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Merge branch 'kokkospod' of https://github.com/cesmix-mit/lammps into kokkospod

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This commit is contained in:
exapde
2024-05-18 08:17:51 -04:00
parent b5fe3d5b06 b434c4d119
commit 83d5edb032
1201 changed files with 86073 additions and 44250 deletions
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7
.github/CODEOWNERS vendored
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@ -37,7 +37,7 @@ src/MESONT/* @iafoss
src/ML-HDNNP/* @singraber
src/ML-IAP/* @athomps
src/ML-PACE/* @yury-lysogorskiy
src/ML-POD/* @exapde @rohskopf
src/ML-POD/* @exapde
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
@ -65,9 +65,12 @@ src/MANYBODY/pair_nb3b_screened.* @flodesani
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
src/MISC/*_tracker.* @jtclemm
src/MC/fix_gcmc.* @athomps
src/MC/fix_sgcmc.* @athomps
src/REAXFF/compute_reaxff_atom.* @rbberger
src/KOKKOS/compute_reaxff_atom_kokkos.* @rbberger
src/REPLICA/fix_pimd_langevin.* @Yi-FanLi
# core LAMMPS classes
@ -80,7 +83,7 @@ src/bond.* @sjplimp
src/comm*.* @sjplimp
src/compute.* @sjplimp
src/dihedral.* @sjplimp
src/domain.* @sjplimp
src/domain.* @sjplimp @stanmoore1
src/dump*.* @sjplimp
src/error.* @sjplimp
src/finish.* @sjplimp

4
.github/workflows/unittest-macos.yml vendored
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@ -15,7 +15,7 @@ jobs:
build:
name: MacOS Unit Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: macos-latest
runs-on: macos-13
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
@ -43,6 +43,8 @@ jobs:
working-directory: build
run: |
ccache -z
python3 -m venv macosenv
source macosenv/bin/activate
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -C ../cmake/presets/clang.cmake \

32
cmake/CMakeLists.txt
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@ -222,6 +222,10 @@ endif()
add_executable(lmp ${MAIN_SOURCES})
target_link_libraries(lmp PRIVATE lammps)
set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
# re-export all symbols for plugins
if(PKG_PLUGIN AND (NOT ((CMAKE_SYSTEM_NAME STREQUAL "Windows"))))
set_target_properties(lmp PROPERTIES ENABLE_EXPORTS TRUE)
endif()
install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
@ -428,6 +432,7 @@ if(BUILD_OMP)
(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
@ -438,6 +443,21 @@ if(BUILD_OMP)
target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=${LAMMPS_OMP_COMPAT_LEVEL})
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
# this hack is required to correctly link with OpenMP support when using CrayClang version 15.0.2
# CrayClang is only directly recognized by version 3.28 and later
if(CMAKE_VERSION VERSION_LESS 3.28)
get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
endif()
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
endif()
endif()
endif()
# lower C++ standard for fmtlib sources when using Intel classic compiler
@ -552,12 +572,12 @@ endforeach()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
foreach(HEADER cmath)
check_include_file_cxx(${HEADER} FOUND_${HEADER})
if(NOT FOUND_${HEADER})
message(FATAL_ERROR "Could not find needed header - ${HEADER}")
endif(NOT FOUND_${HEADER})
endforeach(HEADER)
if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")))
check_include_file_cxx(cmath FOUND_CMATH)
if(NOT FOUND_CMATH)
message(FATAL_ERROR "Could not find the required 'cmath' header")
endif(NOT FOUND_CMATH)
endif()
# make the standard math library overrideable and autodetected (for systems that don't have it)
find_library(STANDARD_MATH_LIB m DOC "Standard Math library")

4
cmake/Modules/OpenCLLoader.cmake
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@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.02.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "f3573cf9daa3558ba46fd5866517f38f" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.05.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "e7796826b21c059224fabe997e0f2075" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)

3
cmake/Modules/Packages/INTEL.cmake
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@ -111,6 +111,9 @@ if(PKG_KSPACE)
list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
endif()
if(PKG_ML-SNAP)
list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/sna_intel.cpp)
endif()
target_sources(lammps PRIVATE ${INTEL_SOURCES})
target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

9
cmake/Modules/Packages/KOKKOS.cmake
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@ -45,8 +45,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.3.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "889dcea2b5ced3debdc5b0820044bdc4" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -71,7 +71,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 4.2.00 REQUIRED CONFIG)
find_package(Kokkos 4.3.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@ -139,8 +139,9 @@ if(PKG_KSPACE)
message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
elseif(FFT_KOKKOS STREQUAL "CUFFT")
find_package(CUDAToolkit REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
target_link_libraries(lammps PRIVATE cufft)
target_link_libraries(lammps PRIVATE CUDA::cufft)
endif()
elseif(Kokkos_ENABLE_HIP)
if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "HIPFFT")))

15
cmake/Modules/Packages/ML-IAP.cmake
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@ -10,6 +10,14 @@ endif()
option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
# if ML-PACE package *and* MLIAP with Python is enabled is included we may also include ML-PACE support in ML-IAP
set(MLIAP_ENABLE_ACE_DEFAULT OFF)
if(PKG_ML-PACE)
set(MLIAP_ENABLE_ACE_DEFAULT ON)
endif()
option(MLIAP_ENABLE_ACE "Build ML-IAP package with ACE support" ${MLIAP_ENABLE_ACE_DEFAULT})
if(MLIAP_ENABLE_PYTHON)
find_package(Cythonize REQUIRED)
find_package(Python COMPONENTS NumPy REQUIRED)
@ -36,3 +44,10 @@ if(MLIAP_ENABLE_PYTHON)
target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
endif()
if(MLIAP_ENABLE_ACE)
if(NOT PKG_ML-PACE)
message(FATAL_ERROR "Must enable ML-PACE package for including ACE support in ML-IAP")
endif()
target_compile_definitions(lammps PRIVATE -DMLIAP_ACE)
endif()

2
cmake/presets/kokkos-cuda.cmake
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@ -10,7 +10,7 @@ get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokko
set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
# If KSPACE is also enabled, use CUFFT for FFTs
set(FFT_KOKKOS "CUFFT" CACHE STRING FORCE)
set(FFT_KOKKOS "CUFFT" CACHE STRING "" FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

2
cmake/presets/kokkos-hip.cmake
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@ -13,7 +13,7 @@ set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE)
set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE)
# If KSPACE is also enabled, use CUFFT for FFTs
set(FFT_KOKKOS "HIPFFT" CACHE STRING FORCE)
set(FFT_KOKKOS "HIPFFT" CACHE STRING "" FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

6
doc/lammps.1
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@ -1,7 +1,7 @@
.TH LAMMPS "1" "7 February 2024" "2024-02-07"
.TH LAMMPS "1" "17 April 2024" "2024-04-17"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 7 February 2024
\- Molecular Dynamics Simulator. Version 17 April 2024
.SH SYNOPSIS
.B lmp
@ -297,7 +297,7 @@ the chapter on errors in the
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2022 Sandia Corporation
© 2003--2024 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as

3
doc/src/Bibliography.rst
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@ -877,6 +877,9 @@ Bibliography
**(PLUMED)**
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Pavlov)**
D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
**(Paquay)**
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

14
doc/src/Build_extras.rst
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@ -533,9 +533,6 @@ They must be specified in uppercase.
* - A64FX
- HOST
- ARMv8.2 with SVE Support
* - WSM
- HOST
- Intel Westmere CPU (SSE 4.2)
* - SNB
- HOST
- Intel Sandy/Ivy Bridge CPU (AVX 1)
@ -566,18 +563,15 @@ They must be specified in uppercase.
* - KNL
- HOST
- Intel Knights Landing Xeon Phi
* - BGQ
- HOST
- IBM Blue Gene/Q CPU
* - POWER7
- HOST
- IBM POWER7 CPU
* - POWER8
- HOST
- IBM POWER8 CPU
* - POWER9
- HOST
- IBM POWER9 CPU
* - RISCV_SG2042
- HOST
- SG2042 (RISC-V) CPU
* - KEPLER30
- GPU
- NVIDIA Kepler generation CC 3.0 GPU
@ -666,7 +660,7 @@ They must be specified in uppercase.
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 4.2 of the Kokkos library.
This list was last updated for version 4.3.0 of the Kokkos library.
.. tabs::

2
doc/src/Commands_bond.rst
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@ -89,6 +89,7 @@ OPT.
* :doc:`cosine/shift (o) <angle_cosine_shift>`
* :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
* :doc:`cosine/squared (o) <angle_cosine_squared>`
* :doc:`cosine/squared/restricted (o) <angle_cosine_squared_restricted>`
* :doc:`cross <angle_cross>`
* :doc:`dipole (o) <angle_dipole>`
* :doc:`fourier (o) <angle_fourier>`
@ -127,6 +128,7 @@ OPT.
* :doc:`charmmfsw (k) <dihedral_charmm>`
* :doc:`class2 (ko) <dihedral_class2>`
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
* :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>`
* :doc:`fourier (io) <dihedral_fourier>`
* :doc:`harmonic (iko) <dihedral_harmonic>`
* :doc:`helix (o) <dihedral_helix>`

2
doc/src/Commands_fix.rst
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@ -61,6 +61,7 @@ OPT.
* :doc:`controller <fix_controller>`
* :doc:`damping/cundall <fix_damping_cundall>`
* :doc:`deform (k) <fix_deform>`
* :doc:`deform/pressure <fix_deform_pressure>`
* :doc:`deposit <fix_deposit>`
* :doc:`dpd/energy (k) <fix_dpd_energy>`
* :doc:`drag <fix_drag>`
@ -262,6 +263,7 @@ OPT.
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
* :doc:`wall/colloid <fix_wall>`
* :doc:`wall/ees <fix_wall_ees>`
* :doc:`wall/flow (k) <fix_wall_flow>`
* :doc:`wall/gran (k) <fix_wall_gran>`
* :doc:`wall/gran/region <fix_wall_gran_region>`
* :doc:`wall/harmonic <fix_wall>`

2
doc/src/Commands_pair.rst
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@ -245,6 +245,7 @@ OPT.
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation (k) <pair_pace>`
* :doc:`pedone (o) <pair_pedone>`
* :doc:`pod <pair_pod>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
@ -256,6 +257,7 @@ OPT.
* :doc:`rann <pair_rann>`
* :doc:`reaxff (ko) <pair_reaxff>`
* :doc:`rebo (io) <pair_airebo>`
* :doc:`rebomos (o) <pair_rebomos>`
* :doc:`resquared (go) <pair_resquared>`
* :doc:`saip/metal (t) <pair_saip_metal>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`

47
doc/src/Developer_updating.rst
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@ -18,6 +18,7 @@ Available topics in mostly chronological order are:
- `Setting flags in the constructor`_
- `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_
- `Use ev_init() to initialize variables derived from eflag and vflag`_
- `Use utils::count_words() functions instead of atom->count_words()`_
- `Use utils::numeric() functions instead of force->numeric()`_
- `Use utils::open_potential() function to open potential files`_
- `Use symbolic Atom and AtomVec constants instead of numerical values`_
@ -130,6 +131,41 @@ Not applying this change will not cause a compilation error, but
can lead to inconsistent behavior and incorrect tallying of
energy or virial.
Use utils::count_words() functions instead of atom->count_words()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 2Jun2020
The "count_words()" functions for parsing text have been moved from the
Atom class to the :doc:`utils namespace <Developer_utils>`. The
"count_words()" function in "utils" uses the Tokenizer class internally
to split a line into words and count them, thus it will not modify the
argument string as the function in the Atoms class did and thus had a
variant using a copy buffer. Unlike the old version, the new version
does not remove comments. For that you can use the
:cpp:func:`utils::trim_comment() function
<LAMMPS_NS::utils::trim_comment>` as shown in the example below.
Old:
.. code-block:: c++
nwords = atom->count_words(line);
int nwords = atom->count_words(buf);
New:
.. code-block:: c++
nwords = utils::count_words(line);
int nwords = utils::count_words(utils::trim_comment(buf));
.. seealso::
:cpp:func:`utils::count_words() <LAMMPS_NS::utils::count_words>`,
:cpp:func:`utils::trim_comments() <LAMMPS_NS::utils::trim_comments>`
Use utils::numeric() functions instead of force->numeric()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -137,11 +173,12 @@ Use utils::numeric() functions instead of force->numeric()
The "numeric()" conversion functions (including "inumeric()",
"bnumeric()", and "tnumeric()") have been moved from the Force class to
the utils namespace. Also they take an additional argument that selects
whether the ``Error::all()`` or ``Error::one()`` function should be
called in case of an error. The former should be used when *all* MPI
processes call the conversion function and the latter *must* be used
when they are called from only one or a subset of the MPI processes.
the :doc:`utils namespace <Developer_utils>`. Also they take an
additional argument that selects whether the ``Error::all()`` or
``Error::one()`` function should be called in case of an error. The
former should be used when *all* MPI processes call the conversion
function and the latter *must* be used when they are called from only
one or a subset of the MPI processes.
Old:

4
doc/src/Developer_utils.rst
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@ -635,10 +635,10 @@ Tohoku University (under MIT license)
----------
.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec)
.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec, int sort)
:project: progguide
.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3])
.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort)
:project: progguide
---------------------------

49
doc/src/Errors_details.rst
View File

@ -13,15 +13,44 @@ discussions of such cases.
Unknown identifier in data file
-------------------------------
This error happens when LAMMPS encounters a line of text in an unexpected format
while reading a data file. This is most commonly cause by inconsistent header and
section data. The header section informs LAMMPS how many entries or lines are expected in the
various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file.
If there is a mismatch, LAMMPS will either keep reading beyond the end of a section
or stop reading before the section has ended.
This error happens when LAMMPS encounters a line of text with an
unexpected keyword while :doc:`reading a data file <read_data>`. This
would be either header keywords or section header keywords. This is
most commonly due to a mistyped keyword or due to a keyword that is
inconsistent with the :doc:`atom style <atom_style>` used.
Such a mismatch can happen unexpectedly when the first line of the data
is *not* a comment as required by the format. That would result in
LAMMPS expecting, for instance, 0 atoms because the "atoms" header line
is treated as a comment.
The header section informs LAMMPS how many entries or lines are expected
in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of
the data file. If there is a mismatch, LAMMPS will either keep reading
beyond the end of a section or stop reading before the section has
ended. In that case the next line will not contain a recognized keyword.
Such a mismatch can also happen when the first line of the data
is *not* a comment as required by the format, but a line with a valid
header keyword. That would result in LAMMPS expecting, for instance,
0 atoms because the "atoms" header line is the first line and thus
treated as a comment.
Another possibility to trigger this error is to have a keyword in the
data file that corresponds to a fix (e.g. :doc:`fix cmap <fix_cmap>`)
but the :doc:`read_data <read_data>` command is missing the (optional)
arguments that identify the fix and the header keyword and section
keyword or those arguments are inconsistent with the keywords in the
data file.
.. _err0002:
Incorrect format in ... section of data file
--------------------------------------------
This error happens when LAMMPS reads the contents of a section of a
:doc:`data file <read_data>` and the number of parameters in the line
differs from what is expected. This most commonly happens, when the
atom style is different from what is expected for a specific data file
since changing the atom style usually changes the format of the line.
This error can also happen when the number of entries indicated in the
header of a data file (e.g. the number of atoms) is larger than the
number of lines provided (e.g. in the corresponding Atoms section)
and then LAMMPS will continue reading into the next section and that
would have a completely different format.

6
doc/src/Errors_messages.rst
View File

@ -7883,12 +7883,6 @@ keyword to allow for additional bonds to be formed
Fix poems cannot (yet) work with coupled bodies whose joints connect
the bodies in a tree structure.
*Triclinic box skew is too large*
The displacement in a skewed direction must be less than half the box
length in that dimension. E.g. the xy tilt must be between -half and
+half of the x box length. This constraint can be relaxed by using
the box tilt command.
*Tried to convert a double to int, but input_double > INT_MAX*
Self-explanatory.

7
doc/src/Errors_warnings.rst
View File

@ -752,13 +752,6 @@ This will most likely cause errors in kinetic fluctuations.
More than the maximum # of neighbors was found multiple times. This
was unexpected.
*Triclinic box skew is large*
The displacement in a skewed direction is normally required to be less
than half the box length in that dimension. E.g. the xy tilt must be
between -half and +half of the x box length. You have relaxed the
constraint using the box tilt command, but the warning means that a
LAMMPS simulation may be inefficient as a result.
*Use special bonds = 0,1,1 with bond style fene*
Most FENE models need this setting for the special_bonds command.

4
doc/src/Fortran.rst
View File

@ -1255,8 +1255,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
three elements of the global vector calculated by fix recenter into the
variables *dx*, *dy*, and *dz*, respectively.
If asked for per-atom or local data, :f:func:`extract_compute` returns a
pointer to actual LAMMPS data. The pointer so returned will have the
If asked for per-atom or local data, :f:func:`extract_fix` returns a
pointer to actual LAMMPS data. The pointer returned will have the
appropriate size to match the internal data, and will be
type/kind/rank-checked at the time of the assignment. For example,

124
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@ -1,42 +1,112 @@
2d simulations
==============
================
2d simulations
================
Use the :doc:`dimension <dimension>` command to specify a 2d simulation.
You must use the :doc:`dimension <dimension>` command to specify a 2d
simulation. The default is 3d.
Make the simulation box periodic in z via the :doc:`boundary <boundary>`
command. This is the default.
A 2d simulation box must be periodic in z as set by the :doc:`boundary
<boundary>` command. This is the default.
If using the :doc:`create_box <create_box>` command to define a
simulation box, set the z dimensions narrow, but finite, so that the
:doc:`create_atoms <create_atoms>` command will fill the 3d simulation
box with a single z plane of atoms - e.g.
Simulation boxes in LAMMPS can be either orthogonal or triclinic in
shape. Orthogonal boxes in 2d are a rectangle with 4 edges that are
each perpendicular to either the x or y coordinate axes. Triclinic
boxes in 2d are a parallelogram with opposite pairs of faces parallel
to each other. LAMMPS supports two forms of triclinic boxes,
restricted and general, which for 2d differ in how the box is oriented
with respect to the xy coordinate axes. See the :doc:`Howto triclinic
<Howto_triclinic>` for a detailed description of all 3 kinds of
simulation boxes.
Here are examples of using the :doc:`create_box <create_box>` command
to define the simulation box for a 2d system.
.. code-block:: LAMMPS
create_box 1 -10 10 -10 10 -0.25 0.25
# 2d orthogonal box using a block-style region
region mybox block -10 10 0 10 -0.5 0.5
create_box 1 mybox
If using the :doc:`read_data <read_data>` command to read in a file of
atom coordinates, set the "zlo zhi" values to be finite but narrow,
similar to the create_box command settings just described. For each
atom in the file, assign a z coordinate so it falls inside the
z-boundaries of the box - e.g. 0.0.
# 2d restricted triclinic box using a prism-style region with only xy tilt
region mybox prism 0 10 0 10 -0.5 0.5 2.0 0.0 0.0
create_box 1 mybox
Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last
defined fix to ensure that the z-components of velocities and forces
are zeroed out every timestep. The reason to make it the last fix is
so that any forces induced by other fixes will be zeroed out.
# 2d general triclinic box using a primitive cell for a 2d hex lattice
lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 &
a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
create_box 1 NULL 0 5 0 5 -0.5 0.5
Many of the example input scripts included in the LAMMPS distribution
Note that for 2d orthogonal or restricted triclinic boxes, the box has
a 3rd dimension which must straddle z = 0.0 in the z dimension.
Typically the width of box in the z dimension should be narrow,
e.g. -0.5 to 0.5, but that is not required. For a 2d general
triclinic box, the *a3* vector defined by the :doc:`lattice <lattice>`
command must be (0.0,0.0,1.0), which is its default value. Also the
*clo* and *chi* arguments of the :doc:`create_box <create_box>`
command must be -0.5 and 0.5.
Here are examples of using the :doc:`read_data <read_data>` command
to define the simulation box for a 2d system via keywords in the
header section of the data file. These are the same boxes as the examples
for the :doc:`create_box <create_box>` command
.. code-block:: LAMMPS
# 2d orthogonal box
-10 10 xlo xhi
0 10 ylo yhi
-0.5 0.5 zlo zhi # this is the default, so no need to specify
# 2d restricted triclinic box with only xy tilt
-10 10 xlo xhi
0 10 ylo yhi
-0.5 0.5 zlo zhi # this is the default, so no need to specify
2.0 0.0 0.0 xy xz yz
# 3d general triclinic box using a primitive cell for a 2d hex lattice
5 0 0 avec
2.5 4.3301270189 0 bvec
0 0 1 cvec # this is the default, so no need to specify
0 0 -0.5 abc origin # this is the default for 2d, so no need to specify
Note that for 2d orthogonal or restricted triclinic boxes, the box has
a 3rd dimension specified by the *zlo zhi* values, which must straddle
z = 0.0. Typically the width of box in the z dimension should be
narrow, e.g. -0.5 to 0.5, but that is not required. For a 2d general
triclinic box, the z component of *avec* and *bvec* must be zero, and
*cvec* must be (0,0,1), which is the default. The z component of *abc
origin* must also be -0.5, which is the default.
If using the :doc:`create_atoms <create_atoms>` command to create
atoms in the 2d simulation box, all the z coordinates of created atoms
will be zero.
If using the :doc:`read_data <read_data>` command to read in a data
file of atom coordinates for a 2d system, the z coordinates of all
atoms should be zero. A value within epsilon of zero is also allowed
in case the data file was generated by another program with finite
numeric precision, in which case the z coord for the atom will be set
to zero.
Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last fix
defined in the input script. It ensures that the z-components of
velocities and forces are zeroed out every timestep. The reason to
make it the last fix is so that any forces added by other fixes will
also be zeroed out.
Many of the example input scripts included in the examples directory
are for 2d models.
.. note::
Some models in LAMMPS treat particles as finite-size spheres, as
opposed to point particles. See the :doc:`atom_style sphere <atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>`
commands for details. By default, for 2d simulations, such particles
will still be modeled as 3d spheres, not 2d discs (circles), meaning
opposed to point particles. See the :doc:`atom_style sphere
<atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>` commands
for details. By default, for 2d simulations, such particles will
still be modeled as 3d spheres, not 2d discs (circles), meaning
their moment of inertia will be that of a sphere. If you wish to
model them as 2d discs, see the :doc:`set density/disc <set>` command
and the *disc* option for the :doc:`fix nve/sphere <fix_nve_sphere>`,
:doc:`fix nvt/sphere <fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>`
commands.
model them as 2d discs, see the :doc:`set density/disc <set>`
command and the *disc* option for the :doc:`fix nve/sphere
<fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
<fix_npt_sphere>` commands.

33
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@ -102,8 +102,19 @@ particles of different styles
| :doc:`dump image <dump_image>` | output body particle attributes as an image |
+------------------------------------------------+-----------------------------------------------------+
The pair styles defined for use with specific body styles are listed
in the sections below.
The pair styles currently defined for use with specific body styles
are listed in the sections below.
Note that for all the body styles, if the data file defines a general
triclinic box, then the orientation of the body particle and its
corresponding 6 moments of inertia and other orientation-dependent
values should reflect the fact the body is defined withing a general
triclinic box with edge vectors **A**,**B**,**C**. LAMMPS will rotate
the box to convert it to a restricted triclinic box. This operation
will also rotate the orientation of the body particles. See the
:doc:`Howto triclinic <Howto_triclinic>` doc page for more details.
The sections below highlight the orientation-dependent values specific
to each body style.
----------
@ -154,12 +165,18 @@ values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each sub-particle are specified as its x,y,z
displacement from the center-of-mass of the body particle. The
center-of-mass position of the particle is specified by the x,y,z
values in the *Atoms* section of the data file, as is the total mass
of the body particle.
Note that if the data file defines a general triclinic simulation box,
these sub-particle displacements are orientation-dependent and, as
mentioned above, should reflect the body particle's orientation within
the general triclinic box.
The :doc:`pair_style body/nparticle <pair_body_nparticle>` command can be used
with this body style to compute body/body and body/non-body interactions.
@ -226,6 +243,7 @@ values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each vertex are specified as its x,y,z displacement
from the center-of-mass of the body particle. The center-of-mass
position of the particle is specified by the x,y,z values in the
@ -270,6 +288,11 @@ A disk, whose diameter is 3.0, mass 1.0, is specified as follows:
0 0 0
3.0
Note that if the data file defines a general triclinic simulation box,
these polygon vertex displacements are orientation-dependent and, as
mentioned above, should reflect the body particle's orientation within
the general triclinic box.
The :doc:`pair_style body/rounded/polygon <pair_body_rounded_polygon>`
command can be used with this body style to compute body/body
interactions. The :doc:`fix wall/body/polygon <fix_wall_body_polygon>`
@ -366,6 +389,7 @@ values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the principal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each vertex are specified as its x,y,z displacement
from the center-of-mass of the body particle. The center-of-mass
position of the particle is specified by the x,y,z values in the
@ -435,6 +459,11 @@ A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
The number of edges and faces for a rod or sphere must be listed,
but is ignored.
Note that if the data file defines a general triclinic simulation box,
these polyhedron vertex displacements are orientation-dependent and,
as mentioned above, should reflect the body particle's orientation
within the general triclinic box.
The :doc:`pair_style body/rounded/polhedron
<pair_body_rounded_polyhedron>` command can be used with this body
style to compute body/body interactions. The :doc:`fix

9
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@ -15,7 +15,8 @@ orientation for rotational models. This produces a stress-free initial
state. Furthermore, bonds are allowed to break under large strains,
producing fracture. The examples/bpm directory has sample input scripts
for simulations of the fragmentation of an impacted plate and the
pouring of extended, elastic bodies.
pouring of extended, elastic bodies. See :ref:`(Clemmer) <howto-Clemmer>`
for more general information on the approach and the LAMMPS implementation.
----------
@ -150,3 +151,9 @@ the following are currently compatible with BPM bond styles:
interactions, one will need to switch between different *special_bonds*
settings in the input script. An example is found in
``examples/bpm/impact``.
----------
.. _howto-Clemmer:
**(Clemmer)** Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).

5
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@ -45,10 +45,15 @@ atoms, and should be used for granular system instead of the fix style
To model heat conduction, one must add the temperature and heatflow
atom variables with:
* :doc:`fix property/atom <fix_property_atom>`
a temperature integration fix
* :doc:`fix heat/flow <fix_heat_flow>`
and a heat conduction option defined in both
* :doc:`pair_style granular <pair_granular>`
* :doc:`fix wall/gran <fix_wall_gran>`

431
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@ -2,43 +2,195 @@ Triclinic (non-orthogonal) simulation boxes
===========================================
By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The :doc:`boundary <boundary>` command sets the boundary
conditions of the box (periodic, non-periodic, etc). The orthogonal
box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
starting from the origin given by **a** = (xhi-xlo,0,0); **b** =
(0,yhi-ylo,0); **c** = (0,0,zhi-zlo). The 6 parameters
particles. The orthogonal box has its "origin" at (xlo,ylo,zlo) and
extends to (xhi,yhi,zhi). Conceptually it is defined by 3 edge
vectors starting from the origin given by **A** = (xhi-xlo,0,0); **B**
= (0,yhi-ylo,0); **C** = (0,0,zhi-zlo). The :doc:`boundary
<boundary>` command sets the boundary conditions for the 6 faces of
the box (periodic, non-periodic, etc). The 6 parameters
(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
is created, e.g. by the :doc:`create_box <create_box>` or
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
parameters, as well as lx,ly,lz, can be output via the
:doc:`thermo_style custom <thermo_style>` command.
is created by one of these commands:
LAMMPS also allows simulations to be performed in triclinic
(non-orthogonal) simulation boxes shaped as a parallelepiped with
triclinic symmetry. The parallelepiped has its "origin" at
(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
origin given by **a** = (xhi-xlo,0,0); **b** = (xy,yhi-ylo,0); **c** =
(xz,yz,zhi-zlo). *xy,xz,yz* can be 0.0 or positive or negative values
and are called "tilt factors" because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped. In LAMMPS the triclinic
simulation box edge vectors **a**, **b**, and **c** cannot be arbitrary
vectors. As indicated, **a** must lie on the positive x axis. **b** must
lie in the xy plane, with strictly positive y component. **c** may have
any orientation with strictly positive z component. The requirement
that **a**, **b**, and **c** have strictly positive x, y, and z components,
respectively, ensures that **a**, **b**, and **c** form a complete
right-handed basis. These restrictions impose no loss of generality,
since it is possible to rotate/invert any set of 3 crystal basis
vectors so that they conform to the restrictions.
* :doc:`create_box <create_box>`
* :doc:`read_data <read_data>`
* :doc:`read_restart <read_restart>`
* :doc:`read_dump <read_dump>`
For example, assume that the 3 vectors **A**,\ **B**,\ **C** are the edge
vectors of a general parallelepiped, where there is no restriction on
**A**,\ **B**,\ **C** other than they form a complete right-handed basis i.e.
**A** x **B** . **C** > 0. The equivalent LAMMPS **a**,\ **b**,\ **c** are a linear
rotation of **A**, **B**, and **C** and can be computed as follows:
Internally, LAMMPS defines box size parameters lx,ly,lz where lx =
xhi-xlo, and similarly in the y and z dimensions. The 6 parameters, as
well as lx,ly,lz, can be output via the :doc:`thermo_style custom
<thermo_style>` command. See the :doc:`Howto 2d <Howto_2d>` doc page
for info on how zlo and zhi are defined for 2d simulations.
----------
Triclinic simulation boxes
""""""""""""""""""""""""""
LAMMPS also allows simulations to be performed using triclinic
(non-orthogonal) simulation boxes shaped as a 3d parallelepiped with
triclinic symmetry. For 2d simulations a triclinic simulation box is
effectively a parallelogram; see the :doc:`Howto 2d <Howto_2d>` doc
page for details.
One use of triclinic simulation boxes is to model solid-state crystals
with triclinic symmetry. The :doc:`lattice <lattice>` command can be
used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the :doc:`create_atoms
<create_atoms>` command.
A second use is to run Parrinello-Rahman dynamics via the :doc:`fix
npt <fix_nh>` command, which will adjust the xy, xz, yz tilt factors
to compensate for off-diagonal components of the pressure tensor. The
analog for an :doc:`energy minimization <minimize>` is the :doc:`fix
box/relax <fix_box_relax>` command.
A third use is to shear a bulk solid to study the response of the
material. The :doc:`fix deform <fix_deform>` command can be used for
this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the :doc:`Howto
NEMD <Howto_nemd>` doc page on non-equilibrium MD (NEMD) simulations.
Conceptually, a triclinic parallelepiped is defined with an "origin"
at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** =
(bx,by,bz), **C** = (cx,cy,cz) which can be arbitrary vectors, so long
as they are non-zero, distinct, and not co-planar. In addition, they
must define a right-handed system, such that (**A** cross **B**)
points in the direction of **C**. Note that a left-handed system can
be converted to a right-handed system by simply swapping the order of
any pair of the **A**, **B**, **C** vectors.
The 4 commands listed above for defining orthogonal simulation boxes
have triclinic options which allow for specification of the origin and
edge vectors **A**, **B**, **C**. For each command, this can be done
in one of two ways, for what LAMMPS calls a *general* triclinic box or
a *restricted* triclinic box.
A *general* triclinic box is specified by an origin (xlo, ylo, zlo)
and arbitrary edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), and
**C** = (cx,cy,cz). So there are 12 parameters in total.
A *restricted* triclinic box also has an origin (xlo,ylo,zlo), but its
edge vectors are of the following restricted form: **A** =
(xhi-xlo,0,0), **B** = (xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So
there are 9 parameters in total. Note that the restricted form
requires **A** to be along the x-axis, **B** to be in the xy plane
with a y-component in the +y direction, and **C** to have its
z-component in the +z direction. Note that a restricted triclinic box
is *right-handed* by construction since (**A** cross **B**) points in
the direction of **C**.
The *xy,xz,yz* values can be zero or positive or negative. They are
called "tilt factors" because they are the amount of displacement
applied to edges of faces of an orthogonal box to change it into a
restricted triclinic parallelepiped.
.. note::
Any right-handed general triclinic box (i.e. solid-state crystal
basis vectors) can be rotated in 3d around its origin in order to
conform to the LAMMPS definition of a restricted triclinic box.
See the discussion in the next sub-section about general triclinic
simulation boxes in LAMMPS.
Note that the :doc:`thermo_style custom <thermo_style>` command has
keywords for outputting the various parameters that define the size
and shape of orthogonal, restricted triclinic, and general triclinic
simulation boxes.
For orthogonal boxes there 6 thermo keywords (xlo,ylo,zlo) and
(xhi,yhi,zhi).
For restricted triclinic boxes there are 9 thermo keywords for
(xlo,ylo,zlo), (xhi,yhi,zhi), and the (xy,xz,yz) tilt factors.
For general triclinic boxes there are 12 thermo keywords for
(xlo,ylo,zhi) and the components of the **A**, **B**, **C** edge
vectors, namely (avecx,avecy,avecz), (bvecx,bvecy,bvecz), and
(cvecx,cvecy,cvecz),
The remainder of this doc page explains (a) how LAMMPS operates with
general triclinic simulation boxes, (b) mathematical transformations
between general and restricted triclinic boxes which may be useful
when creating LAMMPS inputs or interpreting outputs for triclinic
simulations, and (c) how LAMMPS uses tilt factors for restricted
triclinic simulation boxes.
----------
General triclinic simulation boxes in LAMMPS
""""""""""""""""""""""""""""""""""""""""""""
LAMMPS allows specification of general triclinic simulation boxes with
their atoms as a convenience for users who may be converting data from
solid-state crystallographic representations or from DFT codes for
input to LAMMPS. Likewise it allows output of dump files, data files,
and thermodynamic data (e.g. pressure tensor) in a general triclinic
format.
However internally, LAMMPS only uses restricted triclinic simulation
boxes. This is for parallel efficiency and to formulate partitioning
of the simulation box across processors, neighbor list building, and
inter-processor communication of per-atom data with methods similar to
those used for orthogonal boxes.
This means 4 things which are important to understand:
* Input of a general triclinic system is immediately converted to a
restricted triclinic system.
* If output of per-atom data for a general triclinic system is
requested (e.g. for atom coordinates in a dump file),
conversion from a restricted to general triclinic system is done at
the time of output.
* The conversion of the simulation box and per-atom data from general
triclinic to restricted triclinic (and vice versa) is a 3d rotation
operation around an origin, which is the lower left corner of the
simulation box. This means an input data file for a general
triclinic system should specify all per-atom quantities consistent
with the general triclinic box and its orientation relative to the
standard x,y,z coordinate axes. For example, atom coordinates
should be inside the general triclinic simulation box defined by the
edge vectors **A**, **B**, **C** and its origin. Likewise per-atom
velocities should be in directions consistent with the general
triclinic box orientation. E.g. a velocity vector which will be in
the +x direction once LAMMPS converts from a general to restricted
triclinic box, should be specified in the data file in the direction
of the **A** edge vector. See the :doc:`read_data <read_data>` doc
page for info on all the per-atom vector quantities to which this
rule applies when a data file for a general triclinic box is input.
* If commands such as :doc:`write_data <write_data>` or :doc:`dump
custom <dump>` are used to output general triclinic information, it
is effectively the inverse of the operation described in the
preceding bullet.
* Other LAMMPS commands such as :doc:`region <region>` or
:doc:`velocity <velocity>` or :doc:`set <set>`, operate on a
restricted triclinic system even if a general triclinic system was
defined initially.
This is the list of commands which have general triclinic options:
* :doc:`create_box <create_box>` - define a general triclinic box
* :doc:`create_atoms <create_atoms>` - add atoms to a general triclinic box
* :doc:`lattice <lattice>` - define a custom lattice consistent with the **A**, **B**, **C** edge vectors of a general triclinic box
* :doc:`read_data <read_data>` - read a data file for a general triclinic system
* :doc:`write_data <write_data>` - write a data file for a general triclinic system
* :doc:`dump atom, dump custom <dump>` - output dump snapshots in general triclinic format
* :doc:`dump_modify triclinic/general <dump_modify>` - select general triclinic format for dump output
* :doc:`thermo_style <thermo_style>` - output the pressure tensor in
general triclinic format
* :doc:`thermo_modify triclinic/general <thermo_modify>` - select general triclinic format for thermo output
* :doc:`read_restart <read_restart>` - read a restart file for a general triclinic system
* :doc:`write_restart <read_restart>` - write a restart file for a general triclinic system
----------
Transformation from general to restricted triclinic boxes
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Let **A**,\ **B**,\ **C** be the right-handed edge vectors of a
general triclinic simulation box. The equivalent LAMMPS **a**,\
**b**,\ **c** for a restricted triclinic box are a 3d rotation of
**A**, **B**, and **C** and can be computed as follows:
.. math::
@ -55,23 +207,17 @@ rotation of **A**, **B**, and **C** and can be computed as follows:
c_y = & \mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})} \times \mathbf{\hat{A}} \quad = \quad \frac{\mathbf{B} \cdot \mathbf{C} - b_x c_x}{b_y} \\
c_z = & |\mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})}|\quad = \quad \sqrt{C^2 - {c_x}^2 - {c_y}^2}
where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^)
indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles
between the vectors described below. Note that by construction,
**a**, **b**, and **c** have strictly positive x, y, and z components, respectively.
If it should happen that
**A**, **B**, and **C** form a left-handed basis, then the above equations
are not valid for **c**\ . In this case, it is necessary
to first apply an inversion. This can be achieved
by interchanging two basis vectors or by changing the sign of one of them.
where A = \| **A** \| indicates the scalar length of **A**\ . The hat
symbol (\^) indicates the corresponding unit vector. :math:`\beta` and
:math:`\gamma` are angles between the **A**, **B**, **C** vectors
as described below.
For consistency, the same rotation/inversion applied to the basis vectors
must also be applied to atom positions, velocities,
and any other vector quantities.
This can be conveniently achieved by first converting to
fractional coordinates in the
old basis and then converting to distance coordinates in the new basis.
The transformation is given by the following equation:
For consistency, the same rotation applied to the triclinic box edge
vectors can also be applied to atom positions, velocities, and other
vector quantities. This can be conveniently achieved by first
converting to fractional coordinates in the general triclinic
coordinates and then converting to coordinates in the restricted
triclinic basis. The transformation is given by the following equation:
.. math::
@ -82,87 +228,24 @@ The transformation is given by the following equation:
\mathbf{A \times B}
\end{pmatrix} \cdot \mathbf{X}
where *V* is the volume of the box, **X** is the original vector quantity and
**x** is the vector in the LAMMPS basis.
where *V* is the volume of the box (same in either basis), **X** is
the fractional vector in the general triclinic basis and **x** is the
resulting vector in the restricted triclinic basis.
There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in at least the second dimension
of the tilt (y in xy) if you want to enforce a shift in periodic
boundary conditions across that boundary. Some commands that work
with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap
boundary conditions in specific dimensions. See the command doc pages
for details.
----------
The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
time the simulation box is created. This happens in one of 3 ways.
If the :doc:`create_box <create_box>` command is used with a region of
style *prism*, then a triclinic box is setup. See the
:doc:`region <region>` command for details. If the
:doc:`read_data <read_data>` command is used to define the simulation
box, and the header of the data file contains a line with the "xy xz
yz" keyword, then a triclinic box is setup. See the
:doc:`read_data <read_data>` command for details. Finally, if the
:doc:`read_restart <read_restart>` command reads a restart file which
was written from a simulation using a triclinic box, then a triclinic
box will be setup for the restarted simulation.
Crystallographic general triclinic representation of a simulation box
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Note that you can define a triclinic box with all 3 tilt factors =
0.0, so that it is initially orthogonal. This is necessary if the box
will become non-orthogonal, e.g. due to the :doc:`fix npt <fix_nh>` or
:doc:`fix deform <fix_deform>` commands. Alternatively, you can use the
:doc:`change_box <change_box>` command to convert a simulation box from
orthogonal to triclinic and vice versa.
As with orthogonal boxes, LAMMPS defines triclinic box size parameters
lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
The 9 parameters, as well as lx,ly,lz, can be output via the
:doc:`thermo_style custom <thermo_style>` command.
To avoid extremely tilted boxes (which would be computationally
inefficient), LAMMPS normally requires that no tilt factor can skew
the box more than half the distance of the parallel box length, which
is the first dimension in the tilt factor (x for xz). This is required
both when the simulation box is created, e.g. via the
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands,
as well as when the box shape changes dynamically during a simulation,
e.g. via the :doc:`fix deform <fix_deform>` or :doc:`fix npt <fix_nh>`
commands.
For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
the xy tilt factor must be between -5 and 5. Similarly, both xz and
yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
not a limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are geometrically all equivalent. If the box tilt exceeds this
limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
command), then the box is "flipped" to an equivalent shape with a tilt
factor within the bounds, so the run can continue. See the :doc:`fix deform <fix_deform>` page for further details.
One exception to this rule is if the first dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.
Box flips that may occur using the :doc:`fix deform <fix_deform>` or
:doc:`fix npt <fix_nh>` commands can be turned off using the *flip no*
option with either of the commands.
Note that if a simulation box has a large tilt factor, LAMMPS will run
less efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor's irregular-shaped subdomain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.
Triclinic crystal structures are often defined using three lattice
constants *a*, *b*, and *c*, and three angles :math:`\alpha`,
:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature,
the a, b, and c lattice constants are the scalar lengths of the edge
General triclinic crystal structures are often defined using three
lattice constants *a*, *b*, and *c*, and three angles :math:`\alpha`,
:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, the
a, b, and c lattice constants are the scalar lengths of the edge
vectors **a**, **b**, and **c** defined above. The relationship
between these 6 quantities (a, b, c, :math:`\alpha`, :math:`\beta`,
:math:`\gamma`) and the LAMMPS box sizes (lx,ly,lz) =
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
:math:`\gamma`) and the LAMMPS restricted triclinic box sizes
(lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is
as follows:
.. math::
@ -186,15 +269,19 @@ The inverse relationship can be written as follows:
The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
:math:`\gamma` can be printed out or accessed by computes using the
:doc:`thermo_style custom <thermo_style>` keywords
*cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma*,
respectively.
:doc:`thermo_style custom <thermo_style>` keywords *cella*, *cellb*,
*cellc*, *cellalpha*, *cellbeta*, *cellgamma*, respectively.
----------
Output of restricted and general triclinic boxes in a dump file
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
As discussed on the :doc:`dump <dump>` command doc page, when the BOX
BOUNDS for a snapshot is written to a dump file for a triclinic box,
an orthogonal bounding box which encloses the triclinic simulation box
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
box, formatted as follows:
BOUNDS for a snapshot is written to a dump file for a restricted
triclinic box, an orthogonal bounding box which encloses the triclinic
simulation box is output, along with the 3 tilt factors (xy, xz, yz) of
the restricted triclinic box, formatted as follows:
.. parsed-literal::
@ -204,7 +291,7 @@ box, formatted as follows:
zlo_bound zhi_bound yz
This bounding box is convenient for many visualization programs and is
calculated from the 9 triclinic box parameters
calculated from the 9 restricted triclinic box parameters
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
.. parsed-literal::
@ -217,22 +304,66 @@ calculated from the 9 triclinic box parameters
zhi_bound = zhi
These formulas can be inverted if you need to convert the bounding box
back into the triclinic box parameters, e.g. xlo = xlo_bound -
MIN(0.0,xy,xz,xy+xz).
back into the restricted triclinic box parameters, e.g. xlo =
xlo_bound - MIN(0.0,xy,xz,xy+xz).
One use of triclinic simulation boxes is to model solid-state crystals
with triclinic symmetry. The :doc:`lattice <lattice>` command can be
used with non-orthogonal basis vectors to define a lattice that will
tile a triclinic simulation box via the
:doc:`create_atoms <create_atoms>` command.
----------
A second use is to run Parrinello-Rahman dynamics via the :doc:`fix npt <fix_nh>` command, which will adjust the xy, xz, yz tilt
factors to compensate for off-diagonal components of the pressure
tensor. The analog for an :doc:`energy minimization <minimize>` is
the :doc:`fix box/relax <fix_box_relax>` command.
Periodicity and tilt factors for triclinic simulation boxes
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
A third use is to shear a bulk solid to study the response of the
material. The :doc:`fix deform <fix_deform>` command can be used for
this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the next section
on non-equilibrium MD (NEMD) simulations.
There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in y or z if you wish to
enforce a shift in coordinates due to periodic boundary conditions
across the y or z boundaries. See the doc page for the :doc:`boundary
<boundary>` command for an explanation of shifted coordinates for
restricted triclinic boxes which are periodic.
Some commands that work with triclinic boxes, e.g. the :doc:`fix
deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require
periodicity or non-shrink-wrap boundary conditions in specific
dimensions. See the command doc pages for details.
A restricted triclinic box can be defined with all 3 tilt factors =
0.0, so that it is initially orthogonal. This is necessary if the box
will become non-orthogonal, e.g. due to use of the :doc:`fix npt
<fix_nh>` or :doc:`fix deform <fix_deform>` commands. Alternatively,
you can use the :doc:`change_box <change_box>` command to convert a
simulation box from orthogonal to restricted triclinic and vice versa.
.. note::
Highly tilted restricted triclinic simulation boxes can be
computationally inefficient. This is due to the large volume of
communication needed to acquire ghost atoms around a processor's
irregular-shaped subdomain. For extreme values of tilt, LAMMPS may
also lose atoms and generate an error.
LAMMPS will issue a warning if you define a restricted triclinic box
with a tilt factor which skews the box more than half the distance of
the parallel box length, which is the first dimension in the tilt
factor (e.g. x for xz).
For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
the xy tilt factor should be between -5 and 5 to avoid the warning.
Similarly, both xz and yz should be between -(xhi-xlo)/2 and
+(yhi-ylo)/2. Note that these are not limitations, since if the
maximum tilt factor is 5 (as in this example), then simulations boxes
and atom configurations with tilt = ..., -15, -5, 5, 15, 25, ... are
all geometrically equivalent.
If the box tilt exceeds this limit during a dynamics run (e.g. due to
the :doc:`fix deform <fix_deform>` command), then by default the box
is "flipped" to an equivalent shape with a tilt factor within the
warning bounds, and the run continues. See the :doc:`fix deform
<fix_deform>` page for further details. Box flips that would normally
occur using the :doc:`fix deform <fix_deform>` or :doc:`fix npt
<fix_nh>` commands can be suppressed using the *flip no* option with
either of the commands.
One exception to box flipping is if the first dimension in the tilt
factor (e.g. x for xy) is non-periodic. In that case, the limits on
the tilt factor are not enforced, since flipping the box in that
dimension would not change the atom positions due to non-periodicity.
In this mode, if the system tilts to large angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.

