From 878795e64aba8ce4d1ab4d138087ec757a1039da Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 29 Jun 2021 19:49:18 -0400 Subject: [PATCH] bulk rename of remaining USER- packages --- .github/CODEOWNERS | 42 +- .github/CONTRIBUTING.md | 6 +- cmake/CMakeLists.txt | 46 +-- .../{USER-COLVARS.cmake => COLVARS.cmake} | 0 .../Packages/{USER-H5MD.cmake => H5MD.cmake} | 0 .../{USER-INTEL.cmake => INTEL.cmake} | 46 +-- .../Packages/{USER-MDI.cmake => MDI.cmake} | 0 .../{USER-MOLFILE.cmake => MOLFILE.cmake} | 0 .../{USER-NETCDF.cmake => NETCDF.cmake} | 2 +- .../{USER-PLUMED.cmake => PLUMED.cmake} | 0 .../Packages/{USER-QMMM.cmake => QMMM.cmake} | 0 .../{USER-SCAFACOS.cmake => SCAFACOS.cmake} | 0 .../Packages/{USER-SDPD.cmake => SDPD.cmake} | 0 .../Packages/{USER-VTK.cmake => VTK.cmake} | 0 cmake/presets/all_off.cmake | 14 +- cmake/presets/all_on.cmake | 14 +- cmake/presets/download.cmake | 2 +- cmake/presets/mingw-cross.cmake | 14 +- cmake/presets/most.cmake | 8 +- 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rename src/{USER-MOLFILE => MOLFILE}/molfile_interface.cpp (100%) rename src/{USER-MOLFILE => MOLFILE}/molfile_interface.h (100%) rename src/{USER-MOLFILE => MOLFILE}/reader_molfile.cpp (100%) rename src/{USER-MOLFILE => MOLFILE}/reader_molfile.h (100%) rename src/{USER-NETCDF => NETCDF}/Install.sh (100%) rename src/{USER-NETCDF => NETCDF}/README (99%) rename src/{USER-NETCDF => NETCDF}/dump_netcdf.cpp (100%) rename src/{USER-NETCDF => NETCDF}/dump_netcdf.h (100%) rename src/{USER-NETCDF => NETCDF}/dump_netcdf_mpiio.cpp (100%) rename src/{USER-NETCDF => NETCDF}/dump_netcdf_mpiio.h (100%) rename src/{USER-PHONON => PHONON}/Install.sh (88%) rename src/{USER-PHONON => PHONON}/README (100%) rename src/{USER-PHONON => PHONON}/dynamical_matrix.cpp (100%) rename src/{USER-PHONON => PHONON}/dynamical_matrix.h (100%) rename src/{USER-PHONON => PHONON}/fix_phonon.cpp (100%) rename src/{USER-PHONON => PHONON}/fix_phonon.h (100%) rename src/{USER-PHONON => PHONON}/third_order.cpp (100%) rename src/{USER-PHONON => PHONON}/third_order.h (100%) rename src/{USER-PLUMED => PLUMED}/Install.sh (100%) rename src/{USER-PLUMED => PLUMED}/README (97%) rename src/{USER-PLUMED => PLUMED}/fix_plumed.cpp (100%) rename src/{USER-PLUMED => PLUMED}/fix_plumed.h (100%) rename src/{USER-PTM => PTM}/LICENSE (100%) rename src/{USER-PTM => PTM}/README (100%) rename src/{USER-PTM => PTM}/compute_ptm_atom.cpp (99%) rename src/{USER-PTM => PTM}/compute_ptm_atom.h (100%) rename src/{USER-PTM => PTM}/ptm_alloy_types.cpp (100%) rename src/{USER-PTM => PTM}/ptm_alloy_types.h (100%) rename src/{USER-PTM => PTM}/ptm_alt_templates.h (100%) rename src/{USER-PTM => PTM}/ptm_canonical_coloured.cpp (100%) rename src/{USER-PTM => PTM}/ptm_canonical_coloured.h (100%) rename src/{USER-PTM => PTM}/ptm_constants.cpp (100%) rename src/{USER-PTM => PTM}/ptm_constants.h (100%) rename src/{USER-PTM => PTM}/ptm_convex_hull_incremental.cpp (100%) rename src/{USER-PTM => PTM}/ptm_convex_hull_incremental.h (100%) rename src/{USER-PTM => PTM}/ptm_deformation_gradient.cpp (100%) rename src/{USER-PTM => PTM}/ptm_deformation_gradient.h (100%) rename src/{USER-PTM => PTM}/ptm_functions.h (100%) rename src/{USER-PTM => PTM}/ptm_fundamental_mappings.h (100%) rename src/{USER-PTM => PTM}/ptm_graph_data.cpp (100%) rename src/{USER-PTM => PTM}/ptm_graph_data.h (100%) rename src/{USER-PTM => PTM}/ptm_graph_tools.cpp (100%) rename src/{USER-PTM => PTM}/ptm_graph_tools.h (100%) rename src/{USER-PTM => PTM}/ptm_index.cpp (100%) rename src/{USER-PTM => PTM}/ptm_initialize_data.cpp (100%) rename src/{USER-PTM => PTM}/ptm_initialize_data.h (100%) rename src/{USER-PTM => PTM}/ptm_neighbour_ordering.cpp (100%) rename src/{USER-PTM => PTM}/ptm_neighbour_ordering.h (100%) rename src/{USER-PTM => PTM}/ptm_normalize_vertices.cpp (100%) rename src/{USER-PTM => PTM}/ptm_normalize_vertices.h (100%) rename src/{USER-PTM => PTM}/ptm_polar.cpp (100%) rename src/{USER-PTM => PTM}/ptm_polar.h (100%) rename src/{USER-PTM => PTM}/ptm_quat.cpp (100%) rename src/{USER-PTM => PTM}/ptm_quat.h (100%) rename src/{USER-PTM => PTM}/ptm_structure_matcher.cpp (100%) rename src/{USER-PTM => PTM}/ptm_structure_matcher.h (100%) rename src/{USER-PTM => PTM}/ptm_voronoi_cell.cpp (100%) rename src/{USER-PTM => PTM}/ptm_voronoi_cell.h (100%) rename src/{USER-PTM => PTM}/ptm_voronoi_config.h (100%) rename src/{USER-QMMM => QMMM}/Install.sh (100%) rename src/{USER-QMMM => QMMM}/README (100%) rename src/{USER-QMMM => QMMM}/fix_qmmm.cpp (100%) rename src/{USER-QMMM => QMMM}/fix_qmmm.h (100%) rename src/{USER-QTB => QTB}/README (100%) rename src/{USER-QTB => QTB}/fix_qbmsst.cpp (100%) rename src/{USER-QTB => QTB}/fix_qbmsst.h (100%) rename src/{USER-QTB => QTB}/fix_qtb.cpp (100%) rename src/{USER-QTB => QTB}/fix_qtb.h (100%) rename src/{USER-REACTION => REACTION}/README (100%) rename src/{USER-REACTION => REACTION}/fix_bond_react.cpp (100%) rename src/{USER-REACTION => REACTION}/fix_bond_react.h (100%) rename src/{USER-REACTION => REACTION}/superpose3d.h (100%) rename src/{USER-SCAFACOS => SCAFACOS}/Install.sh (100%) rename src/{USER-SCAFACOS => SCAFACOS}/README (100%) rename src/{USER-SCAFACOS => SCAFACOS}/scafacos.cpp (100%) rename src/{USER-SCAFACOS => SCAFACOS}/scafacos.h (100%) rename src/{USER-SMTBQ => SMTBQ}/README (100%) rename src/{USER-SMTBQ => SMTBQ}/pair_smtbq.cpp (100%) rename src/{USER-SMTBQ => SMTBQ}/pair_smtbq.h (100%) rename src/{USER-SPH => SPH}/README (100%) rename src/{USER-SPH => SPH}/atom_vec_sph.cpp (100%) rename src/{USER-SPH => SPH}/atom_vec_sph.h (100%) rename src/{USER-SPH => SPH}/compute_sph_e_atom.cpp (100%) rename src/{USER-SPH => SPH}/compute_sph_e_atom.h (100%) rename src/{USER-SPH => SPH}/compute_sph_rho_atom.cpp (100%) rename src/{USER-SPH => SPH}/compute_sph_rho_atom.h (100%) rename src/{USER-SPH => SPH}/compute_sph_t_atom.cpp (100%) rename src/{USER-SPH => SPH}/compute_sph_t_atom.h (100%) rename src/{USER-SPH => SPH}/fix_sph.cpp (100%) rename src/{USER-SPH => SPH}/fix_sph.h (100%) rename src/{USER-SPH => SPH}/fix_sph_stationary.cpp (100%) rename src/{USER-SPH => SPH}/fix_sph_stationary.h (100%) rename src/{USER-SPH => SPH}/pair_sph_heatconduction.cpp (100%) rename src/{USER-SPH => SPH}/pair_sph_heatconduction.h (100%) rename src/{USER-SPH => SPH}/pair_sph_idealgas.cpp (100%) rename src/{USER-SPH => SPH}/pair_sph_idealgas.h (100%) rename src/{USER-SPH => SPH}/pair_sph_lj.cpp (100%) rename src/{USER-SPH => SPH}/pair_sph_lj.h (100%) rename src/{USER-SPH => SPH}/pair_sph_rhosum.cpp (100%) rename src/{USER-SPH => SPH}/pair_sph_rhosum.h (100%) rename src/{USER-SPH => SPH}/pair_sph_taitwater.cpp (100%) rename src/{USER-SPH => SPH}/pair_sph_taitwater.h (100%) rename src/{USER-SPH => SPH}/pair_sph_taitwater_morris.cpp (100%) rename src/{USER-SPH => SPH}/pair_sph_taitwater_morris.h (100%) rename src/{USER-TALLY => TALLY}/README (100%) rename src/{USER-TALLY => TALLY}/compute_force_tally.cpp (100%) rename src/{USER-TALLY => TALLY}/compute_force_tally.h (100%) rename src/{USER-TALLY => TALLY}/compute_heat_flux_tally.cpp (100%) rename src/{USER-TALLY => TALLY}/compute_heat_flux_tally.h (100%) rename src/{USER-TALLY => TALLY}/compute_pe_mol_tally.cpp (100%) rename src/{USER-TALLY => TALLY}/compute_pe_mol_tally.h (100%) rename src/{USER-TALLY => TALLY}/compute_pe_tally.cpp (100%) rename src/{USER-TALLY => TALLY}/compute_pe_tally.h (100%) rename src/{USER-TALLY => TALLY}/compute_stress_tally.cpp (100%) rename src/{USER-TALLY => TALLY}/compute_stress_tally.h (100%) rename src/{USER-UEF => UEF}/README (95%) rename src/{USER-UEF => UEF}/compute_pressure_uef.cpp (100%) rename src/{USER-UEF => UEF}/compute_pressure_uef.h (100%) rename src/{USER-UEF => UEF}/compute_temp_uef.cpp (100%) rename src/{USER-UEF => UEF}/compute_temp_uef.h (100%) rename src/{USER-UEF => UEF}/dump_cfg_uef.cpp (100%) rename src/{USER-UEF => UEF}/dump_cfg_uef.h (100%) rename src/{USER-UEF => UEF}/fix_nh_uef.cpp (99%) rename src/{USER-UEF => UEF}/fix_nh_uef.h (100%) rename src/{USER-UEF => UEF}/fix_npt_uef.cpp (100%) rename src/{USER-UEF => UEF}/fix_npt_uef.h (100%) rename src/{USER-UEF => UEF}/fix_nvt_uef.cpp (100%) rename src/{USER-UEF => UEF}/fix_nvt_uef.h (100%) rename src/{USER-UEF => UEF}/uef_utils.cpp (100%) rename src/{USER-UEF => UEF}/uef_utils.h (100%) rename src/{USER-VTK => VTK}/Install.sh (100%) rename src/{USER-VTK => VTK}/README (100%) rename src/{USER-VTK => VTK}/dump_vtk.cpp (100%) rename src/{USER-VTK => VTK}/dump_vtk.h (100%) rename src/{USER-YAFF => YAFF}/README (100%) rename src/{USER-YAFF => YAFF}/angle_cross.cpp (100%) rename src/{USER-YAFF => YAFF}/angle_cross.h (100%) rename src/{USER-YAFF => YAFF}/angle_mm3.cpp (100%) rename src/{USER-YAFF => YAFF}/angle_mm3.h (100%) rename src/{USER-YAFF => YAFF}/bond_mm3.cpp (100%) rename src/{USER-YAFF => YAFF}/bond_mm3.h (100%) rename src/{USER-YAFF => YAFF}/improper_distharm.cpp (100%) rename src/{USER-YAFF => YAFF}/improper_distharm.h (100%) rename src/{USER-YAFF => YAFF}/improper_sqdistharm.cpp (100%) rename src/{USER-YAFF => YAFF}/improper_sqdistharm.h (100%) rename src/{USER-YAFF => YAFF}/pair_lj_switch3_coulgauss_long.cpp (100%) rename src/{USER-YAFF => YAFF}/pair_lj_switch3_coulgauss_long.h (100%) rename src/{USER-YAFF => YAFF}/pair_mm3_switch3_coulgauss_long.cpp (100%) rename src/{USER-YAFF => YAFF}/pair_mm3_switch3_coulgauss_long.h (100%) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index d1d87f2576..