rename from src/USER-INTEL/math_extra_intel.h rename to src/INTEL/math_extra_intel.h diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/INTEL/nbin_intel.cpp similarity index 99% rename from src/USER-INTEL/nbin_intel.cpp rename to src/INTEL/nbin_intel.cpp index 5227b6c521..94f18002a0 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/INTEL/nbin_intel.cpp @@ -68,7 +68,7 @@ NBinIntel::~NBinIntel() { void NBinIntel::bin_atoms_setup(int nall) { // binhead = per-bin vector, mbins in length - // add 1 bin for USER-INTEL package + // add 1 bin for INTEL package if (mbins > maxbin) { #ifdef _LMP_INTEL_OFFLOAD diff --git a/src/USER-INTEL/nbin_intel.h b/src/INTEL/nbin_intel.h similarity index 100% rename from src/USER-INTEL/nbin_intel.h rename to src/INTEL/nbin_intel.h diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/INTEL/npair_full_bin_ghost_intel.cpp similarity index 99% rename from src/USER-INTEL/npair_full_bin_ghost_intel.cpp rename to src/INTEL/npair_full_bin_ghost_intel.cpp index 50f98bf746..082f95721f 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/INTEL/npair_full_bin_ghost_intel.cpp @@ -42,11 +42,11 @@ void NPairFullBinGhostIntel::build(NeighList *list) #ifdef _LMP_INTEL_OFFLOAD if (_fix->offload_noghost()) error->all(FLERR, - "The 'ghost no' option cannot be used with this USER-INTEL pair style."); + "The 'ghost no' option cannot be used with this INTEL pair style."); #endif if (nstencil > INTEL_MAX_STENCIL_CHECK) - error->all(FLERR, "Too many neighbor bins for USER-INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package."); #ifdef _LMP_INTEL_OFFLOAD if (exclude) diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.h b/src/INTEL/npair_full_bin_ghost_intel.h similarity index 100% rename from src/USER-INTEL/npair_full_bin_ghost_intel.h rename to src/INTEL/npair_full_bin_ghost_intel.h diff --git a/src/USER-INTEL/npair_full_bin_intel.cpp b/src/INTEL/npair_full_bin_intel.cpp similarity index 98% rename from src/USER-INTEL/npair_full_bin_intel.cpp rename to src/INTEL/npair_full_bin_intel.cpp index 4b84c72081..82c73ec940 100644 --- a/src/USER-INTEL/npair_full_bin_intel.cpp +++ b/src/INTEL/npair_full_bin_intel.cpp @@ -37,7 +37,7 @@ NPairFullBinIntel::NPairFullBinIntel(LAMMPS *lmp) : NPairIntel(lmp) {} void NPairFullBinIntel::build(NeighList *list) { if (nstencil > INTEL_MAX_STENCIL_CHECK) - error->all(FLERR, "Too many neighbor bins for USER-INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package."); #ifdef _LMP_INTEL_OFFLOAD if (exclude) diff --git a/src/USER-INTEL/npair_full_bin_intel.h b/src/INTEL/npair_full_bin_intel.h similarity index 100% rename from src/USER-INTEL/npair_full_bin_intel.h rename to src/INTEL/npair_full_bin_intel.h diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.cpp b/src/INTEL/npair_half_bin_newton_intel.cpp similarity index 98% rename from src/USER-INTEL/npair_half_bin_newton_intel.cpp rename to src/INTEL/npair_half_bin_newton_intel.cpp index abaddde84c..21145ad647 100644 --- a/src/USER-INTEL/npair_half_bin_newton_intel.cpp +++ b/src/INTEL/npair_half_bin_newton_intel.cpp @@ -39,7 +39,7 @@ NPairHalfBinNewtonIntel::NPairHalfBinNewtonIntel(LAMMPS *lmp) : void NPairHalfBinNewtonIntel::build(NeighList *list) { if (nstencil / 2 > INTEL_MAX_STENCIL_CHECK) - error->all(FLERR, "Too many neighbor bins for USER-INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package."); #ifdef _LMP_INTEL_OFFLOAD if (exclude) diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.h b/src/INTEL/npair_half_bin_newton_intel.h similarity index 100% rename from src/USER-INTEL/npair_half_bin_newton_intel.h rename to src/INTEL/npair_half_bin_newton_intel.h diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp b/src/INTEL/npair_half_bin_newton_tri_intel.cpp similarity index 98% rename from src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp rename to src/INTEL/npair_half_bin_newton_tri_intel.cpp index 264407b1bf..1ad4d5fc68 100644 --- a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp +++ b/src/INTEL/npair_half_bin_newton_tri_intel.cpp @@ -39,7 +39,7 @@ NPairHalfBinNewtonTriIntel::NPairHalfBinNewtonTriIntel(LAMMPS *lmp) : void NPairHalfBinNewtonTriIntel::build(NeighList *list) { if (nstencil > INTEL_MAX_STENCIL) - error->all(FLERR, "Too many neighbor bins for USER-INTEL package."); + error->all(FLERR, "Too many neighbor bins for INTEL package."); #ifdef _LMP_INTEL_OFFLOAD if (exclude) diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.h b/src/INTEL/npair_half_bin_newton_tri_intel.h similarity index 100% rename from src/USER-INTEL/npair_half_bin_newton_tri_intel.h rename to src/INTEL/npair_half_bin_newton_tri_intel.h diff --git a/src/USER-INTEL/npair_halffull_newtoff_intel.h b/src/INTEL/npair_halffull_newtoff_intel.h similarity index 100% rename from src/USER-INTEL/npair_halffull_newtoff_intel.h rename to src/INTEL/npair_halffull_newtoff_intel.h diff --git a/src/USER-INTEL/npair_halffull_newton_intel.cpp b/src/INTEL/npair_halffull_newton_intel.cpp similarity index 100% rename from src/USER-INTEL/npair_halffull_newton_intel.cpp rename to src/INTEL/npair_halffull_newton_intel.cpp diff --git a/src/USER-INTEL/npair_halffull_newton_intel.h b/src/INTEL/npair_halffull_newton_intel.h similarity index 100% rename from src/USER-INTEL/npair_halffull_newton_intel.h rename to src/INTEL/npair_halffull_newton_intel.h diff --git a/src/USER-INTEL/npair_intel.cpp b/src/INTEL/npair_intel.cpp similarity index 100% rename from src/USER-INTEL/npair_intel.cpp rename to src/INTEL/npair_intel.cpp diff --git a/src/USER-INTEL/npair_intel.h b/src/INTEL/npair_intel.h similarity index 98% rename from src/USER-INTEL/npair_intel.h rename to src/INTEL/npair_intel.h index 7c21e683ad..8035f6f9be 100644 --- a/src/USER-INTEL/npair_intel.h +++ b/src/INTEL/npair_intel.h @@ -113,7 +113,7 @@ E: The 'package intel' command is required for /intel styles Self explanatory. -E: Too many neighbor bins for USER-INTEL package. +E: Too many neighbor bins for INTEL package. The number of bins used in the stencil to check for neighboring atoms is too high for the Intel package. Either increase the bin size in the input script diff --git a/src/USER-INTEL/npair_skip_intel.cpp b/src/INTEL/npair_skip_intel.cpp similarity index 100% rename from src/USER-INTEL/npair_skip_intel.cpp rename to src/INTEL/npair_skip_intel.cpp diff --git a/src/USER-INTEL/npair_skip_intel.h b/src/INTEL/npair_skip_intel.h similarity index 100% rename from src/USER-INTEL/npair_skip_intel.h rename to src/INTEL/npair_skip_intel.h diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/INTEL/pair_airebo_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_airebo_intel.cpp rename to src/INTEL/pair_airebo_intel.cpp index 12afce046b..8b2eadbe72 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/INTEL/pair_airebo_intel.cpp @@ -293,7 +293,7 @@ void PairAIREBOIntel::compute( ) { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); pvector[0] = pvector[1] = pvector[2] = 0.0; diff --git a/src/USER-INTEL/pair_airebo_intel.h b/src/INTEL/pair_airebo_intel.h similarity index 100% rename from src/USER-INTEL/pair_airebo_intel.h rename to src/INTEL/pair_airebo_intel.h diff --git a/src/USER-INTEL/pair_airebo_morse_intel.cpp b/src/INTEL/pair_airebo_morse_intel.cpp similarity index 100% rename from src/USER-INTEL/pair_airebo_morse_intel.cpp rename to src/INTEL/pair_airebo_morse_intel.cpp diff --git a/src/USER-INTEL/pair_airebo_morse_intel.h b/src/INTEL/pair_airebo_morse_intel.h similarity index 100% rename from src/USER-INTEL/pair_airebo_morse_intel.h rename to src/INTEL/pair_airebo_morse_intel.h diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/INTEL/pair_buck_coul_cut_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_buck_coul_cut_intel.cpp rename to src/INTEL/pair_buck_coul_cut_intel.cpp index e2ff70e392..1859edb732 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/INTEL/pair_buck_coul_cut_intel.cpp @@ -76,7 +76,7 @@ void PairBuckCoulCutIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.h b/src/INTEL/pair_buck_coul_cut_intel.h similarity index 100% rename from src/USER-INTEL/pair_buck_coul_cut_intel.h rename to src/INTEL/pair_buck_coul_cut_intel.h diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/INTEL/pair_buck_coul_long_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_buck_coul_long_intel.cpp rename to src/INTEL/pair_buck_coul_long_intel.cpp index 689a874bce..dc5eed7521 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/INTEL/pair_buck_coul_long_intel.cpp @@ -76,7 +76,7 @@ void PairBuckCoulLongIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.h b/src/INTEL/pair_buck_coul_long_intel.h similarity index 100% rename from src/USER-INTEL/pair_buck_coul_long_intel.h rename to src/INTEL/pair_buck_coul_long_intel.h diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/INTEL/pair_buck_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_buck_intel.cpp rename to src/INTEL/pair_buck_intel.cpp index 017774f8f6..23f7852486 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/INTEL/pair_buck_intel.cpp @@ -69,7 +69,7 @@ void PairBuckIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_buck_intel.h b/src/INTEL/pair_buck_intel.h similarity index 100% rename from src/USER-INTEL/pair_buck_intel.h rename to src/INTEL/pair_buck_intel.h diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/INTEL/pair_dpd_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_dpd_intel.cpp rename to src/INTEL/pair_dpd_intel.cpp index 18c039572b..0e872efdf6 100644 --- a/src/USER-INTEL/pair_dpd_intel.cpp +++ b/src/INTEL/pair_dpd_intel.cpp @@ -85,7 +85,7 @@ void PairDPDIntel::compute(int eflag, int vflag, { ev_init(eflag, vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_dpd_intel.h b/src/INTEL/pair_dpd_intel.h similarity index 100% rename from src/USER-INTEL/pair_dpd_intel.h rename to src/INTEL/pair_dpd_intel.h diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/INTEL/pair_eam_alloy_intel.cpp similarity index 100% rename from src/USER-INTEL/pair_eam_alloy_intel.cpp rename to src/INTEL/pair_eam_alloy_intel.cpp diff --git a/src/USER-INTEL/pair_eam_alloy_intel.h b/src/INTEL/pair_eam_alloy_intel.h similarity index 100% rename from src/USER-INTEL/pair_eam_alloy_intel.h rename to src/INTEL/pair_eam_alloy_intel.h diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/INTEL/pair_eam_fs_intel.cpp similarity index 100% rename from src/USER-INTEL/pair_eam_fs_intel.cpp rename to src/INTEL/pair_eam_fs_intel.cpp diff --git a/src/USER-INTEL/pair_eam_fs_intel.h b/src/INTEL/pair_eam_fs_intel.h similarity index 100% rename from src/USER-INTEL/pair_eam_fs_intel.h rename to src/INTEL/pair_eam_fs_intel.h diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/INTEL/pair_eam_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_eam_intel.cpp rename to src/INTEL/pair_eam_intel.cpp index 58573eca5f..04724f599c 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/INTEL/pair_eam_intel.cpp @@ -81,7 +81,7 @@ void PairEAMIntel::compute(int eflag, int vflag, { ev_init(eflag, vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_eam_intel.h b/src/INTEL/pair_eam_intel.h similarity index 100% rename from src/USER-INTEL/pair_eam_intel.h rename to src/INTEL/pair_eam_intel.h diff --git a/src/USER-INTEL/pair_gayberne_intel.cpp b/src/INTEL/pair_gayberne_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_gayberne_intel.cpp rename to src/INTEL/pair_gayberne_intel.cpp index e51b7758e6..8b81b1ea81 100644 --- a/src/USER-INTEL/pair_gayberne_intel.cpp +++ b/src/INTEL/pair_gayberne_intel.cpp @@ -75,7 +75,7 @@ void PairGayBerneIntel::compute(int eflag, int vflag, { ev_init(eflag, vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nall = atom->nlocal + atom->nghost; diff --git a/src/USER-INTEL/pair_gayberne_intel.h b/src/INTEL/pair_gayberne_intel.h similarity index 100% rename from src/USER-INTEL/pair_gayberne_intel.h rename to src/INTEL/pair_gayberne_intel.h diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp rename to src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp index 59809cc839..f67f5156b8 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -72,7 +72,7 @@ void PairLJCharmmCoulCharmmIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h b/src/INTEL/pair_lj_charmm_coul_charmm_intel.h similarity index 100% rename from src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h rename to src/INTEL/pair_lj_charmm_coul_charmm_intel.h diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/INTEL/pair_lj_charmm_coul_long_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp rename to src/INTEL/pair_lj_charmm_coul_long_intel.cpp index 0ce7e1e1fd..40a18be7d5 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp +++ b/src/INTEL/pair_lj_charmm_coul_long_intel.cpp @@ -73,7 +73,7 @@ void PairLJCharmmCoulLongIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h b/src/INTEL/pair_lj_charmm_coul_long_intel.h similarity index 100% rename from src/USER-INTEL/pair_lj_charmm_coul_long_intel.h rename to src/INTEL/pair_lj_charmm_coul_long_intel.h diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/INTEL/pair_lj_cut_coul_long_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp rename to src/INTEL/pair_lj_cut_coul_long_intel.cpp index 9e024b35c8..47d14186f6 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/INTEL/pair_lj_cut_coul_long_intel.cpp @@ -75,7 +75,7 @@ void PairLJCutCoulLongIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.h b/src/INTEL/pair_lj_cut_coul_long_intel.h similarity index 100% rename from src/USER-INTEL/pair_lj_cut_coul_long_intel.h rename to src/INTEL/pair_lj_cut_coul_long_intel.h diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/INTEL/pair_lj_cut_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_lj_cut_intel.cpp rename to src/INTEL/pair_lj_cut_intel.cpp index 029b1eca5b..71e12d7b24 100644 --- a/src/USER-INTEL/pair_lj_cut_intel.cpp +++ b/src/INTEL/pair_lj_cut_intel.cpp @@ -65,7 +65,7 @@ void PairLJCutIntel::compute(int eflag, int vflag, { ev_init(eflag, vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_lj_cut_intel.h b/src/INTEL/pair_lj_cut_intel.h similarity index 100% rename from src/USER-INTEL/pair_lj_cut_intel.h rename to src/INTEL/pair_lj_cut_intel.h diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp b/src/INTEL/pair_lj_long_coul_long_intel.cpp similarity index 100% rename from src/USER-INTEL/pair_lj_long_coul_long_intel.cpp rename to src/INTEL/pair_lj_long_coul_long_intel.cpp diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.h b/src/INTEL/pair_lj_long_coul_long_intel.h similarity index 100% rename from src/USER-INTEL/pair_lj_long_coul_long_intel.h rename to src/INTEL/pair_lj_long_coul_long_intel.h diff --git a/src/USER-INTEL/pair_rebo_intel.cpp b/src/INTEL/pair_rebo_intel.cpp similarity index 100% rename from src/USER-INTEL/pair_rebo_intel.cpp rename to src/INTEL/pair_rebo_intel.cpp diff --git a/src/USER-INTEL/pair_rebo_intel.h b/src/INTEL/pair_rebo_intel.h similarity index 100% rename from src/USER-INTEL/pair_rebo_intel.h rename to src/INTEL/pair_rebo_intel.h diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/INTEL/pair_sw_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_sw_intel.cpp rename to src/INTEL/pair_sw_intel.cpp index b7c92bf1ee..421e8b2fc5 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/INTEL/pair_sw_intel.cpp @@ -96,7 +96,7 @@ void PairSWIntel::compute(int eflag, int vflag, { ev_init(eflag, vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_sw_intel.h b/src/INTEL/pair_sw_intel.h similarity index 100% rename from src/USER-INTEL/pair_sw_intel.h rename to src/INTEL/pair_sw_intel.h diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/INTEL/pair_tersoff_intel.cpp similarity index 99% rename from src/USER-INTEL/pair_tersoff_intel.cpp rename to src/INTEL/pair_tersoff_intel.cpp index 975b600bfa..707e8404ff 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/INTEL/pair_tersoff_intel.cpp @@ -110,7 +110,7 @@ void PairTersoffIntel::compute(int eflag, int vflag, { ev_init(eflag,vflag); if (vflag_atom) - error->all(FLERR,"USER-INTEL package does not support per-atom stress"); + error->all(FLERR,"INTEL package does not support per-atom stress"); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_tersoff_intel.h b/src/INTEL/pair_tersoff_intel.h similarity index 100% rename from src/USER-INTEL/pair_tersoff_intel.h rename to src/INTEL/pair_tersoff_intel.h diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/INTEL/pppm_disp_intel.cpp similarity index 99% rename from src/USER-INTEL/pppm_disp_intel.cpp rename to src/INTEL/pppm_disp_intel.cpp index ff045983db..8d4ed1778d 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/INTEL/pppm_disp_intel.cpp @@ -160,7 +160,7 @@ void PPPMDispIntel::init() precompute_rho(); } if (order > INTEL_P3M_MAXORDER) - error->all(FLERR,"PPPM order greater than supported by USER-INTEL\n"); + error->all(FLERR,"PPPM order greater than supported by INTEL\n"); } /* ---------------------------------------------------------------------- diff --git a/src/USER-INTEL/pppm_disp_intel.h b/src/INTEL/pppm_disp_intel.h similarity index 100% rename from src/USER-INTEL/pppm_disp_intel.h rename to src/INTEL/pppm_disp_intel.h diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/INTEL/pppm_intel.cpp similarity index 99% rename from src/USER-INTEL/pppm_intel.cpp rename to src/INTEL/pppm_intel.cpp index b369e25284..8b0542d770 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/INTEL/pppm_intel.cpp @@ -135,7 +135,7 @@ void PPPMIntel::init() } if (order > INTEL_P3M_MAXORDER) - error->all(FLERR,"PPPM order greater than supported by USER-INTEL\n"); + error->all(FLERR,"PPPM order greater than supported by INTEL\n"); } diff --git a/src/USER-INTEL/pppm_intel.h b/src/INTEL/pppm_intel.h similarity index 96% rename from src/USER-INTEL/pppm_intel.h rename to src/INTEL/pppm_intel.h index b6ffe206b1..c0e66996c1 100644 --- a/src/USER-INTEL/pppm_intel.h +++ b/src/INTEL/pppm_intel.h @@ -116,9 +116,9 @@ class PPPMIntel : public PPPM { /* ERROR/WARNING messages: -E: PPPM order greater than supported by USER-INTEL +E: PPPM order greater than supported by INTEL There is a compile time limit on the maximum order for PPPM -in the USER-INTEL package that might be different from LAMMPS +in the INTEL package that might be different from LAMMPS */ diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/INTEL/verlet_lrt_intel.cpp similarity index 100% rename from src/USER-INTEL/verlet_lrt_intel.cpp rename to src/INTEL/verlet_lrt_intel.cpp diff --git a/src/USER-INTEL/verlet_lrt_intel.h b/src/INTEL/verlet_lrt_intel.h similarity index 100% rename from src/USER-INTEL/verlet_lrt_intel.h rename to src/INTEL/verlet_lrt_intel.h diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index a8527989d7..ce97510d7a 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -83,7 +83,7 @@ AtomKokkos::~AtomKokkos() memoryKK->destroy_kokkos(k_fm, fm); memoryKK->destroy_kokkos(k_fm_long, fm_long); - // USER-DPD package + // DPD-REACT package memoryKK->destroy_kokkos(k_uCond,uCond); memoryKK->destroy_kokkos(k_uMech,uMech); memoryKK->destroy_kokkos(k_uChem,uChem); diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index e807180f35..1c3953ddf3 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -61,7 +61,7 @@ class AtomKokkos : public Atom { DAT::tdual_f_array k_fm; DAT::tdual_f_array k_fm_long; -// USER-DPD package +// DPD-REACT package DAT::tdual_efloat_1d k_uCond, k_uMech, k_uChem, k_uCG, k_uCGnew, k_rho,k_dpdTheta,k_duChem; diff --git a/src/KOKKOS/min_kokkos.cpp b/src/KOKKOS/min_kokkos.cpp index aaf883c881..715d77f293 100644 --- a/src/KOKKOS/min_kokkos.cpp +++ b/src/KOKKOS/min_kokkos.cpp @@ -348,7 +348,7 @@ void MinKokkos::setup_minimal(int flag) void MinKokkos::run(int n) { if (nextra_atom) - error->all(FLERR,"Cannot yet use extra atom DOFs (e.g. USER-AWPMD and USER-EFF packages) " + error->all(FLERR,"Cannot yet use extra atom DOFs (e.g. AWPMD and EFF packages) " "with Kokkos minimize"); // minimizer iterations diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index eed0026af3..a7db309b1d 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -190,7 +190,7 @@ void NeighBondKokkos::init_topology_kk() { /* ---------------------------------------------------------------------- build all topology neighbor lists every few timesteps - normally built with pair lists, but USER-CUDA separates them + normally built with pair lists, but CUDA separates them ------------------------------------------------------------------------- */ template diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp index e4a2b02cc0..207ff7501b 100644 --- a/src/KOKKOS/neighbor_kokkos.cpp +++ b/src/KOKKOS/neighbor_kokkos.cpp @@ -226,7 +226,7 @@ void NeighborKokkos::operator()(TagNeighborCheckDistance, const int /* ---------------------------------------------------------------------- build perpetuals neighbor lists called at setup and every few timesteps during run or minimization - topology lists also built if topoflag = 1, USER-CUDA calls with topoflag = 0 + topology lists also built if topoflag = 1, CUDA calls with topoflag = 0 ------------------------------------------------------------------------- */ @@ -377,7 +377,7 @@ void NeighborKokkos::init_topology() { /* ---------------------------------------------------------------------- build all topology neighbor lists every few timesteps - normally built with pair lists, but USER-CUDA separates them + normally built with pair lists, but CUDA separates them ------------------------------------------------------------------------- */ void NeighborKokkos::build_topology() { diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 2385d1977a..dbda29d807 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -1532,7 +1532,7 @@ void PPPMKokkos::operator()(TagPPPM_make_rho_atomic, const int &i) c template KOKKOS_INLINE_FUNCTION void PPPMKokkos::operator() (TagPPPM_make_rho, typename Kokkos::TeamPolicy::member_type dev) const { - // adapted from USER-OMP/pppm.cpp: + // adapted from OPENMP/pppm.cpp: // determine range of grid points handled by this thread int tid = dev.league_rank(); diff --git a/src/USER-LB/README b/src/LATBOLTZ/README similarity index 98% rename from src/USER-LB/README rename to src/LATBOLTZ/README index 4f22986d84..6f2e06178c 100644 --- a/src/USER-LB/README +++ b/src/LATBOLTZ/README @@ -16,7 +16,7 @@ brief descriptions of other fixes below, each of which have their own doc page. There are example scripts for using this package in -examples/USER/lb. +examples/PACKAGES/latboltz. IMPORTANT NOTE: This package can only be used if LAMMPS is compiled with MPI (i.e. the serial makefile should not be used to compile the diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/LATBOLTZ/fix_lb_fluid.cpp similarity index 100% rename from src/USER-LB/fix_lb_fluid.cpp rename to src/LATBOLTZ/fix_lb_fluid.cpp diff --git a/src/USER-LB/fix_lb_fluid.h b/src/LATBOLTZ/fix_lb_fluid.h similarity index 98% rename from src/USER-LB/fix_lb_fluid.h rename to src/LATBOLTZ/fix_lb_fluid.h index 3b0ce872ba..0842acbe64 100644 --- a/src/USER-LB/fix_lb_fluid.h +++ b/src/LATBOLTZ/fix_lb_fluid.h @@ -23,7 +23,7 @@ FixStyle(lb/fluid,FixLbFluid); #include "fix.h" #if defined(MPI_STUBS) -#error "The USER-LB package cannot be compiled in serial with MPI STUBS" +#error "The LATBOLTZ package cannot be compiled in serial with MPI STUBS" #endif namespace LAMMPS_NS { diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/LATBOLTZ/fix_lb_momentum.cpp similarity index 100% rename from src/USER-LB/fix_lb_momentum.cpp rename to src/LATBOLTZ/fix_lb_momentum.cpp diff --git a/src/USER-LB/fix_lb_momentum.h b/src/LATBOLTZ/fix_lb_momentum.h similarity index 100% rename from src/USER-LB/fix_lb_momentum.h rename to src/LATBOLTZ/fix_lb_momentum.h diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/LATBOLTZ/fix_lb_pc.cpp similarity index 100% rename from src/USER-LB/fix_lb_pc.cpp rename to src/LATBOLTZ/fix_lb_pc.cpp diff --git a/src/USER-LB/fix_lb_pc.h b/src/LATBOLTZ/fix_lb_pc.h similarity index 100% rename from src/USER-LB/fix_lb_pc.h rename to src/LATBOLTZ/fix_lb_pc.h diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/LATBOLTZ/fix_lb_rigid_pc_sphere.cpp similarity index 100% rename from src/USER-LB/fix_lb_rigid_pc_sphere.cpp rename to src/LATBOLTZ/fix_lb_rigid_pc_sphere.cpp diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.h b/src/LATBOLTZ/fix_lb_rigid_pc_sphere.h similarity index 100% rename from src/USER-LB/fix_lb_rigid_pc_sphere.h rename to src/LATBOLTZ/fix_lb_rigid_pc_sphere.h diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/LATBOLTZ/fix_lb_viscous.cpp similarity index 100% rename from src/USER-LB/fix_lb_viscous.cpp rename to src/LATBOLTZ/fix_lb_viscous.cpp diff --git a/src/USER-LB/fix_lb_viscous.h b/src/LATBOLTZ/fix_lb_viscous.h similarity index 100% rename from src/USER-LB/fix_lb_viscous.h rename to src/LATBOLTZ/fix_lb_viscous.h diff --git a/src/USER-SMD/Install.sh b/src/MACHDYN/Install.sh similarity index 61% rename from src/USER-SMD/Install.sh rename to src/MACHDYN/Install.sh index cb9aa5452b..bf18c332f3 100755 --- a/src/USER-SMD/Install.sh +++ b/src/MACHDYN/Install.sh @@ -37,29 +37,29 @@ done if (test $1 = 1) then if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*smd[^ \t]* //g' ../Makefile.package - sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/smd/includelink |' ../Makefile.package - sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(user-smd_SYSINC) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-smd_SYSLIB) |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-smd_SYSPATH) |' ../Makefile.package + sed -i -e 's/[^ \t]*machdyn[^ \t]* //g' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/machdyn/includelink |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(machdyn_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(machdyn_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(machdyn_SYSPATH) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*smd.*$/d' ../Makefile.package.settings + sed -i -e '/^include.*machdyn.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ -include ..\/..\/lib\/smd\/Makefile.lammps +include ..\/..\/lib\/machdyn\/Makefile.lammps ' ../Makefile.package.settings fi elif (test $1 = 0) then if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*smd[^ \t]* //g' ../Makefile.package + sed -i -e 's/[^ \t]*machdyn[^ \t]* //g' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*smd.*$/d' ../Makefile.package.settings + sed -i -e '/^include.*machdyn.*$/d' ../Makefile.package.settings fi fi diff --git a/src/USER-SMD/README b/src/MACHDYN/README similarity index 92% rename from src/USER-SMD/README rename to src/MACHDYN/README index 924157ac97..4bbf3cb3a9 100644 --- a/src/USER-SMD/README +++ b/src/MACHDYN/README @@ -19,7 +19,7 @@ from *.STL files. See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started. -There are example scripts for using this package in examples/USER/smd. +There are example scripts for using this package in examples/PACKAGES/machdyn. The person who created this package is Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/MACHDYN/atom_vec_smd.cpp similarity index 99% rename from src/USER-SMD/atom_vec_smd.cpp rename to src/MACHDYN/atom_vec_smd.cpp index 2cae7517ec..b798425e19 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/MACHDYN/atom_vec_smd.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/atom_vec_smd.h b/src/MACHDYN/atom_vec_smd.h similarity index 97% rename from src/USER-SMD/atom_vec_smd.h rename to src/MACHDYN/atom_vec_smd.h index 8ad6448bba..ada2c2c936 100644 --- a/src/USER-SMD/atom_vec_smd.h +++ b/src/MACHDYN/atom_vec_smd.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/MACHDYN/compute_smd_contact_radius.cpp similarity index 98% rename from src/USER-SMD/compute_smd_contact_radius.cpp rename to src/MACHDYN/compute_smd_contact_radius.cpp index 82186c96b4..7a10b563f8 100644 --- a/src/USER-SMD/compute_smd_contact_radius.cpp +++ b/src/MACHDYN/compute_smd_contact_radius.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_contact_radius.h b/src/MACHDYN/compute_smd_contact_radius.h similarity index 96% rename from src/USER-SMD/compute_smd_contact_radius.h rename to src/MACHDYN/compute_smd_contact_radius.h index 503ae386a7..87f3208dd3 100644 --- a/src/USER-SMD/compute_smd_contact_radius.h +++ b/src/MACHDYN/compute_smd_contact_radius.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/MACHDYN/compute_smd_damage.cpp similarity index 98% rename from src/USER-SMD/compute_smd_damage.cpp rename to src/MACHDYN/compute_smd_damage.cpp index 23a74123bf..f3b52ccfce 100644 --- a/src/USER-SMD/compute_smd_damage.cpp +++ b/src/MACHDYN/compute_smd_damage.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_damage.h b/src/MACHDYN/compute_smd_damage.h similarity index 96% rename from src/USER-SMD/compute_smd_damage.h rename to src/MACHDYN/compute_smd_damage.h index 21956c9819..ac1fcb1bb4 100644 --- a/src/USER-SMD/compute_smd_damage.h +++ b/src/MACHDYN/compute_smd_damage.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_hourglass_error.cpp b/src/MACHDYN/compute_smd_hourglass_error.cpp similarity index 98% rename from src/USER-SMD/compute_smd_hourglass_error.cpp rename to src/MACHDYN/compute_smd_hourglass_error.cpp index 53289c6d12..b0d01d2b14 100644 --- a/src/USER-SMD/compute_smd_hourglass_error.cpp +++ b/src/MACHDYN/compute_smd_hourglass_error.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_hourglass_error.h b/src/MACHDYN/compute_smd_hourglass_error.h similarity index 96% rename from src/USER-SMD/compute_smd_hourglass_error.h rename to src/MACHDYN/compute_smd_hourglass_error.h index b7e513f182..32b5b90d56 100644 --- a/src/USER-SMD/compute_smd_hourglass_error.h +++ b/src/MACHDYN/compute_smd_hourglass_error.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/MACHDYN/compute_smd_internal_energy.cpp similarity index 98% rename from src/USER-SMD/compute_smd_internal_energy.cpp rename to src/MACHDYN/compute_smd_internal_energy.cpp index aa59d7cc00..0d17588b13 100644 --- a/src/USER-SMD/compute_smd_internal_energy.cpp +++ b/src/MACHDYN/compute_smd_internal_energy.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_internal_energy.h b/src/MACHDYN/compute_smd_internal_energy.h similarity index 96% rename from src/USER-SMD/compute_smd_internal_energy.h rename to src/MACHDYN/compute_smd_internal_energy.h index 3277bf028c..b4aaaf6b40 100644 --- a/src/USER-SMD/compute_smd_internal_energy.h +++ b/src/MACHDYN/compute_smd_internal_energy.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/MACHDYN/compute_smd_plastic_strain.cpp similarity index 98% rename from src/USER-SMD/compute_smd_plastic_strain.cpp rename to src/MACHDYN/compute_smd_plastic_strain.cpp index 5d98650226..3f5fbdf090 100644 --- a/src/USER-SMD/compute_smd_plastic_strain.cpp +++ b/src/MACHDYN/compute_smd_plastic_strain.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_plastic_strain.h b/src/MACHDYN/compute_smd_plastic_strain.h similarity index 96% rename from src/USER-SMD/compute_smd_plastic_strain.h rename to src/MACHDYN/compute_smd_plastic_strain.h index 92409afbf8..7e319610a3 100644 --- a/src/USER-SMD/compute_smd_plastic_strain.h +++ b/src/MACHDYN/compute_smd_plastic_strain.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/MACHDYN/compute_smd_plastic_strain_rate.cpp similarity index 98% rename from src/USER-SMD/compute_smd_plastic_strain_rate.cpp rename to src/MACHDYN/compute_smd_plastic_strain_rate.cpp index da9f4846cc..d215b0e321 100644 --- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp +++ b/src/MACHDYN/compute_smd_plastic_strain_rate.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.h b/src/MACHDYN/compute_smd_plastic_strain_rate.h similarity index 96% rename from src/USER-SMD/compute_smd_plastic_strain_rate.h rename to src/MACHDYN/compute_smd_plastic_strain_rate.h index 745b9ed3cc..d0ea09af26 100644 --- a/src/USER-SMD/compute_smd_plastic_strain_rate.h +++ b/src/MACHDYN/compute_smd_plastic_strain_rate.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/MACHDYN/compute_smd_rho.cpp similarity index 98% rename from src/USER-SMD/compute_smd_rho.cpp rename to src/MACHDYN/compute_smd_rho.cpp index cffe71ade3..f05c7c6e83 100644 --- a/src/USER-SMD/compute_smd_rho.cpp +++ b/src/MACHDYN/compute_smd_rho.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_rho.h b/src/MACHDYN/compute_smd_rho.h similarity index 96% rename from src/USER-SMD/compute_smd_rho.h rename to src/MACHDYN/compute_smd_rho.h index 85335bbce8..954caade5d 100644 --- a/src/USER-SMD/compute_smd_rho.h +++ b/src/MACHDYN/compute_smd_rho.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/MACHDYN/compute_smd_tlsph_defgrad.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_defgrad.cpp rename to src/MACHDYN/compute_smd_tlsph_defgrad.cpp index 0611dab47b..e8c78821dc 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp +++ b/src/MACHDYN/compute_smd_tlsph_defgrad.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.h b/src/MACHDYN/compute_smd_tlsph_defgrad.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_defgrad.h rename to src/MACHDYN/compute_smd_tlsph_defgrad.h index ece997771b..eed4066867 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.h +++ b/src/MACHDYN/compute_smd_tlsph_defgrad.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_dt.cpp b/src/MACHDYN/compute_smd_tlsph_dt.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_dt.cpp rename to src/MACHDYN/compute_smd_tlsph_dt.cpp index 8000de9c59..ca1973309f 100644 --- a/src/USER-SMD/compute_smd_tlsph_dt.cpp +++ b/src/MACHDYN/compute_smd_tlsph_dt.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_dt.h b/src/MACHDYN/compute_smd_tlsph_dt.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_dt.h rename to src/MACHDYN/compute_smd_tlsph_dt.h index 1fedd6d36d..e57db2dd74 100644 --- a/src/USER-SMD/compute_smd_tlsph_dt.h +++ b/src/MACHDYN/compute_smd_tlsph_dt.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp b/src/MACHDYN/compute_smd_tlsph_num_neighs.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_num_neighs.cpp rename to src/MACHDYN/compute_smd_tlsph_num_neighs.cpp index f7d95410ae..230a5946f8 100644 --- a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp +++ b/src/MACHDYN/compute_smd_tlsph_num_neighs.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.h b/src/MACHDYN/compute_smd_tlsph_num_neighs.h similarity index 97% rename from src/USER-SMD/compute_smd_tlsph_num_neighs.h rename to src/MACHDYN/compute_smd_tlsph_num_neighs.h index ad6311d60d..e3531a47ea 100644 --- a/src/USER-SMD/compute_smd_tlsph_num_neighs.h +++ b/src/MACHDYN/compute_smd_tlsph_num_neighs.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/MACHDYN/compute_smd_tlsph_shape.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_shape.cpp rename to src/MACHDYN/compute_smd_tlsph_shape.cpp index b2d38b2af2..1887de683c 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.cpp +++ b/src/MACHDYN/compute_smd_tlsph_shape.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_shape.h b/src/MACHDYN/compute_smd_tlsph_shape.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_shape.h rename to src/MACHDYN/compute_smd_tlsph_shape.h index c1b9b69bfb..76298cf30c 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.h +++ b/src/MACHDYN/compute_smd_tlsph_shape.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/MACHDYN/compute_smd_tlsph_strain.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_strain.cpp rename to src/MACHDYN/compute_smd_tlsph_strain.cpp index 19ce976509..30f158a3f1 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.cpp +++ b/src/MACHDYN/compute_smd_tlsph_strain.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_strain.h b/src/MACHDYN/compute_smd_tlsph_strain.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_strain.h rename to src/MACHDYN/compute_smd_tlsph_strain.h index f94385b7fe..426cb6dea9 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.h +++ b/src/MACHDYN/compute_smd_tlsph_strain.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/MACHDYN/compute_smd_tlsph_strain_rate.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_strain_rate.cpp rename to src/MACHDYN/compute_smd_tlsph_strain_rate.cpp index adb0bbcf6d..1889cbcc0f 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp +++ b/src/MACHDYN/compute_smd_tlsph_strain_rate.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.h b/src/MACHDYN/compute_smd_tlsph_strain_rate.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_strain_rate.h rename to src/MACHDYN/compute_smd_tlsph_strain_rate.h index 35d2a80519..7fd851725c 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain_rate.h +++ b/src/MACHDYN/compute_smd_tlsph_strain_rate.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/MACHDYN/compute_smd_tlsph_stress.cpp similarity index 98% rename from src/USER-SMD/compute_smd_tlsph_stress.cpp rename to src/MACHDYN/compute_smd_tlsph_stress.cpp index 75a06a45e9..038e09a3c0 100644 --- a/src/USER-SMD/compute_smd_tlsph_stress.cpp +++ b/src/MACHDYN/compute_smd_tlsph_stress.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_tlsph_stress.h b/src/MACHDYN/compute_smd_tlsph_stress.h similarity index 96% rename from src/USER-SMD/compute_smd_tlsph_stress.h rename to src/MACHDYN/compute_smd_tlsph_stress.h index 7bb0250620..4ef4199e48 100644 --- a/src/USER-SMD/compute_smd_tlsph_stress.h +++ b/src/MACHDYN/compute_smd_tlsph_stress.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_triangle_vertices.cpp b/src/MACHDYN/compute_smd_triangle_vertices.cpp similarity index 98% rename from src/USER-SMD/compute_smd_triangle_vertices.cpp rename to src/MACHDYN/compute_smd_triangle_vertices.cpp index c4b832faa3..016ae3e85f 100644 --- a/src/USER-SMD/compute_smd_triangle_vertices.cpp +++ b/src/MACHDYN/compute_smd_triangle_vertices.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_triangle_vertices.h b/src/MACHDYN/compute_smd_triangle_vertices.h similarity index 96% rename from src/USER-SMD/compute_smd_triangle_vertices.h rename to src/MACHDYN/compute_smd_triangle_vertices.h index fe369580aa..06be1a4e1a 100644 --- a/src/USER-SMD/compute_smd_triangle_vertices.h +++ b/src/MACHDYN/compute_smd_triangle_vertices.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_effm.cpp b/src/MACHDYN/compute_smd_ulsph_effm.cpp similarity index 98% rename from src/USER-SMD/compute_smd_ulsph_effm.cpp rename to src/MACHDYN/compute_smd_ulsph_effm.cpp index edf9355f20..24cae6b14e 100644 --- a/src/USER-SMD/compute_smd_ulsph_effm.cpp +++ b/src/MACHDYN/compute_smd_ulsph_effm.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_effm.h b/src/MACHDYN/compute_smd_ulsph_effm.h similarity index 96% rename from src/USER-SMD/compute_smd_ulsph_effm.h rename to src/MACHDYN/compute_smd_ulsph_effm.h index 8839f1dcbc..836a3d2a74 100644 --- a/src/USER-SMD/compute_smd_ulsph_effm.h +++ b/src/MACHDYN/compute_smd_ulsph_effm.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp b/src/MACHDYN/compute_smd_ulsph_num_neighs.cpp similarity index 98% rename from src/USER-SMD/compute_smd_ulsph_num_neighs.cpp rename to src/MACHDYN/compute_smd_ulsph_num_neighs.cpp index 5b900fc15d..7c181a6a82 100644 --- a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp +++ b/src/MACHDYN/compute_smd_ulsph_num_neighs.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.h b/src/MACHDYN/compute_smd_ulsph_num_neighs.h similarity index 97% rename from src/USER-SMD/compute_smd_ulsph_num_neighs.h rename to src/MACHDYN/compute_smd_ulsph_num_neighs.h index 75217d7685..527ba17737 100644 --- a/src/USER-SMD/compute_smd_ulsph_num_neighs.h +++ b/src/MACHDYN/compute_smd_ulsph_num_neighs.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/MACHDYN/compute_smd_ulsph_strain.cpp similarity index 98% rename from src/USER-SMD/compute_smd_ulsph_strain.cpp rename to src/MACHDYN/compute_smd_ulsph_strain.cpp index 3dbfc02391..eed26821b0 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain.cpp +++ b/src/MACHDYN/compute_smd_ulsph_strain.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_strain.h b/src/MACHDYN/compute_smd_ulsph_strain.h similarity index 96% rename from src/USER-SMD/compute_smd_ulsph_strain.h rename to src/MACHDYN/compute_smd_ulsph_strain.h index 6265a9ab5e..54f53f6782 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain.h +++ b/src/MACHDYN/compute_smd_ulsph_strain.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp b/src/MACHDYN/compute_smd_ulsph_strain_rate.cpp similarity index 98% rename from src/USER-SMD/compute_smd_ulsph_strain_rate.cpp rename to src/MACHDYN/compute_smd_ulsph_strain_rate.cpp index d44a6bac70..9e2709eb0a 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp +++ b/src/MACHDYN/compute_smd_ulsph_strain_rate.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.h b/src/MACHDYN/compute_smd_ulsph_strain_rate.h similarity index 96% rename from src/USER-SMD/compute_smd_ulsph_strain_rate.h rename to src/MACHDYN/compute_smd_ulsph_strain_rate.h index 8ccd5695c1..ab97d7a924 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain_rate.h +++ b/src/MACHDYN/compute_smd_ulsph_strain_rate.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/MACHDYN/compute_smd_ulsph_stress.cpp similarity index 98% rename from src/USER-SMD/compute_smd_ulsph_stress.cpp rename to src/MACHDYN/compute_smd_ulsph_stress.cpp index eadfbfc1b0..9aa75b76e8 100644 --- a/src/USER-SMD/compute_smd_ulsph_stress.cpp +++ b/src/MACHDYN/compute_smd_ulsph_stress.