25
doc/src/Howto_type_labels.rst
View File

@ -14,16 +14,17 @@ wherever they appear in LAMMPS input or output files. The total number
Ntypes for each interaction is "locked in" when the simulation box
is created.
A recent addition to LAMMPS is the option to use strings - referred
to as type labels - as an alternative. Using type labels instead of
A recent addition to LAMMPS is the option to use strings - referred to
as type labels - as an alternative. Using type labels instead of
numeric types can be advantageous in various scenarios. For example,
type labels can make inputs more readable and generic (i.e. usable through
the :doc:`include command <include>` for different systems with different
numerical values assigned to types. This generality also applies to
other inputs like data files read by :doc:`read_data <read_data>` or
molecule template files read by the :doc:`molecule <molecule>`
command. See below for a list of other commands that can use
type labels in different ways.
type labels can make inputs more readable and generic (i.e. usable
through the :doc:`include command <include>` for different systems with
different numerical values assigned to types. This generality also
applies to other inputs like data files read by :doc:`read_data
<read_data>` or molecule template files read by the :doc:`molecule
<molecule>` command. A discussion of the current type label support can
be found in :ref:`(Gissinger) <Typelabel24>`. See below for a list of
other commands that can use type labels in different ways.
LAMMPS will *internally* continue to use numeric types, which means
that many previous restrictions still apply. For example, the total
@ -124,3 +125,9 @@ between the files. The creation of simulation-ready reaction templates
for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
type labels, and results in templates that can be used without
modification in multiple simulations or different systems.
-----------
.. _Typelabel24:
**(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).

2
doc/src/Intro_citing.rst
View File

@ -47,6 +47,8 @@ In addition there are DOIs generated for individual stable releases:
- 3 March 2020 version: `DOI:10.5281/zenodo.3726417 <https://dx.doi.org/10.5281/zenodo.3726417>`_
- 29 October 2020 version: `DOI:10.5281/zenodo.4157471 <https://dx.doi.org/10.5281/zenodo.4157471>`_
- 29 September 2021 version: `DOI:10.5281/zenodo.6386596 <https://dx.doi.org/10.5281/zenodo.6386596>`_
- 23 June 2022 version: `DOI:10.5281/zenodo.10806836 <https://doi.org/10.5281/zenodo.10806836>`_
- 2 August 2023 version: `DOI:10.5281/zenodo.10806852 <https://doi.org/10.5281/zenodo.10806852>`_
Home page
^^^^^^^^^

4
doc/src/Intro_features.rst
View File

@ -29,7 +29,7 @@ General features
* spatial decomposition of simulation domain for MPI parallelism
* particle decomposition inside spatial decomposition for OpenMP and GPU parallelism
* GPLv2 licensed open-source distribution
* highly portable C++-11
* highly portable C++-11 (optional packages may require C++17)
* modular code with most functionality in optional packages
* only depends on MPI library for basic parallel functionality, MPI stub for serial compilation
* other libraries are optional and only required for specific packages
@ -81,7 +81,7 @@ commands)
* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, Class II (COMPASS), hydrogen bond, harmonic, gaussian, tabulated, scripted
* charged pairwise potentials: Coulombic, point-dipole
* many-body potentials: EAM, Finnis/Sinclair, MEAM, MEAM+SW, EIM, EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, Streitz-Mintmire, 3-body polymorphic, BOP, Vashishta
* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN
* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN, SNAP
* interfaces to ML potentials distributed by external groups: ANI, ChIMES, DeepPot, HIPNN, MTP
* long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM, ScaFaCoS
* polarization models: :doc:`QEq <fix_qeq>`, :doc:`core/shell model <Howto_coreshell>`, :doc:`Drude dipole model <Howto_drude>`

17
doc/src/Python_scatter.rst
View File

@ -54,8 +54,21 @@ like this:
x[3] = x coord of atom with ID 2
...
x[n3-1] = z coord of atom with ID natoms
lmp.scatter_atoms("x",1,3,x)
lmp.scatter_atoms("x", 1, 3, x)
The coordinates can also be provided as arguments to the initializer of x:
.. code-block:: python
from ctypes import c_double
natoms = 2
n3 = 3*natoms
# init in constructor
x = (n3*c_double)(0.0, 0.0, 0.0, 1.0, 1.0, 1.0)
lmp.scatter_atoms("x", 1, 3, x)
# or using a list
coords = [1.0, 2.0, 3.0, -3.0, -2.0, -1.0]
x = (c_double*len(coords))(*coords)
Alternatively, you can just change values in the vector returned by
the gather methods, since they are also ctypes vectors.

64
doc/src/Speed_kokkos.rst
View File

@ -20,11 +20,28 @@ including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
(Sandia). For more information on developing using Kokkos abstractions
see the `Kokkos Wiki <https://github.com/kokkos/kokkos/wiki>`_.
Kokkos currently provides support for 4 modes of execution (per MPI
.. note::
The Kokkos library is under active development and tracking the
availability of accelerator hardware, so is the KOKKOS package in
LAMMPS. This means that only a certain range of versions of the
Kokkos library are compatible with the KOKKOS package of a certain
range of LAMMPS versions. For that reason LAMMPS comes with a
bundled version of the Kokkos library that has been validated on
multiple platforms and may contain selected back-ported bug fixes
from upstream Kokkos versions. While it is possible to build LAMMPS
with an external version of Kokkos, it is untested and may result in
incorrect execution or crashes.
Kokkos currently provides full support for 4 modes of execution (per MPI
task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA
GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
produce an executable compatible with a specific hardware.
(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA GPUs) and
HIP (for AMD GPUs). Additional modes (e.g. OpenMP target, Intel data
center GPUs) are under development. You choose the mode at build time
to produce an executable compatible with a specific hardware.
The following compatibility notes have been last updated for LAMMPS
version 23 November 2023 and Kokkos version 4.2.
.. admonition:: C++17 support
:class: note
@ -54,22 +71,22 @@ produce an executable compatible with a specific hardware.
:class: note
Kokkos with CUDA currently implicitly assumes that the MPI library is
GPU-aware. This is not always the case, especially when using
GPU-aware. This is not always the case, especially when using
pre-compiled MPI libraries provided by a Linux distribution. This is
not a problem when using only a single GPU with a single MPI
rank. When running with multiple MPI ranks, you may see segmentation
rank. When running with multiple MPI ranks, you may see segmentation
faults without GPU-aware MPI support. These can be avoided by adding
the flags :doc:`-pk kokkos gpu/aware off <Run_options>` to the
LAMMPS command line or by using the command :doc:`package kokkos
gpu/aware off <package>` in the input file.
.. admonition:: AMD GPU support
.. admonition:: Intel Data Center GPU support
:class: note
To build with Kokkos the HIPCC compiler from the AMD ROCm software
version 3.5 or later is required. Supporting this Kokkos mode in
LAMMPS is still work in progress. Please contact the LAMMPS developers
if you run into problems.
Support for Kokkos with Intel Data Center GPU accelerators (formerly
known under the code name "Ponte Vecchio") in LAMMPS is still a work
in progress. Only a subset of the functionality works correctly.
Please contact the LAMMPS developers if you run into problems.
Building LAMMPS with the KOKKOS package
"""""""""""""""""""""""""""""""""""""""
@ -292,6 +309,10 @@ one or more nodes, each with two GPUs:
settings. Experimenting with its options can provide a speed-up for
specific calculations. For example:
.. code-block:: bash
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
.. note::
The default binsize for :doc:`atom sorting <atom_modify>` on GPUs
@ -302,9 +323,15 @@ one or more nodes, each with two GPUs:
frequent sorting than default (e.g. sorting every 100 time steps
instead of 1000) may improve performance.
.. code-block:: bash
.. note::
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
When running on GPUs with many MPI ranks (tens of thousands and
more), the creation of the atom map (required for molecular systems)
on the GPU can slow down significantly or run out of GPU memory and
thus slow down the whole calculation or cause a crash. You can use
the "-pk kokkos atom/map no" :doc:`command-line switch <Run_options>`
of the :doc:`package kokkos atom/map no <package>` command to create
the atom map on the CPU instead.
.. note::
@ -416,15 +443,22 @@ Generally speaking, the following rules of thumb apply:
performance of a KOKKOS style is a bit slower than the OPENMP
package.
* When running large number of atoms per GPU, KOKKOS is typically faster
than the GPU package when compiled for double precision. The benefit
than the GPU package when compiled for double precision. The benefit
of using single or mixed precision with the GPU package depends
significantly on the hardware in use and the simulated system and pair
style.
* When running on Intel hardware, KOKKOS is not as fast as
* When running on Intel Phi hardware, KOKKOS is not as fast as
the INTEL package, which is optimized for x86 hardware (not just
from Intel) and compilation with the Intel compilers. The INTEL
package also can increase the vector length of vector instructions
by switching to single or mixed precision mode.
* The KOKKOS package by default assumes that you are using exactly one
MPI rank per GPU. When trying to use multiple MPI ranks per GPU it is
mandatory to enable `CUDA Multi-Process Service (MPS)
<https://docs.nvidia.com/deploy/mps/index.html>`_ to get good
performance. In this case it is better to not use all available
MPI ranks in order to avoid competing with the MPS daemon for
CPU resources.
See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
LAMMPS website for performance of the KOKKOS package on different

80
doc/src/angle_cosine_squared_restricted.rst Normal file
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@ -0,0 +1,80 @@
.. index:: angle_style cosine/squared/restricted
.. index:: angle_style cosine/squared/restricted/omp
angle_style cosine/squared/restricted command
=============================================
Accelerator Variants: *cosine/squared/restricted/omp*
Syntax
""""""
.. code-block:: LAMMPS
angle_style cosine/squared/restricted
Examples
""""""""
.. code-block:: LAMMPS
angle_style cosine/squared/restricted
angle_coeff 2*4 75.0 100.0
Description
"""""""""""
.. versionadded:: 17Apr2024
The *cosine/squared/restricted* angle style uses the potential
.. math::
E = K [\cos(\theta) - \cos(\theta_0)]^2 / \sin^2(\theta)
, which is commonly used in the MARTINI force field,
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K`
is a prefactor. Note that the usual 1/2 factor is included in :math:`K`.
See :ref:`(Bulacu) <restricted-Bulacu>` for a description of the restricted angle for the MARTINI force field.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_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` (energy)
* :math:`\theta_0` (degrees)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc page
for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none
----------
.. _restricted-Bulacu:
**(Bulacu)** Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
(2013).

3
doc/src/angle_style.rst
View File

@ -10,7 +10,7 @@ Syntax
angle_style style
* style = *none* or *zero* or *hybrid* or *amoeba* or *charmm* or *class2* or *class2/p6* or *cosine* or *cosine/buck6d* or *cosine/delta* or *cosine/periodic* or *cosine/shift* or *cosine/shift/exp* or *cosine/squared* or *cross* or *dipole* or *fourier* or *fourier/simple* or *gaussian* or *harmonic* or *lepton* or *mm3* or *quartic* or *spica* or *table*
* style = *none* or *zero* or *hybrid* or *amoeba* or *charmm* or *class2* or *class2/p6* or *cosine* or *cosine/buck6d* or *cosine/delta* or *cosine/periodic* or *cosine/shift* or *cosine/shift/exp* or *cosine/squared* or *cosine/squared/restricted* or *cross* or *dipole* or *fourier* or *fourier/simple* or *gaussian* or *harmonic* or *lepton* or *mm3* or *quartic* or *spica* or *table*
Examples
""""""""
@ -84,6 +84,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`cosine/shift <angle_cosine_shift>` - angle cosine with a shift
* :doc:`cosine/shift/exp <angle_cosine_shift_exp>` - cosine with shift and exponential term in spring constant
* :doc:`cosine/squared <angle_cosine_squared>` - angle with cosine squared term
* :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` - angle with restricted cosine squared term
* :doc:`cross <angle_cross>` - cross term coupling angle and bond lengths
* :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole
* :doc:`fourier <angle_fourier>` - angle with multiple cosine terms

27
doc/src/atom_style.rst
View File

@ -283,21 +283,22 @@ Note that there may be additional arguments required along with the
arguments are described on the :doc:`Howto body <Howto_body>` doc page.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element between two regions of different dielectric constant. For
interface particles, in addition to the properties associated with
atom_style full, each particle also should be assigned a normal unit
vector (defined by normx, normy, normz), an area (area/patch), the
particle (e.g. an ion), or an interface particle representing a
boundary element between two regions of different dielectric
constant. For interface particles, in addition to the properties
associated with atom_style full, each particle also should be assigned
a unit dipole vector (mu) representing the direction of the induced
dipole moment at each interface particle, an area (area/patch), the
difference and mean of the dielectric constants of two sides of the
interface along the direction of the normal vector (ed and em), the
local dielectric constant at the boundary element (epsilon), and a mean
local curvature (curv). Physical particles must be assigned these
values, as well, but only their local dielectric constants will be used;
see documentation for associated :doc:`pair styles <pair_dielectric>`
and :doc:`fixes <fix_polarize>`. The distinction between the physical
and interface particles is only meaningful when :doc:`fix polarize
<fix_polarize>` commands are applied to the interface particles. This
style is part of the DIELECTRIC package.
local dielectric constant at the boundary element (epsilon), and a
mean local curvature (curv). Physical particles must be assigned
these values, as well, but only their local dielectric constants will
be used; see documentation for associated :doc:`pair styles
<pair_dielectric>` and :doc:`fixes <fix_polarize>`. The distinction
between the physical and interface particles is only meaningful when
:doc:`fix polarize <fix_polarize>` commands are applied to the
interface particles. This style is part of the DIELECTRIC package.
For the *dipole* style, a point dipole vector mu is defined for each
point particle. Note that if you wish the particles to be finite-size

54
doc/src/boundary.rst
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@ -42,8 +42,10 @@ commands.
The style *p* means the box is periodic, so that particles interact
across the boundary, and they can exit one end of the box and re-enter
the other end. A periodic dimension can change in size due to
constant pressure boundary conditions or box deformation (see the :doc:`fix npt <fix_nh>` and :doc:`fix deform <fix_deform>` commands). The *p*
style must be applied to both faces of a dimension.
constant pressure boundary conditions or box deformation (see the
:doc:`fix npt <fix_nh>` and :doc:`fix deform <fix_deform>` commands).
The *p* style must be applied to both faces of a dimension. For 2d
simulations the z dimension must be periodic (which is the default).
The styles *f*, *s*, and *m* mean the box is non-periodic, so that
particles do not interact across the boundary and do not move from one
@ -76,28 +78,44 @@ atoms becomes less than 50.0. This can be useful if you start a
simulation with an empty box or if you wish to leave room on one side
of the box, e.g. for atoms to evaporate from a surface.
For triclinic (non-orthogonal) simulation boxes, if the second dimension
of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
enforced with the tilt factor offset. If the first dimension is
shrink-wrapped, then the shrink wrapping is applied to the tilted box
face, to encompass the atoms. E.g. for a positive xy tilt, the xlo
and xhi faces of the box are planes tilting in the +y direction as y
increases. These tilted planes are shrink-wrapped around the atoms to
determine the x extent of the box.
LAMMPS also allows use of triclinic (non-orthogonal) simulation boxes.
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
triclinic representations.
description of both general and restricted triclinic boxes and how to
define them. General triclinic boxes (arbitrary edge vectors **A**,
**B**, and **C**) are converted internally to restricted triclinic
boxes with tilt factors (xy,xz,yz) which skew an otherwise orthogonal
box.
The boundary <boundary> command settings explained above for the 6
faces of an orthogonal box also apply in similar manner to the 6 faces
of a restricted triclinic box (and thus to the corresponding 6 faces
of a general triclinic box), with the following context.
if the second dimension of a tilt factor (e.g. y for xy) is periodic,
then the periodicity is enforced with the tilt factor offset. This
means that for y periodicity a particle which exits the lower y
boundary is displaced in the x-direction by xy before it re-enters the
upper y boundary. And vice versa if a particle exits the upper y
boundary. Likewise the ghost atoms surrounding a particle near the
lower y boundary include images of particles near the upper y-boundary
which are displaced in the x-direction by xy. Similar rules apply for
z-periodicity and the xz and/or yz tilt factors.
If the first dimension of a tilt factor is shrink-wrapped, then the
shrink wrapping is applied to the tilted box face, to encompass the
atoms. E.g. for a positive xy tilt, the xlo and xhi faces of the box
are planes tilting in the +y direction as y increases. The position
of these tilted planes are adjusted dynamically to shrink-wrap around
the atoms to determine the xlo and xhi extents of the box.
Restrictions
""""""""""""
This command cannot be used after the simulation box is defined by a
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or
:doc:`read_restart <read_restart>` command. See the
:doc:`change_box <change_box>` command for how to change the simulation
box boundaries after it has been defined.
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command
or :doc:`read_restart <read_restart>` command. See the
:doc:`change_box <change_box>` command for how to change the
simulation box boundaries after it has been defined.
For 2d simulations, the z dimension must be periodic.

19
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@ -204,8 +204,23 @@ angles per atom satisfying the ADF criteria.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
By default, the ADF is not computed for distances longer than the
largest force cutoff, since the neighbor list creation will only contain
pairs up to that distance (plus neighbor list skin). If you use outer
cutoffs larger than that, you must use :doc:`neighbor style 'bin' or
'nsq' <neighbor>`.
If you want an ADF for a larger outer cutoff, you can also use the
:doc:`rerun <rerun>` command to post-process a dump file, use :doc:`pair
style zero <pair_zero>` and set the force cutoff to be larger in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary and with pair style zero you are not computing any forces, and
since you are not running dynamics you are not changing the model that
generated the trajectory.
The ADF is not computed for neighbors outside the force cutoff,
since processors (in parallel) don't know about atom coordinates for

2
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@ -102,6 +102,8 @@ This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
Related commands
""""""""""""""""

2
doc/src/compute_composition_atom.rst
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@ -107,6 +107,8 @@ This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
Related commands
""""""""""""""""

38
doc/src/compute_count_type.rst
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@ -12,7 +12,7 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command
* count/type = style name of this compute command
* mode = {atom} or {bond} or {angle} or {dihedral} or {improper}
* mode = *atom* or *bond* or *angle* or *dihedral* or *improper*
Examples
""""""""
@ -69,29 +69,42 @@ for each type:
----------
If the {mode} setting is {atom} then the count of atoms for each atom
If the *mode* setting is *atom* then the count of atoms for each atom
type is tallied. Only atoms in the specified group are counted.
If the {mode} setting is {bond} then the count of bonds for each bond
The atom count for each type can be normalized by the total number of
atoms like so:
.. code-block:: LAMMPS
compute typevec all count/type atom # number of atoms of each type
variable normtypes vector c_typevec/atoms # divide by total number of atoms
variable ntypes equal extract_setting(ntypes) # number of atom types
thermo_style custom step v_normtypes[*${ntypes}] # vector variable needs upper limit
Similarly, bond counts can be normalized by the total number of bonds.
The same goes for angles, dihedrals, and impropers (see below).
If the *mode* setting is *bond* then the count of bonds for each bond
type is tallied. Only bonds with both atoms in the specified group
are counted.
For {mode} = {bond}, broken bonds with a bond type of zero are also
For *mode* = *bond*, broken bonds with a bond type of zero are also
counted. The :doc:`bond_style quartic <bond_quartic>` and :doc:`BPM
bond styles <Howto_bpm>` break bonds by doing this. See the :doc:`
Howto broken bonds <Howto_broken_bonds>` doc page for more details.
bond styles <Howto_bpm>` break bonds by doing this. See the
:doc:`Howto broken bonds <Howto_broken_bonds>` doc page for more details.
Note that the group setting is ignored for broken bonds; all broken
bonds in the system are counted.
If the {mode} setting is {angle} then the count of angles for each
If the *mode* setting is *angle* then the count of angles for each
angle type is tallied. Only angles with all 3 atoms in the specified
group are counted.
If the {mode} setting is {dihedral} then the count of dihedrals for
If the *mode* setting is *dihedral* then the count of dihedrals for
each dihedral type is tallied. Only dihedrals with all 4 atoms in the
specified group are counted.
If the {mode} setting is {improper} then the count of impropers for
If the *mode* setting is *improper* then the count of impropers for
each improper type is tallied. Only impropers with all 4 atoms in the
specified group are counted.
@ -101,18 +114,19 @@ Output info
"""""""""""
This compute calculates a global vector of counts. If the mode is
{atom} or {bond} or {angle} or {dihedral} or {improper}, then the
*atom* or *bond* or *angle* or *dihedral* or *improper*, then the
vector length is the number of atom types or bond types or angle types
or dihedral types or improper types, respectively.
If the mode is {bond} this compute also calculates a global scalar
If the mode is *bond* this compute also calculates a global scalar
which is the number of broken bonds with type = 0, as explained above.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See the :doc:`Howto output
<Howto_output>` page for an overview of LAMMPS output options.
The scalar and vector values calculated by this compute are "extensive".
The scalar and vector values calculated by this compute are both
"intensive".
Restrictions
""""""""""""

2
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@ -106,6 +106,8 @@ Restrictions
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package.
This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
Related commands
""""""""""""""""

8
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@ -64,7 +64,7 @@ tangential force tensor. The contact tensor is calculated as
.. math::
C_{ab} = \frac{15}{2} (\phi_{ab} - \mathrm{Tr}(\phi) \delta_{ab})
C_{ab} = \frac{15}{2} (\phi_{ab} - \frac{1}{3} \mathrm{Tr}(\phi) \delta_{ab})
where :math:`a` and :math:`b` are the :math:`x`, :math:`y`, :math:`z`
directions, :math:`\delta_{ab}` is the Kronecker delta function, and
@ -83,7 +83,7 @@ The branch tensor is calculated as
.. math::
B_{ab} = \frac{15}{6 \mathrm{Tr}(D)} (D_{ab} - \mathrm{Tr}(D) \delta_{ab})
B_{ab} = \frac{15}{2\, \mathrm{Tr}(D)} (D_{ab} - \frac{1}{3} \mathrm{Tr}(D) \delta_{ab})
where the tensor :math:`D` is defined as
@ -101,7 +101,7 @@ The normal force fabric tensor is calculated as
.. math::
F^n_{ab} = \frac{15}{6\, \mathrm{Tr}(N)} (N_{ab} - \mathrm{Tr}(N) \delta_{ab})
F^n_{ab} = \frac{15}{2\, \mathrm{Tr}(N)} (N_{ab} - \frac{1}{3} \mathrm{Tr}(N) \delta_{ab})
where the tensor :math:`N` is defined as
@ -119,7 +119,7 @@ as
.. math::
F^t_{ab} = \frac{15}{9\, \mathrm{Tr}(N)} (T_{ab} - \mathrm{Tr}(T) \delta_{ab})
F^t_{ab} = \frac{5}{\mathrm{Tr}(N)} (T_{ab} - \frac{1}{3} \mathrm{Tr}(T) \delta_{ab})
where the tensor :math:`T` is defined as

54
doc/src/compute_mliap.rst
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@ -20,7 +20,7 @@ Syntax
*model* values = style
style = *linear* or *quadratic* or *mliappy*
*descriptor* values = style filename
style = *sna*
style = *sna* or *ace*
filename = name of file containing descriptor definitions
*gradgradflag* value = 0/1
toggle gradgrad method for force gradient
@ -31,6 +31,7 @@ Examples
.. code-block:: LAMMPS
compute mliap model linear descriptor sna Ta06A.mliap.descriptor
compute mliap model linear descriptor ace H_N_O_ccs.yace gradgradflag 1
Description
"""""""""""
@ -40,18 +41,15 @@ of machine-learning interatomic potentials with respect to model parameters.
It is used primarily for calculating the gradient of energy, force, and
stress components with respect to model parameters, which is useful when
training :doc:`mliap pair_style <pair_mliap>` models to match target data.
It provides separate
definitions of the interatomic potential functional form (*model*)
and the geometric quantities that characterize the atomic positions
(*descriptor*). By defining *model* and *descriptor* separately,
It provides separate definitions of the interatomic potential functional
form (*model*) and the geometric quantities that characterize the atomic
positions (*descriptor*). By defining *model* and *descriptor* separately,
it is possible to use many different models with a given descriptor,
or many different descriptors with a given model. Currently, the
compute supports just two models, *linear* and *quadratic*,
and one descriptor, *sna*, the SNAP descriptor used by
:doc:`pair_style snap <pair_snap>`, including the linear, quadratic,
and chem variants. Work is currently underway to extend
the interface to handle neural network energy models,
and it is also straightforward to add new descriptor styles.
or many different descriptors with a given model. Currently, the compute
supports *linear* and *quadratic* SNAP descriptor computes used in
:doc:`pair_style snap <pair_snap>`, *linear* SO3 descriptor computes, and
*linear* ACE descriptor computes used in :doc:`pair_style pace <pair_pace>`,
and it is straightforward to add new descriptor styles.
The compute *mliap* command must be followed by two keywords
*model* and *descriptor* in either order.
@ -60,19 +58,31 @@ The *model* keyword is followed by the model style (*linear*,
*quadratic* or *mliappy*). The *mliappy* model is only available if
LAMMPS is built with the *mliappy* Python module. There are
:ref:`specific installation instructions <mliap>` for that module.
For the *mliap* compute, specifying a *linear* model will compute the
specified descriptors and gradients with respect to linear model parameters
whereas *quadratic* will do the same, but for the quadratic products of
descriptors.
The *descriptor* keyword is followed by a descriptor style, and
additional arguments. The compute currently supports two descriptor
styles *sna* and *so3*, but it is is straightforward to add additional
descriptor styles. The SNAP descriptor style *sna* is the same as that
used by :doc:`pair_style snap <pair_snap>`, including the linear,
quadratic, and chem variants. A single additional argument specifies
the descriptor filename containing the parameters and setting used by
the SNAP descriptor. The descriptor filename usually ends in the
additional arguments. The compute currently supports three descriptor
styles: *sna*, *so3*, and *ace*, but it is is straightforward to add
additional descriptor styles. The SNAP descriptor style *sna* is the
same as that used by :doc:`pair_style snap <pair_snap>`, including the
linear, quadratic, and chem variants. A single additional argument
specifies the descriptor filename containing the parameters and setting used
by the SNAP descriptor. The descriptor filename usually ends in the
*.mliap.descriptor* extension. The format of this file is identical to
the descriptor file in the :doc:`pair_style mliap <pair_mliap>`, and is
described in detail there.
The ACE descriptor style *ace* is the same as :doc:`pair_style pace <pair_pace>`.
A single additional argument specifies the *ace* descriptor filename
that contains parameters and settings for the ACE descriptors. This file
format differs from the SNAP or SO3 descriptor files, and has a *.yace* or
*.ace* extension. However, as with other mliap descriptor styles, this file
is identical to the ace descriptor file in :doc:`pair_style mliap <pair_mliap>`,
where it is described in further detail.
.. note::
The number of LAMMPS atom types (and the value of *nelems* in the model)
@ -172,8 +182,10 @@ This compute is part of the ML-IAP package. It is only enabled if
LAMMPS was built with that package. In addition, building LAMMPS with
the ML-IAP package requires building LAMMPS with the ML-SNAP package.
The *mliappy* model also requires building LAMMPS with the PYTHON
package. See the :doc:`Build package <Build_package>` page for more
info.
package. The *ace* descriptor also requires building LAMMPS with the
ML-PACE package. See the :doc:`Build package <Build_package>` page for
more info. Note that `kk` (KOKKOS) accelerated variants of SNAP and
ACE descriptors are not compatible with `mliap descriptor`.
Related commands
""""""""""""""""

3
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@ -153,7 +153,8 @@ Related commands
Default
"""""""
none
By default the compute includes contributions from the keywords:
``ke pair bond angle dihedral improper kspace fix``
----------

5
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@ -23,8 +23,9 @@ Syntax
spx, spy, spz, sp, fmx, fmy, fmz,
nbonds,
radius, diameter, omegax, omegay, omegaz,
temperature, heatflow,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
shapex, shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
end1x, end1y, end1z, end2x, end2y, end2z,
corner1x, corner1y, corner1z,
@ -56,6 +57,8 @@ Syntax
*nbonds* = number of bonds assigned to an atom
*radius,diameter* = radius,diameter of spherical particle
*omegax,omegay,omegaz* = angular velocity of spherical particle
*temperature* = internal temperature of spherical particle
*heatflow* = internal heat flow of spherical particle
*angmomx,angmomy,angmomz* = angular momentum of aspherical particle
*shapex,shapey,shapez* = 3 diameters of aspherical particle
*quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles

37
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@ -176,22 +176,29 @@ also numbers :math:`\ge 0.0`.
Restrictions
""""""""""""
The RDF is not computed for distances longer than the force cutoff,
since processors (in parallel) do not know about atom coordinates for
atoms further away than that distance. If you want an RDF for larger
distances, you can use the :doc:`rerun <rerun>` command to post-process
a dump file and set the cutoff for the potential to be longer in the
By default, the RDF is not computed for distances longer than the
largest force cutoff, since the neighbor list creation will only contain
pairs up to that distance (plus neighbor list skin). This distance can
be increased using the *cutoff* keyword but this keyword is only valid
with :doc:`neighbor styles 'bin' and 'nsq' <neighbor>`.
If you want an RDF for larger distances, you can also use the
:doc:`rerun <rerun>` command to post-process a dump file, use :doc:`pair
style zero <pair_zero>` and set the force cutoff to be longer in the
rerun script. Note that in the rerun context, the force cutoff is
arbitrary, since you are not running dynamics and thus are not changing
your model. The definition of :math:`g(r)` used by LAMMPS is only appropriate
for characterizing atoms that are uniformly distributed throughout the
simulation cell. In such cases, the coordination number is still
correct and meaningful. As an example, if a large simulation cell
contains only one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)`
will register an arbitrarily large spike at whatever distance they
happen to be at, and zero everywhere else.
The function :math:`\text{coord}(r)` will show a step
change from zero to one at the location of the spike in :math:`g(r)`.
arbitrary and with pair style zero you are not computing any forces, and
you are not running dynamics you are not changing the model that
generated the trajectory.
The definition of :math:`g(r)` used by LAMMPS is only appropriate for
characterizing atoms that are uniformly distributed throughout the
simulation cell. In such cases, the coordination number is still correct
and meaningful. As an example, if a large simulation cell contains only
one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)` will
register an arbitrarily large spike at whatever distance they happen to
be at, and zero everywhere else. The function :math:`\text{coord}(r)`
will show a step change from zero to one at the location of the spike in
:math:`g(r)`.
.. note::

3
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@ -56,8 +56,9 @@ Examples
compute 1 all reduce sum c_force
compute 1 all reduce/region subbox sum c_force
compute 2 all reduce min c_press[2] f_ave v_myKE
compute 2 all reduce min c_press[*] f_ave v_myKE
compute 2 all reduce min c_press[*] f_ave v_myKE inputs peratom
compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
compute 4 all reduce max c_bond inputs local
Description
"""""""""""

3
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@ -289,7 +289,8 @@ Related commands
Default
"""""""
none
By default the compute includes contributions from the keywords:
``ke pair bond angle dihedral improper kspace fix``
----------

9
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@ -126,16 +126,19 @@ These styles are part of the EXTRA-COMPUTE package. They are only
enabled if LAMMPS is built with that package. See the :doc:`Build
package <Build_package>` doc page on for more info.
The method is only implemented for 3d orthogonal simulation boxes whose
The method is implemented for orthogonal simulation boxes whose
size does not change in time, and axis-aligned planes.
The method only works with two-body pair interactions, because it
requires the class method ``Pair::single()`` to be implemented, which is
not possible for manybody potentials. In particular, compute
*stress/mop/profile* and *stress/mop* do not work with more than two-body pair
interactions, long range (kspace) interactions and
*stress/mop/profile* and *stress/mop* do not work with more than two-body
pair interactions, long range (kspace) interactions and
improper intramolecular interactions.
The impact of fixes that affect the stress (e.g. fix langevin) is
also not included in the stress computed here.
Related commands
""""""""""""""""

261
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@ -86,25 +86,46 @@ Description
"""""""""""
This command creates atoms (or molecules) within the simulation box,
either on a lattice, or a single atom (or molecule), or on a surface
defined by a triangulated mesh, or a random collection of atoms (or
molecules). It is an alternative to reading in atom coordinates
either on a lattice, or at random points, or on a surface defined by a
triangulated mesh. Or it creates a single atom (or molecule) at a
specified point. It is an alternative to reading in atom coordinates
explicitly via a :doc:`read_data <read_data>` or :doc:`read_restart
<read_restart>` command. A simulation box must already exist, which is
<read_restart>` command.
To use this command a simulation box must already exist, which is
typically created via the :doc:`create_box <create_box>` command.
Before using this command, a lattice must also be defined using the
:doc:`lattice <lattice>` command, unless you specify the *single* style
with units = box or the *random* style. For the remainder of this doc
page, a created atom or molecule is referred to as a "particle".
Before using this command, a lattice must typically also be defined
using the :doc:`lattice <lattice>` command, unless you specify the
*single* or *mesh* style with units = box or the *random* style. To
create atoms on a lattice for general triclinic boxes, see the
discussion below.
For the remainder of this doc page, a created atom or molecule is
referred to as a "particle".
If created particles are individual atoms, they are assigned the
specified atom *type*, though this can be altered via the *basis*
keyword as discussed below. If molecules are being created, the type
of each atom in the created molecule is specified in the file read by
the :doc:`molecule <molecule>` command, and those values are added to
the specified atom *type* (e.g., if *type* = 2 and the file specifies
atom types 1, 2, and 3, then each created molecule will have atom types
3, 4, and 5).
of each atom in the created molecule is specified in a specified file
read by the :doc:`molecule <molecule>` command, and those values are
added to the specified atom *type* (e.g., if *type* = 2 and the file
specifies atom types 1, 2, and 3, then each created molecule will have
atom types 3, 4, and 5).
.. note::
You cannot use this command to create atoms that are outside the
simulation box; they will just be ignored by LAMMPS. This is true
even if you are using shrink-wrapped box boundaries, as specified
by the :doc:`boundary <boundary>` command. However, you can first
use the :doc:`change_box <change_box>` command to temporarily
expand the box, then add atoms via create_atoms, then finally use
change_box command again if needed to re-shrink-wrap the new atoms.
See the :doc:`change_box <change_box>` doc page for an example of
how to do this, using the create_atoms *single* style to insert a
new atom outside the current simulation box.
----------
For the *box* style, the create_atoms command fills the entire
simulation box with particles on the lattice. If your simulation box
@ -126,10 +147,117 @@ periodic boundaries. If this is desired, you should either use the
*box* style, or tweak the region size to get precisely the particles
you want.
----------
If the simulation box is formulated as a general triclinic box defined
by arbitrary edge vectors **A**, **B**, **C**, then the *box* and
*region* styles will create atoms on a lattice commensurate with those
edge vectors. See the :doc:`Howto_triclinic <Howto_triclinic>` doc
page for a detailed explanation of orthogonal, restricted triclinic,
and general triclinic simulation boxes. As with the :doc:`create_box
<create_box>` command, the :doc:`lattice <lattice>` command used by
this command must be of style *custom* and use its *triclinic/general*
option. The *a1, *a2*, *a3* settings of the :doc:`lattice <lattice>`
command define the edge vectors of a unit cell of the general
triclinic lattice. The :doc:`create_box <create_box>` command creates
a simulation box which replicates that unit cell along each of the
**A**, **B**, **C** edge vectors.
.. note::
LAMMPS allows specification of general triclinic simulation boxes
as a convenience for users who may be converting data from
solid-state crystallographic representations or from DFT codes for
input to LAMMPS. However, as explained on the
:doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
LAMMPS only uses restricted triclinic simulation boxes. This means
the box created by the :doc:`create_box <create_box>` command as
well as the atoms created by this command with their per-atom
information (e.g. coordinates, velocities) are converted (rotated)
from general to restricted triclinic form when the two commands are
invoked. The <Howto_triclinic>` doc page also discusses other
LAMMPS commands which can input/output general triclinic
representations of the simulation box and per-atom data.
The *box* style will fill the entire general triclinic box with
particles on the lattice, as explained above.
.. note::
The *region* style also operates as explained above, but the check
for particles inside the region is performed *after* the particle
coordinates have been converted to the restricted triclinic box.
This means the region must also be defined with respect to the
restricted triclinic box, not the general triclinic box.
If the simulation box is general triclinic, the *single*, *random*,
and *mesh* styles described next operate on the box *after* it has
been converted to restricted triclinic. So all the settings for those
styles should be made in that context.
----------
For the *single* style, a single particle is added to the system at
the specified coordinates. This can be useful for debugging purposes
or to create a tiny system with a handful of particles at specified
positions.
positions. For a 2d simulation the specified z coordinate must be
0.0.
.. versionchanged:: 2Jun2022
The *porosity* style has been renamed to *random* with added functionality.
For the *random* style, *N* particles are added to the system at
randomly generated coordinates, which can be useful for generating an
amorphous system. For 2d simulations, the z coordinates of all added
atoms will be 0.0.
The particles are created one by one using the specified random number
*seed*, resulting in the same set of particle coordinates, independent
of how many processors are being used in the simulation. Unless the
*overlap* keyword is specified, particles created by the *random*
style will typically be highly overlapped. Various additional
criteria can be used to accept or reject a random particle insertion;
see the keyword discussion below. Multiple attempts per particle are
made (see the *maxtry* keyword) until the insertion is either
successful or fails. If this command fails to add all requested *N*
particles, a warning will be output.
If the *region-ID* argument is specified as NULL, then the randomly
created particles will be anywhere in the simulation box. If a
*region-ID* is specified, a geometric volume is filled that is both
inside the simulation box and is also consistent with the region
volume. See the :doc:`region <region>` command for details. Note
that a region can be specified so that its "volume" is either inside
or outside its geometric boundary.
Note that the create_atoms command adds particles to those that
already exist. This means it can be used to add particles to a system
previously read in from a data or restart file. Or the create_atoms
command can be used multiple times, to add multiple sets of particles
to the simulation. For example, grain boundaries can be created, by
interleaving the create_atoms command with :doc:`lattice <lattice>`
commands specifying different orientations.
When this command is used, care should be taken to ensure the
resulting system does not contain particles that are highly
overlapped. Such overlaps will cause many interatomic potentials to
compute huge energies and forces, leading to bad dynamics. There are
several strategies to avoid this problem:
* Use the :doc:`delete_atoms overlap <delete_atoms>` command after
create_atoms. For example, this strategy can be used to overlay and
surround a large protein molecule with a volume of water molecules,
then delete water molecules that overlap with the protein atoms.
* For the *random* style, use the optional *overlap* keyword to avoid
overlaps when each new particle is created.
* Before running dynamics on an overlapped system, perform an
:doc:`energy minimization <minimize>`. Or run initial dynamics with
:doc:`pair_style soft <pair_soft>` or with :doc:`fix nve/limit
<fix_nve_limit>` to un-overlap the particles, before running normal
dynamics.
.. figure:: img/marble_race.jpg
:figwidth: 33%
@ -189,73 +317,6 @@ to the area of that triangle.
beneficial to exclude computing interactions between the created
particles using :doc:`neigh_modify exclude <neigh_modify>`.
.. versionchanged:: 2Jun2022
The *porosity* style has been renamed to *random* with added functionality.
For the *random* style, *N* particles are added to the system at
randomly generated coordinates, which can be useful for generating an
amorphous system. The particles are created one by one using the
specified random number *seed*, resulting in the same set of particle
coordinates, independent of how many processors are being used in the
simulation. Unless the *overlap* keyword is specified, particles
created by the *random* style will typically be highly overlapped.
Various additional criteria can be used to accept or reject a random
particle insertion; see the keyword discussion below. Multiple
attempts per particle are made (see the *maxtry* keyword) until the
insertion is either successful or fails. If this command fails to add
all requested *N* particles, a warning will be output.
If the *region-ID* argument is specified as NULL, then the randomly
created particles will be anywhere in the simulation box. If a
*region-ID* is specified, a geometric volume is filled that is both
inside the simulation box and is also consistent with the region
volume. See the :doc:`region <region>` command for details. Note
that a region can be specified so that its "volume" is either inside
or outside its geometric boundary.
Note that the create_atoms command adds particles to those that
already exist. This means it can be used to add particles to a system
previously read in from a data or restart file. Or the create_atoms
command can be used multiple times, to add multiple sets of particles
to the simulation. For example, grain boundaries can be created, by
interleaving the create_atoms command with :doc:`lattice <lattice>`
commands specifying different orientations.
When this command is used, care should be taken to ensure the
resulting system does not contain particles that are highly
overlapped. Such overlaps will cause many interatomic potentials to
compute huge energies and forces, leading to bad dynamics. There are
several strategies to avoid this problem:
* Use the :doc:`delete_atoms overlap <delete_atoms>` command after
create_atoms. For example, this strategy can be used to overlay and
surround a large protein molecule with a volume of water molecules,
then delete water molecules that overlap with the protein atoms.
* For the *random* style, use the optional *overlap* keyword to avoid
overlaps when each new particle is created.
* Before running dynamics on an overlapped system, perform an
:doc:`energy minimization <minimize>`. Or run initial dynamics with
:doc:`pair_style soft <pair_soft>` or with :doc:`fix nve/limit
<fix_nve_limit>` to un-overlap the particles, before running normal
dynamics.
.. note::
You cannot use any of the styles explained above to create atoms
that are outside the simulation box; they will just be ignored by
LAMMPS. This is true even if you are using shrink-wrapped box
boundaries, as specified by the :doc:`boundary <boundary>` command.
However, you can first use the :doc:`change_box <change_box>`
command to temporarily expand the box, then add atoms via
create_atoms, then finally use change_box command again if needed
to re-shrink-wrap the new atoms. See the :doc:`change_box
<change_box>` doc page for an example of how to do this, using the
create_atoms *single* style to insert a new atom outside the
current simulation box.
----------
Individual atoms are inserted by this command, unless the *mol*
@ -268,6 +329,12 @@ molecule can be specified in the molecule file. See the
required to be in this file are the coordinates and types of atoms in
the molecule.
.. note::
If you are using the *mol* keyword in combination with the
:doc:`atom style template <atom_style>` command, they must use
the same molecule template-ID.
Using a lattice to add molecules, e.g. via the *box* or *region* or
*single* styles, is exactly the same as adding atoms on lattice
points, except that entire molecules are added at each point, i.e. on
@ -401,12 +468,13 @@ to.
The *overlap* keyword only applies to the *random* style. It prevents
newly created particles from being created closer than the specified
*Doverlap* distance from any other particle. When the particles being
created are molecules, the radius of the molecule (from its geometric
center) is added to *Doverlap*. If particles have finite size (see
:doc:`atom_style sphere <atom_style>` for example) *Doverlap* should
be specified large enough to include the particle size in the
non-overlapping criterion.
*Doverlap* distance from any other particle. If particles have finite
size (see :doc:`atom_style sphere <atom_style>` for example) *Doverlap*
should be specified large enough to include the particle size in the
non-overlapping criterion. If molecules are being randomly inserted, then
an insertion is only accepted if each particle in the molecule meets the
overlap criterion with respect to other particles (not including particles
in the molecule itself).
.. note::
@ -463,12 +531,19 @@ on a single CPU core.
-----
The *units* keyword determines the meaning of the distance units used
to specify the coordinates of the one particle created by the *single*
style, or the overlap distance *Doverlap* by the *overlap* keyword. A
*box* value selects standard distance units as defined by the
:doc:`units <units>` command (e.g., :math:`\AA` for
units = *real* or *metal*\ . A *lattice* value means the distance units are in
lattice spacings.
by parameters for various styles. A *box* value selects standard
distance units as defined by the :doc:`units <units>` command (e.g.,
:math:`\AA` for units = *real* or *metal*\ . A *lattice* value means
the distance units are in lattice spacings. These are affected settings:
* for *single* style: coordinates of the particle created
* for *random* style: overlap distance *Doverlap* by the *overlap* keyword
* for *mesh* style: *bisect* threshold value for *meshmode* = *bisect*
* for *mesh* style: *radthresh* value for *meshmode* = *bisect*
* for *mesh* style: *density* value for *meshmode* = *qrand*
Since *density* represents an area (distance ^2), the lattice spacing
factor is also squared.
----------

241
doc/src/create_box.rst
View File

@ -9,9 +9,11 @@ Syntax
.. code-block:: LAMMPS
create_box N region-ID keyword value ...
create_box N NULL alo ahi blo bhi clo chi keyword value ...
* N = # of atom types to use in this simulation
* region-ID = ID of region to use as simulation domain
* region-ID = ID of region to use as simulation domain or NULL for general triclinic box
* alo,ahi,blo,bhi,clo,chi = multipliers on a1,a2,a3 vectors defined by :doc"`lattice <lattice>` command (only when region-ID = NULL)
* zero or more keyword/value pairs may be appended
* keyword = *bond/types* or *angle/types* or *dihedral/types* or *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*
@ -32,121 +34,204 @@ Examples
.. code-block:: LAMMPS
# orthogonal or restricted triclinic box using regionID = mybox
create_box 2 mybox
create_box 2 mybox bond/types 2 extra/bond/per/atom 1
.. code-block:: LAMMPS
# 2d general triclinic box using primitive cell for 2d hex lattice
lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 &
a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
create_box 1 NULL 0 5 0 5 -0.5 0.5
.. code-block:: LAMMPS
# 3d general triclinic box using primitive cell for 3d fcc lattice
lattice custom 1.0 a2 0.0 0.5 0.5 a1 0.5 0.0 0.5 a3 0.5 0.5 0.0 basis 0.0 0.0 0.0 triclinic/general
create box 1 NULL -5 5 -10 10 0 20
Description
"""""""""""
This command creates a simulation box based on the specified region.
Thus a :doc:`region <region>` command must first be used to define a
geometric domain. It also partitions the simulation box into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors being used and the settings of the
:doc:`processors <processors>` command. The partitioning can later be
changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
This command creates a simulation box. It also partitions the box into
a regular 3d grid of smaller sub-boxes, one per processor (MPI task).
The geometry of the partitioning is based on the size and shape of the
simulation box, the number of processors being used and the settings
of the :doc:`processors <processors>` command. The partitioning can
later be changed by the :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands.
The argument N is the number of atom types that will be used in the
Simulation boxes in LAMMPS can be either orthogonal or triclinic in
shape. Orthogonal boxes are a brick in 3d (rectangle in 2d) with 6
faces that are each perpendicular to one of the standard xyz
coordinate axes. Triclinic boxes are a parallelepiped in 3d
(parallelogram in 2d) with opposite pairs of faces parallel to each
other. LAMMPS supports two forms of triclinic boxes, restricted and
general, which differ in how the box is oriented with respect to the
xyz coordinate axes. See the :doc:`Howto triclinic <Howto_triclinic>`
for a detailed description of all 3 kinds of simulation boxes.
The argument *N* is the number of atom types that will be used in the
simulation.
Orthogonal and restricted triclinic boxes are created by specifying a
region ID previously defined by the :doc:`region <region>` command.
General triclinic boxes are discussed below.
If the region is not of style *prism*, then LAMMPS encloses the region
(block, sphere, etc.) with an axis-aligned orthogonal bounding box
which becomes the simulation domain.
which becomes the simulation domain. For a 2d simulation, the zlo and
zhi values of the simulation box must straddle zero.
If the region is of style *prism*, LAMMPS creates a non-orthogonal
simulation domain shaped as a parallelepiped with triclinic symmetry.
As defined by the :doc:`region prism <region>` command, the
parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by three
edge vectors starting from the origin given by
:math:`\vec a = (x_\text{hi}-x_\text{lo},0,0)`;
:math:`\vec b = (xy,y_\text{hi}-y_\text{lo},0)`; and
:math:`\vec c = (xz,yz,z_\text{hi}-z_\text{lo})`.
The parameters *xy*\ , *xz*\ , and *yz* can be 0.0 or
positive or negative values and are called "tilt factors" because they
are the amount of displacement applied to faces of an originally
orthogonal box to transform it into the parallelepiped.
parallelepiped has an "origin" at (xlo,ylo,zlo) and three edge vectors
starting from the origin given by :math:`\vec a =
(x_\text{hi}-x_\text{lo},0,0)`; :math:`\vec b =
(xy,y_\text{hi}-y_\text{lo},0)`; and :math:`\vec c =
(xz,yz,z_\text{hi}-z_\text{lo})`. In LAMMPS lingo, this is a
restricted triclinic box because the three edge vectors cannot be
defined in arbitrary (general) directions. The parameters *xy*\ ,
*xz*\ , and *yz* can be 0.0 or positive or negative values and are
called "tilt factors" because they are the amount of displacement
applied to faces of an originally orthogonal box to transform it into
the parallelepiped. For a 2d simulation, the zlo and zhi values of
the simulation box must straddle zero.
By default, a *prism* region used with the create_box command must have
tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half
the distance of the parallel box length. For example, if
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x`
box length is 10 and the :math:`xy` tilt factor must be between
:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz`
must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
Typically a *prism* region used with the create_box command should
have tilt factors :math:`(xy,xz,yz)` that do not skew the box more
than half the distance of the parallel box length. For example, if
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the
:math:`x` box length is 10 and the :math:`xy` tilt factor must be
between :math:`-5` and :math:`5`. Similarly, both :math:`xz` and
:math:`yz` must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a
limitation, since if the maximum tilt factor is 5 (as in this example),
then configurations with tilt :math:`= \dots, -15`, :math:`-5`,
:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically
equivalent. Simulations with large tilt factors will run inefficiently,
since they require more ghost atoms and thus more communication. With
very large tilt factors, LAMMPS will eventually produce incorrect
trajectories and stop with errors due to lost atoms or similar.
limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt :math:`= \dots, -15`,
:math:`-5`, :math:`5`, :math:`15`, :math:`25, \dots` are all
geometrically equivalent.
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
triclinic representations.
LAMMPS will issue a warning if the tilt factors of the created box do
not meet this criterion. This is because simulations with large tilt
factors may run inefficiently, since they require more ghost atoms and
thus more communication. With very large tilt factors, LAMMPS may
eventually produce incorrect trajectories and stop with errors due to
lost atoms or similar issues.
When a prism region is used, the simulation domain should normally be periodic
in the dimension that the tilt is applied to, which is given by the second
dimension of the tilt factor (e.g., :math:`y` for :math:`xy` tilt). This is so
that pairs of atoms interacting across that boundary will have one of them
shifted by the tilt factor. Periodicity is set by the
:doc:`boundary <boundary>` command. For example, if the :math:`xy` tilt factor
is non-zero, then the :math:`y` dimension should be periodic. Similarly, the
:math:`z` dimension should be periodic if :math:`xz` or :math:`yz` is non-zero.
LAMMPS does not require this periodicity, but you may lose atoms if this is not
the case.
See the :doc:`Howto triclinic <Howto_triclinic>` page for geometric
descriptions of triclinic boxes and tilt factors, as well as how to
transform the restricted triclinic parameters to and from other
commonly used triclinic representations.
When a prism region is used, the simulation domain should normally be
periodic in the dimension that the tilt is applied to, which is given
by the second dimension of the tilt factor (e.g., :math:`y` for
:math:`xy` tilt). This is so that pairs of atoms interacting across
that boundary will have one of them shifted by the tilt factor.
Periodicity is set by the :doc:`boundary <boundary>` command. For
example, if the :math:`xy` tilt factor is non-zero, then the :math:`y`
dimension should be periodic. Similarly, the :math:`z` dimension
should be periodic if :math:`xz` or :math:`yz` is non-zero. LAMMPS
does not require this periodicity, but you may lose atoms if this is
not the case.
Note that if your simulation will tilt the box (e.g., via the
:doc:`fix deform <fix_deform>` command), the simulation box must be set up to
be triclinic, even if the tilt factors are initially 0.0. You can
also change an orthogonal box to a triclinic box or vice versa by
:doc:`fix deform <fix_deform>` command), the simulation box must be
created as triclinic, even if the tilt factors are initially 0.0. You
can also change an orthogonal box to a triclinic box or vice versa by
using the :doc:`change box <change_box>` command with its *ortho* and
*triclinic* options.
.. note::
If the system is non-periodic (in a dimension), then you should
not make the lo/hi box dimensions (as defined in your
:doc:`region <region>` command) radically smaller/larger than the extent
of the atoms you eventually plan to create (e.g., via the
:doc:`create_atoms <create_atoms>` command). For example, if your atoms
extend from 0 to 50, you should not specify the box bounds as :math:`-10000`
and :math:`10000`. This is because as described above, LAMMPS uses the
specified box size to lay out the 3d grid of processors. A huge
(mostly empty) box will be sub-optimal for performance when using
"fixed" boundary conditions (see the :doc:`boundary <boundary>`
command). When using "shrink-wrap" boundary conditions (see the
:doc:`boundary <boundary>` command), a huge (mostly empty) box may cause
a parallel simulation to lose atoms the first time that LAMMPS
shrink-wraps the box around the atoms.
If the system is non-periodic (in a dimension), then you should not
make the lo/hi box dimensions (as defined in your :doc:`region
<region>` command) radically smaller/larger than the extent of the
atoms you eventually plan to create (e.g., via the
:doc:`create_atoms <create_atoms>` command). For example, if your
atoms extend from 0 to 50, you should not specify the box bounds as
:math:`-10000` and :math:`10000`. This is because as described
above, LAMMPS uses the specified box size to lay out the 3d grid of
processors. A huge (mostly empty) box will be sub-optimal for
performance when using "fixed" boundary conditions (see the
:doc:`boundary <boundary>` command). When using "shrink-wrap"
boundary conditions (see the :doc:`boundary <boundary>` command), a
huge (mostly empty) box may cause a parallel simulation to lose
atoms the first time that LAMMPS shrink-wraps the box around the
atoms.
----------
As noted above, general triclinic boxes in LAMMPS allow the box to
have arbitrary edge vectors **A**, **B**, **C**. The only
restrictions are that the three vectors be distinct, non-zero, and not
co-planar. They must also define a right-handed system such that
(**A** x **B**) points in the direction of **C**. Note that a
left-handed system can be converted to a right-handed system by simply
swapping the order of any pair of the **A**, **B**, **C** vectors.
To create a general triclinic boxes, the region is specified as NULL
and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three
edge vectors **A**, **B**, **C** using additional information
previously defined by the :doc:`lattice <lattice>` command.
The lattice must be of style *custom* and use its *triclinic/general*
option. This insures the lattice satisfies the restrictions listed
above. The *a1, *a2*, *a3* settings of the :doc:`lattice <lattice>`
command define the edge vectors of a unit cell of the general
triclinic lattice. This command uses them to define the three edge
vectors and origin of the general triclinic box as:
* **A** = (ahi-alo) * *a1*
* **B** = (bhi-blo) * *a2*
* **C** = (chi-clo) * *a3*
* origin = (alo*a1 + blo*a2 + clo*a3)
For 2d general triclinic boxes, clo = -0.5 and chi = 0.5 is required.
.. note::
LAMMPS allows specification of general triclinic simulation boxes
as a convenience for users who may be converting data from
solid-state crystallographic representations or from DFT codes for
input to LAMMPS. However, as explained on the
:doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
LAMMPS only uses restricted triclinic simulation boxes. This means
the box defined by this command and per-atom information
(e.g. coordinates, velocities) defined by the :doc:`create_atoms
<create_atoms>` command are converted (rotated) from general to
restricted triclinic form when the two commands are invoked. The
<Howto_triclinic>` doc page also discusses other LAMMPS commands
which can input/output general triclinic representations of the
simulation box and per-atom data.
----------
The optional keywords can be used to create a system that allows for
bond (angle, dihedral, improper) interactions, or for molecules with
special 1--2, 1--3, or 1--4 neighbors to be added later. These optional
keywords serve the same purpose as the analogous keywords that can be
used in a data file which are recognized by the
special 1--2, 1--3, or 1--4 neighbors to be added later. These
optional keywords serve the same purpose as the analogous keywords
that can be used in a data file which are recognized by the
:doc:`read_data <read_data>` command when it sets up a system.
Note that if these keywords are not used, then the create_box command
creates an atomic (non-molecular) simulation that does not allow bonds
between pairs of atoms to be defined, or a
:doc:`bond potential <bond_style>` to be specified, or for molecules with
special neighbors to be added to the system by commands such as
:doc:`create_atoms mol <create_atoms>`, :doc:`fix deposit <fix_deposit>`
or :doc:`fix pour <fix_pour>`.
between pairs of atoms to be defined, or a :doc:`bond potential
<bond_style>` to be specified, or for molecules with special neighbors
to be added to the system by commands such as :doc:`create_atoms mol
<create_atoms>`, :doc:`fix deposit <fix_deposit>` or :doc:`fix pour
<fix_pour>`.
As an example, see the examples/deposit/in.deposit.molecule script,
which deposits molecules onto a substrate. Initially there are no
molecules in the system, but they are added later by the
:doc:`fix deposit <fix_deposit>` command. The create_box command in the
script uses the bond/types and extra/bond/per/atom keywords to allow
this. If the added molecule contained more than one special bond
(allowed by default), an extra/special/per/atom keyword would also
need to be specified.
molecules in the system, but they are added later by the :doc:`fix
deposit <fix_deposit>` command. The create_box command in the script
uses the bond/types and extra/bond/per/atom keywords to allow this.
If the added molecule contained more than one special bond (allowed by
default), an extra/special/per/atom keyword would also need to be
specified.
----------

71
doc/src/dihedral_cosine_squared_restricted.rst Normal file
View File

@ -0,0 +1,71 @@
.. index:: dihedral_style cosine/squared/restricted
dihedral_style cosine/squared/restricted command
================================================
Syntax
""""""
.. code-block:: LAMMPS
dihedral_style cosine/squared/restricted
Examples
""""""""
.. code-block:: LAMMPS
dihedral_style cosine/squared/restricted
dihedral_coeff 1 10.0 120
Description
"""""""""""
.. versionadded:: 17Apr2024
The *cosine/squared/restricted* dihedral style uses the potential
.. math::
E = K [\cos(\phi) - \cos(\phi_0)]^2 / \sin^2(\phi)
, which is commonly used in the MARTINI force field.
See :ref:`(Bulacu) <restricted-Bul>` for a description of the restricted dihedral for the MARTINI force field.
The following coefficients must be defined for each dihedral type via the
:doc:`dihedral_coeff <dihedral_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` (energy)
* :math:`\phi_0` (degrees)
:math:`\phi_0` is specified in degrees, but LAMMPS converts it to radians internally.
----------
Restrictions
""""""""""""
This dihedral style can only be used if LAMMPS was built with the
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc page
for more info.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`
Default
"""""""
none
----------
.. _restricted-Bul:
**(Bulacu)** Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
(2013).

3
doc/src/dihedral_style.rst
View File

@ -10,7 +10,7 @@ Syntax
dihedral_style style
* style = *none* or *zero* or *hybrid* or *charmm* or *charmmfsw* or *class2* or *cosine/shift/exp* or *fourier* or *harmonic* or *helix* or *lepton* or *multi/harmonic* or *nharmonic* or *opls* or *spherical* or *table* or *table/cut*
* style = *none* or *zero* or *hybrid* or *charmm* or *charmmfsw* or *class2* or *cosine/shift/exp* or *cosine/squared/restricted* or *fourier* or *harmonic* or *helix* or *lepton* or *multi/harmonic* or *nharmonic* or *opls* or *spherical* or *table* or *table/cut*
Examples
""""""""
@ -105,6 +105,7 @@ exist.
* :doc:`charmmfsw <dihedral_charmm>` - CHARMM dihedral with force switching
* :doc:`class2 <dihedral_class2>` - COMPASS (class 2) dihedral
* :doc:`cosine/shift/exp <dihedral_cosine_shift_exp>` - dihedral with exponential in spring constant
* :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>` - squared cosine dihedral with restricted term
* :doc:`fourier <dihedral_fourier>` - dihedral with multiple cosine terms
* :doc:`harmonic <dihedral_harmonic>` - harmonic dihedral
* :doc:`helix <dihedral_helix>` - helix dihedral

111
doc/src/dump.rst
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@ -104,7 +104,6 @@ Syntax
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
heatflow, temperature,
c_ID, c_ID[I], f_ID, f_ID[I], v_name,
i_name, d_name, i2_name[I], d2_name[I]
@ -131,8 +130,6 @@ Syntax
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
heatflow = rate of heat flow into particle
temperature = temperature of particle
c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom vector calculated by a fix with ID
@ -278,16 +275,20 @@ format <dump_modify>` command and its options.
Format of native LAMMPS format dump files:
The *atom*, *custom*, *grid*, and *local* styles create files in a
simple LAMMPS-specific text format that is self-explanatory when
viewing a dump file. Many post-processing tools either included with
LAMMPS or third-party tools can read this format, as does the
simple LAMMPS-specific text format that is mostly self-explanatory
when viewing a dump file. Many post-processing tools either included
with LAMMPS or third-party tools can read this format, as does the
:doc:`rerun <rerun>` command. See tools described on the :doc:`Tools
<Tools>` doc page for examples, including `Pizza.py
<https://lammps.github.io/pizza>`_.
For all these styles, the dimensions of the simulation box are
included in each snapshot. For an orthogonal simulation box this
information is formatted as:
included in each snapshot. The simulation box in LAMMPS can be
defined in one of 3 ways: orthogonal, restricted triclinic, and
general triclinic. See the :doc:`Howto triclinic <Howto_triclinic>`
doc page for a detailed description of all 3 options.
For an orthogonal simulation box the box information is formatted as:
.. parsed-literal::
@ -304,10 +305,10 @@ the six characters is one of *p* (periodic), *f* (fixed), *s* (shrink wrap),
or *m* (shrink wrapped with a minimum value). See the
:doc:`boundary <boundary>` command for details.
For triclinic simulation boxes (non-orthogonal), an orthogonal
bounding box which encloses the triclinic simulation box is output,
along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic box,
formatted as follows:
For a restricted triclinic simulation box, an orthogonal bounding box
which encloses the restricted triclinic simulation box is output,
along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic
box, formatted as follows:
.. parsed-literal::
@ -329,6 +330,10 @@ bounding box extents (xlo_bound, xhi_bound, etc.) are calculated from the
triclinic parameters, and how to transform those parameters to and
from other commonly used triclinic representations.
For a general triclinic simulation box, see the "General triclinic"
section below for a description of the ITEM: BOX BOUNDS format as well
as how per-atom coordinates and per-atom vector quantities are output.
The *atom* and *custom* styles output a "ITEM: NUMBER OF ATOMS" line
with the count of atoms in the snapshot. Likewise they output an
"ITEM: ATOMS" line which includes column descriptors for the per-atom
@ -400,7 +405,6 @@ command.
Dump files in other popular formats:
.. note::
This section only discusses file formats relevant to this doc page.
@ -656,6 +660,87 @@ how to control the compression level in both variants.
----------
General triclinic simulation box output for the *atom* and *custom* styles:
As mentioned above, the simulation box can be defined as a general
triclinic box, which means that 3 arbitrary box edge vectors **A**,
**B**, **C** can be specified. See the :doc:`Howto triclinic
<Howto_triclinic>` doc page for a detailed description of general
triclinic boxes.
This option is provided as a convenience for users who may be
converting data from solid-state crystallographic representations or
from DFT codes for input to LAMMPS. However, as explained on the
:doc:`Howto_triclinic <Howto_triclinic>` doc page, internally, LAMMPS
only uses restricted triclinic simulation boxes. This means the box
and per-atom information (e.g. coordinates, velocities) LAMMPS stores
are converted (rotated) from general to restricted triclinic form when
the system is created.
For dump output, if the :doc:`dump_modify triclinic/general
<dump_modify>` command is used, the box description and per-atom
coordinates and other per-atom vectors will be converted (rotated)
from restricted to general form when each dump file snapshots is
output. This option can only be used if the simulation box was
initially created as general triclinic. If the option is not used,
and the simulation box is general triclinic, then the dump file
snapshots will reflect the internal restricted triclinic geometry.
The dump_modify triclinic/general option affects 3 aspects of the dump
file output.
First, the format for the BOX BOUNDS is as follows
.. parsed-literal::
ITEM: BOX BOUNDS abc origin
ax ay az originx
bx by bz originy
cx cy cz originz
where the **A** edge vector of the box is (ax,ay,az) and similarly
for **B** and **C**. The origin of all 3 edge vectors is (originx,
originy, originz).
Second, the coordinates of each atom are converted (rotated) so that
the atom is inside (or near) the general triclinic box defined by the
**A**, **B**, **C** edge vectors. For style *atom*, this only alters
output for unscaled atom coords, via the :doc:`dump_modify scaled no
<dump_modify>` setting. For style *custom*, this alters output for
either unscaled or unwrapped output of atom coords, via the *x,y,z* or
*xu,yu,zu* attributes. For output of scaled atom coords by both
styles, there is no difference between restricted and general
triclinic values.
Third, the output for any attribute of the *custom* style which
represents a per-atom vector quantity will be converted (rotated) to
be oriented consistent with the general triclinic box and its
orientation relative to the standard xyz coordinate axes.
This applies to the following *custom* style attributes:
* vx,vy,vz = atom velocities
* fx,fy,fz = forces on atoms
* mux,muy,muz = orientation of dipole moment of atom
* omegax,omegay,omegaz = angular velocity of spherical particle
* angmomx,angmomy,angmomz = angular momentum of aspherical particle
* tqx,tqy,tqz = torque on finite-size particles
For example, if the velocity of an atom in a restricted triclinic box
is along the x-axis, then it will be output for a general triclinic
box as a vector along the **A** edge vector of the box.
.. note::
For style *custom*, the :doc:`dump_modify thresh <dump_modify>`
command may access per-atom attributes either directly or
indirectly through a compute or variable. If the attribute is an
atom coordinate or one of the vectors mentioned above, its value
will *NOT* be a general triclinic (rotated) value. Rather it will
be a restricted triclinic value.
----------
Arguments for different styles:
The sections below describe per-atom, local, and per grid cell

