Loading cmake/CMakeLists.txt +3 −4 Original line number Diff line number Diff line Loading @@ -218,10 +218,9 @@ if(BUILD_OMP) message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support") endif() if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 9.99.9)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 18.99.9)) ) if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0))) # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts. # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe. target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=4) Loading cmake/Modules/Packages/USER-PLUMED.cmake +2 −2 Original line number Diff line number Diff line Loading @@ -55,8 +55,8 @@ if(DOWNLOAD_PLUMED) endif() include(ExternalProject) ExternalProject_Add(plumed_build URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz URL_MD5 204d2edae58d9b10ba3ad460cad64191 URL https://github.com/plumed/plumed2/releases/download/v2.6.1/plumed-src-2.6.1.tgz URL_MD5 89a9a450fc6025299fe16af235957163 BUILD_IN_SOURCE 1 CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC} Loading doc/src/fix_property_atom.rst +23 −13 Original line number Diff line number Diff line Loading @@ -105,7 +105,7 @@ keyword with a value of *yes*\ . This will invoke extra communication when ghost atoms are created (at every re-neighboring) to insure the new properties are also defined for the ghost atoms. .. note:: .. admonition:: Properties on ghost atoms If you use this command with the *mol*\ , *q* or *rmass* vectors, then you most likely want to set *ghost* yes, since these properties Loading @@ -115,7 +115,7 @@ new properties are also defined for the ghost atoms. atoms to have these values. LAMMPS will issue a warning it you define those vectors but do not set *ghost* yes. .. note:: .. admonition:: Limitations on ghost atom properties The properties for ghost atoms are not updated every timestep, but only once every few steps when neighbor lists are re-built. Thus Loading @@ -126,12 +126,6 @@ new properties are also defined for the ghost atoms. that can be invoked from within a :doc:`pair style <pair_style>` or :doc:`fix <fix>` or :doc:`compute <compute>` that you write. .. note:: If this fix is defined **after** the simulation box is created, a 'run 0' command should be issued to properly initialize the storage created by this fix. ---------- This fix is one of a small number that can be defined in an input Loading @@ -139,6 +133,12 @@ script before the simulation box is created or atoms are defined. This is so it can be used with the :doc:`read_data <read_data>` command as described below. .. note:: If this fix is defined **after** the simulation box is created, a 'run 0' command may be needed to properly initialize the storage created by this fix. Per-atom properties that are defined by the :doc:`atom style <atom_style>` are initialized when atoms are created, e.g. by the :doc:`read_data <read_data>` or :doc:`create_atoms <create_atoms>` commands. The per-atom properties defined by this fix are not. So Loading Loading @@ -271,11 +271,21 @@ example to heavy water: Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. .. warning:: When reading data from a restart, the fix command has to be specified **exactly** the same way as before. LAMMPS will only check whether a fix is of the same style and has the same fix ID and in case of a match will then try to initialize the fix with the data stored in the binary restart file. If the fix property/atom command does not match exactly, data can be corrupted or LAMMPS may crash. None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix. No global or per-atom quantities are stored by this fix for Loading doc/src/fix_store_state.rst +9 −0 Original line number Diff line number Diff line Loading @@ -111,6 +111,15 @@ command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. .. warning:: When reading data from a restart, the fix command has to be specified **exactly** the same way as before. LAMMPS will only check whether a fix is of the same style and has the same fix ID and in case of a match will then try to initialize the fix with the data stored in the binary restart file. If the fix store/state command does not match exactly, data can be corrupted or LAMMPS may crash. None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix. Loading doc/src/pg_developer.rst +3 −0 Original line number Diff line number Diff line Loading @@ -909,6 +909,9 @@ Convenience functions .. doxygenfunction:: timespec2seconds :project: progguide .. doxygenfunction:: date2num :project: progguide --------------------------- Tokenizer classes Loading Loading
cmake/CMakeLists.txt +3 −4 Original line number Diff line number Diff line Loading @@ -218,10 +218,9 @@ if(BUILD_OMP) message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support") endif() if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 9.99.9)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 18.99.9)) ) if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0))) # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts. # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe. target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=4) Loading
cmake/Modules/Packages/USER-PLUMED.cmake +2 −2 Original line number Diff line number Diff line Loading @@ -55,8 +55,8 @@ if(DOWNLOAD_PLUMED) endif() include(ExternalProject) ExternalProject_Add(plumed_build URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz URL_MD5 204d2edae58d9b10ba3ad460cad64191 URL https://github.com/plumed/plumed2/releases/download/v2.6.1/plumed-src-2.6.1.tgz URL_MD5 89a9a450fc6025299fe16af235957163 BUILD_IN_SOURCE 1 CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC} Loading
doc/src/fix_property_atom.rst +23 −13 Original line number Diff line number Diff line Loading @@ -105,7 +105,7 @@ keyword with a value of *yes*\ . This will invoke extra communication when ghost atoms are created (at every re-neighboring) to insure the new properties are also defined for the ghost atoms. .. note:: .. admonition:: Properties on ghost atoms If you use this command with the *mol*\ , *q* or *rmass* vectors, then you most likely want to set *ghost* yes, since these properties Loading @@ -115,7 +115,7 @@ new properties are also defined for the ghost atoms. atoms to have these values. LAMMPS will issue a warning it you define those vectors but do not set *ghost* yes. .. note:: .. admonition:: Limitations on ghost atom properties The properties for ghost atoms are not updated every timestep, but only once every few steps when neighbor lists are re-built. Thus Loading @@ -126,12 +126,6 @@ new properties are also defined for the ghost atoms. that can be invoked from within a :doc:`pair style <pair_style>` or :doc:`fix <fix>` or :doc:`compute <compute>` that you write. .. note:: If this fix is defined **after** the simulation box is created, a 'run 0' command should be issued to properly initialize the storage created by this fix. ---------- This fix is one of a small number that can be defined in an input Loading @@ -139,6 +133,12 @@ script before the simulation box is created or atoms are defined. This is so it can be used with the :doc:`read_data <read_data>` command as described below. .. note:: If this fix is defined **after** the simulation box is created, a 'run 0' command may be needed to properly initialize the storage created by this fix. Per-atom properties that are defined by the :doc:`atom style <atom_style>` are initialized when atoms are created, e.g. by the :doc:`read_data <read_data>` or :doc:`create_atoms <create_atoms>` commands. The per-atom properties defined by this fix are not. So Loading Loading @@ -271,11 +271,21 @@ example to heavy water: Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. .. warning:: When reading data from a restart, the fix command has to be specified **exactly** the same way as before. LAMMPS will only check whether a fix is of the same style and has the same fix ID and in case of a match will then try to initialize the fix with the data stored in the binary restart file. If the fix property/atom command does not match exactly, data can be corrupted or LAMMPS may crash. None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix. No global or per-atom quantities are stored by this fix for Loading
doc/src/fix_store_state.rst +9 −0 Original line number Diff line number Diff line Loading @@ -111,6 +111,15 @@ command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. .. warning:: When reading data from a restart, the fix command has to be specified **exactly** the same way as before. LAMMPS will only check whether a fix is of the same style and has the same fix ID and in case of a match will then try to initialize the fix with the data stored in the binary restart file. If the fix store/state command does not match exactly, data can be corrupted or LAMMPS may crash. None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix. Loading
doc/src/pg_developer.rst +3 −0 Original line number Diff line number Diff line Loading @@ -909,6 +909,9 @@ Convenience functions .. doxygenfunction:: timespec2seconds :project: progguide .. doxygenfunction:: date2num :project: progguide --------------------------- Tokenizer classes Loading