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_ulsph_stress.h b/src/MACHDYN/compute_smd_ulsph_stress.h similarity index 96% rename from src/USER-SMD/compute_smd_ulsph_stress.h rename to src/MACHDYN/compute_smd_ulsph_stress.h index bcb6098b64..6f3182f5f4 100644 --- a/src/USER-SMD/compute_smd_ulsph_stress.h +++ b/src/MACHDYN/compute_smd_ulsph_stress.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/MACHDYN/compute_smd_vol.cpp similarity index 98% rename from src/USER-SMD/compute_smd_vol.cpp rename to src/MACHDYN/compute_smd_vol.cpp index 873699a591..2fdc4e34d2 100644 --- a/src/USER-SMD/compute_smd_vol.cpp +++ b/src/MACHDYN/compute_smd_vol.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/compute_smd_vol.h b/src/MACHDYN/compute_smd_vol.h similarity index 96% rename from src/USER-SMD/compute_smd_vol.h rename to src/MACHDYN/compute_smd_vol.h index ab9143d41c..c0fd4550b4 100644 --- a/src/USER-SMD/compute_smd_vol.h +++ b/src/MACHDYN/compute_smd_vol.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/MACHDYN/fix_smd_adjust_dt.cpp similarity index 99% rename from src/USER-SMD/fix_smd_adjust_dt.cpp rename to src/MACHDYN/fix_smd_adjust_dt.cpp index dc5dbd08a9..f45364713a 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/MACHDYN/fix_smd_adjust_dt.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_adjust_dt.h b/src/MACHDYN/fix_smd_adjust_dt.h similarity index 97% rename from src/USER-SMD/fix_smd_adjust_dt.h rename to src/MACHDYN/fix_smd_adjust_dt.h index 5f6b350be3..41203cf472 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.h +++ b/src/MACHDYN/fix_smd_adjust_dt.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/MACHDYN/fix_smd_integrate_tlsph.cpp similarity index 99% rename from src/USER-SMD/fix_smd_integrate_tlsph.cpp rename to src/MACHDYN/fix_smd_integrate_tlsph.cpp index a8257dfebe..8bde3b3d07 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp +++ b/src/MACHDYN/fix_smd_integrate_tlsph.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.h b/src/MACHDYN/fix_smd_integrate_tlsph.h similarity index 97% rename from src/USER-SMD/fix_smd_integrate_tlsph.h rename to src/MACHDYN/fix_smd_integrate_tlsph.h index c5f86092a4..582b4588a4 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.h +++ b/src/MACHDYN/fix_smd_integrate_tlsph.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/MACHDYN/fix_smd_integrate_ulsph.cpp similarity index 99% rename from src/USER-SMD/fix_smd_integrate_ulsph.cpp rename to src/MACHDYN/fix_smd_integrate_ulsph.cpp index 2c9b71c400..967cf33095 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp +++ b/src/MACHDYN/fix_smd_integrate_ulsph.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.h b/src/MACHDYN/fix_smd_integrate_ulsph.h similarity index 96% rename from src/USER-SMD/fix_smd_integrate_ulsph.h rename to src/MACHDYN/fix_smd_integrate_ulsph.h index 36afceeaaa..af75685a4b 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.h +++ b/src/MACHDYN/fix_smd_integrate_ulsph.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/MACHDYN/fix_smd_move_triangulated_surface.cpp similarity index 99% rename from src/USER-SMD/fix_smd_move_triangulated_surface.cpp rename to src/MACHDYN/fix_smd_move_triangulated_surface.cpp index 15ba0ef828..c790720e99 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/MACHDYN/fix_smd_move_triangulated_surface.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.h b/src/MACHDYN/fix_smd_move_triangulated_surface.h similarity index 97% rename from src/USER-SMD/fix_smd_move_triangulated_surface.h rename to src/MACHDYN/fix_smd_move_triangulated_surface.h index 8fce159121..aec2fcb688 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.h +++ b/src/MACHDYN/fix_smd_move_triangulated_surface.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/MACHDYN/fix_smd_setvel.cpp similarity index 99% rename from src/USER-SMD/fix_smd_setvel.cpp rename to src/MACHDYN/fix_smd_setvel.cpp index c0c0fccd46..7b76e08ec6 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/MACHDYN/fix_smd_setvel.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/MACHDYN/fix_smd_setvel.h similarity index 97% rename from src/USER-SMD/fix_smd_setvel.h rename to src/MACHDYN/fix_smd_setvel.h index 8791d58c3f..1e91a8d602 100644 --- a/src/USER-SMD/fix_smd_setvel.h +++ b/src/MACHDYN/fix_smd_setvel.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp similarity index 99% rename from src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp rename to src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp index 77d8bcc804..32d96e3d7f 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/MACHDYN/fix_smd_tlsph_reference_configuration.h similarity index 97% rename from src/USER-SMD/fix_smd_tlsph_reference_configuration.h rename to src/MACHDYN/fix_smd_tlsph_reference_configuration.h index a5a26797e0..98108b8ffd 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h +++ b/src/MACHDYN/fix_smd_tlsph_reference_configuration.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/MACHDYN/fix_smd_wall_surface.cpp similarity index 100% rename from src/USER-SMD/fix_smd_wall_surface.cpp rename to src/MACHDYN/fix_smd_wall_surface.cpp diff --git a/src/USER-SMD/fix_smd_wall_surface.h b/src/MACHDYN/fix_smd_wall_surface.h similarity index 100% rename from src/USER-SMD/fix_smd_wall_surface.h rename to src/MACHDYN/fix_smd_wall_surface.h diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/MACHDYN/pair_smd_hertz.cpp similarity index 99% rename from src/USER-SMD/pair_smd_hertz.cpp rename to src/MACHDYN/pair_smd_hertz.cpp index 24e6802a14..a5355e46e0 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/MACHDYN/pair_smd_hertz.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_hertz.h b/src/MACHDYN/pair_smd_hertz.h similarity index 97% rename from src/USER-SMD/pair_smd_hertz.h rename to src/MACHDYN/pair_smd_hertz.h index 0d3c5b880b..b736764de3 100644 --- a/src/USER-SMD/pair_smd_hertz.h +++ b/src/MACHDYN/pair_smd_hertz.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/MACHDYN/pair_smd_tlsph.cpp similarity index 99% rename from src/USER-SMD/pair_smd_tlsph.cpp rename to src/MACHDYN/pair_smd_tlsph.cpp index 62e8e5e1c1..280e0173e3 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/MACHDYN/pair_smd_tlsph.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_tlsph.h b/src/MACHDYN/pair_smd_tlsph.h similarity index 99% rename from src/USER-SMD/pair_smd_tlsph.h rename to src/MACHDYN/pair_smd_tlsph.h index b641ca71e5..86e2bbe52b 100644 --- a/src/USER-SMD/pair_smd_tlsph.h +++ b/src/MACHDYN/pair_smd_tlsph.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/MACHDYN/pair_smd_triangulated_surface.cpp similarity index 99% rename from src/USER-SMD/pair_smd_triangulated_surface.cpp rename to src/MACHDYN/pair_smd_triangulated_surface.cpp index 36a34b5f1c..0d6abb6dfb 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/MACHDYN/pair_smd_triangulated_surface.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_triangulated_surface.h b/src/MACHDYN/pair_smd_triangulated_surface.h similarity index 97% rename from src/USER-SMD/pair_smd_triangulated_surface.h rename to src/MACHDYN/pair_smd_triangulated_surface.h index 5e2c8e3fc4..57865e7983 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.h +++ b/src/MACHDYN/pair_smd_triangulated_surface.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/MACHDYN/pair_smd_ulsph.cpp similarity index 99% rename from src/USER-SMD/pair_smd_ulsph.cpp rename to src/MACHDYN/pair_smd_ulsph.cpp index 38a80195e9..0958cbc7c3 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/MACHDYN/pair_smd_ulsph.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/pair_smd_ulsph.h b/src/MACHDYN/pair_smd_ulsph.h similarity index 98% rename from src/USER-SMD/pair_smd_ulsph.h rename to src/MACHDYN/pair_smd_ulsph.h index b9ae311917..6d58168b5a 100644 --- a/src/USER-SMD/pair_smd_ulsph.h +++ b/src/MACHDYN/pair_smd_ulsph.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/smd_kernels.h b/src/MACHDYN/smd_kernels.h similarity index 98% rename from src/USER-SMD/smd_kernels.h rename to src/MACHDYN/smd_kernels.h index 67244b64d3..07155f13a5 100644 --- a/src/USER-SMD/smd_kernels.h +++ b/src/MACHDYN/smd_kernels.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/smd_material_models.cpp b/src/MACHDYN/smd_material_models.cpp similarity index 99% rename from src/USER-SMD/smd_material_models.cpp rename to src/MACHDYN/smd_material_models.cpp index a49b5b034d..cee0a3822e 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/MACHDYN/smd_material_models.cpp @@ -3,7 +3,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/smd_material_models.h b/src/MACHDYN/smd_material_models.h similarity index 98% rename from src/USER-SMD/smd_material_models.h rename to src/MACHDYN/smd_material_models.h index 89dca2155a..df1d830445 100644 --- a/src/USER-SMD/smd_material_models.h +++ b/src/MACHDYN/smd_material_models.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/USER-SMD/smd_math.h b/src/MACHDYN/smd_math.h similarity index 99% rename from src/USER-SMD/smd_math.h rename to src/MACHDYN/smd_math.h index de8658b59c..369adb2321 100644 --- a/src/USER-SMD/smd_math.h +++ b/src/MACHDYN/smd_math.h @@ -2,7 +2,7 @@ * * *** Smooth Mach Dynamics *** * - * This file is part of the USER-SMD package for LAMMPS. + * This file is part of the MACHDYN package for LAMMPS. * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. diff --git a/src/MAKE/OPTIONS/Makefile.intel_coprocessor b/src/MAKE/OPTIONS/Makefile.intel_coprocessor index b11256baa1..2b66c20f4a 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_coprocessor +++ b/src/MAKE/OPTIONS/Makefile.intel_coprocessor @@ -1,4 +1,4 @@ -# intel_coprocessor = USER-INTEL package with Phi offload support, Intel MPI, MKL FFT +# intel_coprocessor = INTEL package with Phi offload support, Intel MPI, MKL FFT SHELL = /bin/sh diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi index 4adc427d91..04ec1fdc64 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi @@ -1,4 +1,4 @@ -# intel_cpu_intelmpi = USER-INTEL package, Intel MPI, MKL FFT +# intel_cpu_intelmpi = INTEL package, Intel MPI, MKL FFT SHELL = /bin/sh diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich index 762899722c..dece0092f1 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich @@ -1,4 +1,4 @@ -# intel_cpu_mpich = USER-INTEL package, MPICH with compiler set to Intel icc +# intel_cpu_mpich = INTEL package, MPICH with compiler set to Intel icc SHELL = /bin/sh diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi index 9adb5b1af2..0053aef20a 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi @@ -1,4 +1,4 @@ -# intel_cpu_openmpi = USER-INTEL package, OpenMPI with compiler set to Intel icc +# intel_cpu_openmpi = INTEL package, OpenMPI with compiler set to Intel icc SHELL = /bin/sh diff --git a/src/MAKE/OPTIONS/Makefile.mgptfast b/src/MAKE/OPTIONS/Makefile.mgptfast index dc8682c3a6..da10701a9a 100644 --- a/src/MAKE/OPTIONS/Makefile.mgptfast +++ b/src/MAKE/OPTIONS/Makefile.mgptfast @@ -1,4 +1,4 @@ -# mgptfast = MPI with its default compiler, optimizations for USER-MGPT +# mgptfast = MPI with its default compiler, optimizations for MGPT SHELL = /bin/sh diff --git a/src/MAKE/OPTIONS/Makefile.omp b/src/MAKE/OPTIONS/Makefile.omp index a6b45f7a31..0f49cdb15c 100644 --- a/src/MAKE/OPTIONS/Makefile.omp +++ b/src/MAKE/OPTIONS/Makefile.omp @@ -1,4 +1,4 @@ -# omp = USER-OMP package, MPI with its default compiler +# omp = OPENMP package, MPI with its default compiler SHELL = /bin/sh diff --git a/src/MAKE/README b/src/MAKE/README index 95f6c72a1a..bd883948a2 100644 --- a/src/MAKE/README +++ b/src/MAKE/README @@ -44,7 +44,7 @@ These Makefiles derive from src/MAKE/Makefile.mpi with added settings to illustrate how they can be added to any Makefile. Makefile.big use of -DLAMMPS_BIGBIG setting -Makefile.fastmgpt optimzations for USER-MGPT package +Makefile.fastmgpt optimzations for MGPT package Makefile.fftw FFTW support for long-range Coulombics (PPPM) Makefile.jpeg JPEG support for dump image Makefile.png PNG support for dump image @@ -63,14 +63,14 @@ the compiler wrapped by mpicxx. Setting this requires a different syntax for different MPIs. Makefile.opt OPT package, using default MPI -Makefile.omp USER-OMP package, using default MPI +Makefile.omp OPENMP package, using default MPI Makefile.gpu GPU package, using default MPI -Makefile.intel_cpu_intelmpi USER-INTEL package for CPU with Intel MPI -Makefile.intel_cpu_mpich USER-INTEL package for CPU with MPICH -Makefile.intel_cpu_openmpi USER-INTEL package for CPU with OpenMPI -Makefile.intel_coprocessor USER-INTEL package with Xeon Phi support -Makefile.knl USER-INTEL package with KNL support +Makefile.intel_cpu_intelmpi INTEL package for CPU with Intel MPI +Makefile.intel_cpu_mpich INTEL package for CPU with MPICH +Makefile.intel_cpu_openmpi INTEL package for CPU with OpenMPI +Makefile.intel_coprocessor INTEL package with Xeon Phi support +Makefile.knl INTEL package with KNL support Makefile.kokkos_cuda_mpich KOKKOS package with GPU support for MPICH Makefile.kokkos_cuda_openmpi KOKKOS package with GPU support for OpenMPI diff --git a/src/USER-MANIFOLD/README b/src/MANIFOLD/README similarity index 97% rename from src/USER-MANIFOLD/README rename to src/MANIFOLD/README index 24c645232d..3dd496ad03 100644 --- a/src/USER-MANIFOLD/README +++ b/src/MANIFOLD/README @@ -1,5 +1,5 @@ +==============================================================================+ -This file is a part of the USER-MANIFOLD package. +This file is a part of the MANIFOLD package. This package allows LAMMPS to perform MD simulations of particles constrained on a manifold (i.e., a 2D subspace of the 3D simulation @@ -21,7 +21,7 @@ This software is distributed under the GNU General Public License. +==============================================================================+ At the moment we have a few manifolds available, extending them is very easy: -To add a new manifold, do the following in the "USER-MANIFOLD" directory: +To add a new manifold, do the following in the "MANIFOLD" directory: 0. Create a new pair of source/header files, and name them "manifold_*.cpp/h", where you should replace '*' with some (descriptive) name. @@ -69,7 +69,7 @@ a relatively simple manifold. With those things in place, the install script should be able to add your manifold to LAMMPS without any extra work, so just running -make yes-user-manifold +make yes-manifold make should (re)compile LAMMPS with the manifolds added. diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/MANIFOLD/fix_manifoldforce.cpp similarity index 100% rename from src/USER-MANIFOLD/fix_manifoldforce.cpp rename to src/MANIFOLD/fix_manifoldforce.cpp diff --git a/src/USER-MANIFOLD/fix_manifoldforce.h b/src/MANIFOLD/fix_manifoldforce.h similarity index 97% rename from src/USER-MANIFOLD/fix_manifoldforce.h rename to src/MANIFOLD/fix_manifoldforce.h index 285fcd5578..d58fe6001b 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.h +++ b/src/MANIFOLD/fix_manifoldforce.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2015) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/MANIFOLD/fix_nve_manifold_rattle.cpp similarity index 99% rename from src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp rename to src/MANIFOLD/fix_nve_manifold_rattle.cpp index b340869ea9..b4644a1350 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/MANIFOLD/fix_nve_manifold_rattle.cpp @@ -12,7 +12,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h b/src/MANIFOLD/fix_nve_manifold_rattle.h similarity index 98% rename from src/USER-MANIFOLD/fix_nve_manifold_rattle.h rename to src/MANIFOLD/fix_nve_manifold_rattle.h index e112b9bc7e..e2bf6b5639 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h +++ b/src/MANIFOLD/fix_nve_manifold_rattle.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/MANIFOLD/fix_nvt_manifold_rattle.cpp similarity index 99% rename from src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp rename to src/MANIFOLD/fix_nvt_manifold_rattle.cpp index 57ae8ef109..f675cdff73 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -12,7 +12,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h b/src/MANIFOLD/fix_nvt_manifold_rattle.h similarity index 98% rename from src/USER-MANIFOLD/fix_nvt_manifold_rattle.h rename to src/MANIFOLD/fix_nvt_manifold_rattle.h index 2e6115e692..d8439b1ad0 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h +++ b/src/MANIFOLD/fix_nvt_manifold_rattle.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/manifold.h b/src/MANIFOLD/manifold.h similarity index 98% rename from src/USER-MANIFOLD/manifold.h rename to src/MANIFOLD/manifold.h index f2f46a6647..92a5a02222 100644 --- a/src/USER-MANIFOLD/manifold.h +++ b/src/MANIFOLD/manifold.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. This package allows LAMMPS to perform MD simulations of particles constrained on a manifold (i.e., a 2D subspace of the 3D simulation diff --git a/src/USER-MANIFOLD/manifold_cylinder.cpp b/src/MANIFOLD/manifold_cylinder.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_cylinder.cpp rename to src/MANIFOLD/manifold_cylinder.cpp diff --git a/src/USER-MANIFOLD/manifold_cylinder.h b/src/MANIFOLD/manifold_cylinder.h similarity index 100% rename from src/USER-MANIFOLD/manifold_cylinder.h rename to src/MANIFOLD/manifold_cylinder.h diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp b/src/MANIFOLD/manifold_cylinder_dent.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_cylinder_dent.cpp rename to src/MANIFOLD/manifold_cylinder_dent.cpp diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.h b/src/MANIFOLD/manifold_cylinder_dent.h similarity index 100% rename from src/USER-MANIFOLD/manifold_cylinder_dent.h rename to src/MANIFOLD/manifold_cylinder_dent.h diff --git a/src/USER-MANIFOLD/manifold_dumbbell.cpp b/src/MANIFOLD/manifold_dumbbell.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_dumbbell.cpp rename to src/MANIFOLD/manifold_dumbbell.cpp diff --git a/src/USER-MANIFOLD/manifold_dumbbell.h b/src/MANIFOLD/manifold_dumbbell.h similarity index 100% rename from src/USER-MANIFOLD/manifold_dumbbell.h rename to src/MANIFOLD/manifold_dumbbell.h diff --git a/src/USER-MANIFOLD/manifold_ellipsoid.cpp b/src/MANIFOLD/manifold_ellipsoid.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_ellipsoid.cpp rename to src/MANIFOLD/manifold_ellipsoid.cpp diff --git a/src/USER-MANIFOLD/manifold_ellipsoid.h b/src/MANIFOLD/manifold_ellipsoid.h similarity index 100% rename from src/USER-MANIFOLD/manifold_ellipsoid.h rename to src/MANIFOLD/manifold_ellipsoid.h diff --git a/src/USER-MANIFOLD/manifold_factory.cpp b/src/MANIFOLD/manifold_factory.cpp similarity index 98% rename from src/USER-MANIFOLD/manifold_factory.cpp rename to src/MANIFOLD/manifold_factory.cpp index 8b3e3d02d0..6fa73643b5 100644 --- a/src/USER-MANIFOLD/manifold_factory.cpp +++ b/src/MANIFOLD/manifold_factory.cpp @@ -12,7 +12,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/MANIFOLD/manifold_factory.h similarity index 97% rename from src/USER-MANIFOLD/manifold_factory.h rename to src/MANIFOLD/manifold_factory.h index ddaf965169..4cf27b0b83 100644 --- a/src/USER-MANIFOLD/manifold_factory.h +++ b/src/MANIFOLD/manifold_factory.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology. License: GNU General Public License. diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/MANIFOLD/manifold_gaussian_bump.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_gaussian_bump.cpp rename to src/MANIFOLD/manifold_gaussian_bump.cpp diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.h b/src/MANIFOLD/manifold_gaussian_bump.h similarity index 98% rename from src/USER-MANIFOLD/manifold_gaussian_bump.h rename to src/MANIFOLD/manifold_gaussian_bump.h index 75c0ce6644..8c72db080f 100644 --- a/src/USER-MANIFOLD/manifold_gaussian_bump.h +++ b/src/MANIFOLD/manifold_gaussian_bump.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- - This file is a part of the USER-MANIFOLD package. + This file is a part of the MANIFOLD package. This package allows LAMMPS to perform MD simulations of particles constrained on a manifold (i.e., a 2D subspace of the 3D simulation diff --git a/src/USER-MANIFOLD/manifold_plane.cpp b/src/MANIFOLD/manifold_plane.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_plane.cpp rename to src/MANIFOLD/manifold_plane.cpp diff --git a/src/USER-MANIFOLD/manifold_plane.h b/src/MANIFOLD/manifold_plane.h similarity index 100% rename from src/USER-MANIFOLD/manifold_plane.h rename to src/MANIFOLD/manifold_plane.h diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp b/src/MANIFOLD/manifold_plane_wiggle.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_plane_wiggle.cpp rename to src/MANIFOLD/manifold_plane_wiggle.cpp diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.h b/src/MANIFOLD/manifold_plane_wiggle.h similarity index 100% rename from src/USER-MANIFOLD/manifold_plane_wiggle.h rename to src/MANIFOLD/manifold_plane_wiggle.h diff --git a/src/USER-MANIFOLD/manifold_sphere.h b/src/MANIFOLD/manifold_sphere.h similarity index 100% rename from src/USER-MANIFOLD/manifold_sphere.h rename to src/MANIFOLD/manifold_sphere.h diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/MANIFOLD/manifold_spine.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_spine.cpp rename to src/MANIFOLD/manifold_spine.cpp diff --git a/src/USER-MANIFOLD/manifold_spine.h b/src/MANIFOLD/manifold_spine.h similarity index 100% rename from src/USER-MANIFOLD/manifold_spine.h rename to src/MANIFOLD/manifold_spine.h diff --git a/src/USER-MANIFOLD/manifold_supersphere.h b/src/MANIFOLD/manifold_supersphere.h similarity index 100% rename from src/USER-MANIFOLD/manifold_supersphere.h rename to src/MANIFOLD/manifold_supersphere.h diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/MANIFOLD/manifold_thylakoid.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_thylakoid.cpp rename to src/MANIFOLD/manifold_thylakoid.cpp diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/MANIFOLD/manifold_thylakoid.h similarity index 100% rename from src/USER-MANIFOLD/manifold_thylakoid.h rename to src/MANIFOLD/manifold_thylakoid.h diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp b/src/MANIFOLD/manifold_thylakoid_shared.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_thylakoid_shared.cpp rename to src/MANIFOLD/manifold_thylakoid_shared.cpp diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.h b/src/MANIFOLD/manifold_thylakoid_shared.h similarity index 100% rename from src/USER-MANIFOLD/manifold_thylakoid_shared.h rename to src/MANIFOLD/manifold_thylakoid_shared.h diff --git a/src/USER-MANIFOLD/manifold_torus.cpp b/src/MANIFOLD/manifold_torus.cpp similarity index 100% rename from src/USER-MANIFOLD/manifold_torus.cpp rename to src/MANIFOLD/manifold_torus.cpp diff --git a/src/USER-MANIFOLD/manifold_torus.h b/src/MANIFOLD/manifold_torus.h similarity index 100% rename from src/USER-MANIFOLD/manifold_torus.h rename to src/MANIFOLD/manifold_torus.h diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 5ec89cbe7e..2b206689d6 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -28,7 +28,7 @@ class PairEAM : public Pair { public: friend class FixSemiGrandCanonicalMC; // Alex Stukowski option - // public variables so USER-ATC package can access them + // public variables so ATC package can access them double cutmax; diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index e275cd8c11..6598890ea4 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -2315,7 +2315,7 @@ double FixGCMC::energy_full() // unlike Verlet, not performing a reverse_comm() or forces here // b/c GCMC does not care about forces // don't think it will mess up energy due to any post_force() fixes - // but Modify::pre_reverse() is needed for USER-INTEL + // but Modify::pre_reverse() is needed for INTEL if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag); if (modify->n_post_force) modify->post_force(vflag); diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index 3dd0d2d3c9..7b4a749f2e 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -1049,7 +1049,7 @@ double FixWidom::energy_full() // unlike Verlet, not performing a reverse_comm() or forces here // b/c Widom does not care about forces // don't think it will mess up energy due to any post_force() fixes - // but Modify::pre_reverse() is needed for USER-INTEL + // but Modify::pre_reverse() is needed for INTEL if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag); if (modify->n_pre_force) modify->pre_force(vflag); diff --git a/src/USER-MDI/Install.sh b/src/MDI/Install.sh similarity index 100% rename from src/USER-MDI/Install.sh rename to src/MDI/Install.sh diff --git a/src/USER-MDI/README b/src/MDI/README similarity index 93% rename from src/USER-MDI/README rename to src/MDI/README index 045fbea518..cad9ae3f39 100644 --- a/src/USER-MDI/README +++ b/src/MDI/README @@ -1,4 +1,4 @@ -The USER-MDI package adds an mdi/engine command which enables LAMMPS +The MDI package adds an mdi/engine command which enables LAMMPS to operate as a MolSSI Driver Interface (MDI) engine, responding to commands from an external MDI driver. diff --git a/src/USER-MDI/fix_mdi_engine.cpp b/src/MDI/fix_mdi_engine.cpp similarity index 100% rename from src/USER-MDI/fix_mdi_engine.cpp rename to src/MDI/fix_mdi_engine.cpp diff --git a/src/USER-MDI/fix_mdi_engine.h b/src/MDI/fix_mdi_engine.h similarity index 100% rename from src/USER-MDI/fix_mdi_engine.h rename to src/MDI/fix_mdi_engine.h diff --git a/src/USER-MDI/library_mdi.cpp b/src/MDI/library_mdi.cpp similarity index 100% rename from src/USER-MDI/library_mdi.cpp rename to src/MDI/library_mdi.cpp diff --git a/src/USER-MDI/library_mdi.h b/src/MDI/library_mdi.h similarity index 100% rename from src/USER-MDI/library_mdi.h rename to src/MDI/library_mdi.h diff --git a/src/USER-MDI/mdi_engine.cpp b/src/MDI/mdi_engine.cpp similarity index 100% rename from src/USER-MDI/mdi_engine.cpp rename to src/MDI/mdi_engine.cpp diff --git a/src/USER-MDI/mdi_engine.h b/src/MDI/mdi_engine.h similarity index 100% rename from src/USER-MDI/mdi_engine.h rename to src/MDI/mdi_engine.h diff --git a/src/MEAM/README b/src/MEAM/README new file mode 100644 index 0000000000..8015f6c699 --- /dev/null +++ b/src/MEAM/README @@ -0,0 +1,26 @@ +This package implements the MEAM potential as a LAMMPS pair style. + +============================================================================== + +This package is a translation and extension of the Fortran MEAM +package to native C++. + +Translation by + Sebastian Hütter, sebastian.huetter@ovgu.de + Institute of Materials and Joining Technology + Otto-von-Guericke University Magdeburg, Germany + +The original Fortran implementation was created by + Greg Wagner (while at Sandia, now at Northwestern U). + +============================================================================== + +Use "make yes-meam" to enable this package or use +-DPKG_MEAM=on when configuring building LAMMPS + + +In your LAMMPS input script, specify + pair_style meam +to enable the use of this implementation. parameters, input files and +outputs are compatible to those for the Fortran version of pair_style meam. + diff --git a/src/USER-MEAMC/meam.h b/src/MEAM/meam.h similarity index 100% rename from src/USER-MEAMC/meam.h rename to src/MEAM/meam.h diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/MEAM/meam_dens_final.cpp similarity index 100% rename from src/USER-MEAMC/meam_dens_final.cpp rename to src/MEAM/meam_dens_final.cpp diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/MEAM/meam_dens_init.cpp similarity index 100% rename from src/USER-MEAMC/meam_dens_init.cpp rename to src/MEAM/meam_dens_init.cpp diff --git a/src/USER-MEAMC/meam_force.cpp b/src/MEAM/meam_force.cpp similarity index 100% rename from src/USER-MEAMC/meam_force.cpp rename to src/MEAM/meam_force.cpp diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/MEAM/meam_funcs.cpp similarity index 100% rename from src/USER-MEAMC/meam_funcs.cpp rename to src/MEAM/meam_funcs.cpp diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/MEAM/meam_impl.cpp similarity index 100% rename from src/USER-MEAMC/meam_impl.cpp rename to src/MEAM/meam_impl.cpp diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/MEAM/meam_setup_done.cpp similarity index 100% rename from src/USER-MEAMC/meam_setup_done.cpp rename to src/MEAM/meam_setup_done.cpp diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/MEAM/meam_setup_global.cpp similarity index 100% rename from src/USER-MEAMC/meam_setup_global.cpp rename to src/MEAM/meam_setup_global.cpp diff --git a/src/USER-MEAMC/meam_setup_param.cpp b/src/MEAM/meam_setup_param.cpp similarity index 100% rename from src/USER-MEAMC/meam_setup_param.cpp rename to src/MEAM/meam_setup_param.cpp diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/MEAM/pair_meam.cpp similarity index 95% rename from src/USER-MEAMC/pair_meamc.cpp rename to src/MEAM/pair_meam.cpp index a4ea3abdce..0d607b8fb2 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/MEAM/pair_meam.cpp @@ -16,7 +16,7 @@ Contributing author: Greg Wagner (SNL) ------------------------------------------------------------------------- */ -#include "pair_meamc.h" +#include "pair_meam.h" #include "atom.h" #include "comm.h" @@ -47,7 +47,7 @@ static const char *keywords[] = { /* ---------------------------------------------------------------------- */ -PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp) +PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; restartinfo = 0; @@ -72,7 +72,7 @@ PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp) check if allocated, since class can be destructed when incomplete ------------------------------------------------------------------------- */ -PairMEAMC::~PairMEAMC() +PairMEAM::~PairMEAM() { delete meam_inst; @@ -85,7 +85,7 @@ PairMEAMC::~PairMEAMC() /* ---------------------------------------------------------------------- */ -void PairMEAMC::compute(int eflag, int vflag) +void PairMEAM::compute(int eflag, int vflag) { int i,ii,n,inum_half,errorflag; int *ilist_half,*numneigh_half,**firstneigh_half; @@ -173,7 +173,7 @@ void PairMEAMC::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -void PairMEAMC::allocate() +void PairMEAM::allocate() { allocated = 1; int n = atom->ntypes; @@ -189,7 +189,7 @@ void PairMEAMC::allocate() global settings ------------------------------------------------------------------------- */ -void PairMEAMC::settings(int narg, char ** /*arg*/) +void PairMEAM::settings(int narg, char ** /*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -198,7 +198,7 @@ void PairMEAMC::settings(int narg, char ** /*arg*/) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairMEAMC::coeff(int narg, char **arg) +void PairMEAM::coeff(int narg, char **arg) { int m,n; @@ -309,7 +309,7 @@ void PairMEAMC::coeff(int narg, char **arg) init specific to this pair style ------------------------------------------------------------------------- */ -void PairMEAMC::init_style() +void PairMEAM::init_style() { if (force->newton_pair == 0) error->all(FLERR,"Pair style MEAM requires newton pair on"); @@ -329,7 +329,7 @@ void PairMEAMC::init_style() half or full ------------------------------------------------------------------------- */ -void PairMEAMC::init_list(int id, NeighList *ptr) +void PairMEAM::init_list(int id, NeighList *ptr) { if (id == 1) listfull = ptr; else if (id == 2) listhalf = ptr; @@ -339,7 +339,7 @@ void PairMEAMC::init_list(int id, NeighList *ptr) init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairMEAMC::init_one(int i, int j) +double PairMEAM::init_one(int i, int j) { if (setflag[i][j] == 0) scale[i][j] = 1.0; scale[j][i] = scale[i][j]; @@ -348,16 +348,16 @@ double PairMEAMC::init_one(int i, int j) /* ---------------------------------------------------------------------- */ -void PairMEAMC::read_files(const std::string &globalfile, +void PairMEAM::read_files(const std::string &globalfile, const std::string &userfile) { - read_global_meamc_file(globalfile); - read_user_meamc_file(userfile); + read_global_meam_file(globalfile); + read_user_meam_file(userfile); } /* ---------------------------------------------------------------------- */ -void PairMEAMC::read_global_meamc_file(const std::string &globalfile) +void PairMEAM::read_global_meam_file(const std::string &globalfile) { // allocate parameter arrays std::vector lat(nlibelements); @@ -498,7 +498,7 @@ void PairMEAMC::read_global_meamc_file(const std::string &globalfile) /* ---------------------------------------------------------------------- */ -void PairMEAMC::read_user_meamc_file(const std::string &userfile) +void PairMEAM::read_user_meam_file(const std::string &userfile) { // done if user param file is "NULL" @@ -577,7 +577,7 @@ void PairMEAMC::read_user_meamc_file(const std::string &userfile) /* ---------------------------------------------------------------------- */ -int PairMEAMC::pack_forward_comm(int n, int *list, double *buf, +int PairMEAM::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,m; @@ -621,7 +621,7 @@ int PairMEAMC::pack_forward_comm(int n, int *list, double *buf, /* ---------------------------------------------------------------------- */ -void PairMEAMC::unpack_forward_comm(int n, int first, double *buf) +void PairMEAM::unpack_forward_comm(int n, int first, double *buf) { int i,k,m,last; @@ -662,7 +662,7 @@ void PairMEAMC::unpack_forward_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -int PairMEAMC::pack_reverse_comm(int n, int first, double *buf) +int PairMEAM::pack_reverse_comm(int n, int first, double *buf) { int i,k,m,last; @@ -697,7 +697,7 @@ int PairMEAMC::pack_reverse_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -void PairMEAMC::unpack_reverse_comm(int n, int *list, double *buf) +void PairMEAM::unpack_reverse_comm(int n, int *list, double *buf) { int i,j,k,m; @@ -732,7 +732,7 @@ void PairMEAMC::unpack_reverse_comm(int n, int *list, double *buf) memory usage of local atom-based arrays ------------------------------------------------------------------------- */ -double PairMEAMC::memory_usage() +double PairMEAM::memory_usage() { double bytes = 11 * meam_inst->nmax * sizeof(double); bytes += (double)(3 + 6 + 10 + 3 + 3 + 3) * meam_inst->nmax * sizeof(double); @@ -747,7 +747,7 @@ double PairMEAMC::memory_usage() done once per reneighbor so that neigh_f2c and neigh_c2f don't see them ------------------------------------------------------------------------- */ -void PairMEAMC::neigh_strip(int inum, int *ilist, +void PairMEAM::neigh_strip(int inum, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jnum; @@ -763,7 +763,7 @@ void PairMEAMC::neigh_strip(int inum, int *ilist, /* ---------------------------------------------------------------------- */ -void *PairMEAMC::extract(const char *str, int &dim) +void *PairMEAM::extract(const char *str, int &dim) { dim = 2; if (strcmp(str,"scale") == 0) return (void *) scale; diff --git a/src/USER-MEAMC/pair_meamc.h b/src/MEAM/pair_meam.h similarity index 92% rename from src/USER-MEAMC/pair_meamc.h rename to src/MEAM/pair_meam.h index 08166c7bd7..06be670eb9 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/MEAM/pair_meam.h @@ -13,13 +13,13 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(meam/c,PairMEAMC); -PairStyle(meam,PairMEAMC); +PairStyle(meam,PairMEAM); +PairStyle(meam/c,PairMEAM); // clang-format on #else -#ifndef LMP_PAIR_MEAMC_H -#define LMP_PAIR_MEAMC_H +#ifndef LMP_PAIR_MEAM_H +#define LMP_PAIR_MEAM_H #include "pair.h" @@ -27,10 +27,10 @@ PairStyle(meam,PairMEAMC); namespace LAMMPS_NS { -class PairMEAMC : public Pair { +class PairMEAM : public Pair { public: - PairMEAMC(class LAMMPS *); - ~PairMEAMC(); + PairMEAM(class LAMMPS *); + ~PairMEAM(); void compute(int, int); void settings(int, char **); void coeff(int, char **); @@ -56,8 +56,8 @@ class PairMEAMC : public Pair { void allocate(); void read_files(const std::string &, const std::string &); - void read_global_meamc_file(const std::string &); - void read_user_meamc_file(const std::string &); + void read_global_meam_file(const std::string &); + void read_user_meam_file(const std::string &); void neigh_strip(int, int *, int *, int **); }; diff --git a/src/USER-MESONT/Install.sh b/src/MESONT/Install.sh similarity index 100% rename from src/USER-MESONT/Install.sh rename to src/MESONT/Install.sh diff --git a/src/USER-MESONT/README b/src/MESONT/README similarity index 97% rename from src/USER-MESONT/README rename to src/MESONT/README index ce08731734..0c66cb7b82 100644 --- a/src/USER-MESONT/README +++ b/src/MESONT/README @@ -1,4 +1,4 @@ -USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon +MESONT is a LAMMPS package for simulation of nanomechanics of carbon nanotubes (CNTs). The model is based on a coarse-grained representation of CNTs as "flexible cylinders" consisting of a variable number of segments. Internal interactions within a CNT and the van der Waals @@ -22,7 +22,7 @@ The following commands are contained in this package: atom_style mesont This command enables mesont atom_style containing variables used for - further commands in USER-MESONT. + further commands in MESONT. pair_style mesont/tpm cut table_path BendingMode TPMType This command activates a pair_style describing CNT mesoscopic tubular diff --git a/src/USER-MESONT/atom_vec_mesont.cpp b/src/MESONT/atom_vec_mesont.cpp similarity index 100% rename from src/USER-MESONT/atom_vec_mesont.cpp rename to src/MESONT/atom_vec_mesont.cpp diff --git a/src/USER-MESONT/atom_vec_mesont.h b/src/MESONT/atom_vec_mesont.h similarity index 100% rename from src/USER-MESONT/atom_vec_mesont.h rename to src/MESONT/atom_vec_mesont.h diff --git a/src/USER-MESONT/compute_mesont.cpp b/src/MESONT/compute_mesont.cpp similarity index 100% rename from src/USER-MESONT/compute_mesont.cpp rename to src/MESONT/compute_mesont.cpp diff --git a/src/USER-MESONT/compute_mesont.h b/src/MESONT/compute_mesont.h similarity index 100% rename from src/USER-MESONT/compute_mesont.h rename to src/MESONT/compute_mesont.h diff --git a/src/USER-MESONT/export_mesont.h b/src/MESONT/export_mesont.h similarity index 100% rename from src/USER-MESONT/export_mesont.h rename to src/MESONT/export_mesont.h diff --git a/src/USER-MESONT/pair_mesocnt.cpp b/src/MESONT/pair_mesocnt.cpp similarity index 100% rename from src/USER-MESONT/pair_mesocnt.cpp rename to src/MESONT/pair_mesocnt.cpp diff --git a/src/USER-MESONT/pair_mesocnt.h b/src/MESONT/pair_mesocnt.h similarity index 100% rename from src/USER-MESONT/pair_mesocnt.h rename to src/MESONT/pair_mesocnt.h diff --git a/src/USER-MESONT/pair_mesont_tpm.cpp b/src/MESONT/pair_mesont_tpm.cpp similarity index 100% rename from src/USER-MESONT/pair_mesont_tpm.cpp rename to src/MESONT/pair_mesont_tpm.cpp diff --git a/src/USER-MESONT/pair_mesont_tpm.h b/src/MESONT/pair_mesont_tpm.h similarity index 100% rename from src/USER-MESONT/pair_mesont_tpm.h rename to src/MESONT/pair_mesont_tpm.h diff --git a/src/USER-MESONT/potentials.txt b/src/MESONT/potentials.txt similarity index 100% rename from src/USER-MESONT/potentials.txt rename to src/MESONT/potentials.txt diff --git a/src/USER-MGPT/README b/src/MGPT/README similarity index 92% rename from src/USER-MGPT/README rename to src/MGPT/README index 151bd02b5d..1f29a68385 100644 --- a/src/USER-MGPT/README +++ b/src/MGPT/README @@ -17,7 +17,7 @@ See the doc page for the pair_style mgpt command for full details on using this package in LAMMPS. In particular, the user should note that the MGPT potentials are explicitly volume dependent, requiring special attention in their application. Useful example scripts are given in -the "examples/USER/mgpt" directory. These scripts show the necessary +the "examples/PACKAGES/mgpt" directory. These scripts show the necessary steps to perform constant-volume calculations and simulations. It is strongly recommended that the user work through and understand these examples before proceeding to more complex simulations. @@ -28,6 +28,6 @@ vanadium (V6.1 potentials) are contained in the LAMMPS "potentials" directory. It is expected that MGPT potentials for additional materials will be added over time. -The persons who created the USER-MGPT package are Tomas Oppelstrup +The persons who created the MGPT package are Tomas Oppelstrup (oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) Contact them directly if you have any questions. diff --git a/src/USER-MGPT/mgpt_bgmul_7.c.h b/src/MGPT/mgpt_bgmul_7.c.h similarity index 100% rename from src/USER-MGPT/mgpt_bgmul_7.c.h rename to src/MGPT/mgpt_bgmul_7.c.h diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/MGPT/mgpt_linalg.cpp similarity index 100% rename from src/USER-MGPT/mgpt_linalg.cpp rename to src/MGPT/mgpt_linalg.cpp diff --git a/src/USER-MGPT/mgpt_linalg.h b/src/MGPT/mgpt_linalg.h similarity index 100% rename from src/USER-MGPT/mgpt_linalg.h rename to src/MGPT/mgpt_linalg.h diff --git a/src/USER-MGPT/mgpt_mmul3_538.c.h b/src/MGPT/mgpt_mmul3_538.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul3_538.c.h rename to src/MGPT/mgpt_mmul3_538.c.h diff --git a/src/USER-MGPT/mgpt_mmul3_748.c.h b/src/MGPT/mgpt_mmul3_748.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul3_748.c.h rename to src/MGPT/mgpt_mmul3_748.c.h diff --git a/src/USER-MGPT/mgpt_mmul3d_526.c.h b/src/MGPT/mgpt_mmul3d_526.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul3d_526.c.h rename to src/MGPT/mgpt_mmul3d_526.c.h diff --git a/src/USER-MGPT/mgpt_mmul3d_744.c.h b/src/MGPT/mgpt_mmul3d_744.