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Merge branch 'develop' into group-bitmap-accessor

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This commit is contained in:
Axel Kohlmeyer
2024-07-24 00:08:55 -04:00
parent 7a3dd2231b fbd37bd5e9
commit 25a4117e67
434 changed files with 38492 additions and 13867 deletions
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3
.github/CODEOWNERS vendored
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@ -59,7 +59,8 @@ src/VTK/* @rbberger
# individual files in packages
src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane @stanmoore1
src/KOSSOS/pair_pod_kokkos.* @exapde @stanmoore1
src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/MANYBODY/pair_nb3b_screened.* @flodesani

11
.gitignore vendored
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@ -43,12 +43,12 @@ Thumbs.db
#cmake
/build*
/CMakeCache.txt
/CMakeFiles/
/Testing
CMakeCache.txt
CMakeFiles
/Makefile
/Testing
/cmake_install.cmake
Testing
Temporary
cmake_install.cmake
/lmp
out/Debug
out/RelWithDebInfo
@ -60,3 +60,4 @@ src/Makefile.package.settings-e
/cmake/build/x64-Debug-Clang
/install/x64-GUI-MSVC
/install
.Rhistory

32
cmake/CMakeLists.txt
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@ -23,6 +23,7 @@ project(lammps CXX)
set(SOVERSION 0)
get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
include(GNUInstallDirs)
get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
# collect all executables and shared libs in the top level build folder
@ -163,6 +164,22 @@ if(MSVC)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# warn about potentially problematic GCC compiler versions
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
if (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
"with C++17 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 9.x or later")
endif()
endif()
if (CMAKE_CXX_STANDARD GREATER_EQUAL 11)
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
"with C++11 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
endif()
endif()
endif()
# export all symbols when building a .dll file on windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@ -197,18 +214,17 @@ set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
option(BUILD_SHARED_LIBS "Build shared library" OFF)
option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
# Support using clang-tidy for C++ files with selected options
set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
if(ENABLE_CLANG_TIDY)
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-qualified-auto,misc-unused-parameters,modernize-deprecated-ios-base-aliases,modernize-loop-convert,modernize-shrink-to-fit,modernize-use-auto,modernize-use-using,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
else()
unset(CMAKE_CXX_CLANG_TIDY CACHE)
endif()
include(GNUInstallDirs)
file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
@ -282,10 +298,10 @@ set(STANDARD_PACKAGES
ML-HDNNP
ML-IAP
ML-PACE
ML-POD
ML-QUIP
ML-RANN
ML-SNAP
ML-POD
ML-UF3
MOFFF
MOLECULE
@ -305,6 +321,7 @@ set(STANDARD_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SCAFACOS
SHOCK
@ -409,6 +426,7 @@ pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
pkg_depends(MESONT MOLECULE)
pkg_depends(RHEO BPM)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
@ -549,7 +567,7 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -939,6 +957,7 @@ message(STATUS "<<< Compilers and Flags: >>>
-- C++ Compiler: ${CMAKE_CXX_COMPILER}
Type: ${CMAKE_CXX_COMPILER_ID}
Version: ${CMAKE_CXX_COMPILER_VERSION}
C++ Standard: ${CMAKE_CXX_STANDARD}
C++ Flags: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
Defines: ${DEFINES}")
get_target_property(OPTIONS lammps COMPILE_OPTIONS)
@ -1045,9 +1064,6 @@ endif()
if(BUILD_TOOLS)
message(STATUS "<<< Building Tools >>>")
endif()
if(BUILD_LAMMPS_SHELL)
message(STATUS "<<< Building LAMMPS Shell >>>")
endif()
if(BUILD_LAMMPS_GUI)
message(STATUS "<<< Building LAMMPS GUI >>>")
if(LAMMPS_GUI_USE_PLUGIN)

2
cmake/Modules/Packages/ML-QUIP.cmake
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@ -27,7 +27,7 @@ if(DOWNLOAD_QUIP)
else()
message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
endif()
set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
set(temp "${temp}CFLAGS += -fPIC -Wno-return-mismatch \nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
set(temp "${temp}MATH_LINKOPTS=")
foreach(flag ${BLAS_LIBRARIES})
set(temp "${temp} ${flag}")

2
cmake/Modules/Packages/RHEO.cmake Normal file
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@ -0,0 +1,2 @@
find_package(GSL 2.7 REQUIRED)
target_link_libraries(lammps PRIVATE GSL::gsl)

4
cmake/Modules/Testing.cmake
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@ -102,9 +102,9 @@ endif()
#######################################
# select code sanitizer options
#######################################
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, hwaddress, leak, thread, undefined)")
mark_as_advanced(ENABLE_SANITIZER)
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
set(ENABLE_SANITIZER_VALUES none address hwaddress leak thread undefined)
set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)

31
cmake/Modules/Tools.cmake
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@ -37,37 +37,6 @@ if(BUILD_TOOLS)
add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
endif()
find_package(PkgConfig QUIET)
if(BUILD_LAMMPS_SHELL)
if(NOT PkgConfig_FOUND)
message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
endif()
find_package(PkgConfig REQUIRED)
pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
# include resource compiler to embed icons into the executable on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
enable_language(RC)
set(ICON_RC_FILE ${LAMMPS_TOOLS_DIR}/lammps-shell/lmpicons.rc)
endif()
add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
# workaround for broken readline pkg-config file on FreeBSD
if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
target_include_directories(lammps-shell PRIVATE /usr/local/include)
endif()
if(CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
pkg_check_modules(TERMCAP IMPORTED_TARGET REQUIRED termcap)
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::TERMCAP)
endif()
install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
endif()
if(BUILD_LAMMPS_GUI)
get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)

3
cmake/presets/all_off.cmake
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@ -26,8 +26,8 @@ set(ALL_PACKAGES
DPD-REACT
DPD-SMOOTH
DRUDE
ELECTRODE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
@ -82,6 +82,7 @@ set(ALL_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SCAFACOS
SHOCK

3
cmake/presets/all_on.cmake
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@ -28,8 +28,8 @@ set(ALL_PACKAGES
DPD-REACT
DPD-SMOOTH
DRUDE
ELECTRODE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
@ -84,6 +84,7 @@ set(ALL_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SCAFACOS
SHOCK

3
cmake/presets/mingw-cross.cmake
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@ -22,8 +22,8 @@ set(WIN_PACKAGES
DPD-REACT
DPD-SMOOTH
DRUDE
ELECTRODE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
@ -33,7 +33,6 @@ set(WIN_PACKAGES
FEP
GPU
GRANULAR
INTEL
INTERLAYER
KSPACE
LEPTON

2
cmake/presets/windows.cmake
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@ -52,8 +52,8 @@ set(WIN_PACKAGES
ORIENT
PERI
PHONON
POEMS
PLUGIN
POEMS
PTM
QEQ
QTB

4
doc/lammps.1
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@ -1,7 +1,7 @@
.TH LAMMPS "1" "17 April 2024" "2024-04-17"
.TH LAMMPS "1" "27 June 2024" "2024-06-27"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 17 April 2024
\- Molecular Dynamics Simulator. Version 27 June 2024
.SH SYNOPSIS
.B lmp

8
doc/src/Build_basics.rst
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@ -489,8 +489,7 @@ using CMake or Make.
.. code-block:: bash
-D BUILD_TOOLS=value # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt
-D BUILD_LAMMPS_SHELL=value # yes or no (default). Build lammps-shell
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build lammps-gui
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build LAMMPS-GUI
The generated binaries will also become part of the LAMMPS installation
(see below).
@ -505,8 +504,9 @@ using CMake or Make.
make chain # build only chain tool
make micelle2d # build only micelle2d tool
cd lammps/tools/lammps-shell
make # build LAMMPS shell
.. note::
Building the LAMMPS-GUI *requires* building LAMMPS with CMake.
----------

5
doc/src/Build_development.rst
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@ -88,8 +88,8 @@ on recording all commands required to do the compilation.
.. _sanitizer:
Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
----------------------------------------------------------------------
Address, Leak, Undefined Behavior, and Thread Sanitizer Support (CMake only)
----------------------------------------------------------------------------
Compilers such as GCC and Clang support generating instrumented binaries
which use different sanitizer libraries to detect problems in the code
@ -110,6 +110,7 @@ compilation and linking stages. This is done through setting the
-D ENABLE_SANITIZER=none # no sanitizer active (default)
-D ENABLE_SANITIZER=address # enable address sanitizer / memory leak checker
-D ENABLE_SANITIZER=hwaddress # enable hardware assisted address sanitizer / memory leak checker
-D ENABLE_SANITIZER=leak # enable memory leak checker (only)
-D ENABLE_SANITIZER=undefined # enable undefined behavior sanitizer
-D ENABLE_SANITIZER=thread # enable thread sanitizer

40
doc/src/Build_extras.rst
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@ -59,6 +59,7 @@ This is the list of packages that may require additional steps.
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`QMMM <qmmm>`
* :ref:`RHEO <rheo>`
* :ref:`SCAFACOS <scafacos>`
* :ref:`VORONOI <voronoi>`
* :ref:`VTK <vtk>`
@ -1566,10 +1567,11 @@ LAMMPS build.
.. tab:: CMake build
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
linked into LAMMPS.
command you must ensure that `the GNU Scientific Library (GSL)
<https://www.gnu.org/software/gsl/>` is installed in locations
that are accessible in your environment. There are then two
additional variables that control the manner in which PLUMED is
obtained and linked into LAMMPS.
.. code-block:: bash
@ -2040,6 +2042,36 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
----------
.. _rheo:
RHEO package
------------
To build with this package you must have the `GNU Scientific Library
(GSL) <https://www.gnu.org/software/gsl/>` installed in locations that
are accessible in your environment. The GSL library should be at least
version 2.7.
.. tabs::
.. tab:: CMake build
If CMake cannot find the GSL library or include files, you can set:
.. code-block:: bash
-D GSL_ROOT_DIR=path # path to root of GSL installation
.. tab:: Traditional make
LAMMPS will try to auto-detect the GSL compiler and linker flags
from the corresponding ``pkg-config`` file (``gsl.pc``), otherwise
you can edit the file ``lib/rheo/Makefile.lammps``
to specify the paths and library names where indicated by comments.
This must be done **before** the package is installed.
----------
.. _scafacos:
SCAFACOS package

8
doc/src/Build_link.rst
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@ -45,8 +45,8 @@ executable code from the library is copied into the calling executable.
.. code-block:: bash
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
mpicc -c -O $(pkg-config --cflags liblammps) caller.c
mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
.. tab:: Traditional make
@ -155,8 +155,8 @@ POEMS package installed becomes:
.. code-block:: bash
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf --libs)
mpicc -c -O $(pkg-config --cflags liblammps) caller.c
mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
.. tab:: Traditional make

1
doc/src/Build_package.rst
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@ -62,6 +62,7 @@ packages:
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`QMMM <qmmm>`
* :ref:`RHEO <rheo>`
* :ref:`SCAFACOS <scafacos>`
* :ref:`VORONOI <voronoi>`
* :ref:`VTK <vtk>`

1
doc/src/Commands_bond.rst
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@ -54,6 +54,7 @@ OPT.
* :doc:`oxdna2/fene <bond_oxdna>`
* :doc:`oxrna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`rheo/shell <bond_rheo_shell>`
* :doc:`special <bond_special>`
* :doc:`table (o) <bond_table>`

5
doc/src/Commands_compute.rst
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@ -108,6 +108,10 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`pe/mol/tally <compute_tally>`
* :doc:`pe/tally <compute_tally>`
* :doc:`plasticity/atom <compute_plasticity_atom>`
* :doc:`pod/atom <compute_pod_atom>`
* :doc:`podd/atom <compute_pod_atom>`
* :doc:`pod/local <compute_pod_atom>`
* :doc:`pod/global <compute_pod_atom>`
* :doc:`pressure <compute_pressure>`
* :doc:`pressure/alchemy <compute_pressure_alchemy>`
* :doc:`pressure/uef <compute_pressure_uef>`
@ -122,6 +126,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`reduce <compute_reduce>`
* :doc:`reduce/chunk <compute_reduce_chunk>`
* :doc:`reduce/region <compute_reduce>`
* :doc:`rheo/property/atom <compute_rheo_property_atom>`
* :doc:`rigid/local <compute_rigid_local>`
* :doc:`saed <compute_saed>`
* :doc:`slcsa/atom <compute_slcsa_atom>`

6
doc/src/Commands_fix.rst
View File

@ -28,6 +28,7 @@ OPT.
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
* :doc:`add/heat <fix_add_heat>`
* :doc:`addtorque <fix_addtorque>`
* :doc:`alchemy <fix_alchemy>`
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
@ -204,6 +205,11 @@ OPT.
* :doc:`reaxff/species (k) <fix_reaxff_species>`
* :doc:`recenter <fix_recenter>`
* :doc:`restrain <fix_restrain>`
* :doc:`rheo <fix_rheo>`
* :doc:`rheo/oxidation <fix_rheo_oxidation>`
* :doc:`rheo/pressure <fix_rheo_pressure>`
* :doc:`rheo/thermal <fix_rheo_thermal>`
* :doc:`rheo/viscosity <fix_rheo_viscosity>`
* :doc:`rhok <fix_rhok>`
* :doc:`rigid (o) <fix_rigid>`
* :doc:`rigid/meso <fix_rigid_meso>`

8
doc/src/Commands_pair.rst
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@ -35,6 +35,10 @@ OPT.
*
*
*
*
*
*
*
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@ -247,7 +251,7 @@ OPT.
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation (k) <pair_pace>`
* :doc:`pedone (o) <pair_pedone>`
* :doc:`pod <pair_pod>`
* :doc:`pod (k) <pair_pod>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`
@ -260,6 +264,8 @@ OPT.
* :doc:`rebo (io) <pair_airebo>`
* :doc:`rebomos (o) <pair_rebomos>`
* :doc:`resquared (go) <pair_resquared>`
* :doc:`rheo <pair_rheo>`
* :doc:`rheo/solid <pair_rheo_solid>`
* :doc:`saip/metal (t) <pair_saip_metal>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
* :doc:`smatb <pair_smatb>`

31
doc/src/Commands_removed.rst
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@ -8,6 +8,18 @@ stop LAMMPS and print a suitable error message in most cases, when a
style/command is used that has been removed or will replace the command
with the direct alternative (if available) and print a warning.
restart2data tool
-----------------
.. versionchanged:: 23Nov2013
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command line flags <Run_options>`
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
@ -151,17 +163,16 @@ and allow running LAMMPS with GPU acceleration.
i-PI tool
---------
.. versionchanged:: TBD
.. versionchanged:: 27Jun2024
The i-PI tool has been removed from the LAMMPS distribution. Instead,
instructions to install i-PI from PyPi via pip are provided.
instructions to install i-PI from PyPI via pip are provided.
restart2data tool
-----------------
LAMMPS shell
------------
.. versionchanged:: TBD
The LAMMPS shell has been removed from the LAMMPS distribution. Users
are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command line flags <Run_options>`

3
doc/src/Developer_utils.rst
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@ -211,6 +211,9 @@ Argument processing
.. doxygenfunction:: bounds
:project: progguide
.. doxygenfunction:: bounds_typelabel
:project: progguide
.. doxygenfunction:: expand_args
:project: progguide

24
doc/src/Developer_write_pair.rst
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@ -50,6 +50,30 @@ We are looking at the following cases:
- `Case 3: a potential requiring communication`_
- `Case 4: potentials without a compute() function`_
Package and build system considerations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In general, new pair styles should be added to the :ref:`EXTRA-PAIR
package <PKG-EXTRA-PAIR>` unless they are an accelerated pair style and
then they should be added to the corresponding accelerator package
(:ref:`GPU <PKG-GPU>`, :ref:`INTEL <PKG-INTEL>`, :ref:`KOKKOS
<PKG-KOKKOS>`, :ref:`OPENMP <PKG-OPENMP>`, :ref:`OPT <PKG-OPT>`). If
you feel that your contribution should be added to a different package,
please consult with the LAMMPS developers first.
The contributed code needs to support the :doc:`traditional GNU make
build process <Build_make>` **and** the :doc:`CMake build process
<Build_cmake>`. For the GNU make process and if the package has an
``Install.sh`` file, most likely that file needs to be updated to
correctly copy the sources when installing the package and properly
delete them when uninstalling. This is particularly important when
added a new pair style that is a derived class from an existing pair
style in a package, so that its installation depends on the the
installation status of the package of the derived class. For the CMake
process, it is sometimes necessary to make changes to the package
specific CMake scripting in ``cmake/Modules/Packages``.
----
Case 1: a pairwise additive model

2
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@ -134,6 +134,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| rerun | use of rerun and read_dump commands |
+-------------+------------------------------------------------------------------+
| rheo | RHEO simulations of fluid flows and phase transitions |
+-------------+------------------------------------------------------------------+
| rigid | rigid bodies modeled as independent or coupled |
+-------------+------------------------------------------------------------------+
| shear | sideways shear applied to 2d solid, with and without a void |

2
doc/src/Fortran.rst
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@ -2327,7 +2327,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
retrieved via :f:func:`get_last_error_message`. This allows to
restart a calculation or delete and recreate the LAMMPS instance when
a C++ exception occurs. One application of using exceptions this way
is the :ref:`lammps_shell`.
is the :ref:`lammps_gui`.
:to: :cpp:func:`lammps_config_has_exceptions`
:r has_exceptions:

1
doc/src/Howto.rst
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@ -89,6 +89,7 @@ Packages howto
Howto_drude2
Howto_peri
Howto_manifold
Howto_rheo
Howto_spins
Tutorials howto

198
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@ -1,6 +1,10 @@
CHARMM, AMBER, COMPASS, and DREIDING force fields
=================================================
A compact summary of the concepts, definitions, and properties of
force fields with explicit bonded interactions (like the ones discussed
in this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly used
@ -11,12 +15,42 @@ commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
<bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc page for
additional tools that can use CHARMM, AMBER, or Materials Studio
generated files to assign force field coefficients and convert their
output into LAMMPS input.
output into LAMMPS input. LAMMPS input scripts can also be generated by
`charmm-gui.org <https://charmm-gui.org/>`_.
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
force field. See :ref:`(Cornell) <howto-Cornell>` for a description of
the AMBER force field. See :ref:`(Sun) <howto-Sun>` for a description
of the COMPASS force field.
CHARMM and AMBER
----------------
The `CHARMM force field
<https://mackerell.umaryland.edu/charmm_ff.shtml>`_ :ref:`(MacKerell)
<howto-MacKerell>` and `AMBER force field
<https://ambermd.org/AmberModels.php>`_ :ref:`(Cornell) <howto-Cornell>`
have potential energy function of the form
.. math::
V & = \sum_{bonds} E_b + \sum_{angles} \!E_a + \!\overbrace{\sum_{dihedral} \!\!E_d}^{\substack{
\text{charmm} \\
\text{charmmfsw}
}} +\!\!\! \sum_{impropers} \!\!\!E_i \\[.6em]
& \quad + \!\!\!\!\!\!\!\!\!\!\underbrace{~\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}_{\substack{
\text{lj/charmm/coul/charmm} \\
\text{lj/charmm/coul/charmm/implicit} \\
\text{lj/charmm/coul/long} \\
\text{lj/charmm/coul/msm} \\
\text{lj/charmmfsw/coul/charmmfsh} \\
\text{lj/charmmfsw/coul/long}
}} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{CMAP}(\phi,\psi)}
The terms are computed by bond styles (relationship between 2 atoms),
angle styles (between 3 atoms) , dihedral/improper styles (between 4
atoms), pair styles (non-covalently bonded pair interactions) and
special bonds. The CMAP term (see :doc:`fix cmap <fix_cmap>` command for
details) corrects for pairs of dihedral angles ("Correction MAP") to
significantly improve the structural and dynamic properties of proteins
in crystalline and solution environments :ref:`(Brooks)
<howto-Brooks>`. The AMBER force field does not include the CMAP term.
The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each
@ -31,10 +65,81 @@ command's documentation for the formula it computes.
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm/implicit
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/long
* :doc:`special_bonds <special_bonds>` charmm
* :doc:`special_bonds <special_bonds>` amber
The pair styles compute Lennard Jones (LJ) and Coulombic interactions
with additional switching or shifting functions that ramp the energy
and/or force smoothly to zero between an inner :math:`(a)` and outer
:math:`(b)` cutoff. The older styles with *charmm* (not *charmmfsw* or
*charmmfsh*\ ) in their name compute the LJ and Coulombic interactions
with an energy switching function (esw) S(r) which ramps the energy
smoothly to zero between the inner and outer cutoff. This can cause
irregularities in pairwise forces (due to the discontinuous second
derivative of energy at the boundaries of the switching region), which
in some cases can result in complications in energy minimization and
detectable artifacts in MD simulations.
.. grid:: 1 1 2 2
.. grid-item::
.. math::
LJ(r) &= 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]\\[.6em]
C(r) &= \frac{C q_i q_j}{ \epsilon r}\\[.6em]
S(r) &= \frac{ \left(b^2 - r^2\right)^2 \left(b^2 + 2r^2 - 3{a^2}\right)}
{ \left(b^2 - a^2\right)^3 }\\[.6em]
E_{LJ}(r) &= \begin{cases}
LJ(r), & r \leq a \\
LJ(r) S(r), & a < r \leq b \\
0, &r > b
\end{cases} \\[.6em]
E_{coul}(r) &= \begin{cases}
C(r), & r \leq a \\
C(r) S(r), & a < r \leq b \\
0, & r > b
\end{cases}
.. grid-item::
.. image:: img/howto_charmm_ELJ.png
:align: center
The newer styles with *charmmfsw* or *charmmfsh* in their name replace
energy switching with force switching (fsw) for LJ interactions and
force shifting (fsh) functions for Coulombic interactions
:ref:`(Steinbach) <howto-Steinbach>`
.. grid:: 1 1 2 2
.. grid-item::
.. math::
E_{LJ}(r) = & \begin{cases}
4 \epsilon \sigma^6 \left(\frac{\displaystyle\sigma
^6-r^6}{\displaystyle r^{12}}-\frac{\displaystyle\sigma ^6}{\displaystyle a^6
b^6}+\frac{\displaystyle 1}{\displaystyle a^3 b^3}\right) & r\leq a \\
\frac{\displaystyle 4 \epsilon \sigma^6 \left(\sigma ^6
\left(b^6-r^6\right)^2-b^3 r^6 \left(a^3+b^3\right)
\left(b^3-r^3\right)^2\right)}{\displaystyle b^6 r^{12}
\left(b^6-a^6\right)} & a<r \leq b\\
0, & r>b
\end{cases}\\[.6em]
E_{coul}(r) & = \begin{cases}
C(r) \frac{\displaystyle (b-r)^2}{\displaystyle r b^2}, & r \leq b \\
0, & r > b
\end{cases}
.. grid-item::
.. image:: img/howto_charmmfsw_ELJ.png
:align: center
These styles are used by LAMMPS input scripts generated by
https://charmm-gui.org/ :ref:`(Brooks) <howto-Brooks>`.
.. note::
For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
@ -43,17 +148,33 @@ command's documentation for the formula it computes.
<pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
pages.
.. note::
The TIP3P water model is strongly recommended for use with the CHARMM
force field. In fact, `"using the SPC model with CHARMM parameters is
a bad idea"
<https://matsci.org/t/using-spc-water-with-charmm-ff/24715>`_ and `"to
enable TIP4P style water in CHARMM, you would have to write a new pair
style"
<https://matsci.org/t/hybrid-pair-styles-for-charmm-and-tip4p-ew/32609>`_
. LAMMPS input scripts generated by Solution Builder on https://charmm-gui.org
use TIP3P molecules for solvation. Any other water model can and
probably will lead to false conclusions.
COMPASS
-------
COMPASS is a general force field for atomistic simulation of common
organic molecules, inorganic small molecules, and polymers which was
developed using ab initio and empirical parameterization techniques.
See the :doc:`Tools <Tools>` page for the msi2lmp tool for creating
LAMMPS template input and data files from BIOVIA's Materials Studio
files. Please note that the msi2lmp tool is very old and largely
unmaintained, so it does not support all features of Materials Studio
provided force field files, especially additions during the last decade.
You should watch the output carefully and compare results, where
possible. See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS force
field.
developed using ab initio and empirical parameterization techniques
:ref:`(Sun) <howto-Sun>`. See the :doc:`Tools <Tools>` page for the
msi2lmp tool for creating LAMMPS template input and data files from
BIOVIA's Materials Studio files. Please note that the msi2lmp tool is
very old and largely unmaintained, so it does not support all features
of Materials Studio provided force field files, especially additions
during the last decade. You should watch the output carefully and
compare results, where possible. See :ref:`(Sun) <howto-Sun>` for a
description of the COMPASS force field.
These interaction styles listed below compute force field formulas that
are consistent with the COMPASS force field. See each command's
@ -70,14 +191,21 @@ documentation for the formula it computes.
* :doc:`special_bonds <special_bonds>` lj/coul 0 0 1
DREIDING is a generic force field developed by the `Goddard group <http://www.wag.caltech.edu>`_ at Caltech and is useful for
predicting structures and dynamics of organic, biological and main-group
inorganic molecules. The philosophy in DREIDING is to use general force
constants and geometry parameters based on simple hybridization
considerations, rather than individual force constants and geometric
parameters that depend on the particular combinations of atoms involved
in the bond, angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond term <pair_hbond_dreiding>` to describe interactions involving a
hydrogen atom on very electronegative atoms (N, O, F).
DREIDING
--------
DREIDING is a generic force field developed by the `Goddard group
<http://www.wag.caltech.edu>`_ at Caltech and is useful for predicting
structures and dynamics of organic, biological and main-group inorganic
molecules. The philosophy in DREIDING is to use general force constants
and geometry parameters based on simple hybridization considerations,
rather than individual force constants and geometric parameters that
depend on the particular combinations of atoms involved in the bond,
angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond
term <pair_hbond_dreiding>` to describe interactions involving a
hydrogen atom on very electronegative atoms (N, O, F). Unlike CHARMM
or AMBER, the DREIDING force field has not been parameterized for
considering solvents (like water).
See :ref:`(Mayo) <howto-Mayo>` for a description of the DREIDING force field
@ -110,21 +238,31 @@ documentation for the formula it computes.
----------
.. _Typelabel2:
**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
.. _howto-MacKerell:
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al (1998). J Phys Chem, 102, 3586 . https://doi.org/10.1021/jp973084f
.. _howto-Cornell:
**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman (1995). JACS 117, 5179-5197. https://doi.org/10.1021/ja00124a002
.. _howto-Steinbach:
**(Steinbach)** Steinbach, Brooks (1994). J Comput Chem, 15, 667. https://doi.org/10.1002/jcc.540150702
.. _howto-Brooks:
**(Brooks)** Brooks, et al (2009). J Comput Chem, 30, 1545. https://onlinelibrary.wiley.com/doi/10.1002/jcc.21287
.. _howto-Sun:
**(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
**(Sun)** Sun (1998). J. Phys. Chem. B, 102, 7338-7364. https://doi.org/10.1021/jp980939v
.. _howto-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
**(Mayo)** Mayo, Olfason, Goddard III (1990). J Phys Chem, 94, 8897-8909. https://doi.org/10.1021/j100389a010

18
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@ -1,7 +1,7 @@
Use chunks to calculate system properties
=========================================
In LAMMS, "chunks" are collections of atoms, as defined by the
In LAMMPS, "chunks" are collections of atoms, as defined by the
:doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns
each atom to a chunk ID (or to no chunk at all). The number of chunks
and the assignment of chunk IDs to atoms can be static or change over
@ -148,14 +148,14 @@ Example calculations with chunks
Here are examples using chunk commands to calculate various
properties:
(1) Average velocity in each of 1000 2d spatial bins:
1. Average velocity in each of 1000 2d spatial bins:
.. code-block:: LAMMPS
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
(2) Temperature in each spatial bin, after subtracting a flow
2. Temperature in each spatial bin, after subtracting a flow
velocity:
.. code-block:: LAMMPS
@ -164,7 +164,7 @@ velocity:
compute vbias all temp/profile 1 0 0 y 10
fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
(3) Center of mass of each molecule:
3. Center of mass of each molecule:
.. code-block:: LAMMPS
@ -172,7 +172,7 @@ velocity:
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
(4) Total force on each molecule and ave/max across all molecules:
4. Total force on each molecule and ave/max across all molecules:
.. code-block:: LAMMPS
@ -183,7 +183,7 @@ velocity:
thermo 1000
thermo_style custom step temp v_xave v_xmax
(5) Histogram of cluster sizes:
5. Histogram of cluster sizes:
.. code-block:: LAMMPS
@ -192,16 +192,16 @@ velocity:
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
(6) An example for using a per-chunk value to apply per-atom forces to
6. An example for using a per-chunk value to apply per-atom forces to
compress individual polymer chains (molecules) in a mixture, is
explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
(7) An example for using one set of per-chunk values for molecule
7. An example for using one set of per-chunk values for molecule
chunks, to create a second set of micelle-scale chunks (clustered
molecules, due to hydrophobicity), is explained on the
:doc:`compute reduce/chunk <compute_reduce_chunk>` command doc page.
(8) An example for using one set of per-chunk values (dipole moment
8. An example for using one set of per-chunk values (dipole moment
vectors) for molecule chunks, spreading the values to each atom in
each chunk, then defining a second set of chunks as spatial bins, and
using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an

2
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@ -339,8 +339,6 @@ Some common LAMMPS specific variables
- build LAMMPS with OpenMP support (default: ``on`` if compiler supports OpenMP fully, else ``off``)
* - ``BUILD_TOOLS``
- compile some additional executables from the ``tools`` folder (default: ``off``)
* - ``BUILD_LAMMPS_SHELL``
- compile the LAMMPS shell from the ``tools/lammps-shell`` folder (default: ``off``)
* - ``BUILD_DOC``
- include building the HTML format documentation for packaging/installing (default: ``off``)
* - ``CMAKE_TUNE_FLAGS``