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/BROWNIAN/* @samueljmcameron src/CG-DNA/* @ohenrich src/CG-SDK/* @akohlmey -src/USER-COLVARS/* @giacomofiorin -src/USER-DIELECTRIC/* @ndtrung81 -src/USER-FEP/* @agiliopadua +src/COLVARS/* @giacomofiorin +src/DIELECTRIC/* @ndtrung81 +src/FEP/* @agiliopadua src/ML-HDNNP/* @singraber -src/USER-INTEL/* @wmbrownintel -src/USER-MANIFOLD/* @Pakketeretet2 -src/USER-MDI/* @taylor-a-barnes +src/INTEL/* @wmbrownintel +src/MANIFOLD/* @Pakketeretet2 +src/MDI/* @taylor-a-barnes src/MEAM/* @martok -src/USER-MESONT/* @iafoss -src/USER-MOFFF/* @hheenen -src/USER-MOLFILE/* @akohlmey -src/USER-NETCDF/* @pastewka +src/MESONT/* @iafoss +src/MOFFF/* @hheenen +src/MOLFILE/* @akohlmey +src/NETCDF/* @pastewka src/ML-PACE/* @yury-lysogorskiy -src/USER-PLUMED/* @gtribello -src/USER-PHONON/* @lingtikong -src/USER-PTM/* @pmla +src/PLUMED/* @gtribello +src/PHONON/* @lingtikong +src/PTM/* @pmla src/OPENMP/* @akohlmey -src/USER-QMMM/* @akohlmey +src/QMMM/* @akohlmey src/REAXFF/* @hasanmetin -src/USER-REACTION/* @jrgissing -src/USER-SCAFACOS/* @rhalver -src/USER-TALLY/* @akohlmey -src/USER-UEF/* @danicholson -src/USER-VTK/* @rbberger +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 fe95d9ba73..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`. +* 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/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 580625d187..5e80a16d6b 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -141,14 +141,14 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE PERI POEMS PLUGIN QEQ REPLICA RIGID SHOCK SPIN ML-SNAP SRD KIM PYTHON MSCG MPIIO VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BOCS CG-DNA DPD-MESO CG-SDK - USER-COLVARS USER-DIELECTRIC USER-DIFFRACTION DPD-REACT USER-DRUDE USER-EFF USER-FEP - USER-H5MD ML-HDNNP LATBOLTZ USER-MANIFOLD USER-MDI MEAM USER-MESONT USER-MGPT - USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB - ML-RANN USER-REACTION REAXFF USER-SCAFACOS DPD-SMOOTH MACHDYN USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK ML-QUIP USER-QMMM USER-YAFF ML-PACE USER-BROWNIAN) + ADIOS ATC AWPMD BOCS CG-DNA DPD-MESO CG-SDK + COLVARS DIELECTRIC DIFFRACTION DPD-REACT DRUDE EFF FEP + H5MD ML-HDNNP LATBOLTZ MANIFOLD MDI MEAM MESONT MGPT + USER-MISC MOFFF MOLFILE NETCDF PHONON PLUMED PTM QTB + ML-RANN REACTION REAXFF SCAFACOS DPD-SMOOTH MACHDYN SMTBQ SPH + TALLY UEF VTK ML-QUIP QMMM YAFF ML-PACE BROWNIAN) -set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL OPENMP) +set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP) foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) @@ -159,7 +159,7 @@ endforeach() ###################################################### target_include_directories(lammps PUBLIC $) -if(PKG_USER-ADIOS) +if(PKG_ADIOS) # The search for ADIOS2 must come before MPI because # it includes its own MPI search with the latest FindMPI.cmake # script that defines the MPI::MPI_C target @@ -231,11 +231,11 @@ endif() # in an error instead of skipping over files pkg_depends(ML-IAP ML-SNAP) pkg_depends(MPIIO MPI) -pkg_depends(USER-ATC MANYBODY) +pkg_depends(ATC MANYBODY) pkg_depends(LATBOLTZ MPI) -pkg_depends(USER-PHONON KSPACE) -pkg_depends(USER-SCAFACOS MPI) -pkg_depends(USER-DIELECTRIC KSPACE) +pkg_depends(PHONON KSPACE) +pkg_depends(SCAFACOS MPI) +pkg_depends(DIELECTRIC KSPACE) # detect if we may enable OpenMP support by default set(BUILD_OMP_DEFAULT OFF) @@ -271,7 +271,7 @@ if(BUILD_OMP) target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX) endif() -if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_ML-QUIP OR PKG_LATTE) +if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE) enable_language(C) find_package(LAPACK) find_package(BLAS) @@ -350,8 +350,8 @@ else() set(CUDA_REQUEST_PIC) endif() -foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI USER-COLVARS ML-HDNNP USER-MDI USER-MOLFILE USER-NETCDF - USER-PLUMED USER-QMMM ML-QUIP USER-SCAFACOS MACHDYN USER-VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE) +foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF + PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() @@ -444,9 +444,9 @@ endforeach() ############################################## # add lib sources of (simple) enabled packages ############################################ -foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT) +foreach(SIMPLE_LIB POEMS ATC AWPMD H5MD MESONT) if(PKG_${SIMPLE_LIB}) - string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") + string(REGEX REPLACE "^" "" PKG_LIB "${SIMPLE_LIB}") string(TOLOWER "${PKG_LIB}" PKG_LIB) if(PKG_LIB STREQUAL "mesont") enable_language(Fortran) @@ -470,13 +470,13 @@ 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 ${LAPACK_LIBRARIES}) if(BUILD_MPI) @@ -488,15 +488,15 @@ if(PKG_USER-ATC) target_compile_definitions(atc PRIVATE -DLAMMPS_${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 OPENMP DPD-SMOOTH 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/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-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/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-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/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-SDPD.cmake b/cmake/Modules/Packages/SDPD.cmake similarity index 100% rename from cmake/Modules/Packages/USER-SDPD.cmake rename to cmake/Modules/Packages/SDPD.cmake 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 0f30bb56ad..86f12c98f1 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -5,13 +5,13 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS CG-DNA CG-SDK - USER-COLVARS USER-DIFFRACTION DPD-REACT USER-DRUDE USER-EFF USER-FEP USER-H5MD - ML-HDNNP USER-INTEL LATBOLTZ USER-MANIFOLD USER-MDI MEAM DPD-MESO - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF OPENMP - ML-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB ML-QUIP ML-RANN - USER-REACTION REAXFF USER-SCAFACOS DPD-SMOOTH MACHDYN USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC) + ADIOS ATC AWPMD BROWNIAN BOCS CG-DNA CG-SDK + COLVARS DIFFRACTION DPD-REACT DRUDE EFF FEP H5MD + ML-HDNNP INTEL LATBOLTZ MANIFOLD MDI MEAM DPD-MESO + MESONT MGPT USER-MISC MOFFF MOLFILE NETCDF OPENMP + ML-PACE PHONON PLUMED PTM QMMM QTB ML-QUIP ML-RANN + REACTION REAXFF SCAFACOS DPD-SMOOTH MACHDYN SMTBQ SPH + TALLY UEF VTK YAFF DIELECTRIC) 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 685303c21e..909af2edff 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -7,13 +7,13 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS CG-DNA CG-SDK - USER-COLVARS USER-DIFFRACTION DPD-REACT USER-DRUDE USER-EFF USER-FEP USER-H5MD - ML-HDNNP USER-INTEL LATBOLTZ USER-MANIFOLD USER-MDI MEAM DPD-MESO - USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF OPENMP - ML-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB ML-QUIP ML-RANN - USER-REACTION REAXFF USER-SCAFACOS DPD-SMOOTH MACHDYN USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-YAFF USER-DIELECTRIC) + ADIOS ATC AWPMD BROWNIAN BOCS CG-DNA CG-SDK + COLVARS DIFFRACTION DPD-REACT DRUDE EFF FEP H5MD + ML-HDNNP INTEL LATBOLTZ MANIFOLD MDI MEAM DPD-MESO + MESONT MGPT USER-MISC MOFFF MOLFILE NETCDF OPENMP + ML-PACE PHONON PLUMED PTM QMMM QTB ML-QUIP ML-RANN + REACTION REAXFF SCAFACOS DPD-SMOOTH MACHDYN SMTBQ SPH + TALLY UEF VTK YAFF DIELECTRIC) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/download.cmake b/cmake/presets/download.cmake index 8610a5078b..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 MACHDYN USER-MESONT USER-MDI ML-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 4f87048797..ba6089935f 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -1,13 +1,13 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU GRANULAR KSPACE LATTE MANYBODY MC MISC ML-IAP MOLECULE OPT PERI POEMS QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI - USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN CG-DNA CG-SDK - USER-COLVARS USER-DIFFRACTION DPD-REACT USER-DRUDE USER-EFF USER-FEP - ML-HDNNP USER-INTEL USER-MANIFOLD USER-MDI MEAM DPD-MESO - USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE OPENMP - USER-PHONON USER-PTM USER-QTB USER-REACTION REAXFF - DPD-SMOOTH MACHDYN USER-SMTBQ USER-SPH USER-TALLY USER-UEF - USER-YAFF USER-DIELECTRIC) + ATC AWPMD BOCS BROWNIAN CG-DNA CG-SDK + COLVARS DIFFRACTION DPD-REACT DRUDE EFF FEP + ML-HDNNP INTEL MANIFOLD MDI MEAM DPD-MESO + MESONT USER-MISC MGPT MOFFF MOLFILE OPENMP + PHONON PTM QTB REACTION REAXFF + DPD-SMOOTH MACHDYN SMTBQ SPH TALLY UEF + YAFF DIELECTRIC) foreach(PKG ${WIN_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 2abb87bb51..9c66607ddf 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -5,10 +5,10 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MISC ML-IAP MOLECULE OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI - USER-BROWNIAN USER-BOCS CG-DNA CG-SDK USER-COLVARS - USER-DIFFRACTION DPD-REACT USER-DRUDE USER-EFF USER-FEP MEAM - DPD-MESO USER-MISC USER-MOFFF OPENMP USER-PHONON USER-REACTION - REAXFF DPD-SMOOTH USER-SPH MACHDYN USER-UEF USER-YAFF USER-DIELECTRIC) + BROWNIAN BOCS CG-DNA CG-SDK COLVARS + DIFFRACTION DPD-REACT DRUDE EFF FEP MEAM + DPD-MESO USER-MISC MOFFF OPENMP PHONON REACTION + REAXFF DPD-SMOOTH SPH MACHDYN UEF YAFF DIELECTRIC) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index a500270011..d4b3497855 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -3,9 +3,9 @@ set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG PYTHON VORONOI - USER-ADIOS USER-ATC USER-AWPMD USER-H5MD ML-HDNNP LATBOLTZ USER-MOLFILE - USER-MESONT USER-MDI USER-NETCDF ML-PACE USER-PLUMED USER-QMMM ML-QUIP - USER-SCAFACOS MACHDYN USER-VTK) + ADIOS ATC AWPMD H5MD ML-HDNNP LATBOLTZ MOLFILE + MESONT MDI NETCDF ML-PACE PLUMED QMMM ML-QUIP + SCAFACOS MACHDYN 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 67857da68e..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 REAXFF, 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 616f1dac8b..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 OPENMP 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 207d767649..9ef209b3b3 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -121,18 +121,18 @@ documentation to find out how to build and link with it. The majority of OpenMP (threading) support in LAMMPS is provided by the ``OPENMP`` package; see the :doc:`Speed_omp` -page for details. The ``USER-INTEL`` package also includes OpenMP +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 ``USER-INTEL`` does not exist) +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``, -``ML-SNAP``, ``USER-DIFFRACTION``, and ``DPD-REACT`` 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 @@ -326,8 +326,8 @@ LAMMPS. Makefile.opt # OPT package Makefile.omp # OPENMP package - Makefile.intel_cpu # USER-INTEL package for CPUs - Makefile.intel_coprocessor # USER-INTEL package for KNLs + 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_development.rst b/doc/src/Build_development.rst index a306984a3d..