47
doc/src/dump_modify.rst
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@ -17,7 +17,7 @@ Syntax
* one or more keyword/value pairs may be appended
* these keywords apply to various dump styles
* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *triclinic/general* or *units* or *unwrap*
.. parsed-literal::
@ -74,12 +74,13 @@ Syntax
-N = sort per-atom lines in descending order by the Nth column
*tfactor* arg = time scaling factor (> 0.0)
*thermo* arg = *yes* or *no*
*time* arg = *yes* or *no*
*thresh* args = attribute operator value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^"
value = numeric value to compare to, or LAST
these 3 args can be replaced by the word "none" to turn off thresholding
*time* arg = *yes* or *no*
*triclinic/general* arg = *yes* or *no*
*units* arg = *yes* or *no*
*unwrap* arg = *yes* or *no*
@ -802,8 +803,9 @@ region since the last dump.
dump_modify ... thresh v_charge |^ LAST
This will dump atoms whose charge has changed from an absolute value
less than :math:`\frac12` to greater than :math:`\frac12` (or vice versa) since the last dump (e.g., due to reactions and subsequent charge equilibration in a
reactive force field).
less than :math:`\frac12` to greater than :math:`\frac12` (or vice
versa) since the last dump (e.g., due to reactions and subsequent
charge equilibration in a reactive force field).
The choice of operators listed above are the usual comparison
operators. The XOR operation (exclusive or) is also included as "\|\^".
@ -811,6 +813,18 @@ In this context, XOR means that if either the attribute or value is
0.0 and the other is non-zero, then the result is "true" and the
threshold criterion is met. Otherwise it is not met.
.. note::
For style *custom*, the *triclinic/general* keyword can alter dump
output for general triclinic simulation boxes and their atoms. See
the :doc:`dump <dump>` command for details of how this changes the
format of dump file snapshots. The thresh keyword may access
per-atom attributes either directly or indirectly through a compute
or variable. If the attribute is an atom coordinate or a per-atom
vector (such as velocity, force, or dipole moment), its value will
*NOT* be a general triclinic (rotated) value. Rather it will be a
restricted triclinic value.
----------
The *time* keyword only applies to the dump *atom*, *custom*, *local*,
@ -835,6 +849,29 @@ The default setting is *no*\ .
----------
The *triclinic/general* keyword only applies to the dump *atom* and
*custom* styles. It can only be used with a value of *yes* if the
simulation box was created as a general triclinic box. See the
:doc:`Howto_triclinic <Howto_triclinic>` doc page for a detailed
explanation of orthogonal, restricted triclinic, and general triclinic
simulation boxes.
If this keyword is used with a value of *yes*, the box information at
the beginning of each snapshot will include information about the 3
arbitrary edge vectors **A**, **B**, **C** that define the general
triclinic box as well as their origin. The format is described on the
:doc:`dump <dump>` doc page.
The coordinates of each atom will likewise be output as values in (or
near) the general triclinic box. Likewise, per-atom vector quantities
such as velocity, omega, dipole moment, etc will have orientations
consistent with the general triclinic box, meaning they will be
rotated relative to the standard xyz coordinate axes. See the
:doc:`dump <dump>` doc page for a full list of which dump attributes
this affects.
----------
The *units* keyword only applies to the dump *atom*, *custom*, and
*local* styles (and their COMPRESS package versions *atom/gz*,
*custom/gz* and *local/gz*\ ). If set to *yes*, each individual dump
@ -922,6 +959,8 @@ The option defaults are
* sort = off for dump styles *atom*, *custom*, *cfg*, and *local*
* sort = id for dump styles *dcd*, *xtc*, and *xyz*
* thresh = none
* time = no
* triclinic/general no
* units = no
* unwrap = no

2
doc/src/fix.rst
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@ -226,6 +226,7 @@ accelerated styles exist.
* :doc:`controller <fix_controller>` - apply control loop feedback mechanism
* :doc:`damping/cundall <fix_damping_cundall>` - Cundall non-viscous damping for granular simulations
* :doc:`deform <fix_deform>` - change the simulation box size/shape
* :doc:`deform/pressure <fix_deform_pressure>` - change the simulation box size/shape with additional loading conditions
* :doc:`deposit <fix_deposit>` - add new atoms above a surface
* :doc:`dpd/energy <fix_dpd_energy>` - constant energy dissipative particle dynamics
* :doc:`drag <fix_drag>` - drag atoms towards a defined coordinate
@ -427,6 +428,7 @@ accelerated styles exist.
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` - time integration for body particles of style :doc:`rounded/polyhedron <Howto_body>`
* :doc:`wall/colloid <fix_wall>` - Lennard-Jones wall interacting with finite-size particles
* :doc:`wall/ees <fix_wall_ees>` - wall for ellipsoidal particles
* :doc:`wall/flow <fix_wall_flow>` - flow boundary conditions
* :doc:`wall/gran <fix_wall_gran>` - frictional wall(s) for granular simulations
* :doc:`wall/gran/region <fix_wall_gran_region>` - :doc:`fix wall/region <fix_wall_region>` equivalent for use with granular particles
* :doc:`wall/harmonic <fix_wall>` - harmonic spring wall

2
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@ -168,7 +168,7 @@ the following global cumulative quantities:
* 1 = swap attempts
* 2 = swap accepts
The vector values calculated by this fix are "extensive".
The vector values calculated by this fix are "intensive".
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

28
doc/src/fix_ave_chunk.rst
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@ -31,7 +31,7 @@ Syntax
v_name = per-atom vector calculated by an atom-style variable with name
* zero or more keyword/arg pairs may be appended
* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *format* or *title1* or *title2* or *title3*
* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *append* or *overwrite* or *format* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -51,6 +51,8 @@ Syntax
dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
*file* arg = filename
filename = file to write results to
*append* arg = filename
filename = file to append results to
*overwrite* arg = none = overwrite output file with only latest output
*format* arg = string
string = C-style format string
@ -433,15 +435,21 @@ molecule.
----------
The *file* keyword allows a filename to be specified. Every
:math:`N_\text{freq}` timesteps, a section of chunk info will be written to a
text file in the following format. A line with the timestep and number of
chunks is written. Then one line per chunk is written, containing the chunk
ID :math:`(1-N_\text{chunk}),` an optional original ID value, optional
coordinate values for chunks that represent spatial bins, the number of atoms
in the chunk, and one or more calculated values. More explanation of the
optional values is given below. The number of values in each line
corresponds to the number of values specified in the fix ave/chunk
.. versionadded:: 17Apr2024
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every :math:`N_\text{freq}`
timesteps, a section of chunk info will be written to a text file in the
following format. A line with the timestep and number of chunks is
written. Then one line per chunk is written, containing the chunk ID
:math:`(1-N_\text{chunk}),` an optional original ID value, optional
coordinate values for chunks that represent spatial bins, the number of
atoms in the chunk, and one or more calculated values. More explanation
of the optional values is given below. The number of values in each
line corresponds to the number of values specified in the fix ave/chunk
command. The number of atoms and the value(s) are summed or average
quantities, as explained above.

1
doc/src/fix_ave_correlate.rst
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@ -65,7 +65,6 @@ Examples
fix 1 all ave/correlate 1 50 10000 &
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
type upper ave running title1 "My correlation data"
fix 1 all ave/correlate 1 50 10000 c_thermo_press[*]
Description

13
doc/src/fix_ave_correlate_long.rst
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@ -20,11 +20,11 @@ Syntax
.. parsed-literal::
c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
v_name = global value calculated by an equal-style variable with name
v_name[I] = Ith component of global vector calculated by a vector-style variable with name
v_name[I] = Ith component of a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount*
@ -63,6 +63,7 @@ Examples
fix 1 all ave/correlate/long 1 10000 &
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
type upper title1 "My correlation data" nlen 15 ncount 3
fix 1 all ave/correlate/long 1 10000 c_thermo_press[*]
Description
"""""""""""
@ -80,8 +81,10 @@ specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each listed value can be the result of a compute or fix or the
evaluation of an equal-style variable. See the
:doc:`fix ave/correlate <fix_ave_correlate>` page for details.
evaluation of an equal-style or vector-style variable. For
vector-style variables, the specified indices can include a wildcard
character. See the :doc:`fix ave/correlate <fix_ave_correlate>` page
for details.
The *Nevery* and *Nfreq* arguments specify on what time steps the input
values will be used to calculate correlation data and the frequency

36
doc/src/fix_ave_histo.rst
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@ -35,7 +35,7 @@ Syntax
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *mode* or *kind* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
* keyword = *mode* or *kind* or *file* or *append* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -45,6 +45,8 @@ Syntax
*kind* arg = *global* or *peratom* or *local*
*file* arg = filename
filename = name of file to output histogram(s) to
*append* arg = filename
filename = name of file to append histogram(s) to
*ave* args = *one* or *running* or *window*
one = output a new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
@ -317,19 +319,25 @@ on. The default is step 0. Often input values can be 0.0 at time 0,
so setting *start* to a larger value can avoid including a 0.0 in
a running or windowed histogram.
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, one histogram is written to the file. This includes a leading
line that contains the timestep, number of bins, the total count of
values contributing to the histogram, the count of values that were
not histogrammed (see the *beyond* keyword), the minimum value
encountered, and the maximum value encountered. The min/max values
include values that were not histogrammed. Following the leading
line, one line per bin is written into the file. Each line contains
the bin #, the coordinate for the center of the bin (between *lo* and
*hi*\ ), the count of values in the bin, and the normalized count. The
normalized count is the bin count divided by the total count (not
including values not histogrammed), so that the normalized values sum
to 1.0 across all bins.
.. versionadded:: 17Apr2024
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every *Nfreq* steps, one
histogram is written to the file. This includes a leading line that
contains the timestep, number of bins, the total count of values
contributing to the histogram, the count of values that were not
histogrammed (see the *beyond* keyword), the minimum value encountered,
and the maximum value encountered. The min/max values include values
that were not histogrammed. Following the leading line, one line per
bin is written into the file. Each line contains the bin #, the
coordinate for the center of the bin (between *lo* and *hi*\ ), the
count of values in the bin, and the normalized count. The normalized
count is the bin count divided by the total count (not including values
not histogrammed), so that the normalized values sum to 1.0 across all
bins.
The *overwrite* keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of

29
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@ -28,7 +28,7 @@ Syntax
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3*
* keyword = *mode* or *file* or *append* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -45,6 +45,8 @@ Syntax
M = value # from 1 to Nvalues
*file* arg = filename
filename = name of file to output time averages to
*append* arg = filename
filename = name of file to append time averages to
*overwrite* arg = none = overwrite output file with only latest output
*format* arg = string
string = C-style format string
@ -270,16 +272,21 @@ are effectively constant or are simply current values (e.g., they are
being written to a file with other time-averaged values for purposes
of creating well-formatted output).
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, one quantity or vector of quantities is written to the file for
each input value specified in the fix ave/time command. For *mode* =
scalar, this means a single line is written each time output is
performed. Thus the file ends up to be a series of lines, i.e. one
column of numbers for each input value. For *mode* = vector, an array
of numbers is written each time output is performed. The number of rows
is the length of the input vectors, and the number of columns is the
number of values. Thus the file ends up to be a series of these array
sections.
.. versionadded:: 17Apr2024
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every *Nfreq* steps, one
quantity or vector of quantities is written to the file for each input
value specified in the fix ave/time command. For *mode* = scalar, this
means a single line is written each time output is performed. Thus the
file ends up to be a series of lines, i.e. one column of numbers for
each input value. For *mode* = vector, an array of numbers is written
each time output is performed. The number of rows is the length of the
input vectors, and the number of columns is the number of values. Thus
the file ends up to be a series of these array sections.
.. versionadded:: 4May2022

13
doc/src/fix_balance.rst
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@ -14,15 +14,15 @@ Syntax
* balance = style name of this fix command
* Nfreq = perform dynamic load balancing every this many steps
* thresh = imbalance threshold that must be exceeded to perform a re-balance
* style = *shift* or *rcb*
* style = *shift* or *rcb* or *report*
.. parsed-literal::
shift args = dimstr Niter stopthresh
*shift* args = dimstr Niter stopthresh
dimstr = sequence of letters containing *x* or *y* or *z*, each not more than once
Niter = # of times to iterate within each dimension of dimstr sequence
stopthresh = stop balancing when this imbalance threshold is reached
*rcb* args = none
*report* args = none
* zero or more keyword/arg pairs may be appended
* keyword = *weight* or *out*
@ -70,6 +70,13 @@ re-balancing is performed periodically during the simulation. To
perform "static" balancing, before or between runs, see the
:doc:`balance <balance>` command.
.. versionadded:: 17Apr2024
The *report* balance style only computes the load imbalance but
does not attempt any re-balancing. This way the load imbalance
information can be used otherwise, for instance for stopping a
run with :doc:`fix halt <fix_halt>`.
Load-balancing is typically most useful if the particles in the
simulation box have a spatially-varying density distribution or
where the computational cost varies significantly between different

10
doc/src/fix_charge_regulation.rst
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@ -253,11 +253,11 @@ built with that package. See the :doc:`Build package <Build_package>`
page for more info.
The :doc:`atom_style <atom_style>`, used must contain the charge
property, for example, the style could be *charge* or *full*. Only
usable for 3D simulations. Atoms specified as free ions cannot be part
of rigid bodies or molecules and cannot have bonding interactions. The
scheme is limited to integer charges, any atoms with non-integer charges
will not be considered by the fix.
property and have per atom type masses, for example, the style could be
*charge* or *full*. Only usable for 3D simulations. Atoms specified as
free ions cannot be part of rigid bodies or molecules and cannot have
bonding interactions. The scheme is limited to integer charges, any
atoms with non-integer charges will not be considered by the fix.
All interaction potentials used must be continuous, otherwise the MD
integration and the particle exchange MC moves do not correspond to the

181
doc/src/fix_deform.rst
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@ -4,6 +4,9 @@
fix deform command
==================
:doc:`fix deform/pressure <fix_deform_pressure>` command
========================================================
Accelerator Variants: *deform/kk*
Syntax
@ -11,18 +14,18 @@ Syntax
.. code-block:: LAMMPS
fix ID group-ID deform N parameter args ... keyword value ...
fix ID group-ID fix_style N parameter style args ... keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* deform = style name of this fix command
* fix_style = *deform* or *deform/pressure*
* N = perform box deformation every this many timesteps
* one or more parameter/arg pairs may be appended
* one or more parameter/style/args sequences of arguments may be appended
.. parsed-literal::
parameter = *x* or *y* or *z* or *xy* or *xz* or *yz*
*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*
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
@ -43,8 +46,15 @@ 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*
style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable*
*final* value = tilt
tilt = tilt factor at end of run (distance units)
*delta* value = dtilt
@ -62,9 +72,12 @@ 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*
* keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
.. parsed-literal::
@ -77,6 +90,15 @@ 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
""""""""
@ -88,6 +110,8 @@ 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
"""""""""""
@ -95,29 +119,46 @@ Change the volume and/or shape of the simulation box during a dynamics
run. Orthogonal simulation boxes have 3 adjustable parameters
(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6
adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be
adjusted independently and simultaneously by this command.
adjusted independently and simultaneously.
This fix can be used to perform non-equilibrium MD (NEMD) simulations
of a continuously strained system. See the :doc:`fix nvt/sllod <fix_nvt_sllod>` and :doc:`compute temp/deform <compute_temp_deform>` commands for more details. Note
that 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>`.
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.
Both these fixes can be used to perform non-equilibrium MD (NEMD)
simulations of a continuously strained system. See the :doc:`fix
nvt/sllod <fix_nvt_sllod>` and :doc:`compute temp/deform
<compute_temp_deform>` commands for more details. Note that
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>`.
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 this
command can be periodic or non-periodic. Dimensions corresponding to
unspecified parameters can also be controlled by a :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
second dimension cannot be shrink-wrapped. Dimensions not varied by
this command can be periodic or non-periodic. Dimensions
corresponding to unspecified parameters can also be controlled by a
:doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
The size and shape of the simulation box at the beginning of the
simulation run were either specified by the
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` command used to setup the simulation
initially if it is the first run, or they are the values from the end
of the previous run. The :doc:`create_box <create_box>`, :doc:`read data <read_data>`, and :doc:`read_restart <read_restart>` commands
specify whether the simulation box is orthogonal or non-orthogonal
(triclinic) and explain the meaning of the xy,xz,yz tilt factors. If
fix deform changes the xy,xz,yz tilt factors, then the simulation box
must be triclinic, even if its initial tilt factors are 0.0.
simulation run were either specified by the :doc:`create_box
<create_box>` or :doc:`read_data <read_data>` or :doc:`read_restart
<read_restart>` command used to setup the simulation initially if it
is the first run, or they are the values from the end of the previous
run. The :doc:`create_box <create_box>`, :doc:`read data
<read_data>`, and :doc:`read_restart <read_restart>` commands specify
whether the simulation box is orthogonal or non-orthogonal (triclinic)
and explain the meaning of the xy,xz,yz tilt factors. If fix deform
changes the xy,xz,yz tilt factors, then the simulation box must be
triclinic, even if its initial tilt factors are 0.0.
As described below, the desired simulation box size and shape at the
end of the run are determined by the parameters of the fix deform
@ -258,21 +299,22 @@ of the units keyword below.
The *variable* style changes the specified box length dimension by
evaluating a variable, which presumably is a function of time. The
variable with *name1* must be an :doc:`equal-style variable <variable>`
and should calculate a change in box length in units of distance.
Note that this distance is in box units, not lattice units; see the
discussion of the *units* keyword below. The formula associated with
variable *name1* can reference the current timestep. Note that it
should return the "change" in box length, not the absolute box length.
This means it should evaluate to 0.0 when invoked on the initial
timestep of the run following the definition of fix deform. It should
evaluate to a value > 0.0 to dilate the box at future times, or a
value < 0.0 to compress the box.
variable with *name1* must be an :doc:`equal-style variable
<variable>` and should calculate a change in box length in units of
distance. Note that this distance is in box units, not lattice units;
see the discussion of the *units* keyword below. The formula
associated with variable *name1* can reference the current timestep.
Note that it should return the "change" in box length, not the
absolute box length. This means it should evaluate to 0.0 when
invoked on the initial timestep of the run following the definition of
fix deform. It should evaluate to a value > 0.0 to dilate the box at
future times, or a value < 0.0 to compress the box.
The variable *name2* must also be an :doc:`equal-style variable <variable>` and should calculate the rate of box length
change, in units of distance/time, i.e. the time-derivative of the
*name1* variable. This quantity is used internally by LAMMPS to reset
atom velocities when they cross periodic boundaries. It is computed
The variable *name2* must also be an :doc:`equal-style variable
<variable>` and should calculate the rate of box length change, in
units of distance/time, i.e. the time-derivative of the *name1*
variable. This quantity is used internally by LAMMPS to reset atom
velocities when they cross periodic boundaries. It is computed
internally for the other styles, but you must provide it when using an
arbitrary variable.
@ -414,12 +456,13 @@ can reference the current timestep. Note that it should return the
should evaluate to 0.0 when invoked on the initial timestep of the run
following the definition of fix deform.
The variable *name2* must also be an :doc:`equal-style variable <variable>` and should calculate the rate of tilt change,
in units of distance/time, i.e. the time-derivative of the *name1*
variable. This quantity is used internally by LAMMPS to reset atom
velocities when they cross periodic boundaries. It is computed
internally for the other styles, but you must provide it when using an
arbitrary variable.
The variable *name2* must also be an :doc:`equal-style variable
<variable>` and should calculate the rate of tilt change, in units of
distance/time, i.e. the time-derivative of the *name1* variable. This
quantity is used internally by LAMMPS to reset atom velocities when
they cross periodic boundaries. It is computed internally for the
other styles, but you must provide it when using an arbitrary
variable.
Here is an example of using the *variable* style to perform the same
box deformation as the *wiggle* style formula listed above, where we
@ -510,33 +553,40 @@ box without explicit remapping of their coordinates.
.. note::
For non-equilibrium MD (NEMD) simulations using "remap v" it is
usually desirable that the fluid (or flowing material, e.g. granular
particles) stream with a velocity profile consistent with the
deforming box. As mentioned above, using a thermostat such as :doc:`fix nvt/sllod <fix_nvt_sllod>` or :doc:`fix lavgevin <fix_langevin>`
(with a bias provided by :doc:`compute temp/deform <compute_temp_deform>`), will typically accomplish
that. If you do not use a thermostat, then there is no driving force
pushing the atoms to flow in a manner consistent with the deforming
box. E.g. for a shearing system the box deformation velocity may vary
usually desirable that the fluid (or flowing material,
e.g. granular particles) stream with a velocity profile consistent
with the deforming box. As mentioned above, using a thermostat
such as :doc:`fix nvt/sllod <fix_nvt_sllod>` or :doc:`fix lavgevin
<fix_langevin>` (with a bias provided by :doc:`compute temp/deform
<compute_temp_deform>`), will typically accomplish that. If you do
not use a thermostat, then there is no driving force pushing the
atoms to flow in a manner consistent with the deforming box.
E.g. for a shearing system the box deformation velocity may vary
from 0 at the bottom to 10 at the top of the box. But the stream
velocity profile of the atoms may vary from -5 at the bottom to +5 at
the top. You can monitor these effects using the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`compute temp/deform <compute_temp_deform>`, and :doc:`compute temp/profile <compute_temp_profile>` commands. One way to induce
atoms to stream consistent with the box deformation is to give them an
velocity profile of the atoms may vary from -5 at the bottom to +5
at the top. You can monitor these effects using the :doc:`fix
ave/chunk <fix_ave_chunk>`, :doc:`compute temp/deform
<compute_temp_deform>`, and :doc:`compute temp/profile
<compute_temp_profile>` commands. One way to induce atoms to
stream consistent with the box deformation is to give them an
initial velocity profile, via the :doc:`velocity ramp <velocity>`
command, that matches the box deformation rate. This also typically
helps the system come to equilibrium more quickly, even if a
thermostat is used.
command, that matches the box deformation rate. This also
typically helps the system come to equilibrium more quickly, even
if a thermostat is used.
.. note::
If a :doc:`fix rigid <fix_rigid>` is defined for rigid bodies, and
*remap* is set to *x*, then the center-of-mass coordinates of rigid
bodies will be remapped to the changing simulation box. This will be
done regardless of whether atoms in the rigid bodies are in the fix
deform group or not. The velocity of the centers of mass are not
remapped even if *remap* is set to *v*, since :doc:`fix nvt/sllod <fix_nvt_sllod>` does not currently do anything special
bodies will be remapped to the changing simulation box. This will
be done regardless of whether atoms in the rigid bodies are in the
fix deform group or not. The velocity of the centers of mass are
not remapped even if *remap* is set to *v*, since :doc:`fix
nvt/sllod <fix_nvt_sllod>` does not currently do anything special
for rigid particles. If you wish to perform a NEMD simulation of
rigid particles, you can either thermostat them independently or
include a background fluid and thermostat the fluid via :doc:`fix nvt/sllod <fix_nvt_sllod>`.
include a background fluid and thermostat the fluid via :doc:`fix
nvt/sllod <fix_nvt_sllod>`.
The *flip* keyword allows the tilt factors for a triclinic box to
exceed half the distance of the parallel box length, as discussed
@ -568,7 +618,8 @@ command if you want to include lattice spacings in a variable formula.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix will restore the initial box settings from :doc:`binary restart files <restart>`, which allows the fix to be properly continue
This fix will restore the initial box settings from :doc:`binary
restart files <restart>`, which allows the fix to be properly continue
deformation, when using the start/stop options of the :doc:`run <run>`
command. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global or per-atom quantities are stored by
@ -586,12 +637,14 @@ Restrictions
You cannot apply x, y, or z deformations to a dimension that is
shrink-wrapped via the :doc:`boundary <boundary>` command.
You cannot apply xy, yz, or xz deformations to a second dimension (y in
xy) that is shrink-wrapped via the :doc:`boundary <boundary>` command.
You cannot apply xy, yz, or xz deformations to a second dimension (y
in xy) that is shrink-wrapped via the :doc:`boundary <boundary>`
command.
Related commands
""""""""""""""""
:doc:`fix deform/pressure <fix_deform_pressure>`,
:doc:`change_box <change_box>`
Default

336
doc/src/fix_deform_pressure.rst Normal file
View File

@ -0,0 +1,336 @@
.. index:: fix deform/pressure
fix deform/pressure command
===========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID deform/pressure N parameter style args ... keyword value ...
* 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
.. 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*
*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*
*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*
*volume* value = none = isotropically adjust system to preserve volume of system
*pressure* values = target gain
target = target mean 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*
.. parsed-literal::
*couple* value = *none* or *xyz* or *xy* or *yz* or *xz*
couple pressure values of various dimensions
*vol/balance/p* value = *yes* or *no*
Modifies the behavior of the *volume* option to try and balance pressures
*max/rate* value = *rate*
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
""""""""
.. code-block:: LAMMPS
fix 1 all deform/pressure 1 x pressure 2.0 0.1 normalize/pressure yes max/rate 0.001
fix 1 all deform/pressure 1 x trate 0.1 y volume z volume vol/balance/p yes
fix 1 all deform/pressure 1 x trate 0.1 y pressure/mean 0.0 1.0 z pressure/mean 0.0 1.0
Description
"""""""""""
.. versionadded:: 17Apr2024
This fix is an extension of the :doc:`fix deform <fix_deform>`
command, which allows all of its options to be used as well as new
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
simulation can define only a single deformation command: fix deform or
fix deform/pressure.
----------
For the *x*, *y*, and *z* parameters, this is the meaning of the
styles and values provided by this fix.
The *pressure* style adjusts a dimension's box length to control the
corresponding component of the pressure tensor. This option attempts to
maintain a specified target pressure using a linear controller where the
box length :math:`L` evolves according to the equation
.. math::
\frac{d L(t)}{dt} = L(t) k (P_t - P)
where :math:`k` is a proportional gain constant, :math:`P_t` is the target
pressure, and :math:`P` is the current pressure along that dimension. This
approach is similar to the method used to control the pressure by
:doc:`fix press/berendsen <fix_press_berendsen>`. The target pressure
accepts either a constant numeric value or a LAMMPS :ref:`variable <variable>`.
Notably, this variable can be a function of time or other components of
the pressure tensor. By default, :math:`k` has units of 1/(time * pressure)
although this will change if the *normalize/pressure* option is set as
:ref:`discussed below <deform_normalize>`. There is no proven method
to choosing an appropriate value of :math:`k` as it will depend on the
specific details of a simulation. Testing different values is recommended.
By default, there is no limit on the resulting strain rate in any dimension.
A maximum limit can be applied using the :ref:`max/rate <deform_max_rate>`
option. Akin to :doc:`fix nh <fix_nh>`, pressures in different dimensions
can be coupled using the :ref:`couple <deform_couple>` option. This means
the instantaneous pressure along coupled dimensions are averaged and the box
strains identically along the coupled dimensions.
The *pressure/mean* style changes a dimension's box length to maintain
a constant mean pressure defined as the trace of the pressure tensor.
This option has identical arguments to the *pressure* style and a similar
functional equation, except the current and target pressures refer to the
mean trace of the pressure tensor. All options for the *pressure* style
also apply to the *pressure/mean* style except for the
:ref:`couple <deform_couple>` option.
Note that while this style can be identical to coupled *pressure* styles,
it is generally not the same. For instance in 2D, a coupled *pressure*
style in the *x* and *y* dimensions would be equivalent to using the
*pressure/mean* style with identical settings in each dimension. However,
it would not be the same if settings (e.g. gain constants) were used in
the *x* and *y* dimensions or if the *pressure/mean* command was only applied
along one dimension.
----------
For the *xy*, *xz*, and *yz* parameters, this is the meaning of the
styles and values provided by this fix. Note that changing the
tilt factors of a triclinic box does not change its volume.
The *pressure* style adjusts a tilt factor to control the corresponding
off-diagonal component of the pressure tensor. This option attempts to
maintain a specified target value using a linear controller where the
tilt factor T evolves according to the equation
.. parsed-literal::
\frac{d T(t)}{dt} = L(t) k (P - P_t)
where :math:`k` is a proportional gain constant, :math:`P_t` is the
target pressure, :math:`P` is the current pressure, and :math:`L` is
the perpendicular box length. The target pressure accepts either a
constant numeric value or a LAMMPS :ref:`variable
<variable>`. Notably, this variable can be a function of time or other
components of the pressure tensor. By default, :math:`k` has units of
1/(time * pressure) although this will change if the
*normalize/pessure* option is set as :ref:`discussed below
<deform_normalize>`. There is no proven method to choosing an
appropriate value of :math:`k` as it will depend on the specific
details of a simulation and testing different values is
recommended. One can also apply a maximum limit to the magnitude of
the applied strain using the :ref:`max/rate <deform_max_rate>` option.
The *erate/rescale* style operates similarly to the *erate* style with
a specified strain rate in units of 1/time. The difference is that
the change in the tilt factor will depend on the current length of
the box perpendicular to the shear direction, L, instead of the
original length, L0. The tilt factor T as a function of time will
change as
.. parsed-literal::
T(t) = T(t-1) + L\*erate\* \Delta t
where T(t-1) is the tilt factor on the previous timestep and :math:`\Delta t`
is the timestep size. This option may be useful in scenarios where
L changes in time.
----------
The *box* parameter provides an additional control over the *x*, *y*,
and *z* box lengths by isotropically dilating or contracting the box
to either maintain a fixed mean pressure or volume. This isotropic
scaling is applied after the box is deformed by the above *x*, *y*,
*z*, *xy*, *xz*, and *yz* styles, acting as a second deformation
step. This parameter will change the overall strain rate in the *x*,
*y*, or *z* dimensions. This parameter can only be used in
combination with the *x*, *y*, or *z* commands: *vel*, *erate*,
*trate*, *pressure*, or *wiggle*. This is the meaning of its styles
and values.
The *volume* style isotropically scales box lengths to maintain a constant
box volume in response to deformation from other parameters. This style
may be useful in scenarios where one wants to apply a constant deviatoric
pressure using *pressure* styles in the *x*, *y*, and *z* dimensions (
deforming the shape of the box), while maintaining a constant volume.
The *pressure* style isotropically scales box lengths in an attempt to
maintain a target mean pressure (the trace of the pressure tensor) of the
system. This is accomplished by isotropically scaling all box lengths
:math:`L` by an additional factor of :math:`k (P_t - P_m)` where :math:`k`
is the proportional gain constant, :math:`P_t` is the target pressure, and
:math:`P_m` is the current mean pressure. This style may be useful in
scenarios where one wants to apply a constant deviatoric strain rate
using various strain-based styles (e.g. *trate*) along the *x*, *y*, and *z*
dimensions (deforming the shape of the box), while maintaining a mean pressure.
----------
The optional keywords provided by this fix are described below.
.. _deform_normalize:
The *normalize/pressure* keyword changes how box dimensions evolve when
using the *pressure* or *pressure/mean* deformation styles. If the
*deform/normalize* value is set to *yes*, then the deviation from the
target pressure is normalized by the absolute value of the target
pressure such that the proportional gain constant scales a percentage
error and has units of 1/time. If the target pressure is ever zero, this
will produce an error unless the *max/rate* keyword is defined,
described below, which will cap the divergence.
.. _deform_max_rate:
The *max/rate* keyword sets an upper threshold, *rate*, that limits the
maximum magnitude of the instantaneous strain rate applied in any dimension.
This keyword only applies to the *pressure* and *pressure/mean* options. If
a pressure-controlled rate is used for both *box* and either *x*, *y*, or
*z*, then this threshold will apply separately to each individual controller
such that the cumulative strain rate on a box dimension may be up to twice
the value of *rate*.
.. _deform_couple:
The *couple* keyword allows two or three of the diagonal components of
the pressure tensor to be "coupled" together for the *pressure* option.
The value specified with the keyword determines which are coupled. For
example, *xz* means the *Pxx* and *Pzz* components of the stress tensor
are coupled. *Xyz* means all 3 diagonal components are coupled. Coupling
means two things: the instantaneous stress will be computed as an average
of the corresponding diagonal components, and the coupled box dimensions
will be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. If a *pressure*
style is defined for more than one coupled dimension, the target pressures
and gain constants must be identical. Alternatively, if a *pressure*
style is only defined for one of the coupled dimensions, its settings are
copied to other dimensions with undefined styles. *Couple xyz* can be used
for a 2d simulation; the *z* dimension is simply ignored.
.. _deform_balance:
The *vol/balance/p* keyword modifies the behavior of the *volume* style when
applied to two of the *x*, *y*, and *z* dimensions. Instead of straining
the two dimensions in lockstep, the two dimensions are allowed to
separately dilate or contract in a manner to maintain a constant
volume while simultaneously trying to keep the pressure along each
dimension equal using a method described in :ref:`(Huang2014) <Huang2014>`.
----------
If any pressure controls are used, this fix computes a temperature and
pressure each timestep. To do this, the fix creates its own computes
of style "temp" and "pressure", as if these commands had been issued:
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure
<compute_pressure>` commands for details. Note that the IDs of the
new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press", and the group for the new computes is the same
as the fix group.
Note that these are NOT the computes used by thermodynamic output (see
the :doc:`thermo_style <thermo_style>` command) with ID =
*thermo_temp* and *thermo_press*. This means you can change the
attributes of this fix's temperature or pressure via the
:doc:`compute_modify <compute_modify>` command or print this
temperature or pressure during thermodynamic output via the
:doc:`thermo_style custom <thermo_style>` command using the
appropriate compute-ID. It also means that changing attributes of
*thermo_temp* or *thermo_press* will have no effect on this fix.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix will restore the initial box settings from :doc:`binary
restart files <restart>`, which allows the fix to be properly continue
deformation, when using the start/stop options of the :doc:`run <run>`
command. No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`.
If any pressure controls are used, the :doc:`fix_modify <fix_modify>`
*temp* and *press* options are supported by this fix, unlike in
:doc:`fix deform <fix_deform>`. You can use them to assign a
:doc:`compute <compute>` you have defined to this fix which will be
used in its temperature and pressure calculations. If you do this,
note that the kinetic energy derived from the compute temperature
should be consistent with the virial term computed using all atoms for
the pressure. LAMMPS will warn you if you choose to compute
temperature on a subset of atoms.
This fix can perform deformation over multiple runs, using the *start*
and *stop* keywords of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this.
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
You cannot apply x, y, or z deformations to a dimension that is
shrink-wrapped via the :doc:`boundary <boundary>` command.
You cannot apply xy, yz, or xz deformations to a second dimension (y
in xy) that is shrink-wrapped via the :doc:`boundary <boundary>`
command.
Related commands
""""""""""""""""
:doc:`fix deform <fix_deform>`, :doc:`change_box <change_box>`
Default
"""""""
The option defaults are normalize/pressure = no.
----------
.. _Huang2014:
**(Huang2014)** X. Huang, "Exploring critical-state behavior using DEM",
Doctoral dissertation, Imperial College. (2014). https://doi.org/10.25560/25316

27
doc/src/fix_electrode.rst
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@ -45,7 +45,7 @@ Syntax
rng_v = integer used to initialize random number generator
* zero or more keyword/value pairs may be appended
* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv*
* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* or *qtotal* or *eta*
.. parsed-literal::
@ -68,6 +68,10 @@ Syntax
filename = file from which to read elastance matrix
*read_inv* value = filename
filename = file from which to read inverted matrix
*qtotal* value = number or *v_* equal-style variable
add overall potential so that all electrode charges add up to *qtotal*
*eta* value = d_propname
d_propname = a custom double vector defined via fix property/atom
Examples
""""""""
@ -249,6 +253,27 @@ be enabled if any electrode particle has the same type as any
electrolyte particle (which would be unusual in a typical simulation)
and the fix will issue an error in that case.
.. versionadded:: 17Apr2024
The keyword *qtotal* causes *fix electrode/conp* and *fix
electrode/thermo* to add an overall potential to all electrodes so that
the total charge on the electrodes is a specified amount (which may be
an equal-style variable). For example, if a user wanted to simulate a
solution of excess cations such that the total electrolyte charge is +2,
setting *qtotal -2* would cause the total electrode charge to be -2, so
that the simulation box remains overall electroneutral. Since *fix
electrode/conq* constrains the total charges of individual electrodes,
and since *symm on* constrains the total charge of all electrodes to be
zero, either option is incompatible with the *qtotal* keyword (even if
*qtotal* is set to zero).
.. versionadded:: 17Apr2024
The keyword *eta* takes the name of a custom double vector defined via
fix property/atom. The values will be used instead of the standard eta
value. The property/atom fix must be for vector of double values and
use the *ghost on* option.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

7
doc/src/fix_gcmc.rst
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@ -427,7 +427,7 @@ the following global cumulative quantities:
* 7 = rotation attempts
* 8 = rotation successes
The vector values calculated by this fix are "extensive".
The vector values calculated by this fix are "intensive".
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
@ -440,8 +440,11 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
This fix style requires an :doc:`atom style <atom_style>` with per atom
type masses.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
called. Reneighboring is **required**.
Only usable for 3D simulations.