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@ -1,11 +1,11 @@
Using the LAMMPS GUI
Using the LAMMPS-GUI
====================
This document describes **LAMMPS GUI version 1.5**.
This document describes **LAMMPS-GUI version 1.6**.
-----
LAMMPS GUI is a graphical text editor customized for editing LAMMPS
LAMMPS-GUI is a graphical text editor customized for editing LAMMPS
input files that is linked to the :ref:`LAMMPS library <lammps_c_api>`
and thus can run LAMMPS directly using the contents of the editor's text
buffer as input. It can retrieve and display information from LAMMPS
@ -16,58 +16,60 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
.. note::
Pre-compiled, ready-to-use LAMMPS GUI executables for Linux (Ubuntu
Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux (Ubuntu
20.04LTS or later and compatible), macOS (version 11 aka Big Sur or
later), and Windows (version 10 or later) :ref:`are available
<lammps_gui_install>` for download. They may be linked to a
development version of LAMMPS in case they need features not yet
available in a released version. Serial LAMMPS executables of the
same LAMMPS version are included as well. The source code for the
LAMMPS GUI is included in the LAMMPS source code and can be found in
the ``tools/lammps-gui`` folder. It can be compiled alongside LAMMPS
when :doc:`compiling with CMake <Build_cmake>`.
<lammps_gui_install>` for download. None-MPI LAMMPS executables of
the same LAMMPS version are included in these packages as well. The
source code for the LAMMPS-GUI is included in the LAMMPS source code
distribution and can be found in the ``tools/lammps-gui`` folder. It
can be compiled alongside LAMMPS when :doc:`compiling with CMake
<Build_cmake>`.
LAMMPS GUI tries to provide an experience similar to what people
traditionally would do to run LAMMPS using a command line window:
LAMMPS-GUI tries to provide an experience similar to what people
traditionally would do to run LAMMPS using a command line window
but just rolled into a single executable:
- editing LAMMPS input files with a text editor
- run LAMMPS on those input file with selected command line flags
- use or extract data from the created files and visualize it with
either a molecular visualization program or a plotting program
- editing inputs with a text editor
- run LAMMPS on the input with selected command line flags
- and then use or extract data from the created files and visualize it
That procedure is quite effective for people proficient in using the
command line, as that allows them to use tools for the individual steps
which they are most comfortable with. It is often required when running
LAMMPS on high-performance computing facilities.
that they are most comfortable with. It is often *required* to adopt
this workflow when running LAMMPS simulations on high-performance
computing facilities.
The main benefit of using the LAMMPS GUI application instead is that
The main benefit of using the LAMMPS-GUI application instead is that
many basic tasks can be done directly from the GUI without switching to
a text console window or using external programs, let alone writing
scripts to extract data from the generated output. It also integrates
well with graphical desktop environments.
LAMMPS GUI thus makes it easier for beginners to get started running
LAMMPS-GUI thus makes it easier for beginners to get started running
simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS
since you only need to learn how to use a single program for most tasks
and thus time can be saved and people can focus on learning LAMMPS. It
is also designed to keep the barrier low when you decide to switch to a
full featured, standalone programming editor and more sophisticated
visualization and analysis tools and run LAMMPS from a command line.
visualization and analysis tools, and run LAMMPS from the command line
or a batch script.
The following text provides a detailed tour of the features and
functionality of the LAMMPS GUI.
Suggestions for new features and reports of bugs are always welcome.
You can use the :doc:`the same channels as for LAMMPS itself
<Errors_bugs>` for that purpose.
functionality of the LAMMPS-GUI. Suggestions for new features and
reports of bugs are always welcome. You can use the :doc:`the same
channels as for LAMMPS itself <Errors_bugs>` for that purpose.
-----
Main window
-----------
Starting LAMMPS-GUI
-------------------
When LAMMPS GUI starts, it will show a main window with either an
empty buffer or the contents of a loaded file. In the latter case it
may look like the following:
When LAMMPS-GUI starts, it shows the main window, labeled *Editor*, with
either an empty buffer or the contents of the file used as argument. In
the latter case it may look like the following:
.. image:: JPG/lammps-gui-main.png
:align: center
@ -80,32 +82,34 @@ the LAMMPS input file syntax. The status bar shows the status of
LAMMPS execution on the left (e.g. "Ready." when idle) and the current
working directory on the right. The name of the current file in the
buffer is shown in the window title; the word `*modified*` is added if
the buffer edits have not yet saved to a file. The size of the main
window will be stored when exiting and restored when starting again.
the buffer edits have not yet saved to a file. The geometry of the main
window is stored when exiting and restored when starting again.
Opening Files
^^^^^^^^^^^^^
The LAMMPS GUI application will try to open the first command line
argument as a LAMMPS input script, further arguments are ignored.
When no argument is given, LAMMPS GUI will start with an empty buffer.
Files can also be opened via the ``File`` menu or by drag-and-drop of
a file from a graphical file manager into the editor window. Only one
file can be open at a time, so opening a new file with a filled buffer
will close the buffer. If the buffer has unsaved modifications, you
will be asked to either cancel the operation, discard the changes, or
save them.
The LAMMPS-GUI application tries to open the first command line argument
as a LAMMPS input script, further arguments are ignored. When no
argument is given, LAMMPS-GUI starts with an empty buffer. Files can
also be opened via the ``File`` menu or by drag-and-drop of a file from
a graphical file manager into the editor window. Only one file can be
edited at a time, so opening a new file with a filled buffer closes that
buffer. If the buffer has unsaved modifications, you are asked to
either cancel the operation, discard the changes, or save them. A
buffer with modifications can be saved any time from the "File" menu, by
the keyboard shortcut `Ctrl-S` (`Command-S` on macOS), or by clicking on
the "Save" button at the very left in the status bar.
Running LAMMPS
^^^^^^^^^^^^^^
From within the LAMMPS GUI main window LAMMPS can be started either from
From within the LAMMPS-GUI main window LAMMPS can be started either from
the ``Run`` menu using the ``Run LAMMPS from Editor Buffer`` entry, by
the keyboard shortcut `Ctrl-Enter` (`Command-Enter` on macOS), or by
clicking on the green "Run" button in the status bar. All of these
operations will cause LAMMPS to process the entire input script, which
may contain multiple :doc:`run <run>` or :doc:`minimize <minimize>`
commands.
operations causes LAMMPS to process the entire input script in the
editor buffer, which may contain multiple :doc:`run <run>` or
:doc:`minimize <minimize>` commands.
LAMMPS runs in a separate thread, so the GUI stays responsive and is
able to interact with the running calculation and access data it
@ -128,33 +132,30 @@ before LAMMPS can be run from a file.
While LAMMPS is running, the contents of the status bar change. On
the left side there is a text indicating that LAMMPS is running, which
will also show the number of active threads, if thread-parallel
also indicates the number of active threads, when thread-parallel
acceleration was selected in the ``Preferences`` dialog. On the right
side, a progress bar is shown that displays the estimated progress for
the current :doc:`run command <run>`.
the current :doc:`run <run>` or :doc:`minimize <minimize>` command.
Also, the line number of the currently executed command will be
highlighted in green.
.. image:: JPG/lammps-gui-run-highlight.png
:align: center
:scale: 75%
Also, the line number of the currently executed command is highlighted
in green.
If an error occurs (in the example below the command :doc:`label
<label>` was incorrectly capitalized as "Label"), an error message
dialog will be shown and the line of the input which triggered the
error will be highlighted. The state of LAMMPS in the status bar will
be set to "Failed." instead of "Ready."
dialog is shown and the line of the input which triggered the error is
highlighted. The state of LAMMPS in the status bar is set to "Failed."
instead of "Ready."
.. image:: JPG/lammps-gui-run-error.png
:align: center
:scale: 75%
Up to three additional windows will open during a run:
Up to three additional windows may open during a run:
- a log window with the captured screen output
- a chart window with a line graph created from the thermodynamic output of the run
- a slide show window with images created by a :doc:`dump image command <dump_image>`
- an *Output* window with the captured screen output from LAMMPS
- a *Charts* window with a line graph created from thermodynamic output of the run
- a *Slide Show* window with images created by a :doc:`dump image command <dump_image>`
in the input
More information on those windows and how to adjust their behavior and
contents is given below.
@ -171,55 +172,68 @@ This is equivalent to the input script command :doc:`timer timeout 0
interface. Please see the corresponding documentation pages to
understand the implications of this operation.
Log Window
----------
Output Window
-------------
By default, when starting a run, a "Log Window" will open that displays
the current screen output of the LAMMPS calculation, that would normally
be seen in the command line window, as shown below.
By default, when starting a run, an *Output* window opens that displays
the screen output of the running LAMMPS calculation, as shown below.
This text would normally be seen in the command line window.
.. image:: JPG/lammps-gui-log.png
:align: center
:scale: 50%
LAMMPS GUI captures the screen output as it is generated and updates
the log window regularly during a run.
LAMMPS-GUI captures the screen output from LAMMPS as it is generated and
updates the *Output* window regularly during a run.
By default, the log window will be replaced each time a run is started.
By default, the *Output* window is replaced each time a run is started.
The runs are counted and the run number for the current run is displayed
in the window title. It is possible to change the behavior of LAMMPS
GUI in the preferences dialog to create a *new* log window for every run
or to not show the current log window. It is also possible to show or
hide the *current* log window from the ``View`` menu.
in the window title. It is possible to change the behavior of
LAMMPS-GUI in the preferences dialog to create a *new* *Output* window
for every run or to not show the current *Output* window. It is also
possible to show or hide the *current* *Output* window from the ``View``
menu.
The text in the log window is read-only and cannot be modified, but
The text in the *Output* window is read-only and cannot be modified, but
keyboard shortcuts to select and copy all or parts of the text can be
used to transfer text to another program. Also, the keyboard shortcut
`Ctrl-S` (`Command-S` on macOS) is available to save the log buffer to a
`Ctrl-S` (`Command-S` on macOS) is available to save the *Output* buffer to a
file. The "Select All" and "Copy" functions, as well as a "Save Log to
File" option are also available from a context menu by clicking with the
right mouse button into the log window text area.
right mouse button into the *Output* window text area.
Chart Window
------------
By default, when starting a run, a "Chart Window" will open that
displays a plot of thermodynamic output of the LAMMPS calculation as
shown below.
.. image:: JPG/lammps-gui-chart.png
.. image:: JPG/lammps-gui-yaml.png
:align: center
:scale: 50%
.. versionadded:: 1.6
Should the *Output* window contain embedded YAML format text (see above for a
demonstration), for example from using :doc:`thermo_style yaml
<thermo_style>` or :doc:`thermo_modify line yaml <thermo_modify>`, the
keyboard shortcut `Ctrl-Y` (`Command-Y` on macOS) is available to save
only the YAML parts to a file. This option is also available from a
context menu by clicking with the right mouse button into the *Output* window
text area.
Charts Window
-------------
By default, when starting a run, a *Charts* window opens that displays a
plot of thermodynamic output of the LAMMPS calculation as shown below.
.. image:: JPG/lammps-gui-chart.png
:align: center
:scale: 33%
The drop down menu on the top right allows selection of different
properties that are computed and written to thermo output. Only one
property can be shown at a time. The plots will be updated with new
data as the run progresses, so they can be used to visually monitor the
evolution of available properties. The window title will show the
current run number that this chart window corresponds to. Same as
explained for the log window above, by default, the chart window will
be replaced on each new run, but the behavior can be changed in the
preferences dialog.
property can be shown at a time. The plots are updated with new data as
the run progresses, so they can be used to visually monitor the
evolution of available properties. The window title shows the current
run number that this chart window corresponds to. Same as for the
*Output* window, the chart window is replaced on each new run, but the
behavior can be changed in the preferences dialog.
From the ``File`` menu on the top left, it is possible to save an image
of the currently displayed plot or export the data in either plain text
@ -229,19 +243,20 @@ columns (for use by plotting tools like `gnuplot
be imported for further processing with Microsoft Excel or `pandas
<https://pandas.pydata.org/>`_
Thermo output data from successive run commands in the input script will
be combined into a single data set unless the format, number, or names
of output columns are changed with a :doc:`thermo_style <thermo_style>`
or a :doc:`thermo_modify <thermo_modify>` command, or the current time
step is reset with :doc:`reset_timestep <reset_timestep>`, or if a
Thermo output data from successive run commands in the input script is
combined into a single data set unless the format, number, or names of
output columns are changed with a :doc:`thermo_style <thermo_style>` or
a :doc:`thermo_modify <thermo_modify>` command, or the current time step
is reset with :doc:`reset_timestep <reset_timestep>`, or if a
:doc:`clear <clear>` command is issued.
Image Slide Show
----------------
By default, if the LAMMPS input contains a :doc:`dump image
<dump_image>` command, a "Slide Show" window will open which loads and
displays the images created by LAMMPS as they are written.
<dump_image>` command, a "Slide Show" window opens which loads and
displays the images created by LAMMPS as they are written. This is a
convenient way to visually monitor the progress of the simulation.
.. image:: JPG/lammps-gui-slideshow.png
:align: center
@ -250,9 +265,17 @@ displays the images created by LAMMPS as they are written.
The various buttons at the bottom right of the window allow single
stepping through the sequence of images or playing an animation (as a
continuous loop or once from first to last). It is also possible to
zoom in or zoom out of the displayed images, and to export the slide
show animation to a movie file, if `ffmpeg <https://ffmpeg.org/>`_ is
installed.
zoom in or zoom out of the displayed images. The button on the very
left triggers an export of the slide show animation to a movie file,
provided the `FFmpeg program <https://ffmpeg.org/>`_ is installed.
.. versionadded:: 1.6
When clicking on the "garbage can" icon, all image files of the slide
show will be deleted. Since their number can be large for long
simulations, this option enables to safely and quickly clean up the
clutter caused in the working directory by those image files without
risk of deleting other files by accident when using wildcards.
Variable Info
-------------
@ -260,23 +283,22 @@ Variable Info
During a run, it may be of interest to monitor the value of input script
variables, for example to monitor the progress of loops. This can be
done by enabling the "Variables Window" in the ``View`` menu or by using
the `Ctrl-Shift-W` keyboard shortcut. This will show info similar to
the :doc:`info variables <info>` command in a separate window as shown
the `Ctrl-Shift-W` keyboard shortcut. This shows info similar to the
:doc:`info variables <info>` command in a separate window as shown
below.
.. image:: JPG/lammps-gui-variable-info.png
:align: center
:scale: 75%
Like the log and chart windows, its content is continuously updated
during a run. It will show "(none)" if there are no variables
Like for the *Output* and *Charts* windows, its content is continuously
updated during a run. It will show "(none)" if there are no variables
defined. Note that it is also possible to *set* :doc:`index style
variables <variable>`, that would normally be set via command line
flags, via the "Set Variables..." dialog from the ``Run`` menu.
LAMMPS GUI will automatically set the variable "gui_run" to the
current value of the run counter. That way it would be possible
to automatically record a log for each run attempt by using the
command
LAMMPS-GUI automatically defines the variable "gui_run" to the current
value of the run counter. That way it is possible to automatically
record a separate log for each run attempt by using the command
.. code-block:: LAMMPS
@ -285,26 +307,34 @@ command
at the beginning of an input file. That would record logs to files
``logfile-1.txt``, ``logfile-2.txt``, and so on for successive runs.
Viewing Snapshot Images
-----------------------
Snapshot Image Viewer
---------------------
By selecting the ``Create Image`` entry in the ``Run`` menu, or by
hitting the `Ctrl-I` (`Command-I` on macOS) keyboard shortcut, or by
clicking on the "palette" button in the status bar, LAMMPS GUI will send
a custom :doc:`write_dump image <dump_image>` command to LAMMPS and read
the resulting snapshot image with the current state of the system into
an image viewer window. This functionality is not available *during* an
ongoing run. When LAMMPS is not yet initialized, LAMMPS GUI will try to
identify the line with the first run or minimize command and execute all
command up to that line from the input buffer and then add a "run 0"
command. This will initialize the system so an image of the initial
state of the system can be rendered. If there was an error, the
snapshot image viewer will not appear.
clicking on the "palette" button in the status bar of the *Editor*
window, LAMMPS-GUI sends a custom :doc:`write_dump image <dump_image>`
command to LAMMPS and reads back the resulting snapshot image with the
current state of the system into an image viewer. This functionality is
*not* available *during* an ongoing run. In case LAMMPS is not yet
initialized, LAMMPS-GUI tries to identify the line with the first run or
minimize command and execute all commands from the input buffer up to
that line, and then executes a "run 0" command. This initializes the
system so an image of the initial state of the system can be rendered.
If there was an error in that process, the snapshot image viewer does
not appear.
When possible, LAMMPS GUI will try to detect which elements the atoms
correspond to (via their mass) and then colorize them in the image
accordingly. Otherwise the default predefined sequence of colors is
assigned to the different atom types.
When possible, LAMMPS-GUI tries to detect which elements the atoms
correspond to (via their mass) and then colorize them in the image and
set their atom diameters accordingly. If this is not possible, for
instance when using reduced (= 'lj') :doc:`units <units>`, then
LAMMPS-GUI will check the current pair style and if it is a
Lennard-Jones type potential, it will extract the *sigma* parameter
for each atom type and assign atom diameters from those numbers.
Otherwise the default sequence of colors of the :doc:`dump image
<dump_image>` command is assigned to the different atom types and the
diameters are all the same.
.. image:: JPG/lammps-gui-image.png
:align: center
@ -314,33 +344,43 @@ The default image size, some default image quality settings, the view
style and some colors can be changed in the ``Preferences`` dialog
window. From the image viewer window further adjustments can be made:
actual image size, high-quality (SSAO) rendering, anti-aliasing, view
style, display of box or axes, zoom factor. The view of the system
can be rotated horizontally and vertically. It is also possible to
only display the atoms within a group defined in the input script
(default is "all"). After each change, the image is rendered again
and the display updated. The small palette icon on the top left will
be colored while LAMMPS is running to render the new image; it will be
grayed out when it is finished. When there are many atoms to render
and high quality images with anti-aliasing are requested, re-rendering
may take several seconds. From the ``File`` menu of the image window,
the current image can be saved to a file or copied into the
cut-n-paste buffer for pasting into another application.
style, display of box or axes, zoom factor. The view of the system can
be rotated horizontally and vertically. It is also possible to only
display the atoms within a group defined in the input script (default is
"all"). After each change, the image is rendered again and the display
updated. The small palette icon on the top left is colored while LAMMPS
is running to render the new image; it is grayed out when LAMMPS is
finished. When there are many atoms to render and high quality images
with anti-aliasing are requested, re-rendering may take several seconds.
From the ``File`` menu of the image window, the current image can be
saved to a file (keyboard shortcut `Ctrl-S`) or copied to the clipboard
(keyboard shortcut `Ctrl-C`) for pasting the image into another
application.
Editor Functions
----------------
.. versionadded:: 1.6
The editor has most of the usual functionality that similar programs
have: text selection via mouse or with cursor moves while holding the
Shift key, Cut (`Ctrl-X`), Copy (`Ctrl-C`), Paste (`Ctrl-V`), Undo
(`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All (`Ctrl-A`). When trying
to exit the editor with a modified buffer, a dialog will pop up asking
whether to cancel the exit operation, or to save or not save the buffer
contents to a file.
From the ``File`` menu it is also possible to copy the current
:doc:`dump image <dump_image>` and :doc:`dump_modify <dump_image>`
commands to the clipboard so they can be pasted into a LAMMPS input file
so that the visualization settings of the snapshot image can be repeated
for the entire simulation (and thus be repeated in the slide show
viewer). This feature has the keyboard shortcut `Ctrl-D`.
Editor Window
-------------
The *Editor* window of LAMMPS-GUI has most of the usual functionality
that similar programs have: text selection via mouse or with cursor
moves while holding the Shift key, Cut (`Ctrl-X`), Copy (`Ctrl-C`),
Paste (`Ctrl-V`), Undo (`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All
(`Ctrl-A`). When trying to exit the editor with a modified buffer, a
dialog will pop up asking whether to cancel the exit operation, or to
save or not save the buffer contents to a file.
Context Specific Word Completion
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
By default, LAMMPS GUI will display a small pop-up frame with possible
By default, LAMMPS-GUI displays a small pop-up frame with possible
choices for LAMMPS input script commands or styles after 2 characters of
a word have been typed.
@ -354,10 +394,10 @@ by clicking on the entry with the mouse. The automatic completion
pop-up can be disabled in the ``Preferences`` dialog, but the completion
can still be requested manually by either hitting the 'Shift-TAB' key or
by right-clicking with the mouse and selecting the option from the
context menu. Most of the completion information is taken from the
LAMMPS instance and thus it will be adjusted to only show available
options that have been enabled while compiling LAMMPS. That, however,
excludes accelerated styles and commands; for improved clarity, only the
context menu. Most of the completion information is retrieved from the
active LAMMPS instance and thus it shows only available options that
have been enabled when compiling LAMMPS. That list, however, excludes
accelerated styles and commands; for improved clarity, only the
non-suffix version of styles are shown.
Line Reformatting
@ -369,8 +409,8 @@ whitespace padding to commands, type specifiers, IDs and names. This
reformatting is performed by default when hitting the 'Enter' key to
start a new line. This feature can be turned on or off in the
``Preferences`` dialog, but it can still be manually performed by
hitting the 'TAB' key. The amount of padding can also be changed in the
``Preferences`` dialog.
hitting the 'TAB' key. The amount of padding can be adjusted in the
``Preferences`` dialog for the *Editor*.
Internally this functionality is achieved by splitting the line into
"words" and then putting it back together with padding added where the
@ -379,17 +419,26 @@ context can be detected; otherwise a single space is used between words.
Context Specific Help
^^^^^^^^^^^^^^^^^^^^^
.. image:: JPG/lammps-gui-popup-help.png
:align: center
:scale: 50%
.. |gui-popup1| image:: JPG/lammps-gui-popup-help.png
:width: 48%
A unique feature of the LAMMPS GUI is the option to look up the
.. |gui-popup2| image:: JPG/lammps-gui-popup-view.png
:width: 48%
|gui-popup1| |gui-popup2|
A unique feature of the LAMMPS-GUI is the option to look up the
documentation for the command in the current line. This can be done by
either clicking the right mouse button or by using the `Ctrl-?` keyboard
shortcut. When clicking the mouse there are additional entries in the
context menu that will open the corresponding documentation page in the
online LAMMPS documentation. When using the keyboard, the first of
those entries will be chosen directly.
shortcut. When using the mouse, there are additional entries in the
context menu that open the corresponding documentation page in the
online LAMMPS documentation in a web browser window. When using the
keyboard, the first of those entries is chosen.
If the word under the cursor is a file, then additionally the context
menu has an entry to open the file in a read-only text viewer window.
This is a convenient way to view the contents of files that are
referenced in the input.
Menu
----
@ -397,9 +446,9 @@ Menu
The menu bar has entries ``File``, ``Edit``, ``Run``, ``View``, and
``About``. Instead of using the mouse to click on them, the individual
menus can also be activated by hitting the `Alt` key together with the
corresponding underlined letter, that is `Alt-F` will activate the
corresponding underlined letter, that is `Alt-F` activates the
``File`` menu. For the corresponding activated sub-menus, the key
corresponding the underlined letters can again be used to select entries
corresponding the underlined letters can be used to select entries
instead of using the mouse.
File
@ -407,19 +456,22 @@ File
The ``File`` menu offers the usual options:
- ``New`` will clear the current buffer and reset the file name to ``*unknown*``
- ``Open`` will open a dialog to select a new file
- ``Save`` will save the current file; if the file name is ``*unknown*``
- ``New`` clears the current buffer and resets the file name to ``*unknown*``
- ``Open`` opens a dialog to select a new file for editing in the *Editor*
- ``View`` opens a dialog to select a file for viewing in a *separate* window (read-only)
- ``Save`` saves the current file; if the file name is ``*unknown*``
a dialog will open to select a new file name
- ``Save As`` will open a dialog to select and new file name and save
the buffer to it
- ``Quit`` will exit LAMMPS GUI. If there are unsaved changes, a dialog
will appear to either cancel the operation, or to save or not save the
edited file.
- ``Save As`` opens a dialog to select and new file name (and folder, if
desired) and saves the buffer to it. Writing the buffer to a
different folder will also switch the current working directory to
that folder.
- ``Quit`` exits LAMMPS-GUI. If there are unsaved changes, a dialog will
appear to either cancel the operation, or to save, or to not save the
modified buffer.
In addition, up to 5 recent file names will be listed after the
``Open`` entry that allows re-opening recent files. This list is
stored when quitting and recovered when starting again.
In addition, up to 5 recent file names will be listed after the ``Open``
entry that allows re-opening recently opened files. This list is stored
when quitting and recovered when starting again.
Edit
^^^^
@ -427,19 +479,20 @@ Edit
The ``Edit`` menu offers the usual editor functions like ``Undo``,
``Redo``, ``Cut``, ``Copy``, ``Paste``. It can also open a
``Preferences`` dialog (keyboard shortcut `Ctrl-P`) and allows deletion
of all stored preferences so they will be reset to default values.
of all stored preferences and settings, so they are reset to their
default values.
Run
^^^
The ``Run`` menu has options to start and stop a LAMMPS process.
Rather than calling the LAMMPS executable as a separate executable,
the LAMMPS GUI is linked to the LAMMPS library and thus can run LAMMPS
internally through the :ref:`LAMMPS C-library interface
<lammps_c_api>`.
The ``Run`` menu has options to start and stop a LAMMPS process. Rather
than calling the LAMMPS executable as a separate executable, the
LAMMPS-GUI is linked to the LAMMPS library and thus can run LAMMPS
internally through the :ref:`LAMMPS C-library interface <lammps_c_api>`
in a separate thread.
Specifically, a LAMMPS instance will be created by calling
:cpp:func:`lammps_open_no_mpi`. The buffer contents then executed by
:cpp:func:`lammps_open_no_mpi`. The buffer contents are then executed by
calling :cpp:func:`lammps_commands_string`. Certain commands and
features are only available after a LAMMPS instance is created. Its
presence is indicated by a small LAMMPS ``L`` logo in the status bar
@ -449,16 +502,16 @@ reading the file. This is mainly provided as a fallback option in
case the input uses some feature that is not available when running
from a string buffer.
The LAMMPS calculation will be run in a concurrent thread so that the
GUI can stay responsive and be updated during the run. This can be
used to tell the running LAMMPS instance to stop at the next timestep.
The ``Stop LAMMPS`` entry will do this by calling
:cpp:func:`lammps_force_timeout`, which is equivalent to a :doc:`timer
timeout 0 <timer>` command.
The LAMMPS calculations are run in a concurrent thread so that the GUI
can stay responsive and be updated during the run. The GUI can retrieve
data from the running LAMMPS instance and tell it to stop at the next
timestep. The ``Stop LAMMPS`` entry will do this by calling the
:cpp:func:`lammps_force_timeout` library function, which is equivalent
to a :doc:`timer timeout 0 <timer>` command.
The ``Set Variables...`` entry will open a dialog box where
The ``Set Variables...`` entry opens a dialog box where
:doc:`index style variables <variable>` can be set. Those variables
will be passed to the LAMMPS instance when it is created and are thus
are passed to the LAMMPS instance when it is created and are thus
set *before* a run is started.
.. image:: JPG/lammps-gui-variables.png
@ -478,12 +531,12 @@ in an ``Image Viewer`` window.
The ``View in OVITO`` entry will launch `OVITO <https://ovito.org>`_
with a :doc:`data file <write_data>` containing the current state of
the system. This option is only available if the LAMMPS GUI can find
the system. This option is only available if the LAMMPS-GUI can find
the OVITO executable in the system path.
The ``View in VMD`` entry will launch VMD with a :doc:`data file
<write_data>` containing the current state of the system. This option
is only available if the LAMMPS GUI can find the VMD executable in the
is only available if the LAMMPS-GUI can find the VMD executable in the
system path.
View
@ -498,14 +551,14 @@ About
^^^^^
The ``About`` menu finally offers a couple of dialog windows and an
option to launch the LAMMPS online documentation in a web browser.
The ``About LAMMPS`` entry displays a dialog with a summary of the
option to launch the LAMMPS online documentation in a web browser. The
``About LAMMPS-GUI`` entry displays a dialog with a summary of the
configuration settings of the LAMMPS library in use and the version
number of LAMMPS GUI itself. The ``Quick Help`` displays a dialog
with a minimal description of LAMMPS GUI. The ``LAMMPS GUI Howto``
entry will open this documentation page from the online documentation
in a web browser window. The ``LAMMPS Manual`` entry will open the
main page of the LAMMPS documentation in the web browser.
number of LAMMPS-GUI itself. The ``Quick Help`` displays a dialog with
a minimal description of LAMMPS-GUI. The ``LAMMPS-GUI Howto`` entry
will open this documentation page from the online documentation in a web
browser window. The ``LAMMPS Manual`` entry will open the main page of
the LAMMPS online documentation in a web browser window.
-----
@ -513,7 +566,7 @@ Preferences
-----------
The ``Preferences`` dialog allows customization of the behavior and
look of the LAMMPS GUI application. The settings are grouped and each
look of the LAMMPS-GUI application. The settings are grouped and each
group is displayed within a tab.
.. |guiprefs1| image:: JPG/lammps-gui-prefs-general.png
@ -534,9 +587,9 @@ General Settings:
^^^^^^^^^^^^^^^^^
- *Echo input to log:* when checked, all input commands, including
variable expansions, will be echoed to the log window. This is
variable expansions, are echoed to the *Output* window. This is
equivalent to using `-echo screen` at the command line. There is no
log *file* produced by default, since LAMMPS GUI uses `-log none`.
log *file* produced by default, since LAMMPS-GUI uses `-log none`.
- *Include citation details:* when checked full citation info will be
included to the log window. This is equivalent to using `-cite
screen` on the command line.
@ -558,12 +611,12 @@ General Settings:
chart window will be replaced when a new snapshot image is requested,
otherwise each command will create a new image window.
- *Path to LAMMPS Shared Library File:* this option is only visible
when LAMMPS GUI was compiled to load the LAMMPS library at run time
when LAMMPS-GUI was compiled to load the LAMMPS library at run time
instead of being linked to it directly. With the ``Browse..`` button
or by changing the text, a different shared library file with a
different compilation of LAMMPS with different settings or from a
different version can be loaded. After this setting was changed,
LAMMPS GUI needs to be re-launched.
LAMMPS-GUI needs to be re-launched.
- *Select Default Font:* Opens a font selection dialog where the type
and size for the default font (used for everything but the editor and
log) of the application can be set.
@ -571,11 +624,12 @@ General Settings:
size for the text editor and log font of the application can be set.
- *GUI update interval:* Allows to set the time interval between GUI
and data updates during a LAMMPS run in milliseconds. The default is
to update the GUI every 100 milliseconds. This is good for most cases.
For LAMMPS runs that run very fast, however, data may be missed and
to update the GUI every 10 milliseconds. This is good for most cases.
For LAMMPS runs that run *very* fast, however, data may be missed and
through lowering this interval, this can be corrected. However, this
will make the GUI use more resources, which may be a problem on some
computers with slower CPUs. The default value is 100 milliseconds.
computers with slower CPUs and a small number of CPU cores. This
setting may be changed to a value between 1 and 1000 milliseconds.
Accelerators:
^^^^^^^^^^^^^
@ -648,48 +702,54 @@ available (On macOS use the Command key instead of Ctrl/Control).
- Redo edit
- Ctrl+/
- Stop Active Run
* - Ctrl+S
- Save File
* - Ctrl+Shift+F
- View File
- Ctrl+C
- Copy text
- Ctrl+Shift+V
- Set Variables
* - Ctrl+Shift+S
- Save File As
* - Ctrl+S
- Save File
- Ctrl+X
- Cut text
- Ctrl+I
- Snapshot Image
* - Ctrl+Q
- Quit Application
* - Ctrl+Shift+S
- Save File As
- Ctrl+V
- Paste text
- Ctrl+L
- Slide Show
* - Ctrl+W
- Close Window
* - Ctrl+Q
- Quit Application
- Ctrl+A
- Select All
- Ctrl+P
- Preferences
* - Ctrl+Shift+A
- About LAMMPS
* - Ctrl+W
- Close Window
- Ctrl+Shift+H
- Quick Help
- Ctrl+Shift+G
- LAMMPS GUI Howto
* - Ctrl+Shift+M
- LAMMPS Manual
- LAMMPS-GUI Howto
* - Ctrl+Shift+A
- About LAMMPS
- Ctrl+?
- Context Help
- Ctrl+Shift+W
- Show Variables
* - Ctrl+Shift+Enter
- Run File
* - Ctrl+Shift+M
- LAMMPS Manual
- TAB
- Reformat line
- Shift+TAB
- Show Completions
* - Ctrl+Shift+Enter
- Run File
-
-
-
-
Further editing keybindings `are documented with the Qt documentation
<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_. In