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, OPENMP 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. diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index bf624adcb3..c20c3788df 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -43,25 +43,25 @@ This is the list of packages that may require additional steps. * :ref:`POEMS ` * :ref:`PYTHON ` * :ref:`VORONOI ` - * :ref:`USER-ADIOS ` - * :ref:`USER-ATC ` - * :ref:`USER-AWPMD ` - * :ref:`USER-COLVARS ` - * :ref:`USER-H5MD ` + * :ref:`ADIOS ` + * :ref:`ATC ` + * :ref:`AWPMD ` + * :ref:`COLVARS ` + * :ref:`H5MD ` * :ref:`ML-HDNNP ` - * :ref:`USER-INTEL ` - * :ref:`USER-MDI ` - * :ref:`USER-MESONT ` - * :ref:`USER-MOLFILE ` - * :ref:`USER-NETCDF ` + * :ref:`INTEL ` + * :ref:`MDI ` + * :ref:`MESONT ` + * :ref:`MOLFILE ` + * :ref:`NETCDF ` * :ref:`ML-PACE ` - * :ref:`USER-PLUMED ` + * :ref:`PLUMED ` * :ref:`OPENMP ` - * :ref:`USER-QMMM ` + * :ref:`QMMM ` * :ref:`ML-QUIP ` - * :ref:`USER-SCAFACOS ` + * :ref:`SCAFACOS ` * :ref:`MACHDYN ` - * :ref:`USER-VTK ` + * :ref:`VTK ` ---------- @@ -1058,10 +1058,10 @@ binary package provided by your operating system. .. _user-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 @@ -1077,38 +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: -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 @@ -1153,14 +1153,14 @@ The USER-ATC package requires the MANYBODY package also be installed. .. _user-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 @@ -1204,7 +1204,7 @@ USER-AWPMD package .. _user-colvars: -USER-COLVARS package +COLVARS package --------------------------------------- This package includes the `Colvars library @@ -1218,7 +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 @@ -1303,7 +1303,7 @@ 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. @@ -1347,7 +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 @@ -1380,7 +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 @@ -1405,12 +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 @@ -1425,7 +1425,7 @@ 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. @@ -1433,7 +1433,7 @@ LAMMPS build. .. _user-h5md: -USER-H5MD package +H5MD package --------------------------------- To build with this package you must have the HDF5 software package @@ -1444,7 +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 @@ -1530,15 +1530,15 @@ 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 OPENMP package `, as it can be -used in tandem with the USER-INTEL package to good effect, as explained +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 @@ -1547,7 +1547,7 @@ 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:: @@ -1564,7 +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: @@ -1602,7 +1602,7 @@ TBB and MKL. .. _user-mdi: -USER-MDI package +MDI package ----------------------------- .. tabs:: @@ -1631,7 +1631,7 @@ USER-MDI package .. _user-mesont: -USER-MESONT package +MESONT package ------------------------- This package includes a library written in Fortran 90 in the @@ -1644,7 +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 @@ -1673,7 +1673,7 @@ they will be downloaded the first time this package is installed. .. _user-molfile: -USER-MOLFILE package +MOLFILE package --------------------------------------- .. tabs:: @@ -1683,9 +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 @@ -1711,7 +1711,7 @@ USER-MOLFILE package .. _user-netcdf: -USER-NETCDF package +NETCDF package ------------------------------------- To build with this package you must have the NetCDF library installed @@ -1721,7 +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 @@ -1775,10 +1775,10 @@ OPENMP package .. _user-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 @@ -1801,11 +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/minimal.cmake -D PKG_QMMM=yes \ -D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake After completing the LAMMPS build and also configuring and @@ -1885,7 +1885,7 @@ to be downloaded and configured. See step 1 and step 1.1 in the .. _user-scafacos: -USER-SCAFACOS package +SCAFACOS package ----------------------------------------- To build with this package, you must download and build the @@ -1976,7 +1976,7 @@ Eigen3 is a template library, so you do not need to build it. .. _user-vtk: -USER-VTK package +VTK package ------------------------------- To build with this package you must have the VTK library installed on @@ -1986,7 +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 a28d074e0b..c7b063e8a9 100644 --- a/doc/src/Build_make.rst +++ b/doc/src/Build_make.rst @@ -117,8 +117,8 @@ 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 OPENMP package optimized for OpenMP make kokkos_omp # build with the KOKKOS package for OpenMP diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index 06f4cf0a42..faea51901e 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -33,13 +33,13 @@ 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:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`ADIOS ` | +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`ML-HDNNP ` | :ref:`USER-INTEL ` | +| :ref:`ATC ` | :ref:`AWPMD ` | :ref:`COLVARS ` | :ref:`H5MD ` | :ref:`ML-HDNNP ` | :ref:`INTEL ` | +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`USER-MOLFILE ` | :ref:`USER-NETCDF ` | :ref:`ML-PACE ` | :ref:`USER-PLUMED ` | :ref:`OPENMP ` | :ref:`USER-QMMM ` | +| :ref:`MOLFILE ` | :ref:`NETCDF ` | :ref:`ML-PACE ` | :ref:`PLUMED ` | :ref:`OPENMP ` | :ref:`QMMM ` | +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ -| :ref:`ML-QUIP ` | :ref:`USER-SCAFACOS ` | :ref:`MACHDYN ` | :ref:`USER-VTK ` | | | +| :ref:`ML-QUIP ` | :ref:`SCAFACOS ` | :ref:`MACHDYN ` | :ref:`VTK ` | | | +--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+ The mechanism for including packages is simple but different for CMake @@ -58,7 +58,7 @@ 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 @@ -89,7 +89,7 @@ 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. @@ -225,7 +225,7 @@ 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. diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index 227291e9c7..074a6349e6 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -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 b6817f720e..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 = OPENMP, 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 = OPENMP, 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 = OPENMP, 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 = OPENMP, 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 eb34d71679..1fa84fe370 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -16,7 +16,7 @@ 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 = +additional letters in parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index e3d79489e3..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 = OPENMP, 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 0bb99cdf28..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 = OPENMP, 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 a621f1a903..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 = OPENMP, t = +parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT. .. table_from_list:: diff --git a/doc/src/Developer_unittest.rst b/doc/src/Developer_unittest.rst index 74940c0f9b..820e911a8f 100644 --- a/doc/src/Developer_unittest.rst +++ b/doc/src/Developer_unittest.rst @@ -405,7 +405,7 @@ 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, OPENMP, -USER-INTEL) and for the latter two with 4 OpenMP threads enabled. For +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_messages.rst b/doc/src/Errors_messages.rst index cb1386f2d8..fba3b1bb39 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -6344,8 +6344,8 @@ 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* @@ -8064,7 +8064,7 @@ 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* diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index 785475d12f..46d400c9e8 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -2,10 +2,10 @@ 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. @@ -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/Install_windows.rst b/doc/src/Install_windows.rst index c3f256cfad..1e5c9684ac 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -18,7 +18,7 @@ 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, ML-QUIP, and USER-VTK. +ADIOS, H5MD, NETCDF, QMMM, ML-QUIP, and VTK. The serial version also does not include the MPIIO and LATBOLTZ packages. The GPU package is compiled for OpenCL with mixed precision kernels. diff --git a/doc/src/Intro_authors.rst b/doc/src/Intro_authors.rst index 355dd02b9b..720221d4b7 100644 --- a/doc/src/Intro_authors.rst +++ b/doc/src/Intro_authors.rst @@ -30,18 +30,18 @@ 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), REAXFF package for C version of ReaxFF -* Mike Brown (Intel), GPU and USER-INTEL packages +* Mike Brown (Intel), GPU and INTEL packages * Colin Denniston (U Western Ontario), LATBOLTZ package -* Georg Ganzenmuller (EMI), MACHDYN 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 +* 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 38c5df5246..b347b95201 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -169,7 +169,7 @@ packages in the src directory for examples. If you are uncertain, please ask. * 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 + 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 @@ -177,7 +177,7 @@ packages in the src directory for examples. If you are uncertain, please ask. 