3
doc/src/fix_hyper_local.rst
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@ -512,8 +512,7 @@ Value 27 computes the average boost for biased bonds only on this step.
Value 28 is the count of bonds with an absolute value of strain >= q
on this step.
The scalar value is an "extensive" quantity since it grows with the
system size; the vector values are all "intensive".
The scalar value and vector values are all "intensive".
This fix also computes a local vector of length the number of bonds
currently in the system. The value for each bond is its :math:`C_{ij}`

90
doc/src/fix_indent.rst
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@ -8,33 +8,44 @@ Syntax
.. code-block:: LAMMPS
fix ID group-ID indent K keyword values ...
fix ID group-ID indent K gstyle args keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* indent = style name of this fix command
* K = force constant for indenter surface (force/distance\^2 units)
* one or more keyword/value pairs may be appended
* keyword = *sphere* or *cylinder* or *plane* or *side* or *units*
* gstyle = *sphere* or *cylinder* or *cone* or *plane*
.. parsed-literal::
*sphere* args = x y z R
x,y,z = position of center of indenter (distance units)
x, y, z = position of center of indenter (distance units)
R = sphere radius of indenter (distance units)
any of x,y,z,R can be a variable (see below)
any of x, y, z, R can be a variable (see below)
*cylinder* args = dim c1 c2 R
dim = *x* or *y* or *z* = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
c1, c2 = coords of cylinder axis in other 2 dimensions (distance units)
R = cylinder radius of indenter (distance units)
any of c1,c2,R can be a variable (see below)
*cone* args = dim c1 c2 radlo radhi lo hi
dim = *x* or *y* or *z* = axis of cone
c1, c2 = coords of cone axis in other 2 dimensions (distance units)
radlo,radhi = cone radii at lo and hi end (distance units)
lo,hi = bounds of cone in dim (distance units)
any of c1, c2, radlo, radhi, lo, hi can be a variable (see below)
*plane* args = dim pos side
dim = *x* or *y* or *z* = plane perpendicular to this dimension
pos = position of plane in dimension x, y, or z (distance units)
pos can be a variable (see below)
side = *lo* or *hi*
* zero or more keyword/value pairs may be appended
* keyword = *side* or *units*
.. parsed-literal::
*side* value = *in* or *out*
*in* = the indenter acts on particles inside the sphere or cylinder
*out* = the indenter acts on particles outside the sphere or cylinder
*in* = the indenter acts on particles inside the sphere or cylinder or cone
*out* = the indenter acts on particles outside the sphere or cylinder or cone
*units* value = *lattice* or *box*
lattice = the geometry is defined in lattice units
box = the geometry is defined in simulation box units
@ -53,12 +64,12 @@ Description
Insert an indenter within a simulation box. The indenter repels all
atoms in the group that touch it, so it can be used to push into a
material or as an obstacle in a flow. Or it can be used as a
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 indenter can either be spherical or cylindrical or planar. You
must set one of those 3 keywords.
The *gstyle* geometry of the indenter can either be a sphere, a
cylinder, a cone, or a plane.
A spherical indenter exerts a force of magnitude
@ -75,15 +86,20 @@ 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.
Spherical and cylindrical indenters account for periodic boundaries in
two ways. First, the center point of a spherical indenter (x,y,z) or
axis of a cylindrical indenter (c1,c2) is remapped back into the
simulation box, if the box is periodic in a particular dimension.
This occurs every timestep if the indenter geometry is specified with
a variable (see below), e.g. it is moving over time. Second, the
calculation of distance to the indenter center 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 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.
Spherical, cylindrical, and conical indenters account for periodic
boundaries in two ways. First, the center point of a spherical
indenter (x,y,z) or axis of a cylindrical/conical indenter (c1,c2) is
remapped back into the simulation box, if the box is periodic in a
particular dimension. This occurs every timestep if the indenter
geometry is specified with a variable (see below), e.g. it is moving
over time. Second, the calculation of distance to the indenter center
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
@ -97,9 +113,13 @@ 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*,
*y*, *z*, or *R*\ . Similarly, for a cylindrical indenter, any of *c1*,
*c2*, or *R*, can be a variable. For a planar indenter, *pos* can be
a variable. If the value is a variable, it should be specified as
*y*, *z*, or *R*\ . For a cylindrical indenter, any of the 3
quantities *c1*, *c2*, or *R*, can be a variable. For a conical
indenter, any of the 6 quantities *c1*, *c2*, *radlo*, *radhi*, *lo*,
or *hi* can be a variable. For a planar indenter, the single value
*pos* can be a variable.
If any of these values 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 timestep, and its value used to define the
indenter geometry.
@ -110,7 +130,8 @@ command keywords for the simulation box parameters and timestep and
elapsed time. Thus it is easy to specify indenter properties that
change as a function of time or span consecutive runs in a continuous
fashion. For the latter, see the *start* and *stop* keywords of the
:doc:`run <run>` command and the *elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for details.
:doc:`run <run>` command and the *elaplong* keyword of
:doc:`thermo_style custom <thermo_style>` for details.
For example, if a spherical indenter's x-position is specified as v_x,
then this variable definition will keep it's center at a relative
@ -141,12 +162,13 @@ rate.
If the *side* keyword is specified as *out*, which is the default,
then particles outside the indenter are pushed away from its outer
surface, as described above. This only applies to spherical or
cylindrical indenters. If the *side* keyword is specified as *in*,
the action of the indenter is reversed. Particles inside the indenter
are pushed away from its inner surface. In other words, the indenter
is now a containing wall that traps the particles inside it. If the
radius shrinks over time, it will squeeze the particles.
surface, as described above. This only applies to spherical,
cylindrical, and conical indenters. If the *side* keyword is
specified as *in*, the action of the indenter is reversed. Particles
inside the indenter are pushed away from its inner surface. In other
words, the indenter is now a containing wall that traps the particles
inside it. If the radius shrinks over time, it will squeeze the
particles.
The *units* keyword determines the meaning of the distance units used
to define the indenter geometry. A *box* value selects standard
@ -166,10 +188,10 @@ lattice spacings in a variable formula.
The force constant *K* is not affected by the *units* keyword. It is
always in force/distance\^2 units where force and distance are defined
by the :doc:`units <units>` command. If you wish K to be scaled by the
lattice spacing, you can define K with a variable whose formula
contains *xlat*, *ylat*, *zlat* keywords of the
:doc:`thermo_style <thermo_style>` command, e.g.
by the :doc:`units <units>` command. If you wish K to be scaled by
the lattice spacing, you can define K with a variable whose formula
contains *xlat*, *ylat*, *zlat* keywords of the :doc:`thermo_style
<thermo_style>` command, e.g.
.. code-block:: LAMMPS

2
doc/src/fix_mol_swap.rst
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@ -146,7 +146,7 @@ the following global cumulative quantities:
* 1 = swap attempts
* 2 = swap accepts
The vector values calculated by this fix are "extensive".
The vector values calculated by this fix are "intensive".
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

19
doc/src/fix_nonaffine_displacement.rst
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@ -8,7 +8,7 @@ Syntax
.. parsed-literal::
fix ID group nonaffine/displacement style args reference/style nstep
fix ID group nonaffine/displacement style args reference/style nstep keyword values
* ID, group are documented in :doc:`fix <fix>` command
* nonaffine/displacement = style name of this fix command
@ -32,6 +32,13 @@ Syntax
*update* = update the reference frame every *nstep* timesteps
*offset* = update the reference frame *nstep* timesteps before calculating the nonaffine displacement
* zero or more keyword/value pairs may be appended
.. parsed-literal::
*z/min* values = zmin
zmin = minimum coordination number to calculate D2min
Examples
""""""""
@ -76,6 +83,12 @@ is the identity tensor. This calculation is only performed on timesteps that
are a multiple of *nevery* (including timestep zero). Data accessed before
this occurs will simply be zeroed.
For particles with low coordination numbers, calculations of :math:`D^2_\mathrm{min}`
may not be accurate. An optional minimum coordination number can be defined using
the *z/min* keyword. If any particle has fewer than the specified number of particles
in the cutoff distance or in contact, the above calculations will be skipped and the
corresponding peratom array entries will be zero.
The *integrated* style simply integrates the velocity of particles
every timestep to calculate a displacement. This style only works if
used in conjunction with another fix that deforms the box and displaces
@ -86,8 +99,8 @@ Both of these methods require defining a reference state. With the *fixed* refer
style, the user picks a specific timestep *nstep* at which particle positions are saved.
If peratom data is accessed from this compute prior to this timestep, it will simply be
zeroed. The *update* reference style implies the reference state will be updated every
*nstep* timesteps. The *offset* reference only applies to the *d2min* metric and will
update the reference state *nstep* timesteps before a multiple of *nevery* timesteps.
*nstep* timesteps. The *offset* reference will update the reference state *nstep*
timesteps before a multiple of *nevery* timesteps.
----------

17
doc/src/fix_property_atom.rst
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@ -22,6 +22,8 @@ Syntax
*mol* = molecule IDs
*q* = charge
*rmass* = per-atom mass
*temperature* = internal temperature of atom
*heatflow* = internal heat flow of atom
i_name = new integer vector referenced by name
d_name = new floating-point vector referenced by name
i2_name = new integer array referenced by name
@ -59,14 +61,18 @@ these properties for each atom in the system when a data file is read.
This fix augments the set of per-atom properties with new custom
ones. This can be useful in several scenarios.
If the atom style does not define molecule IDs, per-atom charge, or
per-atom mass, they can be added using the *mol*\ , *q* or *rmass*
If the atom style does not define molecule IDs, per-atom charge,
per-atom mass, internal temperature, or internal heat flow, they can
be added using the *mol*\ , *q*, *rmass*, *temperature*, or *heatflow*
keywords. This could be useful to define "molecules" to use as rigid
bodies with the :doc:`fix rigid <fix_rigid>` command, or to carry
around an extra flag with atoms (stored as a molecule ID) that can be
used by various commands like :doc:`compute chunk/atom
<compute_chunk_atom>` to group atoms without having to use the group
command (which is limited to a total of 32 groups including *all*\ ).
For finite-size particles, an internal temperature and heat flow can
be used to model heat conduction as in the
:doc:`GRANULAR package <Howto_granular>`.
Another application is to use the *rmass* flag in order to have
per-atom masses instead of per-type masses. This could be used to
@ -85,9 +91,10 @@ properties that are not needed such as bond lists, which incurs some
overhead when there are no bonds.
In the future, we may add additional existing per-atom properties to
fix property/atom, similar to *mol*\ , *q* or *rmass*\ , which
"turn-on" specific properties defined by some atom styles, so they can
be easily used by atom styles that do not define them.
fix property/atom, similar to *mol*\ , *q*, *rmass*\ , *temperature*\ ,
or *heatflow* which "turn-on" specific properties defined by some atom
styles, so they can be easily used by atom styles that do not define
them.
More generally, the *i_name* and *d_name* options allow one or more
new custom per-atom vectors to be defined. Likewise the *i2_name* and

12
doc/src/fix_reaxff_species.rst
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@ -20,7 +20,7 @@ Syntax
* Nfreq = calculate average bond-order every this many timesteps
* filename = name of output file
* zero or more keyword/value pairs may be appended
* keyword = *cutoff* or *element* or *position* or *delete*
* keyword = *cutoff* or *element* or *position* or *delete* or *delete_rate_limit*
.. parsed-literal::
@ -110,10 +110,10 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
The optional keyword *element* can be used to specify the chemical
symbol printed for each LAMMPS atom type. The number of symbols must
match the number of LAMMPS atom types and each symbol must consist of
1 or 2 alphanumeric characters. Normally, these symbols should be
chosen to match the chemical identity of each LAMMPS atom type, as
specified using the :doc:`reaxff pair_coeff <pair_reaxff>` command and
the ReaxFF force field file.
1 or 2 alphanumeric characters. By default, these symbols are the same
as the chemical identity of each LAMMPS atom type, as specified by the
:doc:`ReaxFF pair_coeff <pair_reaxff>` command and the ReaxFF force
field file.
The optional keyword *position* writes center-of-mass positions of
each identified molecules to file *filepos* every *posfreq* timesteps.
@ -233,5 +233,5 @@ Default
"""""""
The default values for bond-order cutoffs are 0.3 for all I-J pairs.
The default element symbols are C, H, O, N.
The default element symbols are taken from the ReaxFF pair_coeff command.
Position files are not written by default.

281
doc/src/fix_rigid.rst
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@ -171,14 +171,15 @@ Examples of large rigid bodies are a colloidal particle, or portions
of a biomolecule such as a protein.
Example of small rigid bodies are patchy nanoparticles, such as those
modeled in :ref:`this paper <Zhang1>` by Sharon Glotzer's group, clumps of
granular particles, lipid molecules consisting of one or more point
dipoles connected to other spheroids or ellipsoids, irregular
particles built from line segments (2d) or triangles (3d), and
coarse-grain models of nano or colloidal particles consisting of a
small number of constituent particles. Note that the :doc:`fix shake <fix_shake>` command can also be used to rigidify small
molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats
the constituent atoms as point masses.
modeled in :ref:`this paper <Zhang1>` by Sharon Glotzer's group,
clumps of granular particles, lipid molecules consisting of one or
more point dipoles connected to other spheroids or ellipsoids,
irregular particles built from line segments (2d) or triangles (3d),
and coarse-grain models of nano or colloidal particles consisting of a
small number of constituent particles. Note that the :doc:`fix shake
<fix_shake>` command can also be used to rigidify small molecules of
2, 3, or 4 atoms, e.g. water molecules. That fix treats the
constituent atoms as point masses.
These fixes also update the positions and velocities of the atoms in
each rigid body via time integration, in the NVE, NVT, NPT, or NPH
@ -212,13 +213,14 @@ processors when ghost atom info is accumulated.
.. note::
To use the *rigid/small* styles the ghost atom cutoff must be
large enough to span the distance between the atom that owns the body
and every other atom in the body. This distance value is printed out
when the rigid bodies are defined. If the
:doc:`pair_style <pair_style>` cutoff plus neighbor skin does not span
this distance, then you should use the :doc:`comm_modify cutoff <comm_modify>` command with a setting epsilon larger than
the distance.
To use the *rigid/small* styles the ghost atom cutoff must be large
enough to span the distance between the atom that owns the body and
every other atom in the body. This distance value is printed out
when the rigid bodies are defined. If the :doc:`pair_style
<pair_style>` cutoff plus neighbor skin does not span this
distance, then you should use the :doc:`comm_modify cutoff
<comm_modify>` command with a setting epsilon larger than the
distance.
Which of the two variants is faster for a particular problem is hard
to predict. The best way to decide is to perform a short test run.
@ -229,49 +231,54 @@ differences may accumulate to produce divergent trajectories.
.. note::
You should not update the atoms in rigid bodies via other
time-integration fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`fix move <fix_move>`),
or you will have conflicting updates to positions and velocities
resulting in unphysical behavior in most cases. When performing a hybrid
simulation with some atoms in rigid bodies, and some not, a separate
time integration fix like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` should be used for the non-rigid particles.
time-integration fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix
nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`fix move
<fix_move>`), or you will have conflicting updates to positions and
velocities resulting in unphysical behavior in most cases. When
performing a hybrid simulation with some atoms in rigid bodies, and
some not, a separate time integration fix like :doc:`fix nve
<fix_nve>` or :doc:`fix nvt <fix_nh>` should be used for the
non-rigid particles.
.. note::
These fixes are overkill if you simply want to hold a collection
of atoms stationary or have them move with a constant velocity. A
simpler way to hold atoms stationary is to not include those atoms in
your time integration fix. E.g. use "fix 1 mobile nve" instead of
"fix 1 all nve", where "mobile" is the group of atoms that you want to
move. You can move atoms with a constant velocity by assigning them
an initial velocity (via the :doc:`velocity <velocity>` command),
setting the force on them to 0.0 (via the :doc:`fix setforce <fix_setforce>` command), and integrating them as usual
(e.g. via the :doc:`fix nve <fix_nve>` command).
These fixes are overkill if you simply want to hold a collection of
atoms stationary or have them move with a constant velocity. A
simpler way to hold atoms stationary is to not include those atoms
in your time integration fix. E.g. use "fix 1 mobile nve" instead
of "fix 1 all nve", where "mobile" is the group of atoms that you
want to move. You can move atoms with a constant velocity by
assigning them an initial velocity (via the :doc:`velocity
<velocity>` command), setting the force on them to 0.0 (via the
:doc:`fix setforce <fix_setforce>` command), and integrating them
as usual (e.g. via the :doc:`fix nve <fix_nve>` command).
.. warning::
The aggregate properties of each rigid body are
calculated at the start of a simulation run and are maintained in
internal data structures. The properties include the position and
velocity of the center-of-mass of the body, its moments of inertia, and
its angular momentum. This is done using the properties of the
constituent atoms of the body at that point in time (or see the *infile*
keyword option). Thereafter, changing these properties of individual
atoms in the body will have no effect on a rigid body's dynamics, unless
they effect any computation of per-atom forces or torques. If the
keyword *reinit* is set to *yes* (the default), the rigid body data
structures will be recreated at the beginning of each *run* command;
if the keyword *reinit* is set to *no*, the rigid body data structures
will be built only at the very first *run* command and maintained for
as long as the rigid fix is defined. For example, you might think you
could displace the atoms in a body or add a large velocity to each atom
in a body to make it move in a desired direction before a second run is
performed, using the :doc:`set <set>` or
:doc:`displace_atoms <displace_atoms>` or :doc:`velocity <velocity>`
commands. But these commands will not affect the internal attributes
of the body unless *reinit* is set to *yes*\ . With *reinit* set to *no*
(or using the *infile* option, which implies *reinit* *no*\ ) the position
and velocity of individual atoms in the body will be reset when time
integration starts again.
The aggregate properties of each rigid body are calculated at the
start of a simulation run and are maintained in internal data
structures. The properties include the position and velocity of the
center-of-mass of the body, its moments of inertia, and its angular
momentum. This is done using the properties of the constituent
atoms of the body at that point in time (or see the *infile*
keyword option). Thereafter, changing these properties of
individual atoms in the body will have no effect on a rigid body's
dynamics, unless they effect any computation of per-atom forces or
torques. If the keyword *reinit* is set to *yes* (the default), the
rigid body data structures will be recreated at the beginning of
each *run* command; if the keyword *reinit* is set to *no*, the
rigid body data structures will be built only at the very first
*run* command and maintained for as long as the rigid fix is
defined. For example, you might think you could displace the atoms
in a body or add a large velocity to each atom in a body to make it
move in a desired direction before a second run is performed, using
the :doc:`set <set>` or :doc:`displace_atoms <displace_atoms>` or
:doc:`velocity <velocity>` commands. But these commands will not
affect the internal attributes of the body unless *reinit* is set
to *yes*\ . With *reinit* set to *no* (or using the *infile*
option, which implies *reinit* *no*\ ) the position and velocity of
individual atoms in the body will be reset when time integration
starts again.
----------
@ -316,17 +323,17 @@ to be part of rigid bodies.
.. note::
To compute the initial center-of-mass position and other
properties of each rigid body, the image flags for each atom in the
body are used to "unwrap" the atom coordinates. Thus you must ensure
that these image flags are consistent so that the unwrapping creates a
To compute the initial center-of-mass position and other properties
of each rigid body, the image flags for each atom in the body are
used to "unwrap" the atom coordinates. Thus you must ensure that
these image flags are consistent so that the unwrapping creates a
valid rigid body (one where the atoms are close together),
particularly if the atoms in a single rigid body straddle a periodic
boundary. This means the input data file or restart file must define
the image flags for each atom consistently or that you have used the
:doc:`set <set>` command to specify them correctly. If a dimension is
non-periodic then the image flag of each atom must be 0 in that
dimension, else an error is generated.
particularly if the atoms in a single rigid body straddle a
periodic boundary. This means the input data file or restart file
must define the image flags for each atom consistently or that you
have used the :doc:`set <set>` command to specify them correctly.
If a dimension is non-periodic then the image flag of each atom
must be 0 in that dimension, else an error is generated.
The *force* and *torque* keywords discussed next are only allowed for
the *rigid* styles.
@ -362,12 +369,13 @@ settings from the final keyword are used.
.. note::
For computational efficiency, you may wish to turn off pairwise
and bond interactions within each rigid body, as they no longer
contribute to the motion. The :doc:`neigh_modify exclude <neigh_modify>` and :doc:`delete_bonds <delete_bonds>`
commands are used to do this. If the rigid bodies have strongly
overlapping atoms, you may need to turn off these interactions to
avoid numerical problems due to large equal/opposite intra-body forces
For computational efficiency, you may wish to turn off pairwise and
bond interactions within each rigid body, as they no longer
contribute to the motion. The :doc:`neigh_modify exclude
<neigh_modify>` and :doc:`delete_bonds <delete_bonds>` commands are
used to do this. If the rigid bodies have strongly overlapping
atoms, you may need to turn off these interactions to avoid
numerical problems due to large equal/opposite intra-body forces
swamping the contribution of small inter-body forces.
For computational efficiency, you should typically define one fix
@ -379,7 +387,8 @@ is more expensive.
The constituent particles within a rigid body can be point particles
(the default in LAMMPS) or finite-size particles, such as spheres or
ellipsoids or line segments or triangles. See the :doc:`atom_style sphere and ellipsoid and line and tri <atom_style>` commands for more
ellipsoids or line segments or triangles. See the :doc:`atom_style
sphere and ellipsoid and line and tri <atom_style>` commands for more
details on these kinds of particles. Finite-size particles contribute
differently to the moment of inertia of a rigid body than do point
particles. Finite-size particles can also experience torque (e.g. due
@ -389,7 +398,8 @@ orientation. These contributions are accounted for by these fixes.
Forces between particles within a body do not contribute to the
external force or torque on the body. Thus for computational
efficiency, you may wish to turn off pairwise and bond interactions
between particles within each rigid body. The :doc:`neigh_modify exclude <neigh_modify>` and :doc:`delete_bonds <delete_bonds>`
between particles within each rigid body. The :doc:`neigh_modify
exclude <neigh_modify>` and :doc:`delete_bonds <delete_bonds>`
commands are used to do this. For finite-size particles this also
means the particles can be highly overlapped when creating the rigid
body.
@ -401,16 +411,17 @@ perform constant NVE time integration. They are referred to below as
the 4 NVE rigid styles. The only difference is that the *rigid* and
*rigid/small* styles use an integration technique based on Richardson
iterations. The *rigid/nve* and *rigid/small/nve* styles uses the
methods described in the paper by :ref:`Miller <Miller3>`, which are thought
to provide better energy conservation than an iterative approach.
methods described in the paper by :ref:`Miller <Miller3>`, which are
thought to provide better energy conservation than an iterative
approach.
The *rigid/nvt* and *rigid/nvt/small* styles performs constant NVT
integration using a Nose/Hoover thermostat with chains as described
originally in :ref:`(Hoover) <Hoover>` and :ref:`(Martyna) <Martyna2>`, which
thermostats both the translational and rotational degrees of freedom
of the rigid bodies. They are referred to below as the 2 NVT rigid
styles. The rigid-body algorithm used by *rigid/nvt* is described in
the paper by :ref:`Kamberaj <Kamberaj>`.
originally in :ref:`(Hoover) <Hoover>` and :ref:`(Martyna)
<Martyna2>`, which thermostats both the translational and rotational
degrees of freedom of the rigid bodies. They are referred to below as
the 2 NVT rigid styles. The rigid-body algorithm used by *rigid/nvt*
is described in the paper by :ref:`Kamberaj <Kamberaj>`.
The *rigid/npt*, *rigid/nph*, *rigid/npt/small*, and *rigid/nph/small*
styles perform constant NPT or NPH integration using a Nose/Hoover
@ -436,12 +447,12 @@ The target pressures for each of the 6 components of the stress tensor
can be specified independently via the *x*, *y*, *z* keywords, which
correspond to the 3 simulation box dimensions. For each component,
the external pressure or tensor component at each timestep is a ramped
value during the run from *Pstart* to *Pstop*\ . If a target pressure is
specified for a component, then the corresponding box dimension will
change during a simulation. For example, if the *y* keyword is used,
the y-box length will change. A box dimension will not change if that
component is not specified, although you have the option to change
that dimension via the :doc:`fix deform <fix_deform>` command.
value during the run from *Pstart* to *Pstop*\ . If a target pressure
is specified for a component, then the corresponding box dimension
will change during a simulation. For example, if the *y* keyword is
used, the y-box length will change. A box dimension will not change
if that component is not specified, although you have the option to
change that dimension via the :doc:`fix deform <fix_deform>` command.
For all barostat keywords, the *Pdamp* parameter operates like the
*Tdamp* parameter, determining the time scale on which pressure is
@ -525,11 +536,11 @@ discussed below.
The *langevin* keyword applies a Langevin thermostat to the constant
NVE time integration performed by any of the 4 NVE rigid styles:
*rigid*, *rigid/nve*, *rigid/small*, *rigid/small/nve*\ . It cannot be
used with the 2 NVT rigid styles: *rigid/nvt*, *rigid/small/nvt*\ . The
desired temperature at each timestep is a ramped value during the run
from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in time
units and determines how rapidly the temperature is relaxed. For
*rigid*, *rigid/nve*, *rigid/small*, *rigid/small/nve*\ . It cannot
be used with the 2 NVT rigid styles: *rigid/nvt*, *rigid/small/nvt*\ .
The desired temperature at each timestep is a ramped value during the
run from *Tstart* to *Tstop*\ . The *Tdamp* parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (:math:`\tau` or fs or ps - see the
:doc:`units <units>` command). The random # *seed* must be a positive
@ -564,29 +575,30 @@ used. *Tchain* is the number of thermostats in the Nose Hoover chain.
This value, along with *Tdamp* can be varied to dampen undesirable
oscillations in temperature that can occur in a simulation. As a rule
of thumb, increasing the chain length should lead to smaller
oscillations. The keyword *pchain* specifies the number of
thermostats in the chain thermostatting the barostat degrees of
freedom.
oscillations. The keyword *pchain* specifies the number of thermostats
in the chain thermostatting the barostat degrees of freedom.
.. note::
There are alternate ways to thermostat a system of rigid bodies.
You can use :doc:`fix langevin <fix_langevin>` to treat the individual
particles in the rigid bodies as effectively immersed in an implicit
solvent, e.g. a Brownian dynamics model. For hybrid systems with both
rigid bodies and solvent particles, you can thermostat only the
solvent particles that surround one or more rigid bodies by
appropriate choice of groups in the compute and fix commands for
temperature and thermostatting. The solvent interactions with the
rigid bodies should then effectively thermostat the rigid body
temperature as well without use of the Langevin or Nose/Hoover options
associated with the fix rigid commands.
You can use :doc:`fix langevin <fix_langevin>` to treat the
individual particles in the rigid bodies as effectively immersed in
an implicit solvent, e.g. a Brownian dynamics model. For hybrid
systems with both rigid bodies and solvent particles, you can
thermostat only the solvent particles that surround one or more
rigid bodies by appropriate choice of groups in the compute and fix
commands for temperature and thermostatting. The solvent
interactions with the rigid bodies should then effectively
thermostat the rigid body temperature as well without use of the
Langevin or Nose/Hoover options associated with the fix rigid
commands.
----------
The *mol* keyword can only be used with the *rigid/small* styles. It
must be used when other commands, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`, add rigid
bodies on-the-fly during a simulation. You specify a *template-ID*
must be used when other commands, such as :doc:`fix deposit
<fix_deposit>` or :doc:`fix pour <fix_pour>`, add rigid bodies
on-the-fly during a simulation. You specify a *template-ID*
previously defined using the :doc:`molecule <molecule>` command, which
reads a file that defines the molecule. You must use the same
*template-ID* that the other fix which is adding rigid bodies uses.
@ -670,16 +682,16 @@ cross periodic boundaries during the simulation.
.. note::
If you use the *infile* or *mol* keywords and write restart
files during a simulation, then each time a restart file is written,
the fix also write an auxiliary restart file with the name
rfile.rigid, where "rfile" is the name of the restart file,
If you use the *infile* or *mol* keywords and write restart files
during a simulation, then each time a restart file is written, the
fix also write an auxiliary restart file with the name rfile.rigid,
where "rfile" is the name of the restart file,
e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
file is in the same format described above. Thus it can be used in a
new input script that restarts the run and re-specifies a rigid fix
using an *infile* keyword and the appropriate filename. Note that the
auxiliary file will contain one line for every rigid body, even if the
original file only listed a subset of the rigid bodies.
file is in the same format described above. Thus it can be used in
a new input script that restarts the run and re-specifies a rigid
fix using an *infile* keyword and the appropriate filename. Note
that the auxiliary file will contain one line for every rigid body,
even if the original file only listed a subset of the rigid bodies.
If the system has rigid bodies with finite-size overlapping particles
and the model uses the :doc:`fix gravity <fix_gravity>` command to
@ -728,10 +740,11 @@ also accounted for by this fix.
----------
If your simulation is a hybrid model with a mixture of rigid bodies and
non-rigid particles (e.g. solvent) there are several ways these rigid
fixes can be used in tandem with :doc:`fix nve <fix_nve>`, :doc:`fix nvt
<fix_nh>`, :doc:`fix npt <fix_nh>`, and :doc:`fix nph <fix_nh>`.
If your simulation is a hybrid model with a mixture of rigid bodies
and non-rigid particles (e.g. solvent) there are several ways these
rigid fixes can be used in tandem with :doc:`fix nve <fix_nve>`,
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, and :doc:`fix nph
<fix_nh>`.
If you wish to perform NVE dynamics (no thermostatting or
barostatting), use one of 4 NVE rigid styles to integrate the rigid
@ -741,14 +754,14 @@ particles.
If you wish to perform NVT dynamics (thermostatting, but no
barostatting), you can use one of the 2 NVT rigid styles for the rigid
bodies, and any thermostatting fix for the non-rigid particles
(:doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix
temp/berendsen <fix_temp_berendsen>`). You can also use one of the 4
NVE rigid styles for the rigid bodies and thermostat them using
:doc:`fix langevin <fix_langevin>` on the group that contains all the
particles in the rigid bodies. The net force added by :doc:`fix
langevin <fix_langevin>` to each rigid body effectively thermostats its
translational center-of-mass motion. Not sure how well it does at
thermostatting its rotational motion.
(:doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`,
:doc:`fix temp/berendsen <fix_temp_berendsen>`). You can also use one
of the 4 NVE rigid styles for the rigid bodies and thermostat them
using :doc:`fix langevin <fix_langevin>` on the group that contains
all the particles in the rigid bodies. The net force added by
:doc:`fix langevin <fix_langevin>` to each rigid body effectively
thermostats its translational center-of-mass motion. Not sure how
well it does at thermostatting its rotational motion.
If you wish to perform NPT or NPH dynamics (barostatting), you cannot
use both :doc:`fix npt <fix_nh>` and the NPT or NPH rigid styles. This
@ -774,12 +787,12 @@ to the global pressure and the box is scaled the same by any of the
barostatting fixes.
You could even use the second and third options for a non-hybrid
simulation consisting of only rigid bodies, assuming you give :doc:`fix
npt <fix_nh>` an empty group, though it's an odd thing to do. The
barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen
<fix_press_berendsen>`) will monitor the pressure and change the box
dimensions, but not time integrate any particles. The integration of
the rigid bodies will be performed by fix rigid/nvt.
simulation consisting of only rigid bodies, assuming you give
:doc:`fix npt <fix_nh>` an empty group, though it's an odd thing to
do. The barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix
press/berensen <fix_press_berendsen>`) will monitor the pressure and
change the box dimensions, but not time integrate any particles. The
integration of the rigid bodies will be performed by fix rigid/nvt.
----------
@ -824,10 +837,10 @@ various :doc:`output commands <Howto_output>`. The scalar value
calculated by these fixes is "intensive". The scalar is the current
temperature of the collection of rigid bodies. This is averaged over
all rigid bodies and their translational and rotational degrees of
freedom. The translational energy of a rigid body is 1/2 m v\^2, where
m = total mass of the body and v = the velocity of its center of mass.
The rotational energy of a rigid body is 1/2 I w\^2, where I = the
moment of inertia tensor of the body and w = its angular velocity.
freedom. The translational energy of a rigid body is 1/2 m v\^2,
where m = total mass of the body and v = the velocity of its center of
mass. The rotational energy of a rigid body is 1/2 I w\^2, where I =
the moment of inertia tensor of the body and w = its angular velocity.
Degrees of freedom constrained by the *force* and *torque* keywords
are removed from this calculation, but only for the *rigid* and
*rigid/nve* fixes.

