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Merge branch 'develop' of github.com:lammps/lammps into kk_occupancy

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This commit is contained in:
Stan Gerald Moore
2022-12-22 09:18:24 -07:00
parent a21a09f6d3 8b8c0ee72d
commit 33f3adf85c
851 changed files with 166043 additions and 21047 deletions
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3
.github/CODEOWNERS vendored
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@ -37,6 +37,7 @@ src/MESONT/* @iafoss
src/ML-HDNNP/* @singraber
src/ML-IAP/* @athomps
src/ML-PACE/* @yury-lysogorskiy
src/ML-POD/* @exapde @rohskopf
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
@ -63,6 +64,8 @@ src/MANYBODY/pair_atm.* @sergeylishchuk
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/MISC/*_tracker.* @jtclemm
src/MC/fix_gcmc.* @athomps
src/MC/fix_sgcmc.* @athomps
# core LAMMPS classes
src/lammps.* @sjplimp

6
.github/workflows/compile-msvc.yml vendored
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@ -26,7 +26,7 @@ jobs:
- name: Select Python version
uses: actions/setup-python@v4
with:
python-version: '3.10'
python-version: '3.11'
- name: Building LAMMPS via CMake
shell: bash
@ -37,6 +37,8 @@ jobs:
nuget install MSMPIDIST
cmake -C cmake/presets/windows.cmake \
-D PKG_PYTHON=on \
-D WITH_PNG=off \
-D WITH_JPEG=off \
-S cmake -B build \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on \
@ -52,4 +54,4 @@ jobs:
- name: Run Unit Tests
working-directory: build
shell: bash
run: ctest -V -C Release
run: ctest -V -C Release -E FixTimestep:python_move_nve

7
cmake/CMakeLists.txt
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@ -266,6 +266,7 @@ set(STANDARD_PACKAGES
ML-QUIP
ML-RANN
ML-SNAP
ML-POD
MOFFF
MOLECULE
MOLFILE
@ -432,7 +433,7 @@ if(BUILD_OMP)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR PKG_ELECTRODE)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
@ -638,7 +639,7 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
endif()
endforeach()
if(PKG_ELECTRODE)
if(PKG_ELECTRODE OR PKG_ML-POD)
target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES})
endif()
@ -667,7 +668,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()

2
cmake/Modules/Packages/KOKKOS.cmake
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@ -124,7 +124,7 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
if(PKG_KSPACE)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
if(Kokkos_ENABLE_CUDA)
if(NOT (FFT STREQUAL "KISS"))

9
cmake/Modules/Packages/MC.cmake Normal file
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@ -0,0 +1,9 @@
# fix sgcmc may only be installed if also the EAM pair style from MANYBODY is installed
if(NOT PKG_MANYBODY)
get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.h)
set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

1
cmake/presets/all_off.cmake
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@ -56,6 +56,7 @@ set(ALL_PACKAGES
ML-HDNNP
ML-IAP
ML-PACE
ML-POD
ML-QUIP
ML-RANN
ML-SNAP

1
cmake/presets/all_on.cmake
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@ -58,6 +58,7 @@ set(ALL_PACKAGES
ML-HDNNP
ML-IAP
ML-PACE
ML-POD
ML-QUIP
ML-RANN
ML-SNAP

1
cmake/presets/mingw-cross.cmake
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@ -47,6 +47,7 @@ set(WIN_PACKAGES
MISC
ML-HDNNP
ML-IAP
ML-POD
ML-RANN
ML-SNAP
MOFFF

1
cmake/presets/most.cmake
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@ -41,6 +41,7 @@ set(ALL_PACKAGES
MEAM
MISC
ML-IAP
ML-POD
ML-SNAP
MOFFF
MOLECULE