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. + 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 @@ -212,7 +212,7 @@ 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 + USER-MISC or 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 @@ -234,7 +234,7 @@ 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/Packages_details.rst b/doc/src/Packages_details.rst index fae4ede453..ea4a6a172b 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -65,54 +65,54 @@ page gives those details. .. table_from_list:: :columns: 6 - * :ref:`USER-ADIOS ` - * :ref:`USER-ATC ` - * :ref:`USER-AWPMD ` - * :ref:`USER-BOCS ` - * :ref:`USER-BROWNIAN ` + * :ref:`ADIOS ` + * :ref:`ATC ` + * :ref:`AWPMD ` + * :ref:`BOCS ` + * :ref:`BROWNIAN ` * :ref:`CG-DNA ` * :ref:`CG-SDK ` - * :ref:`USER-COLVARS ` - * :ref:`USER-DIELECTRIC ` - * :ref:`USER-DIFFRACTION ` + * :ref:`COLVARS ` + * :ref:`DIELECTRIC ` + * :ref:`DIFFRACTION ` * :ref:`DPD-REACT ` - * :ref:`USER-DRUDE ` - * :ref:`USER-EFF ` - * :ref:`USER-FEP ` - * :ref:`USER-H5MD ` + * :ref:`DRUDE ` + * :ref:`EFF ` + * :ref:`FEP ` + * :ref:`H5MD ` * :ref:`ML-HDNNP ` - * :ref:`USER-INTEL ` + * :ref:`INTEL ` * :ref:`LATBOLTZ ` - * :ref:`USER-MANIFOLD ` - * :ref:`USER-MDI ` + * :ref:`MANIFOLD ` + * :ref:`MDI ` * :ref:`MEAM ` * :ref:`DPD-MESO ` - * :ref:`USER-MESONT ` - * :ref:`USER-MGPT ` + * :ref:`MESONT ` + * :ref:`MGPT ` * :ref:`USER-MISC ` - * :ref:`USER-MOFFF ` - * :ref:`USER-MOLFILE ` - * :ref:`USER-NETCDF ` + * :ref:`MOFFF ` + * :ref:`MOLFILE ` + * :ref:`NETCDF ` * :ref:`OPENMP ` * :ref:`ML-PACE ` - * :ref:`USER-PHONON ` - * :ref:`USER-PLUMED ` - * :ref:`USER-PTM ` - * :ref:`USER-QMMM ` - * :ref:`USER-QTB ` + * :ref:`PHONON ` + * :ref:`PLUMED ` + * :ref:`PTM ` + * :ref:`QMMM ` + * :ref:`QTB ` * :ref:`ML-QUIP ` * :ref:`ML-RANN ` - * :ref:`USER-REACTION ` + * :ref:`REACTION ` * :ref:`REAXFF ` - * :ref:`USER-SCAFACOS ` + * :ref:`SCAFACOS ` * :ref:`DPD-SMOOTH ` * :ref:`MACHDYN ` - * :ref:`USER-SMTBQ ` - * :ref:`USER-SPH ` - * :ref:`USER-TALLY ` - * :ref:`USER-UEF ` - * :ref:`USER-VTK ` - * :ref:`USER-YAFF ` + * :ref:`SMTBQ ` + * :ref:`SPH ` + * :ref:`TALLY ` + * :ref:`UEF ` + * :ref:`VTK ` + * :ref:`YAFF ` ---------- @@ -447,7 +447,7 @@ 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:`OPENMP ` 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. @@ -802,7 +802,7 @@ 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:`OPENMP ` packages, which +:ref:`INTEL `, and :ref:`OPENMP ` packages, which have styles optimized for CPU performance. **Authors:** James Fischer (High Performance Technologies), David Richie, @@ -1154,9 +1154,9 @@ This package has :ref:`specific installation instructions ` on the :doc ---------- -.. _PKG-USER-ADIOS: +.. _PKG-ADIOS: -USER-ADIOS package +ADIOS package ------------------ **Contents:** @@ -1170,12 +1170,12 @@ commands to write and read data using the ADIOS library. **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-ADIOS: filenames -> commands -* src/USER-ADIOS/README +* src/ADIOS: filenames -> commands +* src/ADIOS/README * examples/PACKAGES/adios * https://github.com/ornladios/ADIOS2 * :doc:`dump atom/adios ` @@ -1184,9 +1184,9 @@ This package has :ref:`specific installation instructions ` on the : ---------- -.. _PKG-USER-ATC: +.. _PKG-ATC: -USER-ATC package +ATC package ---------------- **Contents:** @@ -1199,21 +1199,21 @@ atomic information to continuum fields. **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-ATC: filenames -> commands -* src/USER-ATC/README +* src/ATC: filenames -> commands +* src/ATC/README * :doc:`fix atc ` * examples/PACKAGES/atc * https://www.lammps.org/pictures.html#atc ---------- -.. _PKG-USER-AWPMD: +.. _PKG-AWPMD: -USER-AWPMD package +AWPMD package ------------------ **Contents:** @@ -1227,20 +1227,20 @@ model. **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-AWPMD: filenames -> commands -* src/USER-AWPMD/README +* src/AWPMD: filenames -> commands +* src/AWPMD/README * :doc:`pair_style awpmd/cut ` * examples/PACKAGES/awpmd ---------- -.. _PKG-USER-BOCS: +.. _PKG-BOCS: -USER-BOCS package +BOCS package ----------------- **Contents:** @@ -1258,7 +1258,7 @@ Pennsylvania State University) **Supporting info:** -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: @@ -1271,9 +1271,9 @@ Example inputs are in the examples/PACKAGES/bocs folder. ---------- -.. _PKG-USER-BROWNIAN: +.. _PKG-BROWNIAN: -USER-BROWNIAN package +BROWNIAN package --------------------- **Contents:** @@ -1344,9 +1344,9 @@ acids. ---------- -.. _PKG-USER-COLVARS: +.. _PKG-COLVARS: -USER-COLVARS package +COLVARS package -------------------- **Contents:** @@ -1366,22 +1366,22 @@ the NAMD MD code, but with portability in mind. Axel Kohlmeyer **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-COLVARS: filenames -> commands +* src/COLVARS: filenames -> commands * `doc/PDF/colvars-refman-lammps.pdf `_ -* src/USER-COLVARS/README +* src/COLVARS/README * lib/colvars/README * :doc:`fix colvars ` * examples/PACKAGES/colvars ---------- -.. _PKG-USER-DIELECTRIC: +.. _PKG-DIELECTRIC: -USER-DIELECTRIC package +DIELECTRIC package ------------------------ **Contents:** @@ -1395,16 +1395,16 @@ different dielectric constants. **Supporting info:** -* src/USER-DIELECTRIC: filenames -> commands +* src/DIELECTRIC: filenames -> commands * :doc:`compute efield/atom ` * TODO: add all styles * examples/PACKAGES/dielectric ---------- -.. _PKG-USER-DIFFRACTION: +.. _PKG-DIFFRACTION: -USER-DIFFRACTION package +DIFFRACTION package ------------------------ **Contents:** @@ -1416,7 +1416,7 @@ intensities based on kinematic diffraction theory. **Supporting info:** -* src/USER-DIFFRACTION: filenames -> commands +* src/DIFFRACTION: filenames -> commands * :doc:`compute saed ` * :doc:`compute xrd ` * :doc:`fix saed/vtk ` @@ -1465,9 +1465,9 @@ Brennan (ARL). ---------- -.. _PKG-USER-DRUDE: +.. _PKG-DRUDE: -USER-DRUDE package +DRUDE package ------------------ **Contents:** @@ -1482,11 +1482,11 @@ Devemy (CNRS), and Agilio Padua (ENS de Lyon). **Supporting info:** -* src/USER-DRUDE: filenames -> commands +* src/DRUDE: filenames -> commands * :doc:`Howto drude ` * :doc:`Howto drude2 ` * :doc:`Howto polarizable ` -* src/USER-DRUDE/README +* src/DRUDE/README * :doc:`fix drude ` * :doc:`fix drude/transform/\* ` * :doc:`compute temp/drude ` @@ -1497,9 +1497,9 @@ Devemy (CNRS), and Agilio Padua (ENS de Lyon). ---------- -.. _PKG-USER-EFF: +.. _PKG-EFF: -USER-EFF package +EFF package ---------------- **Contents:** @@ -1516,8 +1516,8 @@ tools/eff; see its README file. **Supporting info:** -* src/USER-EFF: filenames -> commands -* src/USER-EFF/README +* src/EFF: filenames -> commands +* src/EFF/README * :doc:`atom_style electron ` * :doc:`fix nve/eff ` * :doc:`fix nvt/eff ` @@ -1533,9 +1533,9 @@ tools/eff; see its README file. ---------- -.. _PKG-USER-FEP: +.. _PKG-FEP: -USER-FEP package +FEP package ---------------- **Contents:** @@ -1549,8 +1549,8 @@ for using this package in tools/fep; see its README file. **Supporting info:** -* src/USER-FEP: filenames -> commands -* src/USER-FEP/README +* src/FEP: filenames -> commands +* src/FEP/README * :doc:`fix adapt/fep ` * :doc:`compute fep ` * :doc:`pair_style \*/soft ` @@ -1560,9 +1560,9 @@ for using this package in tools/fep; see its README file. ---------- -.. _PKG-USER-H5MD: +.. _PKG-H5MD: -USER-H5MD package +H5MD package ----------------- **Contents:** @@ -1583,12 +1583,12 @@ H5MD format. **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 +* src/H5MD: filenames -> commands +* src/H5MD/README * lib/h5md/README * :doc:`dump h5md ` @@ -1628,9 +1628,9 @@ This package has :ref:`specific installation instructions ` on the ---------- -.. _PKG-USER-INTEL: +.. _PKG-INTEL: -USER-INTEL package +INTEL package ------------------ **Contents:** @@ -1638,7 +1638,7 @@ USER-INTEL package 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 +: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 @@ -1651,27 +1651,27 @@ supported, performance will be sub-optimal. .. note:: - the USER-INTEL package contains styles that require using the + 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. +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. **Supporting info:** -* src/USER-INTEL: filenames -> commands -* src/USER-INTEL/README +* src/INTEL: filenames -> commands +* src/INTEL/README * :doc:`Accelerator packages ` -* :doc:`USER-INTEL package ` +* :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/USER-INTEL/TEST +* src/INTEL/TEST * `Benchmarks page `_ of web site ---------- @@ -1700,9 +1700,9 @@ Ontario). ---------- -.. _PKG-USER-MGPT: +.. _PKG-MGPT: -USER-MGPT package +MGPT package ----------------- **Contents:** @@ -1720,8 +1720,8 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. **Supporting info:** -* src/USER-MGPT: filenames -> commands -* src/USER-MGPT/README +* src/MGPT: filenames -> commands +* src/MGPT/README * :doc:`pair_style mgpt ` * examples/PACKAGES/mgpt @@ -1750,9 +1750,9 @@ src/USER-MISC/README file. ---------- -.. _PKG-USER-MANIFOLD: +.. _PKG-MANIFOLD: -USER-MANIFOLD package +MANIFOLD package --------------------- **Contents:** @@ -1770,8 +1770,8 @@ Waltham, MA, USA) **Supporting info:** -* src/USER-MANIFOLD: filenames -> commands -* src/USER-MANIFOLD/README +* src/MANIFOLD: filenames -> commands +* src/MANIFOLD/README * :doc:`Howto manifold ` * :doc:`fix manifoldforce ` * :doc:`fix nve/manifold/rattle ` @@ -1781,9 +1781,9 @@ Waltham, MA, USA) ---------- -.. _PKG-USER-MDI: +.. _PKG-MDI: -USER-MDI package +MDI package ---------------- **Contents:** @@ -1796,7 +1796,7 @@ other atomic or molecular simulation codes via the `MolSSI Driver Interface **Supporting info:** -* src/USER-MDI/README +* src/MDI/README * :doc:`mdi/engine ` * :doc:`fix mdi/engine ` * examples/PACKAGES/mdi @@ -1859,14 +1859,14 @@ algorithm. ---------- -.. _PKG-USER-MESONT: +.. _PKG-MESONT: -USER-MESONT package +MESONT package ------------------- **Contents:** -USER-MESONT is a LAMMPS package for simulation of nanomechanics of +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 @@ -1895,8 +1895,8 @@ Philipp Kloza (U Cambridge) **Supporting