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul3d_744.c.h rename to src/MGPT/mgpt_mmul3d_744.c.h diff --git a/src/USER-MGPT/mgpt_mmul_bg_552.c.h b/src/MGPT/mgpt_mmul_bg_552.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul_bg_552.c.h rename to src/MGPT/mgpt_mmul_bg_552.c.h diff --git a/src/USER-MGPT/mgpt_mmul_bg_722.c.h b/src/MGPT/mgpt_mmul_bg_722.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul_bg_722.c.h rename to src/MGPT/mgpt_mmul_bg_722.c.h diff --git a/src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h b/src/MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h rename to src/MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h diff --git a/src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h b/src/MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h similarity index 100% rename from src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h rename to src/MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h diff --git a/src/USER-MGPT/mgpt_readpot.cpp b/src/MGPT/mgpt_readpot.cpp similarity index 100% rename from src/USER-MGPT/mgpt_readpot.cpp rename to src/MGPT/mgpt_readpot.cpp diff --git a/src/USER-MGPT/mgpt_readpot.h b/src/MGPT/mgpt_readpot.h similarity index 100% rename from src/USER-MGPT/mgpt_readpot.h rename to src/MGPT/mgpt_readpot.h diff --git a/src/USER-MGPT/mgpt_splinetab.cpp b/src/MGPT/mgpt_splinetab.cpp similarity index 100% rename from src/USER-MGPT/mgpt_splinetab.cpp rename to src/MGPT/mgpt_splinetab.cpp diff --git a/src/USER-MGPT/mgpt_splinetab.h b/src/MGPT/mgpt_splinetab.h similarity index 100% rename from src/USER-MGPT/mgpt_splinetab.h rename to src/MGPT/mgpt_splinetab.h diff --git a/src/USER-MGPT/mgpt_ttr_5022.c.h b/src/MGPT/mgpt_ttr_5022.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_5022.c.h rename to src/MGPT/mgpt_ttr_5022.c.h diff --git a/src/USER-MGPT/mgpt_ttr_5042.c.h b/src/MGPT/mgpt_ttr_5042.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_5042.c.h rename to src/MGPT/mgpt_ttr_5042.c.h diff --git a/src/USER-MGPT/mgpt_ttr_5123.c.h b/src/MGPT/mgpt_ttr_5123.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_5123.c.h rename to src/MGPT/mgpt_ttr_5123.c.h diff --git a/src/USER-MGPT/mgpt_ttr_5141.c.h b/src/MGPT/mgpt_ttr_5141.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_5141.c.h rename to src/MGPT/mgpt_ttr_5141.c.h diff --git a/src/USER-MGPT/mgpt_ttr_7022.c.h b/src/MGPT/mgpt_ttr_7022.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_7022.c.h rename to src/MGPT/mgpt_ttr_7022.c.h diff --git a/src/USER-MGPT/mgpt_ttr_7042.c.h b/src/MGPT/mgpt_ttr_7042.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_7042.c.h rename to src/MGPT/mgpt_ttr_7042.c.h diff --git a/src/USER-MGPT/mgpt_ttr_7123.c.h b/src/MGPT/mgpt_ttr_7123.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_7123.c.h rename to src/MGPT/mgpt_ttr_7123.c.h diff --git a/src/USER-MGPT/mgpt_ttr_7141.c.h b/src/MGPT/mgpt_ttr_7141.c.h similarity index 100% rename from src/USER-MGPT/mgpt_ttr_7141.c.h rename to src/MGPT/mgpt_ttr_7141.c.h diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/MGPT/pair_mgpt.cpp similarity index 100% rename from src/USER-MGPT/pair_mgpt.cpp rename to src/MGPT/pair_mgpt.cpp diff --git a/src/USER-MGPT/pair_mgpt.h b/src/MGPT/pair_mgpt.h similarity index 100% rename from src/USER-MGPT/pair_mgpt.h rename to src/MGPT/pair_mgpt.h diff --git a/src/USER-MISC/fix_imd.cpp b/src/MISC/fix_imd.cpp similarity index 100% rename from src/USER-MISC/fix_imd.cpp rename to src/MISC/fix_imd.cpp diff --git a/src/USER-MISC/fix_imd.h b/src/MISC/fix_imd.h similarity index 100% rename from src/USER-MISC/fix_imd.h rename to src/MISC/fix_imd.h diff --git a/src/USER-HDNNP/Install.sh b/src/ML-HDNNP/Install.sh similarity index 100% rename from src/USER-HDNNP/Install.sh rename to src/ML-HDNNP/Install.sh diff --git a/src/USER-HDNNP/README b/src/ML-HDNNP/README similarity index 91% rename from src/USER-HDNNP/README rename to src/ML-HDNNP/README index 690db8a714..1d9590f7d7 100644 --- a/src/USER-HDNNP/README +++ b/src/ML-HDNNP/README @@ -5,9 +5,9 @@ neural network potentials[1] via an interface to the n2p2 library Please see the main documentation for the "pair_style hdnnp" command for further details on how the pair style is used. An example is provided in the -"examples/USER/hdnnp" directory of LAMMPS. +"examples/PACKAGES/hdnnp" directory of LAMMPS. -The USER-HDNNP package requires the external library n2p2 which must be +The ML-HDNNP package requires the external library n2p2 which must be downloaded and compiled before starting the build process of LAMMPS. A guideline on how to build n2p2 is presented in "lib/hdnnp/README". This package supports the LAMMPS build process via CMake and traditional makefiles, please diff --git a/src/USER-HDNNP/pair_hdnnp.cpp b/src/ML-HDNNP/pair_hdnnp.cpp similarity index 99% rename from src/USER-HDNNP/pair_hdnnp.cpp rename to src/ML-HDNNP/pair_hdnnp.cpp index af64f98f75..7aeacad588 100644 --- a/src/USER-HDNNP/pair_hdnnp.cpp +++ b/src/ML-HDNNP/pair_hdnnp.cpp @@ -35,7 +35,7 @@ using namespace LAMMPS_NS; static const char cite_user_hdnnp_package[] = - "USER-HDNNP package: 10.1021/acs.jctc.8b00770\n\n" + "ML-HDNNP package: 10.1021/acs.jctc.8b00770\n\n" "@Article{Singraber19,\n" " author = {Singraber, Andreas and Behler, J{\"o}rg and Dellago, Christoph},\n" " title = {Library-{{Based LAMMPS Implementation}} of {{High}}-{{Dimensional Neural Network Potentials}}},\n" diff --git a/src/USER-HDNNP/pair_hdnnp.h b/src/ML-HDNNP/pair_hdnnp.h similarity index 100% rename from src/USER-HDNNP/pair_hdnnp.h rename to src/ML-HDNNP/pair_hdnnp.h diff --git a/src/MLIAP/Install.sh b/src/ML-IAP/Install.sh similarity index 76% rename from src/MLIAP/Install.sh rename to src/ML-IAP/Install.sh index e6ba4042a9..08cdfecd88 100755 --- a/src/MLIAP/Install.sh +++ b/src/ML-IAP/Install.sh @@ -29,17 +29,20 @@ action () { # enforce package dependency if (test $1 = 1 || test $1 = 2) then if (test ! -e ../sna.h) then - echo "Must install SNAP package to use MLIAP package" + echo "Must install SNAP package to use ML-IAP package" exit 1 fi fi -# all package files with no dependencies +# all package C++ files with no dependencies -for file in *.cpp *.h *.pyx; do +for file in *.cpp *.h; do test -f ${file} && action $file done +# Install cython pyx file only if also Python is available +action mliap_model_python_couple.pyx python_impl.cpp + # edit 2 Makefile.package files to include/exclude package info if (test $1 = 1) then @@ -64,4 +67,11 @@ elif (test $1 = 0) then fi rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings + +elif (test $1 = 2) then + if (test "$(type cythonize 2> /dev/null)" != "" && test -e ../python_impl.cpp) then + cythonize -3 ../mliap_model_python_couple.pyx + else + rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h + fi fi diff --git a/src/ML-IAP/README.md b/src/ML-IAP/README.md new file mode 100644 index 0000000000..f6db495099 --- /dev/null +++ b/src/ML-IAP/README.md @@ -0,0 +1,56 @@ +This package provides a general interface to families of +machine-learning interatomic potentials (MLIAPs). This interface +consists of a `mliap pair style` and a `mliap compute`. The `mliap pair +style` is used when running simulations with energies and forces +calculated by an MLIAP. The interface allows separate definitions of the +interatomic potential functional form (`model`) and the geometric +quantities that characterize the atomic positions (`descriptor`). By +defining `model` and `descriptor` separately, it is possible to use many +different models with a given descriptor, or many different descriptors +with a given model. The mliap pair_style supports the following models: + +- `linear`, +- `quadratic`, +- `nn` (neural networks) +- `mliappy` (general Python interface to things like PyTorch). + +It currently supports two classes of descriptors, `sna` (the SNAP +descriptors) and `so3` (the SO3 descriptor). It is straightforward to +add new descriptor and model styles. + +The `compute mliap` style provides gradients of the energy, force, and +stress tensor w.r.t. model parameters. These are useful when training +MLIAPs to match target data. Any `model` or `descriptor` that has been +implemented for the `mliap` pair style can also be accessed by the +`mliap` compute. In addition to the energy, force, and stress +gradients, w.r.t. each `model` parameter, the compute also calculates +the energy, force, and stress contributions from a user-specified +reference potential. + +## Generating the model files from the third-party packages +- To train the `linear` and `quadratic` models with the SNAP descriptors, see the examples in [FitSNAP](https://github.com/FitSNAP/FitSNAP). +- To train the `nn` model with the SNAP descriptors, check the examples in [PyXtal\_FF](https://github.com/qzhu2017/PyXtal_FF). + +## Building the ML-IAP package with Python support + +The `mliappy` energy model requires that the MLIAP package is compiled +with Python support enabled. This extension, written by Nick Lubbers +(LANL), provides a coupling to PyTorch and other Python modules. This +should be automatically enabled by default if the prerequisite software +is installed when compiling with CMake. It can be enforced during CMake +configuration by setting the variable `MLIAP_ENABLE_PYTHON=yes` or for +conventional build by adding `-DMLIAP_PYTHON` to the `LMP_INC` variable +in your makefile and running the cythonize script on the .pyx file(s) +copied to the src folder. + +Using the `mliappy` energy model also requires to install the PYTHON +package and have the [cython](https://cython.org) software +installed. During configuration/compilation the cythonize script will be +used to convert the provided .pyx file(s) to C++ code. Please do *NOT* +run the cythonize script manually in the src/ML-IAP folder. If you have +done so by accident, you need to delete the generated .cpp and .h +file(s) in the src/ML-IAP folder or there may be problems during +compilation. + +More information on building LAMMPS with this package is +[here](https://docs.lammps.org/Build_extras.html#mliap). diff --git a/src/MLIAP/compute_mliap.cpp b/src/ML-IAP/compute_mliap.cpp similarity index 100% rename from src/MLIAP/compute_mliap.cpp rename to src/ML-IAP/compute_mliap.cpp diff --git a/src/MLIAP/compute_mliap.h b/src/ML-IAP/compute_mliap.h similarity index 100% rename from src/MLIAP/compute_mliap.h rename to src/ML-IAP/compute_mliap.h diff --git a/src/MLIAP/mliap_data.cpp b/src/ML-IAP/mliap_data.cpp similarity index 100% rename from src/MLIAP/mliap_data.cpp rename to src/ML-IAP/mliap_data.cpp diff --git a/src/MLIAP/mliap_data.h b/src/ML-IAP/mliap_data.h similarity index 100% rename from src/MLIAP/mliap_data.h rename to src/ML-IAP/mliap_data.h diff --git a/src/MLIAP/mliap_descriptor.cpp b/src/ML-IAP/mliap_descriptor.cpp similarity index 100% rename from src/MLIAP/mliap_descriptor.cpp rename to src/ML-IAP/mliap_descriptor.cpp diff --git a/src/MLIAP/mliap_descriptor.h b/src/ML-IAP/mliap_descriptor.h similarity index 100% rename from src/MLIAP/mliap_descriptor.h rename to src/ML-IAP/mliap_descriptor.h diff --git a/src/MLIAP/mliap_descriptor_snap.cpp b/src/ML-IAP/mliap_descriptor_snap.cpp similarity index 100% rename from src/MLIAP/mliap_descriptor_snap.cpp rename to src/ML-IAP/mliap_descriptor_snap.cpp diff --git a/src/MLIAP/mliap_descriptor_snap.h b/src/ML-IAP/mliap_descriptor_snap.h similarity index 100% rename from src/MLIAP/mliap_descriptor_snap.h rename to src/ML-IAP/mliap_descriptor_snap.h diff --git a/src/MLIAP/mliap_descriptor_so3.cpp b/src/ML-IAP/mliap_descriptor_so3.cpp similarity index 100% rename from src/MLIAP/mliap_descriptor_so3.cpp rename to src/ML-IAP/mliap_descriptor_so3.cpp diff --git a/src/MLIAP/mliap_descriptor_so3.h b/src/ML-IAP/mliap_descriptor_so3.h similarity index 100% rename from src/MLIAP/mliap_descriptor_so3.h rename to src/ML-IAP/mliap_descriptor_so3.h diff --git a/src/MLIAP/mliap_model.cpp b/src/ML-IAP/mliap_model.cpp similarity index 72% rename from src/MLIAP/mliap_model.cpp rename to src/ML-IAP/mliap_model.cpp index f6491c926d..47c3cd54a6 100644 --- a/src/MLIAP/mliap_model.cpp +++ b/src/ML-IAP/mliap_model.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -51,9 +50,7 @@ MLIAPModel::~MLIAPModel() placeholder ------------------------------------------------------------------------- */ -void MLIAPModel::init() -{ -} +void MLIAPModel::init() {} /* ---------------------------------------------------------------------- set number of elements @@ -75,8 +72,8 @@ void MLIAPModel::set_ndescriptors(int ndescriptors_in) /* ---------------------------------------------------------------------- */ - -MLIAPModelSimple::MLIAPModelSimple(LAMMPS *lmp, char *coefffilename) : MLIAPModel(lmp, coefffilename) +MLIAPModelSimple::MLIAPModelSimple(LAMMPS *lmp, char *coefffilename) : + MLIAPModel(lmp, coefffilename) { if (coefffilename) read_coeffs(coefffilename); } @@ -90,37 +87,37 @@ void MLIAPModelSimple::read_coeffs(char *coefffilename) FILE *fpcoeff; if (comm->me == 0) { - fpcoeff = utils::open_potential(coefffilename,lmp,nullptr); + fpcoeff = utils::open_potential(coefffilename, lmp, nullptr); if (fpcoeff == nullptr) - error->one(FLERR,"Cannot open MLIAPModel coeff file {}: {}", - coefffilename,utils::getsyserror()); + error->one(FLERR, "Cannot open MLIAPModel coeff file {}: {}", coefffilename, + utils::getsyserror()); } - char line[MAXLINE],*ptr; + char line[MAXLINE], *ptr; int eof = 0; int n; int nwords = 0; while (nwords == 0) { if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fpcoeff); + ptr = fgets(line, MAXLINE, fpcoeff); if (ptr == nullptr) { eof = 1; fclose(fpcoeff); - } else n = strlen(line) + 1; + } else + n = strlen(line) + 1; } - MPI_Bcast(&eof,1,MPI_INT,0,world); + MPI_Bcast(&eof, 1, MPI_INT, 0, world); if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); + MPI_Bcast(&n, 1, MPI_INT, 0, world); + MPI_Bcast(line, n, MPI_CHAR, 0, world); // strip comment, skip line if blank - if ((ptr = strchr(line,'#'))) *ptr = '\0'; + if ((ptr = strchr(line, '#'))) *ptr = '\0'; nwords = utils::count_words(line); } - if (nwords != 2) - error->all(FLERR,"Incorrect format in MLIAPModel coefficient file"); + if (nwords != 2) error->all(FLERR, "Incorrect format in MLIAPModel coefficient file"); // words = ptrs to all words in line // strip single and double quotes from words @@ -130,45 +127,47 @@ void MLIAPModelSimple::read_coeffs(char *coefffilename) nelements = coeffs.next_int(); nparams = coeffs.next_int(); } catch (TokenizerException &e) { - error->all(FLERR,"Incorrect format in MLIAPModel coefficient " - "file: {}",e.what()); + error->all(FLERR, + "Incorrect format in MLIAPModel coefficient " + "file: {}", + e.what()); } // set up coeff lists memory->destroy(coeffelem); - memory->create(coeffelem,nelements,nparams,"mliap_snap_model:coeffelem"); + memory->create(coeffelem, nelements, nparams, "mliap_snap_model:coeffelem"); // Loop over nelements blocks in the coefficient file for (int ielem = 0; ielem < nelements; ielem++) { for (int icoeff = 0; icoeff < nparams; icoeff++) { if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fpcoeff); + ptr = fgets(line, MAXLINE, fpcoeff); if (ptr == nullptr) { eof = 1; fclose(fpcoeff); - } else n = strlen(line) + 1; + } else + n = strlen(line) + 1; } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) - error->all(FLERR,"Incorrect format in MLIAPModel coefficient file"); - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); + MPI_Bcast(&eof, 1, MPI_INT, 0, world); + if (eof) error->all(FLERR, "Incorrect format in MLIAPModel coefficient file"); + MPI_Bcast(&n, 1, MPI_INT, 0, world); + MPI_Bcast(line, n, MPI_CHAR, 0, world); try { ValueTokenizer coeffs(utils::trim_comment(line)); - if (coeffs.count() != 1) - throw TokenizerException("Wrong number of items",""); + if (coeffs.count() != 1) throw TokenizerException("Wrong number of items", ""); coeffelem[ielem][icoeff] = coeffs.next_double(); } catch (TokenizerException &e) { - error->all(FLERR,"Incorrect format in MLIAPModel " - "coefficient file: {}",e.what()); + error->all(FLERR, + "Incorrect format in MLIAPModel " + "coefficient file: {}", + e.what()); } } } - if (comm->me == 0) fclose(fpcoeff); } @@ -180,7 +179,6 @@ double MLIAPModelSimple::memory_usage() { double bytes = 0; - bytes += (double)nelements*nparams*sizeof(double); // coeffelem + bytes += (double) nelements * nparams * sizeof(double); // coeffelem return bytes; } - diff --git a/src/MLIAP/mliap_model.h b/src/ML-IAP/mliap_model.h similarity index 100% rename from src/MLIAP/mliap_model.h rename to src/ML-IAP/mliap_model.h diff --git a/src/MLIAP/mliap_model_linear.cpp b/src/ML-IAP/mliap_model_linear.cpp similarity index 100% rename from src/MLIAP/mliap_model_linear.cpp rename to src/ML-IAP/mliap_model_linear.cpp diff --git a/src/MLIAP/mliap_model_linear.h b/src/ML-IAP/mliap_model_linear.h similarity index 100% rename from src/MLIAP/mliap_model_linear.h rename to src/ML-IAP/mliap_model_linear.h diff --git a/src/MLIAP/mliap_model_nn.cpp b/src/ML-IAP/mliap_model_nn.cpp similarity index 100% rename from src/MLIAP/mliap_model_nn.cpp rename to src/ML-IAP/mliap_model_nn.cpp diff --git a/src/MLIAP/mliap_model_nn.h b/src/ML-IAP/mliap_model_nn.h similarity index 100% rename from src/MLIAP/mliap_model_nn.h rename to src/ML-IAP/mliap_model_nn.h diff --git a/src/MLIAP/mliap_model_python.cpp b/src/ML-IAP/mliap_model_python.cpp similarity index 81% rename from src/MLIAP/mliap_model_python.cpp rename to src/ML-IAP/mliap_model_python.cpp index cd985f273a..3d91107449 100644 --- a/src/MLIAP/mliap_model_python.cpp +++ b/src/ML-IAP/mliap_model_python.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -18,63 +17,63 @@ #ifdef MLIAP_PYTHON -#include #include "mliap_model_python.h" + +#include "error.h" +#include "lmppython.h" +#include "mliap_data.h" #include "mliap_model_python_couple.h" #include "pair_mliap.h" -#include "mliap_data.h" -#include "error.h" -#include "utils.h" -#include "lmppython.h" #include "python_compat.h" +#include "utils.h" +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -MLIAPModelPython::MLIAPModelPython(LAMMPS* lmp, char* coefffilename) : - MLIAPModel(lmp, coefffilename) +MLIAPModelPython::MLIAPModelPython(LAMMPS *lmp, char *coefffilename) : + MLIAPModel(lmp, coefffilename) { model_loaded = 0; python->init(); PyGILState_STATE gstate = PyGILState_Ensure(); - PyObject * pyMain = PyImport_AddModule("__main__"); + PyObject *pyMain = PyImport_AddModule("__main__"); if (!pyMain) { PyGILState_Release(gstate); - error->all(FLERR,"Could not initialize embedded Python"); + error->all(FLERR, "Could not initialize embedded Python"); } - PyObject* coupling_module = PyImport_ImportModule("mliap_model_python_couple"); + PyObject *coupling_module = PyImport_ImportModule("mliap_model_python_couple"); if (!coupling_module) { PyErr_Print(); PyErr_Clear(); PyGILState_Release(gstate); - error->all(FLERR,"Loading MLIAPPY coupling module failure."); + error->all(FLERR, "Loading MLIAPPY coupling module failure."); } // Recipe from lammps/src/pair_python.cpp : // add current directory to PYTHONPATH - PyObject * py_path = PySys_GetObject((char *)"path"); + PyObject *py_path = PySys_GetObject((char *) "path"); PyList_Append(py_path, PY_STRING_FROM_STRING(".")); // if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well - const char * potentials_path = getenv("LAMMPS_POTENTIALS"); - if (potentials_path != NULL) { - PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path)); - } + const char *potentials_path = getenv("LAMMPS_POTENTIALS"); + if (potentials_path != NULL) { PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path)); } PyGILState_Release(gstate); if (coefffilename) read_coeffs(coefffilename); - nonlinearflag=1; + nonlinearflag = 1; } /* ---------------------------------------------------------------------- */ -MLIAPModelPython::~MLIAPModelPython() { +MLIAPModelPython::~MLIAPModelPython() +{ MLIAPPY_unload_model(this); } @@ -82,7 +81,6 @@ MLIAPModelPython::~MLIAPModelPython() { get number of parameters ---------------------------------------------------------------------- */ - int MLIAPModelPython::get_nparams() { return nparams; @@ -97,15 +95,14 @@ void MLIAPModelPython::read_coeffs(char *fname) PyErr_Print(); PyErr_Clear(); PyGILState_Release(gstate); - error->all(FLERR,"Loading python model failure."); + error->all(FLERR, "Loading python model failure."); } PyGILState_Release(gstate); if (loaded) { this->connect_param_counts(); - } - else { - utils::logmesg(lmp,"Loading python model deferred.\n"); + } else { + utils::logmesg(lmp, "Loading python model deferred.\n"); } } @@ -121,15 +118,13 @@ void MLIAPModelPython::connect_param_counts() PyErr_Print(); PyErr_Clear(); PyGILState_Release(gstate); - error->all(FLERR,"Loading python model failure."); + error->all(FLERR, "Loading python model failure."); } PyGILState_Release(gstate); model_loaded = 1; - utils::logmesg(lmp,"Loading python model complete.\n"); - + utils::logmesg(lmp, "Loading python model complete.\n"); } - /* ---------------------------------------------------------------------- Calculate model gradients w.r.t descriptors for each atom beta_i = dE(B_i)/dB_i @@ -137,9 +132,7 @@ void MLIAPModelPython::connect_param_counts() void MLIAPModelPython::compute_gradients(MLIAPData *data) { - if (not model_loaded) { - error->all(FLERR,"Model not loaded."); - } + if (not model_loaded) { error->all(FLERR, "Model not loaded."); } PyGILState_STATE gstate = PyGILState_Ensure(); MLIAPPY_compute_gradients(this, data); @@ -147,10 +140,9 @@ void MLIAPModelPython::compute_gradients(MLIAPData *data) PyErr_Print(); PyErr_Clear(); PyGILState_Release(gstate); - error->all(FLERR,"Running python model failure."); + error->all(FLERR, "Running python model failure."); } PyGILState_Release(gstate); - } /* ---------------------------------------------------------------------- @@ -170,7 +162,7 @@ void MLIAPModelPython::compute_gradients(MLIAPData *data) void MLIAPModelPython::compute_gradgrads(class MLIAPData *) { - error->all(FLERR,"compute_gradgrads not implemented"); + error->all(FLERR, "compute_gradgrads not implemented"); } /* ---------------------------------------------------------------------- @@ -180,7 +172,7 @@ void MLIAPModelPython::compute_gradgrads(class MLIAPData *) void MLIAPModelPython::compute_force_gradients(class MLIAPData *) { - error->all(FLERR,"compute_force_gradients not implemented"); + error->all(FLERR, "compute_force_gradients not implemented"); } /* ---------------------------------------------------------------------- @@ -193,7 +185,6 @@ int MLIAPModelPython::get_gamma_nnz(class MLIAPData *) return 0; } - double MLIAPModelPython::memory_usage() { // todo: get approximate memory usage in coupling code. diff --git a/src/MLIAP/mliap_model_python.h b/src/ML-IAP/mliap_model_python.h similarity index 100% rename from src/MLIAP/mliap_model_python.h rename to src/ML-IAP/mliap_model_python.h diff --git a/src/MLIAP/mliap_model_python_couple.pyx b/src/ML-IAP/mliap_model_python_couple.pyx similarity index 100% rename from src/MLIAP/mliap_model_python_couple.pyx rename to src/ML-IAP/mliap_model_python_couple.pyx diff --git a/src/MLIAP/mliap_model_quadratic.cpp b/src/ML-IAP/mliap_model_quadratic.cpp similarity index 100% rename from src/MLIAP/mliap_model_quadratic.cpp rename to src/ML-IAP/mliap_model_quadratic.cpp diff --git a/src/MLIAP/mliap_model_quadratic.h b/src/ML-IAP/mliap_model_quadratic.h similarity index 100% rename from src/MLIAP/mliap_model_quadratic.h rename to src/ML-IAP/mliap_model_quadratic.h diff --git a/src/MLIAP/mliap_so3.cpp b/src/ML-IAP/mliap_so3.cpp similarity index 100% rename from src/MLIAP/mliap_so3.cpp rename to src/ML-IAP/mliap_so3.cpp diff --git a/src/MLIAP/mliap_so3.h b/src/ML-IAP/mliap_so3.h similarity index 100% rename from src/MLIAP/mliap_so3.h rename to src/ML-IAP/mliap_so3.h diff --git a/src/MLIAP/mliap_so3_math.h b/src/ML-IAP/mliap_so3_math.h similarity index 100% rename from src/MLIAP/mliap_so3_math.h rename to src/ML-IAP/mliap_so3_math.h diff --git a/src/MLIAP/pair_mliap.cpp b/src/ML-IAP/pair_mliap.cpp similarity index 100% rename from src/MLIAP/pair_mliap.cpp rename to src/ML-IAP/pair_mliap.cpp diff --git a/src/MLIAP/pair_mliap.h b/src/ML-IAP/pair_mliap.h similarity index 100% rename from src/MLIAP/pair_mliap.h rename to src/ML-IAP/pair_mliap.h diff --git a/src/USER-PACE/Install.sh b/src/ML-PACE/Install.sh similarity index 100% rename from src/USER-PACE/Install.sh rename to src/ML-PACE/Install.sh diff --git a/src/USER-PACE/README b/src/ML-PACE/README similarity index 89% rename from src/USER-PACE/README rename to src/ML-PACE/README index c701a615f7..7909b68dd3 100644 --- a/src/USER-PACE/README +++ b/src/ML-PACE/README @@ -1,4 +1,4 @@ -The USER-PACE package provides the pace pair style, +The ML-PACE package provides the pace pair style, an efficient implementation of the Atomic Cluster Expansion potential (ACE). @@ -17,7 +17,7 @@ provided to help automate the process. Also see the LAMMPS manual for general information on building LAMMPS with external libraries using either traditional make or CMake. -More information about the USER-PACE implementation of ACE +More information about the ML-PACE implementation of ACE is available here: https://github.com/ICAMS/lammps-user-pace diff --git a/src/USER-PACE/pair_pace.cpp b/src/ML-PACE/pair_pace.cpp similarity index 100% rename from src/USER-PACE/pair_pace.cpp rename to src/ML-PACE/pair_pace.cpp diff --git a/src/USER-PACE/pair_pace.h b/src/ML-PACE/pair_pace.h similarity index 100% rename from src/USER-PACE/pair_pace.h rename to src/ML-PACE/pair_pace.h diff --git a/src/USER-QUIP/Install.sh b/src/ML-QUIP/Install.sh similarity index 100% rename from src/USER-QUIP/Install.sh rename to src/ML-QUIP/Install.sh diff --git a/src/USER-QUIP/README b/src/ML-QUIP/README similarity index 82% rename from src/USER-QUIP/README rename to src/ML-QUIP/README index 5bd9c45181..0e82248dd5 100644 --- a/src/USER-QUIP/README +++ b/src/ML-QUIP/README @@ -6,5 +6,5 @@ Potential (GAP) models. See lib/quip/README for more information on how to build LAMMPS with this package. -See examples/USER/quip for several test examples that run QUIP +See examples/PACKAGES/quip for several test examples that run QUIP potentials. diff --git a/src/USER-QUIP/pair_quip.cpp b/src/ML-QUIP/pair_quip.cpp similarity index 100% rename from src/USER-QUIP/pair_quip.cpp rename to src/ML-QUIP/pair_quip.cpp diff --git a/src/USER-QUIP/pair_quip.h b/src/ML-QUIP/pair_quip.h similarity index 100% rename from src/USER-QUIP/pair_quip.h rename to src/ML-QUIP/pair_quip.h diff --git a/src/USER-RANN/pair_rann.cpp b/src/ML-RANN/pair_rann.cpp similarity index 99% rename from src/USER-RANN/pair_rann.cpp rename to src/ML-RANN/pair_rann.cpp index 59ad688cb5..66e5bb107e 100644 --- a/src/USER-RANN/pair_rann.cpp +++ b/src/ML-RANN/pair_rann.cpp @@ -62,7 +62,7 @@ DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918 using namespace LAMMPS_NS; static const char cite_user_rann_package[] = - "USER-RANN package:\n\n" + "ML-RANN package:\n\n" "@Article{Nitol2021,\n" " author = {Nitol, Mashroor S and Dickel, Doyl E and Barrett, Christopher D},\n" " title = {Artificial neural network potential for pure zinc},\n" diff --git a/src/USER-RANN/pair_rann.h b/src/ML-RANN/pair_rann.h similarity index 100% rename from src/USER-RANN/pair_rann.h rename to src/ML-RANN/pair_rann.h diff --git a/src/USER-RANN/rann_activation.h b/src/ML-RANN/rann_activation.h similarity index 100% rename from src/USER-RANN/rann_activation.h rename to src/ML-RANN/rann_activation.h diff --git a/src/USER-RANN/rann_activation_linear.h b/src/ML-RANN/rann_activation_linear.h similarity index 100% rename from src/USER-RANN/rann_activation_linear.h rename to src/ML-RANN/rann_activation_linear.h diff --git a/src/USER-RANN/rann_activation_sig_i.h b/src/ML-RANN/rann_activation_sig_i.h similarity index 100% rename from src/USER-RANN/rann_activation_sig_i.h rename to src/ML-RANN/rann_activation_sig_i.h diff --git a/src/USER-RANN/rann_fingerprint.cpp b/src/ML-RANN/rann_fingerprint.cpp similarity index 100% rename from src/USER-RANN/rann_fingerprint.cpp rename to src/ML-RANN/rann_fingerprint.cpp diff --git a/src/USER-RANN/rann_fingerprint.h b/src/ML-RANN/rann_fingerprint.h similarity index 100% rename from src/USER-RANN/rann_fingerprint.h rename to src/ML-RANN/rann_fingerprint.h diff --git a/src/USER-RANN/rann_fingerprint_bond.cpp b/src/ML-RANN/rann_fingerprint_bond.cpp similarity index 100% rename from src/USER-RANN/rann_fingerprint_bond.cpp rename to src/ML-RANN/rann_fingerprint_bond.cpp diff --git a/src/USER-RANN/rann_fingerprint_bond.h b/src/ML-RANN/rann_fingerprint_bond.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_bond.h rename to src/ML-RANN/rann_fingerprint_bond.h diff --git a/src/USER-RANN/rann_fingerprint_bondscreened.cpp b/src/ML-RANN/rann_fingerprint_bondscreened.cpp similarity index 100% rename from src/USER-RANN/rann_fingerprint_bondscreened.cpp rename to src/ML-RANN/rann_fingerprint_bondscreened.cpp diff --git a/src/USER-RANN/rann_fingerprint_bondscreened.h b/src/ML-RANN/rann_fingerprint_bondscreened.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_bondscreened.h rename to src/ML-RANN/rann_fingerprint_bondscreened.h diff --git a/src/USER-RANN/rann_fingerprint_bondscreenedspin.cpp b/src/ML-RANN/rann_fingerprint_bondscreenedspin.cpp similarity index 100% rename from src/USER-RANN/rann_fingerprint_bondscreenedspin.cpp rename to src/ML-RANN/rann_fingerprint_bondscreenedspin.cpp diff --git a/src/USER-RANN/rann_fingerprint_bondscreenedspin.h b/src/ML-RANN/rann_fingerprint_bondscreenedspin.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_bondscreenedspin.h rename to src/ML-RANN/rann_fingerprint_bondscreenedspin.h diff --git a/src/USER-RANN/rann_fingerprint_bondspin.cpp b/src/ML-RANN/rann_fingerprint_bondspin.cpp similarity index 100% rename from src/USER-RANN/rann_fingerprint_bondspin.cpp rename to src/ML-RANN/rann_fingerprint_bondspin.cpp diff --git a/src/USER-RANN/rann_fingerprint_bondspin.h b/src/ML-RANN/rann_fingerprint_bondspin.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_bondspin.h rename to src/ML-RANN/rann_fingerprint_bondspin.h diff --git a/src/USER-RANN/rann_fingerprint_radial.cpp b/src/ML-RANN/rann_fingerprint_radial.cpp similarity index 100% rename from src/USER-RANN/rann_fingerprint_radial.cpp rename to src/ML-RANN/rann_fingerprint_radial.cpp diff --git a/src/USER-RANN/rann_fingerprint_radial.h b/src/ML-RANN/rann_fingerprint_radial.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_radial.h rename to src/ML-RANN/rann_fingerprint_radial.h diff --git a/src/USER-RANN/rann_fingerprint_radialscreened.cpp b/src/ML-RANN/rann_fingerprint_radialscreened.cpp similarity index 100% rename from src/USER-RANN/rann_fingerprint_radialscreened.cpp rename to src/ML-RANN/rann_fingerprint_radialscreened.cpp diff --git a/src/USER-RANN/rann_fingerprint_radialscreened.h b/src/ML-RANN/rann_fingerprint_radialscreened.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_radialscreened.h rename to src/ML-RANN/rann_fingerprint_radialscreened.h diff --git a/src/USER-RANN/rann_fingerprint_radialscreenedspin.cpp b/src/ML-RANN/rann_fingerprint_radialscreenedspin.cpp similarity index 100% rename from src/USER-RANN/rann_fingerprint_radialscreenedspin.cpp rename to src/ML-RANN/rann_fingerprint_radialscreenedspin.cpp diff --git a/src/USER-RANN/rann_fingerprint_radialscreenedspin.h b/src/ML-RANN/rann_fingerprint_radialscreenedspin.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_radialscreenedspin.h rename to src/ML-RANN/rann_fingerprint_radialscreenedspin.h diff --git a/src/USER-RANN/rann_fingerprint_radialspin.cpp b/src/ML-RANN/rann_fingerprint_radialspin.cpp similarity index 100% rename from src/USER-RANN/rann_fingerprint_radialspin.cpp rename to src/ML-RANN/rann_fingerprint_radialspin.cpp diff --git a/src/USER-RANN/rann_fingerprint_radialspin.h b/src/ML-RANN/rann_fingerprint_radialspin.h similarity index 100% rename from src/USER-RANN/rann_fingerprint_radialspin.h rename to src/ML-RANN/rann_fingerprint_radialspin.h diff --git a/src/SNAP/compute_sna_atom.cpp b/src/ML-SNAP/compute_sna_atom.cpp similarity index 100% rename from src/SNAP/compute_sna_atom.cpp rename to src/ML-SNAP/compute_sna_atom.cpp diff --git a/src/SNAP/compute_sna_atom.h b/src/ML-SNAP/compute_sna_atom.h similarity index 100% rename from src/SNAP/compute_sna_atom.h rename to src/ML-SNAP/compute_sna_atom.h diff --git a/src/SNAP/compute_snad_atom.cpp b/src/ML-SNAP/compute_snad_atom.cpp similarity index 100% rename from src/SNAP/compute_snad_atom.cpp rename to src/ML-SNAP/compute_snad_atom.cpp diff --git a/src/SNAP/compute_snad_atom.h b/src/ML-SNAP/compute_snad_atom.h similarity index 100% rename from src/SNAP/compute_snad_atom.h rename to src/ML-SNAP/compute_snad_atom.h diff --git a/src/SNAP/compute_snap.cpp b/src/ML-SNAP/compute_snap.cpp similarity index 100% rename from src/SNAP/compute_snap.cpp rename to src/ML-SNAP/compute_snap.cpp diff --git a/src/SNAP/compute_snap.h b/src/ML-SNAP/compute_snap.h similarity index 100% rename from src/SNAP/compute_snap.h rename to src/ML-SNAP/compute_snap.h diff --git a/src/SNAP/compute_snav_atom.cpp b/src/ML-SNAP/compute_snav_atom.cpp similarity index 100% rename from src/SNAP/compute_snav_atom.cpp rename to src/ML-SNAP/compute_snav_atom.cpp diff --git a/src/SNAP/compute_snav_atom.h b/src/ML-SNAP/compute_snav_atom.h similarity index 100% rename from src/SNAP/compute_snav_atom.h rename to src/ML-SNAP/compute_snav_atom.h diff --git a/src/SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp similarity index 100% rename from src/SNAP/pair_snap.cpp rename to src/ML-SNAP/pair_snap.cpp diff --git a/src/SNAP/pair_snap.h b/src/ML-SNAP/pair_snap.h similarity index 100% rename from src/SNAP/pair_snap.h rename to src/ML-SNAP/pair_snap.h diff --git a/src/SNAP/sna.cpp b/src/ML-SNAP/sna.cpp similarity index 100% rename from src/SNAP/sna.cpp rename to src/ML-SNAP/sna.cpp diff --git a/src/SNAP/sna.h b/src/ML-SNAP/sna.h similarity index 100% rename from src/SNAP/sna.h rename to src/ML-SNAP/sna.h diff --git a/src/MLIAP/README.md b/src/MLIAP/README.md deleted file mode 100644 index b5cdc337f5..0000000000 --- a/src/MLIAP/README.md +++ /dev/null @@ -1,41 +0,0 @@ -This package provides a general interface to families of machine-learning interatomic potentials (MLIAPs). -This interface consists of a `mliap pair style` and a `mliap compute`. -The `mliap pair style` is used when running simulations with energies and -forces calculated by an MLIAP. The interface allows separate -definitions of the interatomic potential functional form (`model`) -and the geometric quantities that characterize the atomic positions -(`descriptor`). By defining `model` and `descriptor` separately, -it is possible to use many different models with a given descriptor, -or many different descriptors with a given model. The pair_style -supports the following models: - -- `linear`, -- `quadratic`, -- `nn` (neural networks) -- `mliappy` (general Python interface to things like PyTorch). - -It currently supports only one class of descriptors, `sna`, the SNAP descriptors. -It is straightforward to add new descriptor and model styles. - -The `mliap compute` style provides gradients of the energy, force, -and stress tensor w.r.t. model parameters. -These are useful when training MLIAPs to match target data. -Any `model` or `descriptor` that has been implemented for the -`mliap` pair style can also be accessed by the `mliap` compute. -In addition to the energy, force, and stress gradients, w.r.t. -each `model` parameter, the compute also calculates the energy, -force, and stress contributions from a user-specified -reference potential. - -## Generating the model files from the third-party packages -- To train the `linear` and `quadratic` models with the SNAP descriptors, see the examples in [FitSNAP](https://github.com/FitSNAP/FitSNAP). -- To train the `nn` model with the SNAP descriptors, check the examples in [PyXtal\_FF](https://github.com/qzhu2017/PyXtal_FF). - -## Building MLIAP with Python support - -The `mliappy` energy model requires that the MLIAP package be compiled with Python support enabled. This extension, written by Nick Lubbers (LANL), provides a coupling to PyTorch and other Python modules. This should be automatically enabled by default if the prerequisite software is installed. It can be enforced during CMake configuration by setting the variable `MLIAP_ENABLE_PYTHON=yes` or for conventional build by adding `-DMLIAP_PYTHON` to the `LMP_INC` variable in your makefile and running the cythonize script on the .pyx file(s) copied to the src folder. - -This requires to also install the PYTHON package and have the [cython](https://cython.org) software installed. During configuration/compilation -the cythonize script will be used to convert the provided .pyx file(s) to C++ code. Please do not run the cythonize script in the src/MLIAP folder. If you have done so by accident, you need to delete the generated .cpp and .h file(s) in the src/MLIAP folder or there may be problems during compilation. - -More information on building LAMMPS with this package is [here](https://docs.lammps.org/Build_extras.html#mliap). diff --git a/src/USER-MOFFF/README b/src/MOFFF/README similarity index 98% rename from src/USER-MOFFF/README rename to src/MOFFF/README index 237ac9ba53..fa3cb0ef87 100644 --- a/src/USER-MOFFF/README +++ b/src/MOFFF/README @@ -25,7 +25,7 @@ See the doc pages for "pair_style buck6d/coul/gauss", "anlge_style class2", commands to get started. Also see the above mentioned website and literature for further documentation about the force field. -There are example scripts for using this force field in examples/USER/mofff. +There are example scripts for using this force field in examples/PACKAGES/mofff. The creators of this package are Hendrik Heenen (hendrik.heenen at mytum.de) and Rochus Schmid (rochus.schmid at rub.de). Contact them directly if you diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/MOFFF/angle_class2_p6.cpp similarity index 100% rename from src/USER-MOFFF/angle_class2_p6.cpp rename to src/MOFFF/angle_class2_p6.cpp diff --git a/src/USER-MOFFF/angle_class2_p6.h b/src/MOFFF/angle_class2_p6.h similarity index 100% rename from src/USER-MOFFF/angle_class2_p6.h rename to src/MOFFF/angle_class2_p6.h diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/MOFFF/angle_cosine_buck6d.cpp similarity index 100% rename from src/USER-MOFFF/angle_cosine_buck6d.cpp rename to src/MOFFF/angle_cosine_buck6d.cpp diff --git a/src/USER-MOFFF/angle_cosine_buck6d.h b/src/MOFFF/angle_cosine_buck6d.h similarity index 100% rename from src/USER-MOFFF/angle_cosine_buck6d.h rename to src/MOFFF/angle_cosine_buck6d.h diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/MOFFF/improper_inversion_harmonic.cpp similarity index 100% rename from src/USER-MOFFF/improper_inversion_harmonic.cpp rename to src/MOFFF/improper_inversion_harmonic.cpp diff --git a/src/USER-MOFFF/improper_inversion_harmonic.h b/src/MOFFF/improper_inversion_harmonic.h similarity index 100% rename from src/USER-MOFFF/improper_inversion_harmonic.h rename to src/MOFFF/improper_inversion_harmonic.h diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp similarity index 100% rename from src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp rename to src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.h b/src/MOFFF/pair_buck6d_coul_gauss_dsf.h similarity index 100% rename from src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.h rename to src/MOFFF/pair_buck6d_coul_gauss_dsf.h diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/MOFFF/pair_buck6d_coul_gauss_long.cpp similarity index 100% rename from src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp rename to src/MOFFF/pair_buck6d_coul_gauss_long.cpp diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.h b/src/MOFFF/pair_buck6d_coul_gauss_long.h similarity index 100% rename from src/USER-MOFFF/pair_buck6d_coul_gauss_long.h rename to src/MOFFF/pair_buck6d_coul_gauss_long.h diff --git a/src/USER-MOLFILE/Install.sh b/src/MOLFILE/Install.sh similarity index 100% rename from src/USER-MOLFILE/Install.sh rename to src/MOLFILE/Install.sh diff --git a/src/USER-MOLFILE/README b/src/MOLFILE/README similarity index 100% rename from src/USER-MOLFILE/README rename to src/MOLFILE/README diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/MOLFILE/dump_molfile.cpp similarity index 100% rename from src/USER-MOLFILE/dump_molfile.cpp rename to src/MOLFILE/dump_molfile.cpp diff --git a/src/USER-MOLFILE/dump_molfile.h b/src/MOLFILE/dump_molfile.h similarity index 100% rename from src/USER-MOLFILE/dump_molfile.h rename to src/MOLFILE/dump_molfile.h diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/MOLFILE/molfile_interface.cpp similarity index 100% rename from src/USER-MOLFILE/molfile_interface.cpp rename to src/MOLFILE/molfile_interface.cpp diff --git a/src/USER-MOLFILE/molfile_interface.h b/src/MOLFILE/molfile_interface.h similarity index 100% rename from src/USER-MOLFILE/molfile_interface.h rename to src/MOLFILE/molfile_interface.h diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/MOLFILE/reader_molfile.cpp similarity index 100% rename from src/USER-MOLFILE/reader_molfile.cpp rename to src/MOLFILE/reader_molfile.cpp diff --git a/src/USER-MOLFILE/reader_molfile.h b/src/MOLFILE/reader_molfile.h similarity index 100% rename from