116
doc/src/Howto_rheo.rst Normal file
View File

@ -0,0 +1,116 @@
Reproducing hydrodynamics and elastic objects (RHEO)
====================================================
The RHEO package is a hybrid implementation of smoothed particle
hydrodynamics (SPH) for fluid flow, which can couple to the :doc:`BPM package
<Howto_bpm>` to model solid elements. RHEO combines these methods to enable
mesh-free modeling of multi-phase material systems. Its SPH solver supports
many advanced options including reproducing kernels, particle shifting, free
surface identification, and solid surface reconstruction. To model fluid-solid
systems, the status of particles can dynamically change between a fluid and
solid state, e.g. during melting/solidification, which determines how they
interact and their physical behavior. The package is designed with modularity
in mind, so one can easily turn various features on/off, adjust physical
details of the system, or develop new capabilities. For instance, the numerics
associated with calculating gradients, reproducing kernels, etc. are separated
into distinct classes to simplify the development of new integration schemes
which can call these calculations. Additional numerical details can be found in
:ref:`(Palermo) <howto_rheo_palermo>` and
:ref:`(Clemmer) <howto_rheo_clemmer>`.
Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package
<PKG-SPH>` package is likely better suited for your application. It has fewer advanced
features and therefore benefits from improved performance. The :ref:`MACHDYN
<PKG-MACHDYN>` package for solids may also be relevant for fluid-solid problems.
----------
At the core of the package is :doc:`fix rheo <fix_rheo>` which integrates
particle trajectories and controls many optional features (e.g. the use
of reproducing kernels). In conjunction to fix rheo, one must specify an
instance of :doc:`fix rheo/pressure <fix_rheo_pressure>` and
:doc:`fix rheo/viscosity <fix_rheo_viscosity>` to define a pressure equation
of state and viscosity model, respectively. Optionally, one can model
a heat equation with :doc:`fix rheo/thermal <fix_rheo_thermal>`, which also
allows the user to specify equations for a particle's thermal conductivity,
specific heat, latent heat, and melting temperature. The ordering of these
fixes in an an input script matters. Fix rheo must be defined prior to all
other RHEO fixes.
Typically, RHEO requires atom style rheo. In addition to typical atom
properties like positions and forces, particles store a local density,
viscosity, pressure, and status. If thermal evolution is modeled, one must
use atom style rheo/thermal which also includes a local energy, temperature, and
conductivity. Note that the temperature is always derived from the energy.
This implies the *temperature* attribute of :doc:`the set command <set>` does not
affect particles. Instead, one should use the *sph/e* attribute.
The status variable uses bit-masking to track various properties of a particle
such as its current state of matter (fluid or solid) and its location relative
to a surface. Some of these properties (and others) can be accessed using
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`. The *status*
attribute in :doc:`the set command <set>` only allows control over the first bit
which sets the state of matter, 0 is fluid and 1 is solid.
Fluid interactions, including pressure forces, viscous forces, and heat exchange,
are calculated using :doc:`pair rheo <pair_rheo>`. Unlike typical pair styles,
pair rheo ignores the :doc:`special bond <special_bonds>` settings. Instead,
it determines whether to calculate forces based on the status of particles: e.g.,
hydrodynamic forces are only calculated if a fluid particle is involved.
----------
To model elastic objects, there are currently two mechanisms in RHEO, one designed
for bulk solid bodies and the other for thin shells. Both mechanisms rely on
introducing bonded forces between particles and therefore require a hybrid of atom
style bond and rheo (or rheo/thermal).
To create an elastic solid body, one has to (a) change the status of constituent
particles to solid (e.g. with the :doc:`set <set>` command), (b) create bpm
bonds between the particles (see the :doc:`bpm howto <Howto_bpm>` page for
more details), and (c) use :doc:`pair rheo/solid <pair_rheo_solid>` to
apply repulsive contact forces between distinct solid bodies. Akin to pair rheo,
pair rheo/solid considers a particles fluid/solid phase to determine whether to
apply forces. However, unlike pair rheo, pair rheo/solid does obey special bond
settings such that contact forces do not have to be calculated between two bonded
solid particles in the same elastic body.
In systems with thermal evolution, fix rheo/thermal can optionally set a
melting/solidification temperature allowing particles to dynamically swap their
state between fluid and solid when the temperature exceeds or drops below the
critical temperature, respectively. Using the *react* option, one can specify a maximum
bond length and a bond type. Then, when solidifying, particles will search their
local neighbors and automatically create bonds with any neighboring solid particles
in range. For BPM bond styles, bonds will then use the immediate position of the two
particles to calculate a reference state. When melting, particles will delete any
bonds of the specified type when reverting to a fluid state. Special bonds are updated
as bonds are created/broken.
The other option for elastic objects is an elastic shell that is nominally much
thinner than a particle diameter, e.g. a oxide skin which gradually forms over time
on the surface of a fluid. Currently, this is implemented using
:doc:`fix rheo/oxidation <fix_rheo_oxidation>` and bond style
:doc:`rheo/shell <bond_rheo_shell>`. Essentially, fix rheo/oxidation creates candidate
bonds of a specified type between surface fluid particles within a specified distance.
a newly created rheo/shell bond will then start a timer. While the timer is counting
down, the bond will delete itself if particles move too far apart or move away from the
surface. However, if the timer reaches a user-defined threshold, then the bond will
activate and apply additional forces to the fluid particles. Bond style rheo/shell
then operates very similarly to a BPM bond style, storing a reference length and
breaking if stretched too far. Unlike the above method, this option does not remove
the underlying fluid interactions (although particle shifting is turned off) and does
not modify special bond settings of particles.
While these two options are not expected to be appropriate for every system,
either framework can be modified to create more suitable models (e.g. by changing the
criteria for creating/deleting a bond or altering force calculations).
----------
.. _howto_rheo_palermo:
**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.
.. _howto_rheo_clemmer:
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

10
doc/src/Install_linux.rst
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@ -35,11 +35,11 @@ packages listed below), they do not depend on any installed software and
thus should run on *any* 64-bit x86 machine with *any* Linux version.
These executable include most of the available packages and multi-thread
parallelization (via INTEL, KOKKOS, or OPENMP package). They are **not**
compatible with MPI. Several of the LAMMPS tools executables (e.g. ``msi2lmp``)
and the ``lammps-shell`` program are included as well. Because of the
static linkage, there is no ``liblammps.so`` library file and thus also the
LAMMPS python module, which depends on it, is not included.
parallelization (via INTEL, KOKKOS, or OPENMP package). They are
**not** compatible with MPI. Several of the LAMMPS tools executables
(e.g. ``msi2lmp``) are included as well. Because of the static linkage,
there is no ``liblammps.so`` library file and thus also the LAMMPS
python module, which depends on it, is not included.
The compressed tar archives available for download have names following
the pattern ``lammps-linux-x86_64-<version>.tar.gz`` and will all unpack

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12
doc/src/Library_properties.rst
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@ -13,6 +13,8 @@ This section documents the following functions:
- :cpp:func:`lammps_extract_setting`
- :cpp:func:`lammps_extract_global_datatype`
- :cpp:func:`lammps_extract_global`
- :cpp:func:`lammps_extract_pair_dimension`
- :cpp:func:`lammps_extract_pair`
- :cpp:func:`lammps_map_atom`
--------------------
@ -123,6 +125,16 @@ subdomains and processors.
-----------------------
.. doxygenfunction:: lammps_extract_pair_dimension
:project: progguide
-----------------------
.. doxygenfunction:: lammps_extract_pair
:project: progguide
-----------------------
.. doxygenfunction:: lammps_map_atom
:project: progguide

71
doc/src/Packages_details.rst
View File

@ -8,12 +8,12 @@ info on how to download or build any extra library it requires. It also
gives links to documentation, example scripts, and pictures/movies (if
available) that illustrate use of the package.
The majority of packages can be included in a LAMMPS build with a
single setting (``-D PKG_<NAME>=on`` for CMake) or command
(``make yes-<name>`` for make). See the :doc:`Build package <Build_package>`
page for more info. A few packages may require additional steps;
this is indicated in the descriptions below. The :doc:`Build extras <Build_extras>`
page gives those details.
The majority of packages can be included in a LAMMPS build with a single
setting (``-D PKG_<NAME>=on`` for CMake) or command (``make yes-<name>``
for make). See the :doc:`Build package <Build_package>` page for more
info. A few packages may require additional steps; this is indicated in
the descriptions below. The :doc:`Build extras <Build_extras>` page
gives those details.
.. note::
@ -103,6 +103,7 @@ page gives those details.
* :ref:`QEQ <PKG-QEQ>`
* :ref:`QMMM <PKG-QMMM>`
* :ref:`QTB <PKG-QTB>`
* :ref:`RHEO <PKG-RHEO>`
* :ref:`REACTION <PKG-REACTION>`
* :ref:`REAXFF <PKG-REAXFF>`
* :ref:`REPLICA <PKG-REPLICA>`
@ -1323,18 +1324,19 @@ KSPACE package
**Contents:**
A variety of long-range Coulombic solvers, as well as pair styles
which compute the corresponding short-range pairwise Coulombic
interactions. These include Ewald, particle-particle particle-mesh
(PPPM), and multilevel summation method (MSM) solvers.
A variety of long-range Coulombic solvers, as well as pair styles which
compute the corresponding short-range pairwise Coulombic interactions.
These include Ewald, particle-particle particle-mesh (PPPM), and
multilevel summation method (MSM) solvers.
**Install:**
Building with this package requires a 1d FFT library be present on
your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, third party libraries like FFTW, or a
vendor-supplied FFT library. See the :doc:`Build settings <Build_settings>` page for details on how to select
different FFT options for your LAMPMS build.
Building with this package requires a 1d FFT library be present on your
system for use by the PPPM solvers. This can be the KISS FFT library
provided with LAMMPS, third party libraries like FFTW, or a
vendor-supplied FFT library. See the :doc:`Build settings
<Build_settings>` page for details on how to select different FFT
options for your LAMMPS build.
**Supporting info:**
@ -2621,6 +2623,45 @@ another set.
----------
.. _PKG-RHEO:
RHEO package
------------
**Contents:**
Pair styles, bond styles, fixes, and computes for reproducing
hydrodynamics and elastic objects. See the :doc:`Howto rheo
<Howto_rheo>` page for an overview.
**Install:**
This package has :ref:`specific installation instructions <rheo>` on the :doc:`Build extras <Build_extras>` page.
**Authors:** Joel T. Clemmer (Sandia National Labs),
Thomas C. O'Connor (Carnegie Mellon University)
.. versionadded:: TBD
**Supporting info:**
* src/RHEO filenames -> commands
* :doc:`Howto_rheo <Howto_rheo>`
* :doc:`atom_style rheo <atom_style>`
* :doc:`atom_style rheo/thermal <atom_style>`
* :doc:`bond_style rheo/shell <bond_rheo_shell>`
* :doc:`compute rheo/property/atom <compute_rheo_property_atom>`
* :doc:`fix rheo <fix_rheo>`
* :doc:`fix rheo/oxidation <fix_rheo_oxidation>`
* :doc:`fix rheo/pressure <fix_rheo_pressure>`
* :doc:`fix rheo/thermal <fix_rheo_thermal>`
* :doc:`fix rheo/viscosity <fix_rheo_viscosity>`
* :doc:`pair_style rheo <pair_rheo>`
* :doc:`pair_style rheo/solid <pair_rheo_solid>`
* examples/rheo
----------
.. _PKG-RIGID:
RIGID package

5
doc/src/Packages_list.rst
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@ -413,6 +413,11 @@ whether an extra library is needed to build and use the package:
- :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>`
- qtb
- no
* - :ref:`RHEO <PKG-RHEO>`
- reproducing hydrodynamics and elastic objects
- :doc:`Howto rheo <Howto_rheo>`
- rheo
- no
* - :ref:`REACTION <PKG-REACTION>`
- chemical reactions in classical MD
- :doc:`fix bond/react <fix_bond_react>`

299
doc/src/Tools.rst
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@ -92,7 +92,6 @@ Miscellaneous tools
* :ref:`emacs <emacs>`
* :ref:`i-PI <ipi>`
* :ref:`kate <kate>`
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS GUI <lammps_gui>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`Offline build tool <offline>`
@ -379,7 +378,7 @@ See README file in the tools/fep directory.
i-PI tool
-------------------
.. versionchanged:: TBD
.. versionchanged:: 27June2024
The tools/i-pi directory used to contain a bundled version of the i-PI
software package for use with LAMMPS. This version, however, was
@ -389,7 +388,7 @@ The i-PI package was created and is maintained by Michele Ceriotti,
michele.ceriotti at gmail.com, to interface to a variety of molecular
dynamics codes.
i-PI is now available via PyPi using the pip package manager at:
i-PI is now available via PyPI using the pip package manager at:
https://pypi.org/project/ipi/
Here are the commands to set up a virtual environment and install
@ -444,219 +443,9 @@ The file was provided by Alessandro Luigi Sellerio
----------
.. _lammps_shell:
LAMMPS shell
------------
.. versionadded:: 9Oct2020
Overview
^^^^^^^^
The LAMMPS Shell, ``lammps-shell`` is a program that functions very
similar to the regular LAMMPS executable but has several modifications
and additions that make it more powerful for interactive sessions,
i.e. where you type LAMMPS commands from the prompt instead of reading
them from a file.
- It uses the readline and history libraries to provide command line
editing and context aware TAB-expansion (details on that below).
- When processing an input file with the '-in' or '-i' flag from the
command line, it does not exit at the end of that input file but
stops at a prompt, so that additional commands can be issued
- Errors will not abort the shell but return to the prompt.
- It has additional commands aimed at interactive use (details below).
- Interrupting a calculation with CTRL-C will not terminate the
session but rather enforce a timeout to cleanly stop an ongoing
run (more info on timeouts is in the :doc:`timer command <timer>`
documentation).
These enhancements make the LAMMPS shell an attractive choice for
interactive LAMMPS sessions in graphical desktop environments
(e.g. Gnome, KDE, Cinnamon, XFCE, Windows).
TAB-expansion
^^^^^^^^^^^^^
When writing commands interactively at the shell prompt, you can hit
the TAB key at any time to try and complete the text. This completion
is context aware and will expand any first word only to commands
available in that executable.
- For style commands it will expand to available styles of the
corresponding category (e.g. pair styles after a
:doc:`pair_style <pair_style>` command).
- For :doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`dump <dump>`
it will also expand only to already defined groups for the group-ID
keyword.
- For commands like :doc:`compute_modify <compute_modify>`,
:doc:`fix_modify <fix_modify>`, or :doc:`dump_modify <dump_modify>`
it will expand to known compute/fix/dump IDs only.
- When typing references to computes, fixes, or variables with a
"c\_", "f\_", or "v\_" prefix, respectively, then the expansion will
be to known compute/fix IDs and variable names. Variable name
expansion is also available for the ${name} variable syntax.
- In all other cases TAB expansion will complete to names of files
and directories.
Command line editing and history
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
When typing commands, command line editing similar to what BASH
provides is available. Thus it is possible to move around the
currently line and perform various cut and insert and edit operations.
Previous commands can be retrieved by scrolling up (and down)
or searching (e.g. with CTRL-r).
Also history expansion through using the exclamation mark '!'
can be performed. Examples: '!!' will be replaced with the previous
command, '!-2' will repeat the command before that, '!30' will be
replaced with event number 30 in the command history list, and
'!run' with the last command line that started with "run". Adding
a ":p" to such a history expansion will result that the expansion is
printed and added to the history list, but NOT executed.
On exit the LAMMPS shell will write the history list to a file
".lammps_history" in the current working directory. If such a
file exists when the LAMMPS shell is launched it will be read to
populate the history list.
This is realized via the readline library and can thus be customized
with an ``.inputrc`` file in the home directory. For application
specific customization, the LAMMPS shell uses the name "lammps-shell".
For more information about using and customizing an application using
readline, please see the available documentation at:
https://www.gnu.org/software/readline/
Additional commands
^^^^^^^^^^^^^^^^^^^
The following commands are added to the LAMMPS shell on top of the
regular LAMMPS commands:
.. parsed-literal::
help (or ?) print a brief help message
history display the current command history list
clear_history wipe out the current command history list
save_history <range> <file>
write commands from the history to file.
The range is given as <from>-<to>, where <from> and <to>
may be empty. Example: save_history 100- in.recent
source <file> read commands from file (same as "include")
pwd print current working directory
cd <directory> change current working directory (same as pwd if no directory)
mem print current and maximum memory usage
\|<command> execute <command> as a shell command and return to the command prompt
exit exit the LAMMPS shell cleanly (unlike the "quit" command)
Please note that some known shell operations are implemented in the
LAMMPS :doc:`shell command <shell>` in a platform neutral fashion,
while using the '\|' character will always pass the following text
to the operating system's shell command.
Compilation
^^^^^^^^^^^
Compilation of the LAMMPS shell can be enabled by setting the CMake
variable ``BUILD_LAMMPS_SHELL`` to "on" or using the makefile in the
``tools/lammps-shell`` folder to compile after building LAMMPS using
the conventional make procedure. The makefile will likely need
customization depending on the features and settings used for
compiling LAMMPS.
Limitations
^^^^^^^^^^^
The LAMMPS shell was not designed for use with MPI parallelization
via ``mpirun`` or ``mpiexec`` or ``srun``.
Readline customization
^^^^^^^^^^^^^^^^^^^^^^
The behavior of the readline functionality can be customized in the
``${HOME}/.inputrc`` file. This can be used to alter the default
settings or change the key-bindings. The LAMMPS Shell sets the
application name ``lammps-shell``, so settings can be either applied
globally or only for the LAMMPS shell by bracketing them between
``$if lammps-shell`` and ``$endif`` like in the following example:
.. code-block:: bash
$if lammps-shell
# disable "beep" or "screen flash"
set bell-style none
# bind the "Insert" key to toggle overwrite mode
"\e[2~": overwrite-mode
$endif
More details about this are in the `readline documentation <https://tiswww.cwru.edu/php/chet/readline/rluserman.html#SEC9>`_.
LAMMPS Shell tips and tricks
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Below are some suggestions for how to use and customize the LAMMPS shell.
Enable tilde expansion
""""""""""""""""""""""
Adding ``set expand-tilde on`` to ``${HOME}/.inputrc`` is recommended as
this will change the filename expansion behavior to replace any text
starting with "~" by the full path to the corresponding user's home
directory. While the expansion of filenames **will** happen on all
arguments where the context is not known (e.g. ``~/compile/lamm<TAB>``
will expand to ``~/compile/lammps/``), it will not replace the tilde by
default. But since LAMMPS does not do tilde expansion itself (unlike a
shell), this will result in errors. Instead the tilde-expression should
be expanded into a valid path, where the plain "~/" stands for the
current user's home directory and "~someuser/" stands for
"/home/someuser" or whatever the full path to that user's home directory
is.
File extension association
""""""""""""""""""""""""""
Since the LAMMPS shell (unlike the regular LAMMPS executable) does not
exit when an input file is passed on the command line with the "-in" or
"-i" flag (the behavior is like for ``python -i <filename>``), it makes
the LAMMPS shell suitable for associating it with input files based on
their filename extension (e.g. ".lmp"). Since ``lammps-shell`` is a
console application, you have to run it inside a terminal program with a
command line like this:
.. code-block:: bash
xterm -title "LAMMPS Shell" -e /path/to/lammps-shell -i in.file.lmp
Use history to create an input file
"""""""""""""""""""""""""""""""""""
When experimenting with commands to interactively to figure out a
suitable choice of settings or simply the correct syntax, you may want
to record part of your commands to a file for later use. This can be
done with the ``save_history`` commands, which allows to selectively
write a section of the command history to a file (Example:
``save_history 25-30 in.run``). This file can be further edited
(Example: ``|vim in.run``) and then the file read back in and tried out
(Example: ``source in.run``). If the input also creates a system box,
you first need to use the :doc:`clear` command.
----------
.. _lammps_gui:
LAMMPS GUI
LAMMPS-GUI
----------
.. versionadded:: 2Aug2023
@ -664,25 +453,28 @@ LAMMPS GUI
Overview
^^^^^^^^
LAMMPS GUI is a graphical text editor customized for editing LAMMPS
LAMMPS-GUI is a graphical text editor customized for editing LAMMPS
input files that is linked to the :ref:`LAMMPS C-library <lammps_c_api>`
and thus can run LAMMPS directly using the contents of the editor's text
buffer as input. It can retrieve and display information from LAMMPS
while it is running, display visualizations created with the :doc:`dump
image command <dump_image>`, and is adapted specifically for editing
LAMMPS input files through text completion and reformatting, and linking
to the online LAMMPS documentation for known LAMMPS commands and styles.
LAMMPS input files through syntax highlighting, text completion, and
reformatting, and linking to the online LAMMPS documentation for known
LAMMPS commands and styles.
This is similar to what people traditionally would do to run LAMMPS:
using a regular text editor to edit the input and run the necessary
commands, possibly including the text editor, too, from a command line
terminal window. This similarity is a design goal. While making it easy
for beginners to start with LAMMPS, it is also the intention to simplify
the transition to workflows like most experienced LAMMPS users do.
This is similar to what people traditionally would do to run LAMMPS but
all rolled into a single application: that is, using a text editor,
plotting program, and a visualization program to edit the input, run
LAMMPS, process the output into graphs and visualizations from a command
line window. This similarity is a design goal. While making it easy for
beginners to start with LAMMPS, it is also the expectation that
LAMMPS-GUI users will eventually transition to workflows that most
experienced LAMMPS users employ.
All features have been extensively exposed to keyboard shortcuts, so
that there is also appeal for experienced LAMMPS users for prototyping
and testing simulations setups.
and testing simulation setups.
Features
^^^^^^^^
@ -690,9 +482,10 @@ Features
A detailed discussion and explanation of all features and functionality
are in the :doc:`Howto_lammps_gui` tutorial Howto page.
Here are a few highlights of LAMMPS GUI
Here are a few highlights of LAMMPS-GUI
- Text editor with syntax highlighting customized for LAMMPS
- Text editor features command completion for known commands and styles
- Text editor will switch working directory to folder of file in buffer
- Text editor will remember up to 5 recent files
- Context specific LAMMPS command help via online documentation
@ -704,32 +497,32 @@ Here are a few highlights of LAMMPS GUI
- Thermodynamic output is captured and displayed as line graph in a Chart Window
- Indicator for currently executed command
- Indicator for line that caused an error
- Visualization of current state in Image Viewer (via :doc:`dump image <dump_image>`)
- Visualization of current state in Image Viewer (via calling :doc:`write_dump image <dump_image>`)
- Capture of images created via :doc:`dump image <dump_image>` in Slide show window
- Many adjustable settings and preferences that are persistent
- Dialog to set variables from the LAMMPS command line
- Dialog to set variables, similar to the LAMMPS command line flag '-v' / '-var'
Parallelization
^^^^^^^^^^^^^^^
Due to its nature as a graphical application, it is not possible to use
the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading and GPU
the LAMMPS-GUI in parallel with MPI, but OpenMP multi-threading and GPU
acceleration is available and enabled by default.
Prerequisites and portability
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS GUI is programmed in C++ based on the C++11 standard and using
LAMMPS-GUI is programmed in C++ based on the C++11 standard and using
the `Qt GUI framework <https://www.qt.io/product/framework>`_.
Currently, Qt version 5.12 or later is required; Qt 5.15LTS is
recommended; support for Qt version 6.x is under active development and
thus far only tested with Qt 6.5LTS on Linux. Building LAMMPS with
CMake is required.
recommended; support for Qt version 6.x is available. Building LAMMPS
with CMake is required.
The LAMMPS GUI has been successfully compiled and tested on:
The LAMMPS-GUI has been successfully compiled and tested on:
- Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
- Fedora Linux 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.5LTS
- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.7
- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
@ -745,20 +538,20 @@ available from https://download.lammps.org/static or
https://github.com/lammps/lammps/releases. You can unpack the archives
(or mount the macOS disk image) and run the GUI directly in place. The
folder may also be moved around and added to the ``PATH`` environment
variable so the executables will be found automatically. The LAMMPS GUI
variable so the executables will be found automatically. The LAMMPS-GUI
executable is called ``lammps-gui`` and either takes no arguments or
attempts to load the first argument as LAMMPS input file.
Compilation
^^^^^^^^^^^
The source for the LAMMPS GUI is included with the LAMMPS source code
The source for the LAMMPS-GUI is included with the LAMMPS source code
distribution in the folder ``tools/lammps-gui`` and thus it can be can
be built as part of a regular LAMMPS compilation. :doc:`Using CMake
<Howto_cmake>` is required. To enable its compilation, the CMake
variable ``-D BUILD_LAMMPS_GUI=on`` must be set when creating the CMake
configuration. All other settings (compiler, flags, compile type) for
LAMMPS GUI are then inherited from the regular LAMMPS build. If the Qt
LAMMPS-GUI are then inherited from the regular LAMMPS build. If the Qt
library is packaged for Linux distributions, then its location is
typically auto-detected since the required CMake configuration files are
stored in a location where CMake can find them without additional help.
@ -766,17 +559,17 @@ Otherwise, the location of the Qt library installation must be indicated
by setting ``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to
a folder inside the Qt installation that contains the file
``Qt5Config.cmake``. Similarly, for Qt6 the location of the Qt library
installation can be indicated by setting ``-D Qt6_DIR=/path/to/qt6/lib/cmake/Qt6``,
if necessary. When both, Qt5 and Qt6 are available, Qt6 will be preferred
unless ``-D LAMMPS_GUI_USE_QT5=yes`` is set.
installation can be indicated by setting ``-D
Qt6_DIR=/path/to/qt6/lib/cmake/Qt6``, if necessary. When both, Qt5 and
Qt6 are available, Qt6 will be preferred unless ``-D
LAMMPS_GUI_USE_QT5=yes`` is set.
It should be possible to build the LAMMPS GUI as a standalone
compilation (e.g. when LAMMPS has been compiled with traditional make).
Then the CMake configuration needs to be told where to find the LAMMPS
headers and the LAMMPS library, via ``-D
LAMMPS_SOURCE_DIR=/path/to/lammps/src``. CMake will try to guess a
build folder with the LAMMPS library from that path, but it can also be
set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
It is possible to build the LAMMPS-GUI as a standalone compilation
(e.g. when LAMMPS has been compiled with traditional make). Then the
CMake configuration needs to be told where to find the LAMMPS headers
and the LAMMPS library, via ``-D LAMMPS_SOURCE_DIR=/path/to/lammps/src``.
CMake will try to guess a build folder with the LAMMPS library from that
path, but it can also be set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
Rather than linking to the LAMMPS library during compilation, it is also
possible to compile the GUI with a plugin loader that will load
@ -827,19 +620,19 @@ There is a custom `x64-GUI-MSVC` build configuration provided in the
compilation settings for project. Choosing this configuration will
activate building the `lammps-gui.exe` executable in addition to LAMMPS
through importing package selection from the ``windows.cmake`` preset
file and enabling building the LAMMPS GUI and disabling building with MPI.
file and enabling building the LAMMPS-GUI and disabling building with MPI.
When requesting an installation from the `Build` menu in Visual Studio,
it will create a compressed ``LAMMPS-Win10-amd64.zip`` zip file with the
executables and required dependent .dll files. This zip file can be
uncompressed and ``lammps-gui.exe`` run directly from there. The
uncompressed folder can be added to the ``PATH`` environment and LAMMPS
and LAMMPS GUI can be launched from anywhere from the command line.
and LAMMPS-GUI can be launched from anywhere from the command line.
**MinGW64 Cross-compiler**
The standard CMake build procedure can be applied and the
``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
command will automatically include a suitable CMake toolset file (the
command will automatically include a suitable CMake toolchain file (the
regular cmake command can be used after that to modify the configuration
settings, if needed). After building the libraries and executables,
you can build the target 'zip' (i.e. ``cmake --build <build dir> --target zip``
@ -1329,7 +1122,7 @@ for Tcl with:
.. code-block:: bash
swig -tcl -module tcllammps lammps.i
gcc -fPIC -shared $(pkgconf --cflags tcl) -o tcllammps.so \
gcc -fPIC -shared $(pkg-config tcl --cflags) -o tcllammps.so \
lammps_wrap.c -L ../src/ -llammps
tclsh
@ -1340,8 +1133,8 @@ functions included with:
swig -tcl -module tcllmps lammps_shell.i
gcc -o tcllmpsh lammps_wrap.c -Xlinker -export-dynamic \
-DHAVE_CONFIG_H $(pkgconf --cflags tcl) \
$(pkgconf --libs tcl) -L ../src -llammps
-DHAVE_CONFIG_H $(pkg-config tcl --cflags) \
$(pkg-config tcl --libs) -L ../src -llammps
In both cases it is assumed that the LAMMPS library was compiled
as a shared library in the ``src`` folder. Otherwise the last