5
doc/src/fix_sgcmc.rst
View File

@ -148,6 +148,8 @@ components of the vector represent the following quantities:
* ...
* N+2: The current global concentration of species *X* (= number of atoms of type *N* / total number of atoms)
The vector values calculated by this fix are "intensive".
Restrictions
""""""""""""
@ -155,6 +157,9 @@ This fix is part of the MC 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 style requires an :doc:`atom style <atom_style>` with per atom
type masses.
At present the fix provides optimized subroutines for EAM type
potentials (see above) that calculate potential energy changes due to
*local* atom type swaps very efficiently. Other potentials are

103
doc/src/fix_ttm.rst
View File

@ -96,11 +96,11 @@ each processor, which is acceptable when the overall grid is reasonably
small. For larger grids you should use fix *ttm/grid* instead.
Fix *ttm/mod* adds options to account for external heat sources (e.g. at
a surface) and for specifying parameters that allow the electronic
heat capacity to depend strongly on electronic temperature. It is
more expensive computationally than fix *ttm* because it treats the
thermal diffusion equation as non-linear. More details on fix *ttm/mod*
are given below.
a surface) and for specifying parameters that allow the electronic heat
capacity to depend strongly on electronic temperature. It is more
expensive computationally than fix *ttm* because it treats the thermal
diffusion equation as non-linear. More details on fix *ttm/mod* are
given below.
Heat transfer between the electronic and atomic subsystems is carried
out via an inhomogeneous Langevin thermostat. Only atoms in the fix
@ -136,23 +136,23 @@ transfer between the subsystems:
\bigtriangledown (\kappa_e \bigtriangledown T_e) -
g_p (T_e - T_a) + g_s T_a'
where C_e is the specific heat, rho_e is the density, kappa_e is the
thermal conductivity, T is temperature, the "e" and "a" subscripts
represent electronic and atomic subsystems respectively, g_p is the
coupling constant for the electron-ion interaction, and g_s is the
electron stopping coupling parameter. C_e, rho_e, and kappa_e are
specified as parameters to the fix. The other quantities are derived.
The form of the heat diffusion equation used here is almost the same
as that in equation 6 of :ref:`(Duffy) <Duffy>`, with the exception that the
electronic density is explicitly represented, rather than being part
of the specific heat parameter.
where :math:`C_e` is the specific heat, :math:`\rho_e` is the density,
:math:`\kappa_e` is the thermal conductivity, *T* is temperature, the
"e" and "a" subscripts represent electronic and atomic subsystems
respectively, :math:`g_p` is the coupling constant for the electron-ion
interaction, and :math:`g_s` is the electron stopping coupling
parameter. :math:`C_e`, :math:`\rho_e`, and :math:`\kappa_e` are
specified as parameters to the fix *ttm* or *ttm/grid*. The other
quantities are derived. The form of the heat diffusion equation used
here is almost the same as that in equation 6 of :ref:`(Duffy) <Duffy>`,
with the exception that the electronic density is explicitly
represented, rather than being part of the specific heat parameter.
Currently, the TTM fixes assume that none of the user-supplied
parameters will vary with temperature. Note that :ref:`(Duffy)
<Duffy>` used a tanh() functional form for the temperature dependence
of the electronic specific heat, but ignored temperature dependencies
of any of the other parameters. See more discussion below for fix
ttm/mod.
parameters will vary with temperature. Note that :ref:`(Duffy) <Duffy>`
used a tanh() functional form for the temperature dependence of the
electronic specific heat, but ignored temperature dependencies of any of
the other parameters. See more discussion below for fix *ttm/mod*.
.. note::
@ -265,27 +265,27 @@ heat sources (e.g. laser heating in ablation simulations):
\bigtriangledown (\kappa_e \bigtriangledown T_e) -
g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin})
where theta is the Heaviside step function, I_0 is the (absorbed)
laser pulse intensity for ablation simulations, l_skin is the depth
of skin-layer, and all other designations have the same meaning as in
the former equation. The duration of the pulse is set by the parameter
*tau* in the *init_file*.
where :math:`\theta` is the Heaviside step function, :math:`I_0` is the
(absorbed) laser pulse intensity for ablation simulations,
:math:`l_{skin}` is the depth of the skin-layer, and all other
designations have the same meaning as in the former equation. The
duration of the pulse is set by the parameter *tau* in the *init_file*.
Fix ttm/mod also allows users to specify the dependencies of C_e and
kappa_e on the electronic temperature. The specific heat is expressed
as
Fix *ttm/mod* also allows users to specify the dependencies of
:math:`C_e` and :math:`\kappa_e` on the electronic temperature. The
specific heat is expressed as
.. math::
C_e = C_0 + (a_0 + a_1 X + a_2 X^2 + a_3 X^3 + a_4 X^4) \exp (-(AX)^2)
where *X* = T_e/1000, and the thermal conductivity is defined as
kappa_e = D_e\*rho_e\*C_e, where D_e is the thermal diffusion
coefficient.
where :math:`X = \frac{T_e}{1000}`, and the thermal conductivity is
defined as :math:`\kappa_e = D_e \cdot rho_e \cdot C_e`, where
:math:`D_e` is the thermal diffusion coefficient.
Electronic pressure effects are included in the TTM model to account
for the blast force acting on ions because of electronic pressure
gradient (see :ref:`(Chen) <Chen>`, :ref:`(Norman) <Norman>`). The total force
Electronic pressure effects are included in the TTM model to account for
the blast force acting on ions because of electronic pressure gradient
(see :ref:`(Chen) <Chen>`, :ref:`(Norman) <Norman>`). The total force
acting on an ion is:
.. math::
@ -293,25 +293,26 @@ acting on an ion is:
{\vec F}_i = - \partial U / \partial {\vec r}_i + {\vec
F}_{langevin} - \nabla P_e/n_{ion}
where F_langevin is a force from Langevin thermostat simulating
electron-phonon coupling, and nabla P_e/n_ion is the electron blast
force.
where :math:`F_{langevin}` is a force from Langevin thermostat
simulating electron-phonon coupling, and :math:`\nabla P_e/n_{ion}` is
the electron blast force.
The electronic pressure is taken to be P_e = B\*rho_e\*C_e\*T_e
The electronic pressure is taken to be :math:`P_e = B \cdot rho_e \cdot
C_e \cdot T_e`
The current fix ttm/mod implementation allows TTM simulations with a
The current fix *ttm/mod* implementation allows TTM simulations with a
vacuum. The vacuum region is defined as the grid cells with zero
electronic temperature. The numerical scheme does not allow energy
exchange with such cells. Since the material can expand to previously
unoccupied region in some simulations, the vacuum border can be
allowed to move. It is controlled by the *surface_movement* parameter
in the *init_file*. If it is set to 1, then "vacuum" cells can be
changed to "electron-filled" cells with the temperature *T_e_min* if
atoms move into them (currently only implemented for the case of
1-dimensional motion of flat surface normal to the X axis). The
initial borders of vacuum can be set in the *init_file* via *lsurface*
and *rsurface* parameters. In this case, electronic pressure gradient
is calculated as
unoccupied region in some simulations, the vacuum border can be allowed
to move. It is controlled by the *surface_movement* parameter in the
*init_file*. If it is set to 1, then "vacuum" cells can be changed to
"electron-filled" cells with the temperature *T_e_min* if atoms move
into them (currently only implemented for the case of 1-dimensional
motion of a flat surface normal to the X axis). The initial locations of
the interfaces of the electron density to the vacuum can be set in the
*init_file* via *lsurface* and *rsurface* parameters. In this case,
electronic pressure gradient is calculated as
.. math::
@ -319,10 +320,10 @@ is calculated as
\frac{x}{x+\lambda}\frac{(C_e{}T_e)_{x+\Delta
x}-(C_e{}T_e)_{x}}{\Delta x} \right]
where lambda is the electron mean free path (see :ref:`(Norman) <Norman>`,
:ref:`(Pisarev) <Pisarev>`)
where :math:`\lambda` is the electron mean free path (see :ref:`(Norman)
<Norman>`, :ref:`(Pisarev) <Pisarev>`)
The fix ttm/mod parameter file *init_file* has the following syntax.
The fix *ttm/mod* parameter file *init_file* has the following syntax.
Every line with an odd number is considered as a comment and
ignored. The lines with the even numbers are treated as follows:

175
doc/src/fix_wall_flow.rst Normal file
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@ -0,0 +1,175 @@
.. index:: fix wall/flow
.. index:: fix wall/flow/kk
fix wall/flow command
=====================
Accelerator Variants: *wall/flow/kk*
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID wall/flow axis vflow T seed N coords ... keyword value
* ID, group-ID are documented in :doc:`fix <fix>` command
* wall/flow = style name of this fix command
* axis = flow axis (*x*, *y*, or *z*)
* vflow = generated flow velocity in *axis* direction (velocity units)
* T = flow temperature (temperature units)
* seed = random seed for stochasticity (positive integer)
* N = number of walls
* coords = list of N wall positions along the *axis* direction in ascending order (distance units)
* zero or more keyword/value pairs may be appended
* keyword = *units*
.. parsed-literal::
*units* value = *lattice* or *box*
*lattice* = wall positions are defined in lattice units
*box* = the wall positions are defined in simulation box units
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all wall/flow x 0.4 1.5 593894 4 2.0 4.0 6.0 8.0
Description
"""""""""""
.. versionadded:: 17Apr2024
This fix implements flow boundary conditions (FBC) introduced in
:ref:`(Pavlov1) <fbc-Pavlov1>` and :ref:`(Pavlov2) <fbc-Pavlov2>`.
The goal is to generate a stationary flow with a shifted Maxwell
velocity distribution:
.. math::
f_a(v_a) \propto \exp{\left(-\frac{m (v_a-v_{\text{flow}})^2}{2 kB T}\right)}
where :math:`v_a` is the component of velocity along the specified
*axis* argument (a = x,y,z), :math:`v_{\text{flow}}` is the flow
velocity specified as the *vflow* argument, *T* is the specified flow
temperature, *m* is the particle mass, and *kB* is the Boltzmann
constant.
This is achieved by defining a series of *N* transparent walls along
the flow *axis* direction. Each wall is at the specified position
listed in the *coords* argument. Note that an additional transparent
wall is defined by the code at the boundary of the (periodic)
simulation domain in the *axis* direction. So there are effectively
N+1 walls.
Each time a particle in the specified group passes through one of the
transparent walls, its velocity is re-assigned. Particles not in the
group do not interact with the wall. This can be used, for example, to
add obstacles composed of atoms, or to simulate a solution of complex
molecules in a one-atom liquid (note that the fix has been tested for
one-atom systems only).
Conceptually, the velocity re-assignment represents creation of a new
particle within the system with simultaneous removal of the particle
which passed through the wall. The velocity components in directions
parallel to the wall are re-assigned according to the standard Maxwell
velocity distribution for the specified temperature *T*. The velocity
component perpendicular to the wall is re-assigned according to the
shifted Maxwell distribution defined above:
.. math::
f_{\text{a generated}}(v_a) \propto v_a f_a(v_a)
It can be shown that for an ideal-gas scenario this procedure makes
the velocity distribution of particles between walls exactly as
desired.
Since in most cases simulated systems are not an ideal gas, multiple
walls can be defined, since a single wall may not be sufficient for
maintaining a stationary flow without "congestion" which can manifest
itself as regions in the flow with increased particle density located
upstream from static obstacles.
For the same reason, the actual temperature and velocity of the
generated flow may differ from what is requested. The degree of
discrepancy is determined by how different from an ideal gas the
simulated system is. Therefore, a calibration procedure may be
required for such a system as described in :ref:`(Pavlov)
<fbc-Pavlov2>`.
Note that the interactions between particles on different sides of a
transparent wall are not disabled or neglected. Likewise particle
positions are not altered by the velocity reassignment. This removes
the need to modify the force field to work correctly in cases when a
particle is close to a wall.
For example, if particle positions were uniformly redistributed across
the surface of a wall, two particles could end up too close to each
other, potentially causing the simulation to explode. However due to
this compromise, some collective phenomena such as regions with
increased/decreased density or collective movements are not fully
removed when particles cross a wall. This unwanted consequence can
also be potentially mitigated by using more multiple walls.
.. note::
When the specified flow has a high velocity, a lost atoms error can
occur (see :doc:`error messages <Errors_messages>`). If this
happens, you should ensure the checks for neighbor list rebuilds,
set via the :doc:`neigh_modify <neigh_modify>` command, are as
conservative as possible (every timestep if needed). Those are the
default settings.
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
""""""""""""
Fix *wall_flow* is part of the EXTRA-FIX package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Flow boundary conditions should not be used with rigid bodies such as
those defined by a "fix rigid" command.
This fix can only be used with periodic boundary conditions along the
flow axis. The size of the box in this direction must not change. Also,
the fix is designed to work only in an orthogonal simulation box.
Related commands
""""""""""""""""
:doc:`fix wall/reflect <fix_wall>` command
Default
"""""""
The default for the units keyword is lattice.
----------
.. _fbc-Pavlov1:
**(Pavlov1)** Pavlov, Kolotinskii, Stegailov, "GPU-Based Molecular Dynamics of Turbulent Liquid Flows with OpenMM", Proceedings of PPAM-2022, LNCS (Springer), vol. 13826, pp. 346-358 (2023)
.. _fbc-Pavlov2:
**(Pavlov2)** Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. Appl., (2024)

9
doc/src/fix_widom.rst
View File

@ -179,7 +179,7 @@ the following global cumulative quantities:
* 2 = average difference in potential energy on each timestep
* 3 = volume of the insertion region
The vector values calculated by this fix are "extensive".
The vector values calculated by this fix are "intensive".
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
@ -195,8 +195,11 @@ doc page for more info.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is **required**.
Can be run in parallel, but aspects of the GCMC part will not scale well
in parallel. Only usable for 3D simulations.
This fix style requires an :doc:`atom style <atom_style>` with per atom
type masses.
Can be run in parallel, but some aspects of the insertion procedure
will not scale well in parallel. Only usable for 3D simulations.
Related commands

9
doc/src/labelmap.rst
View File

@ -43,7 +43,8 @@ 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.
labels can be used. See :ref:`(Gissinger) <Typelabel>` 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
@ -98,3 +99,9 @@ Default
"""""""
none
-----------
.. _Typelabel:
**(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).

96
doc/src/lattice.rst
View File

@ -19,7 +19,7 @@ Syntax
scale = lattice constant in distance units (for all other units)
* zero or more keyword/value pairs may be appended
* keyword = *origin* or *orient* or *spacing* or *a1* or *a2* or *a3* or *basis*
* keyword = *origin* or *orient* or *spacing* or *a1* or *a2* or *a3* or *basis* or *triclinic/general*
.. parsed-literal::
@ -34,6 +34,7 @@ Syntax
x,y,z = primitive vector components that define unit cell
*basis* values = x y z
x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1)
*triclinic/general* values = no values
Examples
""""""""
@ -44,7 +45,7 @@ Examples
lattice hex 0.85
lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 triclinic/general
lattice none 2.0
Description
@ -129,10 +130,13 @@ and a3 are 3 orthogonal unit vectors (edges of a unit cube). But you
can specify them to be of any length and non-orthogonal to each other,
so that they describe a tilted parallelepiped. Via the *basis*
keyword you add atoms, one at a time, to the unit cell. Its arguments
are fractional coordinates (0.0 <= x,y,z < 1.0). The position vector
x of a basis atom within the unit cell is thus a linear combination of
the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3,
where bx,by,bz are the 3 values specified for the *basis* keyword.
are fractional coordinates (0.0 <= x,y,z < 1.0). For 2d simulations,
the fractional z coordinate for any basis atom must be 0.0.
The position vector x of a basis atom within the unit cell is a linear
combination of the unit cell's 3 edge vectors, i.e. x = bx a1 + by
a2 + bz a3, where bx,by,bz are the 3 values specified for the *basis*
keyword.
----------
@ -168,18 +172,21 @@ The *origin* option specifies how the unit cell will be shifted or
translated when mapping it into the simulation box. The x,y,z values
are fractional values (0.0 <= x,y,z < 1.0) meaning shift the lattice
by a fraction of the lattice spacing in each dimension. The meaning
of "lattice spacing" is discussed below.
of "lattice spacing" is discussed below. For 2d simulations, the
*origin* z value must be 0.0.
The *orient* option specifies how the unit cell will be rotated when
mapping it into the simulation box. The *dim* argument is one of the
3 coordinate axes in the simulation box. The other 3 arguments are
the crystallographic direction in the lattice that you want to orient
along that axis, specified as integers. E.g. "orient x 2 1 0" means
the x-axis in the simulation box will be the [210] lattice
direction, and similarly for y and z. The 3 lattice directions you
specify do not have to be unit vectors, but they must be mutually
orthogonal and obey the right-hand rule, i.e. (X cross Y) points in
the Z direction.
the x-axis in the simulation box will be the [210] lattice direction,
and similarly for y and z. The 3 lattice directions you specify do
not have to be unit vectors, but they must be mutually orthogonal and
obey the right-hand rule, i.e. (X cross Y) points in the Z direction.
For 2d simulations, the *orient* x and y vectors must define 0 for
their 3rd component. Similarly the *orient* z vector must define 0
for its 1st and 2nd components.
.. note::
@ -193,6 +200,59 @@ the Z direction.
----------
The *triclinic/general* option specifies that the defined lattice is
for use with a general triclinic simulation box, as opposed to an
orthogonal or restricted triclinic box. The :doc:`Howto triclinic
<Howto_triclinic>` doc page explains all 3 kinds of simulation boxes
LAMMPS supports.
If this option is specified, a *custom* lattice style must be used.
The *a1*, *a2*, *a3* vectors should define the edge vectors of a
single unit cell of the lattice with one or more basis atoms. They
edge vectors can be arbitrary so long as they are non-zero, distinct,
and not co-planar. In addition, they must define a right-handed
system, such that (*a1* cross *a2*) points in the direction of *a3*.
Note that a left-handed system can be converted to a right-handed
system by simply swapping the order of any pair of the *a1*, *a2*,
*a3* vectors. For 2d simulations, the *a3* vector must be specified
as (0.0,0.0,1.0), which is its default value.
If this option is used, the *origin* and *orient* settings must have
their default values. Namely (0.0,0.0,0.0) for the *origin* and
(100), (010), (001) for the *orient* vectors.
The :doc:`create_box <create_box>` command can be used to create a
general triclinic box that replicates the *a1*, *a2*, *a3* unit cell
vectors in each direction to create the 3 arbitrary edge vectors of
the overall simulation box. It requires a lattice with the
*triclinic/general* option.
Likewise, the :doc:`create_atoms <create_atoms>` command can be used
to add atoms (or molecules) to a general triclinic box which lie on
the lattice points defined by *a1*, *a2*, *a3* and the unit cell basis
atoms. To do this, it also requires a lattice with the
*triclinic/general* option.
.. note::
LAMMPS allows specification of general triclinic lattices and
simulation boxes as a convenience for users who may be converting
data from solid-state crystallographic representations or from DFT
codes for input to LAMMPS. However, as explained on the
:doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
LAMMPS only uses restricted triclinic simulation boxes. This means
the box and per-atom information (e.g. coordinates, velocities)
defined by the :doc:`create_box <create_box>` and
:doc:`create_atoms <create_atoms>` commands are converted from
general to restricted triclinic form when the two commands are
invoked. It also means that any other commands which use lattice
spacings from this command (e.g. the region command), will be
operating on a restricted triclinic simulation box, even if the
*triclinic/general* option was used to define the lattice. See the
next section for details.
----------
Several LAMMPS commands have the option to use distance units that are
inferred from "lattice spacings" in the x,y,z box directions.
E.g. the :doc:`region <region>` command can create a block of size
@ -216,6 +276,18 @@ coordinates of the 8 corner points of the modified unit cell (4 in
2d). Similarly, the Y and Z lattice spacings are defined as the
difference in the min/max of the y and z coordinates.
.. note::
If the *triclinic/general* option is specified, the unit cell
defined by *a1*, *a2*, *a3* edge vectors is first converted to a
restricted triclinic orientation, which is a rotation operation.
The min/max extent of the 8 corner points is then determined, as
described in the preceding paragraph, to set the lattice
spacings. As explained for the *triclinic/general* option above,
this is because any use of the lattice spacings by other commands
will be for a restricted triclinic simulation box, not a general
triclinic box.
Note that if the unit cell is orthogonal with axis-aligned edges (no
rotation via the *orient* keyword), then the lattice spacings in each
dimension are simply the scale factor (described above) multiplied by

125
doc/src/package.rst
View File

@ -74,7 +74,7 @@ Syntax
*no_affinity* values = none
*kokkos* args = keyword value ...
zero or more keyword/value pairs may be appended
keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *neigh/transpose* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/pair/forward* or *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *sort* or *gpu/aware* or *pair/only*
keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *neigh/transpose* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/pair/forward* or *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *sort* or *atom/map* or *gpu/aware* or *pair/only*
*neigh* value = *full* or *half*
full = full neighbor list
half = half neighbor list built in thread-safe manner
@ -108,6 +108,9 @@ Syntax
*sort* value = *no* or *device*
*no* = perform atom sorting in non-KOKKOS mode
*device* = perform atom sorting on device (e.g. on GPU)
*atom/map* value = *no* or *device*
*no* = build atom map in non-KOKKOS mode
*device* = build atom map on device (e.g. on GPU)
*gpu/aware* = *off* or *on*
*off* = do not use GPU-aware MPI
*on* = use GPU-aware MPI (default)
@ -566,15 +569,19 @@ performing the exchange pack/unpack on the host CPU can give speedup
since it reduces the number of CUDA kernel launches.
The *sort* keyword determines whether the host or device performs atom
sorting, see the :doc:`atom_modify sort <atom_modify>` command. The
value options for the *sort* keyword are *no* or *device* similar to the
*comm* keywords above. If a value of *host* is used it will be
automatically be changed to *no* since the *sort* keyword does not
support *host* mode. The value of *no* will also always be used when
running on the CPU, i.e. setting the value to *device* will have no
effect if the simulation is running on the CPU. Not all fix styles with
extra atom data support *device* mode and in that case a warning will be
given and atom sorting will run in *no* mode instead.
sorting, see the :doc:`atom_modify sort <atom_modify>` command. The value
options for the *sort* keyword are *no* or *device* similar to the *comm*
keywords above. If a value of *host* is used it will be automatically be
changed to *no* since the *sort* keyword does not support *host* mode. Not
all fix styles with extra atom data support *device* mode and in that case
a warning will be given and atom sorting will run in *no* mode instead.
.. versionadded:: 17Apr2024
The *atom/map* keyword determines whether the host or device builds the
atom_map, see the :doc:`atom_modify map <atom_modify>` command. The
value options for the *atom/map* keyword are identical to the *sort*
keyword above.
The *gpu/aware* keyword chooses whether GPU-aware MPI will be used. When
this keyword is set to *on*, buffers in GPU memory are passed directly
@ -593,12 +600,13 @@ for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the
Spectrum MPI when the "-gpu" flag is used.
The *pair/only* keyword can change how the KOKKOS suffix "kk" is applied
when using an accelerator device. By default device acceleration is
always used for all available styles. With *pair/only* set to *on* the
suffix setting will choose device acceleration only for pair styles and
run all other force computations on the host CPU.
The *comm* flags will also automatically be changed to *no*\ . This can
result in better performance for certain configurations and system sizes.
when using an accelerator device. By default device acceleration is always
used for all available styles. With *pair/only* set to *on* the suffix
setting will choose device acceleration only for pair styles and run all
other force computations on the host CPU. The *comm* flags, along with the
*sort* and *atom/map* keywords will also automatically be changed to *no*\ .
This can result in better performance for certain configurations and
system sizes.
----------
@ -684,18 +692,18 @@ Restrictions
This command cannot be used after the simulation box is defined by a
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command.
The gpu style of this command can only be invoked if LAMMPS was built
The *gpu* style of this command can only be invoked if LAMMPS was built
with the GPU package. See the :doc:`Build package <Build_package>` doc
page for more info.
The intel style of this command can only be invoked if LAMMPS was
The *intel* style of this command can only be invoked if LAMMPS was
built with the INTEL package. See the :doc:`Build package <Build_package>` page for more info.
The kk style of this command can only be invoked if LAMMPS was built
The *kokkos* style of this command can only be invoked if LAMMPS was built
with the KOKKOS package. See the :doc:`Build package <Build_package>`
doc page for more info.
The omp style of this command can only be invoked if LAMMPS was built
The *omp* style of this command can only be invoked if LAMMPS was built
with the OPENMP package. See the :doc:`Build package <Build_package>`
doc page for more info.
@ -704,19 +712,27 @@ Related commands
:doc:`suffix <suffix>`, :doc:`-pk command-line switch <Run_options>`
Default
"""""""
Defaults
""""""""
For the GPU package, the default is Ngpu = 0 and the option defaults are neigh
= yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0 to Ngpu-1, tpa = 1,
omp = 0, and platform=-1. These settings are made automatically if the "-sf
gpu" :doc:`command-line switch <Run_options>` is used. If it is not used, you
must invoke the package gpu command in your input script or via the "-pk gpu"
:doc:`command-line switch <Run_options>`.
For the GPU package, the default parameters and settings are:
For the INTEL package, the default is Nphi = 1 and the option defaults are omp
= 0, mode = mixed, lrt = no, balance = -1, tpc = 4, tptask = 240, pppm_table =
yes. The default ghost option is determined by the pair style being used.
.. parsed-literal::
Ngpu = 0, neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0 to Ngpu-1, tpa = 1, omp = 0, platform=-1.
These settings are made automatically if the "-sf gpu"
:doc:`command-line switch <Run_options>` is used. If it is not used,
you must invoke the package gpu command in your input script or via the
"-pk gpu" :doc:`command-line switch <Run_options>`.
For the INTEL package, the default parameters and settings are:
.. parsed-literal::
Nphi = 1, omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4, tptask = 240, pppm_table = yes
The default ghost option is determined by the pair style being used.
This value is output to the screen in the offload report at the end of each
run. Note that all of these settings, except "omp" and "mode", are ignored if
LAMMPS was not built with Xeon Phi co-processor support. These settings are
@ -724,20 +740,35 @@ made automatically if the "-sf intel" :doc:`command-line switch <Run_options>`
is used. If it is not used, you must invoke the package intel command in your
input script or via the "-pk intel" :doc:`command-line switch <Run_options>`.
For the KOKKOS package, the option defaults for GPUs are neigh = full,
neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default value,
comm = device, sort = device, neigh/transpose = off, gpu/aware = on. When
LAMMPS can safely detect that GPU-aware MPI is not available, the default value
of gpu/aware becomes "off". For CPUs or Xeon Phis, the option defaults are
neigh = half, neigh/qeq = half, newton = on, binsize = 0.0, comm = no, and sort
= no. For GPUs, option neigh/thread = on when there are 16k atoms or less on an MPI
rank, otherwise it is "off". These settings are made automatically by the
required "-k on" :doc:`command-line switch <Run_options>`. You can change them
by using the package kokkos command in your input script or via the :doc:`-pk
kokkos command-line switch <Run_options>`.
For the KOKKOS package when using GPUs, the option defaults are:
For the OMP package, the default is Nthreads = 0 and the option defaults are
neigh = yes. These settings are made automatically if the "-sf omp"
:doc:`command-line switch <Run_options>` is used. If it is not used, you must
invoke the package omp command in your input script or via the "-pk omp"
:doc:`command-line switch <Run_options>`.
.. parsed-literal::
neigh = full, neigh/qeq = full, newton = off, binsize = 2x LAMMPS default value, comm = device, sort = device, atom/map = device, neigh/transpose = off, gpu/aware = on
For GPUs, option neigh/thread = on when there are 16k atoms or less on
an MPI rank, otherwise it is "off". When LAMMPS can safely detect that
GPU-aware MPI is not available, the default value of gpu/aware becomes
"off".
For the KOKKOS package when using CPUs or Xeon Phis, the option defaults are:
.. parsed-literal::
neigh = half, neigh/qeq = half, newton = on, binsize = 0.0, comm = no, sort = no, atom/map = no
These settings are made automatically by
the required "-k on" :doc:`command-line switch <Run_options>`. You can
change them by using the package kokkos command in your input script or
via the :doc:`-pk kokkos command-line switch <Run_options>`.
For the OMP package, the defaults are
.. parsed-literal::
Nthreads = 0, neigh = yes
These settings are made automatically if the "-sf omp"
:doc:`command-line switch <Run_options>` is used. If it is not used,
you must invoke the package omp command in your input script or via the
"-pk omp" :doc:`command-line switch <Run_options>`.

14
doc/src/pair_airebo.rst
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@ -156,7 +156,7 @@ pair_coeff command:
The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
The first three C arguments map LAMMPS atom types 1,2,3 to the C
element in the AIREBO file. The final H argument maps LAMMPS atom
type 4 to the H element in the SW file. If a mapping value is
type 4 to the H element in the AIREBO file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when a *airebo* potential is used as part of the *hybrid* pair style.
The NULL values are placeholders for atom types that will be used with
@ -222,12 +222,12 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package <Bui
These pair potentials require the :doc:`newton <newton>` setting to be
"on" for pair interactions.
The CH.airebo and CH.airebo-m potential files provided with LAMMPS
(see the potentials directory) are parameterized for metal :doc:`units <units>`.
You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units,
but you would need to create your own AIREBO or AIREBO-M potential file
with coefficients listed in the appropriate units, if your simulation
does not use "metal" units.
The CH.airebo and CH.airebo-m potential files provided with LAMMPS (see
the potentials directory) are parameterized for metal :doc:`units
<units>`. You can use the pair styles with *any* LAMMPS units, but you
would need to create your own AIREBO or AIREBO-M potential file with
coefficients listed in the appropriate units, if your simulation does
not use "metal" units.
The pair styles provided here **only** support potential files parameterized
for the elements carbon and hydrogen (designated with "C" and "H" in the

8
doc/src/pair_dsmc.rst
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@ -138,8 +138,12 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
This style is part of the MC 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 is part of the MC 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 requires an :doc:`atom style <atom_style>` with per
atom type masses.
Related commands
""""""""""""""""

15
doc/src/pair_eam.rst
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@ -140,6 +140,21 @@ The OpenKIM Project at
provides EAM potentials that can be used directly in LAMMPS with the
:doc:`kim command <kim_commands>` interface.
.. warning::
The EAM potential files tabulate the embedding energy as a function
of the local electron density :math:`\rho`. When atoms get too
close, this electron density may exceed the range for which the
embedding energy was tabulated for. To avoid crashes, LAMMPS will
assume a linearly increasing embedding energy for electron densities
beyond the maximum tabulated value. LAMMPS will print a warning when
this happens. It may be acceptable at the beginning of an
equilibration (e.g. when using randomized coordinates) but would be a
big concern for accuracy if it happens during production runs. The
EAM potential file triggering the warning during production is thus
not a good choice, and the EAM model in general not likely a good
model for the kind of system under investigation.
----------
For style *eam*, potential values are read from a file that is in the

24
doc/src/pair_granular.rst
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@ -187,6 +187,7 @@ for the damping model currently supported are:
2. *mass_velocity*
3. *viscoelastic*
4. *tsuji*
5. *coeff_restitution*
If the *damping* keyword is not specified, the *viscoelastic* model is
used by default.
@ -248,6 +249,29 @@ The dimensionless coefficient of restitution :math:`e` specified as part
of the normal contact model parameters should be between 0 and 1, but
no error check is performed on this.
The *coeff_restitution* model is useful when a specific normal coefficient of
restitution :math:`e` is required. In these models, the normal coefficient of
restitution :math:`e` is specified as an input. Following the approach of
:ref:`(Brilliantov et al) <Brill1996>`, when using the *hooke* normal model,
*coeff_restitution* calculates the damping coefficient as:
.. math::
\eta_n = \sqrt{\frac{4m_{eff}k_n}{1+\left( \frac{\pi}{\log(e)}\right)^2}} ,
For any other normal model, e.g. the *hertz* and *hertz/material* models, the damping
coefficient is:
.. math::
\eta_n = -2\sqrt{\frac{5}{6}}\frac{\log(e)}{\sqrt{\pi^2+(\log(e))^2}}(R_{eff} \delta_{ij})^{\frac{1}{4}}\sqrt{\frac{3}{2}k_n m_{eff}} ,
where :math:`k_n = \frac{4}{3} E_{eff}` for the *hertz/material* model. Since
*coeff_restitution* accounts for the effective mass, effective radius, and
pairwise overlaps (except when used with the *hooke* normal model) when calculating
the damping coefficient, it accurately reproduces the specified coefficient of
restitution for both monodisperse and polydisperse particle pairs.
The total normal force is computed as the sum of the elastic and
damping components:

4
doc/src/pair_meam.rst
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@ -427,8 +427,8 @@ package. They are only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for more info.
The maximum number of elements, that can be read from the MEAM library
file, is determined at compile time. The default is 5. If you need
support for more elements, you have to change the the constant 'maxelt'
file, is determined at compile time. The default is 8. If you need
support for more elements, you have to change the the constant 'MAXELT'
at the beginning of the file ``src/MEAM/meam.h`` and update/recompile
LAMMPS. There is no limit on the number of atoms types.

64
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@ -22,7 +22,7 @@ Syntax
style = *linear* or *quadratic* or *nn* or *mliappy*
filename = name of file containing model definitions
*descriptor* values = style filename
style = *sna* or *so3*
style = *sna* or *so3* or *ace*
filename = name of file containing descriptor definitions
*unified* values = filename ghostneigh_flag
filename = name of file containing serialized unified Python object
@ -36,6 +36,7 @@ Examples
pair_style mliap model linear InP.mliap.model descriptor sna InP.mliap.descriptor
pair_style mliap model quadratic W.mliap.model descriptor sna W.mliap.descriptor
pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor
pair_style mliap model mliappy ACE_NN_Pytorch.pt descriptor ace ccs_single_element.yace
pair_style mliap unified mliap_unified_lj_Ar.pkl 0
pair_coeff * * In P
@ -49,8 +50,8 @@ quantities that characterize the atomic positions (*descriptor*).
By defining *model* and *descriptor* separately, it is possible to use
many different models with a given descriptor, or many different
descriptors with a given model. The pair style currently supports only
*sna* and *so3* descriptor styles, but it is straightforward to add new
descriptors with a given model. The pair style currently supports *sna*,
*so3* and *ace* descriptor styles, but it is straightforward to add new
descriptor styles. By using the *unified* keyword, it is possible to
define a Python model that combines functionalities of both *model* and
*descriptor*.
@ -72,6 +73,26 @@ the smooth SO(3) power spectrum with the explicit inclusion of a radial
basis :ref:`(Bartok) <Bartok2013>` and :ref:`(Zagaceta) <Zagaceta2020>`.
The available models are *linear* and *nn*.
.. versionadded:: 17Apr2024
The descriptor style *ace* is a class of highly general atomic
descriptors, atomic cluster expansion descriptors (ACE) from
:ref:`(Drautz) <Drautz19>`, that include a radial basis, an angular
basis, and bases for other variables (such as chemical species) if
relevant. In descriptor style *ace*, the *ace* descriptors may be
defined up to an arbitrary body order. This descriptor style is the same
as that used in :doc:`pair_style pace <pair_pace>` and :doc:`compute
pace <compute_pace>`. The available models with *ace* in ML-IAP are
*linear* and *mliappy*. The *ace* descriptors and models require
building LAMMPS with the ML-PACE package (see below). The *mliappy*
model style may be used with *ace* descriptors, but it requires that
LAMMPS is also built with the PYTHON package. As with other model
styles, the *mliappy* model style can be used to couple arbitrary python
models that use the *ace* descriptors such as Pytorch NNs. Note that
*ALL* mliap model styles with *ace* descriptors require that descriptors
and hyperparameters are supplied in a `.yace` or `.ace` file, similar to
:doc:`compute pace <compute_pace>`.
The pair_style *mliap* command must be followed by two keywords *model*
and *descriptor* in either order, or the one keyword *unified*. A
single *pair_coeff* command is also required. The first 2 arguments
@ -136,7 +157,7 @@ The detail of *nn* module implementation can be found at :ref:`(Yanxon) <Yanxon2
the mliap-specific python module that is built into LAMMPS.
The *descriptor* keyword is followed by a descriptor style, and additional arguments.
Currently two descriptor styles are available: *sna* and *so3*.
Currently three descriptor styles are available: *sna*, *so3*, and *ace*.
- *sna* indicates the bispectrum component descriptors used by the Spectral
Neighbor Analysis Potential (SNAP) potentials of :doc:`pair_style snap
@ -148,6 +169,16 @@ Currently two descriptor styles are available: *sna* and *so3*.
- *so3* indicated the power spectrum component descriptors. A single additional
argument specifies the descriptor filename containing the parameters and setting.
- *ace* indicates the atomic cluster expansion (ACE) descriptors. A single
additional argument specifies the filename containing parameters, settings, and
definitions of the ace descriptors (through tabulated basis function indices and
corresponding generalized Clebsch-Gordan coefficients) in the ctilde file format,
e.g. in the potential file format with `*.ace` or `*.yace` extensions from
:doc:`pair_style pace <pair_pace>`. Note that unlike the potential file, the
Clebsch-Gordan coefficients in the descriptor file supplied should *NOT* be
multiplied by linear or square root embedding terms.
The SNAP descriptor file closely follows the format of the
:doc:`pair_style snap <pair_snap>` parameter file. The file can contain
blank and comment lines (start with #) anywhere. Each non-blank
@ -169,6 +200,24 @@ contains a few more arguments (e.g., *nmax* and *alpha*). The preparation
of SO3 descriptor and model files can be done with the
`Pyxtal_FF <https://github.com/qzhu2017/PyXtal_FF>`_ package.
The ACE descriptor file differs from the SNAP and SO3 files. It more
closely resembles the potential file format for linear or square-root
embedding ACE potentials used in the :doc:`pair_style pace <pair_pace>`.
As noted above, the key difference is that the Clebsch-Gordan
coefficients in the descriptor file with *mliap descriptor ace* are
*NOT* multiplied by linear or square root embedding terms. In other
words,the model is separated from the descriptor definitions and
hyperparameters. In :doc:`pair_style pace <pair_pace>`, they are
combined. The ACE descriptor files required by *mliap* are generated
automatically in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_ during
linear, pytorch, etc. ACE model fitting. Additional tools are provided
there to prepare *ace* descriptor files and hyperparameters before model
fitting. The *ace* descriptor files can also be extracted from ACE
model fits in `python-ace. <https://github.com/ICAMS/python-ace>`_. It
is important to note that order of the types listed in :doc:`pair_coeff
<pair_coeff>` must match the order of the elements/types listed in the
ACE descriptor file for all *mliap* styles when using *ace* descriptors.
See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
to specify the path for these *model* and *descriptor* files.
@ -245,7 +294,10 @@ This pair style is part of the ML-IAP package. It is only enabled if
LAMMPS was built with that package. In addition, building LAMMPS with
the ML-IAP package requires building LAMMPS with the ML-SNAP package.
The *mliappy* model requires building LAMMPS with the PYTHON package.
See the :doc:`Build package <Build_package>` page for more info.
The *ace* descriptor requires building LAMMPS with the ML-PACE package.
See the :doc:`Build package <Build_package>` page for more info. Note
that `pair_mliap/kk` acceleration will *not* invoke the `kk`
accelerated variants of SNAP or ACE descriptors.
Related commands
@ -271,5 +323,3 @@ none
.. _Yanxon2020:
**(Yanxon2020)** Yanxon, Zagaceta, Tang, Matteson, Zhu, Mach. Learn.: Sci. Technol. 2, 027001 (2020).