src/USER-MOLFILE/reader_molfile.h rename to src/MOLFILE/reader_molfile.h diff --git a/src/MSCG/README b/src/MSCG/README index ab64c26792..3008fbbd22 100644 --- a/src/MSCG/README +++ b/src/MSCG/README @@ -1,4 +1,4 @@ -The USER-MSCG package adds a fix mscg command, which carries out +The MSCG package adds a fix mscg command, which carries out multi-scale coarse-graining for the parameterization of coarse-grained (CG) interactions. diff --git a/src/Makefile b/src/Makefile index 5e7a3c000f..52dff05148 100644 --- a/src/Makefile +++ b/src/Makefile @@ -37,8 +37,9 @@ endif # Package variables -# PACKAGE = standard packages -# PACKUSER = user packagse +# PACKAGE = all packages +# PACKBASIC = a few core packages +# PACKMOST = most packages that do not require additional libs # PACKLIB = all packages that require an additional lib # should be PACKSYS + PACKINT + PACKEXT # PACKSYS = subset that reqiure a common system library @@ -46,35 +47,200 @@ endif # PACKINT = subset that require an internal (provided) library # PACKEXT = subset that require an external (downloaded) library -PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ - granular kim kokkos kspace latte manybody mc message misc \ - mliap molecule mpiio mscg opt peri plugin poems \ - python qeq replica rigid shock snap spin srd voronoi +PACKAGE = \ + adios \ + asphere \ + awpmd \ + bocs \ + body \ + brownian \ + cg-dna \ + cg-sdk\ + class2 \ + colloid \ + colvars \ + compress \ + coreshell \ + diffraction \ + dipole \ + dpd-basic \ + dpd-meso \ + dpd-react \ + dpd-smooth \ + drude \ + eff \ + fep \ + gpu \ + granular \ + h5md \ + intel \ + kim \ + kokkos \ + kspace \ + latboltz \ + latte \ + machdyn \ + manifold \ + manybody \ + mc \ + mdi \ + meam \ + mesont \ + message \ + mgpt \ + misc \ + ml-hdnnp \ + ml-pace \ + ml-quip \ + ml-rann \ + ml-snap \ + mofff \ + molecule \ + molfile \ + mpiio \ + mscg \ + netcdf \ + openmp \ + opt \ + peri \ + plugin \ + plumed \ + poems \ + ptm \ + python \ + qeq \ + qmmm \ + qtb \ + reaction \ + reaxff \ + replica \ + rigid \ + scafacos \ + shock \ + smtbq \ + sph \ + spin \ + srd \ + tally \ + uef \ + user-misc \ + voronoi \ + vtk \ + yaff \ + atc \ + dielectric \ + ml-iap \ + phonon -PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs user-cgdna \ - user-cgsdk user-colvars user-dielectric user-diffraction user-dpd user-drude \ - user-eff user-fep user-h5md user-hdnnp user-intel user-lb user-manifold \ - user-mdi user-meamc user-mesodpd user-mesont user-mgpt user-misc \ - user-mofff user-molfile user-netcdf user-omp user-phonon \ - user-pace user-plumed user-ptm user-qmmm user-qtb user-quip \ - user-rann user-reaction user-reaxc user-scafacos user-smd user-smtbq \ - user-sdpd user-sph user-tally user-uef user-vtk user-yaff +# NOTE: the last four packages must remain at the end since +# they depend on other packages to be installed first. -PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \ - user-adios user-atc user-awpmd user-colvars user-h5md user-hdnnp user-lb user-mdi \ - user-mesont user-molfile user-netcdf user-pace user-plumed user-qmmm user-quip \ - user-scafacos user-smd user-vtk +PACKBASIC = kspace manybody molecule rigid -PACKSYS = compress mpiio python user-lb +PACKMOST = \ + asphere \ + bocs \ + body \ + brownian \ + cg-dna \ + cg-sdk \ + class2 \ + colloid \ + coreshell \ + diffraction \ + dipole \ + dpd-basic \ + dpd-meso \ + dpd-react \ + dpd-smooth \ + drude \ + eff \ + fep \ + granular \ + kspace \ + manybody \ + mc \ + meam \ + misc \ + ml-snap \ + mofff \ + molecule \ + openmp \ + opt \ + peri \ + plugin \ + poems \ + qeq \ + reaction \ + reaxff \ + replica \ + rigid \ + shock \ + sph \ + spin \ + srd \ + uef \ + user-misc \ + yaff \ + dielectric \ + ml-iap \ + phonon -PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont \ - user-mdi +# NOTE: the last three packages must remain at the end since +# they depend on other packages to be installed first. -PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md user-hdnnp user-molfile user-netcdf user-pace user-plumed \ - user-qmmm user-quip user-scafacos user-smd user-vtk +PACKLIB = \ + compress \ + gpu \ + kim \ + kokkos \ + latte \ + message \ + mpiio \ + mscg \ + poems \ + python \ + voronoi \ + adios \ + atc \ + awpmd \ + colvars \ + h5md \ + ml-hdnnp \ + latboltz \ + mdi \ + mesont \ + molfile \ + netcdf \ + ml-pace \ + plumed \ + qmmm \ + ml-quip \ + scafacos \ + machdyn \ + vtk -PACKALL = $(PACKAGE) $(PACKUSER) +PACKSYS = compress latboltz mpiio python + +PACKINT = atc awpmd colvars gpu kokkos mesont message poems + +PACKEXT = \ + adios \ + h5md \ + kim \ + latte \ + machdyn \ + ml-hdnnp \ + ml-pace \ + ml-quip \ + molfile \ + mscg \ + netcdf \ + plumed \ + qmmm \ + scafacos \ + voronoi \ + vtk \ # Helper GNU make function for conversion to upper case without using shell commands uppercase_TABLE:=a,A b,B c,C d,D e,E f,F g,G h,H i,I j,J k,K l,L m,M n,N o,O p,P q,Q r,R s,S t,T u,U v,V w,W x,X y,Y z,Z @@ -87,7 +253,7 @@ PACKUSERUC = $(call uppercase,$(PACKUSER)) YESDIR = $(call uppercase,$(@:yes-%=%)) NODIR = $(call uppercase,$(@:no-%=%)) LIBDIR = $(@:lib-%=%) -LIBUSERDIR = $(@:lib-user-%=%) +LIBUSERDIR = $(@:lib-%=%) # List of all targets @@ -106,10 +272,10 @@ help: @echo 'make no-package remove a single pkg from src dir' @echo 'make yes-all install all pgks in src dir' @echo 'make no-all remove all pkgs from src dir' - @echo 'make yes-standard (yes-std) install all standard pkgs' - @echo 'make no-standard (no-std) remove all standard pkgs' - @echo 'make yes-user install all user pkgs' - @echo 'make no-user remove all user pkgs' + @echo 'make yes-basic install a few commonly used pgks' + @echo 'make no-basic remove a few commonly used pkgs' + @echo 'make yes-most install most pgks w/o libs' + @echo 'make no-most remove most pgks w/o libs' @echo 'make yes-lib install all pkgs with libs (included or ext)' @echo 'make no-lib remove all pkgs with libs (included or ext)' @echo 'make yes-ext install all pkgs with external libs' @@ -314,14 +480,14 @@ package: @echo 'make package-installed (pi) list of installed packages' @echo 'make yes-package install a single pgk in src dir' @echo 'make no-package remove a single pkg from src dir' + @echo 'make yes-basic install a few commonly used pgks in src' + @echo 'make no-basic remove a few commonly used pkgs from src dir' + @echo 'make yes-most install most pgks w/o libs in src' + @echo 'make no-most remove most pkgs w/o libs from src dir' @echo 'make yes-all install all pgks in src dir' @echo 'make no-all remove all pkgs from src dir' - @echo 'make yes-standard (yes-std) install all standard pkgs' - @echo 'make no-standard (no-std) remove all standard pkgs' - @echo 'make yes-user install all user pkgs' - @echo 'make no-user remove all user pkgs' - @echo 'make yes-lib install all pkgs with libs (included or ext)' - @echo 'make no-lib remove all pkgs with libs (included or ext)' + @echo 'make yes-lib install all pkgs with libs (included or ext)' + @echo 'make no-lib remove all pkgs with libs (included or ext)' @echo 'make yes-ext install all pkgs with external libs' @echo 'make no-ext remove all pkgs with external libs' @echo '' @@ -332,22 +498,34 @@ package: @echo 'make lib-package build and/or download a package library' yes-all: - @for p in $(PACKALL); do $(MAKE) yes-$$p; done - -no-all: - @for p in $(PACKALL); do $(MAKE) no-$$p; done - -yes-standard yes-std: @for p in $(PACKAGE); do $(MAKE) yes-$$p; done -no-standard no-std: +no-all: @for p in $(PACKAGE); do $(MAKE) no-$$p; done +yes-standard yes-std: + @echo 'There are no more "standard" or "user" packages in LAMMPS' + +no-standard no-std: + @echo 'There are no more "standard" or "user" packages in LAMMPS' + yes-user: - @for p in $(PACKUSER); do $(MAKE) yes-$$p; done + @echo 'There are no more "standard" or "user" packages in LAMMPS' no-user: - @for p in $(PACKUSER); do $(MAKE) no-$$p; done + @echo 'There are no more "standard" or "user" packages in LAMMPS' + +yes-basic: + @for p in $(PACKBASIC); do $(MAKE) yes-$$p; done + +no-basic: + @for p in $(PACKBASIC); do $(MAKE) no-$$p; done + +yes-most: + @for p in $(PACKMOST); do $(MAKE) yes-$$p; done + +no-most: + @for p in $(PACKMOST); do $(MAKE) no-$$p; done yes-lib: @for p in $(PACKLIB); do $(MAKE) yes-$$p; done @@ -400,7 +578,7 @@ lib-%: echo "Installing lib $(@:lib-%=%)"; \ ( cd ../lib/$(LIBDIR); $(PYTHON) Install.py $(args) ); \ elif [ -e ../lib/$(LIBUSERDIR)/Install.py ]; then \ - echo "Installing lib $(@:lib-user-%=%)"; \ + echo "Installing lib $(@:lib-%=%)"; \ ( cd ../lib/$(LIBUSERDIR); $(PYTHON) Install.py $(args) ); \ else \ echo "Install script for lib $(@:lib-%=%) does not exist"; \ diff --git a/src/Makefile.txt b/src/Makefile.txt deleted file mode 100644 index 5542ed0cc5..0000000000 --- a/src/Makefile.txt +++ /dev/null @@ -1,443 +0,0 @@ -# LAMMPS multiple-machine -*- Makefile -*- - -SHELL = /bin/bash -PYTHON = python - -#.IGNORE: - -# Definitions - -ROOT = lmp -EXE = lmp_$@ -ARLIB = liblammps_$@.a -SHLIB = liblammps_$@.so -ARLINK = liblammps.a -SHLINK = liblammps.so -TMPNAME= tmp_$@_name -LMPLINK= -L. -llammps_$@ - -OBJDIR = Obj_$@ -OBJSHDIR = Obj_shared_$@ - -SRC = $(wildcard *.cpp) -INC = $(filter-out lmpinstalledpkgs.h lmpgitversion.h,$(wildcard *.h)) -OBJ = $(SRC:.cpp=.o) - -SRCLIB = $(filter-out main.cpp,$(SRC)) -OBJLIB = $(filter-out main.o,$(OBJ)) - -# Command-line options for mode: static (default), shared, or print - -mode = static -objdir = $(OBJDIR) - -ifeq ($(mode),shared) -objdir = $(OBJSHDIR) -endif - -# Package variables - -# PACKAGE = standard packages -# PACKUSER = user packagse -# PACKLIB = all packages that require an additional lib -# should be PACKSYS + PACKINT + PACKEXT -# PACKSYS = subset that reqiure a common system library -# include MPIIO and LB b/c require full MPI, not just STUBS -# PACKINT = subset that require an internal (provided) library -# PACKEXT = subset that require an external (downloaded) library - -PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ - granular kim kokkos kspace latte manybody mc message misc \ - mliap molecule mpiio mscg opt peri plugin poems \ - python qeq replica rigid shock snap spin srd voronoi - -PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ - user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ - user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ - user-mgpt user-misc user-mofff user-molfile \ - user-netcdf user-omp user-phonon user-pace user-plumed user-ptm user-qmmm \ - user-qtb user-quip user-rann user-reaction user-reaxc user-scafacos user-smd user-smtbq \ - user-sdpd user-sph user-tally user-uef user-vtk user-yaff - -PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ - python voronoi \ - user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ - user-netcdf user-plumed user-qmmm user-quip user-scafacos \ - user-smd user-vtk user-mesont user-pace - -PACKSYS = compress mpiio python user-lb - -PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont - -PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \ - user-qmmm user-quip user-smd user-vtk - -PACKALL = $(PACKAGE) $(PACKUSER) - -# Helper GNU make function for conversion to upper case without using shell commands -uppercase_TABLE:=a,A b,B c,C d,D e,E f,F g,G h,H i,I j,J k,K l,L m,M n,N o,O p,P q,Q r,R s,S t,T u,U v,V w,W x,X y,Y z,Z -uppercase_internal=$(if $1,$$(subst $(firstword $1),$(call uppercase_internal,$(wordlist 2,$(words $1),$1),$2)),$2) -uppercase=$(eval uppercase_RESULT:=$(call uppercase_internal,$(uppercase_TABLE),$1))$(uppercase_RESULT) - -PACKAGEUC = $(call uppercase,$(PACKAGE)) -PACKUSERUC = $(call uppercase,$(PACKUSER)) - -YESDIR = $(call uppercase,$(@:yes-%=%)) -NODIR = $(call uppercase,$(@:no-%=%)) -LIBDIR = $(@:lib-%=%) -LIBUSERDIR = $(@:lib-user-%=%) - -# List of all targets - -help: - @echo '' - @echo 'make clean-all delete all object files' - @echo 'make clean-machine delete object files for one machine' - @echo 'make mpi-stubs build dummy MPI library in STUBS' - @echo 'make install-python install LAMMPS wrapper in Python' - @echo 'make tar create lmp_src.tar.gz for src dir and packages' - @echo '' - @echo 'make package list available packages and their dependencies' - @echo 'make package-status (ps) status of all packages' - @echo 'make package-installed (pi) list of installed packages' - @echo 'make yes-package install a single pgk in src dir' - @echo 'make no-package remove a single pkg from src dir' - @echo 'make yes-all install all pgks in src dir' - @echo 'make no-all remove all pkgs from src dir' - @echo 'make yes-standard (yes-std) install all standard pkgs' - @echo 'make no-standard (no-std) remove all standard pkgs' - @echo 'make yes-user install all user pkgs' - @echo 'make no-user remove all user pkgs' - @echo 'make yes-lib install all pkgs with libs (included or ext)' - @echo 'make no-lib remove all pkgs with libs (included or ext)' - @echo 'make yes-ext install all pkgs with external libs' - @echo 'make no-ext remove all pkgs with external libs' - @echo '' - @echo 'make package-update (pu) replace src files with updated package files' - @echo 'make package-overwrite replace package files with src files' - @echo 'make package-diff (pd) diff src files against package files' - @echo '' - @echo 'make lib-package help for download/build/install a package library' - @echo 'make lib-package args="..." download/build/install a package library' - @echo 'make purge purge obsolete copies of source files' - @echo '' - @echo 'make machine build LAMMPS for machine with static library' - @echo 'make mode=static machine same as above' - @echo 'make mode=shared machine build LAMMPS for machine with shared library' - @echo 'make mode=print machine print compiler/linker flags' - @echo '' - @echo 'machine is one of these from src/MAKE:' - @echo '' - @files="`ls MAKE/Makefile.*`"; \ - for file in $$files; do head -1 $$file; done - @echo '' - @echo '... or one of these from src/MAKE/OPTIONS:' - @echo '' - @files="`ls MAKE/OPTIONS/Makefile.*`"; \ - for file in $$files; do head -1 $$file; done - @echo '' - @echo '... or one of these from src/MAKE/MACHINES:' - @echo '' - @files="`ls MAKE/MACHINES/Makefile.*`"; \ - for file in $$files; do head -1 $$file; done - @echo '' - @echo '... or one of these from src/MAKE/MINE:' - @echo '' - @files="`ls MAKE/MINE/Makefile.* 2>/dev/null`"; \ - for file in $$files; do head -1 $$file; done - @echo '' - - -lmpinstalledpkgs.h: $(SRC) $(INC) - @echo '#ifndef LMP_INSTALLED_PKGS_H' > ${TMPNAME}.lmpinstalled - @echo '#define LMP_INSTALLED_PKGS_H' >> ${TMPNAME}.lmpinstalled - @echo 'const char * LAMMPS_NS::LAMMPS::installed_packages[] = {' >> ${TMPNAME}.lmpinstalled - @for p in $(PACKAGEUC) $(PACKUSERUC); do info=$$($(SHELL) Package.sh $$p installed); \ - [ -n "$$info" ] && echo "\"$$info\"" | sed -e 's/".*package \(.*\)"/"\1",/' >> ${TMPNAME}.lmpinstalled || :; done - @echo ' NULL };' >> ${TMPNAME}.lmpinstalled - @echo '#endif' >> ${TMPNAME}.lmpinstalled - @if [ -f lmpinstalledpkgs.h ]; \ - then test "`diff --brief ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h`" != "" && \ - mv ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h || rm ${TMPNAME}.lmpinstalled ; \ - else mv ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h ; fi - -gitversion: - @echo 'Gathering git version information' - @echo '#ifndef LMP_GIT_VERSION_H' > ${TMPNAME}.lmpgitversion - @echo '#define LMP_GIT_VERSION_H' >> ${TMPNAME}.lmpgitversion - @if (type git && test -e ../.git ) >> /dev/null 2>> /dev/null ; then \ - git='true'; \ - commit=$$(git rev-parse HEAD); \ - branch=$$(git rev-parse --abbrev-ref HEAD); \ - describe=$$(git describe --dirty=-modified); \ - else \ - git='false' ; \ - commit='(unknown)' ; \ - branch='(unknown)' ; \ - describe='(unknown)' ; \ - fi ; \ - echo "const bool LAMMPS_NS::LAMMPS::has_git_info = $${git};" >> ${TMPNAME}.lmpgitversion ; \ - echo "const char LAMMPS_NS::LAMMPS::git_commit[] = \"$${commit}\";" >> ${TMPNAME}.lmpgitversion ; \ - echo "const char LAMMPS_NS::LAMMPS::git_branch[] = \"$${branch}\";" >> ${TMPNAME}.lmpgitversion ; \ - echo "const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"$${describe}\";" >> ${TMPNAME}.lmpgitversion - @echo '#endif' >> ${TMPNAME}.lmpgitversion - @if [ -f lmpgitversion.h ]; \ - then test "`diff --brief ${TMPNAME}.lmpgitversion lmpgitversion.h`" != "" && \ - mv ${TMPNAME}.lmpgitversion lmpgitversion.h || rm ${TMPNAME}.lmpgitversion ; \ - else mv ${TMPNAME}.lmpgitversion lmpgitversion.h ; fi - -# Build LAMMPS in one of 2 modes -# static = static compile in Obj_machine (default) -# shared = shared compile in Obj_shared_machine - -.DEFAULT: - @if [ $@ = "serial" ]; \ - then cd STUBS; $(MAKE); cd ..; fi - @test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \ - -f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@ - @if [ ! -d $(objdir) ]; then mkdir $(objdir); fi - @echo 'Gathering installed package information (may take a little while)' - @$(SHELL) Make.sh style - @$(SHELL) Make.sh packages - @$(MAKE) $(MFLAGS) lmpinstalledpkgs.h gitversion - @echo 'Compiling LAMMPS for machine $@' - @if [ -f MAKE/MACHINES/Makefile.$@ ]; \ - then cp MAKE/MACHINES/Makefile.$@ $(objdir)/Makefile; fi - @if [ -f MAKE/OPTIONS/Makefile.$@ ]; \ - then cp MAKE/OPTIONS/Makefile.$@ $(objdir)/Makefile; fi - @if [ -f MAKE/Makefile.$@ ]; \ - then cp MAKE/Makefile.$@ $(objdir)/Makefile; fi - @if [ -f MAKE/MINE/Makefile.$@ ]; \ - then cp MAKE/MINE/Makefile.$@ $(objdir)/Makefile; fi - @if [ ! -e Makefile.package ]; \ - then cp Makefile.package.empty Makefile.package; fi - @if [ ! -e Makefile.package.settings ]; \ - then cp Makefile.package.settings.empty Makefile.package.settings; fi - @cp Makefile.package Makefile.package.settings $(objdir) - @cd $(objdir); rm -f .depend; \ - $(MAKE) $(MFLAGS) "SRC = $(SRC)" "INC = $(INC)" depend || : - @rm -f $(ARLINK) $(SHLINK) $(EXE) -ifeq ($(mode),static) - @cd $(objdir); \ - $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" "SHFLAGS =" \ - "LMPLIB = $(ARLIB)" "ARLIB = $(ARLIB)" "SHLIB = $(SHLIB)" \ - "LMPLINK = $(LMPLINK)" "EXE = ../$(EXE)" ../$(EXE) - @ln -s $(ARLIB) $(ARLINK) -endif -ifeq ($(mode),shared) - @cd $(objdir); \ - $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \ - "LMPLIB = $(SHLIB)" "ARLIB = $(ARLIB)" "SHLIB = $(SHLIB)" \ - "LMPLINK = $(LMPLINK)" "EXE = ../$(EXE)" ../$(EXE) - @ln -s $(SHLIB) $(SHLINK) -endif -# backward compatibility -ifeq ($(mode),exe) - $(MAKE) $(MFLAGS) mode=static $@ -endif -ifeq ($(mode),lib) - $(MAKE) $(MFLAGS) mode=static $@ -endif -ifeq ($(mode),shexe) - $(MAKE) $(MFLAGS) mode=shared $@ -endif -ifeq ($(mode),shlib) - $(MAKE) $(MFLAGS) mode=shared $@ -endif - -ifeq ($(mode),print) - @cd $(objdir); \ - $(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \ - "EXE = ../$(ARLIB)" -f ../Makefile.print -endif - -# Remove machine-specific object files - -clean: - @echo 'make clean-all delete all object files' - @echo 'make clean-machine delete object files for one machine' - -clean-all: - rm -rf Obj_* - -clean-%: - @if [ $@ = "clean-serial" ]; \ - then cd STUBS; $(MAKE) clean; cd ..; fi - rm -rf Obj_$(@:clean-%=%) Obj_shared_$(@:clean-%=%) - -# Make MPI STUBS library - -mpi-stubs: - @cd STUBS; $(MAKE) clean; $(MAKE) - -# install LAMMPS shared lib and Python wrapper for Python usage -# include python package settings to automatically adapt name of -# the python interpreter. must purge build folder to not install -# unwanted outdated files. - -sinclude ../lib/python/Makefile.lammps -install-python: - @rm -rf ../python/build - @$(PYTHON) ../python/install.py -v ../src/version.h \ - -p ../python/lammps -l ../src/liblammps.so - -# Create a tarball of src dir and packages - -tar: - @cd STUBS; $(MAKE) clean - @cd ..; tar cvzf src/$(ROOT)_src.tar.gz \ - src/Make* src/Package.sh src/Depend.sh src/Install.sh src/Fetch.sh \ - src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \ - $(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \ - --exclude=*/.svn - @cd STUBS; $(MAKE) - @echo "Created $(ROOT)_src.tar.gz" - -# Package management - -package: - @echo 'Standard packages:' $(PACKAGE) - @echo '' - @echo 'User-contributed packages:' $(PACKUSER) - @echo '' - @echo 'Packages that need system libraries:' $(PACKSYS) - @echo '' - @echo 'Packages that need provided libraries:' $(PACKINT) - @echo '' - @echo 'Packages that need external libraries:' $(PACKEXT) - @echo '' - @echo 'make package list available packages' - @echo 'make package list available packages' - @echo 'make package-status (ps) status of all packages' - @echo 'make package-installed (pi) list of installed packages' - @echo 'make yes-package install a single pgk in src dir' - @echo 'make no-package remove a single pkg from src dir' - @echo 'make yes-all install all pgks in src dir' - @echo 'make no-all remove all pkgs from src dir' - @echo 'make yes-standard (yes-std) install all standard pkgs' - @echo 'make no-standard (no-std) remove all standard pkgs' - @echo 'make yes-user install all user pkgs' - @echo 'make no-user remove all user pkgs' - @echo 'make yes-lib install all pkgs with libs (included or ext)' - @echo 'make no-lib remove all pkgs with libs (included or ext)' - @echo 'make yes-ext install all pkgs with external libs' - @echo 'make no-ext remove all pkgs with external libs' - @echo '' - @echo 'make package-update (pu) replace src files with package files' - @echo 'make package-overwrite replace package files with src files' - @echo 'make package-diff (pd) diff src files against package file' - @echo '' - @echo 'make lib-package build and/or download a package library' - -yes-all: - @for p in $(PACKALL); do $(MAKE) yes-$$p; done - -no-all: - @for p in $(PACKALL); do $(MAKE) no-$$p; done - -yes-standard yes-std: - @for p in $(PACKAGE); do $(MAKE) yes-$$p; done - -no-standard no-std: - @for p in $(PACKAGE); do $(MAKE) no-$$p; done - -yes-user: - @for p in $(PACKUSER); do $(MAKE) yes-$$p; done - -no-user: - @for p in $(PACKUSER); do $(MAKE) no-$$p; done - -yes-lib: - @for p in $(PACKLIB); do $(MAKE) yes-$$p; done - -no-lib: - @for p in $(PACKLIB); do $(MAKE) no-$$p; done - -yes-ext: - @for p in $(PACKEXT); do $(MAKE) yes-$$p; done - -no-ext: - @for p in $(PACKEXT); do $(MAKE) no-$$p; done - -yes-%: - @if [ ! -e Makefile.package ]; \ - then cp Makefile.package.empty Makefile.package; fi - @if [ ! -e Makefile.package.settings ]; \ - then cp Makefile.package.settings.empty Makefile.package.settings; fi - @if [ ! -e $(YESDIR) ]; then \ - echo "Package $(YESDIR) does not exist"; exit 1; \ - elif [ -e $(YESDIR)/Install.sh ]; then \ - echo "Installing package $(@:yes-%=%)"; \ - cd $(YESDIR); $(SHELL) Install.sh 1; cd ..; \ - $(SHELL) Depend.sh $(YESDIR) 1; \ - else \ - echo "Installing package $(@:yes-%=%)"; \ - cd $(YESDIR); $(SHELL) ../Install.sh 1; cd ..; \ - $(SHELL) Depend.sh $(YESDIR) 1; \ - fi; - @$(SHELL) Fetch.sh $(YESDIR) - -no-%: - @if [ ! -e $(NODIR) ]; then \ - echo "Package $(NODIR) does not exist"; exit 1; \ - elif [ -e $(NODIR)/Install.sh ]; then \ - echo "Uninstalling package $(@:no-%=%)"; \ - cd $(NODIR); $(SHELL) Install.sh 0; cd ..; \ - $(SHELL) Depend.sh $(NODIR) 0; \ - else \ - echo "Uninstalling package $(@:no-%=%)"; \ - cd $(NODIR); $(SHELL) ../Install.sh 0; cd ..; \ - $(SHELL) Depend.sh $(NODIR) 0; \ - fi; - -# download/build/install a package library -# update the timestamp on main.cpp to trigger a relink with "make machine" - -lib-%: - @if [ -e ../lib/$(LIBDIR)/Install.py ]; then \ - echo "Installing lib $(@:lib-%=%)"; \ - ( cd ../lib/$(LIBDIR); $(PYTHON) Install.py $(args) ); \ - elif [ -e ../lib/$(LIBUSERDIR)/Install.py ]; then \ - echo "Installing lib $(@:lib-user-%=%)"; \ - ( cd ../lib/$(LIBUSERDIR); $(PYTHON) Install.py $(args) ); \ - else \ - echo "Install script for lib $(@:lib-%=%) does not exist"; \ - fi; touch main.cpp - -# status = list src files that differ from package files -# installed = list of installed packages -# update = replace src files with newer package files -# overwrite = overwrite package files with newer src files -# diff = show differences between src and package files -# purge = delete obsolete and auto-generated package files - -package-status ps: - @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p status; done - @echo '' - @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p status; done - -package-installed pi: - @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p installed; done - @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p installed; done - -package-update pu: purge - @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p update; done - @echo '' - @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p update; done - -package-overwrite: purge - @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p overwrite; done - @echo '' - @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p overwrite; done - -package-diff pd: - @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p diff; done - @echo '' - @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p diff; done - -purge: Purge.list - @echo 'Purging obsolete and auto-generated source files' - @for f in `grep -v '#' Purge.list` ; \ - do test -f $$f && rm $$f && echo $$f || : ; \ - done diff --git a/src/USER-NETCDF/Install.sh b/src/NETCDF/Install.sh similarity index 100% rename from src/USER-NETCDF/Install.sh rename to src/NETCDF/Install.sh diff --git a/src/USER-NETCDF/README b/src/NETCDF/README similarity index 99% rename from src/USER-NETCDF/README rename to src/NETCDF/README index 714cbc67d0..8fdcb9e083 100644 --- a/src/USER-NETCDF/README +++ b/src/NETCDF/README @@ -1,4 +1,4 @@ -USER-NETCDF +NETCDF ============ This package provides the netcdf and netcdf/mpiio dump styles. diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/NETCDF/dump_netcdf.cpp similarity index 100% rename from src/USER-NETCDF/dump_netcdf.cpp rename to src/NETCDF/dump_netcdf.cpp diff --git a/src/USER-NETCDF/dump_netcdf.h b/src/NETCDF/dump_netcdf.h similarity index 100% rename from src/USER-NETCDF/dump_netcdf.h rename to src/NETCDF/dump_netcdf.h diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/NETCDF/dump_netcdf_mpiio.cpp similarity index 100% rename from src/USER-NETCDF/dump_netcdf_mpiio.cpp rename to src/NETCDF/dump_netcdf_mpiio.cpp diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.h b/src/NETCDF/dump_netcdf_mpiio.h similarity index 100% rename from src/USER-NETCDF/dump_netcdf_mpiio.h rename to src/NETCDF/dump_netcdf_mpiio.h diff --git a/src/USER-OMP/Install.sh b/src/OPENMP/Install.sh similarity index 100% rename from src/USER-OMP/Install.sh rename to src/OPENMP/Install.sh diff --git a/src/USER-OMP/README b/src/OPENMP/README similarity index 100% rename from src/USER-OMP/README rename to src/OPENMP/README diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/OPENMP/angle_charmm_omp.cpp similarity index 100% rename from src/USER-OMP/angle_charmm_omp.cpp rename to src/OPENMP/angle_charmm_omp.cpp diff --git a/src/USER-OMP/angle_charmm_omp.h b/src/OPENMP/angle_charmm_omp.h similarity index 100% rename from src/USER-OMP/angle_charmm_omp.h rename to src/OPENMP/angle_charmm_omp.h diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/OPENMP/angle_class2_omp.cpp similarity index 100% rename from src/USER-OMP/angle_class2_omp.cpp rename to src/OPENMP/angle_class2_omp.cpp diff --git a/src/USER-OMP/angle_class2_omp.h b/src/OPENMP/angle_class2_omp.h similarity index 100% rename from src/USER-OMP/angle_class2_omp.h rename to src/OPENMP/angle_class2_omp.h diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/OPENMP/angle_cosine_delta_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_delta_omp.cpp rename to src/OPENMP/angle_cosine_delta_omp.cpp diff --git a/src/USER-OMP/angle_cosine_delta_omp.h b/src/OPENMP/angle_cosine_delta_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_delta_omp.h rename to src/OPENMP/angle_cosine_delta_omp.h diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/OPENMP/angle_cosine_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_omp.cpp rename to src/OPENMP/angle_cosine_omp.cpp diff --git a/src/USER-OMP/angle_cosine_omp.h b/src/OPENMP/angle_cosine_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_omp.h rename to src/OPENMP/angle_cosine_omp.h diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/OPENMP/angle_cosine_periodic_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_periodic_omp.cpp rename to src/OPENMP/angle_cosine_periodic_omp.cpp diff --git a/src/USER-OMP/angle_cosine_periodic_omp.h b/src/OPENMP/angle_cosine_periodic_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_periodic_omp.h rename to src/OPENMP/angle_cosine_periodic_omp.h diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/OPENMP/angle_cosine_shift_exp_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_shift_exp_omp.cpp rename to src/OPENMP/angle_cosine_shift_exp_omp.cpp diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.h b/src/OPENMP/angle_cosine_shift_exp_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_shift_exp_omp.h rename to src/OPENMP/angle_cosine_shift_exp_omp.h diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/OPENMP/angle_cosine_shift_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_shift_omp.cpp rename to src/OPENMP/angle_cosine_shift_omp.cpp diff --git a/src/USER-OMP/angle_cosine_shift_omp.h b/src/OPENMP/angle_cosine_shift_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_shift_omp.h rename to src/OPENMP/angle_cosine_shift_omp.h diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/OPENMP/angle_cosine_squared_omp.cpp similarity index 100% rename from src/USER-OMP/angle_cosine_squared_omp.cpp rename to src/OPENMP/angle_cosine_squared_omp.cpp diff --git a/src/USER-OMP/angle_cosine_squared_omp.h b/src/OPENMP/angle_cosine_squared_omp.h similarity index 100% rename from src/USER-OMP/angle_cosine_squared_omp.h rename to src/OPENMP/angle_cosine_squared_omp.h diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/OPENMP/angle_dipole_omp.cpp similarity index 100% rename from src/USER-OMP/angle_dipole_omp.cpp rename to src/OPENMP/angle_dipole_omp.cpp diff --git a/src/USER-OMP/angle_dipole_omp.h b/src/OPENMP/angle_dipole_omp.h similarity index 100% rename from src/USER-OMP/angle_dipole_omp.h rename to src/OPENMP/angle_dipole_omp.h diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/OPENMP/angle_fourier_omp.cpp similarity index 100% rename from src/USER-OMP/angle_fourier_omp.cpp rename to src/OPENMP/angle_fourier_omp.cpp diff --git a/src/USER-OMP/angle_fourier_omp.h b/src/OPENMP/angle_fourier_omp.h similarity index 100% rename from src/USER-OMP/angle_fourier_omp.h rename to src/OPENMP/angle_fourier_omp.h diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/OPENMP/angle_fourier_simple_omp.cpp similarity index 100% rename from src/USER-OMP/angle_fourier_simple_omp.cpp rename to src/OPENMP/angle_fourier_simple_omp.cpp diff --git a/src/USER-OMP/angle_fourier_simple_omp.h b/src/OPENMP/angle_fourier_simple_omp.h similarity index 100% rename from src/USER-OMP/angle_fourier_simple_omp.h rename to src/OPENMP/angle_fourier_simple_omp.h diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/OPENMP/angle_harmonic_omp.cpp similarity index 100% rename from src/USER-OMP/angle_harmonic_omp.cpp rename to src/OPENMP/angle_harmonic_omp.cpp diff --git a/src/USER-OMP/angle_harmonic_omp.h b/src/OPENMP/angle_harmonic_omp.h similarity index 100% rename from src/USER-OMP/angle_harmonic_omp.h rename to src/OPENMP/angle_harmonic_omp.h diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/OPENMP/angle_quartic_omp.cpp similarity index 100% rename from src/USER-OMP/angle_quartic_omp.cpp rename to src/OPENMP/angle_quartic_omp.cpp diff --git a/src/USER-OMP/angle_quartic_omp.h b/src/OPENMP/angle_quartic_omp.h similarity index 100% rename from src/USER-OMP/angle_quartic_omp.h rename to src/OPENMP/angle_quartic_omp.h diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/OPENMP/angle_sdk_omp.cpp similarity index 100% rename from src/USER-OMP/angle_sdk_omp.cpp rename to src/OPENMP/angle_sdk_omp.cpp diff --git a/src/USER-OMP/angle_sdk_omp.h b/src/OPENMP/angle_sdk_omp.h similarity index 100% rename from src/USER-OMP/angle_sdk_omp.h rename to src/OPENMP/angle_sdk_omp.h diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/OPENMP/angle_table_omp.cpp similarity index 100% rename from src/USER-OMP/angle_table_omp.cpp rename to src/OPENMP/angle_table_omp.cpp diff --git a/src/USER-OMP/angle_table_omp.h b/src/OPENMP/angle_table_omp.h similarity index 100% rename from src/USER-OMP/angle_table_omp.h rename to src/OPENMP/angle_table_omp.h diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/OPENMP/bond_class2_omp.cpp similarity index 100% rename from src/USER-OMP/bond_class2_omp.cpp rename to src/OPENMP/bond_class2_omp.cpp diff --git a/src/USER-OMP/bond_class2_omp.h b/src/OPENMP/bond_class2_omp.h similarity index 100% rename from src/USER-OMP/bond_class2_omp.h rename to src/OPENMP/bond_class2_omp.h diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/OPENMP/bond_fene_expand_omp.cpp similarity index 100% rename from src/USER-OMP/bond_fene_expand_omp.cpp rename to src/OPENMP/bond_fene_expand_omp.cpp diff --git a/src/USER-OMP/bond_fene_expand_omp.h b/src/OPENMP/bond_fene_expand_omp.h similarity index 100% rename from src/USER-OMP/bond_fene_expand_omp.h rename to src/OPENMP/bond_fene_expand_omp.h diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/OPENMP/bond_fene_omp.cpp similarity index 100% rename from src/USER-OMP/bond_fene_omp.cpp rename to src/OPENMP/bond_fene_omp.cpp diff --git a/src/USER-OMP/bond_fene_omp.h b/src/OPENMP/bond_fene_omp.h similarity index 100% rename from src/USER-OMP/bond_fene_omp.h rename to src/OPENMP/bond_fene_omp.h diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/OPENMP/bond_gromos_omp.cpp similarity index 100% rename from src/USER-OMP/bond_gromos_omp.cpp rename to src/OPENMP/bond_gromos_omp.cpp diff --git a/src/USER-OMP/bond_gromos_omp.h b/src/OPENMP/bond_gromos_omp.h similarity index 100% rename from src/USER-OMP/bond_gromos_omp.h rename to src/OPENMP/bond_gromos_omp.h diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/OPENMP/bond_harmonic_omp.cpp similarity index 100% rename from src/USER-OMP/bond_harmonic_omp.cpp rename to src/OPENMP/bond_harmonic_omp.cpp diff --git a/src/USER-OMP/bond_harmonic_omp.h b/src/OPENMP/bond_harmonic_omp.h similarity index 100% rename from src/USER-OMP/bond_harmonic_omp.h rename to src/OPENMP/bond_harmonic_omp.h diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/OPENMP/bond_harmonic_shift_cut_omp.cpp similarity index 100% rename from src/USER-OMP/bond_harmonic_shift_cut_omp.cpp rename to src/OPENMP/bond_harmonic_shift_cut_omp.cpp diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.h b/src/OPENMP/bond_harmonic_shift_cut_omp.h similarity index 100% rename from src/USER-OMP/bond_harmonic_shift_cut_omp.h rename to src/OPENMP/bond_harmonic_shift_cut_omp.h diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/OPENMP/bond_harmonic_shift_omp.cpp similarity index 100% rename from src/USER-OMP/bond_harmonic_shift_omp.cpp rename to src/OPENMP/bond_harmonic_shift_omp.cpp diff --git a/src/USER-OMP/bond_harmonic_shift_omp.h b/src/OPENMP/bond_harmonic_shift_omp.h similarity index 100% rename from src/USER-OMP/bond_harmonic_shift_omp.h rename to src/OPENMP/bond_harmonic_shift_omp.h diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/OPENMP/bond_morse_omp.cpp similarity index 100% rename from src/USER-OMP/bond_morse_omp.cpp rename to src/OPENMP/bond_morse_omp.cpp diff --git a/src/USER-OMP/bond_morse_omp.h b/src/OPENMP/bond_morse_omp.h similarity index 100% rename from src/USER-OMP/bond_morse_omp.h rename to src/OPENMP/bond_morse_omp.h diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/OPENMP/bond_nonlinear_omp.cpp similarity index 100% rename from src/USER-OMP/bond_nonlinear_omp.cpp rename to src/OPENMP/bond_nonlinear_omp.cpp diff --git a/src/USER-OMP/bond_nonlinear_omp.h b/src/OPENMP/bond_nonlinear_omp.h similarity index 100% rename from src/USER-OMP/bond_nonlinear_omp.h rename to src/OPENMP/bond_nonlinear_omp.h diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/OPENMP/bond_quartic_omp.cpp similarity index 100% rename from src/USER-OMP/bond_quartic_omp.cpp rename to src/OPENMP/bond_quartic_omp.cpp diff --git a/src/USER-OMP/bond_quartic_omp.h b/src/OPENMP/bond_quartic_omp.h similarity index 100% rename from src/USER-OMP/bond_quartic_omp.h rename to src/OPENMP/bond_quartic_omp.h diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/OPENMP/bond_table_omp.cpp similarity index 100% rename from src/USER-OMP/bond_table_omp.cpp rename to src/OPENMP/bond_table_omp.cpp diff --git a/src/USER-OMP/bond_table_omp.h b/src/OPENMP/bond_table_omp.h similarity index 100% rename from src/USER-OMP/bond_table_omp.h rename to src/OPENMP/bond_table_omp.h diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/OPENMP/dihedral_charmm_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_charmm_omp.cpp rename to src/OPENMP/dihedral_charmm_omp.cpp diff --git a/src/USER-OMP/dihedral_charmm_omp.h b/src/OPENMP/dihedral_charmm_omp.h similarity index 100% rename from src/USER-OMP/dihedral_charmm_omp.h rename to src/OPENMP/dihedral_charmm_omp.h diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/OPENMP/dihedral_class2_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_class2_omp.cpp rename to src/OPENMP/dihedral_class2_omp.cpp diff --git a/src/USER-OMP/dihedral_class2_omp.h b/src/OPENMP/dihedral_class2_omp.h similarity index 100% rename from src/USER-OMP/dihedral_class2_omp.h rename to src/OPENMP/dihedral_class2_omp.h diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/OPENMP/dihedral_cosine_shift_exp_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp rename to src/OPENMP/dihedral_cosine_shift_exp_omp.cpp diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.h b/src/OPENMP/dihedral_cosine_shift_exp_omp.h similarity index 100% rename from src/USER-OMP/dihedral_cosine_shift_exp_omp.h rename to src/OPENMP/dihedral_cosine_shift_exp_omp.h diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/OPENMP/dihedral_fourier_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_fourier_omp.cpp rename to src/OPENMP/dihedral_fourier_omp.cpp diff --git a/src/USER-OMP/dihedral_fourier_omp.h b/src/OPENMP/dihedral_fourier_omp.h similarity index 100% rename from src/USER-OMP/dihedral_fourier_omp.h rename to src/OPENMP/dihedral_fourier_omp.h diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/OPENMP/dihedral_harmonic_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_harmonic_omp.cpp rename to src/OPENMP/dihedral_harmonic_omp.cpp diff --git a/src/USER-OMP/dihedral_harmonic_omp.h b/src/OPENMP/dihedral_harmonic_omp.h similarity index 100% rename from src/USER-OMP/dihedral_harmonic_omp.h rename to src/OPENMP/dihedral_harmonic_omp.h diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/OPENMP/dihedral_helix_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_helix_omp.cpp rename to src/OPENMP/dihedral_helix_omp.cpp diff --git a/src/USER-OMP/dihedral_helix_omp.h b/src/OPENMP/dihedral_helix_omp.h similarity index 100% rename from src/USER-OMP/dihedral_helix_omp.h rename to src/OPENMP/dihedral_helix_omp.h diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/OPENMP/dihedral_multi_harmonic_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_multi_harmonic_omp.cpp rename to src/OPENMP/dihedral_multi_harmonic_omp.cpp diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.h b/src/OPENMP/dihedral_multi_harmonic_omp.h similarity index 100% rename from src/USER-OMP/dihedral_multi_harmonic_omp.h rename to src/OPENMP/dihedral_multi_harmonic_omp.h diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/OPENMP/dihedral_nharmonic_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_nharmonic_omp.cpp rename to src/OPENMP/dihedral_nharmonic_omp.cpp diff --git a/src/USER-OMP/dihedral_nharmonic_omp.h b/src/OPENMP/dihedral_nharmonic_omp.h similarity index 100% rename from src/USER-OMP/dihedral_nharmonic_omp.h rename to src/OPENMP/dihedral_nharmonic_omp.h diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/OPENMP/dihedral_opls_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_opls_omp.cpp rename to src/OPENMP/dihedral_opls_omp.cpp diff --git a/src/USER-OMP/dihedral_opls_omp.h b/src/OPENMP/dihedral_opls_omp.h similarity index 100% rename from src/USER-OMP/dihedral_opls_omp.h rename to src/OPENMP/dihedral_opls_omp.h diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/OPENMP/dihedral_quadratic_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_quadratic_omp.cpp rename to src/OPENMP/dihedral_quadratic_omp.cpp diff --git a/src/USER-OMP/dihedral_quadratic_omp.h b/src/OPENMP/dihedral_quadratic_omp.h similarity index 100% rename from src/USER-OMP/dihedral_quadratic_omp.h rename to src/OPENMP/dihedral_quadratic_omp.h diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/OPENMP/dihedral_table_omp.cpp similarity index 100% rename from src/USER-OMP/dihedral_table_omp.cpp rename to src/OPENMP/dihedral_table_omp.cpp diff --git a/src/USER-OMP/dihedral_table_omp.h b/src/OPENMP/dihedral_table_omp.h similarity index 100% rename from src/USER-OMP/dihedral_table_omp.h rename to src/OPENMP/dihedral_table_omp.h diff --git a/src/USER-OMP/domain_omp.cpp b/src/OPENMP/domain_omp.cpp similarity index 100% rename from src/USER-OMP/domain_omp.cpp rename to src/OPENMP/domain_omp.cpp diff --git a/src/USER-OMP/ewald_omp.cpp