99
doc/src/atom_modify.rst
View File

@ -71,11 +71,11 @@ all atoms, e.g. in a data or restart file.
atom IDs are required, due to how neighbor lists are built.
The *map* keyword determines how atoms with specific IDs are found
when required. An example are the bond (angle, etc) methods which
need to find the local index of an atom with a specific global ID
which is a bond (angle, etc) partner. LAMMPS performs this operation
efficiently by creating a "map", which is either an *array* or *hash*
table, as described below.
when required. For example, the bond (angle, etc) methods need to
find the local index of an atom with a specific global ID which is a
bond (angle, etc) partner. LAMMPS performs this operation efficiently
by creating a "map", which is either an *array* or *hash* table, as
described below.
When the *map* keyword is not specified in your input script, LAMMPS
only creates a map for :doc:`atom_styles <atom_style>` for molecular
@ -83,34 +83,39 @@ systems which have permanent bonds (angles, etc). No map is created
for atomic systems, since it is normally not needed. However some
LAMMPS commands require a map, even for atomic systems, and will
generate an error if one does not exist. The *map* keyword thus
allows you to force the creation of a map. The *yes* value will
create either an *array* or *hash* style map, as explained in the next
paragraph. The *array* and *hash* values create an array-style or
hash-style map respectively.
allows you to force the creation of a map.
For an *array*\ -style map, each processor stores a lookup table of
length N, where N is the largest atom ID in the system. This is a
fast, simple method for many simulations, but requires too much memory
for large simulations. For a *hash*\ -style map, a hash table is
created on each processor, which finds an atom ID in constant time
(independent of the global number of atom IDs). It can be slightly
slower than the *array* map, but its memory cost is proportional to
the number of atoms owned by a processor, i.e. N/P when N is the total
number of atoms in the system and P is the number of processors.
Specifying a value of *yes* will create either an array-style or
hash-style map, depending on the size of the system. If no atom ID is
larger than 1 million, then an array-style map is used, otherwise a
hash-style map is used. Specifying a value of *array* or *hash*
creates an array-style or hash-style map respectively, regardless of
the size of the system.
The *first* keyword allows a :doc:`group <group>` to be specified whose
atoms will be maintained as the first atoms in each processor's list
of owned atoms. This in only useful when the specified group is a
small fraction of all the atoms, and there are other operations LAMMPS
is performing that will be sped-up significantly by being able to loop
over the smaller set of atoms. Otherwise the reordering required by
this option will be a net slow-down. The :doc:`neigh_modify include <neigh_modify>` and :doc:`comm_modify group <comm_modify>`
commands are two examples of commands that require this setting to
work efficiently. Several :doc:`fixes <fix>`, most notably time
integration fixes like :doc:`fix nve <fix_nve>`, also take advantage of
this setting if the group they operate on is the group specified by
this command. Note that specifying "all" as the group-ID effectively
turns off the *first* option.
For an array-style map, each processor stores a lookup table of length
N, where N is the largest atom ID in the system. This is a fast,
simple method for many simulations, but requires too much memory for
large simulations. For a hash-style map, a hash table is created on
each processor, which finds an atom ID in constant time (independent
of the global number of atom IDs). It can be slightly slower than the
*array* map, but its memory cost is proportional to the number of
atoms owned by a processor, i.e. N/P when N is the total number of
atoms in the system and P is the number of processors.
The *first* keyword allows a :doc:`group <group>` to be specified
whose atoms will be maintained as the first atoms in each processor's
list of owned atoms. This in only useful when the specified group is
a small fraction of all the atoms, and there are other operations
LAMMPS is performing that will be sped-up significantly by being able
to loop over the smaller set of atoms. Otherwise the reordering
required by this option will be a net slow-down. The
:doc:`neigh_modify include <neigh_modify>` and :doc:`comm_modify group
<comm_modify>` commands are two examples of commands that require this
setting to work efficiently. Several :doc:`fixes <fix>`, most notably
time integration fixes like :doc:`fix nve <fix_nve>`, also take
advantage of this setting if the group they operate on is the group
specified by this command. Note that specifying "all" as the group-ID
effectively turns off the *first* option.
It is OK to use the *first* keyword with a group that has not yet been
defined, e.g. to use the atom_modify first command at the beginning of
@ -148,15 +153,16 @@ cache locality will be undermined.
.. note::
Running a simulation with sorting on versus off should not
change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simulations.
Various commands, particularly those which use random numbers
(e.g. :doc:`velocity create <velocity>`, and :doc:`fix langevin <fix_langevin>`), may generate (statistically identical)
results which depend on the order in which atoms are processed. The
order of atoms in a :doc:`dump <dump>` file will also typically change
if sorting is enabled.
Running a simulation with sorting on versus off should not change
the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will
lead to diverging trajectories over time when comparing two
simulations. Various commands, particularly those which use random
numbers (e.g. :doc:`velocity create <velocity>`, and :doc:`fix
langevin <fix_langevin>`), may generate (statistically identical)
results which depend on the order in which atoms are processed.
The order of atoms in a :doc:`dump <dump>` file will also typically
change if sorting is enabled.
.. note::
@ -183,12 +189,13 @@ Default
By default, *id* is yes. By default, atomic systems (no bond topology
info) do not use a map. For molecular systems (with bond topology
info), a map is used. The default map style is array if no atom ID is
larger than 1 million, otherwise the default is hash. By default, a
"first" group is not defined. By default, sorting is enabled with a
frequency of 1000 and a binsize of 0.0, which means the neighbor
cutoff will be used to set the bin size. If no neighbor cutoff is
defined, sorting will be turned off.
info), the default is to use a map of either *array* or *hash* style
depending on the size of the system, as explained above for the *map
yes* keyword/value option. By default, a *first* group is not
defined. By default, sorting is enabled with a frequency of 1000 and
a binsize of 0.0, which means the neighbor cutoff will be used to set
the bin size. If no neighbor cutoff is defined, sorting will be turned
off.
----------

8
doc/src/atom_style.rst
View File

@ -189,6 +189,14 @@ the Additional Information section below.
- *atomic* + molecule, radius, rmass + "smd data"
- :ref:`MACHDYN <PKG-MACHDYN>`
- Smooth Mach Dynamics models
* - *rheo*
- *atomic* + rho, status
- :ref:`RHEO <PKG-RHEO>`
- solid and fluid RHEO particles
* - *rheo/thermal*
- *atomic* + rho, status, energy, temperature
- :ref:`RHEO <PKG-RHEO>`
- RHEO particles with temperature
* - *sph*
- *atomic* + "sph data"
- :ref:`SPH <PKG-SPH>`

188
doc/src/bond_rheo_shell.rst Normal file
View File

@ -0,0 +1,188 @@
.. index:: bond_style rheo/shell
bond_style rheo/shell command
=============================
Syntax
""""""
.. code-block:: LAMMPS
bond_style rheo/shell keyword value attribute1 attribute2 ...
* required keyword = *t/form*
* optional keyword = *store/local*
.. parsed-literal::
*t/form* value = formation time for a bond (time units)
*store/local* values = fix_ID N attributes ...
* fix_ID = ID of associated internal fix to store data
* N = prepare data for output every this many timesteps
* attributes = zero or more of the below attributes may be appended
*id1, id2* = IDs of 2 atoms in the bond
*time* = the timestep the bond broke
*x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
*x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
Examples
""""""""
.. code-block:: LAMMPS
bond_style rheo/shell t/form 10.0
bond_coeff 1 1.0 0.05 0.1
Description
"""""""""""
.. versionadded:: TBD
The *rheo/shell* bond style is designed to work with
:doc:`fix rheo/oxidation <fix_rheo_oxidation>` which creates candidate
bonds between eligible surface or near-surface particles. When a bond
is first created, it computes no forces and starts a timer. Forces are
not computed until the timer reaches the specified bond formation time,
*t/form*, and the bond is enabled and applies forces. If the two particles
move outside of the maximum bond distance or move into the bulk before
the timer reaches *t/form*, the bond automatically deletes itself. This
deletion is not recorded as a broken bond in the optional *store/local* fix.
Before bonds are enabled, they are still treated as regular bonds by
all other parts of LAMMPS. This means they are written to data files
and counted in computes such as :doc:`nbond/atom <compute_nbond_atom>`.
To only count enabled bonds, use the *nbond/shell* attribute in
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`.
When enabled, the bond then computes forces based on deviations from
the initial reference state of the two atoms much like a BPM style
bond (as further discussed in the :doc:`BPM howto page <Howto_bpm>`).
The reference state is stored by each bond when it is first enabled.
Data is then preserved across run commands and is written to
:doc:`binary restart files <restart>` such that restarting the system
will not reset the reference state of a bond or the timer.
This bond style is based on a model described in
:ref:`(Clemmer) <rheo_clemmer>`. The force has a magnitude of
.. math::
F = 2 k (r - r_0) + \frac{2 k}{r_0^2 \epsilon_c^2} (r - r_0)^3
where :math:`k` is a stiffness, :math:`r` is the current distance
and :math:`r_0` is the initial distance between the two particles, and
:math:`\epsilon_c` is maximum strain beyond which a bond breaks. This
is done by setting the bond type to 0 such that forces are no longer
computed.
A damping force proportional to the difference in the normal velocity
of particles is also applied to bonded particles:
.. math::
F_D = - \gamma w (\hat{r} \bullet \vec{v})
where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
displacement normal vector, and :math:`\vec{v}` is the velocity difference
between the two particles.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data
<read_data>` or :doc:`read_restart <read_restart>` commands:
* :math:`k` (force/distance units)
* :math:`\epsilon_c` (unit less)
* :math:`\gamma` (force/velocity units)
Unlike other BPM-style bonds, this bond style does not update special
bond settings when bonds are created or deleted. This bond style also
does not enforce specific :doc:`special_bonds <special_bonds>` settings.
This behavior is purposeful such :doc:`RHEO pair <pair_rheo>` forces
and heat flows are still calculated.
If the *store/local* keyword is used, an internal fix will track bonds that
break during the simulation. Whenever a bond breaks, data is processed
and transferred to an internal fix labeled *fix_ID*. This allows the
local data to be accessed by other LAMMPS commands. Following this optional
keyword, a list of one or more attributes is specified. These include the
IDs of the two atoms in the bond. The other attributes for the two atoms
include the timestep during which the bond broke and the current/initial
center of mass position of the two atoms.
Data is continuously accumulated over intervals of *N*
timesteps. At the end of each interval, all of the saved accumulated
data is deleted to make room for new data. Individual datum may
therefore persist anywhere between *1* to *N* timesteps depending on
when they are saved. This data can be accessed using the *fix_ID* and a
:doc:`dump local <dump>` command. To ensure all data is output,
the dump frequency should correspond to the same interval of *N*
timesteps. A dump frequency of an integer multiple of *N* can be used
to regularly output a sample of the accumulated data.
Note that when unbroken bonds are dumped to a file via the
:doc:`dump local <dump>` command, bonds with type 0 (broken bonds)
are not included.
The :doc:`delete_bonds <delete_bonds>` command can also be used to
query the status of broken bonds or permanently delete them, e.g.:
.. code-block:: LAMMPS
delete_bonds all stats
delete_bonds all bond 0 remove
----------
Restart and other info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This bond style writes the reference state of each bond to
:doc:`binary restart files <restart>`. Loading a restart
file will properly restore bonds. However, the reference state is NOT
written to data files. Therefore reading a data file will not
restore bonds and will cause their reference states to be redefined.
If the *store/local* option is used, an internal fix will calculate
a local vector or local array depending on the number of input values.
The length of the vector or number of rows in the array is the number
of recorded, broken bonds. If a single input is specified, a local
vector is produced. If two or more inputs are specified, a local array
is produced where the number of columns = the number of inputs. The
vector or array can be accessed by any command that uses local values
from a compute as input. See the :doc:`Howto output <Howto_output>` page
for an overview of LAMMPS output options.
The vector or array will be floating point values that correspond to
the specified attribute.
The single() function of this bond style returns 0.0 for the energy
of a bonded interaction, since energy is not conserved in these
dissipative potentials. The single() function also calculates two
extra bond quantities, the initial distance :math:`r_0` and a time.
These extra quantities can be accessed by the
:doc:`compute bond/local <compute_bond_local>` command as *b1* and *b2*\ .
Restrictions
""""""""""""
This bond style is part of the RHEO package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`fix rheo/oxidation <fix_rheo_oxidation>`
Default
"""""""
NA
----------
.. _rheo_clemmer:
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

1
doc/src/bond_style.rst
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@ -105,6 +105,7 @@ accelerated styles exist.
* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
* :doc:`quartic <bond_quartic>` - breakable quartic bond
* :doc:`rheo/shell <bond_rheo_shell>` - shell bond for oxidation modeling in RHEO
* :doc:`special <bond_special>` - enable special bond exclusions for 1-5 pairs and beyond
* :doc:`table <bond_table>` - tabulated by bond length

5
doc/src/compute.rst
View File

@ -272,6 +272,10 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`pe/mol/tally <compute_tally>` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism
* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
* :doc:`pod/atom <compute_pod_atom>` - POD descriptors for each atom
* :doc:`podd/atom <compute_pod_atom>` - derivative of POD descriptors for each atom
* :doc:`pod/local <compute_pod_atom>` - local POD descriptors and their derivatives
* :doc:`pod/global <compute_pod_atom>` - global POD descriptors and their derivatives
* :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
* :doc:`pressure/alchemy <compute_pressure_alchemy>` - mixed system total pressure and pressure tensor for :doc:`fix alchemy <fix_alchemy>` runs
* :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
@ -286,6 +290,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
* :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
* :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region
* :doc:`rheo/property/atom <compute_rheo_property_atom>` - convert atom attributes in RHEO package to per-atom vectors/arrays
* :doc:`rigid/local <compute_rigid_local>` - extract rigid body attributes
* :doc:`saed <compute_saed>` - electron diffraction intensity on a mesh of reciprocal lattice nodes
* :doc:`slcsa/atom <compute_slcsa_atom>` - perform Supervised Learning Crystal Structure Analysis (SL-CSA)

13
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@ -8,10 +8,17 @@ Syntax
.. code-block:: LAMMPS
compute ID group-ID nbond/atom
compute ID group-ID nbond/atom keyword value
* ID, group-ID are documented in :doc:`compute <compute>` command
* nbond/atom = style name of this compute command
* zero or more keyword/value pairs may be appended
* keyword = *bond/type*
.. parsed-literal::
*bond/type* value = *btype*
*btype* = bond type included in count
Examples
""""""""
@ -19,6 +26,7 @@ Examples
.. code-block:: LAMMPS
compute 1 all nbond/atom
compute 1 all nbond/atom bond/type 2
Description
"""""""""""
@ -31,6 +39,9 @@ the :doc:`Howto broken bonds <Howto_bpm>` page for more information.
The number of bonds will be zero for atoms not in the specified
compute group. This compute does not depend on Newton bond settings.
If the keyword *bond/type* is specified, only bonds of *btype* are
counted.
Output info
"""""""""""

145
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@ -0,0 +1,145 @@
.. index:: compute pod/atom
.. index:: compute podd/atom
.. index:: compute pod/local
.. index:: compute pod/global
compute pod/atom command
========================
compute podd/atom command
=========================
compute pod/local command
=========================
compute pod/global command
==========================
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID pod/atom param.pod coefficients.pod
compute ID group-ID podd/atom param.pod coefficients.pod
compute ID group-ID pod/local param.pod coefficients.pod
compute ID group-ID pod/global param.pod coefficients.pod
* ID, group-ID are documented in :doc:`compute <compute>` command
* pod/atom = style name of this compute command
* param.pod = the parameter file specifies parameters of the POD descriptors
* coefficients.pod = the coefficient file specifies coefficients of the POD potential
Examples
""""""""
.. code-block:: LAMMPS
compute d all pod/atom Ta_param.pod
compute dd all podd/atom Ta_param.pod
compute ldd all pod/local Ta_param.pod
compute gdd all podd/global Ta_param.pod
compute d all pod/atom Ta_param.pod Ta_coefficients.pod
compute dd all podd/atom Ta_param.pod Ta_coefficients.pod
compute ldd all pod/local Ta_param.pod Ta_coefficients.pod
compute gdd all podd/global Ta_param.pod Ta_coefficients.pod
Description
"""""""""""
.. versionadded:: 27June2024
Define a computation that calculates a set of quantities related to the
POD descriptors of the atoms in a group. These computes are used
primarily for calculating the dependence of energy and force components
on the linear coefficients in the :doc:`pod pair_style <pair_pod>`,
which is useful when training a POD potential to match target data. POD
descriptors of an atom are characterized by the radial and angular
distribution of neighbor atoms. The detailed mathematical definition is
given in the papers by :ref:`(Nguyen and Rohskopf) <Nguyen20222c>`,
:ref:`(Nguyen2023) <Nguyen20232c>`, :ref:`(Nguyen2024) <Nguyen20242c>`,
and :ref:`(Nguyen and Sema) <Nguyen20243c>`.
Compute *pod/atom* calculates the per-atom POD descriptors.
Compute *podd/atom* calculates derivatives of the per-atom POD
descriptors with respect to atom positions.
Compute *pod/local* calculates the per-atom POD descriptors and their
derivatives with respect to atom positions.
Compute *pod/global* calculates the global POD descriptors and their
derivatives with respect to atom positions.
Examples how to use Compute POD commands are found in the directory
``examples/PACKAGES/pod``.
.. warning::
All of these compute styles produce *very* large per-atom output
arrays that scale with the total number of atoms in the system.
This will result in *very* large memory consumption for systems
with a large number of atoms.
----------
Output info
"""""""""""
Compute *pod/atom* produces an 2D array of size :math:`N \times M`,
where :math:`N` is the number of atoms and :math:`M` is the number of
descriptors. Each column corresponds to a particular POD descriptor.
Compute *podd/atom* produces an 2D array of size :math:`N \times (M * 3
N)`. Each column corresponds to a particular derivative of a POD
descriptor.
Compute *pod/local* produces an 2D array of size :math:`(1 + 3N) \times
(M * N)`. The first row contains the per-atom descriptors, and the last
3N rows contain the derivatives of the per-atom descriptors with respect
to atom positions.
Compute *pod/global* produces an 2D array of size :math:`(1 + 3N) \times
(M)`. The first row contains the global descriptors, and the last 3N
rows contain the derivatives of the global descriptors with respect to
atom positions.
Restrictions
""""""""""""
These computes are part of the ML-POD package. They are only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fitpod <fitpod_command>`,
:doc:`pair_style pod <pair_pod>`
Default
"""""""
none
----------
.. _Nguyen20222c:
**(Nguyen and Rohskopf)** Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).
.. _Nguyen20232c:
**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
.. _Nguyen20242c:
**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
.. _Nguyen20243c:
**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).

143
doc/src/compute_rheo_property_atom.rst Normal file
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@ -0,0 +1,143 @@
.. index:: compute rheo/property/atom
compute rheo/property/atom command
==================================
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID rheo/property/atom input1 input2 ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* rheo/property/atom = style name of this compute command
* input = one or more atom attributes
.. parsed-literal::
possible attributes = phase, surface, surface/r,
surface/divr, surface/n/a, coordination,
shift/v/a, energy, temperature, heatflow,
conductivity, cv, viscosity, pressure, rho,
grad/v/ab, stress/v/ab, stress/t/ab, nbond/shell
.. parsed-literal::
*phase* = atom phase state
*surface* = atom surface status
*surface/r* = atom distance from the surface
*surface/divr* = divergence of position at atom position
*surface/n/a* = a-component of surface normal vector
*coordination* = coordination number
*shift/v/a* = a-component of atom shifting velocity
*energy* = atom energy
*temperature* = atom temperature
*heatflow* = atom heat flow
*conductivity* = atom conductivity
*cv* = atom specific heat
*viscosity* = atom viscosity
*pressure* = atom pressure
*rho* = atom density
*grad/v/ab* = ab-component of atom velocity gradient tensor
*stress/v/ab* = ab-component of atom viscous stress tensor
*stress/t/ab* = ab-component of atom total stress tensor (pressure and viscous)
*nbond/shell* = number of oxide bonds
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all rheo/property/atom phase surface/r surface/n/* pressure
compute 2 all rheo/property/atom shift/v/x grad/v/xx stress/v/*
Description
"""""""""""
.. versionadded:: TBD
Define a computation that stores atom attributes specific to the RHEO
package for each atom in the group. This is useful so that the values
can be used by other :doc:`output commands <Howto_output>` that take
computes as inputs. See for example, the
:doc:`compute reduce <compute_reduce>`,
:doc:`fix ave/atom <fix_ave_atom>`,
:doc:`fix ave/histo <fix_ave_histo>`,
:doc:`fix ave/chunk <fix_ave_chunk>`, and
:doc:`atom-style variable <variable>` commands.
For vector attributes, e.g. *shift/v/*:math:`\alpha`, one must specify
:math:`\alpha` as the *x*, *y*, or *z* component, e.g. *shift/v/x*.
Alternatively, a wild card \* will include all components, *x* and *y* in
2D or *x*, *y*, and *z* in 3D.
For tensor attributes, e.g. *grad/v/*:math:`\alpha \beta`, one must specify
both :math:`\alpha` and :math:`\beta` as *x*, *y*, or *z*, e.g. *grad/v/xy*.
Alternatively, a wild card \* will include all components. In 2D, this
includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
*yx*, *yy*, *yz*, *zx*, *zy*, and *zz*.
Many properties require their respective fixes, listed below in related
commands, be defined. For instance, the *viscosity* attribute is the
viscosity of a particle calculated by
:doc:`fix rheo/viscous <fix_rheo_viscosity>`. The meaning of less obvious
properties is described below.
The *phase* property indicates whether the particle is in a fluid state,
a value of 0, or a solid state, a value of 1.
The *surface* property indicates the surface designation produced by
the *interface/reconstruct* option of :doc:`fix rheo <fix_rheo>`. Bulk
particles have a value of 0, surface particles have a value of 1, and
splash particles have a value of 2. The *surface/r* property is the
distance from the surface, up to the kernel cutoff length. Surface particles
have a value of 0. The *surface/n/*:math:`\alpha` properties are the
components of the surface normal vector.
The *shift/v/*:math:`\alpha` properties are the components of the shifting
velocity produced by the *shift* option of :doc:`fix rheo <fix_rheo>`.
The *nbond/shell* property is the number of shell bonds that have been
activated from :doc:`bond style rheo/shell <bond_rheo_shell>`.
The values are stored in a per-atom vector or array as discussed
below. Zeroes are stored for atoms not in the specified group or for
quantities that are not defined for a particular particle in the group
Output info
"""""""""""
This compute calculates a per-atom vector or per-atom array depending
on the number of input values. Generally, if a single input is specified,
a per-atom vector is produced. If two or more inputs are specified, a
per-atom array is produced where the number of columns = the number of
inputs. However, if a wild card \* is used for a vector or tensor, then
the number of inputs is considered to be incremented by the dimension or
the dimension squared, respectively. The vector or array can be accessed
by any command that uses per-atom values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
The vector or array values will be in whatever :doc:`units <units>` the
corresponding attribute is in (e.g., density units for *rho*).
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`,
:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
:doc:`fix rheo/pressure <fix_rheo_pressure>`,
:doc:`fix rheo/thermal <fix_rheo_thermal>`,
:doc:`fix rheo/oxdiation <fix_rheo_oxidation>`,
:doc:`fix rheo <fix_rheo>`
Default
"""""""
none

28
doc/src/dump_modify.rst
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@ -107,6 +107,13 @@ Syntax
*checksum* args = *yes* or *no* (add checksum at end of zst file)
* these keywords apply only to the vtk* dump style
* keyword = *binary*
.. parsed-literal::
*binary* args = *yes* or *no* (select between binary and text mode VTK files)
Examples
""""""""
@ -907,11 +914,11 @@ box size stored with the snapshot.
----------
The COMPRESS package offers both GZ and Zstd compression variants of
styles atom, custom, local, cfg, and xyz. When using these styles the
compression level can be controlled by the :code:`compression_level`
keyword. File names with these styles have to end in either
:code:`.gz` or :code:`.zst`.
The :ref:`COMPRESS package <PKG-COMPRESS>` offers both GZ and Zstd
compression variants of styles atom, custom, local, cfg, and xyz. When
using these styles the compression level can be controlled by the
:code:`compression_level` keyword. File names with these styles have to
end in either :code:`.gz` or :code:`.zst`.
GZ supports compression levels from :math:`-1` (default), 0 (no compression),
and 1 to 9, 9 being the best compression. The COMPRESS :code:`/gz` styles use 9
@ -930,6 +937,17 @@ default and it can be disabled with the :code:`checksum` keyword.
----------
The :ref:`VTK package <PKG-VTK>` offers writing dump files in `VTK file
formats <https://www.vtk.org/>`_ that can be read by a variety of
visualization tools based on the VTK library. These VTK files follow
naming conventions that collide with the LAMMPS convention to append
".bin" to a file name in order to switch to a binary output. Thus for
:doc:`vtk style dumps <dump_vtk>` the dump_modify command supports the
keyword *binary* which selects between generating text mode and binary
style VTK files.
----------
Restrictions
""""""""""""