info:** -* src/USER-MESONT: filenames -> commands -* src/USER-MESONT/README +* src/MESONT: filenames -> commands +* src/MESONT/README * :doc:`atom_style mesont ` * :doc:`pair_style mesont/tpm ` * :doc:`compute mesont ` @@ -1906,9 +1906,9 @@ Philipp Kloza (U Cambridge) ---------- -.. _PKG-USER-MOFFF: +.. _PKG-MOFFF: -USER-MOFFF package +MOFFF package ------------------ **Contents:** @@ -1929,8 +1929,8 @@ Rochus Schmid (Ruhr-University Bochum). **Supporting info:** -* src/USER-MOFFF: filenames -> commands -* src/USER-MOFFF/README +* src/MOFFF: filenames -> commands +* src/MOFFF/README * :doc:`pair_style buck6d/coul/gauss ` * :doc:`angle_style class2 ` * :doc:`angle_style cosine/buck6d ` @@ -1939,9 +1939,9 @@ Rochus Schmid (Ruhr-University Bochum). ---------- -.. _PKG-USER-MOLFILE: +.. _PKG-MOLFILE: -USER-MOLFILE package +MOLFILE package -------------------- **Contents:** @@ -1970,20 +1970,20 @@ at **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-MOLFILE: filenames -> commands -* src/USER-MOLFILE/README +* src/MOLFILE: filenames -> commands +* src/MOLFILE/README * lib/molfile/README * :doc:`dump molfile ` ---------- -.. _PKG-USER-NETCDF: +.. _PKG-NETCDF: -USER-NETCDF package +NETCDF package ------------------- **Contents:** @@ -2010,12 +2010,12 @@ tools: **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-NETCDF: filenames -> commands -* src/USER-NETCDF/README +* src/NETCDF: filenames -> commands +* src/NETCDF/README * lib/netcdf/README * :doc:`dump netcdf ` @@ -2035,7 +2035,7 @@ 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:`USER-INTEL ` +the :ref:`KOKKOS `, :ref:`OPT `, and :ref:`INTEL ` packages, which have styles optimized for CPUs. **Author:** Axel Kohlmeyer (Temple U). @@ -2117,9 +2117,9 @@ This package has :ref:`specific installation instructions ` on the ---------- -.. _PKG-USER-PHONON: +.. _PKG-PHONON: -USER-PHONON package +PHONON package ------------------- **Contents:** @@ -2136,8 +2136,8 @@ and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" **Supporting info:** -* src/USER-PHONON: filenames -> commands -* src/USER-PHONON/README +* src/PHONON: filenames -> commands +* src/PHONON/README * :doc:`fix phonon ` * :doc:`dynamical_matrix ` * :doc:`third_order ` @@ -2145,9 +2145,9 @@ and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" ---------- -.. _PKG-USER-PLUMED: +.. _PKG-PLUMED: -USER-PLUMED package +PLUMED package ------------------- **Contents:** @@ -2163,20 +2163,20 @@ and Gareth Tribello. **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-PLUMED/README +* src/PLUMED/README * lib/plumed/README * :doc:`fix plumed ` * examples/PACKAGES/plumed ---------- -.. _PKG-USER-PTM: +.. _PKG-PTM: -USER-PTM package +PTM package ---------------- **Contents:** @@ -2189,16 +2189,16 @@ Matching methodology. **Supporting info:** -* src/USER-PTM: filenames not starting with ptm\_ -> commands -* src/USER-PTM: filenames starting with ptm\_ -> supporting code -* src/USER-PTM/LICENSE +* src/PTM: filenames not starting with ptm\_ -> commands +* src/PTM: filenames starting with ptm\_ -> supporting code +* src/PTM/LICENSE * :doc:`compute ptm/atom ` ---------- -.. _PKG-USER-QMMM: +.. _PKG-QMMM: -USER-QMMM package +QMMM package ----------------- **Contents:** @@ -2227,13 +2227,13 @@ changes to LAMMPS itself. **Install:** -This package has :ref:`specific installation instructions ` +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. **Supporting info:** -* src/USER-QMMM: filenames -> commands -* src/USER-QMMM/README +* src/QMMM: filenames -> commands +* src/QMMM/README * lib/qmmm/README * :doc:`fix phonon ` * lib/qmmm/example-ec/README @@ -2241,9 +2241,9 @@ on the :doc:`Build extras ` page. ---------- -.. _PKG-USER-QTB: +.. _PKG-QTB: -USER-QTB package +QTB package ---------------- **Contents:** @@ -2261,8 +2261,8 @@ simulation. **Supporting info:** -* src/USER-QTB: filenames -> commands -* src/USER-QTB/README +* src/QTB: filenames -> commands +* src/QTB/README * :doc:`fix qtb ` * :doc:`fix qbmsst ` * examples/PACKAGES/qtb @@ -2327,9 +2327,9 @@ with contributions by Doyl Dickel, Mississippi State University. ---------- -.. _PKG-USER-REACTION: +.. _PKG-REACTION: -USER-REACTION package +REACTION package --------------------- **Contents:** @@ -2348,8 +2348,8 @@ molecules, and chiral-sensitive reactions. **Supporting info:** -* src/USER-REACTION: filenames -> commands -* src/USER-REACTION/README +* src/REACTION: filenames -> commands +* src/REACTION/README * :doc:`fix bond/react ` * examples/PACKAGES/reaction * `2017 LAMMPS Workshop `_ @@ -2383,9 +2383,9 @@ for monitoring molecules as bonds are created and destroyed. ---------- -.. _PKG-USER-SCAFACOS: +.. _PKG-SCAFACOS: -USER-SCAFACOS package +SCAFACOS package --------------------- **Contents:** @@ -2406,12 +2406,12 @@ the Forschungszentrum Juelich. **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-SCAFACOS: filenames -> commands -* src/USER-SCAFACOS/README +* src/SCAFACOS: filenames -> commands +* src/SCAFACOS/README * :doc:`kspace_style scafacos ` * :doc:`kspace_modify ` * examples/PACKAGES/scafacos @@ -2428,7 +2428,7 @@ DPD-SMOOTH package 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 `). +:ref:`SPH package `). Also two fixes for moving and rigid body integration of SPH/SDPD particles (particles of atom_style meso). @@ -2456,7 +2456,7 @@ MACHDYN package 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 `). +:ref:`SPH package `). This package solves solids mechanics problems via a state of the art stabilized meshless method with hourglass control. It can specify @@ -2484,9 +2484,9 @@ This package has :ref:`specific installation instructions ` on the :doc ---------- -.. _PKG-USER-SMTBQ: +.. _PKG-SMTBQ: -USER-SMTBQ package +SMTBQ package ------------------ **Contents:** @@ -2500,16 +2500,16 @@ Tetot (LAAS-CNRS, France). **Supporting info:** -* src/USER-SMTBQ: filenames -> commands -* src/USER-SMTBQ/README +* src/SMTBQ: filenames -> commands +* src/SMTBQ/README * :doc:`pair_style smtbq ` * examples/PACKAGES/smtbq ---------- -.. _PKG-USER-SPH: +.. _PKG-SPH: -USER-SPH package +SPH package ---------------- **Contents:** @@ -2533,17 +2533,17 @@ Dynamics, Ernst Mach Institute, Germany). **Supporting info:** -* src/USER-SPH: filenames -> commands -* src/USER-SPH/README +* src/SPH: filenames -> commands +* src/SPH/README * doc/PDF/SPH_LAMMPS_userguide.pdf * examples/PACKAGES/sph * https://www.lammps.org/movies.html#sph ---------- -.. _PKG-USER-TALLY: +.. _PKG-TALLY: -USER-TALLY package +TALLY package ------------------ **Contents:** @@ -2556,16 +2556,16 @@ stress, etc) about individual interactions. **Supporting info:** -* src/USER-TALLY: filenames -> commands -* src/USER-TALLY/README +* src/TALLY: filenames -> commands +* src/TALLY/README * :doc:`compute \*/tally ` * examples/PACKAGES/tally ---------- -.. _PKG-USER-UEF: +.. _PKG-UEF: -USER-UEF package +UEF package ---------------- **Contents:** @@ -2578,8 +2578,8 @@ supporting compute styles and an output option. **Supporting info:** -* src/USER-UEF: filenames -> commands -* src/USER-UEF/README +* src/UEF: filenames -> commands +* src/UEF/README * :doc:`fix nvt/uef ` * :doc:`fix npt/uef ` * :doc:`compute pressure/uef ` @@ -2589,9 +2589,9 @@ supporting compute styles and an output option. ---------- -.. _PKG-USER-VTK: +.. _PKG-VTK: -USER-VTK package +VTK package ---------------- **Contents:** @@ -2611,20 +2611,20 @@ system. **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-VTK: filenames -> commands -* src/USER-VTK/README +* src/VTK: filenames -> commands +* src/VTK/README * lib/vtk/README * :doc:`dump vtk ` ---------- -.. _PKG-USER-YAFF: +.. _PKG-YAFF: -USER-YAFF package +YAFF package ----------------- **Contents:** @@ -2646,7 +2646,7 @@ which discuss the `QuickFF `_ methodology. **Supporting info:** -* src/USER-YAFF/README +* src/YAFF/README * :doc:`angle_style cross ` * :doc:`angle_style mm3 ` * :doc:`bond_style mm3 ` diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 2a9104ca04..41eac29290 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -31,101 +31,101 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | Package | Description | Doc page | Example | Library | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-ADIOS ` | dump output via ADIOS | :doc:`dump adios ` | USER/adios | ext | +| :ref:`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:`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:`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:`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:`BROWNIAN ` | Brownian dynamics and self-propelled particles | :doc:`fix brownian `, :doc:`fix propel/self ` | USER/brownian | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`CG-DNA ` | coarse-grained DNA force fields | src/CG-DNA/README | USER/cgdna | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`CG-SDK ` | 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:`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:`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:`DIFFRACTION ` | virtual x-ray and electron diffraction | :doc:`compute xrd ` | USER/diffraction | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`DPD-REACT ` | reactive dissipative particle dynamics | src/DPD-REACT/README | USER/dpd | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-DRUDE ` | Drude oscillators | :doc:`Howto drude ` | USER/drude | no | +| :ref:`DRUDE ` | Drude oscillators | :doc:`Howto drude ` | USER/drude | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-EFF ` | electron force field | :doc:`pair_style eff/cut ` | USER/eff | no | +| :ref:`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:`FEP ` | free energy perturbation | :doc:`compute fep ` | USER/fep | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | +| :ref:`H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`ML-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:`INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`LATBOLTZ ` | Lattice Boltzmann fluid | :doc:`fix lb/fluid ` | USER/lb | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | +| :ref:`MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-MDI ` | client-server coupling | :doc:`MDI Howto ` | USER/mdi | ext | +| :ref:`MDI ` | client-server coupling | :doc:`MDI Howto ` | USER/mdi | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`MEAM ` | modified EAM potential (C++) | :doc:`pair_style meam ` | meam | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`DPD-MESO ` | 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:`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:`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:`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:`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:`NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`OPENMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`ML-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:`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:`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:`PTM ` | Polyhedral Template Matching | :doc:`compute ptm/atom ` | n/a | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-QMMM ` | QM/MM coupling | :doc:`fix qmmm ` | USER/qmmm | ext | +| :ref:`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:`QTB ` | quantum nuclear effects | :doc:`fix qtb ` :doc:`fix qbmsst ` | qtb | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`ML-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`ML-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:`REACTION ` | chemical reactions in classical MD | :doc:`fix bond/react ` | USER/reaction | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`REAXFF ` | 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:`SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos ` | USER/scafacos | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`DPD-SMOOTH ` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal ` | USER/sdpd | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`MACHDYN ` | 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:`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:`SPH ` | smoothed particle hydrodynamics | `SPH User Guide `_ | USER/sph | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-TALLY ` | pairwise tally computes | :doc:`compute XXX/tally ` | USER/tally | no | +| :ref:`TALLY ` | pairwise tally computes | :doc:`compute XXX/tally ` | USER/tally | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-UEF ` | extensional flow | :doc:`fix nvt/uef ` | USER/uef | no | +| :ref:`UEF ` | extensional flow | :doc:`fix nvt/uef ` | USER/uef | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-VTK ` | dump output via VTK | :doc:`compute vtk ` | n/a | ext | +| :ref:`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 | +| :ref:`YAFF ` | additional styles implemented in YAFF | :doc:`angle_style cross ` | USER/yaff | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ .. _MOFplus: https://www.mofplus.org/content/show/MOF-FF diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 8e639a42ac..bfe769a8eb 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -202,7 +202,7 @@ Option -plog will override the name of the partition log files file.N. **-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 OPENMP 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 @@ -540,7 +540,7 @@ 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 OPENMP package. The hybrid style is the only style that accepts arguments. It allows for two packages to be @@ -548,7 +548,7 @@ 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 +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 @@ -570,14 +570,14 @@ 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 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 +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 diff --git a/doc/src/Speed_compare.rst b/doc/src/Speed_compare.rst index 3ae461a82c..7821214c83 100644 --- a/doc/src/Speed_compare.rst +++ b/doc/src/Speed_compare.rst @@ -72,7 +72,7 @@ section below for examples where this has been done. 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 d480a6c766..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 OPENMP 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 01a3537a0b..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:`OPENMP 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, @@ -407,8 +407,8 @@ 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 ` +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 @@ -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 aee5047ef4..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 @@ -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_packages.rst b/doc/src/Speed_packages.rst index 01283ac6fe..32ed314230 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -18,7 +18,7 @@ standard or user packages: +-----------------------------------------+-------------------------------------------------------+ | :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 | +-----------------------------------------+-------------------------------------------------------+ @@ -41,11 +41,11 @@ 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:`OPENMP `, :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 +84,9 @@ 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, OPENMP, 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 +116,15 @@ 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 +156,7 @@ 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 diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index d6b3a823b5..582fc4d3ad 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -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. @@ -861,7 +861,7 @@ 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/PACKAGES/phonon directory diff --git a/doc/src/accel_styles.rst b/doc/src/accel_styles.rst index e50e77478c..bd7d88f9d7 100644 --- a/doc/src/accel_styles.rst +++ b/doc/src/accel_styles.rst @@ -5,7 +5,7 @@ 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, +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/angle_charmm.rst b/doc/src/angle_charmm.rst index 5b98d95b58..d411599eaf 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -63,7 +63,7 @@ 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, +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/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/atom_style.rst b/doc/src/atom_style.rst index 45cfcd5ae7..a54971cf3b 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -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, OPENMP, 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 @@ -352,7 +352,7 @@ 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 DPD-REACT package for dissipative particle dynamics (DPD). @@ -362,14 +362,14 @@ 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/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 6875aa7233..5427538a73 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -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_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_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_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_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_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_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_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 0933cc5337..baf7985ef5 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -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 6db78a5b11..6de30a3d84 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -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_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_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_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_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_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 d93efe341f..5c32ccee99 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -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 8f3db1879c..2667cb5eeb 100644 --- a/doc/src/fix_polarize.rst +++ b/doc/src/fix_polarize.rst @@ -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_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_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 fc9c7737dd..744c7e75f3 100644 --- a/doc/src/fix_tgnh_drude.rst +++ b/doc/src/fix_tgnh_drude.rst @@ -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/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 618f93fff4..41d533eebe 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -71,7 +71,7 @@ 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, +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 886ea86c1d..b3eb6d7000 100644 --- a/doc/src/info.rst +++ b/doc/src/info.rst @@ -89,7 +89,7 @@ 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, +settings of included accelerator support for the GPU, KOKKOS, INTEL, and OPENMP packages. The *styles* category prints the list of styles available in the diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index b1eb46f5f0..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:: @@ -420,7 +420,7 @@ 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, +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. @@ -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 5480d4810b..e997dc6147 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -130,7 +130,7 @@ 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 +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 @@ -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 OPENMP 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 @@ -600,7 +600,7 @@ too. .. note:: - If you build LAMMPS with the GPU, USER-INTEL, and / or OPENMP + 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 @@ -642,7 +642,7 @@ 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 ` @@ -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_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 982e6c538b..d1465ef147 100644 --- a/doc/src/pair_coul_tt.rst +++ b/doc/src/pair_coul_tt.rst @@ -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_eff.rst b/doc/src/pair_eff.rst index 5378483c56..ceb571a58d 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -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_fep_soft.rst b/doc/src/pair_fep_soft.rst index 55317aac77..6f8954a0a7 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -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_hybrid.rst b/doc/src/pair_hybrid.rst index f57139e15c..