b/src/OPENMP/ewald_omp.cpp similarity index 100% rename from src/USER-OMP/ewald_omp.cpp rename to src/OPENMP/ewald_omp.cpp diff --git a/src/USER-OMP/ewald_omp.h b/src/OPENMP/ewald_omp.h similarity index 100% rename from src/USER-OMP/ewald_omp.h rename to src/OPENMP/ewald_omp.h diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/OPENMP/fix_gravity_omp.cpp similarity index 100% rename from src/USER-OMP/fix_gravity_omp.cpp rename to src/OPENMP/fix_gravity_omp.cpp diff --git a/src/USER-OMP/fix_gravity_omp.h b/src/OPENMP/fix_gravity_omp.h similarity index 100% rename from src/USER-OMP/fix_gravity_omp.h rename to src/OPENMP/fix_gravity_omp.h diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/OPENMP/fix_neigh_history_omp.cpp similarity index 100% rename from src/USER-OMP/fix_neigh_history_omp.cpp rename to src/OPENMP/fix_neigh_history_omp.cpp diff --git a/src/USER-OMP/fix_neigh_history_omp.h b/src/OPENMP/fix_neigh_history_omp.h similarity index 100% rename from src/USER-OMP/fix_neigh_history_omp.h rename to src/OPENMP/fix_neigh_history_omp.h diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/OPENMP/fix_nh_asphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nh_asphere_omp.cpp rename to src/OPENMP/fix_nh_asphere_omp.cpp diff --git a/src/USER-OMP/fix_nh_asphere_omp.h b/src/OPENMP/fix_nh_asphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nh_asphere_omp.h rename to src/OPENMP/fix_nh_asphere_omp.h diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/OPENMP/fix_nh_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nh_omp.cpp rename to src/OPENMP/fix_nh_omp.cpp diff --git a/src/USER-OMP/fix_nh_omp.h b/src/OPENMP/fix_nh_omp.h similarity index 100% rename from src/USER-OMP/fix_nh_omp.h rename to src/OPENMP/fix_nh_omp.h diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/OPENMP/fix_nh_sphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nh_sphere_omp.cpp rename to src/OPENMP/fix_nh_sphere_omp.cpp diff --git a/src/USER-OMP/fix_nh_sphere_omp.h b/src/OPENMP/fix_nh_sphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nh_sphere_omp.h rename to src/OPENMP/fix_nh_sphere_omp.h diff --git a/src/USER-OMP/fix_nph_asphere_omp.cpp b/src/OPENMP/fix_nph_asphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nph_asphere_omp.cpp rename to src/OPENMP/fix_nph_asphere_omp.cpp diff --git a/src/USER-OMP/fix_nph_asphere_omp.h b/src/OPENMP/fix_nph_asphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nph_asphere_omp.h rename to src/OPENMP/fix_nph_asphere_omp.h diff --git a/src/USER-OMP/fix_nph_omp.cpp b/src/OPENMP/fix_nph_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nph_omp.cpp rename to src/OPENMP/fix_nph_omp.cpp diff --git a/src/USER-OMP/fix_nph_omp.h b/src/OPENMP/fix_nph_omp.h similarity index 100% rename from src/USER-OMP/fix_nph_omp.h rename to src/OPENMP/fix_nph_omp.h diff --git a/src/USER-OMP/fix_nph_sphere_omp.cpp b/src/OPENMP/fix_nph_sphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nph_sphere_omp.cpp rename to src/OPENMP/fix_nph_sphere_omp.cpp diff --git a/src/USER-OMP/fix_nph_sphere_omp.h b/src/OPENMP/fix_nph_sphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nph_sphere_omp.h rename to src/OPENMP/fix_nph_sphere_omp.h diff --git a/src/USER-OMP/fix_npt_asphere_omp.cpp b/src/OPENMP/fix_npt_asphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_npt_asphere_omp.cpp rename to src/OPENMP/fix_npt_asphere_omp.cpp diff --git a/src/USER-OMP/fix_npt_asphere_omp.h b/src/OPENMP/fix_npt_asphere_omp.h similarity index 100% rename from src/USER-OMP/fix_npt_asphere_omp.h rename to src/OPENMP/fix_npt_asphere_omp.h diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/OPENMP/fix_npt_omp.cpp similarity index 100% rename from src/USER-OMP/fix_npt_omp.cpp rename to src/OPENMP/fix_npt_omp.cpp diff --git a/src/USER-OMP/fix_npt_omp.h b/src/OPENMP/fix_npt_omp.h similarity index 100% rename from src/USER-OMP/fix_npt_omp.h rename to src/OPENMP/fix_npt_omp.h diff --git a/src/USER-OMP/fix_npt_sphere_omp.cpp b/src/OPENMP/fix_npt_sphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_npt_sphere_omp.cpp rename to src/OPENMP/fix_npt_sphere_omp.cpp diff --git a/src/USER-OMP/fix_npt_sphere_omp.h b/src/OPENMP/fix_npt_sphere_omp.h similarity index 100% rename from src/USER-OMP/fix_npt_sphere_omp.h rename to src/OPENMP/fix_npt_sphere_omp.h diff --git a/src/USER-OMP/fix_nve_omp.cpp b/src/OPENMP/fix_nve_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nve_omp.cpp rename to src/OPENMP/fix_nve_omp.cpp diff --git a/src/USER-OMP/fix_nve_omp.h b/src/OPENMP/fix_nve_omp.h similarity index 100% rename from src/USER-OMP/fix_nve_omp.h rename to src/OPENMP/fix_nve_omp.h diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/OPENMP/fix_nve_sphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nve_sphere_omp.cpp rename to src/OPENMP/fix_nve_sphere_omp.cpp diff --git a/src/USER-OMP/fix_nve_sphere_omp.h b/src/OPENMP/fix_nve_sphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nve_sphere_omp.h rename to src/OPENMP/fix_nve_sphere_omp.h diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/OPENMP/fix_nvt_asphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nvt_asphere_omp.cpp rename to src/OPENMP/fix_nvt_asphere_omp.cpp diff --git a/src/USER-OMP/fix_nvt_asphere_omp.h b/src/OPENMP/fix_nvt_asphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nvt_asphere_omp.h rename to src/OPENMP/fix_nvt_asphere_omp.h diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/OPENMP/fix_nvt_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nvt_omp.cpp rename to src/OPENMP/fix_nvt_omp.cpp diff --git a/src/USER-OMP/fix_nvt_omp.h b/src/OPENMP/fix_nvt_omp.h similarity index 100% rename from src/USER-OMP/fix_nvt_omp.h rename to src/OPENMP/fix_nvt_omp.h diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/OPENMP/fix_nvt_sllod_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nvt_sllod_omp.cpp rename to src/OPENMP/fix_nvt_sllod_omp.cpp diff --git a/src/USER-OMP/fix_nvt_sllod_omp.h b/src/OPENMP/fix_nvt_sllod_omp.h similarity index 100% rename from src/USER-OMP/fix_nvt_sllod_omp.h rename to src/OPENMP/fix_nvt_sllod_omp.h diff --git a/src/USER-OMP/fix_nvt_sphere_omp.cpp b/src/OPENMP/fix_nvt_sphere_omp.cpp similarity index 100% rename from src/USER-OMP/fix_nvt_sphere_omp.cpp rename to src/OPENMP/fix_nvt_sphere_omp.cpp diff --git a/src/USER-OMP/fix_nvt_sphere_omp.h b/src/OPENMP/fix_nvt_sphere_omp.h similarity index 100% rename from src/USER-OMP/fix_nvt_sphere_omp.h rename to src/OPENMP/fix_nvt_sphere_omp.h diff --git a/src/USER-OMP/fix_omp.cpp b/src/OPENMP/fix_omp.cpp similarity index 86% rename from src/USER-OMP/fix_omp.cpp rename to src/OPENMP/fix_omp.cpp index eb19c3a2d2..2b7e7eeaf9 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/OPENMP/fix_omp.cpp @@ -112,17 +112,9 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg) #if defined(_OPENMP) const char * const nmode = _neighbor ? "multi-threaded" : "serial"; - if (screen) { - if (reset_thr) - fprintf(screen,"set %d OpenMP thread(s) per MPI task\n", nthreads); - fprintf(screen,"using %s neighbor list subroutines\n", nmode); - } - - if (logfile) { - if (reset_thr) - fprintf(logfile,"set %d OpenMP thread(s) per MPI task\n", nthreads); - fprintf(logfile,"using %s neighbor list subroutines\n", nmode); - } + if (reset_thr) + utils::logmesg(lmp, "set {} OpenMP thread(s) per MPI task\n", nthreads); + utils::logmesg(lmp, "using {} neighbor list subroutines\n", nmode); #else error->warning(FLERR,"OpenMP support not enabled during compilation; " "using 1 thread only."); @@ -170,17 +162,17 @@ int FixOMP::setmask() void FixOMP::init() { - // USER-OMP package cannot be used with atom_style template + // OPENMP package cannot be used with atom_style template if (atom->molecular == Atom::TEMPLATE) - error->all(FLERR,"USER-OMP package does not (yet) work with " + error->all(FLERR,"OPENMP package does not (yet) work with " "atom_style template"); // adjust number of data objects when the number of OpenMP // threads has been changed somehow const int nthreads = comm->nthreads; if (_nthr != nthreads) { - if (screen) fprintf(screen,"Re-init USER-OMP for %d OpenMP thread(s)\n", nthreads); - if (logfile) fprintf(logfile,"Re-init USER-OMP for %d OpenMP thread(s)\n", nthreads); + if (comm->me == 0) + utils::logmesg(lmp,"Re-init OPENMP for {} OpenMP thread(s)\n", nthreads); for (int i=0; i < _nthr; ++i) delete thr[i]; @@ -292,23 +284,11 @@ void FixOMP::init() // diagnostic output if (comm->me == 0) { if (last_omp_style) { - if (last_pair_hybrid) { - if (screen) - fprintf(screen,"Hybrid pair style last /omp style %s\n", last_hybrid_name); - if (logfile) - fprintf(logfile,"Hybrid pair style last /omp style %s\n", last_hybrid_name); - } - if (screen) - fprintf(screen,"Last active /omp style is %s_style %s\n", - last_force_name, last_omp_name); - if (logfile) - fprintf(logfile,"Last active /omp style is %s_style %s\n", - last_force_name, last_omp_name); + if (last_pair_hybrid) + utils::logmesg(lmp,"Hybrid pair style last /omp style {}\n",last_hybrid_name); + utils::logmesg(lmp,"Last active /omp style is {}_style {}\n",last_force_name,last_omp_name); } else { - if (screen) - fprintf(screen,"No /omp style for force computation currently active\n"); - if (logfile) - fprintf(logfile,"No /omp style for force computation currently active\n"); + utils::logmesg(lmp,"No /omp style for force computation currently active\n"); } } } @@ -327,8 +307,8 @@ void FixOMP::set_neighbor_omp() const int neigh_omp = _neighbor ? 1 : 0; const int nrequest = neighbor->nrequest; - // flag *all* neighbor list requests as USER-OMP threaded, - // but skip lists already flagged as USER-INTEL threaded + // flag *all* neighbor list requests as OPENMP threaded, + // but skip lists already flagged as INTEL threaded for (int i = 0; i < nrequest; ++i) if (! neighbor->requests[i]->intel) neighbor->requests[i]->omp = neigh_omp; diff --git a/src/USER-OMP/fix_omp.h b/src/OPENMP/fix_omp.h similarity index 100% rename from src/USER-OMP/fix_omp.h rename to src/OPENMP/fix_omp.h diff --git a/src/USER-OMP/fix_peri_neigh_omp.cpp b/src/OPENMP/fix_peri_neigh_omp.cpp similarity index 100% rename from src/USER-OMP/fix_peri_neigh_omp.cpp rename to src/OPENMP/fix_peri_neigh_omp.cpp diff --git a/src/USER-OMP/fix_peri_neigh_omp.h b/src/OPENMP/fix_peri_neigh_omp.h similarity index 100% rename from src/USER-OMP/fix_peri_neigh_omp.h rename to src/OPENMP/fix_peri_neigh_omp.h diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/OPENMP/fix_qeq_comb_omp.cpp similarity index 99% rename from src/USER-OMP/fix_qeq_comb_omp.cpp rename to src/OPENMP/fix_qeq_comb_omp.cpp index 7dd1bfbb69..900a47bd02 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/OPENMP/fix_qeq_comb_omp.cpp @@ -50,7 +50,7 @@ void FixQEQCombOMP::init() error->all(FLERR,"Fix qeq/comb/omp requires atom attribute q"); if (nullptr != force->pair_match("comb3",0)) - error->all(FLERR,"No support for comb3 currently available in USER-OMP"); + error->all(FLERR,"No support for comb3 currently available in OPENMP"); comb = (PairComb *) force->pair_match("comb/omp",1); if (comb == nullptr) diff --git a/src/USER-OMP/fix_qeq_comb_omp.h b/src/OPENMP/fix_qeq_comb_omp.h similarity index 100% rename from src/USER-OMP/fix_qeq_comb_omp.h rename to src/OPENMP/fix_qeq_comb_omp.h diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/OPENMP/fix_qeq_reax_omp.cpp similarity index 99% rename from src/USER-OMP/fix_qeq_reax_omp.cpp rename to src/OPENMP/fix_qeq_reax_omp.cpp index 91c61cc946..7fe9994fc6 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/OPENMP/fix_qeq_reax_omp.cpp @@ -22,7 +22,7 @@ by Hasan Metin Aktulga (MSU), Chris Knight (ALCF), Paul Coffman (ALCF), Kurt O'Hearn (MSU), Ray Shan (Materials Design), Wei Jiang (ALCF) - Integration of the pair_style reax/c/omp into the User-OMP package + Integration of the pair_style reax/c/omp into the OPENMP package by Axel Kohlmeyer (Temple U.) Please cite the related publication: diff --git a/src/USER-OMP/fix_qeq_reax_omp.h b/src/OPENMP/fix_qeq_reax_omp.h similarity index 100% rename from src/USER-OMP/fix_qeq_reax_omp.h rename to src/OPENMP/fix_qeq_reax_omp.h diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/OPENMP/fix_rigid_nh_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_nh_omp.cpp rename to src/OPENMP/fix_rigid_nh_omp.cpp diff --git a/src/USER-OMP/fix_rigid_nh_omp.h b/src/OPENMP/fix_rigid_nh_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_nh_omp.h rename to src/OPENMP/fix_rigid_nh_omp.h diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/OPENMP/fix_rigid_nph_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_nph_omp.cpp rename to src/OPENMP/fix_rigid_nph_omp.cpp diff --git a/src/USER-OMP/fix_rigid_nph_omp.h b/src/OPENMP/fix_rigid_nph_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_nph_omp.h rename to src/OPENMP/fix_rigid_nph_omp.h diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/OPENMP/fix_rigid_npt_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_npt_omp.cpp rename to src/OPENMP/fix_rigid_npt_omp.cpp diff --git a/src/USER-OMP/fix_rigid_npt_omp.h b/src/OPENMP/fix_rigid_npt_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_npt_omp.h rename to src/OPENMP/fix_rigid_npt_omp.h diff --git a/src/USER-OMP/fix_rigid_nve_omp.cpp b/src/OPENMP/fix_rigid_nve_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_nve_omp.cpp rename to src/OPENMP/fix_rigid_nve_omp.cpp diff --git a/src/USER-OMP/fix_rigid_nve_omp.h b/src/OPENMP/fix_rigid_nve_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_nve_omp.h rename to src/OPENMP/fix_rigid_nve_omp.h diff --git a/src/USER-OMP/fix_rigid_nvt_omp.cpp b/src/OPENMP/fix_rigid_nvt_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_nvt_omp.cpp rename to src/OPENMP/fix_rigid_nvt_omp.cpp diff --git a/src/USER-OMP/fix_rigid_nvt_omp.h b/src/OPENMP/fix_rigid_nvt_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_nvt_omp.h rename to src/OPENMP/fix_rigid_nvt_omp.h diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/OPENMP/fix_rigid_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_omp.cpp rename to src/OPENMP/fix_rigid_omp.cpp diff --git a/src/USER-OMP/fix_rigid_omp.h b/src/OPENMP/fix_rigid_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_omp.h rename to src/OPENMP/fix_rigid_omp.h diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/OPENMP/fix_rigid_small_omp.cpp similarity index 100% rename from src/USER-OMP/fix_rigid_small_omp.cpp rename to src/OPENMP/fix_rigid_small_omp.cpp diff --git a/src/USER-OMP/fix_rigid_small_omp.h b/src/OPENMP/fix_rigid_small_omp.h similarity index 100% rename from src/USER-OMP/fix_rigid_small_omp.h rename to src/OPENMP/fix_rigid_small_omp.h diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/OPENMP/improper_class2_omp.cpp similarity index 100% rename from src/USER-OMP/improper_class2_omp.cpp rename to src/OPENMP/improper_class2_omp.cpp diff --git a/src/USER-OMP/improper_class2_omp.h b/src/OPENMP/improper_class2_omp.h similarity index 100% rename from src/USER-OMP/improper_class2_omp.h rename to src/OPENMP/improper_class2_omp.h diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/OPENMP/improper_cossq_omp.cpp similarity index 100% rename from src/USER-OMP/improper_cossq_omp.cpp rename to src/OPENMP/improper_cossq_omp.cpp diff --git a/src/USER-OMP/improper_cossq_omp.h b/src/OPENMP/improper_cossq_omp.h similarity index 100% rename from src/USER-OMP/improper_cossq_omp.h rename to src/OPENMP/improper_cossq_omp.h diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/OPENMP/improper_cvff_omp.cpp similarity index 100% rename from src/USER-OMP/improper_cvff_omp.cpp rename to src/OPENMP/improper_cvff_omp.cpp diff --git a/src/USER-OMP/improper_cvff_omp.h b/src/OPENMP/improper_cvff_omp.h similarity index 100% rename from src/USER-OMP/improper_cvff_omp.h rename to src/OPENMP/improper_cvff_omp.h diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/OPENMP/improper_fourier_omp.cpp similarity index 100% rename from src/USER-OMP/improper_fourier_omp.cpp rename to src/OPENMP/improper_fourier_omp.cpp diff --git a/src/USER-OMP/improper_fourier_omp.h b/src/OPENMP/improper_fourier_omp.h similarity index 100% rename from src/USER-OMP/improper_fourier_omp.h rename to src/OPENMP/improper_fourier_omp.h diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/OPENMP/improper_harmonic_omp.cpp similarity index 100% rename from src/USER-OMP/improper_harmonic_omp.cpp rename to src/OPENMP/improper_harmonic_omp.cpp diff --git a/src/USER-OMP/improper_harmonic_omp.h b/src/OPENMP/improper_harmonic_omp.h similarity index 100% rename from src/USER-OMP/improper_harmonic_omp.h rename to src/OPENMP/improper_harmonic_omp.h diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/OPENMP/improper_ring_omp.cpp similarity index 100% rename from src/USER-OMP/improper_ring_omp.cpp rename to src/OPENMP/improper_ring_omp.cpp diff --git a/src/USER-OMP/improper_ring_omp.h b/src/OPENMP/improper_ring_omp.h similarity index 100% rename from src/USER-OMP/improper_ring_omp.h rename to src/OPENMP/improper_ring_omp.h diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/OPENMP/improper_umbrella_omp.cpp similarity index 100% rename from src/USER-OMP/improper_umbrella_omp.cpp rename to src/OPENMP/improper_umbrella_omp.cpp diff --git a/src/USER-OMP/improper_umbrella_omp.h b/src/OPENMP/improper_umbrella_omp.h similarity index 100% rename from src/USER-OMP/improper_umbrella_omp.h rename to src/OPENMP/improper_umbrella_omp.h diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/OPENMP/msm_cg_omp.cpp similarity index 100% rename from src/USER-OMP/msm_cg_omp.cpp rename to src/OPENMP/msm_cg_omp.cpp diff --git a/src/USER-OMP/msm_cg_omp.h b/src/OPENMP/msm_cg_omp.h similarity index 100% rename from src/USER-OMP/msm_cg_omp.h rename to src/OPENMP/msm_cg_omp.h diff --git a/src/USER-OMP/msm_omp.cpp b/src/OPENMP/msm_omp.cpp similarity index 100% rename from src/USER-OMP/msm_omp.cpp rename to src/OPENMP/msm_omp.cpp diff --git a/src/USER-OMP/msm_omp.h b/src/OPENMP/msm_omp.h similarity index 100% rename from src/USER-OMP/msm_omp.h rename to src/OPENMP/msm_omp.h diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp b/src/OPENMP/npair_full_bin_atomonly_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_bin_atomonly_omp.cpp rename to src/OPENMP/npair_full_bin_atomonly_omp.cpp diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.h b/src/OPENMP/npair_full_bin_atomonly_omp.h similarity index 100% rename from src/USER-OMP/npair_full_bin_atomonly_omp.h rename to src/OPENMP/npair_full_bin_atomonly_omp.h diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.cpp b/src/OPENMP/npair_full_bin_ghost_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_bin_ghost_omp.cpp rename to src/OPENMP/npair_full_bin_ghost_omp.cpp diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.h b/src/OPENMP/npair_full_bin_ghost_omp.h similarity index 100% rename from src/USER-OMP/npair_full_bin_ghost_omp.h rename to src/OPENMP/npair_full_bin_ghost_omp.h diff --git a/src/USER-OMP/npair_full_bin_omp.cpp b/src/OPENMP/npair_full_bin_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_bin_omp.cpp rename to src/OPENMP/npair_full_bin_omp.cpp diff --git a/src/USER-OMP/npair_full_bin_omp.h b/src/OPENMP/npair_full_bin_omp.h similarity index 100% rename from src/USER-OMP/npair_full_bin_omp.h rename to src/OPENMP/npair_full_bin_omp.h diff --git a/src/USER-OMP/npair_full_multi_old_omp.cpp b/src/OPENMP/npair_full_multi_old_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_multi_old_omp.cpp rename to src/OPENMP/npair_full_multi_old_omp.cpp diff --git a/src/USER-OMP/npair_full_multi_old_omp.h b/src/OPENMP/npair_full_multi_old_omp.h similarity index 100% rename from src/USER-OMP/npair_full_multi_old_omp.h rename to src/OPENMP/npair_full_multi_old_omp.h diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/OPENMP/npair_full_multi_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_multi_omp.cpp rename to src/OPENMP/npair_full_multi_omp.cpp diff --git a/src/USER-OMP/npair_full_multi_omp.h b/src/OPENMP/npair_full_multi_omp.h similarity index 100% rename from src/USER-OMP/npair_full_multi_omp.h rename to src/OPENMP/npair_full_multi_omp.h diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp b/src/OPENMP/npair_full_nsq_ghost_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_nsq_ghost_omp.cpp rename to src/OPENMP/npair_full_nsq_ghost_omp.cpp diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.h b/src/OPENMP/npair_full_nsq_ghost_omp.h similarity index 100% rename from src/USER-OMP/npair_full_nsq_ghost_omp.h rename to src/OPENMP/npair_full_nsq_ghost_omp.h diff --git a/src/USER-OMP/npair_full_nsq_omp.cpp b/src/OPENMP/npair_full_nsq_omp.cpp similarity index 100% rename from src/USER-OMP/npair_full_nsq_omp.cpp rename to src/OPENMP/npair_full_nsq_omp.cpp diff --git a/src/USER-OMP/npair_full_nsq_omp.h b/src/OPENMP/npair_full_nsq_omp.h similarity index 100% rename from src/USER-OMP/npair_full_nsq_omp.h rename to src/OPENMP/npair_full_nsq_omp.h diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp b/src/OPENMP/npair_half_bin_atomonly_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp rename to src/OPENMP/npair_half_bin_atomonly_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.h b/src/OPENMP/npair_half_bin_atomonly_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_bin_atomonly_newton_omp.h rename to src/OPENMP/npair_half_bin_atomonly_newton_omp.h diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp b/src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp rename to src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h b/src/OPENMP/npair_half_bin_newtoff_ghost_omp.h similarity index 100% rename from src/USER-OMP/npair_half_bin_newtoff_ghost_omp.h rename to src/OPENMP/npair_half_bin_newtoff_ghost_omp.h diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_bin_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_bin_newtoff_omp.cpp rename to src/OPENMP/npair_half_bin_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.h b/src/OPENMP/npair_half_bin_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_bin_newtoff_omp.h rename to src/OPENMP/npair_half_bin_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_bin_newton_omp.cpp b/src/OPENMP/npair_half_bin_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_bin_newton_omp.cpp rename to src/OPENMP/npair_half_bin_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_bin_newton_omp.h b/src/OPENMP/npair_half_bin_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_bin_newton_omp.h rename to src/OPENMP/npair_half_bin_newton_omp.h diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_bin_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_bin_newton_tri_omp.cpp rename to src/OPENMP/npair_half_bin_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.h b/src/OPENMP/npair_half_bin_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_bin_newton_tri_omp.h rename to src/OPENMP/npair_half_bin_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/OPENMP/npair_half_multi_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_newtoff_omp.cpp rename to src/OPENMP/npair_half_multi_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.h b/src/OPENMP/npair_half_multi_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_newtoff_omp.h rename to src/OPENMP/npair_half_multi_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/OPENMP/npair_half_multi_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_newton_omp.cpp rename to src/OPENMP/npair_half_multi_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_newton_omp.h b/src/OPENMP/npair_half_multi_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_newton_omp.h rename to src/OPENMP/npair_half_multi_newton_omp.h diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/OPENMP/npair_half_multi_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_newton_tri_omp.cpp rename to src/OPENMP/npair_half_multi_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.h b/src/OPENMP/npair_half_multi_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_newton_tri_omp.h rename to src/OPENMP/npair_half_multi_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp b/src/OPENMP/npair_half_multi_old_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp rename to src/OPENMP/npair_half_multi_old_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_old_newtoff_omp.h b/src/OPENMP/npair_half_multi_old_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newtoff_omp.h rename to src/OPENMP/npair_half_multi_old_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_multi_old_newton_omp.cpp b/src/OPENMP/npair_half_multi_old_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newton_omp.cpp rename to src/OPENMP/npair_half_multi_old_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_old_newton_omp.h b/src/OPENMP/npair_half_multi_old_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newton_omp.h rename to src/OPENMP/npair_half_multi_old_newton_omp.h diff --git a/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp b/src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp rename to src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_multi_old_newton_tri_omp.h b/src/OPENMP/npair_half_multi_old_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_multi_old_newton_tri_omp.h rename to src/OPENMP/npair_half_multi_old_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp b/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp rename to src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h b/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.h similarity index 100% rename from src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.h rename to src/OPENMP/npair_half_nsq_newtoff_ghost_omp.h diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_nsq_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_nsq_newtoff_omp.cpp rename to src/OPENMP/npair_half_nsq_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.h b/src/OPENMP/npair_half_nsq_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_nsq_newtoff_omp.h rename to src/OPENMP/npair_half_nsq_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.cpp b/src/OPENMP/npair_half_nsq_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_nsq_newton_omp.cpp rename to src/OPENMP/npair_half_nsq_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.h b/src/OPENMP/npair_half_nsq_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_nsq_newton_omp.h rename to src/OPENMP/npair_half_nsq_newton_omp.h diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp rename to src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.h b/src/OPENMP/npair_half_respa_bin_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newtoff_omp.h rename to src/OPENMP/npair_half_respa_bin_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp b/src/OPENMP/npair_half_respa_bin_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newton_omp.cpp rename to src/OPENMP/npair_half_respa_bin_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.h b/src/OPENMP/npair_half_respa_bin_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newton_omp.h rename to src/OPENMP/npair_half_respa_bin_newton_omp.h diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp rename to src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h b/src/OPENMP/npair_half_respa_bin_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_respa_bin_newton_tri_omp.h rename to src/OPENMP/npair_half_respa_bin_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp rename to src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h b/src/OPENMP/npair_half_respa_nsq_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_respa_nsq_newtoff_omp.h rename to src/OPENMP/npair_half_respa_nsq_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp b/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp rename to src/OPENMP/npair_half_respa_nsq_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.h b/src/OPENMP/npair_half_respa_nsq_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_respa_nsq_newton_omp.h rename to src/OPENMP/npair_half_respa_nsq_newton_omp.h diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_size_bin_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp rename to src/OPENMP/npair_half_size_bin_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.h b/src/OPENMP/npair_half_size_bin_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newtoff_omp.h rename to src/OPENMP/npair_half_size_bin_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/OPENMP/npair_half_size_bin_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newton_omp.cpp rename to src/OPENMP/npair_half_size_bin_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.h b/src/OPENMP/npair_half_size_bin_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newton_omp.h rename to src/OPENMP/npair_half_size_bin_newton_omp.h diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp rename to src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.h b/src/OPENMP/npair_half_size_bin_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_bin_newton_tri_omp.h rename to src/OPENMP/npair_half_size_bin_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/OPENMP/npair_half_size_multi_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp rename to src/OPENMP/npair_half_size_multi_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h b/src/OPENMP/npair_half_size_multi_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newtoff_omp.h rename to src/OPENMP/npair_half_size_multi_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/OPENMP/npair_half_size_multi_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newton_omp.cpp rename to src/OPENMP/npair_half_size_multi_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.h b/src/OPENMP/npair_half_size_multi_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newton_omp.h rename to src/OPENMP/npair_half_size_multi_newton_omp.h diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp rename to src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.h b/src/OPENMP/npair_half_size_multi_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_multi_newton_tri_omp.h rename to src/OPENMP/npair_half_size_multi_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp b/src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp similarity index 100% rename from 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b/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp rename to src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h b/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h rename to src/OPENMP/npair_half_size_multi_old_newton_tri_omp.h diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp rename to src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.h b/src/OPENMP/npair_half_size_nsq_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_nsq_newtoff_omp.h rename to src/OPENMP/npair_half_size_nsq_newtoff_omp.h diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/OPENMP/npair_half_size_nsq_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_half_size_nsq_newton_omp.cpp rename to src/OPENMP/npair_half_size_nsq_newton_omp.cpp diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.h b/src/OPENMP/npair_half_size_nsq_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_half_size_nsq_newton_omp.h rename to src/OPENMP/npair_half_size_nsq_newton_omp.h diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/OPENMP/npair_halffull_newtoff_omp.cpp similarity index 100% rename from src/USER-OMP/npair_halffull_newtoff_omp.cpp rename to src/OPENMP/npair_halffull_newtoff_omp.cpp diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.h b/src/OPENMP/npair_halffull_newtoff_omp.h similarity index 100% rename from src/USER-OMP/npair_halffull_newtoff_omp.h rename to src/OPENMP/npair_halffull_newtoff_omp.h diff --git a/src/USER-OMP/npair_halffull_newton_omp.cpp b/src/OPENMP/npair_halffull_newton_omp.cpp similarity index 100% rename from src/USER-OMP/npair_halffull_newton_omp.cpp rename to src/OPENMP/npair_halffull_newton_omp.cpp diff --git a/src/USER-OMP/npair_halffull_newton_omp.h b/src/OPENMP/npair_halffull_newton_omp.h similarity index 100% rename from src/USER-OMP/npair_halffull_newton_omp.h rename to src/OPENMP/npair_halffull_newton_omp.h diff --git a/src/USER-OMP/npair_omp.h b/src/OPENMP/npair_omp.h similarity index 100% rename from src/USER-OMP/npair_omp.h rename to src/OPENMP/npair_omp.h diff --git a/src/USER-OMP/npair_skip_omp.h b/src/OPENMP/npair_skip_omp.h similarity index 100% rename from src/USER-OMP/npair_skip_omp.h rename to src/OPENMP/npair_skip_omp.h diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/OPENMP/pair_adp_omp.cpp similarity index 100% rename from src/USER-OMP/pair_adp_omp.cpp rename to src/OPENMP/pair_adp_omp.cpp diff --git a/src/USER-OMP/pair_adp_omp.h b/src/OPENMP/pair_adp_omp.h similarity index 100% rename from src/USER-OMP/pair_adp_omp.h rename to src/OPENMP/pair_adp_omp.h diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/OPENMP/pair_agni_omp.cpp similarity index 100% rename from src/USER-OMP/pair_agni_omp.cpp rename to src/OPENMP/pair_agni_omp.cpp diff --git a/src/USER-OMP/pair_agni_omp.h b/src/OPENMP/pair_agni_omp.h similarity index 100% rename from src/USER-OMP/pair_agni_omp.h rename to src/OPENMP/pair_agni_omp.h diff --git a/src/USER-OMP/pair_airebo_morse_omp.cpp b/src/OPENMP/pair_airebo_morse_omp.cpp similarity index 100% rename from src/USER-OMP/pair_airebo_morse_omp.cpp rename to src/OPENMP/pair_airebo_morse_omp.cpp diff --git a/src/USER-OMP/pair_airebo_morse_omp.h b/src/OPENMP/pair_airebo_morse_omp.h similarity index 100% rename from src/USER-OMP/pair_airebo_morse_omp.h rename to src/OPENMP/pair_airebo_morse_omp.h diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/OPENMP/pair_airebo_omp.cpp similarity index 100% rename from src/USER-OMP/pair_airebo_omp.cpp rename to src/OPENMP/pair_airebo_omp.cpp diff --git a/src/USER-OMP/pair_airebo_omp.h b/src/OPENMP/pair_airebo_omp.h similarity index 100% rename from src/USER-OMP/pair_airebo_omp.h rename to src/OPENMP/pair_airebo_omp.h diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/OPENMP/pair_beck_omp.cpp similarity index 100% rename from src/USER-OMP/pair_beck_omp.cpp rename to src/OPENMP/pair_beck_omp.cpp diff --git a/src/USER-OMP/pair_beck_omp.h b/src/OPENMP/pair_beck_omp.h similarity index 100% rename from src/USER-OMP/pair_beck_omp.h rename to src/OPENMP/pair_beck_omp.h diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/OPENMP/pair_born_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_born_coul_long_omp.cpp rename to src/OPENMP/pair_born_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_born_coul_long_omp.h b/src/OPENMP/pair_born_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_born_coul_long_omp.h rename to src/OPENMP/pair_born_coul_long_omp.h diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/OPENMP/pair_born_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_born_coul_msm_omp.cpp rename to src/OPENMP/pair_born_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_born_coul_msm_omp.h b/src/OPENMP/pair_born_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_born_coul_msm_omp.h rename to src/OPENMP/pair_born_coul_msm_omp.h diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/OPENMP/pair_born_coul_wolf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_born_coul_wolf_omp.cpp rename to src/OPENMP/pair_born_coul_wolf_omp.cpp diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.h b/src/OPENMP/pair_born_coul_wolf_omp.h similarity index 100% rename from src/USER-OMP/pair_born_coul_wolf_omp.h rename to src/OPENMP/pair_born_coul_wolf_omp.h diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/OPENMP/pair_born_omp.cpp similarity index 100% rename from src/USER-OMP/pair_born_omp.cpp rename to src/OPENMP/pair_born_omp.cpp diff --git a/src/USER-OMP/pair_born_omp.h b/src/OPENMP/pair_born_omp.h similarity index 100% rename from src/USER-OMP/pair_born_omp.h rename to src/OPENMP/pair_born_omp.h diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/OPENMP/pair_brownian_omp.cpp similarity index 100% rename from src/USER-OMP/pair_brownian_omp.cpp rename to src/OPENMP/pair_brownian_omp.cpp diff --git a/src/USER-OMP/pair_brownian_omp.h b/src/OPENMP/pair_brownian_omp.h similarity index 100% rename from src/USER-OMP/pair_brownian_omp.h rename to src/OPENMP/pair_brownian_omp.h diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/OPENMP/pair_brownian_poly_omp.cpp similarity index 100% rename from src/USER-OMP/pair_brownian_poly_omp.cpp rename to src/OPENMP/pair_brownian_poly_omp.cpp diff --git a/src/USER-OMP/pair_brownian_poly_omp.h b/src/OPENMP/pair_brownian_poly_omp.h similarity index 100% rename from src/USER-OMP/pair_brownian_poly_omp.h rename to src/OPENMP/pair_brownian_poly_omp.h diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/OPENMP/pair_buck_coul_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_buck_coul_cut_omp.cpp rename to src/OPENMP/pair_buck_coul_cut_omp.cpp diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.h b/src/OPENMP/pair_buck_coul_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_buck_coul_cut_omp.h rename to src/OPENMP/pair_buck_coul_cut_omp.h diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/OPENMP/pair_buck_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_buck_coul_long_omp.cpp rename to src/OPENMP/pair_buck_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_buck_coul_long_omp.h b/src/OPENMP/pair_buck_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_buck_coul_long_omp.h rename to src/OPENMP/pair_buck_coul_long_omp.h diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/OPENMP/pair_buck_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_buck_coul_msm_omp.cpp rename to src/OPENMP/pair_buck_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.h b/src/OPENMP/pair_buck_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_buck_coul_msm_omp.h rename to src/OPENMP/pair_buck_coul_msm_omp.h diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/OPENMP/pair_buck_long_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_buck_long_coul_long_omp.cpp rename to src/OPENMP/pair_buck_long_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.h b/src/OPENMP/pair_buck_long_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_buck_long_coul_long_omp.h rename to src/OPENMP/pair_buck_long_coul_long_omp.h diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/OPENMP/pair_buck_omp.cpp similarity index 100% rename from src/USER-OMP/pair_buck_omp.cpp rename to src/OPENMP/pair_buck_omp.cpp diff --git a/src/USER-OMP/pair_buck_omp.h b/src/OPENMP/pair_buck_omp.h similarity index 100% rename from src/USER-OMP/pair_buck_omp.h rename to src/OPENMP/pair_buck_omp.h diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/OPENMP/pair_colloid_omp.cpp similarity index 100% rename from src/USER-OMP/pair_colloid_omp.cpp rename to src/OPENMP/pair_colloid_omp.cpp diff --git a/src/USER-OMP/pair_colloid_omp.h b/src/OPENMP/pair_colloid_omp.h similarity index 100% rename from src/USER-OMP/pair_colloid_omp.h rename to src/OPENMP/pair_colloid_omp.h diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/OPENMP/pair_comb_omp.cpp similarity index 100% rename from src/USER-OMP/pair_comb_omp.cpp rename to src/OPENMP/pair_comb_omp.cpp diff --git a/src/USER-OMP/pair_comb_omp.h b/src/OPENMP/pair_comb_omp.h similarity index 100% rename from src/USER-OMP/pair_comb_omp.h rename to src/OPENMP/pair_comb_omp.h diff --git a/src/USER-OMP/pair_coul_cut_global_omp.cpp b/src/OPENMP/pair_coul_cut_global_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_cut_global_omp.cpp rename to src/OPENMP/pair_coul_cut_global_omp.cpp diff --git a/src/USER-OMP/pair_coul_cut_global_omp.h b/src/OPENMP/pair_coul_cut_global_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_cut_global_omp.h rename to src/OPENMP/pair_coul_cut_global_omp.h diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/OPENMP/pair_coul_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_cut_omp.cpp rename to src/OPENMP/pair_coul_cut_omp.cpp diff --git a/src/USER-OMP/pair_coul_cut_omp.h b/src/OPENMP/pair_coul_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_cut_omp.h rename to src/OPENMP/pair_coul_cut_omp.h diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/OPENMP/pair_coul_cut_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_cut_soft_omp.cpp rename to src/OPENMP/pair_coul_cut_soft_omp.cpp diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.h b/src/OPENMP/pair_coul_cut_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_cut_soft_omp.h rename to src/OPENMP/pair_coul_cut_soft_omp.h diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/OPENMP/pair_coul_debye_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_debye_omp.cpp rename to src/OPENMP/pair_coul_debye_omp.cpp diff --git a/src/USER-OMP/pair_coul_debye_omp.h b/src/OPENMP/pair_coul_debye_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_debye_omp.h rename to src/OPENMP/pair_coul_debye_omp.h diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/OPENMP/pair_coul_diel_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_diel_omp.cpp rename to src/OPENMP/pair_coul_diel_omp.cpp diff --git a/src/USER-OMP/pair_coul_diel_omp.h b/src/OPENMP/pair_coul_diel_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_diel_omp.h rename to src/OPENMP/pair_coul_diel_omp.h diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/OPENMP/pair_coul_dsf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_dsf_omp.cpp rename to src/OPENMP/pair_coul_dsf_omp.cpp diff --git a/src/USER-OMP/pair_coul_dsf_omp.h b/src/OPENMP/pair_coul_dsf_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_dsf_omp.h rename to src/OPENMP/pair_coul_dsf_omp.h diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/OPENMP/pair_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_long_omp.cpp rename to src/OPENMP/pair_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_coul_long_omp.h b/src/OPENMP/pair_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_long_omp.h rename to src/OPENMP/pair_coul_long_omp.h diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/OPENMP/pair_coul_long_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_long_soft_omp.cpp rename to src/OPENMP/pair_coul_long_soft_omp.cpp diff --git a/src/USER-OMP/pair_coul_long_soft_omp.h b/src/OPENMP/pair_coul_long_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_long_soft_omp.h rename to src/OPENMP/pair_coul_long_soft_omp.h diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/OPENMP/pair_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_msm_omp.cpp rename to src/OPENMP/pair_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_coul_msm_omp.h b/src/OPENMP/pair_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_msm_omp.h rename to src/OPENMP/pair_coul_msm_omp.h diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/OPENMP/pair_coul_wolf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_coul_wolf_omp.cpp rename to src/OPENMP/pair_coul_wolf_omp.cpp diff --git a/src/USER-OMP/pair_coul_wolf_omp.h b/src/OPENMP/pair_coul_wolf_omp.h similarity index 100% rename from src/USER-OMP/pair_coul_wolf_omp.h rename to src/OPENMP/pair_coul_wolf_omp.h diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/OPENMP/pair_dpd_omp.cpp similarity index 100% rename from src/USER-OMP/pair_dpd_omp.cpp rename to src/OPENMP/pair_dpd_omp.cpp diff --git a/src/USER-OMP/pair_dpd_omp.h b/src/OPENMP/pair_dpd_omp.h similarity index 100% rename from src/USER-OMP/pair_dpd_omp.h rename to src/OPENMP/pair_dpd_omp.h diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/OPENMP/pair_dpd_tstat_omp.cpp similarity index 100% rename from src/USER-OMP/pair_dpd_tstat_omp.cpp rename to src/OPENMP/pair_dpd_tstat_omp.cpp diff --git a/src/USER-OMP/pair_dpd_tstat_omp.h b/src/OPENMP/pair_dpd_tstat_omp.h similarity index 100% rename from src/USER-OMP/pair_dpd_tstat_omp.h rename to src/OPENMP/pair_dpd_tstat_omp.h diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/OPENMP/pair_eam_alloy_omp.cpp similarity index 100% rename from src/USER-OMP/pair_eam_alloy_omp.cpp rename to src/OPENMP/pair_eam_alloy_omp.cpp diff --git a/src/USER-OMP/pair_eam_alloy_omp.h b/src/OPENMP/pair_eam_alloy_omp.h similarity index 100% rename from src/USER-OMP/pair_eam_alloy_omp.h rename to src/OPENMP/pair_eam_alloy_omp.h diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/OPENMP/pair_eam_fs_omp.cpp similarity index 100% rename from src/USER-OMP/pair_eam_fs_omp.cpp rename to src/OPENMP/pair_eam_fs_omp.cpp diff --git a/src/USER-OMP/pair_eam_fs_omp.h b/src/OPENMP/pair_eam_fs_omp.h similarity index 100% rename from src/USER-OMP/pair_eam_fs_omp.h rename to src/OPENMP/pair_eam_fs_omp.h diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/OPENMP/pair_eam_omp.cpp similarity index 100% rename from src/USER-OMP/pair_eam_omp.cpp rename to src/OPENMP/pair_eam_omp.cpp diff --git a/src/USER-OMP/pair_eam_omp.h b/src/OPENMP/pair_eam_omp.h similarity index 100% rename from src/USER-OMP/pair_eam_omp.h rename to src/OPENMP/pair_eam_omp.h diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/OPENMP/pair_edip_omp.cpp similarity index 100% rename from src/USER-OMP/pair_edip_omp.cpp rename to src/OPENMP/pair_edip_omp.cpp diff --git a/src/USER-OMP/pair_edip_omp.h b/src/OPENMP/pair_edip_omp.h similarity index 100% rename from src/USER-OMP/pair_edip_omp.h rename to src/OPENMP/pair_edip_omp.h diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/OPENMP/pair_eim_omp.cpp similarity index 100% rename from src/USER-OMP/pair_eim_omp.cpp rename to src/OPENMP/pair_eim_omp.cpp diff --git a/src/USER-OMP/pair_eim_omp.h b/src/OPENMP/pair_eim_omp.h similarity index 100% rename from src/USER-OMP/pair_eim_omp.h rename to src/OPENMP/pair_eim_omp.h diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/OPENMP/pair_gauss_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gauss_cut_omp.cpp rename to src/OPENMP/pair_gauss_cut_omp.cpp diff --git a/src/USER-OMP/pair_gauss_cut_omp.h b/src/OPENMP/pair_gauss_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_gauss_cut_omp.h rename to src/OPENMP/pair_gauss_cut_omp.h diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/OPENMP/pair_gauss_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gauss_omp.cpp rename to src/OPENMP/pair_gauss_omp.cpp diff --git a/src/USER-OMP/pair_gauss_omp.h b/src/OPENMP/pair_gauss_omp.h similarity index 100% rename from src/USER-OMP/pair_gauss_omp.h rename to src/OPENMP/pair_gauss_omp.h diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/OPENMP/pair_gayberne_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gayberne_omp.cpp rename to src/OPENMP/pair_gayberne_omp.cpp diff --git a/src/USER-OMP/pair_gayberne_omp.h b/src/OPENMP/pair_gayberne_omp.h similarity index 100% rename from src/USER-OMP/pair_gayberne_omp.h rename to src/OPENMP/pair_gayberne_omp.h diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/OPENMP/pair_gran_hertz_history_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gran_hertz_history_omp.cpp rename to src/OPENMP/pair_gran_hertz_history_omp.cpp diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.h b/src/OPENMP/pair_gran_hertz_history_omp.h similarity index 100% rename from src/USER-OMP/pair_gran_hertz_history_omp.h rename to src/OPENMP/pair_gran_hertz_history_omp.h diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/OPENMP/pair_gran_hooke_history_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gran_hooke_history_omp.cpp rename to src/OPENMP/pair_gran_hooke_history_omp.cpp diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.h b/src/OPENMP/pair_gran_hooke_history_omp.h similarity index 100% rename from src/USER-OMP/pair_gran_hooke_history_omp.h rename to src/OPENMP/pair_gran_hooke_history_omp.h diff --git a/src/USER-OMP/pair_gran_hooke_omp.cpp b/src/OPENMP/pair_gran_hooke_omp.cpp similarity index 100% rename from src/USER-OMP/pair_gran_hooke_omp.cpp rename to src/OPENMP/pair_gran_hooke_omp.cpp diff --git a/src/USER-OMP/pair_gran_hooke_omp.h b/src/OPENMP/pair_gran_hooke_omp.h similarity index 100% rename from src/USER-OMP/pair_gran_hooke_omp.h rename to src/OPENMP/pair_gran_hooke_omp.h diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/OPENMP/pair_hbond_dreiding_lj_omp.cpp similarity index 100% rename from src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp rename to src/OPENMP/pair_hbond_dreiding_lj_omp.cpp diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.h b/src/OPENMP/pair_hbond_dreiding_lj_omp.h similarity index 100% rename from src/USER-OMP/pair_hbond_dreiding_lj_omp.h rename to src/OPENMP/pair_hbond_dreiding_lj_omp.h diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/OPENMP/pair_hbond_dreiding_morse_omp.cpp similarity index 100% rename from src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp rename to src/OPENMP/pair_hbond_dreiding_morse_omp.cpp diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.h b/src/OPENMP/pair_hbond_dreiding_morse_omp.h similarity index 100% rename from src/USER-OMP/pair_hbond_dreiding_morse_omp.h rename to src/OPENMP/pair_hbond_dreiding_morse_omp.h diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/OPENMP/pair_lj96_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj96_cut_omp.cpp rename to src/OPENMP/pair_lj96_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj96_cut_omp.h b/src/OPENMP/pair_lj96_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj96_cut_omp.h rename to src/OPENMP/pair_lj96_cut_omp.h diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp rename to src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h b/src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h rename to src/OPENMP/pair_lj_charmm_coul_charmm_implicit_omp.h diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_charmm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp rename to src/OPENMP/pair_lj_charmm_coul_charmm_omp.cpp diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h b/src/OPENMP/pair_lj_charmm_coul_charmm_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h rename to src/OPENMP/pair_lj_charmm_coul_charmm_omp.h diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp rename to src/OPENMP/pair_lj_charmm_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.h b/src/OPENMP/pair_lj_charmm_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_long_omp.h rename to src/OPENMP/pair_lj_charmm_coul_long_omp.h diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp rename to src/OPENMP/pair_lj_charmm_coul_long_soft_omp.cpp diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h b/src/OPENMP/pair_lj_charmm_coul_long_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.h rename to src/OPENMP/pair_lj_charmm_coul_long_soft_omp.h diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/OPENMP/pair_lj_charmm_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp rename to src/OPENMP/pair_lj_charmm_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.h b/src/OPENMP/pair_lj_charmm_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_charmm_coul_msm_omp.h rename to src/OPENMP/pair_lj_charmm_coul_msm_omp.h diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/OPENMP/pair_lj_class2_coul_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp rename to src/OPENMP/pair_lj_class2_coul_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.h b/src/OPENMP/pair_lj_class2_coul_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_class2_coul_cut_omp.h rename to src/OPENMP/pair_lj_class2_coul_cut_omp.h diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/OPENMP/pair_lj_class2_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_class2_coul_long_omp.cpp rename to src/OPENMP/pair_lj_class2_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.h b/src/OPENMP/pair_lj_class2_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_class2_coul_long_omp.h rename to src/OPENMP/pair_lj_class2_coul_long_omp.h diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/OPENMP/pair_lj_class2_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_class2_omp.cpp rename to src/OPENMP/pair_lj_class2_omp.cpp diff --git a/src/USER-OMP/pair_lj_class2_omp.h b/src/OPENMP/pair_lj_class2_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_class2_omp.h rename to src/OPENMP/pair_lj_class2_omp.h diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/OPENMP/pair_lj_cubic_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cubic_omp.cpp rename to src/OPENMP/pair_lj_cubic_omp.cpp diff --git a/src/USER-OMP/pair_lj_cubic_omp.h b/src/OPENMP/pair_lj_cubic_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cubic_omp.h rename to src/OPENMP/pair_lj_cubic_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_dielectric_omp.cpp b/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_dielectric_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_dielectric_omp.h b/src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_dielectric_omp.h rename to src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/OPENMP/pair_lj_cut_coul_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.h b/src/OPENMP/pair_lj_cut_coul_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_omp.h rename to src/OPENMP/pair_lj_cut_coul_cut_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_cut_soft_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h b/src/OPENMP/pair_lj_cut_coul_cut_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.h rename to src/OPENMP/pair_lj_cut_coul_cut_soft_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/OPENMP/pair_lj_cut_coul_debye_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_debye_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.h b/src/OPENMP/pair_lj_cut_coul_debye_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_debye_omp.h rename to src/OPENMP/pair_lj_cut_coul_debye_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/OPENMP/pair_lj_cut_coul_dsf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_dsf_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.h b/src/OPENMP/pair_lj_cut_coul_dsf_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_dsf_omp.h rename to src/OPENMP/pair_lj_cut_coul_dsf_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_long_dielectric_omp.cpp b/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_dielectric_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_long_dielectric_omp.h b/src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_dielectric_omp.h rename to src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/OPENMP/pair_lj_cut_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.h b/src/OPENMP/pair_lj_cut_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_omp.h rename to src/OPENMP/pair_lj_cut_coul_long_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/OPENMP/pair_lj_cut_coul_long_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_long_soft_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h b/src/OPENMP/pair_lj_cut_coul_long_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_long_soft_omp.h rename to src/OPENMP/pair_lj_cut_coul_long_soft_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/OPENMP/pair_lj_cut_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.h b/src/OPENMP/pair_lj_cut_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_msm_omp.h rename to src/OPENMP/pair_lj_cut_coul_msm_omp.h diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/OPENMP/pair_lj_cut_coul_wolf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp rename to src/OPENMP/pair_lj_cut_coul_wolf_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.h b/src/OPENMP/pair_lj_cut_coul_wolf_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_coul_wolf_omp.h rename to src/OPENMP/pair_lj_cut_coul_wolf_omp.h diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/OPENMP/pair_lj_cut_dipole_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp rename to src/OPENMP/pair_lj_cut_dipole_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.h b/src/OPENMP/pair_lj_cut_dipole_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_dipole_cut_omp.h rename to src/OPENMP/pair_lj_cut_dipole_cut_omp.h diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/OPENMP/pair_lj_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_omp.cpp rename to src/OPENMP/pair_lj_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_omp.h b/src/OPENMP/pair_lj_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_omp.h rename to src/OPENMP/pair_lj_cut_omp.h diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/OPENMP/pair_lj_cut_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_soft_omp.cpp rename to src/OPENMP/pair_lj_cut_soft_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.h b/src/OPENMP/pair_lj_cut_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_soft_omp.h rename to src/OPENMP/pair_lj_cut_soft_omp.h diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/OPENMP/pair_lj_cut_thole_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_thole_long_omp.cpp rename to src/OPENMP/pair_lj_cut_thole_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.h b/src/OPENMP/pair_lj_cut_thole_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_thole_long_omp.h rename to src/OPENMP/pair_lj_cut_thole_long_omp.h diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp b/src/OPENMP/pair_lj_cut_tip4p_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp rename to src/OPENMP/pair_lj_cut_tip4p_cut_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h b/src/OPENMP/pair_lj_cut_tip4p_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h rename to src/OPENMP/pair_lj_cut_tip4p_cut_omp.h diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/OPENMP/pair_lj_cut_tip4p_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp rename to src/OPENMP/pair_lj_cut_tip4p_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.h b/src/OPENMP/pair_lj_cut_tip4p_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_long_omp.h rename to src/OPENMP/pair_lj_cut_tip4p_long_omp.h diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp b/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp rename to src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.cpp diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h b/src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.h rename to src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.h diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/OPENMP/pair_lj_expand_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_expand_omp.cpp rename to src/OPENMP/pair_lj_expand_omp.cpp diff --git a/src/USER-OMP/pair_lj_expand_omp.h b/src/OPENMP/pair_lj_expand_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_expand_omp.h rename to src/OPENMP/pair_lj_expand_omp.h diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp rename to src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.cpp diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h b/src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h rename to src/OPENMP/pair_lj_gromacs_coul_gromacs_omp.h diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/OPENMP/pair_lj_gromacs_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_gromacs_omp.cpp rename to src/OPENMP/pair_lj_gromacs_omp.cpp diff --git a/src/USER-OMP/pair_lj_gromacs_omp.h b/src/OPENMP/pair_lj_gromacs_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_gromacs_omp.h rename to src/OPENMP/pair_lj_gromacs_omp.h diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/OPENMP/pair_lj_long_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_long_coul_long_omp.cpp rename to src/OPENMP/pair_lj_long_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.h b/src/OPENMP/pair_lj_long_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_long_coul_long_omp.h rename to src/OPENMP/pair_lj_long_coul_long_omp.h diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/OPENMP/pair_lj_long_tip4p_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp rename to src/OPENMP/pair_lj_long_tip4p_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.h b/src/OPENMP/pair_lj_long_tip4p_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_long_tip4p_long_omp.h rename to src/OPENMP/pair_lj_long_tip4p_long_omp.h diff --git a/src/USER-OMP/pair_lj_relres_omp.cpp b/src/OPENMP/pair_lj_relres_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_relres_omp.cpp rename to src/OPENMP/pair_lj_relres_omp.cpp diff --git a/src/USER-OMP/pair_lj_relres_omp.h b/src/OPENMP/pair_lj_relres_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_relres_omp.h rename to src/OPENMP/pair_lj_relres_omp.h diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/OPENMP/pair_lj_sdk_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp rename to src/OPENMP/pair_lj_sdk_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.h b/src/OPENMP/pair_lj_sdk_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_sdk_coul_long_omp.h rename to src/OPENMP/pair_lj_sdk_coul_long_omp.h diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/OPENMP/pair_lj_sdk_coul_msm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp rename to src/OPENMP/pair_lj_sdk_coul_msm_omp.cpp diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.h b/src/OPENMP/pair_lj_sdk_coul_msm_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_sdk_coul_msm_omp.h rename to src/OPENMP/pair_lj_sdk_coul_msm_omp.h diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/OPENMP/pair_lj_sdk_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_sdk_omp.cpp rename to src/OPENMP/pair_lj_sdk_omp.cpp diff --git a/src/USER-OMP/pair_lj_sdk_omp.h b/src/OPENMP/pair_lj_sdk_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_sdk_omp.h rename to src/OPENMP/pair_lj_sdk_omp.h diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/OPENMP/pair_lj_sf_dipole_sf_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp rename to src/OPENMP/pair_lj_sf_dipole_sf_omp.cpp diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.h b/src/OPENMP/pair_lj_sf_dipole_sf_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_sf_dipole_sf_omp.h rename to src/OPENMP/pair_lj_sf_dipole_sf_omp.h diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/OPENMP/pair_lj_smooth_linear_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_smooth_linear_omp.cpp rename to src/OPENMP/pair_lj_smooth_linear_omp.cpp diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.h b/src/OPENMP/pair_lj_smooth_linear_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_smooth_linear_omp.h rename to src/OPENMP/pair_lj_smooth_linear_omp.h diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/OPENMP/pair_lj_smooth_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lj_smooth_omp.cpp rename to src/OPENMP/pair_lj_smooth_omp.cpp diff --git a/src/USER-OMP/pair_lj_smooth_omp.h b/src/OPENMP/pair_lj_smooth_omp.h similarity index 100% rename from src/USER-OMP/pair_lj_smooth_omp.h rename to src/OPENMP/pair_lj_smooth_omp.h diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/OPENMP/pair_lubricate_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lubricate_omp.cpp rename to src/OPENMP/pair_lubricate_omp.cpp diff --git a/src/USER-OMP/pair_lubricate_omp.h b/src/OPENMP/pair_lubricate_omp.h similarity index 100% rename from src/USER-OMP/pair_lubricate_omp.h rename to src/OPENMP/pair_lubricate_omp.h diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/OPENMP/pair_lubricate_poly_omp.cpp similarity index 100% rename from src/USER-OMP/pair_lubricate_poly_omp.cpp rename to src/OPENMP/pair_lubricate_poly_omp.cpp diff --git a/src/USER-OMP/pair_lubricate_poly_omp.h b/src/OPENMP/pair_lubricate_poly_omp.h similarity index 100% rename from src/USER-OMP/pair_lubricate_poly_omp.h rename to src/OPENMP/pair_lubricate_poly_omp.h diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/OPENMP/pair_meam_spline_omp.cpp similarity index 100% rename from src/USER-OMP/pair_meam_spline_omp.cpp rename to src/OPENMP/pair_meam_spline_omp.cpp diff --git a/src/USER-OMP/pair_meam_spline_omp.h b/src/OPENMP/pair_meam_spline_omp.h similarity index 100% rename from src/USER-OMP/pair_meam_spline_omp.h rename to src/OPENMP/pair_meam_spline_omp.h diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/OPENMP/pair_morse_omp.cpp similarity index 100% rename from src/USER-OMP/pair_morse_omp.cpp rename to src/OPENMP/pair_morse_omp.cpp diff --git a/src/USER-OMP/pair_morse_omp.h b/src/OPENMP/pair_morse_omp.h similarity index 100% rename from src/USER-OMP/pair_morse_omp.h rename to src/OPENMP/pair_morse_omp.h diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/OPENMP/pair_morse_smooth_linear_omp.cpp similarity index 100% rename from src/USER-OMP/pair_morse_smooth_linear_omp.cpp rename to src/OPENMP/pair_morse_smooth_linear_omp.cpp diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.h b/src/OPENMP/pair_morse_smooth_linear_omp.h similarity index 100% rename from src/USER-OMP/pair_morse_smooth_linear_omp.h rename to src/OPENMP/pair_morse_smooth_linear_omp.h diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/OPENMP/pair_nm_cut_coul_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp rename to src/OPENMP/pair_nm_cut_coul_cut_omp.cpp diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.h b/src/OPENMP/pair_nm_cut_coul_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_nm_cut_coul_cut_omp.h rename to src/OPENMP/pair_nm_cut_coul_cut_omp.h diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/OPENMP/pair_nm_cut_coul_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_nm_cut_coul_long_omp.cpp rename to src/OPENMP/pair_nm_cut_coul_long_omp.cpp diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.h b/src/OPENMP/pair_nm_cut_coul_long_omp.h similarity index 100% rename from src/USER-OMP/pair_nm_cut_coul_long_omp.h rename to src/OPENMP/pair_nm_cut_coul_long_omp.h diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/OPENMP/pair_nm_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_nm_cut_omp.cpp rename to src/OPENMP/pair_nm_cut_omp.cpp diff --git a/src/USER-OMP/pair_nm_cut_omp.h b/src/OPENMP/pair_nm_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_nm_cut_omp.h rename to src/OPENMP/pair_nm_cut_omp.h diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/OPENMP/pair_peri_lps_omp.cpp similarity index 100% rename from src/USER-OMP/pair_peri_lps_omp.cpp rename to src/OPENMP/pair_peri_lps_omp.cpp diff --git a/src/USER-OMP/pair_peri_lps_omp.h b/src/OPENMP/pair_peri_lps_omp.h similarity index 100% rename from src/USER-OMP/pair_peri_lps_omp.h rename to src/OPENMP/pair_peri_lps_omp.h diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/OPENMP/pair_peri_pmb_omp.cpp similarity index 100% rename from src/USER-OMP/pair_peri_pmb_omp.cpp rename to src/OPENMP/pair_peri_pmb_omp.cpp diff --git a/src/USER-OMP/pair_peri_pmb_omp.h b/src/OPENMP/pair_peri_pmb_omp.h similarity index 100% rename from src/USER-OMP/pair_peri_pmb_omp.h rename to src/OPENMP/pair_peri_pmb_omp.h diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/OPENMP/pair_reaxc_omp.cpp similarity index 99% rename from src/USER-OMP/pair_reaxc_omp.cpp rename to src/OPENMP/pair_reaxc_omp.cpp index 8535b87dbe..66e7a77c92 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/OPENMP/pair_reaxc_omp.cpp @@ -24,7 +24,7 @@ by Hasan Metin Aktulga (MSU), Chris Knight (ALCF), Paul Coffman (ALCF), Kurt O'Hearn (MSU), Ray Shan (Materials Design), Wei Jiang (ALCF) - Integration of the pair_style reax/c/omp into the User-OMP package + Integration of the pair_style reax/c/omp into the OPENMP package by Axel Kohlmeyer (Temple U.) Please cite the related publication: diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/OPENMP/pair_reaxc_omp.h similarity index 100% rename from src/USER-OMP/pair_reaxc_omp.h rename to src/OPENMP/pair_reaxc_omp.h diff --git a/src/USER-OMP/pair_rebo_omp.cpp b/src/OPENMP/pair_rebo_omp.cpp similarity index 100% rename from src/USER-OMP/pair_rebo_omp.cpp rename to src/OPENMP/pair_rebo_omp.cpp diff --git a/src/USER-OMP/pair_rebo_omp.h b/src/OPENMP/pair_rebo_omp.h similarity index 100% rename from src/USER-OMP/pair_rebo_omp.h rename to src/OPENMP/pair_rebo_omp.h diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/OPENMP/pair_resquared_omp.cpp similarity index 100% rename from src/USER-OMP/pair_resquared_omp.cpp rename to src/OPENMP/pair_resquared_omp.cpp diff --git a/src/USER-OMP/pair_resquared_omp.h b/src/OPENMP/pair_resquared_omp.h similarity index 100% rename from src/USER-OMP/pair_resquared_omp.h rename to src/OPENMP/pair_resquared_omp.h diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/OPENMP/pair_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_soft_omp.cpp rename to src/OPENMP/pair_soft_omp.cpp diff --git a/src/USER-OMP/pair_soft_omp.h b/src/OPENMP/pair_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_soft_omp.h rename to src/OPENMP/pair_soft_omp.h diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/OPENMP/pair_sw_omp.cpp similarity index 100% rename from src/USER-OMP/pair_sw_omp.cpp rename to src/OPENMP/pair_sw_omp.cpp diff --git a/src/USER-OMP/pair_sw_omp.h b/src/OPENMP/pair_sw_omp.h similarity index 100% rename from src/USER-OMP/pair_sw_omp.h rename to src/OPENMP/pair_sw_omp.h diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/OPENMP/pair_table_omp.cpp similarity index 100% rename from src/USER-OMP/pair_table_omp.cpp rename to src/OPENMP/pair_table_omp.cpp diff --git a/src/USER-OMP/pair_table_omp.h b/src/OPENMP/pair_table_omp.h similarity index 100% rename from src/USER-OMP/pair_table_omp.h rename to src/OPENMP/pair_table_omp.h diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/OPENMP/pair_tersoff_mod_c_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tersoff_mod_c_omp.cpp rename to src/OPENMP/pair_tersoff_mod_c_omp.cpp diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.h b/src/OPENMP/pair_tersoff_mod_c_omp.h similarity index 100% rename from src/USER-OMP/pair_tersoff_mod_c_omp.h rename to src/OPENMP/pair_tersoff_mod_c_omp.h diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/OPENMP/pair_tersoff_mod_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tersoff_mod_omp.cpp rename to src/OPENMP/pair_tersoff_mod_omp.cpp diff --git a/src/USER-OMP/pair_tersoff_mod_omp.h b/src/OPENMP/pair_tersoff_mod_omp.h similarity index 100% rename from src/USER-OMP/pair_tersoff_mod_omp.h rename to src/OPENMP/pair_tersoff_mod_omp.h diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/OPENMP/pair_tersoff_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tersoff_omp.cpp rename to src/OPENMP/pair_tersoff_omp.cpp diff --git a/src/USER-OMP/pair_tersoff_omp.h b/src/OPENMP/pair_tersoff_omp.h similarity index 100% rename from src/USER-OMP/pair_tersoff_omp.h rename to src/OPENMP/pair_tersoff_omp.h diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/OPENMP/pair_tersoff_table_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tersoff_table_omp.cpp rename to src/OPENMP/pair_tersoff_table_omp.cpp diff --git a/src/USER-OMP/pair_tersoff_table_omp.h b/src/OPENMP/pair_tersoff_table_omp.h similarity index 100% rename from src/USER-OMP/pair_tersoff_table_omp.h rename to src/OPENMP/pair_tersoff_table_omp.h diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/OPENMP/pair_tersoff_zbl_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tersoff_zbl_omp.cpp rename to src/OPENMP/pair_tersoff_zbl_omp.cpp diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.h b/src/OPENMP/pair_tersoff_zbl_omp.h similarity index 100% rename from src/USER-OMP/pair_tersoff_zbl_omp.h rename to src/OPENMP/pair_tersoff_zbl_omp.h diff --git a/src/USER-OMP/pair_tip4p_cut_omp.cpp b/src/OPENMP/pair_tip4p_cut_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tip4p_cut_omp.cpp rename to src/OPENMP/pair_tip4p_cut_omp.cpp diff --git a/src/USER-OMP/pair_tip4p_cut_omp.h b/src/OPENMP/pair_tip4p_cut_omp.h similarity index 100% rename from src/USER-OMP/pair_tip4p_cut_omp.h rename to src/OPENMP/pair_tip4p_cut_omp.h diff --git a/src/USER-OMP/pair_tip4p_long_omp.cpp b/src/OPENMP/pair_tip4p_long_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tip4p_long_omp.cpp rename to src/OPENMP/pair_tip4p_long_omp.cpp diff --git a/src/USER-OMP/pair_tip4p_long_omp.h b/src/OPENMP/pair_tip4p_long_omp.h similarity index 100% rename from src/USER-OMP/pair_tip4p_long_omp.h rename to src/OPENMP/pair_tip4p_long_omp.h diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp b/src/OPENMP/pair_tip4p_long_soft_omp.cpp similarity index 100% rename from src/USER-OMP/pair_tip4p_long_soft_omp.cpp rename to src/OPENMP/pair_tip4p_long_soft_omp.cpp diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.h b/src/OPENMP/pair_tip4p_long_soft_omp.h similarity index 100% rename from src/USER-OMP/pair_tip4p_long_soft_omp.h rename to src/OPENMP/pair_tip4p_long_soft_omp.h diff --git a/src/USER-OMP/pair_ufm_omp.cpp b/src/OPENMP/pair_ufm_omp.cpp similarity index 100% rename from src/USER-OMP/pair_ufm_omp.cpp rename to src/OPENMP/pair_ufm_omp.cpp diff --git a/src/USER-OMP/pair_ufm_omp.h b/src/OPENMP/pair_ufm_omp.h similarity index 100% rename from src/USER-OMP/pair_ufm_omp.h rename to src/OPENMP/pair_ufm_omp.h diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/OPENMP/pair_vashishta_omp.cpp similarity index 100% rename from src/USER-OMP/pair_vashishta_omp.cpp rename to src/OPENMP/pair_vashishta_omp.cpp diff --git a/src/USER-OMP/pair_vashishta_omp.h b/src/OPENMP/pair_vashishta_omp.h similarity index 100% rename from src/USER-OMP/pair_vashishta_omp.h rename to src/OPENMP/pair_vashishta_omp.h diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/OPENMP/pair_vashishta_table_omp.cpp similarity index 100% rename from src/USER-OMP/pair_vashishta_table_omp.cpp rename to src/OPENMP/pair_vashishta_table_omp.cpp diff --git a/src/USER-OMP/pair_vashishta_table_omp.h b/src/OPENMP/pair_vashishta_table_omp.h similarity index 100% rename from src/USER-OMP/pair_vashishta_table_omp.h rename to src/OPENMP/pair_vashishta_table_omp.h diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/OPENMP/pair_yukawa_colloid_omp.cpp similarity index 100% rename from src/USER-OMP/pair_yukawa_colloid_omp.cpp rename to src/OPENMP/pair_yukawa_colloid_omp.cpp diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.h b/src/OPENMP/pair_yukawa_colloid_omp.h similarity index 100% rename from src/USER-OMP/pair_yukawa_colloid_omp.h rename to src/OPENMP/pair_yukawa_colloid_omp.h diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/OPENMP/pair_yukawa_omp.cpp similarity index 100% rename from src/USER-OMP/pair_yukawa_omp.cpp rename to src/OPENMP/pair_yukawa_omp.cpp diff --git a/src/USER-OMP/pair_yukawa_omp.h b/src/OPENMP/pair_yukawa_omp.h similarity index 100% rename from src/USER-OMP/pair_yukawa_omp.h rename to src/OPENMP/pair_yukawa_omp.h diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/OPENMP/pair_zbl_omp.cpp similarity index 100% rename from src/USER-OMP/pair_zbl_omp.cpp rename to src/OPENMP/pair_zbl_omp.cpp diff --git a/src/USER-OMP/pair_zbl_omp.h b/src/OPENMP/pair_zbl_omp.h similarity index 100% rename from src/USER-OMP/pair_zbl_omp.h rename to src/OPENMP/pair_zbl_omp.h diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/OPENMP/pppm_cg_omp.cpp similarity index 100% rename from src/USER-OMP/pppm_cg_omp.cpp rename to src/OPENMP/pppm_cg_omp.cpp diff --git a/src/USER-OMP/pppm_cg_omp.h b/src/OPENMP/pppm_cg_omp.h similarity index 100% rename from src/USER-OMP/pppm_cg_omp.h rename to src/OPENMP/pppm_cg_omp.h diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/OPENMP/pppm_disp_omp.cpp similarity index 100% rename from src/USER-OMP/pppm_disp_omp.cpp rename to src/OPENMP/pppm_disp_omp.cpp diff --git a/src/USER-OMP/pppm_disp_omp.h b/src/OPENMP/pppm_disp_omp.h similarity index 100% rename from src/USER-OMP/pppm_disp_omp.h rename to src/OPENMP/pppm_disp_omp.h diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/OPENMP/pppm_disp_tip4p_omp.cpp similarity index 100% rename from src/USER-OMP/pppm_disp_tip4p_omp.cpp rename to src/OPENMP/pppm_disp_tip4p_omp.cpp diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.h b/src/OPENMP/pppm_disp_tip4p_omp.h similarity index 100% rename from src/USER-OMP/pppm_disp_tip4p_omp.h rename to src/OPENMP/pppm_disp_tip4p_omp.h diff --git a/src/USER-OMP/pppm_omp.cpp b/src/OPENMP/pppm_omp.cpp similarity index 100% rename from src/USER-OMP/pppm_omp.cpp rename to src/OPENMP/pppm_omp.cpp diff --git a/src/USER-OMP/pppm_omp.h b/src/OPENMP/pppm_omp.h similarity index 100% rename from src/USER-OMP/pppm_omp.h rename to src/OPENMP/pppm_omp.h diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/OPENMP/pppm_tip4p_omp.cpp similarity index 100% rename from src/USER-OMP/pppm_tip4p_omp.cpp rename to src/OPENMP/pppm_tip4p_omp.cpp diff --git a/src/USER-OMP/pppm_tip4p_omp.h b/src/OPENMP/pppm_tip4p_omp.h similarity index 100% rename from src/USER-OMP/pppm_tip4p_omp.h rename to src/OPENMP/pppm_tip4p_omp.h diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/OPENMP/reaxc_bond_orders_omp.cpp similarity index 100% rename from src/USER-OMP/reaxc_bond_orders_omp.cpp rename to src/OPENMP/reaxc_bond_orders_omp.cpp diff --git a/src/USER-OMP/reaxc_bond_orders_omp.h b/src/OPENMP/reaxc_bond_orders_omp.h similarity index 100% rename from src/USER-OMP/reaxc_bond_orders_omp.h rename to src/OPENMP/reaxc_bond_orders_omp.h diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/OPENMP/reaxc_bonds_omp.cpp similarity index 100% rename from src/USER-OMP/reaxc_bonds_omp.cpp rename to src/OPENMP/reaxc_bonds_omp.cpp diff --git a/src/USER-OMP/reaxc_bonds_omp.h b/src/OPENMP/reaxc_bonds_omp.h similarity index 100% rename from src/USER-OMP/reaxc_bonds_omp.h rename to src/OPENMP/reaxc_bonds_omp.h diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/OPENMP/reaxc_forces_omp.cpp similarity index 100% rename from src/USER-OMP/reaxc_forces_omp.cpp rename to src/OPENMP/reaxc_forces_omp.cpp diff --git a/src/USER-OMP/reaxc_forces_omp.h b/src/OPENMP/reaxc_forces_omp.h similarity index 100% rename from src/USER-OMP/reaxc_forces_omp.h rename to src/OPENMP/reaxc_forces_omp.h diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/OPENMP/reaxc_hydrogen_bonds_omp.cpp similarity index 100% rename from src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp rename to src/OPENMP/reaxc_hydrogen_bonds_omp.cpp diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.h b/src/OPENMP/reaxc_hydrogen_bonds_omp.h similarity index 100% rename from src/USER-OMP/reaxc_hydrogen_bonds_omp.h rename to src/OPENMP/reaxc_hydrogen_bonds_omp.h diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/OPENMP/reaxc_init_md_omp.cpp similarity index 100% rename from src/USER-OMP/reaxc_init_md_omp.cpp rename to src/OPENMP/reaxc_init_md_omp.cpp diff --git a/src/USER-OMP/reaxc_init_md_omp.h b/src/OPENMP/reaxc_init_md_omp.h similarity index 100% rename from src/USER-OMP/reaxc_init_md_omp.h rename to src/OPENMP/reaxc_init_md_omp.h diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/OPENMP/reaxc_multi_body_omp.cpp similarity index 100% rename from src/USER-OMP/reaxc_multi_body_omp.cpp rename to src/OPENMP/reaxc_multi_body_omp.cpp diff --git a/src/USER-OMP/reaxc_multi_body_omp.h b/src/OPENMP/reaxc_multi_body_omp.h similarity index 100% rename from src/USER-OMP/reaxc_multi_body_omp.h rename to src/OPENMP/reaxc_multi_body_omp.h diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/OPENMP/reaxc_nonbonded_omp.cpp similarity index 100% rename from src/USER-OMP/reaxc_nonbonded_omp.cpp rename to src/OPENMP/reaxc_nonbonded_omp.cpp diff --git a/src/USER-OMP/reaxc_nonbonded_omp.h b/src/OPENMP/reaxc_nonbonded_omp.h similarity index 100% rename from src/USER-OMP/reaxc_nonbonded_omp.h rename to src/OPENMP/reaxc_nonbonded_omp.h diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/OPENMP/reaxc_torsion_angles_omp.cpp similarity index 100% rename from src/USER-OMP/reaxc_torsion_angles_omp.cpp rename to src/OPENMP/reaxc_torsion_angles_omp.cpp diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.h b/src/OPENMP/reaxc_torsion_angles_omp.h similarity index 100% rename from src/USER-OMP/reaxc_torsion_angles_omp.h rename to src/OPENMP/reaxc_torsion_angles_omp.h diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/OPENMP/reaxc_valence_angles_omp.cpp similarity index 100% rename from src/USER-OMP/reaxc_valence_angles_omp.cpp rename to src/OPENMP/reaxc_valence_angles_omp.cpp diff --git a/src/USER-OMP/reaxc_valence_angles_omp.h b/src/OPENMP/reaxc_valence_angles_omp.h similarity index 100% rename from src/USER-OMP/reaxc_valence_angles_omp.h rename to src/OPENMP/reaxc_valence_angles_omp.h diff --git a/src/USER-OMP/respa_omp.cpp b/src/OPENMP/respa_omp.cpp similarity index 100% rename from src/USER-OMP/respa_omp.cpp rename to src/OPENMP/respa_omp.cpp diff --git a/src/USER-OMP/respa_omp.h b/src/OPENMP/respa_omp.h similarity index 100% rename from src/USER-OMP/respa_omp.h rename to src/OPENMP/respa_omp.h diff --git a/src/USER-OMP/thr_data.cpp b/src/OPENMP/thr_data.cpp similarity index 100% rename from src/USER-OMP/thr_data.cpp rename to src/OPENMP/thr_data.cpp diff --git a/src/USER-OMP/thr_data.h b/src/OPENMP/thr_data.h similarity index 100% rename from src/USER-OMP/thr_data.h rename to src/OPENMP/thr_data.h diff --git a/src/USER-OMP/thr_omp.cpp b/src/OPENMP/thr_omp.cpp similarity index 100% rename from src/USER-OMP/thr_omp.cpp rename to src/OPENMP/thr_omp.cpp diff --git a/src/USER-OMP/thr_omp.h b/src/OPENMP/thr_omp.h similarity index 100% rename from src/USER-OMP/thr_omp.h rename to src/OPENMP/thr_omp.h diff --git a/src/USER-PHONON/Install.sh b/src/PHONON/Install.sh similarity index 88% rename from src/USER-PHONON/Install.sh rename to src/PHONON/Install.sh index a73f529cfa..4b64fed114 100755 --- a/src/USER-PHONON/Install.sh +++ b/src/PHONON/Install.sh @@ -26,12 +26,12 @@ action () { fi } -# USER-PHONON uses the parallel FFT wrapper used in PPPM, +# PHONON uses the parallel FFT wrapper used in PPPM, # so we must require the KSPACE package to be installed. if (test $1 = 1) then if (test ! -e ../fft3d_wrap.h) then - echo "Must install KSPACE package with USER-PHONON" + echo "Must install KSPACE package with PHONON" exit 1 fi fi diff --git a/src/USER-PHONON/README b/src/PHONON/README similarity index 98% rename from src/USER-PHONON/README rename to src/PHONON/README index d5ed666c0c..4f4147cc85 100644 --- a/src/USER-PHONON/README +++ b/src/PHONON/README @@ -13,7 +13,7 @@ Use of this package requires building LAMMPS with FFT suppport, as described in doc/Section_start.html. There are example scripts for using commands in this package in -examples/USER/phonon. +examples/PACKAGES/phonon. There is an auxiliary post-processing tool in tools/phonon that will compute phonon frequencies and dispersion relations from the dynamical diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/PHONON/dynamical_matrix.cpp similarity index 100% rename from