741
doc/src/fitpod_command.rst
View File

@ -1,18 +1,19 @@
.. index:: fitpod
fitpod command
======================
==============
Syntax
""""""
.. code-block:: LAMMPS
fitpod Ta_param.pod Ta_data.pod
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
* fitpod = style name of this command
* Ta_param.pod = an input file that describes proper orthogonal descriptors (PODs)
* Ta_data.pod = an input file that specifies DFT data used to fit a POD potential
* Ta_coefficients.pod (optional) = an input file that specifies trainable coefficients of a POD potential
Examples
""""""""
@ -20,20 +21,26 @@ Examples
.. code-block:: LAMMPS
fitpod Ta_param.pod Ta_data.pod
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
Description
"""""""""""
.. versionadded:: 22Dec2022
Fit a machine-learning interatomic potential (ML-IAP) based on proper
orthogonal descriptors (POD). Two input files are required for this
command. The first input file describes a POD potential parameter
settings, while the second input file specifies the DFT data used for
the fitting procedure.
orthogonal descriptors (POD); please see :ref:`(Nguyen and Rohskopf)
<Nguyen20222a>`, :ref:`(Nguyen2023) <Nguyen20232a>`, :ref:`(Nguyen2024)
<Nguyen20242a>`, and :ref:`(Nguyen and Sema) <Nguyen20243a>` for details.
The fitted POD potential can be used to run MD simulations via
:doc:`pair_style pod <pair_pod>`.
The table below has one-line descriptions of all the keywords that can
be used in the first input file (i.e. ``Ta_param.pod`` in the example
above):
Two input files are required for this command. The first input file
describes a POD potential parameter settings, while the second input
file specifies the DFT data used for the fitting procedure. All keywords
except *species* have default values. If a keyword is not set in the
input file, its default value is used. The table below has one-line
descriptions of all the keywords that can be used in the first input
file (i.e. ``Ta_param.pod``)
.. list-table::
:header-rows: 1
@ -52,7 +59,7 @@ above):
- INT
- three integer constants specify boundary conditions
* - rin
- 1.0
- 0.5
- REAL
- a real number specifies the inner cut-off radius
* - rcut
@ -60,46 +67,75 @@ above):
- REAL
- a real number specifies the outer cut-off radius
* - bessel_polynomial_degree
- 3
- 4
- INT
- the maximum degree of Bessel polynomials
* - inverse_polynomial_degree
- 6
- 8
- INT
- the maximum degree of inverse radial basis functions
* - number_of_environment_clusters
- 1
- INT
- the number of clusters for environment-adaptive potentials
* - number_of_principal_components
- 2
- INT
- the number of principal components for dimensionality reduction
* - onebody
- 1
- BOOL
- turns on/off one-body potential
* - twobody_number_radial_basis_functions
- 6
- 8
- INT
- number of radial basis functions for two-body potential
* - threebody_number_radial_basis_functions
- 5
- 6
- INT
- number of radial basis functions for three-body potential
* - threebody_number_angular_basis_functions
* - threebody_angular_degree
- 5
- INT
- number of angular basis functions for three-body potential
* - fourbody_snap_twojmax
- angular degree for three-body potential
* - fourbody_number_radial_basis_functions
- 4
- INT
- number of radial basis functions for four-body potential
* - fourbody_angular_degree
- 3
- INT
- angular degree for four-body potential
* - fivebody_number_radial_basis_functions
- 0
- INT
- band limit for SNAP bispectrum components (0,2,4,6,8... allowed)
* - fourbody_snap_chemflag
- number of radial basis functions for five-body potential
* - fivebody_angular_degree
- 0
- BOOL
- turns on/off the explicit multi-element variant of the SNAP bispectrum components
* - quadratic_pod_potential
- INT
- angular degree for five-body potential
* - sixbody_number_radial_basis_functions
- 0
- BOOL
- turns on/off quadratic POD potential
- INT
- number of radial basis functions for six-body potential
* - sixbody_angular_degree
- 0
- INT
- angular degree for six-body potential
* - sevenbody_number_radial_basis_functions
- 0
- INT
- number of radial basis functions for seven-body potential
* - sevenbody_angular_degree
- 0
- INT
- angular degree for seven-body potential
Note that both the number of radial basis functions and angular degree
must decrease as the body order increases. The next table describes all
keywords that can be used in the second input file (i.e. ``Ta_data.pod``
in the example above):
All keywords except *species* have default values. If a keyword is not
set in the input file, its default value is used. The next table
describes all keywords that can be used in the second input file
(i.e. ``Ta_data.pod`` in the example above):
.. list-table::
:header-rows: 1
@ -125,6 +161,10 @@ describes all keywords that can be used in the second input file
- ""
- STRING
- specifies the path to test data files in double quotes
* - path_to_environment_configuration_set
- ""
- STRING
- specifies the path to environment configuration files in double quotes
* - fraction_training_data_set
- 1.0
- REAL
@ -133,6 +173,14 @@ describes all keywords that can be used in the second input file
- 0
- BOOL
- turns on/off randomization of the training set
* - fraction_test_data_set
- 1.0
- REAL
- a real number (<= 1.0) specifies the fraction of the test set used to validate POD
* - randomize_test_data_set
- 0
- BOOL
- turns on/off randomization of the test set
* - fitting_weight_energy
- 100.0
- REAL
@ -161,6 +209,10 @@ describes all keywords that can be used in the second input file
- 8
- INT
- number of digits after the decimal points for numbers in the coefficient file
* - group_weights
- global
- STRING
- ``table`` uses group weights defined for each group named by filename
All keywords except *path_to_training_data_set* have default values. If
a keyword is not set in the input file, its default value is used. After
@ -172,14 +224,44 @@ successful training, a number of output files are produced, if enabled:
* ``<basename>_test_analysis.pod`` reports detailed errors for all test configurations
* ``<basename>_coefficients.pod`` contains the coefficients of the POD potential
After training the POD potential, ``Ta_param.pod`` and ``<basename>_coefficients.pod``
are the two files needed to use the POD potential in LAMMPS. See
:doc:`pair_style pod <pair_pod>` for using the POD potential. Examples
about training and using POD potentials are found in the directory
lammps/examples/PACKAGES/pod.
After training the POD potential, ``Ta_param.pod`` and
``<basename>_coefficients.pod`` are the two files needed to use the POD
potential in LAMMPS. See :doc:`pair_style pod <pair_pod>` for using the
POD potential. Examples about training and using POD potentials are
found in the directory lammps/examples/PACKAGES/pod and the Github repo
https://github.com/cesmix-mit/pod-examples.
Parameterized Potential Energy Surface
""""""""""""""""""""""""""""""""""""""
Loss Function Group Weights
^^^^^^^^^^^^^^^^^^^^^^^^^^^
The *group_weights* keyword in the ``data.pod`` file is responsible for
weighting certain groups of configurations in the loss function. For
example:
.. code-block:: LAMMPS
group_weights table
Displaced_A15 100.0 1.0
Displaced_BCC 100.0 1.0
Displaced_FCC 100.0 1.0
Elastic_BCC 100.0 1.0
Elastic_FCC 100.0 1.0
GSF_110 100.0 1.0
GSF_112 100.0 1.0
Liquid 100.0 1.0
Surface 100.0 1.0
Volume_A15 100.0 1.0
Volume_BCC 100.0 1.0
Volume_FCC 100.0 1.0
This will apply an energy weight of ``100.0`` and a force weight of
``1.0`` for all groups in the ``Ta`` example. The groups are named by
their respective filename. If certain groups are left out of this table,
then the globally defined weights from the ``fitting_weight_energy`` and
``fitting_weight_force`` keywords will be used.
POD Potential
"""""""""""""
We consider a multi-element system of *N* atoms with :math:`N_{\rm e}`
unique elements. We denote by :math:`\boldsymbol r_n` and :math:`Z_n`
@ -187,535 +269,82 @@ position vector and type of an atom *n* in the system,
respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e}
\}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots,
\boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1,
Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The potential energy surface
(PES) of the system can be expressed as a many-body expansion of the
form
Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The total energy of the
POD potential is expressed as :math:`E(\boldsymbol R, \boldsymbol Z) =
\sum_{i=1}^N E_i(\boldsymbol R_i, \boldsymbol Z_i)`, where
.. math::
E(\boldsymbol R, \boldsymbol Z, \boldsymbol{\eta}, \boldsymbol{\mu}) \ = \ & \sum_{i} V^{(1)}(\boldsymbol r_i, Z_i, \boldsymbol \mu^{(1)} ) + \frac12 \sum_{i,j} V^{(2)}(\boldsymbol r_i, \boldsymbol r_j, Z_i, Z_j, \boldsymbol \eta, \boldsymbol \mu^{(2)}) \\
& + \frac16 \sum_{i,j,k} V^{(3)}(\boldsymbol r_i, \boldsymbol r_j, \boldsymbol r_k, Z_i, Z_j, Z_k, \boldsymbol \eta, \boldsymbol \mu^{(3)}) + \ldots
where :math:`V^{(1)}` is the one-body potential often used for
representing external field or energy of isolated elements, and the
higher-body potentials :math:`V^{(2)}, V^{(3)}, \ldots` are symmetric,
uniquely defined, and zero if two or more indices take identical values.
The superscript on each potential denotes its body order. Each *q*-body
potential :math:`V^{(q)}` depends on :math:`\boldsymbol \mu^{(q)}` which
are sets of parameters to fit the PES. Note that :math:`\boldsymbol \mu`
is a collection of all potential parameters :math:`\boldsymbol
\mu^{(1)}`, :math:`\boldsymbol \mu^{(2)}`, :math:`\boldsymbol
\mu^{(3)}`, etc, and that :math:`\boldsymbol \eta` is a set of
hyper-parameters such as inner cut-off radius :math:`r_{\rm in}` and
outer cut-off radius :math:`r_{\rm cut}`.
Interatomic potentials rely on parameters to learn relationship between
atomic environments and interactions. Since interatomic potentials are
approximations by nature, their parameters need to be set to some
reference values or fitted against data by necessity. Typically,
potential fitting finds optimal parameters, :math:`\boldsymbol \mu^*`,
to minimize a certain loss function of the predicted quantities and
data. Since the fitted potential depends on the data set used to fit it,
different data sets will yield different optimal parameters and thus
different fitted potentials. When fitting the same functional form on
*Q* different data sets, we would obtain *Q* different optimized
potentials, :math:`E(\boldsymbol R,\boldsymbol Z, \boldsymbol \eta,
\boldsymbol \mu_q^*), 1 \le q \le Q`. Consequently, there exist many
different sets of optimized parameters for empirical interatomic
potentials.
Instead of optimizing the potential parameters, inspired by the reduced
basis method :ref:`(Grepl) <Grepl20072>` for parameterized partial
differential equations, we view the parameterized PES as a parametric
manifold of potential energies
.. math::
\mathcal{M} = \{E(\boldsymbol R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu) \ | \ \boldsymbol \mu \in \Omega^{\boldsymbol \mu} \}
where :math:`\Omega^{\boldsymbol \mu}` is a parameter domain in which
:math:`\boldsymbol \mu` resides. The parametric manifold
:math:`\mathcal{M}` contains potential energy surfaces for all values of
:math:`\boldsymbol \mu \in \Omega^{\boldsymbol \mu}`. Therefore, the
parametric manifold yields a much richer and more transferable atomic
representation than any particular individual PES :math:`E(\boldsymbol
R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu^*)`.
We propose specific forms of the parameterized potentials for one-body,
two-body, and three-body interactions. We apply the Karhunen-Loeve
expansion to snapshots of the parameterized potentials to obtain sets of
orthogonal basis functions. These basis functions are aggregated
according to the chemical elements of atoms, thus leading to
multi-element proper orthogonal descriptors.
Proper Orthogonal Descriptors
"""""""""""""""""""""""""""""
Proper orthogonal descriptors are finger prints characterizing the
radial and angular distribution of a system of atoms. The detailed
mathematical definition is given in the paper by Nguyen and Rohskopf
:ref:`(Nguyen) <Nguyen20222>`.
The descriptors for the one-body interaction are used to capture energy
of isolated elements and defined as follows
.. math::
D_{ip}^{(1)} = \left\{
\begin{array}{ll}
1, & \mbox{if } Z_i = p \\
0, & \mbox{if } Z_i \neq p
\end{array}
\right.
for :math:`1 \le i \le N, 1 \le p \le N_{\rm e}`. The number of one-body
descriptors per atom is equal to the number of elements. The one-body
descriptors are independent of atom positions, but dependent on atom
types. The one-body descriptors are active only when the keyword
*onebody* is set to 1.
We adopt the usual assumption that the direct interaction between two
atoms vanishes smoothly when their distance is greater than the outer
cutoff distance :math:`r_{\rm cut}`. Furthermore, we assume that two
atoms can not get closer than the inner cutoff distance :math:`r_{\rm
in}` due to the Pauli repulsion principle. Let :math:`r \in (r_{\rm in},
r_{\rm cut})`, we introduce the following parameterized radial functions
.. math::
\phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) = \frac{\sin (\alpha \pi x) }{r - r_{\rm in}}, \qquad \varphi(r, \gamma) = \frac{1}{r^\gamma} ,
where the scaled distance function :math:`x` is defined below to enrich the two-body manifold
.. math::
x(r, r_{\rm in}, r_{\rm cut}, \beta) = \frac{e^{-\beta(r - r_{\rm in})/(r_{\rm cut} - r_{\rm in})} - 1}{e^{-\beta} - 1} .
We introduce the following function as a convex combination of the two functions
.. math::
\psi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta, \gamma, \kappa) = \kappa \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) + (1- \kappa) \varphi(r, \gamma) .
We see that :math:`\psi` is a function of distance :math:`r`, cut-off
distances :math:`r_{\rm in}` and :math:`r_{\rm cut}`, and parameters
:math:`\alpha, \beta, \gamma, \kappa`. Together these parameters allow
the function :math:`\psi` to characterize a diverse spectrum of two-body
interactions within the cut-off interval :math:`(r_{\rm in}, r_{\rm
cut})`.
Next, we introduce the following parameterized potential
.. math::
W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}) = f_{\rm c}(r_{ij}, \boldsymbol \eta) \psi(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)})
where :math:`\eta_1 = r_{\rm in}, \eta_2 = r_{\rm cut}, \mu_1^{(2)} =
\alpha, \mu_2^{(2)} = \beta, \mu_3^{(2)} = \gamma`, and
:math:`\mu_4^{(2)} = \kappa`. Here the cut-off function :math:`f_{\rm
c}(r_{ij}, \boldsymbol \eta)` proposed in [refs] is used to ensure the
smooth vanishing of the potential and its derivative for :math:`r_{ij}
\ge r_{\rm cut}`:
.. math::
f_{\rm c}(r_{ij}, r_{\rm in}, r_{\rm cut}) = \exp \left(1 -\frac{1}{\sqrt{\left(1 - \frac{(r-r_{\rm in})^3}{(r_{\rm cut} - r_{\rm in})^3} \right)^2 + 10^{-6}}} \right)
Based on the parameterized potential, we form a set of snapshots as
follows. We assume that we are given :math:`N_{\rm s}` parameter tuples
:math:`\boldsymbol \mu^{(2)}_\ell, 1 \le \ell \le N_{\rm s}`. We
introduce the following set of snapshots on :math:`(r_{\rm in}, r_{\rm
cut})`:
.. math::
\xi_\ell(r_{ij}, \boldsymbol \eta) = W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}_\ell), \quad \ell = 1, \ldots, N_{\rm s} .
To ensure adequate sampling of the PES for different parameters, we
choose :math:`N_{\rm s}` parameter points :math:`\boldsymbol
\mu^{(2)}_\ell = (\alpha_\ell, \beta_\ell, \gamma_\ell, \kappa_\ell), 1
\le \ell \le N_{\rm s}` as follows. The parameters :math:`\alpha \in [1,
N_\alpha]` and :math:`\gamma \in [1, N_\gamma]` are integers, where
:math:`N_\alpha` and :math:`N_\gamma` are the highest degrees for
:math:`\alpha` and :math:`\gamma`, respectively. We next choose
:math:`N_\beta` different values of :math:`\beta` in the interval
:math:`[\beta_{\min}, \beta_{\max}]`, where :math:`\beta_{\min} = 0` and
:math:`\beta_{\max} = 4`. The parameter :math:`\kappa` can be set either
0 or 1. Hence, the total number of parameter points is :math:`N_{\rm s}
= N_\alpha N_\beta + N_\gamma`. Although :math:`N_\alpha, N_\beta,
N_\gamma` can be chosen conservatively large, we find that
:math:`N_\alpha = 6, N_\beta = 3, N_\gamma = 8` are adequate for most
problems. Note that :math:`N_\alpha` and :math:`N_\gamma` correspond to
*bessel_polynomial_degree* and *inverse_polynomial_degree*,
respectively.
We employ the Karhunen-Loeve (KL) expansion to generate an orthogonal
basis set which is known to be optimal for representation of the
snapshot family :math:`\{\xi_\ell\}_{\ell=1}^{N_{\rm s}}`. The two-body
orthogonal basis functions are computed as follows
.. math::
U^{(2)}_m(r_{ij}, \boldsymbol \eta) = \sum_{\ell = 1}^{N_{\rm s}} A_{\ell m}(\boldsymbol \eta) \, \xi_\ell(r_{ij}, \boldsymbol \eta), \qquad m = 1, \ldots, N_{\rm 2b} ,
where the matrix :math:`\boldsymbol A \in \mathbb{R}^{N_{\rm s} \times
N_{\rm s}}` consists of eigenvectors of the eigenvalue problem
.. math::
\boldsymbol C \boldsymbol a = \lambda \boldsymbol a
with the entries of :math:`\boldsymbol C \in \mathbb{R}^{N_{\rm s} \times N_{\rm s}}` being given by
.. math::
C_{ij} = \frac{1}{N_{\rm s}} \int_{r_{\rm in}}^{r_{\rm cut}} \xi_i(x, \boldsymbol \eta) \xi_j(x, \boldsymbol \eta) dx, \quad 1 \le i, j \le N_{\rm s}
Note that the eigenvalues :math:`\lambda_\ell, 1 \le \ell \le N_{\rm
s}`, are ordered such that :math:`\lambda_1 \ge \lambda_2 \ge \ldots \ge
\lambda_{N_{\rm s}}`, and that the matrix :math:`\boldsymbol A` is
pe-computed and stored for any given :math:`\boldsymbol \eta`. Owing to
the rapid convergence of the KL expansion, only a small number of
orthogonal basis functions is needed to obtain accurate
approximation. The value of :math:`N_{\rm 2b}` corresponds to
*twobody_number_radial_basis_functions*.
The two-body proper orthogonal descriptors at each atom *i* are computed
by summing the orthogonal basis functions over the neighbors of atom *i*
and numerating on the atom types as follows
.. math::
D^{(2)}_{im l(p, q) }(\boldsymbol \eta) = \left\{
\begin{array}{ll}
\displaystyle \sum_{\{j | Z_j = q\}} U^{(2)}_m(r_{ij}, \boldsymbol \eta), & \mbox{if } Z_i = p \\
0, & \mbox{if } Z_i \neq p
\end{array}
\right.
for :math:`1 \le i \le N, 1 \le m \le N_{\rm 2b}, 1 \le q, p \le N_{\rm
e}`. Here :math:`l(p,q)` is a symmetric index mapping such that
.. math::
l(p,q) = \left\{
\begin{array}{ll}
q + (p-1) N_{\rm e} - p(p-1)/2, & \mbox{if } q \ge p \\
p + (q-1) N_{\rm e} - q(q-1)/2, & \mbox{if } q < p .
\end{array}
\right.
The number of two-body descriptors per atom is thus :math:`N_{\rm 2b}
N_{\rm e}(N_{\rm e}+1)/2`.
It is important to note that the orthogonal basis functions do not
depend on the atomic numbers :math:`Z_i` and :math:`Z_j`. Therefore, the
cost of evaluating the basis functions and their derivatives with
respect to :math:`r_{ij}` is independent of the number of elements
:math:`N_{\rm e}`. Consequently, even though the two-body proper
orthogonal descriptors depend on :math:`\boldsymbol Z`, their
computational complexity is independent of :math:`N_{\rm e}`.
In order to provide proper orthogonal descriptors for three-body
interactions, we need to introduce a three-body parameterized
potential. In particular, the three-body potential is defined as a
product of radial and angular functions as follows
.. math::
W^{(3)}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta, \boldsymbol \mu^{(3)}) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}) \\
\psi(r_{ik}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ik}, r_{\rm min}, r_{\rm max}) \\
\cos (\sigma \theta_{ijk} + \zeta)
where :math:`\sigma` is the periodic multiplicity, :math:`\zeta` is the
equilibrium angle, :math:`\boldsymbol \mu^{(3)} = (\alpha, \beta,
\gamma, \kappa, \sigma, \zeta)`. The three-body potential provides an
angular fingerprint of the atomic environment through the bond angles
:math:`\theta_{ijk}` formed with each pair of neighbors :math:`j` and
:math:`k`. Compared to the two-body potential, the three-body potential
has two extra parameters :math:`(\sigma, \zeta)` associated with the
angular component.
Let :math:`\boldsymbol \varrho = (\alpha, \beta, \gamma, \kappa)`. We
assume that we are given :math:`L_{\rm r}` parameter tuples
:math:`\boldsymbol \varrho_\ell, 1 \le \ell \le L_{\rm r}`. We
introduce the following set of snapshots on :math:`(r_{\min},
r_{\max})`:
.. math::
\zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \boldsymbol \varrho_\ell) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}), \quad 1 \le \ell \le L_{\rm r} .
We apply the Karhunen-Loeve (KL) expansion to this set of snapshots to
obtain orthogonal basis functions as follows
.. math::
U^{r}_m(r_{ij}, r_{\rm min}, r_{\rm max} ) = \sum_{\ell = 1}^{L_{\rm r}} A_{\ell m} \, \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ), \qquad m = 1, \ldots, N_{\rm r} ,
where the matrix :math:`\boldsymbol A \in \mathbb{R}^{L_{\rm r} \times L_{\rm r}}` consists
of eigenvectors of the eigenvalue problem. For the parameterized angular function,
we consider angular basis functions
.. math::
U^{a}_n(\theta_{ijk}) = \cos ((n-1) \theta_{ijk}), \qquad n = 1,\ldots, N_{\rm a},
where :math:`N_{\rm a}` is the number of angular basis functions. The orthogonal
basis functions for the parameterized potential are computed as follows
.. math::
U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta) = U^{r}_m(r_{ij}, \boldsymbol \eta) U^{r}_m(r_{ik}, \boldsymbol \eta) U^{a}_n(\theta_{ijk}),
for :math:`1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}`. The number of three-body
orthogonal basis functions is equal to :math:`N_{\rm 3b} = N_{\rm r} N_{\rm a}` and
independent of the number of elements. The value of :math:`N_{\rm r}` corresponds to
*threebody_number_radial_basis_functions*, while that of :math:`N_{\rm a}` to
*threebody_number_angular_basis_functions*.
The three-body proper orthogonal descriptors at each atom *i*
are obtained by summing over the neighbors *j* and *k* of atom *i* as
.. math::
D^{(3)}_{imn \ell(p, q, s)}(\boldsymbol \eta) = \left\{
\begin{array}{ll}
\displaystyle \sum_{\{j | Z_j = q\}} \sum_{\{k | Z_k = s\}} U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta), & \mbox{if } Z_i = p \\
0, & \mbox{if } Z_i \neq p
\end{array}
\right.
for :math:`1 \le i \le N, 1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}, 1 \le q, p, s \le N_{\rm e}`,
where
.. math::
\ell(p,q,s) = \left\{
\begin{array}{ll}
s + (q-1) N_{\rm e} - q(q-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2 , & \mbox{if } s \ge q \\
q + (s-1) N_{\rm e} - s(s-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2, & \mbox{if } s < q .
\end{array}
\right.
The number of three-body descriptors per atom is thus :math:`N_{\rm 3b} N_{\rm e}^2(N_{\rm e}+1)/2`.
While the number of three-body PODs is cubic function of the number of elements,
the computational complexity of the three-body PODs is independent of the number of elements.
Four-Body SNAP Descriptors
""""""""""""""""""""""""""
In addition to the proper orthogonal descriptors described above, we also employ
the spectral neighbor analysis potential (SNAP) descriptors. SNAP uses bispectrum components
to characterize the local neighborhood of each atom in a very general way. The mathematical definition
of the bispectrum calculation and its derivatives w.r.t. atom positions is described in
:doc:`compute snap <compute_sna_atom>`. In SNAP, the
total energy is decomposed into a sum over atom energies. The energy of
atom *i* is expressed as a weighted sum over bispectrum components.
.. math::
E_i^{\rm SNAP} = \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}
where the SNAP descriptors are related to the bispectrum components by
.. math::
D^{(4)}_{ikp} = \left\{
\begin{array}{ll}
\displaystyle B_{ik}, & \mbox{if } Z_i = p \\
0, & \mbox{if } Z_i \neq p
\end{array}
\right.
Here :math:`B_{ik}` is the *k*\ -th bispectrum component of atom *i*. The number of
bispectrum components :math:`N_{\rm 4b}` depends on the value of *fourbody_snap_twojmax* :math:`= 2 J_{\rm max}`
and *fourbody_snap_chemflag*. If *fourbody_snap_chemflag* = 0
then :math:`N_{\rm 4b} = (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`.
If *fourbody_snap_chemflag* = 1 then :math:`N_{\rm 4b} = N_{\rm e}^3 (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`.
The bispectrum calculation is described in more detail in :doc:`compute sna/atom <compute_sna_atom>`.
Linear Proper Orthogonal Descriptor Potentials
""""""""""""""""""""""""""""""""""""""""""""""
The proper orthogonal descriptors and SNAP descriptors are used to define the atomic energies
in the following expansion
.. math::
E_{i}(\boldsymbol \eta) = \sum_{p=1}^{N_{\rm e}} c^{(1)}_p D^{(1)}_{ip} + \sum_{m=1}^{N_{\rm 2b}} \sum_{l=1}^{N_{\rm e}(N_{\rm e}+1)/2} c^{(2)}_{ml} D^{(2)}_{iml}(\boldsymbol \eta) + \sum_{m=1}^{N_{\rm r}} \sum_{n=1}^{N_{\rm a}} \sum_{\ell=1}^{N_{\rm e}^2(N_{\rm e}+1)/2} c^{(3)}_{mn\ell} D^{(3)}_{imn\ell}(\boldsymbol \eta) + \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}(\boldsymbol \eta),
where :math:`D^{(1)}_{ip}, D^{(2)}_{iml}, D^{(3)}_{imn\ell}, D^{(4)}_{ikp}` are the one-body, two-body, three-body, four-body descriptors,
respectively, and :math:`c^{(1)}_p, c^{(2)}_{ml}, c^{(3)}_{mn\ell}, c^{(4)}_{kp}` are their respective expansion
coefficients. In a more compact notation that implies summation over descriptor indices
the atomic energies can be written as
.. math::
E_i(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m D^{(1)}_{im} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_k D^{(2)}_{im} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m D^{(3)}_{im} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m D^{(4)}_{im}
where :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2`,
:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2`, and
:math:`N_{\rm d}^{(4)} = N_{\rm 4b} N_{\rm e}` are
the number of two-body, three-body, and four-body descriptors, respectively.
The potential energy is then obtained by summing local atomic energies :math:`E_i`
for all atoms :math:`i` in the system
.. math::
E(\boldsymbol \eta) = \sum_{i}^N E_{i}(\boldsymbol \eta)
Because the descriptors are one-body, two-body, and three-body terms,
the resulting POD potential is a three-body PES. We can express the potential
energy as a linear combination of the global descriptors as follows
.. math::
E(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m d^{(1)}_{m} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m d^{(2)}_{m} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m d^{(3)}_{m} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m d^{(4)}_{m}
where the global descriptors are given by
.. math::
d_{m}^{(1)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(1)}(\boldsymbol \eta), \quad d_{m}^{(2)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(2)}(\boldsymbol \eta), \quad d_{m}^{(3)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(3)}(\boldsymbol \eta), \quad d_{m}^{(4)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(4)}(\boldsymbol \eta)
Hence, we obtain the atomic forces as
.. math::
\boldsymbol F = -\nabla E(\boldsymbol \eta) = - \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m \nabla d_m^{(2)} - \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m \nabla d_m^{(3)} - \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m \nabla d_m^{(4)}
where :math:`\nabla d_m^{(2)}`, :math:`\nabla d_m^{(3)}` and :math:`\nabla d_m^{(4)}` are derivatives of the two-body
three-body, and four-body global descriptors with respect to atom positions, respectively.
Note that since the first-body global descriptors are constant, their derivatives are zero.
Quadratic Proper Orthogonal Descriptor Potentials
"""""""""""""""""""""""""""""""""""""""""""""""""
We recall two-body PODs :math:`D^{(2)}_{ik}, 1 \le k \le N_{\rm d}^{(2)}`,
and three-body PODs :math:`D^{(3)}_{im}, 1 \le m \le N_{\rm d}^{(3)}`,
with :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2` and
:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2` being
the number of descriptors per atom for the two-body PODs and three-body PODs,
respectively. We employ them to define a new set of atomic descriptors as follows
.. math::
D^{(2*3)}_{ikm} = \frac{1}{2N}\left( D^{(2)}_{ik} \sum_{j=1}^N D^{(3)}_{jm} + D^{(3)}_{im} \sum_{j=1}^N D^{(2)}_{jk} \right)
for :math:`1 \le i \le N, 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`.
The new descriptors are four-body because they involve central atom :math:`i` together
with three neighbors :math:`j, k` and :math:`l`. The total number of new descriptors per atom is equal to
.. math::
N_{\rm d}^{(2*3)} = N_{\rm d}^{(2)} * N_{\rm d}^{(3)} = N_{\rm 2b} N_{\rm 3b} N_{\rm e}^3 (N_{\rm e}+1)^2/4 .
The new global descriptors are calculated as
.. math::
d^{(2*3)}_{km} = \sum_{i=1}^N D^{(2*3)}_{ikm} = \left( \sum_{i=1}^N D^{(2)}_{ik} \right) \left( \sum_{i=1}^N D^{(3)}_{im} \right) = d^{(2)}_{k} d^{(3)}_m,
for :math:`1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. Hence, the gradient
of the new global descriptors with respect to atom positions is calculated as
.. math::
\nabla d^{(2*3)}_{km} = d^{(3)}_m \nabla d^{(2)}_{k} + d^{(2)}_{k} \nabla d^{(3)}_m, \quad 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)} .
The quadratic POD potential is defined as a linear combination of the
original and new global descriptors as follows
.. math::
E^{(2*3)} = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d^{(2*3)}_{km} .
It thus follows that
.. math::
E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \left( \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)} \right) d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} \left( \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)} \right) d_m^{(3)} ,
which is simplified to
.. math::
E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b_k^{(2)} d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b_m^{(3)} d_m^{(3)}
where
.. math::
b_k^{(2)} & = \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)}, \quad k = 1,\ldots, N_{\rm 2d}^{(2*3)}, \\
b_m^{(3)} & = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)}, \quad m = 1,\ldots, N_{\rm 3d}^{(2*3)} .
The quadratic POD potential results in the following atomic forces
.. math::
\boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} \nabla d^{(2*3)}_{km} .
It can be shown that
.. math::
\boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b^{(2)}_k \nabla d_k^{(2)} - \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b^{(3)}_m \nabla d_m^{(3)} .
The calculation of the atomic forces for the quadratic POD potential
only requires the extra calculation of :math:`b_k^{(2)}` and :math:`b_m^{(3)}` which can be negligible.
As a result, the quadratic POD potential does not increase the computational complexity.
E_i(\boldsymbol R_i, \boldsymbol Z_i) \ = \ \sum_{m=1}^M c_m \mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)
Here :math:`c_m` are trainable coefficients and
:math:`\mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)` are per-atom
POD descriptors. Summing the per-atom descriptors over :math:`i` yields
the global descriptors :math:`d_m(\boldsymbol R, \boldsymbol Z) =
\sum_{i=1}^N \mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)`. It
thus follows that :math:`E(\boldsymbol R, \boldsymbol Z) = \sum_{m=1}^M
c_m d_m(\boldsymbol R, \boldsymbol Z)`.
The per-atom POD descriptors include one, two, three, four, five, six,
and seven-body descriptors, which can be specified in the first input
file. Furthermore, the per-atom POD descriptors also depend on the
number of environment clusters specified in the first input file.
Please see :ref:`(Nguyen2024) <Nguyen20242a>` and :ref:`(Nguyen and Sema)
<Nguyen20243a>` for the detailed description of the per-atom POD
descriptors.
Training
""""""""
POD potentials are trained using the least-squares regression against
A POD potential is trained using the least-squares regression against
density functional theory (DFT) data. Let :math:`J` be the number of
training configurations, with :math:`N_j` being the number of atoms in
the j-th configuration. Let :math:`\{E^{\star}_j\}_{j=1}^{J}` and
:math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` be the DFT energies and
forces for :math:`J` configurations. Next, we calculate the global
descriptors and their derivatives for all training configurations. Let
:math:`d_{jm}, 1 \le m \le M`, be the global descriptors associated with
the j-th configuration, where :math:`M` is the number of global
descriptors. We then form a matrix :math:`\boldsymbol A \in
\mathbb{R}^{J \times M}` with entries :math:`A_{jm} = d_{jm}/ N_j` for
:math:`j=1,\ldots,J` and :math:`m=1,\ldots,M`. Moreover, we form a
matrix :math:`\boldsymbol B \in \mathbb{R}^{\mathcal{N} \times M}` by
stacking the derivatives of the global descriptors for all training
configurations from top to bottom, where :math:`\mathcal{N} =
3\sum_{j=1}^{J} N_j`.
the j-th configuration. The training configurations are extracted from
the extended XYZ files located in a directory (i.e.,
path_to_training_data_set in the second input file). Let
:math:`\{E^{\star}_j\}_{j=1}^{J}` and :math:`\{\boldsymbol
F^{\star}_j\}_{j=1}^{J}` be the DFT energies and forces for :math:`J`
configurations. Next, we calculate the global descriptors and their
derivatives for all training configurations. Let :math:`d_{jm}, 1 \le m
\le M`, be the global descriptors associated with the j-th
configuration, where :math:`M` is the number of global descriptors. We
then form a matrix :math:`\boldsymbol A \in \mathbb{R}^{J \times M}`
with entries :math:`A_{jm} = d_{jm}/ N_j` for :math:`j=1,\ldots,J` and
:math:`m=1,\ldots,M`. Moreover, we form a matrix :math:`\boldsymbol B
\in \mathbb{R}^{\mathcal{N} \times M}` by stacking the derivatives of
the global descriptors for all training configurations from top to
bottom, where :math:`\mathcal{N} = 3\sum_{j=1}^{J} N_j`.
The coefficient vector :math:`\boldsymbol c` of the POD potential is
found by solving the following least-squares problem
.. math::
{\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A(\boldsymbol \eta) \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B(\boldsymbol \eta) \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2,
{\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2,
where :math:`w_E` and :math:`w_F` are weights for the energy
(*fitting_weight_energy*) and force (*fitting_weight_force*),
respectively; and :math:`w_R` is the regularization parameter (*fitting_regularization_parameter*). Here :math:`\bar{\boldsymbol E}^{\star} \in
\mathbb{R}^{J}` is a vector of with entries :math:`\bar{E}^{\star}_j =
E^{\star}_j/N_j` and :math:`\boldsymbol F^{\star}` is a vector of
:math:`\mathcal{N}` entries obtained by stacking :math:`\{\boldsymbol
F^{\star}_j\}_{j=1}^{J}` from top to bottom.
respectively; and :math:`w_R` is the regularization parameter
(*fitting_regularization_parameter*). Here :math:`\bar{\boldsymbol
E}^{\star} \in \mathbb{R}^{J}` is a vector of with entries
:math:`\bar{E}^{\star}_j = E^{\star}_j/N_j` and :math:`\boldsymbol
F^{\star}` is a vector of :math:`\mathcal{N}` entries obtained by
stacking :math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` from top to
bottom.
The training procedure is the same for both the linear and quadratic POD
potentials. However, since the quadratic POD potential has a
significantly larger number of the global descriptors, it is more
expensive to train the linear POD potential. This is because the
training of the quadratic POD potential still requires us to calculate
and store the quadratic global descriptors and their
gradient. Furthermore, the quadratic POD potential may require more
training data in order to prevent over-fitting. In order to reduce the
computational cost of fitting the quadratic POD potential and avoid
over-fitting, we can use subsets of two-body and three-body PODs for
constructing the new descriptors.
Validation
""""""""""
POD potential can be validated on a test dataset in a directory
specified by setting path_to_test_data_set in the second input file. It
is possible to validate the POD potential after the training is
complete. This is done by providing the coefficient file as an input to
:doc:`fitpod <fitpod_command>`, for example,
.. code-block:: LAMMPS
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
Restrictions
""""""""""""
@ -727,7 +356,11 @@ LAMMPS was built with that package. See the :doc:`Build package
Related commands
""""""""""""""""
:doc:`pair_style pod <pair_pod>`
:doc:`pair_style pod <pair_pod>`,
:doc:`compute pod/atom <compute_pod_atom>`,
:doc:`compute podd/atom <compute_pod_atom>`,
:doc:`compute pod/local <compute_pod_atom>`,
:doc:`compute pod/global <compute_pod_atom>`
Default
"""""""
@ -736,10 +369,20 @@ The keyword defaults are also given in the description of the input files.
----------
.. _Grepl20072:
.. _Nguyen20222a:
**(Grepl)** Grepl, Maday, Nguyen, and Patera, ESAIM: Mathematical Modelling and Numerical Analysis 41(3), 575-605, (2007).
**(Nguyen and Rohskopf)** Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).
.. _Nguyen20232a:
**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
.. _Nguyen20242a:
**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
.. _Nguyen20243a:
**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
.. _Nguyen20222:
**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022).