7
doc/Makefile
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@ -45,7 +45,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
# we only want to use explicitly listed files.
DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//')
.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check xmlgen fasthtml
.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml
# ------------------------------------------
@ -96,6 +96,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
rst_anchor_check src/*.rst ;\
python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -175,6 +176,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
rst_anchor_check src/*.rst ;\
python utils/check-packages.py -s ../src -d src ;\
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
python utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -220,6 +222,9 @@ package_check : $(VENV)
char_check :
@( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : )
role_check :
@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
xmlgen : doxygen/xml/index.xml
doxygen/Doxyfile: doxygen/Doxyfile.in

4
doc/lammps.1
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@ -1,7 +1,7 @@
.TH LAMMPS "1" "3 November 2022" "2022-11-3"
.TH LAMMPS "1" "22 December 2022" "2022-12-22"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 3 November 2022
\- Molecular Dynamics Simulator. Version 22 December 2022
.SH SYNOPSIS
.B lmp

45
doc/src/Build_extras.rst
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@ -36,6 +36,7 @@ This is the list of packages that may require additional steps.
* :ref:`AWPMD <awpmd>`
* :ref:`COLVARS <colvars>`
* :ref:`COMPRESS <compress>`
* :ref:`ELECTRODE <electrode>`
* :ref:`GPU <gpu>`
* :ref:`H5MD <h5md>`
* :ref:`INTEL <intel>`
@ -48,6 +49,7 @@ This is the list of packages that may require additional steps.
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`
* :ref:`ML-POD <ml-pod>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
@ -1411,6 +1413,49 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
----------
.. _ml-pod:
ML-POD package
-----------------------------
.. tabs::
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_ML-POD=yes``.
.. tab:: Traditional make
Before building LAMMPS, you must configure the ML-POD support
settings in ``lib/mlpod``. You can do this manually, if you
prefer, or do it in one step from the ``lammps/src`` dir, using a
command like the following, which simply invoke the
``lib/mlpod/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-mlpod # print help message
$ make lib-mlpod args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-mlpod args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-mlpod args="-m mpi -e linalg" # same as above but use the bundled linalg lib
Note that the ``Makefile.lammps`` file has settings to use the BLAS
and LAPACK linear algebra libraries. These can either exist on
your system, or you can use the files provided in ``lib/linalg``.
In the latter case you also need to build the library in
``lib/linalg`` with a command like these:
.. code-block:: bash
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
The package itself is activated with ``make yes-ML-POD``.
----------
.. _plumed:
PLUMED package

5
doc/src/Commands_all.rst
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@ -31,7 +31,6 @@ table above.
* :doc:`bond_style <bond_style>`
* :doc:`bond_write <bond_write>`
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change_box <change_box>`
* :doc:`clear <clear>`
* :doc:`comm_modify <comm_modify>`
@ -90,8 +89,7 @@ table above.
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset_atom_ids <reset_atom_ids>`
* :doc:`reset_mol_ids <reset_mol_ids>`
* :doc:`reset_atoms <reset_atoms>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`
@ -127,6 +125,7 @@ additional letter in parenthesis: k = KOKKOS.
* :doc:`group2ndx <group2ndx>`
* :doc:`hyper <hyper>`
* :doc:`kim <kim_commands>`
* :doc:`fitpod <fitpod_command>`
* :doc:`mdi <mdi>`
* :doc:`ndx2group <group2ndx>`
* :doc:`neb <neb>`

1
doc/src/Commands_category.rst
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@ -25,7 +25,6 @@ Setup simulation box:
:columns: 4
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change_box <change_box>`
* :doc:`create_box <create_box>`
* :doc:`dimension <dimension>`

1
doc/src/Commands_compute.rst
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@ -107,6 +107,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`pressure/uef <compute_pressure_uef>`
* :doc:`property/atom <compute_property_atom>`
* :doc:`property/chunk <compute_property_chunk>`
* :doc:`property/grid <compute_property_grid>`
* :doc:`property/local <compute_property_local>`
* :doc:`ptm/atom <compute_ptm_atom>`
* :doc:`rdf <compute_rdf>`