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, OPENMP, 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_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_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 77d73b531a..ea6621a3fd 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -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_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_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_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_sw.rst b/doc/src/pair_sw.rst index 5bc6649035..a4b39be3c9 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -166,7 +166,7 @@ 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, +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. @@ -174,7 +174,7 @@ 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_thole.rst b/doc/src/pair_thole.rst index e14576fa09..68966a3d9b 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -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/suffix.rst b/doc/src/suffix.rst index 7a046c7dfd..1ece739f55 100644 --- a/doc/src/suffix.rst +++ b/doc/src/suffix.rst @@ -36,7 +36,7 @@ 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 +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. @@ -44,7 +44,7 @@ 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 @@ -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 +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 USER-INTEL variant is available. +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/utils/check-packages.py b/doc/utils/check-packages.py index 339d584c59..f7cbb2795a 100755 --- a/doc/utils/check-packages.py +++ b/doc/utils/check-packages.py @@ -41,7 +41,7 @@ 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-.*") +user = re.compile(".*") stdpkg = [] usrpkg = [] @@ -90,7 +90,7 @@ for p in stdpkg: counter += 1 print(f"Standard package {p} missing in Packages_details.rst") -matches = set(re.findall(':ref:`(USER-[A-Z0-9]+) `', text, re.MULTILINE)) +matches = set(re.findall(':ref:`([A-Z0-9]+) `', text, re.MULTILINE)) for p in usrpkg: if not p in matches: counter +=1 diff --git a/examples/PACKAGES/USER-MISC/pafi/README b/examples/PACKAGES/USER-MISC/pafi/README index c35dff313c..675ce59de4 100644 --- a/examples/PACKAGES/USER-MISC/pafi/README +++ b/examples/PACKAGES/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/PACKAGES/dielectric/README b/examples/PACKAGES/dielectric/README index 6cbb1e204d..fa7ac28c97 100644 --- a/examples/PACKAGES/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/PACKAGES/mesont/README b/examples/PACKAGES/mesont/README index ffbc667120..7d6be7993a 100644 --- a/examples/PACKAGES/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/PACKAGES/qtb/README b/examples/PACKAGES/qtb/README index 41dec0dea3..80cde6395c 100644 --- a/examples/PACKAGES/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/PACKAGES/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 index 16e4deef51..57455b04f4 100644 --- a/examples/PACKAGES/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/PACKAGES/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 index 527d71ce87..b6dcdafc54 100644 --- a/examples/PACKAGES/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/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 index e0b10de95e..179f3bfcb2 100644 --- a/examples/PACKAGES/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/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 index f881ed003a..877cf778fa 100644 --- a/examples/PACKAGES/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/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 index 9410529284..8b6cd7d81e 100644 --- a/examples/PACKAGES/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/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 index 2dc5c07b2b..2d44371649 100644 --- a/examples/PACKAGES/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/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.1 index e6cd7c506f..a4547054c2 100644 --- a/examples/PACKAGES/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/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.ewald.g++.4 index 39e0387491..2036be9b24 100644 --- a/examples/PACKAGES/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/PACKAGES/scafacos/log.27Nov18.scafacos.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.1 index 6b36f0ba91..417c8e9f84 100644 --- a/examples/PACKAGES/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/PACKAGES/scafacos/log.27Nov18.scafacos.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.g++.4 index 23f55fc5a6..9cad97aa6b 100644 --- a/examples/PACKAGES/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/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.1 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.1 index 92e85e072e..3c5a48c251 100644 --- a/examples/PACKAGES/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/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.4 b/examples/PACKAGES/scafacos/log.27Nov18.scafacos.p3m.g++.4 index 18199eca16..4e079da923 100644 --- a/examples/PACKAGES/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/PACKAGES/sph/README b/examples/PACKAGES/sph/README index b5a1acc614..9df07acab7 100644 --- a/examples/PACKAGES/sph/README +++ b/examples/PACKAGES/sph/README @@ -1 +1 @@ -see the USER-SPH user's guide for a detailed explanation of these examples. +see the SPH user's guide for a detailed explanation of these examples. diff --git a/examples/PACKAGES/tally/README b/examples/PACKAGES/tally/README index fcc58e6e0d..074193b0f2 100644 --- a/examples/PACKAGES/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/PACKAGES/uef/README b/examples/PACKAGES/uef/README index aaf53fa2a1..bedffbfb08 100644 --- a/examples/PACKAGES/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/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 b0dfb1d889..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) @@ -33,11 +33,11 @@ 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) 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/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/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/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..ac8215ac05 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/minimal.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/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/python/lammps/core.py b/python/lammps/core.py index 070c0a4ffd..df5e578683 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -1536,7 +1536,7 @@ class lammps(object): """ result = {} - for p in ['GPU', 'KOKKOS', 'USER-INTEL', 'OPENMP']: + for p in ['GPU', 'KOKKOS', 'INTEL', 'OPENMP']: result[p] = {} c = 'api' result[p][c] = [] 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 100% rename from src/USER-ATC/README rename to src/ATC/README 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 100% rename from src/USER-AWPMD/README rename to src/AWPMD/README 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 89% rename from src/USER-BOCS/README rename to src/BOCS/README index 2028333b61..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: 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 100% rename from src/USER-BROWNIAN/fix_brownian.cpp rename to src/BROWNIAN/fix_brownian.cpp 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 100% rename from src/USER-BROWNIAN/fix_brownian_asphere.cpp rename to src/BROWNIAN/fix_brownian_asphere.cpp 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 100% rename from src/USER-BROWNIAN/fix_brownian_base.cpp rename to src/BROWNIAN/fix_brownian_base.cpp 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 100% rename from src/USER-BROWNIAN/fix_brownian_sphere.cpp rename to src/BROWNIAN/fix_brownian_sphere.cpp 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-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 96% rename from src/USER-COLVARS/README rename to src/COLVARS/README index 1ac57d9589..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). 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 92% rename from src/USER-DIELECTRIC/Install.sh rename to src/DIELECTRIC/Install.sh index fd540f3c7e..737d8dc99e 100644 --- a/src/USER-DIELECTRIC/Install.sh +++ b/src/DIELECTRIC/Install.sh @@ -31,7 +31,7 @@ action () { if (test $1 = 1) then if (test ! -e ../ppp.cpp) then - echo "Must install KSPACE package with USER-DIELECTRIC" + echo "Must install KSPACE package with DIELECTRIC" exit 1 fi fi diff --git a/src/USER-DIELECTRIC/README b/src/DIELECTRIC/README similarity index 86% rename from src/USER-DIELECTRIC/README rename to src/DIELECTRIC/README index 9275a1e7ac..