6
doc/src/fix.rst
View File

@ -193,6 +193,7 @@ accelerated styles exist.
* :doc:`adapt <fix_adapt>` - change a simulation parameter over time
* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
* :doc:`addforce <fix_addforce>` - add a force to each atom
* :doc:`add/heat <fix_add_heat>` - add a heat flux to each atom
* :doc:`addtorque <fix_addtorque>` - add a torque to a group of atoms
* :doc:`alchemy <fix_alchemy>` - perform an "alchemical transformation" between two partitions
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>` - torsion/torsion terms in AMOEBA force field
@ -369,6 +370,11 @@ accelerated styles exist.
* :doc:`reaxff/species <fix_reaxff_species>` - write out ReaxFF molecule information
* :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
* :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
* :doc:`rheo <fix_rheo>` - integrator for the RHEO package
* :doc:`rheo/thermal <fix_rheo_thermal>` - thermal integrator for the RHEO package
* :doc:`rheo/oxidation <fix_rheo_oxidation>` - create oxidation bonds for the RHEO package
* :doc:`rheo/pressure <fix_rheo_pressure>` - pressure calculation for the RHEO package
* :doc:`rheo/viscosity <fix_rheo_pressure>` - viscosity calculation for the RHEO package
* :doc:`rhok <fix_rhok>` - add bias potential for long-range ordered systems
* :doc:`rigid <fix_rigid>` - constrain one or more clusters of atoms to move as a rigid body with NVE integration
* :doc:`rigid/meso <fix_rigid_meso>` - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body

111
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@ -0,0 +1,111 @@
.. index:: fix add/heat
fix add/heat command
====================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID add/heat style args keyword values ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* add/heat = style name of this fix command
* style = *constant* or *linear* or *quartic*
.. parsed-literal::
*constant* args = *rate*
*rate* = rate of heat flow (energy/time units)
*linear* args = :math:`T_{target}` *k*
:math:`T_{target}` = target temperature (temperature units)
*k* = prefactor (energy/(time*temperature) units)
*quartic* args = :math:`T_{target}` *k*
:math:`T_{target}` = target temperature (temperature units)
*k* = prefactor (energy/(time*temperature^4) units)
* zero or more keyword/value pairs may be appended to args
* keyword = *overwrite*
.. parsed-literal::
*overwrite* value = *yes* or *no*
*yes* = sets current heat flow of particle
*no* = adds to current heat flow of particle
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all add/heat constant v_heat
fix 1 all add/heat linear 10.0 1.0 overwrite yes
Description
"""""""""""
This fix adds heat to particles with the temperature attribute every timestep.
Note that this is an internal temperature of a particle intended for use with
non-atomistic models like the discrete element method.
For the *constant* style, heat is added at the specified rate. For the *linear* style,
heat is added at a rate of :math:`k (T_{target} - T)` where :math:`k` is the
specified prefactor, :math:`T_{target}` is the specified target temperature, and
:math:`T` is the temperature of the atom. This may be more representative of a
conductive process. For the *quartic* style, heat is added at a rate of
:math:`k (T_{target}^4 - T^4)`, akin to radiative heat transfer.
The rate or temperature can be can be specified as an equal-style or atom-style
:doc:`variable <variable>`. If the value is a variable, it should be
specified as v_name, where name is the variable name. In this case, the
variable will be evaluated each time step, and its value will be used to
determine the rate of heat added.
Equal-style variables can specify formulas with various mathematical
functions and include :doc:`thermo_style <thermo_style>` command
keywords for the simulation box parameters, time step, and elapsed time
to specify time-dependent heating.
Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates to specify spatially-dependent heating.
If the *overwrite* keyword is set to *yes*, this fix will set the total
heat flow on a particle every timestep, overwriting contributions from pair
styles or other fixes. If *overwrite* is *no*, this fix will add heat on
top of other contributions.
----------
Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
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 access by various
:doc:`output commands <Howto_output>`. No parameter of this fix can be used
with the *start/stop* keywords of the :doc:`run <run>` command. This fix is
not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This pair style is part of the GRANULAR package. It is
only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for more info.
This fix requires that atoms store temperature and heat flow
as defined by the :doc:`fix property/atom <fix_property_atom>` command.
Related commands
""""""""""""""""
:doc:`fix heat/flow <fix_heat_flow>`,
:doc:`fix property/atom <fix_property_atom>`,
:doc:`fix rheo/thermal <fix_rheo_thermal>`
Default
"""""""
The default for the *overwrite* keyword is *no*

66
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@ -4,9 +4,6 @@
fix deform command
==================
:doc:`fix deform/pressure <fix_deform_pressure>` command
========================================================
Accelerator Variants: *deform/kk*
Syntax
@ -14,12 +11,11 @@ Syntax
.. code-block:: LAMMPS
fix ID group-ID fix_style N parameter style args ... keyword value ...
fix ID group-ID deform N parameter style args ... keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* fix_style = *deform* or *deform/pressure*
* N = perform box deformation every this many timesteps
* one or more parameter/style/args sequences of arguments may be appended
* one or more parameter/args sequences may be appended
.. parsed-literal::
@ -46,12 +42,6 @@ Syntax
*variable* values = v_name1 v_name2
v_name1 = variable with name1 for box length change as function of time
v_name2 = variable with name2 for change rate as function of time
*pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*pressure/mean* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*xy*, *xz*, *yz* args = style value
style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable*
@ -64,8 +54,6 @@ Syntax
effectively an engineering shear strain rate
*erate* value = R
R = engineering shear strain rate (1/time units)
*erate/rescale* value = R (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
R = engineering shear strain rate (1/time units)
*trate* value = R
R = true shear strain rate (1/time units)
*wiggle* values = A Tp
@ -74,9 +62,6 @@ Syntax
*variable* values = v_name1 v_name2
v_name1 = variable with name1 for tilt change as function of time
v_name2 = variable with name2 for change rate as function of time
*pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
* zero or more keyword/value pairs may be appended
* keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
@ -92,15 +77,6 @@ Syntax
*units* value = *lattice* or *box*
lattice = distances are defined in lattice units
box = distances are defined in simulation box units
*couple* value = *none* or *xyz* or *xy* or *yz* or *xz* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
couple pressure values of various dimensions
*vol/balance/p* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
Modifies the behavior of the *volume* option to try and balance pressures
*max/rate* value = *rate* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
rate = maximum strain rate for pressure control
*normalize/pressure* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
Examples
""""""""
@ -112,8 +88,6 @@ Examples
fix 1 all deform 1 xy erate 0.001 remap v
fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0
See examples for :doc:`fix deform/pressure <fix_deform_pressure>` on its doc page
Description
"""""""""""
@ -123,17 +97,13 @@ run. Orthogonal simulation boxes have 3 adjustable parameters
adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be
adjusted independently and simultaneously.
The fix deform command allows use of all the arguments listed above,
except those flagged as available ONLY for the :doc:`fix
deform/pressure <fix_deform_pressure>` command, which are
pressure-based controls. The fix deform/pressure command allows use
of all the arguments listed above.
The rest of this doc page explains the options common to both
commands. The :doc:`fix deform/pressure <fix_deform_pressure>` doc
page explains the options available ONLY with the fix deform/pressure
command. Note that a simulation can define only a single deformation
command: fix deform or fix deform/pressure.
The :doc:`fix deform/pressure <fix_deform_pressure>` command extends
this command with additional keywords and arguments. The rest of this
page explains the options common to both commands. The :doc:`fix
deform/pressure <fix_deform_pressure>` page explains the options
available ONLY with the fix deform/pressure command. Note that a
simulation can define only a single deformation command: fix deform or
fix deform/pressure.
Both these fixes can be used to perform non-equilibrium MD (NEMD)
simulations of a continuously strained system. See the :doc:`fix
@ -143,6 +113,24 @@ simulation of a continuously extended system (extensional flow) can be
modeled using the :ref:`UEF package <PKG-UEF>` and its :doc:`fix
commands <fix_nh_uef>`.
.. admonition:: Inconsistent trajectories due to image flags
:class: warning
When running long simulations while shearing the box or using a high
shearing rate, it is possible that the image flags used for storing
unwrapped atom positions will "wrap around". When LAMMPS is compiled
with the default settings, case image flags are limited to a range of
:math:`-512 \le i \le 511`, which will overflow when atoms starting
at zero image flag value have passed through a periodic box dimension
more than 512 times.
Changing the :ref:`size of LAMMPS integer types <size>` to the
"bigbig" setting can make this overflow much less likely, since it
increases the image flag value range to :math:`- 1,048,576 \le i \le
1\,048\,575`
----------
For the *x*, *y*, *z* parameters, the associated dimension cannot be
shrink-wrapped. For the *xy*, *yz*, *xz* parameters, the associated
second dimension cannot be shrink-wrapped. Dimensions not varied by

71
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@ -13,29 +13,66 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* deform/pressure = style name of this fix command
* N = perform box deformation every this many timesteps
* one or more parameter/arg sequences may be appended
* one or more parameter/args sequences may be appended
.. parsed-literal::
parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *box*
*x*, *y*, *z* args = style value(s)
style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* or *pressure* or *pressure/mean*
*final* values = lo hi
lo hi = box boundaries at end of run (distance units)
*delta* values = dlo dhi
dlo dhi = change in box boundaries at end of run (distance units)
*scale* values = factor
factor = multiplicative factor for change in box length at end of run
*vel* value = V
V = change box length at this velocity (distance/time units),
effectively an engineering strain rate
*erate* value = R
R = engineering strain rate (1/time units)
*trate* value = R
R = true strain rate (1/time units)
*volume* value = none = adjust this dim to preserve volume of system
*wiggle* values = A Tp
A = amplitude of oscillation (distance units)
Tp = period of oscillation (time units)
*variable* values = v_name1 v_name2
v_name1 = variable with name1 for box length change as function of time
v_name2 = variable with name2 for change rate as function of time
*pressure* values = target gain
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*pressure/mean* values = target gain
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
*xy*, *xz*, *yz* args = style value
style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure* or *erate/rescale*
*final* value = tilt
tilt = tilt factor at end of run (distance units)
*delta* value = dtilt
dtilt = change in tilt factor at end of run (distance units)
*vel* value = V
V = change tilt factor at this velocity (distance/time units),
effectively an engineering shear strain rate
*erate* value = R
R = engineering shear strain rate (1/time units)
*erate/rescale* value = R
R = engineering shear strain rate (1/time units)
*trate* value = R
R = true shear strain rate (1/time units)
*wiggle* values = A Tp
A = amplitude of oscillation (distance units)
Tp = period of oscillation (time units)
*variable* values = v_name1 v_name2
v_name1 = variable with name1 for tilt change as function of time
v_name2 = variable with name2 for change rate as function of time
*pressure* values = target gain
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*erate/rescale* value = R
R = engineering shear strain rate (1/time units)
NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
*box* = style value
style = *volume* or *pressure*
@ -49,6 +86,15 @@ Syntax
.. parsed-literal::
*remap* value = *x* or *v* or *none*
x = remap coords of atoms in group into deforming box
v = remap velocities of atoms in group when they cross periodic boundaries
none = no remapping of x or v
*flip* value = *yes* or *no*
allow or disallow box flips when it becomes highly skewed
*units* value = *lattice* or *box*
lattice = distances are defined in lattice units
box = distances are defined in simulation box units
*couple* value = *none* or *xyz* or *xy* or *yz* or *xz*
couple pressure values of various dimensions
*vol/balance/p* value = *yes* or *no*
@ -57,7 +103,6 @@ Syntax
rate = maximum strain rate for pressure control
*normalize/pressure* value = *yes* or *no*
Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
NOTE: All other keywords are documented by the :doc:`fix deform <fix_deform>` command
Examples
""""""""
@ -79,10 +124,26 @@ pressure-based controls implemented by this command.
All arguments described on the :doc:`fix deform <fix_deform>` doc page
also apply to this fix unless otherwise noted below. The rest of this
doc page explains the arguments specific to this fix. Note that a
page explains the arguments specific to this fix only. Note that a
simulation can define only a single deformation command: fix deform or
fix deform/pressure.
.. admonition:: Inconsistent trajectories due to image flags
:class: warning
When running long simulations while shearing the box or using a high
shearing rate, it is possible that the image flags used for storing
unwrapped atom positions will "wrap around". When LAMMPS is compiled
with the default settings, case image flags are limited to a range of
:math:`-512 \le i \le 511`, which will overflow when atoms starting
at zero image flag value have passed through a periodic box dimension
more than 512 times.
Changing the :ref:`size of LAMMPS integer types <size>` to the
"bigbig" setting can make this overflow much less likely, since it
increases the image flag value range to :math:`- 1,048,576 \le i \le
1\,048\,575`
----------
For the *x*, *y*, and *z* parameters, this is the meaning of the

24
doc/src/fix_electrode.rst
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@ -38,7 +38,7 @@ Syntax
*electrode/thermo* args = potential eta *temp* values
potential = electrode potential
charge = electrode charge
eta = reciprocal width of electrode charge smearing
eta = reciprocal width of electrode charge smearing (can be NULL if eta keyword is used)
*temp* values = T_v tau_v rng_v
T_v = temperature of thermo-potentiostat
tau_v = time constant of thermo-potentiostat
@ -110,7 +110,7 @@ electrostatic configurations:
:ref:`(Deissenbeck)<Deissenbeck>` between two electrodes
* (resulting in changing charges and potentials with appropriate
average potential difference and thermal variance)
average potential difference and thermal variance)
The first group-ID provided to each fix specifies the first electrode
group, and more group(s) are added using the *couple* keyword for each
@ -287,8 +287,18 @@ The *fix_modify tf* option enables the Thomas-Fermi metallicity model
fix_modify ID tf type length voronoi
If this option is used parameters must be set for all atom types of the
electrode.
If this option is used, these two parameters must be set for
all atom types of the electrode:
* `tf` is the Thomas-Fermi length :math:`l_{TF}`
* `voronoi` is the Voronoi volume per atom in units of length cubed
Different types may have different `tf` and `voronoi` values.
The following self-energy term is then added for all electrode atoms:
.. math::
A_{ii} += \frac{1}{4 \pi \epsilon_0} \times \frac{4 \pi l_{TF}^2}{\mathrm{Voronoi volume}}
The *fix_modify timer* option turns on (off) additional timer outputs in the log
file, for code developers to track optimization.
@ -321,9 +331,11 @@ The global array has *N* rows and *2N+1* columns, where the fix manages
array, the elements are:
* array[I][1] = total charge that group *I* would have had *if it were
at 0 V applied potential* * array[I][2 to *N* + 1] = the *N* entries
at 0 V applied potential*
* array[I][2 to *N* + 1] = the *N* entries
of the *I*-th row of the electrode capacitance matrix (definition
follows) * array[I][*N* + 2 to *2N* + 1] = the *N* entries of the
follows)
* array[I][*N* + 2 to *2N* + 1] = the *N* entries of the
*I*-th row of the electrode elastance matrix (the inverse of the
electrode capacitance matrix)

10
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@ -1,7 +1,7 @@
.. index:: fix heat/flow
fix heat/flow command
==========================
=====================
Syntax
""""""
@ -56,13 +56,19 @@ not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This pair style is part of the GRANULAR package. It is
only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for more info.
This fix requires that atoms store temperature and heat flow
as defined by the :doc:`fix property/atom <fix_property_atom>` command.
Related commands
""""""""""""""""
:doc:`pair granular <pair_granular>`, :doc:`fix property/atom <fix_property_atom>`
:doc:`pair granular <pair_granular>`,
:doc:`fix add/heat <fix_add_heat>`,
:doc:`fix property/atom <fix_property_atom>`
Default
"""""""

39
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@ -68,10 +68,10 @@ material or as an obstacle in a flow. Alternatively, it can be used as a
constraining wall around a simulation; see the discussion of the
*side* keyword below.
The *gstyle* geometry of the indenter can either be a sphere, a
cylinder, a cone, or a plane.
The *gstyle* keyword selects the geometry of the indenter and it can
either have the value of *sphere*, *cylinder*, *cone*, or *plane*\ .
A spherical indenter exerts a force of magnitude
A spherical indenter (*gstyle* = *sphere*) exerts a force of magnitude
.. math::
@ -82,13 +82,16 @@ distance from the atom to the center of the indenter, and *R* is the
radius of the indenter. The force is repulsive and F(r) = 0 for *r* >
*R*\ .
A cylindrical indenter exerts the same force, except that *r* is the
distance from the atom to the center axis of the cylinder. The
cylinder extends infinitely along its axis.
A cylindrical indenter (*gstyle* = *cylinder*) follows the same formula
for the force as a sphere, except that *r* is defined the distance
from the atom to the center axis of the cylinder. The cylinder extends
infinitely along its axis.
A conical indenter is similar to a cylindrical indenter except that it
has a finite length (between *lo* and *hi*), and that two different
radii (one at each end, *radlo* and *radhi*) can be defined.
.. versionadded:: 17April2024
A conical indenter (*gstyle* = *cone*) is similar to a cylindrical indenter
except that it has a finite length (between *lo* and *hi*), and that two
different radii (one at each end, *radlo* and *radhi*) can be defined.
Spherical, cylindrical, and conical indenters account for periodic
boundaries in two ways. First, the center point of a spherical
@ -101,15 +104,15 @@ or axis accounts for periodic boundaries. Both of these mean that an
indenter can effectively move through and straddle one or more
periodic boundaries.
A planar indenter is really an axis-aligned infinite-extent wall
exerting the same force on atoms in the system, where *R* is the
position of the plane and *r-R* is the distance from the plane. If
the *side* parameter of the plane is specified as *lo* then it will
indent from the lo end of the simulation box, meaning that atoms with
a coordinate less than the plane's current position will be pushed
towards the hi end of the box and atoms with a coordinate higher than
the plane's current position will feel no force. Vice versa if *side*
is specified as *hi*\ .
A planar indenter (*gstyle* = *plane*) behaves like an axis-aligned
infinite-extent wall with the same force expression on atoms in the
system as before, but where *R* is the position of the plane and *r-R*
is the distance of an from the plane. If the *side* parameter of the
plane is specified as *lo* then it will indent from the lo end of the
simulation box, meaning that atoms with a coordinate less than the
plane's current position will be pushed towards the hi end of the box
and atoms with a coordinate higher than the plane's current position
will feel no force. Vice versa if *side* is specified as *hi*\ .
Any of the 4 quantities defining a spherical indenter's geometry can
be specified as an equal-style :doc:`variable <variable>`, namely *x*,

2
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@ -80,7 +80,7 @@ Obtaining i-PI
""""""""""""""
Here are the commands to set up a virtual environment and install
i-PI into it with all its dependencies via the PyPi repository and
i-PI into it with all its dependencies via the PyPI repository and
the pip package manager.
.. code-block:: sh

180
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@ -0,0 +1,180 @@
.. index:: fix rheo
fix rheo command
================
Syntax
""""""
.. parsed-literal::
fix ID group-ID rheo cut kstyle zmin keyword values...
* ID, group-ID are documented in :doc:`fix <fix>` command
* rheo = style name of this fix command
* cut = cutoff for the kernel (distance)
* kstyle = *quintic* or *RK0* or *RK1* or *RK2*
* zmin = minimal number of neighbors for reproducing kernels
* zero or more keyword/value pairs may be appended to args
* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or
*shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
.. parsed-literal::
*thermal* values = none, turns on thermal evolution
*interface/reconstruct* values = none, reconstructs interfaces with solid particles
*surface/detection* values = *sdstyle* *limit* *limit/splash*
*sdstyle* = *coordination* or *divergence*
*limit* = threshold for surface particles
*limit/splash* = threshold for splash particles
*shift* values = none, turns on velocity shifting
*rho/sum* values = none, uses the kernel to compute the density of particles
*self/mass* values = none, a particle uses its own mass in a rho summation
*density* values = *rho01*, ... *rho0N* (density)
*speed/sound* values = *cs0*, ... *csN* (velocity)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all rheo 3.0 quintic 0 thermal density 0.1 0.1 speed/sound 10.0 1.0
fix 1 all rheo 3.0 RK1 10 shift surface/detection coordination 40
Description
"""""""""""
.. versionadded:: TBD
Perform time integration for RHEO particles, updating positions, velocities,
and densities. For a detailed breakdown of the integration timestep and
numerical details, see :ref:`(Palermo) <rheo_palermo>`. For an
overview of other features available in the RHEO package, see
:doc:`the RHEO howto <Howto_rheo>`.
The type of kernel is specified using *kstyle* and the cutoff is *cut*. Four
kernels are currently available. The *quintic* kernel is a standard quintic
spline function commonly used in SPH. The other options, *RK0*, *RK1*, and
*RK2*, are zeroth, first, and second order reproducing. To generate a
reproducing kernel, a particle must have sufficient neighbors inside the
kernel cutoff distance (a coordination number) to accurately calculate
moments. This threshold is set by *zmin*. If reproducing kernels are
requested but a particle has fewer neighbors, then it will revert to a
non-reproducing quintic kernel until it gains more neighbors.
To model temperature evolution, one must specify the *thermal* keyword,
define a separate instance of :doc:`fix rheo/thermal <fix_rheo_thermal>`,
and use atom style rheo/thermal.
By default, the density of solid RHEO particles does not evolve and forces
with fluid particles are calculated using the current velocity of the solid
particle. If the *interface/reconstruct* keyword is used, then the density
and velocity of solid particles are alternatively reconstructed for every
fluid-solid interaction to ensure no-slip and pressure-balanced boundaries.
This is done by estimating the location of the fluid-solid interface and
extrapolating fluid particle properties across the interface to calculate a
temporary apparent density and velocity for a solid particle. The numerical
details are the same as those described in
:ref:`(Palermo) <howto_rheo_palermo>` except there is an additional
restriction that the reconstructed solid density cannot be less than the
equilibrium density. This prevents fluid particles from sticking to solid
surfaces.
A modified form of Fickian particle shifting can be enabled with the
*shift* keyword. This effectively shifts particle positions to generate a
more uniform spatial distribution. Shifting currently does not consider the
type of a particle and therefore may be inappropriate in systems consisting
of multiple fluid phases.
In systems with free surfaces, the *surface/detection* keyword can be used
to classify the location of particles as being within the bulk fluid, on a
free surface, or isolated from other particles in a splash or droplet.
Shifting is then disabled in the normal direction away from the free surface
to prevent particles from diffusing away. Surface detection can also be used
to control surface-nucleated effects like oxidation when used in combination
with :doc:`fix rheo/oxidation <fix_rheo_oxidation>`. Surface detection is not
performed on solid bodies.
The *surface/detection* keyword takes three arguments: *sdstyle*, *limit*,
and *limit/splash*. The first, *sdstyle*, specifies whether surface particles
are identified using a coordination number (*coordination*) or the divergence
of the local particle positions (*divergence*). The threshold value for a
surface particle for either of these criteria is set by the numerical value
of *limit*. Additionally, if a particle's coordination number is too low,
i.e. if it has separated off from the bulk in a droplet, it is not possible
to define surfaces and the particle is classified as a splash. The coordination
threshold for this classification is set by the numerical value of
*limit/splash*.
By default, RHEO integrates particles' densities using a mass diffusion
equation. Alternatively, one can update densities every timestep by performing
a kernel summation of the masses of neighboring particles by specifying the *rho/sum*
keyword.
The *self/mass* keyword modifies the behavior of the density summation in *rho/sum*.
Typically, the density :math:`\rho` of a particle is calculated as the sum over neighbors
.. math::
\rho_i = \sum_{j} W_{ij} M_j
where :math:`W_{ij}` is the kernel, and :math:`M_j` is the mass of particle :math:`j`.
The *self/mass* keyword augments this expression by replacing :math:`M_j` with
:math:`M_i`. This may be useful in simulations of multiple fluid phases with large
differences in density, :ref:`(Hu) <fix_rheo_hu>`.
The *density* keyword is used to specify the equilibrium density of each of the N
particle types. It must be followed by N numerical values specifying each type's
equilibrium density *rho0*.
The *speed/sound* keyword is used to specify the speed of sound of each of the
N particle types. It must be followed by N numerical values specifying each type's
speed of sound *cs*.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
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 access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix must be used with atom style rheo or rheo/thermal. This fix must
be used in conjunction with :doc:`fix rheo/pressure <fix_rheo_pressure>`.
and :doc:`fix rheo/viscosity <fix_rheo_viscosity>`. If the *thermal* setting
is used, there must also be an instance of
:doc:`fix rheo/thermal <fix_rheo_thermal>`. The fix group must be set to all.
Only one instance of fix rheo may be defined and it must be defined prior
to all other RHEO fixes in the input script.
This fix is part of the RHEO package. It is only enabled if LAMMPS was built
with that package. See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
:doc:`fix rheo/pressure <fix_rheo_pressure>`,
:doc:`fix rheo/thermal <fix_rheo_thermal>`,
:doc:`pair rheo <pair_rheo>`,
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
Default
"""""""
*rho0* and *cs* are set to 1.0 for all atom types.
----------
.. _rheo_palermo:
**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.
.. _fix_rheo_hu:
**(Hu)** Hu, and Adams J. Comp. Physics, 213, 844-861 (2006).

85
doc/src/fix_rheo_oxidation.rst Normal file
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@ -0,0 +1,85 @@
.. index:: fix rheo/oxidation
fix rheo/oxidation command
==========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID rheo/oxidation cut btype rsurf
* ID, group-ID are documented in :doc:`fix <fix>` command
* rheo/oxidation = style name of this fix command
* cut = maximum bond length (distance units)
* btype = type of bonds created
* rsurf = distance from surface to create bonds (distance units)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all rheo/oxidation 1.5 2 0.0
fix 1 all rheo/oxidation 1.0 1 2.0
Description
"""""""""""
.. versionadded:: TBD
This fix dynamically creates bonds on the surface of fluids to
represent physical processes such as oxidation. It is intended
for use with bond style :doc:`bond rheo/shell <bond_rheo_shell>`.
Every timestep, particles check neighbors within a distance of *cut*.
This distance must be smaller than the kernel length defined in
:doc:`fix rheo <fix_rheo>`. Bonds of type *btype* are created between
a fluid particle and either a fluid or solid neighbor. The fluid particles
must also be on the fluid surface, or within a distance of *rsurf* from
the surface. This process is further described in
:ref:`(Clemmer) <howto_rheo_clemmer2>`.
If used in conjunction with solid bodies, such as those generated
by the *react* option of :doc:`fix rheo/thermal <fix_rheo_thermal>`,
it is recommended to use a :doc:`hybrid bond style <bond_hybrid>`
with different bond types for solid and oxide bonds.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
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 access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix must be used with the bond style :doc:`rheo/shell <bond_rheo_shell>`
and :doc:`fix rheo <fix_rheo>` with surface detection enabled.
This fix is part of the RHEO package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
page for more info.
Related commands
""""""""""""""""
:doc:`fix rheo <fix_rheo>`,
:doc:`bond rheo/shell <bond_rheo_shell>`,
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
Default
"""""""
none
----------
.. _howto_rheo_clemmer2:
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

106
doc/src/fix_rheo_pressure.rst Normal file
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@ -0,0 +1,106 @@
.. index:: fix rheo/pressure
fix rheo/pressure command
=========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID rheo/pressure type1 pstyle1 args1 ... typeN pstyleN argsN
* ID, group-ID are documented in :doc:`fix <fix>` command
* rheo/pressure = style name of this fix command
* one or more types and pressure styles must be appended
* types = lists of types (see below)
* pstyle = *linear* or *taitwater* or *cubic*
.. parsed-literal::
*linear* args = none
*taitwater* args = none
*cubic* args = cubic prefactor :math:`A_3` (pressure/density\^2)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all rheo/pressure * linear
fix 1 all rheo/pressure 1 linear 2 cubic 10.0
Description
"""""""""""
.. versionadded:: TBD
This fix defines a pressure equation of state for RHEO particles. One can
define different equations of state for different atom types. An equation
must be specified for every atom type.
One first defines the atom *types*. A wild-card asterisk can be used in place
of or in conjunction with the *types* argument to set the coefficients for
multiple pairs of atom types. This takes the form "\*" or "\*n" or "m\*"
or "m\*n". If :math:`N` is the number of atom types, then an asterisk with
no numeric values means all types from 1 to :math:`N`. A leading asterisk
means all types from 1 to n (inclusive). A trailing asterisk means all types
from m to :math:`N` (inclusive). A middle asterisk means all types from m to n
(inclusive).
The *types* definition is followed by the pressure style, *pstyle*. Current
options *linear*, *taitwater*, and *cubic*. Style *linear* is a linear
equation of state with a particle pressure :math:`P` calculated as
.. math::
P = c (\rho - \rho_0)
where :math:`c` is the speed of sound, :math:`\rho_0` is the equilibrium density,
and :math:`\rho` is the current density of a particle. The numerical values of
:math:`c` and :math:`\rho_0` are set in :doc:`fix rheo <fix_rheo>`. Style *cubic*
is a cubic equation of state which has an extra argument :math:`A_3`,
.. math::
P = c ((\rho - \rho_0) + A_3 (\rho - \rho_0)^3) .
Style *taitwater* is Tait's equation of state:
.. math::
P = \frac{c^2 \rho_0}{7} \biggl[\left(\frac{\rho}{\rho_0}\right)^{7} - 1\biggr].
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
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 access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix must be used with an atom style that includes density
such as atom_style rheo or rheo/thermal. This fix must be used in
conjunction with :doc:`fix rheo <fix_rheo>`. The fix group must be
set to all. Only one instance of fix rheo/pressure can be defined.
This fix is part of the RHEO package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
page for more info.
Related commands
""""""""""""""""
:doc:`fix rheo <fix_rheo>`,
:doc:`pair rheo <pair_rheo>`,
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
Default
"""""""
none

128
doc/src/fix_rheo_thermal.rst Normal file
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@ -0,0 +1,128 @@
.. index:: fix rheo/thermal
fix rheo/thermal command
========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID rheo/thermal attribute values ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* rheo/thermal = style name of this fix command
* one or more attributes may be appended
* attribute = *conductivity* or *specific/heat* or *latent/heat* or *Tfreeze* or *react*
.. parsed-literal::
*conductivity* args = types style args
types = lists of types (see below)
style = *constant*
*constant* arg = conductivity (power/temperature)
*specific/heat* args = types style args
types = lists of types (see below)
style = *constant*
*constant* arg = specific heat (energy/(mass*temperature))
*latent/heat* args = types style args
types = lists of types (see below)
style = *constant*
*constant* arg = latent heat (energy/mass)
*Tfreeze* args = types style args
types = lists of types (see below)
style = *constant*
*constant* arg = freezing temperature (temperature)
*react* args = cut type
cut = maximum bond distance
type = bond type
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all rheo/thermal conductivity * constant 1.0 specific/heat * constant 1.0 Tfreeze * constant 1.0
fix 1 all rheo/pressure conductivity 1*2 constant 1.0 conductivity 3*4 constant 2.0 specific/heat * constant 1.0
Description
"""""""""""
.. versionadded:: TBD
This fix performs time integration of temperature for atom style rheo/thermal.
In addition, it defines multiple thermal properties of particles and handles
melting/solidification, if applicable. For more details on phase transitions
in RHEO, see :doc:`the RHEO howto <Howto_rheo>`.
Note that the temperature of a particle is always derived from the energy.
This implies the *temperature* attribute of :doc:`the set command <set>` does
not affect particles. Instead, one should use the *sph/e* attribute.
For each atom type, one can define expressions for the *conductivity*,
*specific/heat*, *latent/heat*, and critical temperature (*Tfreeze*).
The conductivity and specific heat must be defined for all atom types.
The latent heat and critical temperature are optional. However, a
critical temperature must be defined to specify a latent heat.
Note, if shifting is turned on in :doc:`fix rheo <fix_rheo>`, the gradient
of the energy is used to shift energies. This may be inappropriate in systems
with multiple atom types with different specific heats.
For each property, one must first define a list of atom types. A wild-card
asterisk can be used in place of or in conjunction with the *types* argument
to set the coefficients for multiple pairs of atom types. This takes the
form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is the number of atom
types, then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from m to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
The *types* definition for each property is followed by the style. Currently,
the only option is *constant*. Style *constant* simply applies a constant value
of respective property to each particle of the assigned type.
The *react* keyword controls whether bonds are created/deleted when particles
transition between a fluid and solid state. This option only applies to atom
types that have a defined value of *Tfreeze*. When a fluid particle's
temperature drops below *Tfreeze*, bonds of type *btype* are created between
nearby solid particles within a distance of *cut*. The particle's status also
swaps to a solid state. When a solid particle's temperature rises above
*Tfreeze*, all bonds of type *btype* are broken and the particle's status swaps
to a fluid state.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
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 access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix must be used with an atom style that includes temperature,
heatflow, and conductivity such as atom_style rheo/thermal This fix
must be used in conjunction with :doc:`fix rheo <fix_rheo>` with the
*thermal* setting. The fix group must be set to all. Only one
instance of fix rheo/pressure can be defined.
This fix is part of the RHEO package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
page for more info.
Related commands
""""""""""""""""
:doc:`fix rheo <fix_rheo>`,
:doc:`pair rheo <pair_rheo>`,
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`,
:doc:`fix add/heat <fix_add_heat>`
Default
"""""""
none

117
doc/src/fix_rheo_viscosity.rst Normal file
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@ -0,0 +1,117 @@
.. index:: fix rheo/viscosity
fix rheo/viscosity command
==========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID rheo/viscosity type1 pstyle1 args1 ... typeN pstyleN argsN
* ID, group-ID are documented in :doc:`fix <fix>` command
* rheo/viscosity = style name of this fix command
* one or more types and viscosity styles must be appended
* types = lists of types (see below)
* vstyle = *constant* or *power*
.. parsed-literal::
*constant* args = *eta*
*eta* = viscosity
*power* args = *eta*, *gd0*, *K*, *n*
*eta* = viscosity
*gd0* = critical strain rate
*K* = consistency index
*n* = power-law exponent
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all rheo/viscosity * constant 1.0
fix 1 all rheo/viscosity 1 constant 1.0 2 power 0.1 5e-4 0.001 0.5
Description
"""""""""""
.. versionadded:: TBD
This fix defines a viscosity for RHEO particles. One can define different
viscosities for different atom types, but a viscosity must be specified for
every atom type.
One first defines the atom *types*. A wild-card asterisk can be used in place
of or in conjunction with the *types* argument to set the coefficients for
multiple pairs of atom types. This takes the form "\*" or "\*n" or "m\*"
or "m\*n". If :math:`N` is the number of atom types, then an asterisk with
no numeric values means all types from 1 to :math:`N`. A leading asterisk
means all types from 1 to n (inclusive). A trailing asterisk means all types
from m to :math:`N` (inclusive). A middle asterisk means all types from m to n
(inclusive).
The *types* definition is followed by the viscosity style, *vstyle*. Two
options are available, *constant* and *power*. Style *constant* simply
applies a constant value of the viscosity *eta* to each particle of the
assigned type. Style *power* is a Hershchel-Bulkley constitutive equation
for the stress :math:`\tau`
.. math::
\tau = \left(\frac{\tau_0}{\dot{\gamma}} + K \dot{\gamma}^{n - 1}\right) \dot{\gamma}, \tau \ge \tau_0
where :math:`\dot{\gamma}` is the strain rate and :math:`\tau_0` is the critical
yield stress, below which :math:`\dot{\gamma} = 0.0`. To avoid divergences, this
expression is regularized by defining a critical strain rate *gd0*. If the local
strain rate on a particle falls below this limit, a constant viscosity of *eta*
is assigned. This implies a value of
.. math::
\tau_0 = \eta \dot{\gamma}_0 - K \dot{\gamma}_0^N
as further discussed in :ref:`(Palermo) <rheo_palermo2>`.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
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 access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix must be used with an atom style that includes viscosity
such as atom_style rheo or rheo/thermal. This fix must be used in
conjunction with :doc:`fix rheo <fix_rheo>`. The fix group must be
set to all. Only one instance of fix rheo/viscosity can be defined.
This fix is part of the RHEO package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix rheo <fix_rheo>`,
:doc:`pair rheo <pair_rheo>`,
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
Default
"""""""
none
----------
.. _rheo_palermo2:
**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.