src/USER-PHONON/dynamical_matrix.cpp rename to src/PHONON/dynamical_matrix.cpp diff --git a/src/USER-PHONON/dynamical_matrix.h b/src/PHONON/dynamical_matrix.h similarity index 100% rename from src/USER-PHONON/dynamical_matrix.h rename to src/PHONON/dynamical_matrix.h diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/PHONON/fix_phonon.cpp similarity index 100% rename from src/USER-PHONON/fix_phonon.cpp rename to src/PHONON/fix_phonon.cpp diff --git a/src/USER-PHONON/fix_phonon.h b/src/PHONON/fix_phonon.h similarity index 100% rename from src/USER-PHONON/fix_phonon.h rename to src/PHONON/fix_phonon.h diff --git a/src/USER-PHONON/third_order.cpp b/src/PHONON/third_order.cpp similarity index 100% rename from src/USER-PHONON/third_order.cpp rename to src/PHONON/third_order.cpp diff --git a/src/USER-PHONON/third_order.h b/src/PHONON/third_order.h similarity index 100% rename from src/USER-PHONON/third_order.h rename to src/PHONON/third_order.h diff --git a/src/USER-PLUMED/Install.sh b/src/PLUMED/Install.sh similarity index 100% rename from src/USER-PLUMED/Install.sh rename to src/PLUMED/Install.sh diff --git a/src/USER-PLUMED/README b/src/PLUMED/README similarity index 95% rename from src/USER-PLUMED/README rename to src/PLUMED/README index 31910bc951..9b24e2fbb9 100644 --- a/src/USER-PLUMED/README +++ b/src/PLUMED/README @@ -6,7 +6,7 @@ metadynamics to be used. Furthermore, PLUMED can be used to perform a wide range of analyses on trajectories on the fly as they are generated. The package uses the "PLUMED" library, whose source code is not included -in the LAMMPS source code distribution. The files in the USER-PLUMED package +in the LAMMPS source code distribution. The files in the PLUMED package folder implement an interface between LAMMPS and PLUMED, that are written and maintained by Gareth Tribello (gareth.tribello@gmail.com). @@ -19,7 +19,7 @@ time. However you decide to link PLUMED (statically or dynamically) you must run the command: -make yes-user-plumed +make yes-plumed before compiling LAMMPS in order to enable the module. In addition, if you have chosen to link PLUMED dynamically you must ensure that PLUMED is in your @@ -60,7 +60,7 @@ numerous example scripts for PLUMED as well as citations to articles that dcomen implemented within PLUMED. There are also example scripts for using this package in the folder -examples/USER/plumed, as well as on the GitHub page for PLUMED. +examples/PACKAGES/plumed, as well as on the GitHub page for PLUMED. Please contact Gareth Tribello (gareth.tribello@gmail.com) for questions regarding this package. diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/PLUMED/fix_plumed.cpp similarity index 100% rename from src/USER-PLUMED/fix_plumed.cpp rename to src/PLUMED/fix_plumed.cpp diff --git a/src/USER-PLUMED/fix_plumed.h b/src/PLUMED/fix_plumed.h similarity index 100% rename from src/USER-PLUMED/fix_plumed.h rename to src/PLUMED/fix_plumed.h diff --git a/src/USER-PTM/LICENSE b/src/PTM/LICENSE similarity index 100% rename from src/USER-PTM/LICENSE rename to src/PTM/LICENSE diff --git a/src/USER-PTM/README b/src/PTM/README similarity index 100% rename from src/USER-PTM/README rename to src/PTM/README diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/PTM/compute_ptm_atom.cpp similarity index 99% rename from src/USER-PTM/compute_ptm_atom.cpp rename to src/PTM/compute_ptm_atom.cpp index 301e3d577d..74880adcd5 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/PTM/compute_ptm_atom.cpp @@ -48,7 +48,7 @@ under using namespace LAMMPS_NS; static const char cite_user_ptm_package[] = - "USER-PTM package:\n\n" + "PTM package:\n\n" "@Article{larsen2016ptm,\n" " author={Larsen, Peter Mahler and Schmidt, S{\\o}ren and Schi{\\o}tz, " "Jakob},\n" diff --git a/src/USER-PTM/compute_ptm_atom.h b/src/PTM/compute_ptm_atom.h similarity index 100% rename from src/USER-PTM/compute_ptm_atom.h rename to src/PTM/compute_ptm_atom.h diff --git a/src/USER-PTM/ptm_alloy_types.cpp b/src/PTM/ptm_alloy_types.cpp similarity index 100% rename from src/USER-PTM/ptm_alloy_types.cpp rename to src/PTM/ptm_alloy_types.cpp diff --git a/src/USER-PTM/ptm_alloy_types.h b/src/PTM/ptm_alloy_types.h similarity index 100% rename from src/USER-PTM/ptm_alloy_types.h rename to src/PTM/ptm_alloy_types.h diff --git a/src/USER-PTM/ptm_alt_templates.h b/src/PTM/ptm_alt_templates.h similarity index 100% rename from src/USER-PTM/ptm_alt_templates.h rename to src/PTM/ptm_alt_templates.h diff --git a/src/USER-PTM/ptm_canonical_coloured.cpp b/src/PTM/ptm_canonical_coloured.cpp similarity index 100% rename from src/USER-PTM/ptm_canonical_coloured.cpp rename to src/PTM/ptm_canonical_coloured.cpp diff --git a/src/USER-PTM/ptm_canonical_coloured.h b/src/PTM/ptm_canonical_coloured.h similarity index 100% rename from src/USER-PTM/ptm_canonical_coloured.h rename to src/PTM/ptm_canonical_coloured.h diff --git a/src/USER-PTM/ptm_constants.cpp b/src/PTM/ptm_constants.cpp similarity index 100% rename from src/USER-PTM/ptm_constants.cpp rename to src/PTM/ptm_constants.cpp diff --git a/src/USER-PTM/ptm_constants.h b/src/PTM/ptm_constants.h similarity index 100% rename from src/USER-PTM/ptm_constants.h rename to src/PTM/ptm_constants.h diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/PTM/ptm_convex_hull_incremental.cpp similarity index 100% rename from src/USER-PTM/ptm_convex_hull_incremental.cpp rename to src/PTM/ptm_convex_hull_incremental.cpp diff --git a/src/USER-PTM/ptm_convex_hull_incremental.h b/src/PTM/ptm_convex_hull_incremental.h similarity index 100% rename from src/USER-PTM/ptm_convex_hull_incremental.h rename to src/PTM/ptm_convex_hull_incremental.h diff --git a/src/USER-PTM/ptm_deformation_gradient.cpp b/src/PTM/ptm_deformation_gradient.cpp similarity index 100% rename from src/USER-PTM/ptm_deformation_gradient.cpp rename to src/PTM/ptm_deformation_gradient.cpp diff --git a/src/USER-PTM/ptm_deformation_gradient.h b/src/PTM/ptm_deformation_gradient.h similarity index 100% rename from src/USER-PTM/ptm_deformation_gradient.h rename to src/PTM/ptm_deformation_gradient.h diff --git a/src/USER-PTM/ptm_functions.h b/src/PTM/ptm_functions.h similarity index 100% rename from src/USER-PTM/ptm_functions.h rename to src/PTM/ptm_functions.h diff --git a/src/USER-PTM/ptm_fundamental_mappings.h b/src/PTM/ptm_fundamental_mappings.h similarity index 100% rename from src/USER-PTM/ptm_fundamental_mappings.h rename to src/PTM/ptm_fundamental_mappings.h diff --git a/src/USER-PTM/ptm_graph_data.cpp b/src/PTM/ptm_graph_data.cpp similarity index 100% rename from src/USER-PTM/ptm_graph_data.cpp rename to src/PTM/ptm_graph_data.cpp diff --git a/src/USER-PTM/ptm_graph_data.h b/src/PTM/ptm_graph_data.h similarity index 100% rename from src/USER-PTM/ptm_graph_data.h rename to src/PTM/ptm_graph_data.h diff --git a/src/USER-PTM/ptm_graph_tools.cpp b/src/PTM/ptm_graph_tools.cpp similarity index 100% rename from src/USER-PTM/ptm_graph_tools.cpp rename to src/PTM/ptm_graph_tools.cpp diff --git a/src/USER-PTM/ptm_graph_tools.h b/src/PTM/ptm_graph_tools.h similarity index 100% rename from src/USER-PTM/ptm_graph_tools.h rename to src/PTM/ptm_graph_tools.h diff --git a/src/USER-PTM/ptm_index.cpp b/src/PTM/ptm_index.cpp similarity index 100% rename from src/USER-PTM/ptm_index.cpp rename to src/PTM/ptm_index.cpp diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/PTM/ptm_initialize_data.cpp similarity index 100% rename from src/USER-PTM/ptm_initialize_data.cpp rename to src/PTM/ptm_initialize_data.cpp diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/PTM/ptm_initialize_data.h similarity index 100% rename from src/USER-PTM/ptm_initialize_data.h rename to src/PTM/ptm_initialize_data.h diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/PTM/ptm_neighbour_ordering.cpp similarity index 100% rename from src/USER-PTM/ptm_neighbour_ordering.cpp rename to src/PTM/ptm_neighbour_ordering.cpp diff --git a/src/USER-PTM/ptm_neighbour_ordering.h b/src/PTM/ptm_neighbour_ordering.h similarity index 100% rename from src/USER-PTM/ptm_neighbour_ordering.h rename to src/PTM/ptm_neighbour_ordering.h diff --git a/src/USER-PTM/ptm_normalize_vertices.cpp b/src/PTM/ptm_normalize_vertices.cpp similarity index 100% rename from src/USER-PTM/ptm_normalize_vertices.cpp rename to src/PTM/ptm_normalize_vertices.cpp diff --git a/src/USER-PTM/ptm_normalize_vertices.h b/src/PTM/ptm_normalize_vertices.h similarity index 100% rename from src/USER-PTM/ptm_normalize_vertices.h rename to src/PTM/ptm_normalize_vertices.h diff --git a/src/USER-PTM/ptm_polar.cpp b/src/PTM/ptm_polar.cpp similarity index 100% rename from src/USER-PTM/ptm_polar.cpp rename to src/PTM/ptm_polar.cpp diff --git a/src/USER-PTM/ptm_polar.h b/src/PTM/ptm_polar.h similarity index 100% rename from src/USER-PTM/ptm_polar.h rename to src/PTM/ptm_polar.h diff --git a/src/USER-PTM/ptm_quat.cpp b/src/PTM/ptm_quat.cpp similarity index 100% rename from src/USER-PTM/ptm_quat.cpp rename to src/PTM/ptm_quat.cpp diff --git a/src/USER-PTM/ptm_quat.h b/src/PTM/ptm_quat.h similarity index 100% rename from src/USER-PTM/ptm_quat.h rename to src/PTM/ptm_quat.h diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/PTM/ptm_structure_matcher.cpp similarity index 100% rename from src/USER-PTM/ptm_structure_matcher.cpp rename to src/PTM/ptm_structure_matcher.cpp diff --git a/src/USER-PTM/ptm_structure_matcher.h b/src/PTM/ptm_structure_matcher.h similarity index 100% rename from src/USER-PTM/ptm_structure_matcher.h rename to src/PTM/ptm_structure_matcher.h diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/PTM/ptm_voronoi_cell.cpp similarity index 100% rename from src/USER-PTM/ptm_voronoi_cell.cpp rename to src/PTM/ptm_voronoi_cell.cpp diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/PTM/ptm_voronoi_cell.h similarity index 100% rename from src/USER-PTM/ptm_voronoi_cell.h rename to src/PTM/ptm_voronoi_cell.h diff --git a/src/USER-PTM/ptm_voronoi_config.h b/src/PTM/ptm_voronoi_config.h similarity index 100% rename from src/USER-PTM/ptm_voronoi_config.h rename to src/PTM/ptm_voronoi_config.h diff --git a/src/Purge.list b/src/Purge.list index 88d9e22e59..3debc2ef6d 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -51,6 +51,11 @@ lmpinstalledpkgs.h lmpgitversion.h mliap_model_python_couple.cpp mliap_model_python_couple.h +# moved to DPD-BASIC package on 1 July 2021 +pair_dpd.cpp +pair_dpd.h +pair_dpd_tstat.cpp +pair_dpd_tstat.h # removed on 14 May 2021 nstencil_half_bin_2d_newton_ssa.cpp nstencil_half_bin_2d_newton_ssa.h diff --git a/src/USER-QMMM/Install.sh b/src/QMMM/Install.sh similarity index 100% rename from src/USER-QMMM/Install.sh rename to src/QMMM/Install.sh diff --git a/src/USER-QMMM/README b/src/QMMM/README similarity index 100% rename from src/USER-QMMM/README rename to src/QMMM/README diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/QMMM/fix_qmmm.cpp similarity index 100% rename from src/USER-QMMM/fix_qmmm.cpp rename to src/QMMM/fix_qmmm.cpp diff --git a/src/USER-QMMM/fix_qmmm.h b/src/QMMM/fix_qmmm.h similarity index 100% rename from src/USER-QMMM/fix_qmmm.h rename to src/QMMM/fix_qmmm.h diff --git a/src/USER-QTB/README b/src/QTB/README similarity index 97% rename from src/USER-QTB/README rename to src/QTB/README index 3b2b399d49..7458f60a4f 100644 --- a/src/USER-QTB/README +++ b/src/QTB/README @@ -44,7 +44,7 @@ What command should I use regarding these two cases? Where can I find examples of these two commands? There are example scripts for using this package in - examples/USER/qtb, including one "fix qtb" and one + examples/PACKAGES/qtb, including one "fix qtb" and one "fix qbmsst" example for each of alpha quartz and methane. Running the alpha quartz example requires installation of the kspace package while the methane diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/QTB/fix_qbmsst.cpp similarity index 100% rename from src/USER-QTB/fix_qbmsst.cpp rename to src/QTB/fix_qbmsst.cpp diff --git a/src/USER-QTB/fix_qbmsst.h b/src/QTB/fix_qbmsst.h similarity index 100% rename from src/USER-QTB/fix_qbmsst.h rename to src/QTB/fix_qbmsst.h diff --git a/src/USER-QTB/fix_qtb.cpp b/src/QTB/fix_qtb.cpp similarity index 100% rename from src/USER-QTB/fix_qtb.cpp rename to src/QTB/fix_qtb.cpp diff --git a/src/USER-QTB/fix_qtb.h b/src/QTB/fix_qtb.h similarity index 100% rename from src/USER-QTB/fix_qtb.h rename to src/QTB/fix_qtb.h diff --git a/src/USER-REACTION/README b/src/REACTION/README similarity index 100% rename from src/USER-REACTION/README rename to src/REACTION/README diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp similarity index 100% rename from src/USER-REACTION/fix_bond_react.cpp rename to src/REACTION/fix_bond_react.cpp diff --git a/src/USER-REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h similarity index 100% rename from src/USER-REACTION/fix_bond_react.h rename to src/REACTION/fix_bond_react.h diff --git a/src/USER-REACTION/superpose3d.h b/src/REACTION/superpose3d.h similarity index 100% rename from src/USER-REACTION/superpose3d.h rename to src/REACTION/superpose3d.h diff --git a/src/USER-REAXC/README b/src/REAXFF/README similarity index 97% rename from src/USER-REAXC/README rename to src/REAXFF/README index d21fbb791d..485a56785e 100644 --- a/src/USER-REAXC/README +++ b/src/REAXFF/README @@ -4,7 +4,7 @@ represent the contributions of chemical bonding to the potential energy. It was originally developed by Adri van Duin and the Goddard group at CalTech. -The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in +The REAXFF version of ReaxFF (pair_style reax/c), implemented in C, should give identical or very similar results to pair_style reax, which is a ReaxFF implementation on top of a Fortran library, a version of which library was originally authored by Adri van Duin. diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/REAXFF/compute_spec_atom.cpp similarity index 100% rename from src/USER-REAXC/compute_spec_atom.cpp rename to src/REAXFF/compute_spec_atom.cpp diff --git a/src/USER-REAXC/compute_spec_atom.h b/src/REAXFF/compute_spec_atom.h similarity index 100% rename from src/USER-REAXC/compute_spec_atom.h rename to src/REAXFF/compute_spec_atom.h diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/REAXFF/fix_qeq_reax.cpp similarity index 99% rename from src/USER-REAXC/fix_qeq_reax.cpp rename to src/REAXFF/fix_qeq_reax.cpp index 9663d2ea49..e01c87a1e3 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/REAXFF/fix_qeq_reax.cpp @@ -75,7 +75,7 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) : tolerance = utils::numeric(FLERR,arg[6],false,lmp); pertype_option = utils::strdup(arg[7]); - // dual CG support only available for USER-OMP variant + // dual CG support only available for OPENMP variant // check for compatibility is in Fix::post_constructor() dual_enabled = 0; imax = 200; diff --git a/src/USER-REAXC/fix_qeq_reax.h b/src/REAXFF/fix_qeq_reax.h similarity index 100% rename from src/USER-REAXC/fix_qeq_reax.h rename to src/REAXFF/fix_qeq_reax.h diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/REAXFF/fix_reaxc.cpp similarity index 100% rename from src/USER-REAXC/fix_reaxc.cpp rename to src/REAXFF/fix_reaxc.cpp diff --git a/src/USER-REAXC/fix_reaxc.h b/src/REAXFF/fix_reaxc.h similarity index 100% rename from src/USER-REAXC/fix_reaxc.h rename to src/REAXFF/fix_reaxc.h diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/REAXFF/fix_reaxc_bonds.cpp similarity index 100% rename from src/USER-REAXC/fix_reaxc_bonds.cpp rename to src/REAXFF/fix_reaxc_bonds.cpp diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/REAXFF/fix_reaxc_bonds.h similarity index 100% rename from src/USER-REAXC/fix_reaxc_bonds.h rename to src/REAXFF/fix_reaxc_bonds.h diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/REAXFF/fix_reaxc_species.cpp similarity index 100% rename from src/USER-REAXC/fix_reaxc_species.cpp rename to src/REAXFF/fix_reaxc_species.cpp diff --git a/src/USER-REAXC/fix_reaxc_species.h b/src/REAXFF/fix_reaxc_species.h similarity index 100% rename from src/USER-REAXC/fix_reaxc_species.h rename to src/REAXFF/fix_reaxc_species.h diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/REAXFF/pair_reaxc.cpp similarity index 100% rename from src/USER-REAXC/pair_reaxc.cpp rename to src/REAXFF/pair_reaxc.cpp diff --git a/src/USER-REAXC/pair_reaxc.h b/src/REAXFF/pair_reaxc.h similarity index 100% rename from src/USER-REAXC/pair_reaxc.h rename to src/REAXFF/pair_reaxc.h diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/REAXFF/reaxc_allocate.cpp similarity index 100% rename from src/USER-REAXC/reaxc_allocate.cpp rename to src/REAXFF/reaxc_allocate.cpp diff --git a/src/USER-REAXC/reaxc_allocate.h b/src/REAXFF/reaxc_allocate.h similarity index 100% rename from src/USER-REAXC/reaxc_allocate.h rename to src/REAXFF/reaxc_allocate.h diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/REAXFF/reaxc_bond_orders.cpp similarity index 100% rename from src/USER-REAXC/reaxc_bond_orders.cpp rename to src/REAXFF/reaxc_bond_orders.cpp diff --git a/src/USER-REAXC/reaxc_bond_orders.h b/src/REAXFF/reaxc_bond_orders.h similarity index 100% rename from src/USER-REAXC/reaxc_bond_orders.h rename to src/REAXFF/reaxc_bond_orders.h diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/REAXFF/reaxc_bonds.cpp similarity index 100% rename from src/USER-REAXC/reaxc_bonds.cpp rename to src/REAXFF/reaxc_bonds.cpp diff --git a/src/USER-REAXC/reaxc_bonds.h b/src/REAXFF/reaxc_bonds.h similarity index 100% rename from src/USER-REAXC/reaxc_bonds.h rename to src/REAXFF/reaxc_bonds.h diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/REAXFF/reaxc_control.cpp similarity index 100% rename from src/USER-REAXC/reaxc_control.cpp rename to src/REAXFF/reaxc_control.cpp diff --git a/src/USER-REAXC/reaxc_control.h b/src/REAXFF/reaxc_control.h similarity index 100% rename from src/USER-REAXC/reaxc_control.h rename to src/REAXFF/reaxc_control.h diff --git a/src/USER-REAXC/reaxc_defs.h b/src/REAXFF/reaxc_defs.h similarity index 100% rename from src/USER-REAXC/reaxc_defs.h rename to src/REAXFF/reaxc_defs.h diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/REAXFF/reaxc_ffield.cpp similarity index 100% rename from src/USER-REAXC/reaxc_ffield.cpp rename to src/REAXFF/reaxc_ffield.cpp diff --git a/src/USER-REAXC/reaxc_ffield.h b/src/REAXFF/reaxc_ffield.h similarity index 100% rename from src/USER-REAXC/reaxc_ffield.h rename to src/REAXFF/reaxc_ffield.h diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/REAXFF/reaxc_forces.cpp similarity index 100% rename from src/USER-REAXC/reaxc_forces.cpp rename to src/REAXFF/reaxc_forces.cpp diff --git a/src/USER-REAXC/reaxc_forces.h b/src/REAXFF/reaxc_forces.h similarity index 100% rename from src/USER-REAXC/reaxc_forces.h rename to src/REAXFF/reaxc_forces.h diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/REAXFF/reaxc_hydrogen_bonds.cpp similarity index 100% rename from src/USER-REAXC/reaxc_hydrogen_bonds.cpp rename to src/REAXFF/reaxc_hydrogen_bonds.cpp diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.h b/src/REAXFF/reaxc_hydrogen_bonds.h similarity index 100% rename from src/USER-REAXC/reaxc_hydrogen_bonds.h rename to src/REAXFF/reaxc_hydrogen_bonds.h diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/REAXFF/reaxc_init_md.cpp similarity index 100% rename from src/USER-REAXC/reaxc_init_md.cpp rename to src/REAXFF/reaxc_init_md.cpp diff --git a/src/USER-REAXC/reaxc_init_md.h b/src/REAXFF/reaxc_init_md.h similarity index 100% rename from src/USER-REAXC/reaxc_init_md.h rename to src/REAXFF/reaxc_init_md.h diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/REAXFF/reaxc_io_tools.cpp similarity index 100% rename from src/USER-REAXC/reaxc_io_tools.cpp rename to src/REAXFF/reaxc_io_tools.cpp diff --git a/src/USER-REAXC/reaxc_io_tools.h b/src/REAXFF/reaxc_io_tools.h similarity index 100% rename from src/USER-REAXC/reaxc_io_tools.h rename to src/REAXFF/reaxc_io_tools.h diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/REAXFF/reaxc_list.cpp similarity index 100% rename from src/USER-REAXC/reaxc_list.cpp rename to src/REAXFF/reaxc_list.cpp diff --git a/src/USER-REAXC/reaxc_list.h b/src/REAXFF/reaxc_list.h similarity index 100% rename from src/USER-REAXC/reaxc_list.h rename to src/REAXFF/reaxc_list.h diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/REAXFF/reaxc_lookup.cpp similarity index 100% rename from src/USER-REAXC/reaxc_lookup.cpp rename to src/REAXFF/reaxc_lookup.cpp diff --git a/src/USER-REAXC/reaxc_lookup.h b/src/REAXFF/reaxc_lookup.h similarity index 100% rename from src/USER-REAXC/reaxc_lookup.h rename to src/REAXFF/reaxc_lookup.h diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/REAXFF/reaxc_multi_body.cpp similarity index 100% rename from src/USER-REAXC/reaxc_multi_body.cpp rename to src/REAXFF/reaxc_multi_body.cpp diff --git a/src/USER-REAXC/reaxc_multi_body.h b/src/REAXFF/reaxc_multi_body.h similarity index 100% rename from src/USER-REAXC/reaxc_multi_body.h rename to src/REAXFF/reaxc_multi_body.h diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/REAXFF/reaxc_nonbonded.cpp similarity index 100% rename from src/USER-REAXC/reaxc_nonbonded.cpp rename to src/REAXFF/reaxc_nonbonded.cpp diff --git a/src/USER-REAXC/reaxc_nonbonded.h b/src/REAXFF/reaxc_nonbonded.h similarity index 100% rename from src/USER-REAXC/reaxc_nonbonded.h rename to src/REAXFF/reaxc_nonbonded.h diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/REAXFF/reaxc_reset_tools.cpp similarity index 100% rename from src/USER-REAXC/reaxc_reset_tools.cpp rename to src/REAXFF/reaxc_reset_tools.cpp diff --git a/src/USER-REAXC/reaxc_reset_tools.h b/src/REAXFF/reaxc_reset_tools.h similarity index 100% rename from src/USER-REAXC/reaxc_reset_tools.h rename to src/REAXFF/reaxc_reset_tools.h diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/REAXFF/reaxc_system_props.cpp similarity index 100% rename from src/USER-REAXC/reaxc_system_props.cpp rename to src/REAXFF/reaxc_system_props.cpp diff --git a/src/USER-REAXC/reaxc_system_props.h b/src/REAXFF/reaxc_system_props.h similarity index 100% rename from src/USER-REAXC/reaxc_system_props.h rename to src/REAXFF/reaxc_system_props.h diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/REAXFF/reaxc_tool_box.cpp similarity index 100% rename from src/USER-REAXC/reaxc_tool_box.cpp rename to src/REAXFF/reaxc_tool_box.cpp diff --git a/src/USER-REAXC/reaxc_tool_box.h b/src/REAXFF/reaxc_tool_box.h similarity index 100% rename from src/USER-REAXC/reaxc_tool_box.h rename to src/REAXFF/reaxc_tool_box.h diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/REAXFF/reaxc_torsion_angles.cpp similarity index 100% rename from src/USER-REAXC/reaxc_torsion_angles.cpp rename to src/REAXFF/reaxc_torsion_angles.cpp diff --git a/src/USER-REAXC/reaxc_torsion_angles.h b/src/REAXFF/reaxc_torsion_angles.h similarity index 100% rename from src/USER-REAXC/reaxc_torsion_angles.h rename to src/REAXFF/reaxc_torsion_angles.h diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/REAXFF/reaxc_traj.cpp similarity index 100% rename from src/USER-REAXC/reaxc_traj.cpp rename to src/REAXFF/reaxc_traj.cpp diff --git a/src/USER-REAXC/reaxc_traj.h b/src/REAXFF/reaxc_traj.h similarity index 100% rename from src/USER-REAXC/reaxc_traj.h rename to src/REAXFF/reaxc_traj.h diff --git a/src/USER-REAXC/reaxc_types.h b/src/REAXFF/reaxc_types.h similarity index 100% rename from src/USER-REAXC/reaxc_types.h rename to src/REAXFF/reaxc_types.h diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/REAXFF/reaxc_valence_angles.cpp similarity index 100% rename from src/USER-REAXC/reaxc_valence_angles.cpp rename to src/REAXFF/reaxc_valence_angles.cpp diff --git a/src/USER-REAXC/reaxc_valence_angles.h b/src/REAXFF/reaxc_valence_angles.h similarity index 100% rename from src/USER-REAXC/reaxc_valence_angles.h rename to src/REAXFF/reaxc_valence_angles.h diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/REAXFF/reaxc_vector.cpp similarity index 100% rename from src/USER-REAXC/reaxc_vector.cpp rename to src/REAXFF/reaxc_vector.cpp diff --git a/src/USER-REAXC/reaxc_vector.h b/src/REAXFF/reaxc_vector.h similarity index 100% rename from src/USER-REAXC/reaxc_vector.h rename to src/REAXFF/reaxc_vector.h diff --git a/src/USER-SCAFACOS/Install.sh b/src/SCAFACOS/Install.sh similarity index 100% rename from src/USER-SCAFACOS/Install.sh rename to src/SCAFACOS/Install.sh diff --git a/src/USER-SCAFACOS/README b/src/SCAFACOS/README similarity index 94% rename from src/USER-SCAFACOS/README rename to src/SCAFACOS/README index 42d2e2c0f7..dc3eb65bfa 100644 --- a/src/USER-SCAFACOS/README +++ b/src/SCAFACOS/README @@ -19,7 +19,7 @@ Once you have successfully built LAMMPS with this package and the ScaFaCoS library, you can test it using an input file from the examples scafacos dir, e.g.: -lmp_serial -in lammps/examples/USER/scafacos/in.scafacos.fmm +lmp_serial -in lammps/examples/PACKAGES/scafacos/in.scafacos.fmm For questions about ScaFaCoS, please contact: r.halver@fz-juelich.de or g.sutmann@fz-juelich.de diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/SCAFACOS/scafacos.cpp similarity index 100% rename from src/USER-SCAFACOS/scafacos.cpp rename to src/SCAFACOS/scafacos.cpp diff --git a/src/USER-SCAFACOS/scafacos.h b/src/SCAFACOS/scafacos.h similarity index 100% rename from src/USER-SCAFACOS/scafacos.h rename to src/SCAFACOS/scafacos.h diff --git a/src/USER-SMTBQ/README b/src/SMTBQ/README similarity index 95% rename from src/USER-SMTBQ/README rename to src/SMTBQ/README index e778c65be2..594df29ac6 100644 --- a/src/USER-SMTBQ/README +++ b/src/SMTBQ/README @@ -13,4 +13,4 @@ See the doc page for the pair_style smtbq command to get started. There are potential files for this potential in the potentials dir. There are example scripts for using this package in -examples/USER/smtbq. +examples/PACKAGES/smtbq. diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/SMTBQ/pair_smtbq.cpp similarity index 100% rename from src/USER-SMTBQ/pair_smtbq.cpp rename to src/SMTBQ/pair_smtbq.cpp diff --git a/src/USER-SMTBQ/pair_smtbq.h b/src/SMTBQ/pair_smtbq.h similarity index 100% rename from src/USER-SMTBQ/pair_smtbq.h rename to src/SMTBQ/pair_smtbq.h diff --git a/src/USER-SPH/README b/src/SPH/README similarity index 92% rename from src/USER-SPH/README rename to src/SPH/README index 97afba8d12..948db9a70c 100644 --- a/src/USER-SPH/README +++ b/src/SPH/README @@ -12,7 +12,7 @@ LAMMPS. Currently, the package has the following features: See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started. -There are example scripts for using this package in examples/USER/sph. +There are example scripts for using this package in examples/PACKAGES/sph. The person who created this package is Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in diff --git a/src/USER-SPH/atom_vec_sph.cpp b/src/SPH/atom_vec_sph.cpp similarity index 100% rename from src/USER-SPH/atom_vec_sph.cpp rename to src/SPH/atom_vec_sph.cpp diff --git a/src/USER-SPH/atom_vec_sph.h b/src/SPH/atom_vec_sph.h similarity index 100% rename from src/USER-SPH/atom_vec_sph.h rename to src/SPH/atom_vec_sph.h diff --git a/src/USER-SPH/compute_sph_e_atom.cpp b/src/SPH/compute_sph_e_atom.cpp similarity index 100% rename from src/USER-SPH/compute_sph_e_atom.cpp rename to src/SPH/compute_sph_e_atom.cpp diff --git a/src/USER-SPH/compute_sph_e_atom.h b/src/SPH/compute_sph_e_atom.h similarity index 100% rename from src/USER-SPH/compute_sph_e_atom.h rename to src/SPH/compute_sph_e_atom.h diff --git a/src/USER-SPH/compute_sph_rho_atom.cpp b/src/SPH/compute_sph_rho_atom.cpp similarity index 100% rename from src/USER-SPH/compute_sph_rho_atom.cpp rename to src/SPH/compute_sph_rho_atom.cpp diff --git a/src/USER-SPH/compute_sph_rho_atom.h b/src/SPH/compute_sph_rho_atom.h similarity index 100% rename from src/USER-SPH/compute_sph_rho_atom.h rename to src/SPH/compute_sph_rho_atom.h diff --git a/src/USER-SPH/compute_sph_t_atom.cpp b/src/SPH/compute_sph_t_atom.cpp similarity index 100% rename from src/USER-SPH/compute_sph_t_atom.cpp rename to src/SPH/compute_sph_t_atom.cpp diff --git a/src/USER-SPH/compute_sph_t_atom.h b/src/SPH/compute_sph_t_atom.h similarity index 100% rename from src/USER-SPH/compute_sph_t_atom.h rename to src/SPH/compute_sph_t_atom.h diff --git a/src/USER-SPH/fix_sph.cpp b/src/SPH/fix_sph.cpp similarity index 100% rename from src/USER-SPH/fix_sph.cpp rename to src/SPH/fix_sph.cpp diff --git a/src/USER-SPH/fix_sph.h b/src/SPH/fix_sph.h similarity index 100% rename from src/USER-SPH/fix_sph.h rename to src/SPH/fix_sph.h diff --git a/src/USER-SPH/fix_sph_stationary.cpp b/src/SPH/fix_sph_stationary.cpp similarity index 100% rename from src/USER-SPH/fix_sph_stationary.cpp rename to src/SPH/fix_sph_stationary.cpp diff --git a/src/USER-SPH/fix_sph_stationary.h b/src/SPH/fix_sph_stationary.h similarity index 100% rename from src/USER-SPH/fix_sph_stationary.h rename to src/SPH/fix_sph_stationary.h diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/SPH/pair_sph_heatconduction.cpp similarity index 100% rename from src/USER-SPH/pair_sph_heatconduction.cpp rename to src/SPH/pair_sph_heatconduction.cpp diff --git a/src/USER-SPH/pair_sph_heatconduction.h b/src/SPH/pair_sph_heatconduction.h similarity index 100% rename from src/USER-SPH/pair_sph_heatconduction.h rename to src/SPH/pair_sph_heatconduction.h diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/SPH/pair_sph_idealgas.cpp similarity index 100% rename from src/USER-SPH/pair_sph_idealgas.cpp rename to src/SPH/pair_sph_idealgas.cpp diff --git a/src/USER-SPH/pair_sph_idealgas.h b/src/SPH/pair_sph_idealgas.h similarity index 100% rename from src/USER-SPH/pair_sph_idealgas.h rename to src/SPH/pair_sph_idealgas.h diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/SPH/pair_sph_lj.cpp similarity index 100% rename from src/USER-SPH/pair_sph_lj.cpp rename to src/SPH/pair_sph_lj.cpp diff --git a/src/USER-SPH/pair_sph_lj.h b/src/SPH/pair_sph_lj.h similarity index 100% rename from src/USER-SPH/pair_sph_lj.h rename to src/SPH/pair_sph_lj.h diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/SPH/pair_sph_rhosum.cpp similarity index 100% rename from src/USER-SPH/pair_sph_rhosum.cpp rename to src/SPH/pair_sph_rhosum.cpp diff --git a/src/USER-SPH/pair_sph_rhosum.h b/src/SPH/pair_sph_rhosum.h similarity index 100% rename from src/USER-SPH/pair_sph_rhosum.h rename to src/SPH/pair_sph_rhosum.h diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/SPH/pair_sph_taitwater.cpp similarity index 100% rename from src/USER-SPH/pair_sph_taitwater.cpp rename to src/SPH/pair_sph_taitwater.cpp diff --git a/src/USER-SPH/pair_sph_taitwater.h b/src/SPH/pair_sph_taitwater.h similarity index 100% rename from src/USER-SPH/pair_sph_taitwater.h rename to src/SPH/pair_sph_taitwater.h diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/SPH/pair_sph_taitwater_morris.cpp similarity index 100% rename from src/USER-SPH/pair_sph_taitwater_morris.cpp rename to src/SPH/pair_sph_taitwater_morris.cpp diff --git a/src/USER-SPH/pair_sph_taitwater_morris.h b/src/SPH/pair_sph_taitwater_morris.h similarity index 100% rename from src/USER-SPH/pair_sph_taitwater_morris.h rename to src/SPH/pair_sph_taitwater_morris.h diff --git a/src/USER-TALLY/README b/src/TALLY/README similarity index 93% rename from src/USER-TALLY/README rename to src/TALLY/README index afdf638154..529184de7c 100644 --- a/src/USER-TALLY/README +++ b/src/TALLY/README @@ -15,7 +15,7 @@ Nevertheless, since those compute styles are executed directly using information that has already been computed, they should usually be more efficient than their counterparts. -There are example scripts for using this package in examples/USER/tally +There are example scripts for using this package in examples/PACKAGES/tally The person who created this package is Axel Kohlmeyer (akohlmey@gmail.com) at Temple University with a little help and inspiration from diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/TALLY/compute_force_tally.cpp similarity index 100% rename from src/USER-TALLY/compute_force_tally.cpp rename to src/TALLY/compute_force_tally.cpp diff --git a/src/USER-TALLY/compute_force_tally.h b/src/TALLY/compute_force_tally.h similarity index 100% rename from src/USER-TALLY/compute_force_tally.h rename to src/TALLY/compute_force_tally.h diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/TALLY/compute_heat_flux_tally.cpp similarity index 100% rename from src/USER-TALLY/compute_heat_flux_tally.cpp rename to src/TALLY/compute_heat_flux_tally.cpp diff --git a/src/USER-TALLY/compute_heat_flux_tally.h b/src/TALLY/compute_heat_flux_tally.h similarity index 100% rename from src/USER-TALLY/compute_heat_flux_tally.h rename to src/TALLY/compute_heat_flux_tally.h diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/TALLY/compute_pe_mol_tally.cpp similarity index 100% rename from src/USER-TALLY/compute_pe_mol_tally.cpp rename to src/TALLY/compute_pe_mol_tally.cpp diff --git a/src/USER-TALLY/compute_pe_mol_tally.h b/src/TALLY/compute_pe_mol_tally.h similarity index 100% rename from src/USER-TALLY/compute_pe_mol_tally.h rename to src/TALLY/compute_pe_mol_tally.h diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/TALLY/compute_pe_tally.cpp similarity index 100% rename from src/USER-TALLY/compute_pe_tally.cpp rename to src/TALLY/compute_pe_tally.cpp diff --git a/src/USER-TALLY/compute_pe_tally.h b/src/TALLY/compute_pe_tally.h similarity index 100% rename from src/USER-TALLY/compute_pe_tally.h rename to src/TALLY/compute_pe_tally.h diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/TALLY/compute_stress_tally.cpp similarity index 100% rename from src/USER-TALLY/compute_stress_tally.cpp rename to src/TALLY/compute_stress_tally.cpp diff --git a/src/USER-TALLY/compute_stress_tally.h b/src/TALLY/compute_stress_tally.h similarity index 100% rename from src/USER-TALLY/compute_stress_tally.h rename to src/TALLY/compute_stress_tally.h diff --git a/src/USER-UEF/README b/src/UEF/README similarity index 95% rename from src/USER-UEF/README rename to src/UEF/README index 2f2b872d3b..b2cef5b69b 100644 --- a/src/USER-UEF/README +++ b/src/UEF/README @@ -1,4 +1,4 @@ -USER-UEF is a LAMMPS package for non-equilibrium molecular dynamics +UEF is a LAMMPS package for non-equilibrium molecular dynamics (NEMD) under diagonal flow fields, including uniaxial and biaxial flow. With this package, simulations under extensional flow may be carried out for an indefinite amount of time. It is an implementation diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/UEF/compute_pressure_uef.cpp similarity index 100% rename from src/USER-UEF/compute_pressure_uef.cpp rename to src/UEF/compute_pressure_uef.cpp diff --git a/src/USER-UEF/compute_pressure_uef.h b/src/UEF/compute_pressure_uef.h similarity index 100% rename from src/USER-UEF/compute_pressure_uef.h rename to src/UEF/compute_pressure_uef.h diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/UEF/compute_temp_uef.cpp similarity index 100% rename from src/USER-UEF/compute_temp_uef.cpp rename to src/UEF/compute_temp_uef.cpp diff --git a/src/USER-UEF/compute_temp_uef.h b/src/UEF/compute_temp_uef.h similarity index 100% rename from src/USER-UEF/compute_temp_uef.h rename to src/UEF/compute_temp_uef.h diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/UEF/dump_cfg_uef.cpp similarity index 100% rename from src/USER-UEF/dump_cfg_uef.cpp rename to src/UEF/dump_cfg_uef.cpp diff --git a/src/USER-UEF/dump_cfg_uef.h b/src/UEF/dump_cfg_uef.h similarity index 100% rename from src/USER-UEF/dump_cfg_uef.h rename to src/UEF/dump_cfg_uef.h diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/UEF/fix_nh_uef.cpp similarity index 99% rename from src/USER-UEF/fix_nh_uef.cpp rename to src/UEF/fix_nh_uef.cpp index 9563644ede..a88b389611 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/UEF/fix_nh_uef.cpp @@ -44,7 +44,7 @@ enum{ISO,ANISO,TRICLINIC}; // citation info static const char cite_user_uef_package[] = - "USER-UEF package:\n\n" + "UEF package:\n\n" "@Article{NicholsonRutledge16,\n" "author = {David A. Nicholson and Gregory C. Rutledge},\n" "title = {Molecular simulation of flow-enhanced nucleation in n-eicosane melts under steady shear and uniaxial extension},\n" diff --git a/src/USER-UEF/fix_nh_uef.h b/src/UEF/fix_nh_uef.h similarity index 100% rename from src/USER-UEF/fix_nh_uef.h rename to src/UEF/fix_nh_uef.h diff --git a/src/USER-UEF/fix_npt_uef.cpp b/src/UEF/fix_npt_uef.cpp similarity index 100% rename from src/USER-UEF/fix_npt_uef.cpp rename to src/UEF/fix_npt_uef.cpp diff --git a/src/USER-UEF/fix_npt_uef.h b/src/UEF/fix_npt_uef.h similarity index 100% rename from src/USER-UEF/fix_npt_uef.h rename to src/UEF/fix_npt_uef.h diff --git a/src/USER-UEF/fix_nvt_uef.cpp b/src/UEF/fix_nvt_uef.cpp similarity index 100% rename from src/USER-UEF/fix_nvt_uef.cpp rename to src/UEF/fix_nvt_uef.cpp diff --git a/src/USER-UEF/fix_nvt_uef.h b/src/UEF/fix_nvt_uef.h similarity index 100% rename from src/USER-UEF/fix_nvt_uef.h rename to src/UEF/fix_nvt_uef.h diff --git a/src/USER-UEF/uef_utils.cpp b/src/UEF/uef_utils.cpp similarity index 100% rename from src/USER-UEF/uef_utils.cpp rename to src/UEF/uef_utils.cpp diff --git a/src/USER-UEF/uef_utils.h b/src/UEF/uef_utils.h similarity index 100% rename from src/USER-UEF/uef_utils.h rename to src/UEF/uef_utils.h diff --git a/src/USER-MEAMC/README b/src/USER-MEAMC/README deleted file mode 100644 index dcb70d670c..0000000000 --- a/src/USER-MEAMC/README +++ /dev/null @@ -1,26 +0,0 @@ -This package implements the MEAM/C potential as a LAMMPS pair style. - -============================================================================== - -This package is a translation of the MEAM package to native C++. See -that package as well as the Fortran code distributed in lib/meam for -the original sources and information. - - -Translation by - Sebastian Hütter, sebastian.huetter@ovgu.de - Institute of Materials and Joining Technology - Otto-von-Guericke University Magdeburg, Germany - -The original Fortran implementation was created by - Greg Wagner (while at Sandia, now at Northwestern U). - -============================================================================== - -Use "make yes-user-meamc" to enable this package when building LAMMPS. - -In your LAMMPS input script, specify - pair_style meam/c -to enable the use of this implementation. All parameters, input files and -outputs are exactly identical to these used with pair_style meam. - diff --git a/src/USER-MISC/README b/src/USER-MISC/README index d6f859b359..ea5910203c 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -60,7 +60,6 @@ fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017 fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016 fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 fix grem, David Stelter, dstelter@bu.edu, 22 Nov 16 -fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009 fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 fix momentum/chunk, Jiang Xiao (Hong Kong Polytechnic University), polyu-xiao.jiang at connect.polyu.hk, 19 Aug 2020 fix npt/cauchy, R. E. Miller (Carleton University), F. Pavia and S. Pattamatta, 12 Jan 2020 @@ -89,8 +88,6 @@ pair_style coul/slater/long, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 Fe pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 pair_style e3b, Steven Strong (U Chicago), stevene.strong at gmail dot com, 16 Apr 19 pair_style drip, Mingjian Wen, University of Minnesota, wenxx151 at umn.edu, 17 Apr 19 -pair_style dpd/ext, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP, svobod.martin at gmail dot com, 23 Apr 21 -pair_style dpd/ext/tstat, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP , svobod.martin at gmail dot com, 23 Apr 21 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index c09d3726c2..e3a31dda96 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -21,7 +21,7 @@ soft non-bonded potentials are used, such as DPD polymer chains. See the doc page for pair_style srp command for usage instructions. -There is an example script for this package in examples/USER/srp. +There is an example script for this package in examples/PACKAGES/srp. Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). ------------------------------------------------------------------------- */ diff --git a/src/USER-VTK/Install.sh b/src/VTK/Install.sh similarity index 100% rename from src/USER-VTK/Install.sh rename to src/VTK/Install.sh diff --git a/src/USER-VTK/README b/src/VTK/README similarity index 100% rename from src/USER-VTK/README rename to src/VTK/README diff --git a/src/USER-VTK/dump_vtk.cpp b/src/VTK/dump_vtk.cpp similarity index 100% rename from src/USER-VTK/dump_vtk.cpp rename to src/VTK/dump_vtk.cpp diff --git a/src/USER-VTK/dump_vtk.h b/src/VTK/dump_vtk.h similarity index 100% rename from src/USER-VTK/dump_vtk.h rename to src/VTK/dump_vtk.h diff --git a/src/USER-YAFF/README b/src/YAFF/README similarity index 100% rename from src/USER-YAFF/README rename to src/YAFF/README diff --git a/src/USER-YAFF/angle_cross.cpp b/src/YAFF/angle_cross.cpp similarity index 100% rename from src/USER-YAFF/angle_cross.cpp rename to src/YAFF/angle_cross.cpp diff --git a/src/USER-YAFF/angle_cross.h b/src/YAFF/angle_cross.h similarity index 100% rename from src/USER-YAFF/angle_cross.h rename to src/YAFF/angle_cross.h diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/YAFF/angle_mm3.cpp similarity index 100% rename from src/USER-YAFF/angle_mm3.cpp rename to src/YAFF/angle_mm3.cpp diff --git a/src/USER-YAFF/angle_mm3.h b/src/YAFF/angle_mm3.h similarity index 100% rename from src/USER-YAFF/angle_mm3.h rename to src/YAFF/angle_mm3.h diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/YAFF/bond_mm3.cpp similarity index 100% rename from src/USER-YAFF/bond_mm3.cpp rename to src/YAFF/bond_mm3.cpp diff --git a/src/USER-YAFF/bond_mm3.h b/src/YAFF/bond_mm3.h similarity index 100% rename from src/USER-YAFF/bond_mm3.h rename to src/YAFF/bond_mm3.h diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/YAFF/improper_distharm.cpp similarity index 100% rename from src/USER-YAFF/improper_distharm.cpp rename to src/YAFF/improper_distharm.cpp diff --git a/src/USER-YAFF/improper_distharm.h b/src/YAFF/improper_distharm.h similarity index 100% rename from src/USER-YAFF/improper_distharm.h rename to src/YAFF/improper_distharm.h diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/YAFF/improper_sqdistharm.cpp similarity index 100% rename from src/USER-YAFF/improper_sqdistharm.cpp rename to src/YAFF/improper_sqdistharm.cpp diff --git a/src/USER-YAFF/improper_sqdistharm.h b/src/YAFF/improper_sqdistharm.h similarity index 100% rename from src/USER-YAFF/improper_sqdistharm.h rename to src/YAFF/improper_sqdistharm.h diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/YAFF/pair_lj_switch3_coulgauss_long.cpp similarity index 100% rename from src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp rename to src/YAFF/pair_lj_switch3_coulgauss_long.cpp diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h b/src/YAFF/pair_lj_switch3_coulgauss_long.h similarity index 100% rename from src/USER-YAFF/pair_lj_switch3_coulgauss_long.h rename to src/YAFF/pair_lj_switch3_coulgauss_long.h diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/YAFF/pair_mm3_switch3_coulgauss_long.cpp similarity index 100% rename from src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp rename to src/YAFF/pair_mm3_switch3_coulgauss_long.cpp diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h b/src/YAFF/pair_mm3_switch3_coulgauss_long.h similarity index 100% rename from src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h rename to src/YAFF/pair_mm3_switch3_coulgauss_long.h diff --git a/src/accelerator_omp.h b/src/accelerator_omp.h index 3f3be3c975..437ce3e413 100644 --- a/src/accelerator_omp.h +++ b/src/accelerator_omp.h @@ -15,7 +15,7 @@ #ifdef LMP_USER_OMP -// true interface to USER-OMP +// true interface to OPENMP // provide a DomainOMP class with some overrides for Domain #include "domain.h" diff --git a/src/atom.cpp b/src/atom.cpp index 0a8095116b..6c93161dfd 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -161,7 +161,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) sp = fm = fm_long = nullptr; - // USER-EFF and USER-AWPMD packages + // EFF and AWPMD packages spin = nullptr; eradius = ervel = erforce = nullptr; @@ -169,23 +169,23 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) cs = csforce = vforce = nullptr; etag = nullptr; - // USER-DPD package + // DPD-REACT package uCond = uMech = uChem = uCG = uCGnew = nullptr; duChem = dpdTheta = nullptr; - // USER-MESO package + // MESO package cc = cc_flux = nullptr; edpd_temp = edpd_flux = edpd_cv = nullptr; - // USER-MESONT package + // MESONT package length = nullptr; buckling = nullptr; bond_nt = nullptr; - // USER-SMD package + // MACHDYN package contact_radius = nullptr; smd_data_9 = nullptr; @@ -194,12 +194,12 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) eff_plastic_strain_rate = nullptr; damage = nullptr; - // USER-SPH package + // SPH package rho = drho = esph = desph = cv = nullptr; vest = nullptr; - // USER-DIELECTRIC package + // DIELECTRIC package area = ed = em = epsilon = curvature = q_unscaled = nullptr; @@ -457,14 +457,14 @@ void Atom::peratom_create() add_peratom("fm",&fm,DOUBLE,3,1); add_peratom("fm_long",&fm_long,DOUBLE,3,1); - // USER-EFF package + // EFF package add_peratom("spin",&spin,INT,0); add_peratom("eradius",&eradius,DOUBLE,0); add_peratom("ervel",&ervel,DOUBLE,0); add_peratom("erforce",&erforce,DOUBLE,0,1); // set per-thread flag - // USER-AWPMD package + // AWPMD package add_peratom("cs",&cs,DOUBLE,2); add_peratom("csforce",&csforce,DOUBLE,2); @@ -472,7 +472,7 @@ void Atom::peratom_create() add_peratom("ervelforce",&ervelforce,DOUBLE,0); add_peratom("etag",&etag,INT,0); - // USER-DPD package + // DPD-REACT package add_peratom("dpdTheta",&dpdTheta,DOUBLE,0); add_peratom("uCond",&uCond,DOUBLE,0); @@ -482,7 +482,7 @@ void Atom::peratom_create() add_peratom("uCGnew",&uCGnew,DOUBLE,0); add_peratom("duChem",&duChem,DOUBLE,0); - // USER-MESO package + // MESO package add_peratom("edpd_cv",&edpd_cv,DOUBLE,0); add_peratom("edpd_temp",&edpd_temp,DOUBLE,0); @@ -491,13 +491,13 @@ void Atom::peratom_create() add_peratom("cc",&cc,DOUBLE,1); add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag - // USER-MESONT package + // MESONT package add_peratom("length",&length,DOUBLE,0); add_peratom("buckling",&buckling,INT,0); add_peratom("bond_nt",&bond_nt,tagintsize,2); - // USER-SPH package + // SPH package add_peratom("rho",&rho,DOUBLE,0); add_peratom("drho",&drho,DOUBLE,0,1); // set per-thread flag @@ -506,7 +506,7 @@ void Atom::peratom_create() add_peratom("vest",&vest,DOUBLE,3); add_peratom("cv",&cv,DOUBLE,0); - // USER-SMD package + // MACHDYN package add_peratom("contact_radius",&contact_radius,DOUBLE,0); add_peratom("smd_data_9",&smd_data_9,DOUBLE,1); @@ -515,7 +515,7 @@ void Atom::peratom_create() add_peratom("eff_plastic_strain_rate",&eff_plastic_strain_rate,DOUBLE,0); add_peratom("damage",&damage,DOUBLE,0); - // USER-DIELECTRIC package + // DIELECTRIC package add_peratom("area",&area,DOUBLE,0); add_peratom("ed",&ed,DOUBLE,0); @@ -2646,7 +2646,7 @@ void *Atom::extract(const char *name) if (strcmp(name,"cv") == 0) return (void *) cv; if (strcmp(name,"vest") == 0) return (void *) vest; - // USER-MESONT package + // MESONT package if (strcmp(name,"length") == 0) return (void *) length; if (strcmp(name,"buckling") == 0) return (void *) buckling; if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt; @@ -2663,7 +2663,7 @@ void *Atom::extract(const char *name) if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta; if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp; - // USER-DIELECTRIC + // DIELECTRIC if (strcmp(name,"area") == 0) return (void *) area; if (strcmp(name,"ed") == 0) return (void *) ed; if (strcmp(name,"em") == 0) return (void *) em; @@ -2739,7 +2739,7 @@ int Atom::extract_datatype(const char *name) if (strcmp(name,"cv") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"vest") == 0) return LAMMPS_DOUBLE_2D; - // USER-MESONT package + // MESONT package if (strcmp(name,"length") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"buckling") == 0) return LAMMPS_INT; if (strcmp(name,"bond_nt") == 0) return LAMMPS_TAGINT_2D; @@ -2754,7 +2754,7 @@ int Atom::extract_datatype(const char *name) if (strcmp(name,"dpdTheta") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"edpd_temp") == 0) return LAMMPS_DOUBLE; - // USER-DIELECTRIC + // DIELECTRIC if (strcmp(name,"area") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"ed") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"em") == 0) return LAMMPS_DOUBLE; diff --git a/src/atom.h b/src/atom.h index 392e5c5d5c..c881490b8e 100644 --- a/src/atom.h +++ b/src/atom.h @@ -114,7 +114,7 @@ class Atom : protected Pointers { double **sp, **fm, **fm_long; - // USER_EFF and USER-AWPMD packages + // EFF and AWPMD packages int *spin; double *eradius, *ervel, *erforce; @@ -122,14 +122,14 @@ class Atom : protected Pointers { double **cs, **csforce, **vforce; int *etag; - // USER-DPD package + // DPD-REACT package double *uCond, *uMech, *uChem, *uCGnew, *uCG; double *duChem; double *dpdTheta; int nspecies_dpd; - // USER-MESO package + // MESO package double **cc, **cc_flux; // cc = chemical concentration double *edpd_temp, *edpd_flux; // temperature and heat flux @@ -137,13 +137,13 @@ class Atom : protected Pointers { double *edpd_cv; // heat capacity int cc_species; - // USER-MESONT package + // MESONT package double *length; int *buckling; tagint **bond_nt; - // USER-SMD package + // MACHDYN package double *contact_radius; double **smd_data_9; @@ -152,12 +152,12 @@ class Atom : protected Pointers { double *eff_plastic_strain_rate; double *damage; - // USER-SPH package + // SPH package double *rho, *drho, *esph, *desph, *cv; double **vest; - // USER-DIELECTRIC package + // DIELECTRIC package double *area,*ed,*em,*epsilon,*curvature,*q_unscaled; @@ -187,7 +187,7 @@ class Atom : protected Pointers { int sp_flag; - // USER-SMD package + // MACHDYN package int x0_flag; int smd_flag, damage_flag; diff --git a/src/comm.h b/src/comm.h index e7c07522a9..bc5faa49f4 100644 --- a/src/comm.h +++ b/src/comm.h @@ -281,6 +281,6 @@ UNDOCUMENTED U: OMP_NUM_THREADS environment is not set. This environment variable must be set appropriately to use the -USER-OMP package. +OPENMP package. */ diff --git a/src/info.cpp b/src/info.cpp index 049bdd5bfd..6756c174ca 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -1223,7 +1223,7 @@ bool Info::has_accelerator_feature(const std::string &package, } #endif #if defined(LMP_USER_OMP) - if (package == "USER-OMP") { + if (package == "OPENMP") { if (category == "precision") { if (setting == "double") return true; else return false; @@ -1239,7 +1239,7 @@ bool Info::has_accelerator_feature(const std::string &package, } #endif #if defined(LMP_USER_INTEL) - if (package == "USER-INTEL") { + if (package == "INTEL") { if (category == "precision") { if (setting == "double") return true; else if (setting == "mixed") return true; @@ -1466,24 +1466,24 @@ std::string Info::get_accelerator_info(const std::string &package) if (has_accelerator_feature("KOKKOS","precision","double")) mesg += " double"; mesg += "\n"; } - if ((package.empty() || (package == "USER-OMP")) && has_package("USER-OMP")) { - mesg += "USER-OMP package API:"; - if (has_accelerator_feature("USER-OMP","api","openmp")) mesg += " OpenMP"; - if (has_accelerator_feature("USER-OMP","api","serial")) mesg += " Serial"; - mesg += "\nUSER-OMP package precision:"; - if (has_accelerator_feature("USER-OMP","precision","single")) mesg += " single"; - if (has_accelerator_feature("USER-OMP","precision","mixed")) mesg += " mixed"; - if (has_accelerator_feature("USER-OMP","precision","double")) mesg += " double"; + if ((package.empty() || (package == "OPENMP")) && has_package("OPENMP")) { + mesg += "OPENMP package API:"; + if (has_accelerator_feature("OPENMP","api","openmp")) mesg += " OpenMP"; + if (has_accelerator_feature("OPENMP","api","serial")) mesg += " Serial"; + mesg += "\nOPENMP package precision:"; + if (has_accelerator_feature("OPENMP","precision","single")) mesg += " single"; + if (has_accelerator_feature("OPENMP","precision","mixed")) mesg += " mixed"; + if (has_accelerator_feature("OPENMP","precision","double")) mesg += " double"; mesg += "\n"; } - if ((package.empty() || (package == "USER-INTEL")) && has_package("USER-INTEL")) { - mesg += "USER-INTEL package API:"; - if (has_accelerator_feature("USER-INTEL","api","phi")) mesg += " Phi"; - if (has_accelerator_feature("USER-INTEL","api","openmp")) mesg += " OpenMP"; - mesg += "\nUSER-INTEL package precision:"; - if (has_accelerator_feature("USER-INTEL","precision","single")) mesg += " single"; - if (has_accelerator_feature("USER-INTEL","precision","mixed")) mesg += " mixed"; - if (has_accelerator_feature("USER-INTEL","precision","double")) mesg += " double"; + if ((package.empty() || (package == "INTEL")) && has_package("INTEL")) { + mesg += "INTEL package API:"; + if (has_accelerator_feature("INTEL","api","phi")) mesg += " Phi"; + if (has_accelerator_feature("INTEL","api","openmp")) mesg += " OpenMP"; + mesg += "\nINTEL package precision:"; + if (has_accelerator_feature("INTEL","precision","single")) mesg += " single"; + if (has_accelerator_feature("INTEL","precision","mixed")) mesg += " mixed"; + if (has_accelerator_feature("INTEL","precision","double")) mesg += " double"; mesg += "\n"; } return mesg; diff --git a/src/input.cpp b/src/input.cpp index 1ef88be866..2c2c55f4c4 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1683,7 +1683,7 @@ void Input::package() } else if (strcmp(arg[0],"omp") == 0) { if (!modify->check_package("OMP")) error->all(FLERR, - "Package omp command without USER-OMP package installed"); + "Package omp command without OPENMP package installed"); std::string fixcmd = "package_omp all OMP"; for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i]; @@ -1692,7 +1692,7 @@ void Input::package() } else if (strcmp(arg[0],"intel") == 0) { if (!modify->check_package("INTEL")) error->all(FLERR, - "Package intel command without USER-INTEL package installed"); + "Package intel command without INTEL package installed"); std::string fixcmd = "package_intel all INTEL"; for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i]; diff --git a/src/input.h b/src/input.h index d82816aa04..faf45ab305 100644 --- a/src/input.h +++ b/src/input.h @@ -357,14 +357,14 @@ E: Package kokkos command without KOKKOS package enabled The KOKKOS package must be installed via "make yes-kokkos" before LAMMPS is built, and the "-k on" must be used to enable the package. -E: Package omp command without USER-OMP package installed +E: Package omp command without OPENMP package installed -The USER-OMP package must be installed via "make yes-user-omp" before +The OPENMP package must be installed via "make yes-openmp" before LAMMPS is built. -E: Package intel command without USER-INTEL package installed +E: Package intel command without INTEL package installed -The USER-INTEL package must be installed via "make yes-user-intel" +The INTEL package must be installed via "make yes-intel" before LAMMPS is built. E: Pair_coeff command before simulation box is defined diff --git a/src/lammps.cpp b/src/lammps.cpp index 131d2e66f6..70174b9d14 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -843,19 +843,19 @@ void LAMMPS::post_create() // suffix will always be set if suffix_enable = 1 // check that KOKKOS package classes were instantiated - // check that GPU, INTEL, USER-OMP fixes were compiled with LAMMPS + // check that GPU, INTEL, OPENMP fixes were compiled with LAMMPS if (suffix_enable) { if (strcmp(suffix,"gpu") == 0 && !modify->check_package("GPU")) error->all(FLERR,"Using suffix gpu without GPU package installed"); if (strcmp(suffix,"intel") == 0 && !modify->check_package("INTEL")) - error->all(FLERR,"Using suffix intel without USER-INTEL package installed"); + error->all(FLERR,"Using suffix intel without INTEL package installed"); if (strcmp(suffix,"kk") == 0 && (kokkos == nullptr || kokkos->kokkos_exists == 0)) error->all(FLERR,"Using suffix kk without KOKKOS package enabled"); if (strcmp(suffix,"omp") == 0 && !modify->check_package("OMP")) - error->all(FLERR,"Using suffix omp without USER-OMP package installed"); + error->all(FLERR,"Using suffix omp without OPENMP package installed"); if (strcmp(suffix,"gpu") == 0) input->one("package gpu 0"); if (strcmp(suffix,"intel") == 0) input->one("package intel 1"); diff --git a/src/lammps.h b/src/lammps.h index 9592f9af05..74ae47e9a2 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -199,7 +199,7 @@ E: Using suffix gpu without GPU package installed Self-explanatory. -E: Using suffix intel without USER-INTEL package installed +E: Using suffix intel without INTEL package installed Self-explanatory. @@ -207,7 +207,7 @@ E: Using suffix kk without KOKKOS package enabled Self-explanatory. -E: Using suffix omp without USER-OMP package installed +E: Using suffix omp without OPENMP package installed Self-explanatory. diff --git a/src/library.cpp b/src/library.cpp index 111430ced0..c0dcb4f328 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -4350,7 +4350,7 @@ int lammps_config_package_name(int idx, char *buffer, int buf_size) { \verbatim embed:rst This function checks availability of compile time settings of included :doc:`accelerator packages ` in LAMMPS. -Supported packages names are "GPU", "KOKKOS", "USER-INTEL", and "USER-OMP". +Supported packages names are "GPU", "KOKKOS", "INTEL", and "OPENMP". Supported categories are "api" with possible settings "cuda", "hip", "phi", "pthreads", "opencl", "openmp", and "serial", and "precision" with possible settings "double", "mixed", and "single". If the combination diff --git a/src/modify.cpp b/src/modify.cpp index c395575d7f..c617bf1477 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -1110,7 +1110,7 @@ int Modify::find_fix_by_style(const char *style) check for fix associated with package name in compiled list return 1 if found else 0 used to determine whether LAMMPS was built with - GPU, USER-INTEL, USER-OMP packages, which have their own fixes + GPU, INTEL, OPENMP packages, which have their own fixes ------------------------------------------------------------------------- */ int Modify::check_package(const char *package_fix_name) diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index d10c98835e..aa2a9f6686 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -38,7 +38,7 @@ NBinStandard::NBinStandard(LAMMPS *lmp) : NBin(lmp) {} void NBinStandard::bin_atoms_setup(int nall) { // binhead = per-bin vector, mbins in length - // add 1 bin for USER-INTEL package + // add 1 bin for INTEL package if (mbins > maxbin) { maxbin = mbins; diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp index 5dc56f8c60..dc76b242e9 100644 --- a/src/neigh_list.cpp +++ b/src/neigh_list.cpp @@ -84,7 +84,7 @@ NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp) kk2cpu = 0; execution_space = Host; - // USER-DPD package + // DPD-REACT package np = nullptr; diff --git a/src/neigh_list.h b/src/neigh_list.h index 703d4c13a9..8b920bbe50 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -95,7 +95,7 @@ class NeighList : protected Pointers { int kokkos; // 1 if list stores Kokkos data ExecutionSpace execution_space; - // USER-DPD package and Shardlow Splitting Algorithm (SSA) support + // DPD-REACT package and Shardlow Splitting Algorithm (SSA) support class NPair *np; // ptr to NPair instance I depend on diff --git a/src/neigh_request.h b/src/neigh_request.h index 30cf6592d1..4bdc368317 100644 --- a/src/neigh_request.h +++ b/src/neigh_request.h @@ -66,11 +66,11 @@ class NeighRequest : protected Pointers { int respamiddle; // 1 if need a rRESPA middle list int respaouter; // 1 if need a rRESPA outer list int bond; // 1 if store bond neighbors instead of atom neighs - int omp; // set by USER-OMP package - int intel; // set by USER-INTEL package + int omp; // set by OPENMP package + int intel; // set by INTEL package int kokkos_host; // set by KOKKOS package int kokkos_device; - int ssa; // set by USER-DPD package, for Shardlow lists + int ssa; // set by DPD-REACT package, for Shardlow lists int cut; // 1 if use a non-standard cutoff length double cutoff; // special cutoff distance for this list diff --git a/src/pair.cpp b/src/pair.cpp index 0fcc4bd62f..5448a42e1c 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -959,7 +959,7 @@ void Pair::ev_setup(int eflag, int vflag, int alloc) } } - // run ev_setup option for USER-TALLY computes + // run ev_setup option for TALLY computes if (num_tally_compute > 0) { for (int k=0; k < num_tally_compute; ++k) { diff --git a/src/pair.h b/src/pair.h index b19fa08c48..80d4fc11d1 100644 --- a/src/pair.h +++ b/src/pair.h @@ -246,7 +246,7 @@ class Pair : protected Pointers { float f; } union_int_float_t; - // Accessor for the user-intel package to determine virial calc for hybrid + // Accessor for the INTEL package to determine virial calc for hybrid inline int fdotr_is_set() const { return vflag_fdotr; } diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index ab2fe7803a..545d5d9232 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -923,7 +923,7 @@ again: } // if 2nd keyword (after pair) is compute/tally: - // set flag to register USER-TALLY computes accordingly + // set flag to register TALLY computes accordingly if (iarg < narg && strcmp(arg[iarg],"compute/tally") == 0) { if (narg < iarg+2) diff --git a/tools/README b/tools/README index f803123270..0f6f36e78a 100644 --- a/tools/README +++ b/tools/README @@ -25,7 +25,7 @@ eam_database one tool to generate EAM alloy potential files eam_generate 2nd tool to generate EAM alloy potential files eff scripts for working with the eFF (electron force field) emacs add-ons to EMACS editor for editing LAMMPS input scripts -fep scripts for free-energy perturbation with USER-FEP pkg +fep scripts for free-energy perturbation with FEP pkg i-pi Python wrapper for performing path-integral MD (PIMD) ipp input pre-processor Perl tool for creating input scripts kate add-ons to Kate editor for editing LAMMPS input scripts @@ -34,7 +34,7 @@ lmp2arc convert LAMMPS output to Accelrys Insight format lmp2cfg convert LAMMPS output to CFG files for AtomEye viz magic patterns to detect LAMMPS files with the file(1) command matlab MatLab scripts for post-processing LAMMPS output -mesont Tools for use with the USER-MESONT package +mesont Tools for use with the MESONT package micelle2d create a data file of small lipid chains in solvent moltemplate Instructions for installing the Moltemplate builder program msi2lmp use Accelrys Insight code to setup LAMMPS input diff --git a/tools/drude/polarizer.py b/tools/drude/polarizer.py index 3c17026387..d47ef0e05d 100755 --- a/tools/drude/polarizer.py +++ b/tools/drude/polarizer.py @@ -41,7 +41,7 @@ new bonds to the data file. It will also generate some commands to be included in the LAMMPS input script, which are related to the topology and force field, namely fix drude, pair_style and pair_coeff commands. For information on thermostating please -read the documentation of the USER-DRUDE package. +read the documentation of the DRUDE package. This tool can also be used to revert a Drude-polarized data file to a non-polarizable one. diff --git a/tools/fep/README b/tools/fep/README index ff319d5051..7fd4a8132c 100644 --- a/tools/fep/README +++ b/tools/fep/README @@ -1,4 +1,4 @@ -These are utility scripts provided as part of the USER-FEP package for +These are utility scripts provided as part of the FEP package for free energy perturbation simulations with soft-core pair potentials in LAMMPS. diff --git a/tools/mesont/README b/tools/mesont/README index 9a5289a449..d02679df51 100644 --- a/tools/mesont/README +++ b/tools/mesont/README @@ -1,9 +1,9 @@ -=== USER-MESONT tools === +=== MESONT tools === =============================== The programs in this folder can be used to analyze the output of simulations using the CNT mesoscopic force -field (USER-MESONT). +field (MESONT). dump2vtk.cpp converts output written in *.dump format (the sequence of columns must be "ATOMS id type x y z Es Eb Et diff --git a/unittest/c-library/test_library_open.cpp b/unittest/c-library/test_library_open.cpp index 377f3c53ef..b7a8016a1a 100644 --- a/unittest/c-library/test_library_open.cpp +++ b/unittest/c-library/test_library_open.cpp @@ -137,7 +137,7 @@ TEST(lammps_open_no_mpi, no_screen) TEST(lammps_open_no_mpi, with_omp) { - if (!LAMMPS_NS::LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS_NS::LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); const char *args[] = {"liblammps", "-pk", "omp", "2", "neigh", "no", "-sf", "omp", "-log", "none", "-nocite"}; char **argv = (char **)args; diff --git a/unittest/cplusplus/test_lammps_class.cpp b/unittest/cplusplus/test_lammps_class.cpp index 5288cfc2b6..d25b232fa7 100644 --- a/unittest/cplusplus/test_lammps_class.cpp +++ b/unittest/cplusplus/test_lammps_class.cpp @@ -133,21 +133,21 @@ TEST_F(LAMMPS_plain, TestStyles) found = lmp->match_style("atom", "spin"); EXPECT_STREQ(found, "SPIN"); found = lmp->match_style("atom", "wavepacket"); - EXPECT_STREQ(found, "USER-AWPMD"); + EXPECT_STREQ(found, "AWPMD"); found = lmp->match_style("atom", "dpd"); - EXPECT_STREQ(found, "USER-DPD"); + EXPECT_STREQ(found, "DPD-REACT"); found = lmp->match_style("atom", "edpd"); - EXPECT_STREQ(found, "USER-MESODPD"); + EXPECT_STREQ(found, "DPD-MESO"); found = lmp->match_style("atom", "mdpd"); - EXPECT_STREQ(found, "USER-MESODPD"); + EXPECT_STREQ(found, "DPD-MESO"); found = lmp->match_style("atom", "tdpd"); - EXPECT_STREQ(found, "USER-MESODPD"); + EXPECT_STREQ(found, "DPD-MESO"); found = lmp->match_style("atom", "spin"); EXPECT_STREQ(found, "SPIN"); found = lmp->match_style("atom", "smd"); - EXPECT_STREQ(found, "USER-SMD"); + EXPECT_STREQ(found, "MACHDYN"); found = lmp->match_style("atom", "sph"); - EXPECT_STREQ(found, "USER-SPH"); + EXPECT_STREQ(found, "SPH"); found = lmp->match_style("atom", "i_don't_exist"); EXPECT_STREQ(found, NULL); } @@ -176,9 +176,9 @@ protected: char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); - // only run this test fixture with omp suffix if USER-OMP package is installed + // only run this test fixture with omp suffix if OPENMP package is installed - if (LAMMPS::is_installed_pkg("USER-OMP")) + if (LAMMPS::is_installed_pkg("OPENMP")) lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); else GTEST_SKIP(); @@ -324,7 +324,7 @@ TEST_F(LAMMPS_kokkos, InitMembers) TEST(LAMMPS_init, OpenMP) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (Info::get_openmp_info() == "OpenMP not enabled") GTEST_SKIP(); FILE *fp = fopen("in.lammps_empty", "w"); @@ -340,7 +340,7 @@ TEST(LAMMPS_init, OpenMP) std::string output = ::testing::internal::GetCapturedStdout(); EXPECT_THAT(output, MatchesRegex(".*using 2 OpenMP thread.*per MPI task.*")); - if (LAMMPS_NS::Info::has_accelerator_feature("USER-OMP", "api", "openmp")) + if (LAMMPS_NS::Info::has_accelerator_feature("OPENMP", "api", "openmp")) EXPECT_EQ(lmp->comm->nthreads, 2); else EXPECT_EQ(lmp->comm->nthreads, 1); @@ -356,7 +356,7 @@ TEST(LAMMPS_init, OpenMP) TEST(LAMMPS_init, NoOpenMP) { - if (!LAMMPS_NS::Info::has_accelerator_feature("USER-OMP", "api", "openmp")) + if (!LAMMPS_NS::Info::has_accelerator_feature("OPENMP", "api", "openmp")) GTEST_SKIP() << "No threading enabled"; FILE *fp = fopen("in.lammps_class_noomp", "w"); diff --git a/unittest/force-styles/test_angle_style.cpp b/unittest/force-styles/test_angle_style.cpp index 8f858a3a04..b4300218b7 100644 --- a/unittest/force-styles/test_angle_style.cpp +++ b/unittest/force-styles/test_angle_style.cpp @@ -533,7 +533,7 @@ TEST(AngleStyle, plain) TEST(AngleStyle, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -564,7 +564,7 @@ TEST(AngleStyle, omp) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for USER-OMP package + // relax error a bit for OPENMP package double epsilon = 5.0 * test_config.epsilon; auto f = lmp->atom->f; @@ -628,7 +628,7 @@ TEST(AngleStyle, omp) int id = lmp->modify->find_compute("sum"); double energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with angle style hybrid + // TODO: this is currently broken for OPENMP with angle style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.angle_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(angle->energy, energy, epsilon); @@ -695,7 +695,7 @@ TEST(AngleStyle, omp) id = lmp->modify->find_compute("sum"); energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with angle style hybrid + // TODO: this is currently broken for OPENMP with angle style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.angle_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(angle->energy, energy, epsilon); diff --git a/unittest/force-styles/test_bond_style.cpp b/unittest/force-styles/test_bond_style.cpp index 2b5e11de20..f4c151a394 100644 --- a/unittest/force-styles/test_bond_style.cpp +++ b/unittest/force-styles/test_bond_style.cpp @@ -533,7 +533,7 @@ TEST(BondStyle, plain) TEST(BondStyle, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"BondStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -564,7 +564,7 @@ TEST(BondStyle, omp) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for USER-OMP package + // relax error a bit for OPENMP package double epsilon = 5.0 * test_config.epsilon; auto f = lmp->atom->f; @@ -627,7 +627,7 @@ TEST(BondStyle, omp) int id = lmp->modify->find_compute("sum"); double energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(bond->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with bond style hybrid + // TODO: this is currently broken for OPENMP with bond style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.bond_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(bond->energy, energy, epsilon); @@ -694,7 +694,7 @@ TEST(BondStyle, omp) id = lmp->modify->find_compute("sum"); energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(bond->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with bond style hybrid + // TODO: this is currently broken for OPENMP with bond style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.bond_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(bond->energy, energy, epsilon); diff --git a/unittest/force-styles/test_dihedral_style.cpp b/unittest/force-styles/test_dihedral_style.cpp index 718bcb5332..8cae5d5f7c 100644 --- a/unittest/force-styles/test_dihedral_style.cpp +++ b/unittest/force-styles/test_dihedral_style.cpp @@ -536,7 +536,7 @@ TEST(DihedralStyle, plain) TEST(DihedralStyle, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -567,7 +567,7 @@ TEST(DihedralStyle, omp) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for USER-OMP package + // relax error a bit for OPENMP package double epsilon = 5.0 * test_config.epsilon; auto f = lmp->atom->f; @@ -631,7 +631,7 @@ TEST(DihedralStyle, omp) int id = lmp->modify->find_compute("sum"); double energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(dihedral->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with dihedral style hybrid + // TODO: this is currently broken for OPENMP with dihedral style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.dihedral_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(dihedral->energy, energy, epsilon); @@ -698,7 +698,7 @@ TEST(DihedralStyle, omp) id = lmp->modify->find_compute("sum"); energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(dihedral->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with dihedral style hybrid + // TODO: this is currently broken for OPENMP with dihedral style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.dihedral_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(dihedral->energy, energy, epsilon); diff --git a/unittest/force-styles/test_fix_timestep.cpp b/unittest/force-styles/test_fix_timestep.cpp index 645c41b2ae..34c8ba65d9 100644 --- a/unittest/force-styles/test_fix_timestep.cpp +++ b/unittest/force-styles/test_fix_timestep.cpp @@ -696,7 +696,7 @@ TEST(FixTimestep, plain) TEST(FixTimestep, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); diff --git a/unittest/force-styles/test_improper_style.cpp b/unittest/force-styles/test_improper_style.cpp index 52fc0f0b92..b6d6b9a06b 100644 --- a/unittest/force-styles/test_improper_style.cpp +++ b/unittest/force-styles/test_improper_style.cpp @@ -527,7 +527,7 @@ TEST(ImproperStyle, plain) TEST(ImproperStyle, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -558,7 +558,7 @@ TEST(ImproperStyle, omp) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for USER-OMP package + // relax error a bit for OPENMP package double epsilon = 5.0 * test_config.epsilon; auto f = lmp->atom->f; @@ -622,7 +622,7 @@ TEST(ImproperStyle, omp) int id = lmp->modify->find_compute("sum"); double energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with improper style hybrid + // TODO: this is currently broken for OPENMP with improper style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.improper_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(improper->energy, energy, epsilon); @@ -689,7 +689,7 @@ TEST(ImproperStyle, omp) id = lmp->modify->find_compute("sum"); energy = lmp->modify->compute[id]->compute_scalar(); EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.run_energy, epsilon); - // TODO: this is currently broken for USER-OMP with improper style hybrid + // TODO: this is currently broken for OPENMP with improper style hybrid // needs to be fixed in the main code somewhere. Not sure where, though. if (test_config.improper_style.substr(0, 6) != "hybrid") EXPECT_FP_LE_WITH_EPS(improper->energy, energy, epsilon); diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index b8513237c5..939bf5dbb5 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -598,7 +598,7 @@ TEST(PairStyle, plain) TEST(PairStyle, omp) { - if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("OPENMP")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -632,7 +632,7 @@ TEST(PairStyle, omp) const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); - // relax error a bit for USER-OMP package + // relax error a bit for OPENMP package double epsilon = 5.0 * test_config.epsilon; // relax test precision when using pppm and single precision FFTs #if defined(FFT_SINGLE) @@ -896,7 +896,7 @@ TEST(PairStyle, gpu) TEST(PairStyle, intel) { - if (!LAMMPS::is_installed_pkg("USER-INTEL")) GTEST_SKIP(); + if (!LAMMPS::is_installed_pkg("INTEL")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"PairStyle", "-log", "none", "-echo", "screen", "-nocite", @@ -924,7 +924,7 @@ TEST(PairStyle, intel) GTEST_SKIP(); } - // relax error a bit for USER-INTEL package + // relax error a bit for INTEL package double epsilon = 7.5 * test_config.epsilon; // relax test precision when using pppm and single precision FFTs #if defined(FFT_SINGLE) @@ -1010,7 +1010,7 @@ TEST(PairStyle, intel) EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.run_vdwl, epsilon); EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.run_coul, epsilon); - // rebo family of pair styles will have a large error in per-atom energy for USER-INTEL + // rebo family of pair styles will have a large error in per-atom energy for INTEL if (test_config.pair_style.find("rebo") != std::string::npos) epsilon *= 100000.0; EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl + pair->eng_coul), energy, epsilon); diff --git a/unittest/force-styles/tests/atomic-pair-meam_c.yaml b/unittest/force-styles/tests/atomic-pair-meam.yaml similarity index 99% rename from unittest/force-styles/tests/atomic-pair-meam_c.yaml rename to unittest/force-styles/tests/atomic-pair-meam.yaml index 7d93a698e0..6f262c032a 100644 --- a/unittest/force-styles/tests/atomic-pair-meam_c.yaml +++ b/unittest/force-styles/tests/atomic-pair-meam.yaml @@ -3,13 +3,13 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:03 2021 epsilon: 5e-13 prerequisites: ! | - pair meam/c + pair meam pre_commands: ! | variable newton_pair delete if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.metal -pair_style: meam/c +pair_style: meam pair_coeff: ! | * * library.meam Al Si Mg Cu Fe AlSiMgCuFe.meam Mg Fe extract: ! | diff --git a/unittest/force-styles/tests/kspace-msm.yaml b/unittest/force-styles/tests/kspace-msm.yaml index f3cbb4604d..13e2e0a2c2 100644 --- a/unittest/force-styles/tests/kspace-msm.yaml +++ b/unittest/force-styles/tests/kspace-msm.yaml @@ -11,7 +11,7 @@ post_commands: ! | pair_modify compute no kspace_style msm 1.0e-4 kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/kspace-msm_cg.yaml b/unittest/force-styles/tests/kspace-msm_cg.yaml index 25892a4528..90b5999796 100644 --- a/unittest/force-styles/tests/kspace-msm_cg.yaml +++ b/unittest/force-styles/tests/kspace-msm_cg.yaml @@ -15,7 +15,7 @@ post_commands: ! | pair_modify compute no kspace_style msm/cg 1.0e-4 kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/kspace-msm_nopbc.yaml b/unittest/force-styles/tests/kspace-msm_nopbc.yaml index ce5e3cd0e3..9c071e90eb 100644 --- a/unittest/force-styles/tests/kspace-msm_nopbc.yaml +++ b/unittest/force-styles/tests/kspace-msm_nopbc.yaml @@ -12,7 +12,7 @@ post_commands: ! | pair_modify compute no kspace_style msm 1.0e-4 kspace_modify cutoff/adjust yes - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: coul/msm 10.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/manybody-pair-meam_c.yaml b/unittest/force-styles/tests/manybody-pair-meam.yaml similarity index 99% rename from unittest/force-styles/tests/manybody-pair-meam_c.yaml rename to unittest/force-styles/tests/manybody-pair-meam.yaml index e2867c4dd6..4237f5ffc2 100644 --- a/unittest/force-styles/tests/manybody-pair-meam_c.yaml +++ b/unittest/force-styles/tests/manybody-pair-meam.yaml @@ -3,13 +3,13 @@ lammps_version: 10 Feb 2021 date_generated: Fri Feb 26 23:09:15 2021 epsilon: 7.5e-12 prerequisites: ! | - pair meam/c + pair meam pre_commands: ! | variable newton_pair delete if "$(is_active(package,gpu)) > 0.0" then "variable newton_pair index off" else "variable newton_pair index on" post_commands: ! "" input_file: in.manybody -pair_style: meam/c +pair_style: meam pair_coeff: ! | * * library.meam Si C SiC.meam C C C C Si Si Si Si extract: ! | diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml index c4c907a1e0..f664a72a21 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm.yaml @@ -12,7 +12,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: born/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml index 75f0f76a44..f25e04b008 100644 --- a/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-born_coul_msm_table.yaml @@ -12,7 +12,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: born/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml index 2a41370f62..db5131e253 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml @@ -13,7 +13,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: buck/coul/msm 8.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml index 8538187649..340ae4c9e6 100644 --- a/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: buck/coul/msm 8.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-coul_msm.yaml b/unittest/force-styles/tests/mol-pair-coul_msm.yaml index 83b8550101..fa374d7b13 100644 --- a/unittest/force-styles/tests/mol-pair-coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_msm.yaml @@ -13,7 +13,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml index e07fd6e639..48fe4a1908 100644 --- a/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_msm_table.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml index b3884c3b11..04670511d0 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm.yaml @@ -13,7 +13,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/charmm/coul/msm 10.0 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml index 0755c7e3a6..5f9053fbb8 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_msm_table.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/charmm/coul/msm 10.0 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml index 2bb831e66b..a02cad3f1b 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/cut/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml index ccb0da249f..3c9bf6e724 100644 --- a/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_cut_coul_msm_table.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/cut/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml index 4df3f42891..0a5043adca 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml @@ -13,7 +13,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/sdk/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml index 4f95ee2e34..eff2216f29 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml @@ -14,7 +14,7 @@ post_commands: ! | kspace_style msm 1.0e-4 kspace_modify compute no kspace_modify cutoff/adjust no - kspace_modify pressure/scalar no # required for USER-OMP with msm + kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol pair_style: lj/sdk/coul/msm 12.0 pair_coeff: ! | diff --git a/unittest/python/python-capabilities.py b/unittest/python/python-capabilities.py index 8a3fbbd665..8f72c39670 100644 --- a/unittest/python/python-capabilities.py +++ b/unittest/python/python-capabilities.py @@ -133,23 +133,23 @@ class PythonCapabilities(unittest.TestCase): def test_accelerator_config(self): settings = self.lmp.accelerator_config - if self.cmake_cache['PKG_USER-OMP']: + if self.cmake_cache['PKG_OPENMP']: if self.cmake_cache['BUILD_OMP']: - self.assertIn('openmp',settings['USER-OMP']['api']) + self.assertIn('openmp',settings['OPENMP']['api']) else: - self.assertIn('serial',settings['USER-OMP']['api']) - self.assertIn('double',settings['USER-OMP']['precision']) + self.assertIn('serial',settings['OPENMP']['api']) + self.assertIn('double',settings['OPENMP']['precision']) - if self.cmake_cache['PKG_USER-INTEL']: + if self.cmake_cache['PKG_INTEL']: if 'LMP_INTEL_OFFLOAD' in self.cmake_cache.keys(): - self.assertIn('phi',settings['USER-INTEL']['api']) + self.assertIn('phi',settings['INTEL']['api']) elif self.cmake_cache['BUILD_OMP']: - self.assertIn('openmp',settings['USER-INTEL']['api']) + self.assertIn('openmp',settings['INTEL']['api']) else: - self.assertIn('serial',settings['USER-INTEL']['api']) - self.assertIn('double',settings['USER-INTEL']['precision']) - self.assertIn('mixed',settings['USER-INTEL']['precision']) - self.assertIn('single',settings['USER-INTEL']['precision']) + self.assertIn('serial',settings['INTEL']['api']) + self.assertIn('double',settings['INTEL']['precision']) + self.assertIn('mixed',settings['INTEL']['precision']) + self.assertIn('single',settings['INTEL']['precision']) if self.cmake_cache['PKG_GPU']: if self.cmake_cache['GPU_API'].lower() == 'opencl':