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 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 100% rename from src/USER-DIFFRACTION/README rename to src/DIFFRACTION/README 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/USER-DRUDE/README b/src/DRUDE/README similarity index 100% rename from src/USER-DRUDE/README rename to src/DRUDE/README 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 620421fbd7..9834aa5255 100755 --- a/src/Depend.sh +++ b/src/Depend.sh @@ -49,7 +49,7 @@ if (test $1 = "ASPHERE") then depend GPU depend OPENMP depend CG-DNA - depend USER-INTEL + depend INTEL fi if (test $1 = "CLASS2") then @@ -79,9 +79,9 @@ if (test $1 = "KSPACE") then depend KOKKOS depend OPT depend OPENMP - depend USER-INTEL - depend USER-PHONON - depend USER-FEP + depend INTEL + depend PHONON + depend FEP fi if (test $1 = "MANYBODY") then @@ -97,9 +97,9 @@ if (test $1 = "MOLECULE") then depend GPU depend KOKKOS depend USER-MISC - depend USER-FEP + depend FEP depend OPENMP - depend USER-INTEL + depend INTEL fi if (test $1 = "PERI") then @@ -131,18 +131,18 @@ if (test $1 = "DPD-REACT") then depend KOKKOS fi -if (test $1 = "USER-DRUDE") then +if (test $1 = "DRUDE") then depend OPENMP fi -if (test $1 = "USER-FEP") then +if (test $1 = "FEP") then depend OPENMP fi if (test $1 = "USER-MISC") then depend GPU depend OPENMP - depend USER-INTEL + depend INTEL fi if (test $1 = "REAXFF") then diff --git a/src/USER-EFF/README b/src/EFF/README similarity index 100% rename from src/USER-EFF/README rename to src/EFF/README 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 100% rename from src/USER-FEP/README rename to src/FEP/README 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 541e633675..b59b0619b3 100644 --- a/src/USER-INTEL/README +++ b/src/INTEL/README @@ -43,7 +43,7 @@ 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 OPENMP -is installed, OPENMP styles will be used whenever USER-INTEL styles are not +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 fd64dff72d..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): @@ -111,12 +111,12 @@ mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -v N on 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 51677c8e0e..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 OPENMP + // 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 OPENMP + // 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/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/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/README b/src/MAKE/README index d67f2b576a..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 @@ -66,11 +66,11 @@ Makefile.opt OPT 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/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 96% rename from src/USER-MGPT/README rename to src/MGPT/README index 50c11df5ab..1f29a68385 100644 --- a/src/USER-MGPT/README +++ b/src/MGPT/README @@ -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-MOFFF/README b/src/MOFFF/README similarity index 100% rename from src/USER-MOFFF/README rename to src/MOFFF/README 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 cb10a16337..dc64f48098 100644 --- a/src/Makefile +++ b/src/Makefile @@ -51,28 +51,28 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ ml-iap molecule mpiio mscg opt peri plugin poems \ python qeq replica rigid shock ml-snap spin srd voronoi -PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs cg-dna \ - cg-sdk user-colvars user-dielectric user-diffraction dpd-react user-drude \ - user-eff user-fep user-h5md ml-hdnnp user-intel latboltz user-manifold \ - user-mdi meam dpd-meso user-mesont user-mgpt user-misc \ - user-mofff user-molfile user-netcdf openmp user-phonon \ - ml-pace user-plumed user-ptm user-qmmm user-qtb ml-quip \ - ml-rann user-reaction reaxff user-scafacos machdyn user-smtbq \ - dpd-smooth user-sph user-tally user-uef user-vtk user-yaff +PACKUSER = adios atc awpmd brownian bocs cg-dna \ + cg-sdk colvars dielectric diffraction dpd-react drude \ + eff fep h5md ml-hdnnp intel latboltz manifold \ + mdi meam dpd-meso mesont mgpt user-misc \ + mofff molfile netcdf openmp phonon \ + ml-pace plumed ptm qmmm qtb ml-quip \ + ml-rann reaction reaxff scafacos machdyn smtbq \ + dpd-smooth sph tally uef vtk yaff PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \ - user-adios user-atc user-awpmd user-colvars user-h5md ml-hdnnp latboltz user-mdi \ - user-mesont user-molfile user-netcdf ml-pace user-plumed user-qmmm ml-quip \ - user-scafacos machdyn user-vtk + adios atc awpmd colvars h5md ml-hdnnp latboltz mdi \ + mesont molfile netcdf ml-pace plumed qmmm ml-quip \ + scafacos machdyn vtk PACKSYS = compress mpiio python latboltz -PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont \ - user-mdi +PACKINT = gpu kokkos message poems atc awpmd colvars mesont \ + mdi PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md ml-hdnnp user-molfile user-netcdf ml-pace user-plumed \ - user-qmmm ml-quip user-scafacos machdyn user-vtk + adios h5md ml-hdnnp molfile netcdf ml-pace plumed \ + qmmm ml-quip scafacos machdyn vtk PACKALL = $(PACKAGE) $(PACKUSER) @@ -87,7 +87,7 @@ PACKUSERUC = $(call uppercase,$(PACKUSER)) YESDIR = $(call uppercase,$(@:yes-%=%)) NODIR = $(call uppercase,$(@:no-%=%)) LIBDIR = $(@:lib-%=%) -LIBUSERDIR = $(@:lib-user-%=%) +LIBUSERDIR = $(@:lib-%=%) # List of all targets @@ -400,7 +400,7 @@ 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/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/OPENMP/fix_omp.cpp b/src/OPENMP/fix_omp.cpp index 9f115a74c1..2b7e7eeaf9 100644 --- a/src/OPENMP/fix_omp.cpp +++ b/src/OPENMP/fix_omp.cpp @@ -308,7 +308,7 @@ void FixOMP::set_neighbor_omp() const int nrequest = neighbor->nrequest; // flag *all* neighbor list requests as OPENMP threaded, - // but skip lists already flagged as USER-INTEL 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-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 100% rename from src/USER-PHONON/README rename to src/PHONON/README 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 97% rename from src/USER-PLUMED/README rename to src/PLUMED/README index 3f9860da39..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 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/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 100% rename from src/USER-QTB/README rename to src/QTB/README 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-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 100% rename from src/USER-SCAFACOS/README rename to src/SCAFACOS/README 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 100% rename from src/USER-SMTBQ/README rename to src/SMTBQ/README 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 100% rename from src/USER-SPH/README rename to src/SPH/README 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 100% rename from src/USER-TALLY/README rename to src/TALLY/README 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-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/atom.cpp b/src/atom.cpp index e0681b6dac..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; @@ -174,12 +174,12 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) 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; @@ -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); @@ -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 @@ -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 7e5fc573dc..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; @@ -129,7 +129,7 @@ class Atom : protected Pointers { 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 @@ -137,7 +137,7 @@ class Atom : protected Pointers { double *edpd_cv; // heat capacity int cc_species; - // USER-MESONT package + // MESONT package double *length; int *buckling; @@ -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; diff --git a/src/info.cpp b/src/info.cpp index 13b02df116..6756c174ca 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -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; @@ -1476,14 +1476,14 @@ std::string Info::get_accelerator_info(const std::string &package) 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 9aa5d7f476..2c2c55f4c4 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -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 db006160d8..faf45ab305 100644 --- a/src/input.h +++ b/src/input.h @@ -362,9 +362,9 @@ E: Package omp command without OPENMP package installed 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 9cd3029c8d..70174b9d14 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -850,7 +850,7 @@ void LAMMPS::post_create() 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"); diff --git a/src/lammps.h b/src/lammps.h index 2e7699a281..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. diff --git a/src/library.cpp b/src/library.cpp index 2447ba0a2a..436892683b 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -4327,7 +4327,7 @@ 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 "OPENMP". +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 afa46e9957..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, OPENMP 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_request.h b/src/neigh_request.h index 74802583ac..4bdc368317 100644 --- a/src/neigh_request.h +++ b/src/neigh_request.h @@ -67,7 +67,7 @@ class NeighRequest : protected Pointers { int respaouter; // 1 if need a rRESPA outer list int bond; // 1 if store bond neighbors instead of atom neighs int omp; // set by OPENMP package - int intel; // set by USER-INTEL package + int intel; // set by INTEL package int kokkos_host; // set by KOKKOS package int kokkos_device; int ssa; // set by DPD-REACT package, for Shardlow lists 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/cplusplus/test_lammps_class.cpp b/unittest/cplusplus/test_lammps_class.cpp index e0d2dcf14b..d25b232fa7 100644 --- a/unittest/cplusplus/test_lammps_class.cpp +++ b/unittest/cplusplus/test_lammps_class.cpp @@ -133,7 +133,7 @@ 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, "DPD-REACT"); found = lmp->match_style("atom", "edpd"); @@ -147,7 +147,7 @@ TEST_F(LAMMPS_plain, TestStyles) found = lmp->match_style("atom", "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); } diff --git a/unittest/force-styles/test_pair_style.cpp b/unittest/force-styles/test_pair_style.cpp index f21ebbdb61..939bf5dbb5 100644 --- a/unittest/force-styles/test_pair_style.cpp +++ b/unittest/force-styles/test_pair_style.cpp @@ -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/python/python-capabilities.py b/unittest/python/python-capabilities.py index b3bc46afd3..a0b8bd2618 100644 --- a/unittest/python/python-capabilities.py +++ b/unittest/python/python-capabilities.py @@ -140,16 +140,16 @@ class PythonCapabilities(unittest.TestCase): 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':