26
doc/src/fix_store_force.rst
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@ -23,11 +23,12 @@ Examples
Description
"""""""""""
Store the forces on atoms in the group at the point during each
timestep when the fix is invoked, as described below. This is useful
for storing forces before constraints or other boundary conditions are
computed which modify the forces, so that unmodified forces can be
:doc:`written to a dump file <dump>` or accessed by other :doc:`output commands <Howto_output>` that use per-atom quantities.
Store the forces on atoms in the group at the point during each timestep
when the fix is invoked, as described below. This is useful for storing
forces before constraints or other boundary conditions are computed
which modify the forces, so that unmodified forces can be :doc:`written
to a dump file <dump>` or accessed by other :doc:`output commands
<Howto_output>` that use per-atom quantities.
This fix is invoked at the point in the velocity-Verlet timestepping
immediately after :doc:`pair <pair_style>`, :doc:`bond <bond_style>`,
@ -36,12 +37,13 @@ immediately after :doc:`pair <pair_style>`, :doc:`bond <bond_style>`,
forces have been calculated. It is the point in the timestep when
various fixes that compute constraint forces are calculated and
potentially modify the force on each atom. Examples of such fixes are
:doc:`fix shake <fix_shake>`, :doc:`fix wall <fix_wall>`, and :doc:`fix indent <fix_indent>`.
:doc:`fix shake <fix_shake>`, :doc:`fix wall <fix_wall>`, and :doc:`fix
indent <fix_indent>`.
.. note::
The order in which various fixes are applied which operate at
the same point during the timestep, is the same as the order they are
The order in which various fixes are applied which operate at the
same point during the timestep, is the same as the order they are
specified in the input script. Thus normally, if you want to store
per-atom forces due to force field interactions, before constraints
are applied, you should list this fix first within that set of fixes,
@ -52,8 +54,9 @@ potentially modify the force on each atom. Examples of such fixes are
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
This fix produces a per-atom array which can be accessed by various
:doc:`output commands <Howto_output>`. The number of columns for each
@ -61,7 +64,8 @@ atom is 3, and the columns store the x,y,z forces on each atom. The
per-atom values be accessed on any timestep.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

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6
doc/src/labelmap.rst
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@ -44,8 +44,8 @@ The label map can also be defined by the :doc:`read_data <read_data>`
command when it reads these sections in a data file: Atom Type Labels,
Bond Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for a general discussion of how type
labels can be used. See :ref:`(Gissinger) <Typelabel>` for a discussion
of the type label implementation in LAMMPS and its uses.
labels can be used. See :ref:`(Gissinger) <Typelabel1>` for a
discussion of the type label implementation in LAMMPS and its uses.
Valid type labels can contain any alphanumeric character, but must not
start with a number, a '#', or a '*' character. They can contain other
@ -103,6 +103,6 @@ none
-----------
.. _Typelabel:
.. _Typelabel1:
**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).

42
doc/src/pair_charmm.rst
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@ -112,26 +112,22 @@ Description
These pair styles compute Lennard Jones (LJ) and Coulombic
interactions with additional switching or shifting functions that ramp
the energy and/or force smoothly to zero between an inner and outer
cutoff. They are implementations of the widely used CHARMM force
field used in the `CHARMM <https://www.charmm.org>`_ MD code (and
others). See :ref:`(MacKerell) <pair-MacKerell>` for a description of the
CHARMM force field.
cutoff. They implement the widely used CHARMM force field, see
:doc:`Howto discussion on biomolecular force fields <Howto_bioFF>` for
details.
The styles with *charmm* (not *charmmfsw* or *charmmfsh*\ ) in their
name are the older, original LAMMPS implementations. They compute the
LJ and Coulombic interactions with an energy switching function (esw,
shown in the formula below as S(r)), which ramps the energy smoothly
to zero between the inner and outer cutoff. This can cause
irregularities in pairwise forces (due to the discontinuous second
derivative of energy at the boundaries of the switching region), which
in some cases can result in detectable artifacts in an MD simulation.
LJ and Coulombic interactions with an energy switching function which
ramps the energy smoothly to zero between the inner and outer cutoff.
This can cause irregularities in pairwise forces (due to the discontinuous
second derivative of energy at the boundaries of the switching region),
which in some cases can result in detectable artifacts in an MD simulation.
The newer styles with *charmmfsw* or *charmmfsh* in their name replace
the energy switching with force switching (fsw) and force shifting
(fsh) functions, for LJ and Coulombic interactions respectively.
These follow the formulas and description given in
:ref:`(Steinbach) <Steinbach>` and :ref:`(Brooks) <Brooks1>` to minimize these
artifacts.
.. note::
@ -152,26 +148,6 @@ artifacts.
the CHARMM force field energies and forces, when using one of these
two CHARMM pair styles.
.. math::
E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\
= & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
= & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\
= & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
= & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \\
C(r) = & \frac{C q_i q_j}{ \epsilon r} \\
S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
\left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
{ \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
where S(r) is the energy switching function mentioned above for the
*charmm* styles. See the :ref:`(Steinbach) <Steinbach>` paper for the
functional forms of the force switching and force shifting functions
used in the *charmmfsw* and *charmmfsh* styles.
When using the *lj/charmm/coul/charmm styles*, both the LJ and
Coulombic terms require an inner and outer cutoff. They can be the
same for both formulas or different depending on whether 2 or 4

27
doc/src/pair_coul.rst
View File

@ -2,6 +2,8 @@
.. index:: pair_style coul/cut/gpu
.. index:: pair_style coul/cut/kk
.. index:: pair_style coul/cut/omp
.. index:: pair_style coul/cut/global
.. index:: pair_style coul/cut/global/omp
.. index:: pair_style coul/debye
.. index:: pair_style coul/debye/gpu
.. index:: pair_style coul/debye/kk
@ -11,8 +13,6 @@
.. index:: pair_style coul/dsf/kk
.. index:: pair_style coul/dsf/omp
.. index:: pair_style coul/exclude
.. index:: pair_style coul/cut/global
.. index:: pair_style coul/cut/global/omp
.. index:: pair_style coul/long
.. index:: pair_style coul/long/omp
.. index:: pair_style coul/long/kk
@ -33,6 +33,11 @@ pair_style coul/cut command
Accelerator Variants: *coul/cut/gpu*, *coul/cut/kk*, *coul/cut/omp*
pair_style coul/cut/global command
==================================
Accelerator Variants: *coul/cut/omp*
pair_style coul/debye command
=============================
@ -46,11 +51,6 @@ Accelerator Variants: *coul/dsf/gpu*, *coul/dsf/kk*, *coul/dsf/omp*
pair_style coul/exclude command
===============================
pair_style coul/cut/global command
==================================
Accelerator Variants: *coul/cut/omp*
pair_style coul/long command
============================
@ -79,16 +79,17 @@ pair_style tip4p/long command
Accelerator Variants: *tip4p/long/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style coul/cut cutoff
pair_style coul/cut/global cutoff
pair_style coul/debye kappa cutoff
pair_style coul/dsf alpha cutoff
pair_style coul/exclude cutoff
pair_style coul/cut/global cutoff
pair_style coul/long cutoff
pair_style coul/wolf alpha cutoff
pair_style coul/streitz cutoff keyword alpha
@ -152,6 +153,11 @@ the 2 atoms, and :math:`\epsilon` is the dielectric constant which can be set
by the :doc:`dielectric <dielectric>` command. The cutoff :math:`r_c` truncates
the interaction distance.
Pair style *coul/cut/global* computes the same Coulombic interactions
as style *coul/cut* except that it allows only a single global cutoff
and thus makes it compatible for use in combination with long-range
coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
----------
Style *coul/debye* adds an additional exp() damping factor to the
@ -262,11 +268,6 @@ Streitz-Mintmire parameterization for the material being modeled.
----------
Pair style *coul/cut/global* computes the same Coulombic interactions
as style *coul/cut* except that it allows only a single global cutoff
and thus makes it compatible for use in combination with long-range
coulomb styles in :doc:`hybrid pair styles <pair_hybrid>`.
Pair style *coul/exclude* computes Coulombic interactions like *coul/cut*
but **only** applies them to excluded pairs using a scaling factor
of :math:`\gamma - 1.0` with :math:`\gamma` being the factor assigned

141
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View File

@ -13,16 +13,11 @@ Syntax
pair_style dpd/coul/slater/long T cutoff_DPD seed lambda cutoff_coul
pair_coeff I J a_IJ Gamma is_charged
* T = temperature (temperature units) (dpd only)
* T = temperature (temperature units)
* cutoff_DPD = global cutoff for DPD interactions (distance units)
* seed = random # seed (positive integer)
* lambda = decay length of the charge (distance units)
* cutoff_coul = real part cutoff for Coulombic interactions (distance units)
* I,J = numeric atom types, or type labels
* Gamma = DPD Gamma coefficient
* is_charged (boolean) set to yes if I and J are charged beads
* cutoff_coul = global cutoff for Coulombic interactions (distance units)
Examples
""""""""
@ -30,66 +25,90 @@ Examples
.. code-block:: LAMMPS
pair_style dpd/coul/slater/long 1.0 2.5 34387 0.25 3.0
pair_coeff 1 1 78.0 4.5 # not charged by default
pair_coeff 1 1 78.0 4.5 # not charged by default
pair_coeff 2 2 78.0 4.5 yes
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 27June2024
Style *dpd/coul/slater/long* computes a force field for dissipative particle dynamics
(DPD) following the exposition in :ref:`(Groot) <Groot5>` with the addition of
electrostatic interactions. The coulombic forces in mesoscopic models
employ potentials without explicit excluded-volume interactions.
The goal is to prevent artificial ionic pair formation by including a charge
distribution in the Coulomb potential, following the formulation of
:ref:`(Melchor) <Melchor1>`:
Style *dpd/coul/slater/long* computes a force field for dissipative
particle dynamics (DPD) following the exposition in :ref:`(Groot)
<Groot5>`. It also allows for the use of charged particles in the
model by adding a long-range Coulombic term to the DPD interactions.
The short-range portion of the Coulombics is calculated by this pair
style. The long-range Coulombics are computed by use of the
:doc:`kspace_style <kspace_style>` command, e.g. using the Ewald or
PPPM styles.
The force on bead I due to bead J is given as a sum
of 4 terms
Coulombic forces in mesoscopic models such as DPD employ potentials
without explicit excluded-volume interactions. The goal is to prevent
artificial ionic pair formation by including a charge distribution in
the Coulomb potential, following the formulation in :ref:`(Melchor1)
<Melchor1>`.
.. note::
This pair style is effectively the combination of the
:doc:`pair_style dpd <pair_dpd>` and :doc:`pair_style
coul/slater/long <pair_coul_slater>` commands, but should be more
efficient (especially on GPUs) than using :doc:`pair_style
hybrid/overlay dpd coul/slater/long <pair_hybrid>`. That is
particularly true for the GPU package version of the pair style since
this version is compatible with computing neighbor lists on the GPU
instead of the CPU as is required for hybrid styles.
In the charged DPD model, the force on bead I due to bead J is given
as a sum of 4 terms:
.. math::
\vec{f} = & (F^C + F^D + F^R + F^E) \hat{r_{ij}} \\
F^C = & A w(r) \qquad \qquad \qquad \qquad \qquad r < r_c \\
F^D = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v}_{ij}) \qquad \qquad r < r_c \\
F^R = & \sigma w(r) \alpha (\Delta t)^{-1/2} \qquad \qquad \qquad r < r_c \\
w(r) = & 1 - \frac{r}{r_c} \\
F^E = & \frac{Cq_iq_j}{\epsilon r^2} \left( 1- exp\left( \frac{2r_{ij}}{\lambda} \right) \left( 1 + \frac{2r_{ij}}{\lambda} \left( 1 + \frac{r_{ij}}{\lambda} \right)\right) \right)
F^C = & A w(r) \qquad \qquad \qquad \qquad \qquad r < r_{DPD} \\
F^D = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v}_{ij}) \qquad \qquad r < r_{DPD} \\
F^R = & \sigma w(r) \alpha (\Delta t)^{-1/2} \qquad \qquad \qquad r < r_{DPD} \\
w(r) = & 1 - \frac{r}{r_{DPD}} \\
F^E = & \frac{C q_iq_j}{\epsilon r^2} \left( 1- exp\left( \frac{2r_{ij}}{\lambda} \right) \left( 1 + \frac{2r_{ij}}{\lambda} \left( 1 + \frac{r_{ij}}{\lambda} \right)\right) \right)
where :math:`F^C` is a conservative force, :math:`F^D` is a dissipative
force, :math:`F^R` is a random force, and :math:`F^E` is an electrostatic force.
:math:`\hat{r_{ij}}` is a unit vector in the direction
:math:`r_i - r_j`, :math:`\vec{v}_{ij}` is
the vector difference in velocities of the two atoms :math:`\vec{v}_i -
where :math:`F^C` is a conservative force, :math:`F^D` is a
dissipative force, :math:`F^R` is a random force, and :math:`F^E` is
an electrostatic force. :math:`\hat{r_{ij}}` is a unit vector in the
direction :math:`r_i - r_j`, :math:`\vec{v}_{ij}` is the vector
difference in velocities of the two atoms :math:`\vec{v}_i -
\vec{v}_j`, :math:`\alpha` is a Gaussian random number with zero mean
and unit variance, *dt* is the timestep size, and :math:`w(r)` is a
weighting factor that varies between 0 and 1. :math:`r_c` is the
pairwise cutoff. :math:`\sigma` is set equal to :math:`\sqrt{2 k_B T
\gamma}`, where :math:`k_B` is the Boltzmann constant and *T* is the
temperature parameter in the pair_style command.
C is the same Coulomb conversion factor as in the pair_styles
coul/cut and coul/long. In this way the Coulomb
interaction between ions is corrected at small distances r, and
the long-range interactions are computed either by the Ewald or the PPPM technique.
weighting factor that varies between 0 and 1.
:math:`\sigma` is set equal to :math:`\sqrt{2 k_B T \gamma}`, where
:math:`k_B` is the Boltzmann constant and *T* is the temperature
parameter in the pair_style command.
The following parameters must be defined for each
pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in
the examples above, or in the data file or restart files read by the
:math:`r_{DPD}` is the pairwise cutoff for the first 3 DPD terms in
the formula as specified by *cutoff_DPD*. For the :math:`F^E` term,
pairwise interactions within the specified *cutoff_coul* distance are
computed directly; interactions beyond that distance are computed in
reciprocal space. *C* is the same Coulomb conversion factor used in
the Coulombic formulas described on the :doc:`pair_coul <pair_coul>`
doc page.
The following parameters must be defined for each pair of atoms types
via the :doc:`pair_coeff <pair_coeff>` command as in the examples
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* A (force units)
* :math:`\gamma` (force/velocity units)
* is_charged (boolean)
* is_charged (optional boolean, default = no)
.. note::
This style is the combination of :doc:`pair_style dpd <pair_dpd>` and :doc:`pair_style coul/slater/long <pair_coul_slater>`.
The *is_charged* parameter is optional and can be specified as *yes* or
*no*. *Yes* should be used for interactions between two types of
charged particles. *No* is the default and should be used for
interactions between two types of particles when one or both are
uncharged.
----------
@ -116,17 +135,17 @@ pressure.
This pair style writes its information to :doc:`binary restart files
<restart>`, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file. Note that the
user-specified random number seed is stored in the restart file, so when
a simulation is restarted, each processor will re-initialize its random
number generator the same way it did initially. This means the random
forces will be random, but will not be the same as they would have been
if the original simulation had continued past the restart time.
user-specified random number seed is stored in the restart file, so
when a simulation is restarted, each processor will re-initialize its
random number generator the same way it did initially. This means the
random forces will be random, but will not be the same as they would
have been if the original simulation had continued past the restart
time.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*, *middle*, *outer* keywords.
----------
Restrictions
@ -138,17 +157,17 @@ LAMMPS was built with that package. See the :doc:`Build package
The default frequency for rebuilding neighbor lists is every 10 steps
(see the :doc:`neigh_modify <neigh_modify>` command). This may be too
infrequent since particles move rapidly and
can overlap by large amounts. If this setting yields a non-zero number
of "dangerous" reneighborings (printed at the end of a simulation), you
should experiment with forcing reneighboring more often and see if
system energies/trajectories change.
infrequent since particles move rapidly and can overlap by large
amounts. If this setting yields a non-zero number of "dangerous"
reneighborings (printed at the end of a simulation), you should
experiment with forcing reneighboring more often and see if system
energies/trajectories change.
This pair style requires you to use the :doc:`comm_modify vel yes
This pair style requires use of the :doc:`comm_modify vel yes
<comm_modify>` command so that velocities are stored by ghost atoms.
This pair style also requires the long-range solvers included in the KSPACE package.
This pair style also requires use of a long-range solvers from the
KSPACE package.
This pair style will not restart exactly when using the
:doc:`read_restart <read_restart>` command, though they should provide
@ -160,13 +179,11 @@ Related commands
""""""""""""""""
:doc:`pair_style dpd <pair_dpd>`, :doc:`pair_style coul/slater/long <pair_coul_slater>`,
:doc:`pair_coeff <pair_coeff>`, :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`,
:doc:`pair_style srp <pair_srp>`, :doc:`fix mvv/dpd <fix_mvv_dpd>`.
Default
"""""""
is_charged = no
For the pair_coeff command, the default is is_charged = no.
----------

89
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@ -1,8 +1,11 @@
.. index:: pair_style pod
.. index:: pair_style pod/kk
pair_style pod command
========================
Accelerator Variants: *pod/kk*
Syntax
""""""
@ -24,29 +27,33 @@ Description
.. versionadded:: 22Dec2022
Pair style *pod* defines the proper orthogonal descriptor (POD)
potential :ref:`(Nguyen) <Nguyen20221>`. The mathematical definition of
the POD potential is described from :doc:`fitpod <fitpod_command>`, which is
used to fit the POD potential to *ab initio* energy and force data.
potential :ref:`(Nguyen and Rohskopf) <Nguyen20222b>`,
:ref:`(Nguyen2023) <Nguyen20232b>`, :ref:`(Nguyen2024) <Nguyen20242b>`,
and :ref:`(Nguyen and Sema) <Nguyen20243b>`. The :doc:`fitpod
<fitpod_command>` is used to fit the POD potential.
Only a single pair_coeff command is used with the *pod* style which
specifies a POD parameter file followed by a coefficient file.
specifies a POD parameter file followed by a coefficient file, a
projection matrix file, and a centroid file.
The coefficient file (``Ta_coefficients.pod``) contains coefficients for the
POD potential. The top of the coefficient file can contain any number of
blank and comment lines (start with #), but follows a strict format
after that. The first non-blank non-comment line must contain:
The POD parameter file (``Ta_param.pod``) can contain blank and comment
lines (start with #) anywhere. Each non-blank non-comment line must
contain one keyword/value pair. See :doc:`fitpod <fitpod_command>` for
the description of all the keywords that can be assigned in the
parameter file.
* POD_coefficients: *ncoeff*
The coefficient file (``Ta_coefficients.pod``) contains coefficients for
the POD potential. The top of the coefficient file can contain any
number of blank and comment lines (start with #), but follows a strict
format after that. The first non-blank non-comment line must contain:
This is followed by *ncoeff* coefficients, one per line. The coefficient
* model_coefficients: *ncoeff* *nproj* *ncentroid*
This is followed by *ncoeff* coefficients, *nproj* projection matrix entries,
and *ncentroid* centroid coordinates, one per line. The coefficient
file is generated after training the POD potential using :doc:`fitpod
<fitpod_command>`.
The POD parameter file (``Ta_param.pod``) can contain blank and comment lines
(start with #) anywhere. Each non-blank non-comment line must contain
one keyword/value pair. See :doc:`fitpod <fitpod_command>` for the description
of all the keywords that can be assigned in the parameter file.
As an example, if a LAMMPS indium phosphide simulation has 4 atoms
types, with the first two being indium and the third and fourth being
phophorous, the pair_coeff command would look like this:
@ -67,7 +74,33 @@ the *hybrid* pair style. The NULL values are placeholders for atom
types that will be used with other potentials.
Examples about training and using POD potentials are found in the
directory lammps/examples/PACKAGES/pod.
directory lammps/examples/PACKAGES/pod and the Github repo https://github.com/cesmix-mit/pod-examples.
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS with
user-specifiable parameters as described above. You never need to
specify a pair_coeff command with I != J arguments for this style.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style does not write its information to :doc:`binary restart
files <restart>`, since it is stored in potential files. Thus, you need
to re-specify the pair_style and pair_coeff commands in an input script
that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*, *middle*, *outer* keywords.
----------
.. include:: accel_styles.rst
----------
@ -78,12 +111,14 @@ This style is part of the ML-POD package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This pair style does not compute per-atom energies and per-atom stresses.
Related commands
""""""""""""""""
:doc:`fitpod <fitpod_command>`,
:doc:`compute pod/atom <compute_pod_atom>`,
:doc:`compute podd/atom <compute_pod_atom>`,
:doc:`compute pod/local <compute_pod_atom>`,
:doc:`compute pod/global <compute_pod_atom>`
Default
"""""""
@ -92,6 +127,20 @@ none
----------
.. _Nguyen20221:
.. _Nguyen20222b:
**(Nguyen and Rohskopf)** Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).
.. _Nguyen20232b:
**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
.. _Nguyen20242b:
**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
.. _Nguyen20243b:
**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022).

102
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@ -0,0 +1,102 @@
.. index:: pair_style rheo
pair_style rheo command
=======================
Syntax
""""""
.. code-block:: LAMMPS
pair_style rheo cutoff keyword values
* cutoff = global cutoff for kernel (distance units)
* zero or more keyword/value pairs may be appended to args
* keyword = *rho/damp* or *artificial/visc* or *harmonic/means*
.. parsed-literal::
*rho/damp* args = density damping prefactor :math:`\xi`
*artificial/visc* args = artificial viscosity prefactor :math:`\zeta`
*harmonic/means* args = none
Examples
""""""""
.. code-block:: LAMMPS
pair_style rheo 3.0 rho/damp 1.0 artificial/visc 2.0
pair_coeff * *
Description
"""""""""""
.. versionadded:: TBD
Pair style *rheo* computes pressure and viscous forces between particles
in the :doc:`rheo package <Howto_rheo>`. If thermal evolution is turned
on in :doc:`fix rheo <fix_rheo>`, then the pair style also calculates
heat exchanged between particles.
The *artificial/viscosity* keyword is used to specify the magnitude
:math:`\zeta` of an optional artificial viscosity contribution to forces.
This factor can help stabilize simulations by smoothing out small length
scale variations in velocity fields. Artificial viscous forces typically
are only exchanged by fluid particles. However, if interfaces are not
reconstructed in fix rheo, fluid particles will also exchange artificial
viscous forces with solid particles to improve stability.
The *rho/damp* keyword is used to specify the magnitude :math:`\xi` of
an optional pairwise damping term between the density of particles. This
factor can help stabilize simulations by smoothing out small length
scale variations in density fields. However, in systems that develop
a density gradient in equilibrium (e.g. in a hydrostatic column underlying
gravity), this option may be inappropriate.
If particles have different viscosities or conductivities, the
*harmonic/means* keyword changes how they are averaged before calculating
pairwise forces or heat exchanges. By default, an arithmetic averaged is
used, however, a harmonic mean may improve stability in systems with multiple
fluid phases with large disparities in viscosities.
No coefficients are defined for each pair of atoms types via the
:doc:`pair_coeff <pair_coeff>` command as in the examples
above.
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This style does not write information to :doc:`binary restart files <restart>`.
Thus, you need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the *inner*,
*middle*, *outer* keywords.
Restrictions
""""""""""""
This fix is part of the RHEO package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix rheo <fix_rheo>`,
:doc:`fix rheo/pressure <fix_rheo_pressure>`,
:doc:`fix rheo/thermal <fix_rheo_thermal>`,
:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
Default
"""""""
Density damping and artificial viscous forces are not calculated.
Arithmetic means are used for mixing particle properties.

112
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@ -0,0 +1,112 @@
.. index:: pair_style rheo/solid
pair_style rheo/solid command
=============================
Syntax
""""""
.. code-block:: LAMMPS
pair_style rheo/solid
Examples
""""""""
.. code-block:: LAMMPS
pair_style rheo/solid
pair_coeff * * 1.0 1.5 1.0
Description
"""""""""""
.. versionadded:: TBD
Style *rheo/solid* is effectively a copy of pair style
:doc:`bpm/spring <pair_bpm_spring>` except it only applies forces
between solid RHEO particles, determined by checking the status of
each pair of neighboring particles before calculating forces.
The style computes pairwise forces with the formula
.. math::
F = k (r - r_c)
where :math:`k` is a stiffness and :math:`r_c` is the cutoff length.
An additional damping force is also applied to interacting
particles. The force is proportional to the difference in the
normal velocity of particles
.. math::
F_D = - \gamma w (\hat{r} \bullet \vec{v})
where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
displacement normal vector, :math:`\vec{v}` is the velocity difference
between the two particles, and :math:`w` is a smoothing factor.
This smoothing factor is constructed such that damping forces go to zero
as particles come out of contact to avoid discontinuities. It is
given by
.. math::
w = 1.0 - \left( \frac{r}{r_c} \right)^8 .
The following coefficients must be defined for each pair of atom types
via the :doc:`pair_coeff <pair_coeff>` command as in the examples
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands, or by mixing as described below:
* :math:`k` (force/distance units)
* :math:`r_c` (distance units)
* :math:`\gamma` (force/velocity units)
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is always mixed via a
*geometric* rule. The cutoff is mixed according to the pair_modify
mix value. The default mix value is *geometric*\ . See the
"pair_modify" command for details.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift option, since the pair interaction goes to 0.0 at the cutoff.
The :doc:`pair_modify <pair_modify>` table and tail options are not
relevant for this pair style.
This pair style writes its information to :doc:`binary restart files
<restart>`, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*, *middle*, *outer* keywords.
----------
Restrictions
""""""""""""
This pair style is part of the RHEO package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix rheo <fix_rheo>`,
:doc:`fix rheo/thermal <fix_rheo_thermal>`,
:doc:`pair bpm/spring <pair_bpm_spring>`
Default
"""""""
none

4
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View File

@ -292,6 +292,7 @@ accelerated styles exist.
* :doc:`mesocnt/viscous <pair_mesocnt>` - Mesoscopic vdW potential for (carbon) nanotubes with friction
* :doc:`mgpt <pair_mgpt>` - Simplified model generalized pseudopotential theory (MGPT) potential
* :doc:`mie/cut <pair_mie>` - Mie potential
* :doc:`mliap <pair_mliap>` - Multiple styles of machine-learning potential
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - Smoothed MM3 vdW potential with Gaussian electrostatics
* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
* :doc:`morse <pair_morse>` - Morse potential
@ -337,6 +338,8 @@ accelerated styles exist.
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
* :doc:`rebo <pair_airebo>` - Second generation REBO potential of Brenner
* :doc:`rebomos <pair_rebomos>` - REBOMoS potential for MoS2
* :doc:`rheo <pair_rheo>` - fluid interactions in RHEO package
* :doc:`rheo/solid <pair_rheo_solid>` - solid interactions in RHEO package
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
* :doc:`saip/metal <pair_saip_metal>` - Interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - Smoothed dissipative particle dynamics for water at isothermal conditions
@ -347,7 +350,6 @@ accelerated styles exist.
* :doc:`smd/tri_surface <pair_smd_triangulated_surface>` -
* :doc:`smd/ulsph <pair_smd_ulsph>` -
* :doc:`smtbq <pair_smtbq>` -
* :doc:`mliap <pair_mliap>` - Multiple styles of machine-learning potential
* :doc:`snap <pair_snap>` - SNAP machine-learning potential
* :doc:`soft <pair_soft>` - Soft (cosine) potential
* :doc:`sph/heatconduction <pair_sph_heatconduction>` -

2
doc/src/pair_uf3.rst
View File

@ -36,7 +36,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 27June2024
The *uf3* style computes the :ref:`Ultra-Fast Force Fields (UF3)
<Xie23>` potential, a machine-learning interatomic potential. In UF3,

6
doc/src/read_data.rst
View File

@ -12,7 +12,7 @@ Syntax
* file = name of data file to read in
* zero or more keyword/arg pairs may be appended
* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *group* or *nocoeff* or *fix*
* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom* or *group* or *nocoeff* or *fix*
.. parsed-literal::
@ -859,6 +859,10 @@ of analysis.
- atom-ID molecule-ID atom-type x y z
* - peri
- atom-ID atom-type volume density x y z
* - rheo
- atom-ID atom-type status rho x y z
* - rheo/thermal
- atom-ID atom-type status rho energy x y z
* - smd
- atom-ID atom-type molecule volume mass kradius cradius x0 y0 z0 x y z
* - sph

22
doc/src/reset_atoms.rst
View File

@ -32,7 +32,7 @@ Syntax
.. code-block:: LAMMPS
reset atoms mol group-ID keyword value ...
reset_atoms mol group-ID keyword value ...
* group-ID = ID of group of atoms whose molecule IDs will be reset
* zero or more keyword/value pairs can be appended
@ -66,16 +66,16 @@ Description
.. versionadded:: 22Dec2022
The *reset_atoms* command resets the values of a specified atom
property. In contrast to the set command, it does this in a
property. In contrast to the *set* command, it does this in a
collective manner which resets the values for many atoms in a
self-consistent way. This is often useful when the simulated system
has undergone significant modifications like adding or removing atoms
or molecules, joining data files, changing bonds, or large-scale
self-consistent way. This command is often useful when the simulated
system has undergone significant modifications like adding or removing
atoms or molecules, joining data files, changing bonds, or large-scale
diffusion.
The new values can be thought of as a *reset*, similar to values atoms
would have if a new data file were being read or a new simulation
performed. Note that the set command also resets atom properties to
performed. Note that the *set* command also resets atom properties to
new values, but it treats each atom independently.
The *property* setting can be *id* or *image* or *mol*. For *id*, the
@ -90,7 +90,7 @@ keyword/value settings are given below.
----------
*Property id*
Property: *id*
Reset atom IDs for the entire system, including all the global IDs
stored for bond, angle, dihedral, improper topology data. This will
@ -146,7 +146,7 @@ processor have consecutive IDs, as the :doc:`create_atoms
----------
*Property image*
Property: *image*
Reset the image flags of atoms so that at least one atom in each
molecule has an image flag of 0. Molecular topology is respected so
@ -191,7 +191,7 @@ flags.
----------
*Property mol*
Property: *mol*
Reset molecule IDs for a specified group of atoms based on current
bond connectivity. This will typically create a new set of molecule
@ -203,7 +203,7 @@ For purposes of this operation, molecules are identified by the current
bond connectivity in the system, which may or may not be consistent with
the current molecule IDs. A molecule in this context is a set of atoms
connected to each other with explicit bonds. The specific algorithm
used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`
used is the one of :doc:`compute fragment/atom <compute_cluster_atom>`.
Once the molecules are identified and a new molecule ID computed for
each, this command will update the current molecule ID for all atoms in
the group with the new molecule ID. Note that if the group excludes
@ -266,7 +266,7 @@ The *image* property can only be used when the atom style supports bonds.
Related commands
""""""""""""""""
:doc:`compute fragment/atom <compute_cluster_atom>`
:doc:`compute fragment/atom <compute_cluster_atom>`,
:doc:`fix bond/react <fix_bond_react>`,
:doc:`fix bond/create <fix_bond_create>`,
:doc:`fix bond/break <fix_bond_break>`,

6
doc/src/set.rst
View File

@ -120,6 +120,8 @@ Syntax
*angle* value = numeric angle type or angle type label, for all angles between selected atoms
*dihedral* value = numeric dihedral type or dihedral type label, for all dihedrals between selected atoms
*improper* value = numeric improper type or improper type label, for all impropers between selected atoms
*rheo/rho* value = density of RHEO particles (mass/distance\^3)
*rheo/status* value = status or phase of RHEO particles (unitless)
*sph/e* value = energy of SPH particles (need units)
value can be an atom-style variable (see below)
*sph/cv* value = heat capacity of SPH particles (need units)
@ -506,6 +508,10 @@ by the *bond types* (\ *angle types*, etc) field in the header of the
data file read by the :doc:`read_data <read_data>` command. These
keywords do not allow use of an atom-style variable.
Keywords *rheo/rho* and *rheo/status* set the density and the status of
rheo particles. In particular, one can only set the phase in the status
as described by the :doc:`RHEO howto page <Howto_rheo>`.
Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
and density of smoothed particle hydrodynamics (SPH) particles. See
`this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.