137
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@ -0,0 +1,137 @@
.. index:: pair_style pedone
.. index:: pair_style pedone/omp
pair_style pedone command
=========================
Accelerator Variants: *pedone/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style style args
* style = pedone*
* args = list of arguments for a particular style
.. parsed-literal::
*pedone* args = cutoff
cutoff = global cutoff for Pedone interactions (distance units)
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay pedone 15.0 coul/long 15.0
kspace_style pppm 1.0e-5
pair_coeff * * coul/long
pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0
pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0
Used in input scripts:
.. parsed-literal::
examples/PACKAGES/pedone/in.pedone.relax
examples/PACKAGES/pedone/in.pedone.melt
Description
"""""""""""
.. versionadded:: 17Apr2024
Pair style *pedone* computes the **non-Coulomb** interactions of the Pedone
(or PMMCS) potential :ref:`(Pedone) <Pedone>` which combines Coulomb
interactions, Morse potential, and repulsive :math:`r^{-12}`
Lennard-Jones terms (see below). The *pedone* pair style is meant
to be used in addition to a :doc:`Coulomb pair style <pair_coul>` via
pair style :doc:`hybrid/overlay <pair_hybrid>` (see example above).
Using *coul/long* or *could/dsf* (for solids) is recommended.
The full Pedone potential function from :ref:`(Pedone) <Pedone>` for each
pair of atoms is:
.. math::
E = \frac{C q_i q_j}{\epsilon r}
+ D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
+ \frac{B_0}{r^{12}} \qquad r < r_c
:math:`r_c` is the cutoff and :math:`C` is a conversion factor that is
specific to the choice of :doc:`units <units>` so that the entire
Coulomb term is in energy units with :math:`q_i` and :math:`q_j` as the
assigned charges in multiples of the elementary charge.
The following coefficients must be defined for the selected pairs of
atom types via the :doc:`pair_coeff <pair_coeff>` command as in the
example above:
* :math:`D_0` (energy units)
* :math:`\alpha` (1/distance units)
* :math:`r_0` (distance units)
* :math:`C_0` (energy units)
* cutoff (distance units)
The last coefficient is optional. If not specified, the global *pedone*
cutoff is used.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair style does not support mixing.
This pair style support the :doc:`pair_modify <pair_modify>` shift
option for the energy of the pair interaction.
This pair style does not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to :doc:`binary restart files <restart>`,
so pair_style and pair_coeff commands does 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*, or *outer* keywords.
----------
Restrictions
""""""""""""
The *pedone* pair style is only enabled if LAMMPS was built with the
EXTRA-PAIR package. See the :doc:`Build package <Build_package>` page
for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style <pair_style>`,
:doc:`pair style coul/long and coul/dsf <pair_coul>`,
:doc:`pair style morse <pair_morse>`
Default
"""""""
none
-------------
.. _Pedone:
**(Pedone)** A. Pedone, G. Malavasi, M. C. Menziani, A. N. Cormack, and U. Segre, J. Phys. Chem. B, 110, 11780 (2006)

150
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@ -0,0 +1,150 @@
.. index:: pair_style rebomos
.. index:: pair_style rebomos/omp
pair_style rebomos command
==========================
Accelerator Variants: *rebomos/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style rebomos
* rebomos = name of this pair style
Examples
""""""""
.. code-block:: LAMMPS
pair_style rebomos
pair_coeff * * ../potentials/MoS.rebomos Mo S
Example input scripts available: examples/threebody/
Description
"""""""""""
.. versionadded:: 17Apr2024
The *rebomos* pair style computes the interactions between molybdenum
and sulfur atoms :ref:`(Stewart) <Stewart>` utilizing an adaptive
interatomic reactive empirical bond order potential that is similar in
form to the AIREBO potential :ref:`(Stuart) <Stuart2>`. The potential
is based on an earlier parameterizations for :math:`\text{MoS}_2`
developed by :ref:`(Liang) <Liang>`.
The REBOMoS potential consists of two terms:
.. math::
E & = \frac{1}{2} \sum_i \sum_{j \neq i}
\left[ E^{\text{REBO}}_{ij} + E^{\text{LJ}}_{ij} \right] \\
The :math:`E^{\text{REBO}}` term describes the covalently bonded
interactions between Mo and S atoms while the :math:`E^{\text{LJ}}` term
describes longer range dispersion forces between layers. A cubic spline
function is applied to smoothly switch between covalent bonding at short
distances to dispersion interactions at longer distances. This allows
the model to capture bond formation and breaking events which may occur
between adjacent MoS2 layers, edges, defects, and more.
----------
Only a single pair_coeff command is used with the *rebomos* pair style
which specifies an REBOMoS potential file with parameters for Mo and S.
These are mapped to LAMMPS atom types by specifying N additional
arguments after the filename in the pair_coeff command, where N is the
number of LAMMPS atom types:
* filename
* :math:`N` element names = mapping of REBOMoS elements to atom types
See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
to specify the path for the potential file.
As an example, if your LAMMPS simulation has three atom types and you want
the first two to be Mo, and the third to be S, you would use the following
pair_coeff command:
.. code-block:: LAMMPS
pair_coeff * * MoS.rebomos Mo Mo S
The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
The first two Mo arguments map LAMMPS atom types 1 and 2 to the Mo
element in the REBOMoS file. The final S argument maps LAMMPS atom type
3 to the S element in the REBOMoS file. If a mapping value is specified
as NULL, the mapping is not performed. This can be used when a
*rebomos* potential is used as part of the *hybrid* pair style. The
NULL values are placeholders for atom types that will be used with other
potentials.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair style does not support the :doc:`pair_modify <pair_modify>`
mix, shift, table, and tail options.
This pair style does not write their 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 styles 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 MANYBODY package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
These pair potentials require the :doc:`newton <newton>` setting to be
"on" for pair interactions.
The MoS.rebomos potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal :doc:`units <units>`. You can use
the *rebomos* pair style with any LAMMPS units setting, but you would
need to create your own REBOMoS potential file with coefficients listed
in the appropriate units.
The pair style provided here **only** supports potential files parameterized
for the elements molybdenum and sulfur (designated with "Mo" and "S" in the
*pair_coeff* command. Using potential files for other elements will trigger
an error.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair style rebo <pair_airebo>`
Default
"""""""
none
----------
.. _Stewart:
**(Steward)** Stewart, Spearot, Modelling Simul. Mater. Sci. Eng. 21, 045003, (2013).
.. _Stuart2:
**(Stuart)** Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486, (2000).
.. _Liang:
**(Liang)** Liang, Phillpot, Sinnott Phys. Rev. B79 245110, (2009), Erratum: Phys. Rev. B85 199903(E), (2012)

50
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@ -275,30 +275,30 @@ accelerated styles exist.
* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed LJ vdW potential with Gaussian electrostatics
* :doc:`lj96/cut <pair_lj96>` - Lennard-Jones 9/6 potential
* :doc:`local/density <pair_local_density>` - generalized basic local density potential
* :doc:`lubricate <pair_lubricate>` - hydrodynamic lubrication forces
* :doc:`lubricate/poly <pair_lubricate>` - hydrodynamic lubrication forces with polydispersity
* :doc:`lubricateU <pair_lubricateU>` - hydrodynamic lubrication forces for Fast Lubrication Dynamics
* :doc:`lubricateU/poly <pair_lubricateU>` - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
* :doc:`local/density <pair_local_density>` - Generalized basic local density potential
* :doc:`lubricate <pair_lubricate>` - Hydrodynamic lubrication forces
* :doc:`lubricate/poly <pair_lubricate>` - Hydrodynamic lubrication forces with polydispersity
* :doc:`lubricateU <pair_lubricateU>` - Hydrodynamic lubrication forces for Fast Lubrication Dynamics
* :doc:`lubricateU/poly <pair_lubricateU>` - Hydrodynamic lubrication forces for Fast Lubrication with polydispersity
* :doc:`mdpd <pair_mesodpd>` - mDPD particle interactions
* :doc:`mdpd/rhosum <pair_mesodpd>` - mDPD particle interactions for mass density
* :doc:`meam <pair_meam>` - modified embedded atom method (MEAM)
* :doc:`meam/ms <pair_meam>` - multi-state modified embedded atom method (MS-MEAM)
* :doc:`meam/spline <pair_meam_spline>` - splined version of MEAM
* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
* :doc:`mesocnt <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes
* :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:`meam <pair_meam>` - Modified embedded atom method (MEAM)
* :doc:`meam/ms <pair_meam>` - Multi-state modified embedded atom method (MS-MEAM)
* :doc:`meam/spline <pair_meam_spline>` - Splined version of MEAM
* :doc:`meam/sw/spline <pair_meam_sw_spline>` - Splined version of MEAM with a Stillinger-Weber term
* :doc:`mesocnt <pair_mesocnt>` - Mesoscopic vdW potential for (carbon) nanotubes
* :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:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
* :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
* :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential
* :doc:`morse/smooth/linear <pair_morse>` - Linear smoothed Morse potential
* :doc:`morse/soft <pair_morse>` - Morse potential with a soft core
* :doc:`multi/lucy <pair_multi_lucy>` - DPD potential with density-dependent force
* :doc:`multi/lucy/rx <pair_multi_lucy_rx>` - reactive DPD potential with density-dependent force
* :doc:`nb3b/harmonic <pair_nb3b>` - non-bonded 3-body harmonic potential
* :doc:`nb3b/screened <pair_nb3b>` - non-bonded 3-body screened harmonic potential
* :doc:`nb3b/harmonic <pair_nb3b>` - Non-bonded 3-body harmonic potential
* :doc:`nb3b/screened <pair_nb3b>` - Non-bonded 3-body screened harmonic potential
* :doc:`nm/cut <pair_nm>` - N-M potential
* :doc:`nm/cut/coul/cut <pair_nm>` - N-M potential with cutoff Coulomb
* :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulomb
@ -322,20 +322,22 @@ accelerated styles exist.
* :doc:`oxrna2/xstk <pair_oxrna2>` -
* :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
* :doc:`pace/extrapolation <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades
* :doc:`pedone <pair_pedone>` - Pedone (PMMCS) potential (non-Coulomb part)
* :doc:`pod <pair_pod>` - Proper orthogonal decomposition (POD) machine-learning potential
* :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
* :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
* :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
* :doc:`peri/ves <pair_peri>` - peridynamic VES potential
* :doc:`polymorphic <pair_polymorphic>` - polymorphic 3-body potential
* :doc:`peri/eps <pair_peri>` - Peridynamic EPS potential
* :doc:`peri/lps <pair_peri>` - Peridynamic LPS potential
* :doc:`peri/pmb <pair_peri>` - Peridynamic PMB potential
* :doc:`peri/ves <pair_peri>` - Peridynamic VES potential
* :doc:`polymorphic <pair_polymorphic>` - Polymorphic 3-body potential
* :doc:`python <pair_python>` -
* :doc:`quip <pair_quip>` -
* :doc:`rann <pair_rann>` -
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
* :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
* :doc:`rebo <pair_airebo>` - Second generation REBO potential of Brenner
* :doc:`rebomos <pair_rebomos>` - REBOMoS potential for MoS2
* :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
* :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
* :doc:`smatb <pair_smatb>` - Second Moment Approximation to the Tight Binding
* :doc:`smatb/single <pair_smatb>` - Second Moment Approximation to the Tight Binding for single-element systems
* :doc:`smd/hertz <pair_smd_hertz>` -

42
doc/src/processors.rst
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@ -25,6 +25,8 @@ Syntax
*numa* params = none
*custom* params = infile
infile = file containing grid layout
*numa_nodes* arg = Nn
Nn = number of numa domains per node
*map* arg = *cart* or *cart/reorder* or *xyz* or *xzy* or *yxz* or *yzx* or *zxy* or *zyx*
cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
@ -157,26 +159,30 @@ surface-to-volume ratio of each processor's subdomain.
for most MPI implementations, but some MPIs provide options for this
ordering, e.g. via environment variable settings.
The *numa* style operates similar to the *twolevel* keyword except
that it auto-detects which cores are running on which nodes.
Currently, it does this in only 2 levels, but it may be extended in
the future to account for socket topology and other non-uniform memory
access (NUMA) costs. It also uses a different algorithm than the
*twolevel* keyword for doing the two-level factorization of the
simulation box into a 3d processor grid to minimize off-node
communication, and it does its own MPI-based mapping of nodes and
cores to the regular 3d grid. Thus it may produce a different layout
of the processors than the *twolevel* options.
The *numa* style operates similar to the *twolevel* keyword except that
it auto-detects which cores are running on which nodes. It will also
subdivide the cores into numa domains. Currently, the number of numa
domains is not auto-detected and must be specified using the
*numa_nodes* keyword; otherwise, the default value is used. The *numa*
style uses a different algorithm than the *twolevel* keyword for doing
the two-level factorization of the simulation box into a 3d processor
grid to minimize off-node communication and communication across numa
domains. It does its own MPI-based mapping of nodes and cores to the
regular 3d grid. Thus it may produce a different layout of the
processors than the *twolevel* options.
The *numa* style will give an error if the number of MPI processes is
not divisible by the number of cores used per node, or any of the Px
or Py of Pz values is greater than 1.
or Py or Pz values is greater than 1.
.. note::
Unlike the *twolevel* style, the *numa* style does not require
any particular ordering of MPI ranks i norder to work correctly. This
any particular ordering of MPI ranks in order to work correctly. This
is because it auto-detects which processes are running on which nodes.
However, it assumes that the lowest ranks are in the first numa
domain, and so forth. MPI rank orderings that do not preserve this
property might result in more intra-node communication between CPUs.
The *custom* style uses the file *infile* to define both the 3d
factorization and the mapping of processors to the grid.
@ -207,6 +213,14 @@ any order, but no processor ID should appear more than once.
----------
The *numa_nodes* keyword is used to specify the number of numa domains
per node. It is currently only used by the *numa* style for two-level
factorization to reduce the amount of MPI communications between CPUs.
A good setting for this will typically be equal to the number of CPU
sockets per node.
----------
The *map* keyword affects how the P processor IDs (from 0 to P-1) are
mapped to the 3d grid of processors. It is only used by the
*onelevel* and *twolevel* grid settings.
@ -356,5 +370,5 @@ Related commands
Default
"""""""
The option defaults are Px Py Pz = \* \* \*, grid = onelevel, and map =
cart.
The option defaults are Px Py Pz = \* \* \*, grid = onelevel, map =
cart, and numa_nodes = 2.

562
doc/src/read_data.rst
View File

@ -63,11 +63,16 @@ Description
Read in a data file containing information LAMMPS needs to run a
simulation. The file can be ASCII text or a gzipped text file
(detected by a .gz suffix). This is one of 3 ways to specify initial
atom coordinates; see the :doc:`read_restart <read_restart>` and
:doc:`create_atoms <create_atoms>` commands for alternative methods.
Also see the explanation of the :doc:`-restart command-line switch
<Run_options>` which can convert a restart file to a data file.
(detected by a .gz suffix).
This is one of 3 ways to specify the simulation box: see the
:doc:`create_box <create_box>` and :doc:`read_restart <read_restart>`
and commands for alternative methods. It is also one of 3 ways to
specify initial atom coordinates: see the :doc:`create_atoms
<create_atoms>` and :doc:`read_restart <read_restart>` and commands
for alternative methods. Also see the explanation of the
:doc:`-restart command-line switch <Run_options>` which can convert a
restart file to a data file.
This command can be used multiple times to add new atoms and their
properties to an existing system by using the *add*, *offset*, and
@ -122,37 +127,55 @@ keyword must be used.
.. note::
The simulation box size (xlo to xhi, ylo to yhi, zlo to zhi) in
the new data file will be merged with the existing simulation box to
create a large enough box in each dimension to contain both the
existing and new atoms. Each box dimension never shrinks due to this
merge operation, it only stays the same or grows. Care must be used if
you are growing the existing simulation box in a periodic dimension.
If there are existing atoms with bonds that straddle that periodic
boundary, then the atoms may become far apart if the box size grows.
This will separate the atoms in the bond, which can lead to "lost"
bond atoms or bad dynamics.
If the first read_data command defined an orthogonal or restricted
triclinic or general triclinic simulation box (see the sub-section
below on header keywords), then subsequent data files must define
the same kind of simulation box. For orthogonal boxes, the new box
can be a different size; see the next Note. For a restricted
triclinic box, the 3 new tilt factors ("xy xz yz" keyword) must
have the same values as in the original data file. For a general
triclinic box, the new avec, bvec, cvec, and "abc origin" keywords
must have the same values in the original data file. files. Also
the *shift* keyword cannot be used in subsequent read_data commands
for a general triclinic box.
.. note::
For orthogonal boxes, the simulation box size in the new data file
will be merged with the existing simulation box to create a large
enough box in each dimension to contain both the existing and new
atoms. Each box dimension never shrinks due to this merge
operation, it only stays the same or grows. Care must be used if
you are growing the existing simulation box in a periodic
dimension. If there are existing atoms with bonds that straddle
that periodic boundary, then the atoms may become far apart if the
box size grows. This will separate the atoms in the bond, which
can lead to "lost" bond atoms or bad dynamics.
The three choices for the *add* argument affect how the atom IDs and
molecule IDs of atoms in the data file are treated. If *append* is
specified, atoms in the data file are added to the current system,
with their atom IDs reset so that an atom-ID = M in the data file
becomes atom-ID = N+M, where N is the largest atom ID in the current
system. This rule is applied to all occurrences of atom IDs in the
data file, e.g. in the Velocity or Bonds section. This is also done
for molecule IDs, if the atom style does support molecule IDs or
they are enabled via fix property/atom. If *IDoffset* is specified,
then *IDoffset* is a numeric value is given, e.g. 1000, so that an
atom-ID = M in the data file becomes atom-ID = 1000+M. For systems
with enabled molecule IDs, another numerical argument *MOLoffset*
is required representing the equivalent offset for molecule IDs.
If *merge* is specified, the data file atoms
are added to the current system without changing their IDs. They are
assumed to merge (without duplication) with the currently defined
atoms. It is up to you to ensure there are no multiply defined atom
IDs, as LAMMPS only performs an incomplete check that this is the case
by ensuring the resulting max atom-ID >= the number of atoms. For
molecule IDs, there is no check done at all.
molecule IDs of atoms in the data file are treated.
If *append* is specified, atoms in the data file are added to the
current system, with their atom IDs reset so that an atom-ID = M in
the data file becomes atom-ID = N+M, where N is the largest atom ID in
the current system. This rule is applied to all occurrences of atom
IDs in the data file, e.g. in the Velocity or Bonds section. This is
also done for molecule IDs, if the atom style does support molecule
IDs or they are enabled via fix property/atom.
If *IDoffset* is specified, then *IDoffset* is a numeric value is
given, e.g. 1000, so that an atom-ID = M in the data file becomes
atom-ID = 1000+M. For systems with enabled molecule IDs, another
numerical argument *MOLoffset* is required representing the equivalent
offset for molecule IDs.
If *merge* is specified, the data file atoms are added to the current
system without changing their IDs. They are assumed to merge (without
duplication) with the currently defined atoms. It is up to you to
ensure there are no multiply defined atom IDs, as LAMMPS only performs
an incomplete check that this is the case by ensuring the resulting
max atom-ID >= the number of atoms. For molecule IDs, there is no
check done at all.
The *offset* and *shift* keywords can only be used if the *add*
keyword is also specified.
@ -288,13 +311,16 @@ Format of the header of a data file
"""""""""""""""""""""""""""""""""""
These are the recognized header keywords. Header lines can come in
any order. The value(s) are read from the beginning of the line.
any order. Each keyword takes a single value unless noted in this
list. The value(s) are read from the beginning of the line.
Thus the keyword *atoms* should be in a line like "1000 atoms"; the
keyword *ylo yhi* should be in a line like "-10.0 10.0 ylo yhi"; the
keyword *xy xz yz* should be in a line like "0.0 5.0 6.0 xy xz yz".
All these settings have a default value of 0, except the lo/hi box
size defaults are -0.5 and 0.5. A line need only appear if the value
is different than the default.
All these settings have a default value of 0, except for the
simulation box size settings; their defaults are explained below. A
keyword line need only appear if its value is different than the
default.
* *atoms* = # of atoms in system
* *bonds* = # of bonds in system
@ -315,81 +341,178 @@ is different than the default.
* *lines* = # of line segments in system
* *triangles* = # of triangles in system
* *bodies* = # of bodies in system
* *xlo xhi* = simulation box boundaries in x dimension
* *ylo yhi* = simulation box boundaries in y dimension
* *zlo zhi* = simulation box boundaries in z dimension
* *xy xz yz* = simulation box tilt factors for triclinic system
* *xlo xhi* = simulation box boundaries in x dimension (2 values)
* *ylo yhi* = simulation box boundaries in y dimension (2 values)
* *zlo zhi* = simulation box boundaries in z dimension (2 values)
* *xy xz yz* = simulation box tilt factors for triclinic system (3 values)
* *avec* = first edge vector of a general triclinic simulation box (3 values)
* *bvec* = second edge vector of a general triclinic simulation box (3 values)
* *cvec* = third edge vector of a general triclinic simulation box (3 values)
* *abc origin* = origin of a general triclinic simulation box (3 values)
The initial simulation box size is determined by the lo/hi settings.
In any dimension, the system may be periodic or non-periodic; see the
:doc:`boundary <boundary>` command. When the simulation box is created
it is also partitioned into a regular 3d grid of rectangular bricks,
one per processor, based on the number of processors being used and
the settings of the :doc:`processors <processors>` command. The
partitioning can later be changed by the :doc:`balance <balance>` or
:doc:`fix balance <fix_balance>` commands.
----------
If the *xy xz yz* line does not appear, LAMMPS will set up an
axis-aligned (orthogonal) simulation box. If the line does appear,
LAMMPS creates a non-orthogonal simulation domain shaped as a
parallelepiped with triclinic symmetry. The parallelepiped has its
"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
(xz,yz,zhi-zlo). *Xy,xz,yz* can be 0.0 or positive or negative values
and are called "tilt factors" because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped.
Header specification of the simulation box size and shape
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The tilt factors (xy,xz,yz) should not skew the box more than half the
distance of the corresponding parallel box length. For example, if
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x`
box length is 10 and the :math:`xy` tilt factor must be between
:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz`
must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a
limitation, since if the maximum tilt factor is 5 (as in this example),
then configurations with tilt :math:`= \dots, -15`, :math:`-5`,
:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically
equivalent. Simulations with large tilt factors will run inefficiently,
since they require more ghost atoms and thus more communication. With
very large tilt factors, LAMMPS will eventually produce incorrect
trajectories and stop with errors due to lost atoms or similar.
The last 8 keywords in the list of header keywords are for simulation
boxes of 3 kinds which LAMMPS supports:
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
triclinic representations.
* orthogonal box = faces are perpendicular to the xyz coordinate axes
* restricted triclinic box = a parallelepiped defined by 3 edge vectors oriented in a constrained manner
* general triclinic box = a parallelepiped defined by 3 arbitrary edge vectors
When a triclinic system is used, the simulation domain should normally
be periodic in the dimension that the tilt is applied to, which is
given by the second dimension of the tilt factor (e.g. y for xy tilt).
This is so that pairs of atoms interacting across that boundary will
have one of them shifted by the tilt factor. Periodicity is set by
the :doc:`boundary <boundary>` command. For example, if the xy tilt
factor is non-zero, then the y dimension should be periodic.
Similarly, the z dimension should be periodic if xz or yz is non-zero.
LAMMPS does not require this periodicity, but you may lose atoms if
this is not the case.
For restricted and general triclinic boxes, see the
:doc:`Howto_triclinic <Howto_triclinic>` doc page for a fuller
description than is given here.
Also note that if your simulation will tilt the box, e.g. via the
:doc:`fix deform <fix_deform>` command, the simulation box must be setup
to be triclinic, even if the tilt factors are initially 0.0. You can
also change an orthogonal box to a triclinic box or vice versa by using
the :doc:`change box <change_box>` command with its *ortho* and
*triclinic* options.
The units of the values for all 8 keywords in in distance units; see
the :doc:`units <units>` command for details.
For 2d simulations, the *zlo zhi* values should be set to bound the z
coords for atoms that appear in the file; the default of -0.5 0.5 is
valid if all z coords are 0.0. For 2d triclinic simulations, the xz
and yz tilt factors must be 0.0.
For all 3 kinds of simulation boxes, the system may be periodic or
non-periodic in any dimension; see the :doc:`boundary <boundary>`
command for details.
When the simulation box is created by the read_data command, it is
also partitioned into a regular 3d grid of subdomains, one per
processor, based on the number of processors being used and the
settings of the :doc:`processors <processors>` command. For each kind
of simulation box the subdomains have the same shape as the simulation
box, i.e. smaller orthogonal bricks for orthogonal boxes, smaller
parallelepipeds for triclinic boxes. The partitioning can later be
changed by the :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands.
For an orthogonal box, only the *xlo xhi*, *ylo yhi*, *zlo zhi*
keywords are used. They define the extent of the simulation box in
each dimension so that the resulting edge vectors of an orthogonal box
are:
* **A** = (xhi-xlo,0,0)
* **B** = (0,yhi-ylo,0)
* **C** = (0,0,zhi-zlo)
The origin (lower left corner) of the orthogonal box is at
(xlo,ylo,zlo). The default values for these 3 keywords are -0.5 and
0.5 for each lo/hi pair. For a 2d simulation, the zlo and zhi values
must straddle zero. The default zlo/zhi values do this, so that
keyword is not needed in 2d.
For a restricted triclinic box, the *xy xz yz* keyword is used in
addition to the *xlo xhi*, *ylo yhi*, *zlo zhi* keywords. The three
*xy,xz,yz* values can be 0.0 or positive or negative, and are called
"tilt factors" because they are the amount of displacement applied to
edges of faces of an orthogonal box to transform it into a restricted
triclinic parallelepiped.
The :doc:`Howto_triclinic <Howto_triclinic>` doc page discusses the
tilt factors in detail and explains that the resulting edge vectors of
a restricted triclinic box are:
* **A** = (xhi-xlo,0,0)
* **B** = (xy,yhi-ylo,0)
* **C** = (xz,yz,zhi-zlo)
This restricted form of edge vectors requires that **A** be in the
direction of the x-axis, **B** be in the xy plane with its y-component
in the +y direction, and **C** have its z-component in the +z
direction. The origin (lower left corner) of the restricted triclinic
box is at (xlo,ylo,zlo).
For a 2d simulation, the zlo and zhi values must straddle zero. The
default zlo/zhi values do this, so that keyword is not needed in 2d.
The xz and yz values must also be zero in 2d. The shape of the 2d
restricted triclinic simulation box is effectively a parallelogram.
.. note::
When a restricted triclinic box is used, the simulation domain
should normally be periodic in any dimensions that tilt is applied
to, which is given by the second dimension of the tilt factor
(e.g. y for xy tilt). This is so that pairs of atoms interacting
across that boundary will have one of them shifted by the tilt
factor. Periodicity is set by the :doc:`boundary <boundary>`
command which also describes the shifting by the tilt factor. For
example, if the xy tilt factor is non-zero, then the y dimension
should be periodic. Similarly, the z dimension should be periodic
if xz or yz is non-zero. LAMMPS does not require this periodicity,
but you may lose atoms if this is not the case.
.. note::
Normally, the specified tilt factors (xy,xz,yz) should not skew the
simulation box by more than half the distance of the corresponding
parallel box length for computational efficiency. For example, if
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the
:math:`x` box length is 10 and the :math:`xy` tilt factor should be
between :math:`-5` and :math:`5`. LAMMPS will issue a warning if
this is not the case. See the last sub-section of the
:doc:`Howto_triclinic <Howto_triclinic>` doc page for more details.
.. note::
If a simulation box is initially orthogonal, but will tilt during a
simulation, e.g. via the :doc:`fix deform <fix_deform>` command,
then the box should be defined as restricted triclinic with all 3
tilt factors = 0.0. Alternatively, the :doc:`change box
<change_box>` command can be used to convert an orthogonal box to a
restricted triclinic box.
For a general triclinic box, the *avec*, *bvec*, *cvec*, and *abc
origin* keywords are used. The *xlo xhi*, *ylo yhi*, *zlo zhi*, and
*xy xz yz* keywords are NOT used. The first 3 keywords define the 3
edge vectors **A**, **B**, **C** of the general triclinic box. They
can be arbitrary vectors so long as they are distinct, non-zero, and
not co-planar. They must also define a right-handed system such that
(**A** x **B**) points in the direction of **C**. Note that a
left-handed system can be converted to a right-handed system by simply
swapping the order of any pair of the **A**, **B**, **C** vectors.
The origin of the box (origin of the 3 edge vectors) is set by the
*abc origin* keyword.
The default values for these 4 keywords are as follows:
* avec = (1,0,0)
* bvec = (0,1,0)
* cvec = (0,0,1)
* abc origin = (0,0,0) for 3d, (0,0,-0.5) for 2d
For 2d simulations, *cvec* = (0,0,1) is required, and the 3rd value of
*abc origin* must be -0.5. These are the default values, so the
*cvec* keyword is not needed in 2d.
.. note::
LAMMPS allows specification of general triclinic simulation boxes
as a convenience for users who may be converting data from
solid-state crystallographic representations or from DFT codes for
input to LAMMPS. However, as explained on the
:doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
LAMMPS only uses restricted triclinic simulation boxes. This means
the box and per-atom information (e.g. coordinates, velocities) in
the data file are converted (rotated) from general to restricted
triclinic form when the file is read. Other sections of the data
file must also list their per-atom data appropriately if vector
quantities are specified. This requirement is explained below for
the relevant sections. The :doc:`Howto_triclinic
<Howto_triclinic>` doc page also discusses other LAMMPS commands
which can input/output general triclinic representations of the
simulation box and per-atom data.
The following explanations apply to all 3 kinds of simulation boxes:
orthogonal, restricted triclinic, and general triclinic.
If the system is periodic (in a dimension), then atom coordinates can
be outside the bounds (in that dimension); they will be remapped (in a
periodic sense) back inside the box. Note that if the *add* option is
being used to add atoms to a simulation box that already exists, this
periodic remapping will be performed using simulation box bounds that
are the union of the existing box and the box boundaries in the new
data file.
periodic sense) back inside the box. For triclinic boxes, periodicity
in x,y,z refers to the faces of the parallelepiped defined by the
**A**,**B**,**C** edge vectors of the simulation box. See the
:doc:`boundary <boundary>` command doc page for a fuller discussion.
Note that if the *add* option is being used to add atoms to a
simulation box that already exists, this periodic remapping will be
performed using simulation box bounds that are the union of the
existing box and the box boundaries in the new data file.
If the system is non-periodic (in a dimension), then an image flag for
that direction has no meaning, since there cannot be periodic images
@ -406,7 +529,6 @@ individually back into the principal unit cell in that direction. This
operation is equivalent to the behavior of the :doc:`change_box command
<change_box>` when used to change periodicity.
If those atoms with non-zero image flags are involved in bonded
interactions, this reset can lead to undesired changes, when the image
flag values differ between the atoms, i.e. the bonded interaction
@ -421,73 +543,81 @@ needed, so that the image flag would be zero.
.. note::
If the system is non-periodic (in a dimension), then all atoms in the
data file must have coordinates (in that dimension) that are "greater
than or equal to" the lo value and "less than or equal to" the hi
value. If the non-periodic dimension is of style "fixed" (see the
:doc:`boundary <boundary>` command), then the atom coords must be
strictly "less than" the hi value, due to the way LAMMPS assign atoms
to processors. Note that you should not make the lo/hi values
radically smaller/larger than the extent of the atoms. For example,
if your atoms extend from 0 to 50, you should not specify the box
bounds as -10000 and 10000 unless you also use the :doc:`processors
command <processors>`. This is because LAMMPS uses the specified box
size to layout the 3d grid of processors. A huge (mostly empty) box
will be sub-optimal for performance when using "fixed" boundary
conditions (see the :doc:`boundary <boundary>` command). When using
"shrink-wrap" boundary conditions (see the :doc:`boundary <boundary>`
command), a huge (mostly empty) box may cause a parallel simulation
to lose atoms when LAMMPS shrink-wraps the box around the atoms. The
read_data command will generate an error in this case.
If the system is non-periodic (in a dimension), then all atoms in
the data file must have coordinates (in that dimension) that are
"greater than or equal to" the lo value and "less than or equal to"
the hi value. If the non-periodic dimension is of style "fixed"
(see the :doc:`boundary <boundary>` command), then the atom coords
must be strictly "less than" the hi value, due to the way LAMMPS
assign atoms to processors. Note that you should not make the
lo/hi values radically smaller/larger than the extent of the atoms.
For example, if atoms extend from 0 to 50, you should not specify
the box bounds as -10000 and 10000 unless you also use the
:doc:`processors command <processors>`. This is because LAMMPS
uses the specified box size to layout the 3d grid of processors. A
huge (mostly empty) box will be sub-optimal for performance when
using "fixed" boundary conditions (see the :doc:`boundary
<boundary>` command). When using "shrink-wrap" boundary conditions
(see the :doc:`boundary <boundary>` command), a huge (mostly empty)
box may cause a parallel simulation to lose atoms when LAMMPS
shrink-wraps the box around the atoms. The read_data command will
generate an error in this case.
----------
Meaning of other header keywords
""""""""""""""""""""""""""""""""
The "extra bond per atom" setting (angle, dihedral, improper) is only
needed if new bonds (angles, dihedrals, impropers) will be added to
the system when a simulation runs, e.g. by using the :doc:`fix bond/create <fix_bond_create>` command. Using this header flag
is deprecated; please use the *extra/bond/per/atom* keyword (and
the system when a simulation runs, e.g. by using the :doc:`fix
bond/create <fix_bond_create>` command. Using this header flag is
deprecated; please use the *extra/bond/per/atom* keyword (and
correspondingly for angles, dihedrals and impropers) in the read_data
command instead. Either will pre-allocate space in LAMMPS data
structures for storing the new bonds (angles, dihedrals, impropers).
The "extra special per atom" setting is typically only needed if new
bonds/angles/etc will be added to the system, e.g. by using the :doc:`fix bond/create <fix_bond_create>` command. Or if entire new molecules
will be added to the system, e.g. by using the
:doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` commands,
which will have more special 1-2,1-3,1-4 neighbors than any other
molecules defined in the data file. Using this header flag is
deprecated; please use the *extra/special/per/atom* keyword instead.
Using this setting will pre-allocate space in the LAMMPS data
structures for storing these neighbors. See the
:doc:`special_bonds <special_bonds>` and :doc:`molecule <molecule>` doc
pages for more discussion of 1-2,1-3,1-4 neighbors.
bonds/angles/etc will be added to the system, e.g. by using the
:doc:`fix bond/create <fix_bond_create>` command. Or if entire new
molecules will be added to the system, e.g. by using the :doc:`fix
deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` commands, which
will have more special 1-2,1-3,1-4 neighbors than any other molecules
defined in the data file. Using this header flag is deprecated;
please use the *extra/special/per/atom* keyword instead. Using this
setting will pre-allocate space in the LAMMPS data structures for
storing these neighbors. See the :doc:`special_bonds <special_bonds>`
and :doc:`molecule <molecule>` doc pages for more discussion of
1-2,1-3,1-4 neighbors.
.. note::
All of the "extra" settings are only applied in the first data
file read and when no simulation box has yet been created; as soon as
All of the "extra" settings are only applied in the first data file
read and when no simulation box has yet been created; as soon as
the simulation box is created (and read_data implies that), these
settings are *locked* and cannot be changed anymore. Please see the
description of the *add* keyword above for reading multiple data files.
If they appear in later data files, they are ignored.
description of the *add* keyword above for reading multiple data
files. If they appear in later data files, they are ignored.
The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
only used with :doc:`atom_style ellipsoid or line or tri or body <atom_style>` and specify how many of the atoms are
finite-size ellipsoids or lines or triangles or bodies; the remainder
are point particles. See the discussion of ellipsoidflag and the
*Ellipsoids* section below. See the discussion of lineflag and the
*Lines* section below. See the discussion of triangleflag and the
*Triangles* section below. See the discussion of bodyflag and the
*Bodies* section below.
only used with :doc:`atom_style ellipsoid or line or tri or body
<atom_style>` and specify how many of the atoms are finite-size
ellipsoids or lines or triangles or bodies; the remainder are point
particles. See the discussion of ellipsoidflag and the *Ellipsoids*
section below. See the discussion of lineflag and the *Lines* section
below. See the discussion of triangleflag and the *Triangles* section
below. See the discussion of bodyflag and the *Bodies* section below.
.. note::
For :doc:`atom_style template <atom_style>`, the molecular
topology (bonds,angles,etc) is contained in the molecule templates
read-in by the :doc:`molecule <molecule>` command. This means you
cannot set the *bonds*, *angles*, etc header keywords in the data
file, nor can you define *Bonds*, *Angles*, etc sections as discussed
For :doc:`atom_style template <atom_style>`, the molecular topology
(bonds,angles,etc) is contained in the molecule templates read-in
by the :doc:`molecule <molecule>` command. This means you cannot
set the *bonds*, *angles*, etc header keywords in the data file,
nor can you define *Bonds*, *Angles*, etc sections as discussed
below. You can set the *bond types*, *angle types*, etc header
keywords, though it is not necessary. If specified, they must match
the maximum values defined in any of the template molecules.
keywords, though it is not necessary. If specified, they must
match the maximum values defined in any of the template molecules.
----------
@ -680,6 +810,19 @@ appended to it, which indicate which image of a periodic simulation
box the atom is in. These may be important to include for some kinds
of analysis.
.. note::
For orthogonal and restricted and general triclinic simulation
boxes, the atom coordinates (x,y,z) listed in this section should
be inside the corresponding simulation box. For restricted
triclinic boxes that means the parallelepiped defined by the *xlo
xhi*, *ylo yhi*, *zlo zhi*, and *xy xz yz*, keywords. For general
triclinic boxes that means the parallelepiped defined by the 3 edge
vectors and origin specified by the *avec*, *bvec*, *cvec*, and
*abc origin* header keywords. See the discussion in the header
section above about how atom coordinates outside the simulation box
are (or are not) remapped to be inside the box.
.. list-table::
* - angle
@ -690,10 +833,12 @@ of analysis.
- atom-ID atom-type bodyflag mass x y z
* - bond
- atom-ID molecule-ID atom-type x y z
* - bpm/sphere
- atom-ID molecule-ID atom-type diameter density x y z
* - charge
- atom-ID atom-type q x y z
* - dielectric
- atom-ID atom-type q x y z normx normy normz area ed em epsilon curvature
- atom-ID atom-type q x y z mux muy muz area ed em epsilon curvature
* - dipole
- atom-ID atom-type q x y z mux muy muz
* - dpd
@ -720,8 +865,6 @@ of analysis.
- atom-ID atom-type rho esph cv x y z
* - sphere
- atom-ID atom-type diameter density x y z
* - bpm/sphere
- atom-ID molecule-ID atom-type diameter density x y z
* - spin
- atom-ID atom-type x y z spx spy spz sp
* - tdpd
@ -757,24 +900,42 @@ The per-atom values have these meanings and units, listed alphabetically:
* lineflag = 1 for line segment particles, 0 for point or spherical particles
* mass = mass of particle (mass units)
* molecule-ID = integer ID of molecule the atom belongs to
* mux,muy,muz = components of dipole moment of atom (dipole units)
* mux,muy,muz = components of dipole moment of atom (dipole units) (see general triclinic note below)
* q = charge on atom (charge units)
* rho = density (need units) for SPH particles
* sp = magnitude of magnetic spin of atom (Bohr magnetons)
* spx,spy,spz = components of magnetic spin of atom (unit vector)
* spx,spy,spz = components of magnetic spin of atom (unit vector) (see general triclinic note below)
* template-atom = which atom within a template molecule the atom is
* template-index = which molecule within the molecule template the atom is part of
* theta = internal temperature of a DPD particle
* triangleflag = 1 for triangular particles, 0 for point or spherical particles
* volume = volume of Peridynamic particle (distance\^3 units)
* x,y,z = coordinates of atom (distance units)
* x0,y0,z0 = original (strain-free) coordinates of atom (distance units)
* x0,y0,z0 = original (strain-free) coordinates of atom (distance
units) (see general triclinic note below)
The units for these quantities depend on the unit style; see the
:doc:`units <units>` command for details.
For 2d simulations specify z as 0.0, or a value within the *zlo zhi*
setting in the data file header.
For 2d simulations, the atom coordinate z must be specified as 0.0.
If the data file is created by another program, then z values for a 2d
simulation can be within epsilon of 0.0, and LAMMPS will force them to
zero.
.. note::
If the data file defines a general triclinic box, then the
following per-atom values in the list above are per-atom vectors
which imply an orientation: (mux,muy,muz) and (spx,spy,spz). This
means they should be specified consistent with the general
triclinic box and its orientation relative to the standard x,y,z
coordinate axes. For example a dipole moment vector which will be
in the +x direction once LAMMPS converts from a general to
restricted triclinic box, should be specified in the data file in
the direction of the **A** edge vector. Likewise the (x0,y0,z0)
per-atom strain-free coordinates should be inside the general
triclinic simulation box as explained in the note above. See the
:doc:`Howto triclinic <Howto_triclinic>` doc page for more details.
The atom-ID is used to identify the atom throughout the simulation and
in dump files. Normally, it is a unique value from 1 to Natoms for
@ -922,9 +1083,8 @@ that use unwrapped coordinates internally are as follows:
Atom velocities and other atom quantities not defined above are set to
0.0 when the *Atoms* section is read. Velocities can be set later by
a *Velocities* section in the data file or by a
:doc:`velocity <velocity>` or :doc:`set <set>` command in the input
script.
a *Velocities* section in the data file or by a :doc:`velocity
<velocity>` or :doc:`set <set>` command in the input script.
----------
@ -963,8 +1123,9 @@ the "bodies" keyword.
Each body can have a variable number of integer and/or floating-point
values. The number and meaning of the values is defined by the body
style, as described in the :doc:`Howto body <Howto_body>` doc page. The
body style is given as an argument to the :doc:`atom_style body <atom_style>` command.
style, as described in the :doc:`Howto body <Howto_body>` doc page.
The body style is given as an argument to the :doc:`atom_style body
<atom_style>` command.
The Ninteger and Ndouble values determine how many integer and
floating-point values are specified for this particle. Ninteger and
@ -1179,10 +1340,10 @@ and a general discussion of how type labels can be used.
12 1 2 1 1 0 0 0
The *Ellipsoids* section must appear if :doc:`atom_style ellipsoid <atom_style>` is used and any atoms are listed in the
*Atoms* section with an ellipsoidflag = 1. The number of ellipsoids
should be specified in the header section via the "ellipsoids"
keyword.
The *Ellipsoids* section must appear if :doc:`atom_style ellipsoid
<atom_style>` is used and any atoms are listed in the *Atoms* section
with an ellipsoidflag = 1. The number of ellipsoids should be
specified in the header section via the "ellipsoids" keyword.
The 3 shape values specify the 3 diameters or aspect ratios of a
finite-size ellipsoidal particle, when it is oriented along the 3
@ -1200,6 +1361,12 @@ the quaternion that represents its new orientation is given by
LAMMPS normalizes each atom's quaternion in case (a,b,c) is not
specified as a unit vector.
If the data file defines a general triclinic box, then the quaternion
for each ellipsoid should be specified for its orientation relative to
the standard x,y,z coordinate axes. When the system is converted to a
restricted triclinic box, the ellipsoid quaternions will be altered to
reflect the new orientation of the ellipsoid.
The *Ellipsoids* section must appear after the *Atoms* section.
----------
@ -1316,13 +1483,24 @@ is used and any atoms are listed in the *Atoms* section with a
lineflag = 1. The number of lines should be specified in the header
section via the "lines" keyword.
The 2 end points are the end points of the line segment. The ordering
of the 2 points should be such that using a right-hand rule to cross
the line segment with a unit vector in the +z direction, gives an
"outward" normal vector perpendicular to the line segment.
The 2 end points are the end points of the line segment. They should
be values close to the center point of the line segment specified in
the Atoms section of the data file, even if individual end points are
outside the simulation box.
The ordering of the 2 points should be such that using a right-hand
rule to cross the line segment with a unit vector in the +z direction,
gives an "outward" normal vector perpendicular to the line segment.
I.e. normal = (c2-c1) x (0,0,1). This orientation may be important
for defining some interactions.
If the data file defines a general triclinic box, then the x1,y1 and
x2,y2 values for each line segment should be specified for its
orientation relative to the standard x,y,z coordinate axes. When the
system is converted to a restricted triclinic box, the x1,y1,x2,y2
values will be altered to reflect the new orientation of the line
segment.
The *Lines* section must appear after the *Atoms* section.
----------
@ -1444,15 +1622,27 @@ via the :doc:`pair_coeff <pair_coeff>` command in the input script.
12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0
The *Triangles* section must appear if :doc:`atom_style tri <atom_style>` is used and any atoms are listed in the *Atoms*
section with a triangleflag = 1. The number of lines should be
specified in the header section via the "triangles" keyword.
The *Triangles* section must appear if :doc:`atom_style tri
<atom_style>` is used and any atoms are listed in the *Atoms* section
with a triangleflag = 1. The number of lines should be specified in
the header section via the "triangles" keyword.
The 3 corner points are the corner points of the triangle. The
ordering of the 3 points should be such that using a right-hand rule
to go from point1 to point2 to point3 gives an "outward" normal vector
to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This
orientation may be important for defining some interactions.
The 3 corner points are the corner points of the triangle. They
should be values close to the center point of the triangle specified
in the Atoms section of the data file, even if individual corner
points are outside the simulation box.
The ordering of the 3 points should be such that using a right-hand
rule to go from point1 to point2 to point3 gives an "outward" normal
vector to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1).
This orientation may be important for defining some interactions.
If the data file defines a general triclinic box, then the x1,y1,z1
and x2,y2,z2 and x3,y3,z3 values for each triangle should be specified
for its orientation relative to the standard x,y,z coordinate axes.
When the system is converted to a restricted triclinic box, the
x1,y1,z1,x2,y2,z2,x3,y3,z3 values will be altered to reflect the new
orientation of the triangle.
The *Triangles* section must appear after the *Atoms* section.
@ -1493,6 +1683,12 @@ Vx, vy, vz, and ervel are in :doc:`units <units>` of velocity. Lx, ly,
lz are in units of angular momentum (distance-velocity-mass). Wx, Wy,
Wz are in units of angular velocity (radians/time).
If the data file defines a general triclinic box, then each of the 3
vectors (translational velocity, angular momentum, angular velocity)
should be specified for the rotated coordinate axes of the general
triclinic box. See the :doc:`Howto triclinic <Howto_triclinic>` doc
page for more details.
For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz),
specific values for each sub-style must be listed. The order of the
sub-styles is the same as they were listed in the
@ -1513,8 +1709,8 @@ fields:
atom-ID vx vy vz ervel wx wy wz
Translational velocities can also be set by the
:doc:`velocity <velocity>` command in the input script.
Translational velocities can also be (re)set by the :doc:`velocity
<velocity>` command in the input script.
----------