3
doc/src/Commands_dump.rst
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@ -36,7 +36,8 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
* :doc:`custom/mpiio <dump>`
* :doc:`custom/zstd <dump>`
* :doc:`dcd <dump>`
* :doc:`deprecated <dump>`
* :doc:`grid <dump>`
* :doc:`grid/vtk <dump>`
* :doc:`h5md <dump_h5md>`
* :doc:`image <dump_image>`
* :doc:`local <dump>`

12
doc/src/Commands_fix.rst
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@ -38,6 +38,7 @@ OPT.
* :doc:`ave/chunk <fix_ave_chunk>`
* :doc:`ave/correlate <fix_ave_correlate>`
* :doc:`ave/correlate/long <fix_ave_correlate_long>`
* :doc:`ave/grid <fix_ave_grid>`
* :doc:`ave/histo <fix_ave_histo>`
* :doc:`ave/histo/weight <fix_ave_histo>`
* :doc:`ave/time <fix_ave_time>`
@ -65,13 +66,13 @@ OPT.
* :doc:`drude <fix_drude>`
* :doc:`drude/transform/direct <fix_drude_transform>`
* :doc:`drude/transform/inverse <fix_drude_transform>`
* :doc:`dt/reset <fix_dt_reset>`
* :doc:`dt/reset (k) <fix_dt_reset>`
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electrode/conp (i) <fix_electrode_conp>`
* :doc:`electrode/conq (i) <fix_electrode_conp>`
* :doc:`electrode/thermo (i) <fix_electrode_conp>`
* :doc:`electrode/conp (i) <fix_electrode>`
* :doc:`electrode/conq (i) <fix_electrode>`
* :doc:`electrode/thermo (i) <fix_electrode>`
* :doc:`electron/stopping <fix_electron_stopping>`
* :doc:`electron/stopping/fit <fix_electron_stopping>`
* :doc:`enforce2d (k) <fix_enforce2d>`
@ -213,6 +214,7 @@ OPT.
* :doc:`saed/vtk <fix_saed_vtk>`
* :doc:`setforce (k) <fix_setforce>`
* :doc:`setforce/spin <fix_setforce>`
* :doc:`sgcmc <fix_sgcmc>`
* :doc:`shake (k) <fix_shake>`
* :doc:`shardlow (k) <fix_shardlow>`
* :doc:`smd <fix_smd>`
@ -249,7 +251,7 @@ OPT.
* :doc:`tune/kspace <fix_tune_kspace>`
* :doc:`vector <fix_vector>`
* :doc:`viscosity <fix_viscosity>`
* :doc:`viscous <fix_viscous>`
* :doc:`viscous (k) <fix_viscous>`
* :doc:`viscous/sphere <fix_viscous_sphere>`
* :doc:`wall/body/polygon <fix_wall_body_polygon>`
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`

5
doc/src/Commands_pair.rst
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@ -93,8 +93,8 @@ OPT.
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (giko) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/ext (k) <pair_dpd_ext>`
* :doc:`dpd/ext/tstat (k) <pair_dpd_ext>`
* :doc:`dpd/ext (ko) <pair_dpd_ext>`
* :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (gko) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
@ -237,6 +237,7 @@ OPT.
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation <pair_pace>`
* :doc:`pod <pair_pod>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`