20
doc/src/variable.rst
View File

@ -67,7 +67,7 @@ Syntax
bound(group,dir,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), torque(group,dim,region),
inertia(group,dimdim,region), omega(group,dim,region)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout()
feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
@ -547,7 +547,7 @@ variables.
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label) |
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout() |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Feature functions | is_available(category,feature), is_active(category,feature), is_defined(category,id) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@ -957,7 +957,7 @@ of points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2),
length N. The returned value is the slope of the line. If the line
has a single point or is vertical, it returns 1.0e20.
.. versionadded:: TBD
.. versionadded:: 27June2024
The sort(x) and rsort(x) functions sort the data of the input vector by
their numeric value: sort(x) sorts in ascending order, rsort(x) sorts
@ -1042,6 +1042,20 @@ label2type(), but returns 1 if the type label has been assigned,
otherwise it returns 0. This function can be used to check if a
particular type label already exists in the simulation.
.. versionadded:: TBD
The is_timeout() function returns 1 when the :doc:`timer timeout
<timer>` has expired otherwise it returns 0. This function can be used
to check inputs in combination with the :doc:`if command <if>` to
execute commands after the timer has expired. Example:
.. code-block:: LAMMPS
variable timeout equal is_timeout()
timer timeout 0:10:00 every 10
run 10000
if ${timeout} then "print 'Timer has expired'"
----------
Feature Functions

1
doc/utils/requirements.txt
View File

@ -1,6 +1,7 @@
Sphinx >= 5.3.0, <8.0
sphinxcontrib-spelling
sphinxcontrib-jquery
sphinx-design
git+https://github.com/akohlmey/sphinx-fortran@parallel-read
sphinx-tabs>=3.4.1
breathe

5
doc/utils/sphinx-config/conf.py.in
View File

@ -41,7 +41,7 @@ sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'utils', 'sphinx-config', '_themes'
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
needs_sphinx = '5.2.0'
needs_sphinx = '5.3.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@ -57,6 +57,7 @@ extensions = [
'table_from_list',
'tab_or_note',
'breathe',
'sphinx_design'
]
images_config = {
@ -68,7 +69,7 @@ images_config = {
templates_path = ['_templates']
# The suffix of source filenames.
source_suffix = '.rst'
source_suffix = {'.rst': 'restructuredtext'}
# The encoding of source files.
#source_encoding = 'utf-8-sig'

19
doc/utils/sphinx-config/false_positives.txt
View File

@ -393,6 +393,7 @@ buf
builtin
Bulacu
Bulatov
Bulkley
Bureekaew
burlywood
Bussi
@ -564,6 +565,7 @@ cond
conda
Conda
Condens
conductivities
conf
config
configfile
@ -1099,6 +1101,7 @@ excv
exe
executables
extep
extractable
extrema
extxyz
exy
@ -1173,6 +1176,7 @@ finitecutflag
Finnis
Fiorin
fitpod
fivebody
fixID
fj
Fji
@ -1439,6 +1443,7 @@ henrich
Henrich
Hermitian
Herrmann
Hershchel
Hertizian
hertzian
Hertzsch
@ -1830,6 +1835,7 @@ Kspace
KSpace
KSpaceStyle
Kspring
kstyle
kT
kTequil
kth
@ -2270,6 +2276,7 @@ modelled
modelling
Modelling
Modine
modularity
moduli
mofff
MOFFF
@ -2487,6 +2494,7 @@ Neumann
Nevent
nevery
Nevery
Nevins
newfile
Newns
newtype
@ -2897,6 +2905,7 @@ Pmolrotate
Pmoltrans
pN
png
podd
Podhorszki
Poiseuille
poisson
@ -3065,6 +3074,7 @@ quatw
queryargs
Queteschiner
quickmin
quintic
qw
qx
qy
@ -3076,6 +3086,7 @@ radialscreenedspin
radialspin
radian
radians
radiative
radj
Rafferty
rahman
@ -3179,6 +3190,7 @@ rg
Rg
Rhaphson
Rhe
rheo
rheological
rheology
rhodo
@ -3266,6 +3278,7 @@ rsort
rsq
rst
rstyle
rsurf
Rubensson
Rubia
Rud
@ -3370,6 +3383,7 @@ setmask
Setmask
setpoint
setvel
sevenbody
sfftw
sfree
Sg
@ -3420,6 +3434,7 @@ SiO
Siochi
Sirk
Sival
sixbody
sizeI
sizeJ
sizex
@ -3647,6 +3662,7 @@ Telsa
tempCorrCoeff
templated
Templeton
Tencer
Tequil
ters
tersoff
@ -3735,7 +3751,6 @@ tokyo
tol
tomic
toolchain
toolset
topologies
Toporov
Torder
@ -3813,6 +3828,7 @@ typeJ
typelabel
typeN
typesafe
typestr
Tz
Tzou
ub
@ -3993,6 +4009,7 @@ Vries
Vsevolod
Vsmall
Vstream
vstyle
vtarget
vtk
VTK

2
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -101,6 +101,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(extract_setting);
ADDSYM(extract_global_datatype);
ADDSYM(extract_global);
ADDSYM(extract_pair_dimension);
ADDSYM(extract_pair);
ADDSYM(map_atom);
ADDSYM(extract_atom_datatype);

8
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -144,11 +144,13 @@ struct _liblammpsplugin {
int (*get_mpi_comm)(void *);
int (*extract_setting)(void *, const char *);
int *(*extract_global_datatype)(void *, const char *);
int (*extract_global_datatype)(void *, const char *);
void *(*extract_global)(void *, const char *);
void *(*map_atom)(void *, const void *);
int (*extract_pair_dimension)(void *, const char *);
void *(*extract_pair)(void *, const char *);
int (*map_atom)(void *, const void *);
int *(*extract_atom_datatype)(void *, const char *);
int (*extract_atom_datatype)(void *, const char *);
void *(*extract_atom)(void *, const char *);
void *(*extract_compute)(void *, const char *, int, int);

1
examples/PACKAGES/electrode/madelung/.gitignore vendored
View File

@ -1,2 +1,3 @@
*.csv
*.txt
*.lammpstrj

18
examples/PACKAGES/electrode/madelung/eval.py
View File

@ -17,14 +17,22 @@ q_ref = float(ref_line[3])
inv11_ref = float(ref_line[4])
inv12_ref = float(ref_line[5])
b1_ref = float(ref_line[6])
felec1_ref = float(ref_line[8])
felyt1_ref = float(ref_line[10])
press_ref = float(ref_line[12])
# out.csv
with open(sys.argv[2]) as f:
out_line = f.readlines()[-1].split(", ")
e_out = float(out_line[0])
q_out = float(out_line[1])
press_out = float(out_line[2])
out_lines = [("energy", e_ref, e_out), ("charge", q_ref, q_out)]
out_lines = [
("energy", e_ref, e_out),
("charge", q_ref, q_out),
("pressure", press_ref, press_out),
]
# vec.csv
vec_file = "vec.csv"
@ -44,6 +52,14 @@ if op.isfile(inv_file):
inv12_out = float(inv_line[1])
out_lines.append(("inv11", inv11_ref, inv11_out))
# forces.lammpstrj
force_file = "forces.lammpstrj"
with open(force_file) as f:
lines = f.readlines()[9:]
for name, i, f_ref in [("felec1", "1", felec1_ref), ("felyt1", "3", felyt1_ref)]:
f_out = next(float(y[3]) for x in lines if (y := x.split()) and y[0] == i)
out_lines.append((name, f_ref, f_out))
lines = []
for label, ref, out in out_lines:
error = rel_error(out, ref)

2
examples/PACKAGES/electrode/madelung/in.eta_cg
View File

@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
fix feta all property/atom d_eta ghost on
set group bot d_eta 0.5
set group top d_eta 3.0
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta algo cg 1e-6
fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta algo cg 1e-6
run 0

2
examples/PACKAGES/electrode/madelung/in.eta_mix
View File

@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
fix feta all property/atom d_eta ghost on
set group bot d_eta 0.5
set group top d_eta 3.0
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
run 0

98
examples/PACKAGES/electrode/madelung/plate_cap.py
View File

@ -1,12 +1,17 @@
#!/usr/bin/env python3
import time
import numpy as np
from scipy.special import erf
SQRT2 = np.sqrt(2)
SQRTPI_INV = 1 / np.sqrt(np.pi)
COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units
QE2F = 23.060549
NKTV2P = 68568.415 # pressure in 'real' units
LENGTH = 10000 # convergence parameter
LZ = 20
def lattice(length):
@ -26,6 +31,25 @@ def b_element(r, q, eta):
return q * erf(eta * r) / r
def force_gauss(r, qq, eta):
etar = eta * r
return (qq / np.square(r)) * (
erf(etar) - 2 * etar * SQRTPI_INV * np.exp(-np.square(etar))
)
def force_point(r, qq):
return qq / np.square(r)
def force_component(dx, d, qq, eta=None):
if eta:
return np.sum(dx / d * force_gauss(d, qq, eta))
else:
return np.sum(dx / d * force_point(d, qq))
time_start = time.perf_counter()
a = 1 # nearest neighbor distance i.e. lattice constant / sqrt(2)
x_elec = [-2, 2]
x_elyt = [-1, 1]
@ -36,8 +60,20 @@ v = np.array([-0.5, 0.5]) * (QE2F / COULOMB)
# distances to images within electrode and to opposite electrode
distances = a * np.linalg.norm(lattice(LENGTH), axis=1)
opposite_distances = np.sqrt(np.square(distances) + distance_plates**2)
image_distances = []
for x in x_elec:
image_distances.append([])
for y in x_elyt:
image_distances[-1].append(np.sqrt(np.square(distances) + np.abs(y - x) ** 2))
image_elyt_distances = [[None for _ in range(len(x_elyt))] for _ in range(len(x_elyt))]
for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
image_elyt_distances[i][j] = np.sqrt(
np.square(distances) + np.abs(xj - xi) ** 2
)
for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
# for name, eta_elec in [("", [2.0, 2.0])]:
eta_mix = np.prod(eta_elec) / np.sqrt(np.sum(np.square(eta_elec)))
# self interaction and within original box
A_11 = np.sqrt(2 / np.pi) * eta_elec[0]
@ -55,22 +91,18 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
# electrode-electrolyte interaction
b = []
for x, eta in zip(x_elec, eta_elec):
for i, (x, eta) in enumerate(zip(x_elec, eta_elec)):
bi = 0
for y, q in zip(x_elyt, q_elyt):
d = abs(y - x)
bi += b_element(d, q, eta)
image_distances = np.sqrt(np.square(distances) + d**2)
bi += 4 * np.sum(b_element(image_distances, q, eta))
for j, (y, q) in enumerate(zip(x_elyt, q_elyt)):
bi += b_element(np.abs(y - x), q, eta)
bi += 4 * np.sum(b_element(image_distances[i][j], q, eta))
b.append(bi)
b = np.array(b)
# electrolyte-electrolyte energy
elyt_11 = 4 * np.sum(1 / distances)
distance_elyt = x_elyt[1] - x_elyt[0]
elyt_12 = 1 / distance_elyt + 4 * np.sum(
1 / np.sqrt(np.square(distances) + distance_elyt**2)
)
elyt_12 = 1 / distance_elyt + 4 * np.sum(1 / image_elyt_distances[0][1])
elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]])
energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt))
@ -78,9 +110,48 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
q = np.dot(inv, v - b)
energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt)
# forces in out-of-plane direction
f_elec = np.zeros(len(x_elec))
f_elyt = np.zeros(len(x_elyt))
# electrode-electrode
dx = x_elec[1] - x_elec[0]
fij_box = force_component(dx, np.abs(dx), q[0] * q[1], eta_mix)
fij_img = 4 * force_component(dx, opposite_distances, q[0] * q[1], eta_mix)
f_elec[0] -= fij_box + fij_img
f_elec[1] += fij_box + fij_img
# electrode-electrolyte
for i, (xi, qi, etai) in enumerate(zip(x_elec, q, eta_elec)):
for j, (xj, qj) in enumerate(zip(x_elyt, q_elyt)):
dx = xj - xi
fij_box = force_component(dx, np.abs(dx), qi * qj, etai)
fij_img = 4 * force_component(dx, image_distances[i][j], qi * qj, etai)
f_elec[i] -= fij_box + fij_img
f_elyt[j] += fij_box + fij_img
# electrolyte-electrolyte
for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
dx = xj - xi
fij_box = force_component(dx, np.abs(dx), qi * qj)
fij_img = 4 * force_component(dx, image_elyt_distances[i][j], qi * qj)
f_elyt[i] -= fij_img + fij_box
f_elyt[j] += fij_img + fij_box
# force units
assert np.abs(np.sum(f_elec) + np.sum(f_elyt)) < 1e-8
f_elec *= COULOMB
f_elyt *= COULOMB
# Virial
volume = a**2 * LZ
virial = 0.0
for x, f in [(x_elec, f_elec), (x_elyt, f_elyt)]:
virial += np.dot(x, f)
pressure = NKTV2P * virial / volume
with open(f"plate_cap{name}.csv", "w") as f:
f.write(
"length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A\n"
"length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A"
+ ", b1 / e/A, b2 / e/A, felec1 / kcal/mol/A, felec2 / kcal/mol/A"
+ ", felyt1 / kcal/mol/A, felyt2 / kcal/mol/A, press\n"
)
f.write(
", ".join(
@ -93,7 +164,14 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
f"{inv[0, 1]:.10f}",
f"{b[0]:.8f}",
f"{b[1]:.8f}",
f"{f_elec[0]:.5f}",
f"{f_elec[1]:.5f}",
f"{f_elyt[0]:.5f}",
f"{f_elyt[1]:.5f}",
f"{pressure:.2f}",
]
)
+ "\n"
)
time_end = time.perf_counter()
print(f"{time_end - time_start:0.4f} seconds")

6
examples/PACKAGES/electrode/madelung/settings.mod
View File

@ -19,4 +19,8 @@ compute qtop top reduce sum v_q
compute compute_pe all pe
variable vpe equal c_compute_pe
variable charge equal c_qtop
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
compute press all pressure NULL virial
variable p3 equal c_press[3]
fix fxprint all print 1 "${vpe}, ${charge}, ${p3}" file "out.csv"
dump dump_forces all custom 1 forces.lammpstrj id fx fy fz

4064
examples/PACKAGES/electrode/piston/data.piston.final
View File

File diff suppressed because it is too large Load Diff

6
examples/PACKAGES/electrode/piston/in.piston
View File

@ -42,7 +42,11 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
fix fxforce_wa wall setforce 0.0 0.0 NULL
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
variable atm equal 1/68568.415 # 1/force->nktv2p
variable area equal (xhi-xlo)*(yhi-ylo)
variable wall_force equal -v_atm*v_area/count(wall)
print "Wall force per atom: ${wall_force}"
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
fix fxdrag wall viscous 100
fix fxrigid wall rigid/nve single

97
examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.1 → examples/PACKAGES/electrode/piston/log.22May2024.piston.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (3 Nov 2022)
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
using 1 OpenMP thread(s) per MPI task
# The intention is to find the average position of one wall at atmospheric
# pressure. The output is the wall position over time which can be used to
# find the average position for a run with fixed wall position.
@ -40,8 +41,8 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.011 seconds
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
# ----------------- Settings Section -----------------
@ -77,7 +78,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
fix fxforce_wa wall setforce 0.0 0.0 NULL
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
variable atm equal 1/68568.415 # 1/force->nktv2p
variable area equal (xhi-xlo)*(yhi-ylo)
variable wall_force equal -v_atm*v_area/count(wall)
print "Wall force per atom: ${wall_force}"
Wall force per atom: -0.000109285996244287
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
fix fxpressure wall aveforce 0 0 -0.000109285996244287
fix fxdrag wall viscous 100
fix fxrigid wall rigid/nve single
1 rigid bodies with 48 atoms
@ -134,7 +141,7 @@ PPPM/electrode initialization ...
stencil order = 5
estimated absolute RMS force accuracy = 0.02930901
estimated relative force accuracy = 8.8263214e-05
using double precision MKL FFT
using double precision FFTW3
3d grid and FFT values/proc = 15884 6480
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
@ -157,54 +164,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes
Step c_temp_mobile c_qwa c_qau v_top_wall
0 303.38967 -0.042963484 0.042963484 21.4018
5000 285.08828 -0.26105255 0.26105255 25.155629
10000 323.19176 -0.26264003 0.26264003 24.541676
15000 310.479 -0.27318148 0.27318148 23.141522
20000 295.18544 -0.11313444 0.11313444 23.828735
25000 295.38607 -0.25433086 0.25433086 23.673314
30000 288.0613 -0.30099901 0.30099901 23.438086
35000 278.5591 -0.15823576 0.15823576 24.311915
40000 303.95751 -0.19941381 0.19941381 23.69594
45000 279.026 -0.1659962 0.1659962 23.588604
50000 298.79278 -0.28866703 0.28866703 23.372508
55000 301.03353 -0.078370381 0.078370381 23.192985
60000 306.77965 -0.12807205 0.12807205 23.968574
65000 309.86008 -0.27162663 0.27162663 23.616704
70000 287.31116 -0.029751882 0.029751882 23.667495
75000 312.48654 -0.10759866 0.10759866 23.504105
80000 309.94267 -0.2558548 0.2558548 23.810576
85000 328.04389 -0.1575471 0.1575471 24.013437
90000 302.9806 -0.032002164 0.032002164 24.264432
95000 294.20804 -0.27797238 0.27797238 23.291758
100000 307.63019 -0.19047448 0.19047448 23.632147
Loop time of 530.844 on 1 procs for 100000 steps with 726 atoms
5000 311.85363 0.03543775 -0.03543775 24.79665
10000 285.91321 -0.16873703 0.16873703 23.103088
15000 295.39476 -0.44424612 0.44424612 23.767107
20000 296.12969 -0.14120993 0.14120993 23.96361
25000 306.59629 -0.29333182 0.29333182 23.884488
30000 297.98559 -0.10749684 0.10749684 23.73316
35000 297.98503 -0.11809975 0.11809975 23.984669
40000 300.26292 -0.32784184 0.32784184 23.462748
45000 295.68441 -0.25940165 0.25940165 23.516403
50000 315.12883 -0.36037614 0.36037614 23.627879
55000 290.55151 -0.0032838106 0.0032838106 23.684931
60000 316.4625 -0.17245368 0.17245368 24.126883
65000 296.79343 -0.054061851 0.054061851 23.695094
70000 305.99923 -0.11363801 0.11363801 23.55476
75000 297.40131 -0.27054153 0.27054153 23.928994
80000 306.54811 -0.25409719 0.25409719 23.869448
85000 303.95231 -0.17895561 0.17895561 23.658833
90000 313.43739 -0.059036514 0.059036514 23.36056
95000 290.3077 -0.31394478 0.31394478 23.885538
100000 297.5156 -0.30730083 0.30730083 23.511674
Loop time of 1586.06 on 1 procs for 100000 steps with 726 atoms
Performance: 32.552 ns/day, 0.737 hours/ns, 188.379 timesteps/s, 136.763 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 10.895 ns/day, 2.203 hours/ns, 63.049 timesteps/s, 45.774 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 190.47 | 190.47 | 190.47 | 0.0 | 35.88
Bond | 0.10754 | 0.10754 | 0.10754 | 0.0 | 0.02
Kspace | 73.179 | 73.179 | 73.179 | 0.0 | 13.79
Neigh | 24.209 | 24.209 | 24.209 | 0.0 | 4.56
Comm | 1.6857 | 1.6857 | 1.6857 | 0.0 | 0.32
Output | 0.0016861 | 0.0016861 | 0.0016861 | 0.0 | 0.00
Modify | 240.23 | 240.23 | 240.23 | 0.0 | 45.26
Other | | 0.9595 | | | 0.18
Pair | 460.91 | 460.91 | 460.91 | 0.0 | 29.06
Bond | 0.047873 | 0.047873 | 0.047873 | 0.0 | 0.00
Kspace | 341.4 | 341.4 | 341.4 | 0.0 | 21.53
Neigh | 52.868 | 52.868 | 52.868 | 0.0 | 3.33
Comm | 5.2321 | 5.2321 | 5.2321 | 0.0 | 0.33
Output | 0.00099102 | 0.00099102 | 0.00099102 | 0.0 | 0.00
Modify | 724.63 | 724.63 | 724.63 | 0.0 | 45.69
Other | | 0.9741 | | | 0.06
Nlocal: 726 ave 726 max 726 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2335 ave 2335 max 2335 min
Nghost: 2336 ave 2336 max 2336 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 120271 ave 120271 max 120271 min
Neighs: 120321 ave 120321 max 120321 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 120271
Ave neighs/atom = 165.66253
Total # of neighbors = 120321
Ave neighs/atom = 165.7314
Ave special neighs/atom = 1.7355372
Neighbor list builds = 7722
Neighbor list builds = 7670
Dangerous builds = 0
write_data "data.piston.final"
System init for write_data ...
@ -213,11 +220,11 @@ PPPM/electrode initialization ...
G vector (1/distance) = 0.32814871
grid = 12 15 36
stencil order = 5
estimated absolute RMS force accuracy = 0.029311365
estimated relative force accuracy = 8.8270304e-05
using double precision MKL FFT
estimated absolute RMS force accuracy = 0.029311329
estimated relative force accuracy = 8.8270197e-05
using double precision FFTW3
3d grid and FFT values/proc = 15884 6480
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Average conjugate gradient steps: 1.981
Total wall time: 0:08:50
Total wall time: 0:26:26

109
examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.4 → examples/PACKAGES/electrode/piston/log.22May2024.piston.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (3 Nov 2022)
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
using 1 OpenMP thread(s) per MPI task
# The intention is to find the average position of one wall at atmospheric
# pressure. The output is the wall position over time which can be used to
# find the average position for a run with fixed wall position.
@ -41,8 +42,8 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.017 seconds
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
# ----------------- Settings Section -----------------
@ -66,7 +67,7 @@ Finding SHAKE clusters ...
0 = # of size 3 clusters
0 = # of size 4 clusters
210 = # of frozen angles
find clusters CPU = 0.002 seconds
find clusters CPU = 0.000 seconds
pair_modify mix arithmetic
# ----------------- Run Section -----------------
@ -78,7 +79,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
fix fxforce_wa wall setforce 0.0 0.0 NULL
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
variable atm equal 1/68568.415 # 1/force->nktv2p
variable area equal (xhi-xlo)*(yhi-ylo)
variable wall_force equal -v_atm*v_area/count(wall)
print "Wall force per atom: ${wall_force}"
Wall force per atom: -0.000109285996244287
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
fix fxpressure wall aveforce 0 0 -0.000109285996244287
fix fxdrag wall viscous 100
fix fxrigid wall rigid/nve single
1 rigid bodies with 48 atoms
@ -135,7 +142,7 @@ PPPM/electrode initialization ...
stencil order = 5
estimated absolute RMS force accuracy = 0.02930901
estimated relative force accuracy = 8.8263214e-05
using double precision MKL FFT
using double precision FFTW3
3d grid and FFT values/proc = 8512 2880
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
@ -158,54 +165,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.22 | 10.41 Mbytes
Step c_temp_mobile c_qwa c_qau v_top_wall
0 303.38967 -0.042963484 0.042963484 21.4018
5000 292.03027 -0.19040435 0.19040435 24.581338
10000 309.52764 -0.48308301 0.48308301 23.776985
15000 295.00243 -0.16591109 0.16591109 23.672038
20000 293.5536 -0.086669084 0.086669084 23.426455
25000 303.0079 -0.16488112 0.16488112 23.862966
30000 306.31463 -0.23192653 0.23192653 23.819882
35000 303.66268 -0.2317907 0.2317907 23.495344
40000 301.39435 -0.34661329 0.34661329 23.657835
45000 291.61205 -0.30539427 0.30539427 23.437303
50000 298.65319 -0.096107034 0.096107034 23.57809
55000 282.65069 -0.14943539 0.14943539 23.823728
60000 310.64182 -0.17418813 0.17418813 23.286959
65000 308.47141 -0.02075662 0.02075662 23.91313
70000 292.5186 -0.080163162 0.080163162 23.96283
75000 270.13928 -0.029528648 0.029528648 23.488972
80000 322.10914 0.030761045 -0.030761045 23.47592
85000 310.60347 -0.24069996 0.24069996 23.987091
90000 294.35695 -0.070458235 0.070458235 23.397929
95000 308.69043 -0.2652581 0.2652581 23.473813
100000 318.71883 0.024035956 -0.024035956 23.449863
Loop time of 590.232 on 4 procs for 100000 steps with 726 atoms
5000 291.6303 -0.1820085 0.1820085 24.641399
10000 299.42886 -0.19823095 0.19823095 23.820522
15000 288.23071 -0.065261869 0.065261869 23.360845
20000 299.4644 -0.042993777 0.042993777 23.987554
25000 304.26497 -0.15665293 0.15665293 23.729006
30000 292.29674 -0.25142779 0.25142779 23.960725
35000 295.57492 -0.01269228 0.01269228 23.445383
40000 303.38438 -0.13941727 0.13941727 23.517483
45000 302.211 -0.19589892 0.19589892 23.704043
50000 281.64939 -0.18057298 0.18057298 23.542137
55000 274.90565 -0.15453379 0.15453379 23.734347
60000 290.70459 -0.27977436 0.27977436 23.835365
65000 293.42241 -0.2454241 0.2454241 23.59269
70000 295.20229 -0.041314995 0.041314995 23.73856
75000 297.79519 -0.11231755 0.11231755 23.57262
80000 285.17858 -0.070796508 0.070796508 23.817135
85000 311.71609 -0.068920177 0.068920177 23.861127
90000 287.80446 -0.19183387 0.19183387 23.369393
95000 309.43345 -0.15238671 0.15238671 23.597792
100000 294.12422 -0.14284353 0.14284353 23.526286
Loop time of 876.546 on 4 procs for 100000 steps with 726 atoms
Performance: 29.277 ns/day, 0.820 hours/ns, 169.425 timesteps/s, 123.003 katom-step/s
72.5% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 19.714 ns/day, 1.217 hours/ns, 114.084 timesteps/s, 82.825 katom-step/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 57.391 | 75.867 | 96.292 | 212.1 | 12.85
Bond | 0.10177 | 0.11042 | 0.12415 | 2.7 | 0.02
Kspace | 102.79 | 123.16 | 141.5 | 165.7 | 20.87
Neigh | 12.808 | 12.895 | 12.982 | 2.3 | 2.18
Comm | 18.885 | 19.973 | 21.064 | 24.0 | 3.38
Output | 0.0022573 | 0.0022749 | 0.0023225 | 0.1 | 0.00
Modify | 355.89 | 356.74 | 357.61 | 4.2 | 60.44
Other | | 1.478 | | | 0.25
Pair | 123.63 | 171.23 | 215.73 | 336.6 | 19.53
Bond | 0.068261 | 0.075883 | 0.081822 | 1.9 | 0.01
Kspace | 187.59 | 231.71 | 279.01 | 287.1 | 26.43
Neigh | 29.28 | 29.462 | 29.637 | 2.5 | 3.36
Comm | 12.544 | 13.731 | 14.929 | 29.1 | 1.57
Output | 0.0010182 | 0.0014585 | 0.0016071 | 0.7 | 0.00
Modify | 428.74 | 429.25 | 429.74 | 2.3 | 48.97
Other | | 1.092 | | | 0.12
Nlocal: 181.5 ave 207 max 169 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 1961.5 ave 1984 max 1926 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 30051 ave 41646 max 20775 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nlocal: 181.5 ave 195 max 166 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 1955.5 ave 1978 max 1931 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 30343 ave 39847 max 20428 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 120204
Ave neighs/atom = 165.57025
Total # of neighbors = 121372
Ave neighs/atom = 167.17906
Ave special neighs/atom = 1.7355372
Neighbor list builds = 7663
Neighbor list builds = 7698
Dangerous builds = 0
write_data "data.piston.final"
System init for write_data ...
@ -214,11 +221,11 @@ PPPM/electrode initialization ...
G vector (1/distance) = 0.32814871
grid = 12 15 36
stencil order = 5
estimated absolute RMS force accuracy = 0.029311028
estimated relative force accuracy = 8.8269289e-05
using double precision MKL FFT
estimated absolute RMS force accuracy = 0.029310954
estimated relative force accuracy = 8.8269069e-05
using double precision FFTW3
3d grid and FFT values/proc = 8512 2880
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Average conjugate gradient steps: 1.982
Total wall time: 0:09:50
Average conjugate gradient steps: 1.981
Total wall time: 0:14:36

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