169
doc/src/replicate.rst
View File

@ -8,56 +8,118 @@ Syntax
.. code-block:: LAMMPS
replicate nx ny nz *keyword*
replicate nx ny nz keyword ...
nx,ny,nz = replication factors in each dimension
* optional *keyword* = *bbox*
* zero or more keywords may be appended
* keyword = *bbox* or *bond/periodic*
.. parsed-literal::
*bbox* = only check atoms in replicas that overlap with a processor's subdomain
*bbox* = use a bounding-box algorithm which is faster for large proc counts
*bond/periodic* = use an algorithm that correctly replicates periodic bond loops
Examples
""""""""
For examples of replicating simple linear polymer chains (periodic or
non-periodic) or periodic carbon nanotubes, see examples/replicate.
.. code-block:: LAMMPS
replicate 2 3 2
replicate 2 3 2 bbox
replicate 2 3 2 bond/periodic
Description
"""""""""""
Replicate the current simulation one or more times in each dimension.
For example, replication factors of 2,2,2 will create a simulation
with 8x as many atoms by doubling the simulation domain in each
dimension. A replication factor of 1 in a dimension leaves the
simulation domain unchanged. When the new simulation box is created
it is also partitioned into a regular 3d grid of rectangular bricks,
one per processor, based on the number of processors being used and
the settings of the :doc:`processors <processors>` command. The
partitioning can later be changed by the :doc:`balance <balance>` or
:doc:`fix balance <fix_balance>` commands.
Replicate the current system one or more times in each dimension. For
example, replication factors of 2,2,2 will create a simulation with 8x
as many atoms by doubling the size of the simulation box in each
dimension. A replication factor of 1 leaves the simulation domain
unchanged in that dimension.
All properties of the atoms are replicated, including their
velocities, which may or may not be desirable. New atom IDs are
assigned to new atoms, as are molecule IDs. Bonds and other topology
interactions are created between pairs of new atoms as well as between
old and new atoms. This is done by using the image flag for each atom
to "unwrap" it out of the periodic box before replicating it.
When the new simulation box is created it is partitioned into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors being used and the settings of the
:doc:`processors <processors>` command. The partitioning can be
changed by subsequent :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands.
This means that any molecular bond you specify in the original data
file that crosses a periodic boundary should be between two atoms with
image flags that differ by 1. This will allow the bond to be
unwrapped appropriately.
All properties of each atom are replicated (except per-atom fix data,
see the Restrictions section below). This includes their velocities,
which may or may not be desirable. New atom IDs are assigned to new
atoms, as are new molecule IDs. Bonds and other topology interactions
are created between pairs of new atoms as well as between old and new
atoms.
The optional keyword *bbox* uses a bounding box to only check atoms in
replicas that overlap with a processor's subdomain when assigning
atoms to processors. It typically results in a substantial speedup
when using the replicate command on a large number of processors. It
does require temporary use of more memory, specifically that each
processor can store all atoms in the entire system before it is
replicated.
.. note::
The bond discussion which follows only refers to models with
permanent covalent bonds typically defined in LAMMPS via a data
file. It is not relevant to systems modeled with many-body
potentials which can define bonds on-the-fly, based on the current
positions of nearby atoms, e.g. models using the :doc:`AIREBO
<pair_airebo>` or :doc:`ReaxFF <pair_reaxff>` potentials.
If the *bond/periodic* keyword is not specified, bond replication is
done by using the image flag for each atom to "unwrap" it out of the
periodic box before replicating it. After replication is performed,
atoms outside the new periodic box are wrapped back into it. This
assigns correct images flags to all atoms in the system. For this to
work, all original atoms in the original simulation box must have
consistent image flags. This means that if two atoms have a bond
between them which crosses a periodic boundary, their respective image
flags will differ by 1 in that dimension.
Image flag consistency is not possible if a system has a periodic bond
loop, meaning there is a chain of bonds which crosses an entire
dimension and re-connects to itself across a periodic boundary. In
this case you MUST use the *bond/periodic* keyword to correctly
replicate the system. This option zeroes the image flags for all
atoms and uses a different algorithm to find new (nearby) bond
neighbors in the replicated system. In the final replicated system
all image flags are zero (in each dimension).
.. note::
LAMMPS does not check for image flag consistency before performing
the replication (it does issue a warning about this before a
simulation is run). If the original image flags are inconsistent,
the replicated system will also have inconsistent image flags, but
will otherwise be correctly replicated. This is NOT the case if
there is a periodic bond loop. See the next note.
.. note::
LAMMPS does not check for periodic bond loops. If you use the
*bond/periodic* keyword for a system without periodic bond loops,
the system will be correctly replicated, but image flag information
will be lost (which may or may not be important to your model). If
you do not use the *bond/periodic* keyword for a system with
periodic bond loops, the replicated system will have invalid bonds
(typically very long), resulting in bad dynamics.
If possible, the *bbox* keyword should be used when running on a large
number of processors, as it can result in a substantial speed-up for
the replication operation. It uses a bounding box to only check atoms
in replicas that overlap with each processor's new subdomain when
assigning atoms to processors. It also preserves image flag
information. The only drawback to the *bbox* option is that it
requires a temporary use of more memory. Each processor must be able
to store all atoms (and their per-atom data) in the original system,
before it is replicated.
.. note::
The algorithm used by the *bond/periodic* keyword builds on the
algorithm used by the *bbox* keyword and thus has the same memory
requirements. If you specify only the *bond/peridoic* keyword it
will internally set the *bbox* keyword as well.
----------
Restrictions
""""""""""""
@ -65,49 +127,30 @@ Restrictions
A 2d simulation cannot be replicated in the z dimension.
If a simulation is non-periodic in a dimension, care should be used
when replicating it in that dimension, as it may put atoms nearly on
top of each other.
.. note::
You cannot use the replicate command on a system which has a
molecule that spans the box and is bonded to itself across a periodic
boundary, so that the molecule is effectively a loop. A simple
example would be a linear polymer chain that spans the simulation box
and bonds back to itself across the periodic boundary. More realistic
examples would be a CNT (meant to be an infinitely long CNT) or a
graphene sheet or a bulk periodic crystal where there are explicit
bonds specified between near neighbors. (Note that this only applies
to systems that have permanent bonds as specified in the data file. A
CNT that is just atoms modeled with the :doc:`AIREBO potential <pair_airebo>` has no such permanent bonds, so it can be
replicated.) The reason replication does not work with those systems
is that the image flag settings described above cannot be made
consistent. I.e. it is not possible to define images flags so that
when every pair of bonded atoms is unwrapped (using the image flags),
they will be close to each other. The only way the replicate command
could work in this scenario is for it to break a bond, insert more
atoms, and re-connect the loop for the larger simulation box. But it
is not clever enough to do this. So you will have to construct a
larger version of your molecule as a pre-processing step and input a
new data file to LAMMPS.
when replicating it in that dimension, as it may generate atoms nearly
on top of each other.
If the current simulation was read in from a restart file (before a
run is performed), there must not be any fix information stored in
the file for individual atoms. Similarly, no fixes can be defined at
the time the replicate command is used that require vectors of atom
run is performed), there must not be any fix information stored in the
file for individual atoms. Similarly, no fixes can be defined at the
time the replicate command is used that require vectors of atom
information to be stored. This is because the replicate command does
not know how to replicate that information for new atoms it creates.
To work around this restriction, restart files may be converted into
data files and fixes may be undefined via the :doc:`unfix <unfix>`
command before and redefined after the replicate command.
To work around this restriction two options are possible. (1) Fixes
which use the stored data in the restart file can be defined before
replication and then deleted via the :doc:`unfix <unfix>` command and
re-defined after it. Or (2) the restart file can be converted to a
data file (which deletes the stored fix information) and fixes defined
after the replicate command. In both these scenarios, the per-atom
fix information in the restart file is lost.
Related commands
""""""""""""""""
none
Default
"""""""
none
No settings for using the *bbox* or *bond/periodic* algorithms.

22
doc/src/thermo_modify.rst
View File

@ -11,7 +11,7 @@ Syntax
thermo_modify keyword value ...
* one or more keyword/value pairs may be listed
* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *colname* or *format* or *temp* or *press*
* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *colname* or *format* or *temp* or *press* or *triclinic/general*
.. parsed-literal::
@ -32,6 +32,8 @@ Syntax
*or* a thermo keyword or reference to compute, fix, property or variable.
*temp* value = compute ID that calculates a temperature
*press* value = compute ID that calculates a pressure
*triclinic/general* arg = *yes* or *no*
Examples
""""""""
@ -240,6 +242,19 @@ command, thermo output uses a default compute for pressure with ID =
keyword, then the new pressure compute specified by the *press*
keyword will be unaffected by the *temp* setting.
The *triclinic/general* keyword can only be used with a value of *yes*
if the simulation box was created as a general triclinic box. See the
:doc:`Howto_triclinic <Howto_triclinic>` doc page for a detailed
explanation of orthogonal, restricted triclinic, and general triclinic
simulation boxes.
If this keyword is *yes*, the output of the simulation box edge
vectors and the pressure tensor components for the system are
affected. These are specified by the *avec,bvec,cvec* and
*pxx,pyy,pzz,pxy,pxz,pyz* keywords of the :doc:`thermo_style
<thermo_style>` command. See the :doc:`thermo_style <thermo_style>`
doc page for details.
Restrictions
""""""""""""
none
@ -253,8 +268,9 @@ Default
"""""""
The option defaults are lost = error, warn = 100, norm = yes for unit
style of *lj*, norm = no for unit style of *real* and *metal*,
flush = no, and temp/press = compute IDs defined by thermo_style.
style of *lj*, norm = no for unit style of *real* and *metal*, flush =
no, temp/press = compute IDs defined by thermo_style, and
triclinic/general = no.
The defaults for the line and format options depend on the thermo style.
For styles "one" and "custom", the line and format defaults are "one",

103
doc/src/thermo_style.rst
View File

@ -25,12 +25,18 @@ Syntax
evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
emol, elong, etail,
enthalpy, ecouple, econserve,
vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
xy, xz, yz, xlat, ylat, zlat,
bonds, angles, dihedrals, impropers,
pxx, pyy, pzz, pxy, pxz, pyz,
fmax, fnorm, nbuild, ndanger,
vol, density,
xlo, xhi, ylo, yhi, zlo, zhi,
xy, xz, yz,
avecx, avecy, avecz,
bvecx, bvecy, bvecz,
cvecx, cvecy, cvecz,
lx, ly, lz,
xlat, ylat, zlat,
cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
pxx, pyy, pzz, pxy, pxz, pyz,
bonds, angles, dihedrals, impropers,
fmax, fnorm, nbuild, ndanger,
c_ID, c_ID[I], c_ID[I][J],
f_ID, f_ID[I], f_ID[I][J],
v_name, v_name[I]
@ -66,18 +72,21 @@ Syntax
econserve = pe + ke + ecouple = etotal + ecouple
vol = volume
density = mass density of system
lx,ly,lz = box lengths in x,y,z
xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
xy,xz,yz = box tilt for restricted triclinic (non-orthogonal) simulation boxes
avecx,avecy,avecz = components of edge vector A of the simulation box
bvecx,bvecy,bvecz = components of edge vector B of the simulation box
cvecx,cvecy,cvecz = components of edge vector C of the simulation box
lx,ly,lz = box lengths in x,y,z
xlat,ylat,zlat = lattice spacings as calculated by :doc:`lattice <lattice>` command
bonds,angles,dihedrals,impropers = # of these interactions defined
cella,cellb,cellc = periodic cell lattice constants a,b,c
cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
bonds,angles,dihedrals,impropers = # of these interactions defined
fmax = max component of force on any atom in any dimension
fnorm = length of force vector for all atoms
nbuild = # of neighbor list builds
ndanger = # of dangerous neighbor list builds
cella,cellb,cellc = periodic cell lattice constants a,b,c
cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
c_ID = global scalar value calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
c_ID[I][J] = I,J component of global array calculated by a compute with ID
@ -102,8 +111,11 @@ Examples
Description
"""""""""""
Set the style and content for printing thermodynamic data to the screen
and log files.
Set the style and content for printing thermodynamic data to the
screen and log files. The units for each column of output
corresponding to the list of keywords is determined by the :doc:`units
<units>` command for the simulation. E.g. energies will be in energy
units, temperature in temperature units, pressure in pressure units.
Style *one* prints a single line of thermodynamic info that is the
equivalent of "thermo_style custom step temp epair emol etotal press".
@ -245,7 +257,7 @@ and *pxx*, *pyy*, etc.
----------
Here is more information on other keywords whose meaning may not be
clear:
clear.
The *step*, *elapsed*, and *elaplong* keywords refer to timestep
count. *Step* is the current timestep, or iteration count when a
@ -319,6 +331,63 @@ thermostatting or barostatting to their coupling reservoirs -- that is,
the NVT, NPH, or NPT ensembles, the *econserve* quantity should remain
constant over time even though *etotal* may change.
In LAMMPS, the simulation box can be defined as orthogonal or
triclinic (non-orthogonal). See the :doc:`Howto_triclinic
<Howto_triclinic>` doc page for a detailed explanation of orthogonal,
restricted triclinic, and general triclinic simulation boxes and how
LAMMPS rotates a general triclinic box to be restricted triclinic
internally.
The *lx*, *ly*, *lz* keywords are the extent of the simulation box in
each dimension. The *xlo*, *xhi*, *ylo*, *yhi*, *zlo*, *zhi* keywords
are the lower and upper bounds of the simulation box in each dimension.
I.e. *lx* = *xhi* - *xlo*). These 9 values are the same for all 3 kinds
of boxes. I.e. for a restricted triclinic box, they are the values as
if the box were not tilted. For a general triclinic box, they are the
values after it is internally rotated to be a restricted triclinic box.
The *xy*, *xz*, *yz* are the current tilt factors for a triclinic box.
They are the same for restricted and general triclinic boxes.
The *avecx*, *avecy*, *avecz*, *bvecx*, *bvecy*, *bvecz*, *cvecx*,
*cvecy*, *cvecz* are the components of the 3 edge vectors of the
current general simulation box. If it is an orthogonal box the
vectors are along the x, y, z coordinate axes. If it is a restricted
triclinic box, the **A** vector is along the x axis, the **B** vector
is in the xy plane with a +y coordinate, and the **C** vector has a +z
coordinate, as explained on the :doc:`Howto_triclinic
<Howto_triclinic>` doc page. If the :doc:`thermo_modify
triclinic/general <thermo_modify>` option is set then they are the
**A**, **B**, **C** vector which define the general triclinic box.
The *cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma*
keywords correspond to the usual crystallographic quantities that
define the periodic simulation box of a crystalline system. See the
:doc:`Howto triclinic <Howto_triclinic>` page for a precise definition
of these quantities in terms of the LAMMPS representation of a
restricted triclinic simulation box via *lx*, *ly*, *lz*, *yz*, *xz*,
*xy*\ .
The *pxx,pyy,pzz,pxy,pxz,pyz* keywords are the 6 components of the
symmetric pressure tensor for the system. See the :doc:`compute
pressure <compute_pressure>` command doc page for details of how it is
calculated.
If the :doc:`thermo_modify triclinic/general <thermo_modify>` option
is set then the 6 components will be output as values consistent with
the orientation of the general triclinic box relative to the standard
xyz coordinate axes. If this keyword is not used, the values will be
consistent with the orientation of the restricted triclinic box (which
aligns with the xyz coordinate axes). As explained on the
:doc:`Howto_triclinic <Howto_triclinic>` doc page, even if the
simulation box is created as a general triclinic box, internally
LAMMPS uses a restricted triclinic box.
Note that because the pressure tensor components are computed using
force vectors and atom coordinates, both of which are rotated in the
general versus restricted triclinic representation, the values will
typically be different for the two cases.
The *fmax* and *fnorm* keywords are useful for monitoring the progress
of an :doc:`energy minimization <minimize>`. The *fmax* keyword
calculates the maximum force in any dimension on any atom in the
@ -338,14 +407,6 @@ to reduce the delay factor to ensure no force interactions are missed
by atoms moving beyond the neighbor skin distance before a rebuild
takes place.
The keywords *cella*, *cellb*, *cellc*, *cellalpha*,
*cellbeta*, *cellgamma*, correspond to the usual crystallographic
quantities that define the periodic unit cell of a crystal. See the
:doc:`Howto triclinic <Howto_triclinic>` page for a geometric
description of triclinic periodic cells, including a precise
definition of these quantities in terms of the internal LAMMPS cell
dimensions *lx*, *ly*, *lz*, *yz*, *xz*, *xy*\ .
----------
For output values from a compute or fix or variable, the bracketed

79
doc/src/variable.rst
View File

@ -279,9 +279,9 @@ This means the variable can then be evaluated as many times as desired
and will return those values. There are two ways to cause the next
set of per-atom values from the file to be read: use the
:doc:`next <next>` command or the next() function in an atom-style
variable, as discussed below. Unlike most variable styles
atomfile-style variables are **deleted** during a :doc:`clear <clear>`
command.
variable, as discussed below. Unlike most variable styles, which
remain defined, atomfile-style variables are **deleted** during a
:doc:`clear <clear>` command.
The rules for formatting the file are as follows. Each time a set of
per-atom values is read, a non-blank line is searched for in the file.
@ -289,23 +289,37 @@ The file is read line by line but only up to 254 characters are used.
The rest are ignored. A comment character "#" can be used anywhere
on a line and all text following and the "#" character are ignored;
text starting with the comment character is stripped. Blank lines
are skipped. The first "word" of a non-blank line, delimited by
white-space, is read as the count N of per-atom lines to immediately
follow. N can be the total number of atoms in the system, or only a
subset. The next N lines have the following format
.. parsed-literal::
ID value
where ID is an atom ID and value is the per-atom numeric value that
will be assigned to that atom. IDs can be listed in any order.
are skipped. The first non-blank line is expected to contain a single
integer number as the count *N* of per-atom lines to follow. *N* can
be the total number of atoms in the system or less, indicating that data
for a subset is read. The next N lines must consist of two numbers,
the atom-ID of the atom for which a value is set followed by a floating
point number with the value. The atom-IDs may be listed in any order.
.. note::
Every time a set of per-atom lines is read, the value for all
atoms is first set to 0.0. Thus values for atoms whose ID does not
appear in the set, will remain 0.0.
Every time a set of per-atom lines is read, the value of the atomfile
variable for **all** atoms is first initialized to 0.0. Thus values
for atoms whose ID do not appear in the set in the file will remain
at 0.0.
Below is a small example for the atomfile variable file format:
.. parsed-literal::
# first set
4
# atom-ID value
3 1
4 -4
1 0.5
2 -0.5
# second set
2
2 1.0
4 -1.0
----------
@ -1174,12 +1188,17 @@ custom atom properties are the same; just replace the leading "i" with
+--------+---------------+------------------------------------------+
| equal | i_name[I] | element of per-atom vector (I = atom ID) |
+--------+---------------+------------------------------------------+
| equal | i2_name[I][J] | element of per-atom array (I = atom ID) |
+--------+---------------+------------------------------------------+
+--------+---------------+------------------------------------------+
| vector | i_name[I] | element of per-atom vector (I = atom ID) |
+--------+---------------+------------------------------------------+
| vector | i2_name[I][J] | element of per-atom array (I = atom ID) |
+--------+---------------+------------------------------------------+
+--------+---------------+------------------------------------------+
| atom | i_name | per-atom vector |
+--------+---------------+------------------------------------------+
| atom | i2_name[I] | column of per-atom array |
+--------+---------------+------------------------------------------+
@ -1222,15 +1241,23 @@ table:
+--------+------------+------------------------------------------+
| equal | c_ID | global scalar |
+--------+------------+------------------------------------------+
| equal | c_ID[I] | element of global vector |
+--------+------------+------------------------------------------+
| equal | c_ID[I][J] | element of global array |
+--------+------------+------------------------------------------+
| equal | C_ID[I] | element of per-atom vector (I = atom ID) |
+--------+------------+------------------------------------------+
| equal | C_ID[I][J] | element of per-atom array (I = atom ID) |
+--------+------------+------------------------------------------+
+--------+------------+------------------------------------------+
| vector | c_ID | global vector |
+--------+------------+------------------------------------------+
| vector | c_ID[I] | column of global array |
+--------+------------+------------------------------------------+
+--------+------------+------------------------------------------+
| atom | c_ID | per-atom vector |
+--------+------------+------------------------------------------+
| atom | c_ID[I] | column of per-atom array |
+--------+------------+------------------------------------------+
@ -1286,15 +1313,23 @@ and atom-style variables are listed in the following table:
+--------+------------+------------------------------------------+
| equal | f_ID | global scalar |
+--------+------------+------------------------------------------+
| equal | f_ID[I] | element of global vector |
+--------+------------+------------------------------------------+
| equal | f_ID[I][J] | element of global array |
+--------+------------+------------------------------------------+
| equal | F_ID[I] | element of per-atom vector (I = atom ID) |
+--------+------------+------------------------------------------+
| equal | F_ID[I][J] | element of per-atom array (I = atom ID) |
+--------+------------+------------------------------------------+
+--------+------------+------------------------------------------+
| vector | f_ID | global vector |
+--------+------------+------------------------------------------+
| vector | f_ID[I] | column of global array |
+--------+------------+------------------------------------------+
+--------+------------+------------------------------------------+
| atom | f_ID | per-atom vector |
+--------+------------+------------------------------------------+
| atom | f_ID[I] | column of per-atom array |
+--------+------------+------------------------------------------+
@ -1365,17 +1400,27 @@ per-atom vector.
+--------+-----------+-----------------------------------------------------------------------------------+
| equal | v_name | global scalar from an equal-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| equal | v_name[I] | element of global vector from a vector-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| equal | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
+--------+-----------+-----------------------------------------------------------------------------------+
| vector | v_name | global scalar from an equal-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| vector | v_name | global vector from a vector-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| vector | v_name[I] | element of global vector from a vector-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| vector | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
+--------+-----------+-----------------------------------------------------------------------------------+
| atom | v_name | global scalar from an equal-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| atom | v_name | per-atom vector from an atom-style or atomfile-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| atom | v_name[I] | element of global vector from a vector-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| atom | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+

30
doc/src/write_data.rst
View File

@ -12,13 +12,14 @@ Syntax
* file = name of data file to write out
* zero or more keyword/value pairs may be appended
* keyword = *pair* or *nocoeff* or *nofix* or *nolabelmap*
* keyword = *nocoeff* or *nofix* or *nolabelmap* or *triclinic/general* or *types* or *pair*
.. parsed-literal::
*nocoeff* = do not write out force field info
*nofix* = do not write out extra sections read by fixes
*nolabelmap* = do not write out type labels
*triclinic/general* = write data file in general triclinic format
*types* value = *numeric* or *labels*
*pair* value = *ii* or *ij*
*ii* = write one line of pair coefficient info per atom type
@ -31,6 +32,7 @@ Examples
write_data data.polymer
write_data data.*
write_data data.solid triclinic/general
Description
"""""""""""
@ -85,10 +87,11 @@ using the :doc:`-r command-line switch <Run_options>`.
:doc:`fixes <fix>` are stored. :doc:`Binary restart files <read_restart>`
store more information.
Bond interactions (angle, etc) that have been turned off by the :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>` command will
be written to a data file as if they are turned on. This means they
will need to be turned off again in a new run after the data file is
read.
Bond interactions (angle, etc) that have been turned off by the
:doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>`
command will be written to a data file as if they are turned on. This
means they will need to be turned off again in a new run after the
data file is read.
Bonds that are broken (e.g. by a bond-breaking potential) are not
written to the data file. Thus these bonds will not exist when the
@ -122,6 +125,23 @@ not written to the data file. By default, they are written if they
exist. A type label must be defined for every numeric type (within a
given type-kind) to be written to the data file.
Use of the *triclinic/general* keyword will output a data file which
specifies a general triclinic simulation box as well as per-atom
quantities consistent with the general triclinic box. The latter means
that per-atom vectors, such as velocities and dipole moments will be
oriented consistent with the 3d rotation implied by the general
triclinic box (relative to the associated restricted triclinic box).
This option can only be requested if the simulation box was initially
defined to be general triclinic. If if was and the
*triclinic/general* keyword is not used, then the data file will
specify a restricted triclinic box, since that is the internal format
LAMMPS uses for both general and restricted triclinic simulations.
See the :doc:`Howto triclinic <Howto_triclinic>` doc page for more
explanation of how general triclinic simulation boxes are supported by
LAMMPS. And see the :doc:`read_data <read_data>` doc page for details
of how the format is altered for general triclinic data files.
The *types* keyword determines how atom types, bond types, angle
types, etc are written into these data file sections: Atoms, Bonds,
Angles, etc. The default is the *numeric* setting, even if type label

21
doc/src/write_restart.rst
View File

@ -55,21 +55,22 @@ alter the number of files written.
Restart files can be read by a :doc:`read_restart <read_restart>`
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, you can use the :doc:`-r command-line switch <Run_options>` to convert a restart file to a data file.
another machine. In this case, you can use the :doc:`-r command-line
switch <Run_options>` to convert a restart file to a data file.
.. note::
Although the purpose of restart files is to enable restarting a
simulation from where it left off, not all information about a
simulation is stored in the file. For example, the list of fixes that
were specified during the initial run is not stored, which means the
new input script must specify any fixes you want to use. Even when
restart information is stored in the file, as it is for some fixes,
commands may need to be re-specified in the new input script, in order
to re-use that information. Details are usually given in the
documentation of the respective command. Also, see the
:doc:`read_restart <read_restart>` command for general information about
what is stored in a restart file.
simulation is stored in the file. For example, the list of fixes
that were specified during the initial run is not stored, which
means the new input script must specify any fixes you want to use.
Even when restart information is stored in the file, as it is for
some fixes, commands may need to be re-specified in the new input
script, in order to re-use that information. Details are usually
given in the documentation of the respective command. Also, see the
:doc:`read_restart <read_restart>` command for general information
about what is stored in a restart file.
----------

2
doc/utils/requirements.txt
View File

@ -1,4 +1,4 @@
Sphinx >= 5.3.0, <8.0
Sphinx >= 5.3.0, <7.3
sphinxcontrib-spelling
sphinxcontrib-jquery
git+https://github.com/akohlmey/sphinx-fortran@parallel-read

48
doc/utils/sphinx-config/false_positives.txt
View File

@ -50,6 +50,7 @@ agilio
Agilio
agni
Agnolin
ahi
Ahrens
Ai
Aidan
@ -86,6 +87,7 @@ allocator
allocators
allosws
AlO
alo
Alonso
Alperen
alphak
@ -187,6 +189,10 @@ automagically
Auvergne
Avalos
avalue
avec
avecx
avecy
avecz
aveforce
Avendano
Averett
@ -194,11 +200,14 @@ avi
AVX
awpmd
AWPMD
ax
Axel
Axilrod
Ay
ay
Ayton
Az
az
Azevedo
azimuthal
Azuri
@ -271,6 +280,7 @@ Bext
Bfrac
bgq
Bh
bhi
Bialke
biaxial
bicrystal
@ -307,6 +317,7 @@ Bkappa
blabel
Blaise
blanchedalmond
blo
blocksize
blueviolet
bn
@ -380,12 +391,17 @@ btype
buckPlusAttr
buf
builtin
Bulacu
Bulatov
Bureekaew
burlywood
Bussi
Buturigakkwaishi
Buyl
bvec
bvecx
bvecy
bvecz
Bybee
bz
Cadarache
@ -476,6 +492,7 @@ ChiralIDs
chirality
Cho
Chodera
Choi
ChooseOffset
chris
Christoph
@ -617,6 +634,7 @@ cstdlib
cstring
cstyle
csvr
ctilde
ctrl
ctrn
ctypes
@ -648,14 +666,21 @@ cv
Cv
Cval
cvar
cvec
cvecx
cvecy
cvecz
cvff
cwiggle
cx
cy
cygwin
Cygwin
cylindrically
Cyrot
cyrstals
cython
cz
Daivis
Dammak
dampflag
@ -947,6 +972,7 @@ elastance
Electroneg
electronegative
electronegativity
electroneutral
electroneutrality
Eleftheriou
ElementN
@ -1301,6 +1327,7 @@ gmres
gname
gneb
GNEB
Goga
Goldfarb
Gompper
Gonzalez-Melchor
@ -1478,6 +1505,7 @@ hydroxyl
Hynninen
Hyoungki
hyperdynamics
hyperparameters
hyperplane
hyperradius
hyperspherical
@ -1770,6 +1798,7 @@ Kolafa
Kollman
kolmogorov
Kolmogorov
Kolotinskii
Kondor
konglt
Koning
@ -2038,6 +2067,7 @@ Makefiles
makelist
makepkg
Makse
Malavasi
malloc
Malolepsza
Manby
@ -2147,6 +2177,7 @@ membered
memcheck
Mendelev
Menon
Menziani
mer
Meremianin
Mersenne
@ -2257,6 +2288,7 @@ Montalenti
Monterey
Montero
Monti
Monticelli
Mora
Morefoo
Morfill
@ -2266,6 +2298,7 @@ morris
Morriss
morse
Morteza
MoS
Mosayebi
Moseler
Moskalev
@ -2683,6 +2716,9 @@ organometallic
orientational
orientationsFile
orientorder
originx
originy
originz
Orlikowski
ornl
Ornstein
@ -2726,6 +2762,7 @@ papayawhip
paquay
Paquay
parallelepiped
parallelepipeds
Parallelizable
parallelization
parallelized
@ -2769,11 +2806,14 @@ Peachey
peachpuff
Pearlman
Pedersen
pedone
Pedone
peID
PEigenDense
Peng
peptide
peratom
Perf
Pergamon
pergrid
peri
@ -2781,6 +2821,7 @@ peridynamic
Peridynamic
peridynamics
Peridynamics
Periole
perl
permittivity
perp
@ -3070,6 +3111,7 @@ reaxff
ReaxFF
REAXFF
rebo
rebomos
recurse
recursing
Ree
@ -3195,6 +3237,7 @@ Ronevich
Rosati
Rosato
Rosenberger
Rossi
Rossky
rosybrown
rotationally
@ -3597,6 +3640,7 @@ tesselation
tesselations
Tetot
tex
textrm
tfac
tfmc
tfMC
@ -3637,6 +3681,7 @@ thrid
ThunderX
thylakoid
THz
Tieleman
Tigran
Tij
Tildesley
@ -3884,7 +3929,9 @@ Verlet
versa
Verstraelen
ves
vf
vflag
vflow
vfrac
vhi
vibrational
@ -4115,6 +4162,7 @@ zenodo
Zepeda
zflag
Zhang
Zhao
Zhen
zhi
Zhigilei

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