52
doc/src/Commands_removed.rst
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@ -2,14 +2,17 @@ Removed commands and packages
=============================
This page lists LAMMPS commands and packages that have been removed from
the distribution and provides suggestions for alternatives or replacements.
LAMMPS has special dummy styles implemented, that will stop LAMMPS and
print a suitable error message in most cases, when a style/command is used
that has been removed.
the distribution and provides suggestions for alternatives or
replacements. LAMMPS has special dummy styles implemented, that will
stop LAMMPS and print a suitable error message in most cases, when a
style/command is used that has been removed or will replace the command
with the direct alternative (if available) and print a warning.
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
.. deprecated:: 11Dec2015
The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
since they were superseded by the more general and extensible "chunk
infrastructure". Here the system is partitioned in one of many possible
@ -17,10 +20,23 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
Reset_ids command
-----------------
Box command
-----------
The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`.
.. deprecated:: 22Dec2022
The *box* command has been removed and the LAMMPS code changed so it won't
be needed. If present, LAMMPS will ignore the command and print a warning.
Reset_ids, reset_atom_ids, reset_mol_ids commands
-------------------------------------------------
.. deprecated:: 22Dec2022
The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
been folded into the :doc:`reset_atoms <reset_atoms>` command. If
present, LAMMPS will replace the commands accordingly and print a
warning.
MEAM package
------------
@ -30,18 +46,21 @@ The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
Fortran code of MEAM into C++, which removes several restrictions
(e.g. there can be multiple instances in hybrid pair styles) and allows
for some optimizations leading to better performance. The pair style
:doc:`meam <pair_meam>` has the exact same syntax.
:doc:`meam <pair_meam>` has the exact same syntax. For a transition
period the C++ version of MEAM was called USER-MEAMC so it could
coexist with the Fortran version.
REAX package
------------
The REAX package has been removed since it was superseded by the
:ref:`REAXFF package <PKG-REAXFF>`. The REAXFF
package has been tested to yield equivalent results to the REAX package,
offers better performance, supports OpenMP multi-threading via OPENMP,
and GPU and threading parallelization through KOKKOS. The new pair styles
are not syntax compatible with the removed reax pair style, so input
files will have to be adapted.
:ref:`REAXFF package <PKG-REAXFF>`. The REAXFF package has been tested
to yield equivalent results to the REAX package, offers better
performance, supports OpenMP multi-threading via OPENMP, and GPU and
threading parallelization through KOKKOS. The new pair styles are not
syntax compatible with the removed reax pair style, so input files will
have to be adapted. The REAXFF package was originally called
USER-REAXC.
USER-CUDA package
-----------------
@ -60,5 +79,6 @@ restart2data tool
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For added
convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command line flags <Run_options>`

1
doc/src/Developer.rst
View File

@ -23,3 +23,4 @@ of time and requests from the LAMMPS user community.
Classes
Developer_platform
Developer_utils
Developer_grid

14
doc/src/Developer_code_design.rst
View File

@ -50,7 +50,7 @@ parallel each MPI process creates such an instance. This can be seen
in the ``main.cpp`` file where the core steps of running a LAMMPS
simulation are the following 3 lines of code:
.. code-block:: C++
.. code-block:: c++
LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
lammps->input->file();
@ -78,7 +78,7 @@ LAMMPS makes extensive use of the object oriented programming (OOP)
principles of *compositing* and *inheritance*. Classes like the
``LAMMPS`` class are a **composite** containing pointers to instances
of other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``,
``Modify``, and so on. Each of these classes implement certain
``Modify``, and so on. Each of these classes implements certain
functionality by storing and manipulating data related to the
simulation and providing member functions that trigger certain
actions. Some of those classes like ``Force`` are themselves
@ -87,9 +87,9 @@ interactions. Similarly the ``Modify`` class contains a list of
``Fix`` and ``Compute`` classes. If the input commands that
correspond to these classes include the word *style*, then LAMMPS
stores only a single instance of that class. E.g. *atom_style*,
*comm_style*, *pair_style*, *bond_style*. It the input command does
not include the word *style*, there can be many instances of that
class defined. E.g. *region*, *fix*, *compute*, *dump*.
*comm_style*, *pair_style*, *bond_style*. If the input command does
**not** include the word *style*, then there may be many instances of
that class defined, for example *region*, *fix*, *compute*, *dump*.
**Inheritance** enables creation of *derived* classes that can share
common functionality in their base class while providing a consistent
@ -232,7 +232,7 @@ macro ``PairStyle()`` will associate the style name "lj/cut"
with a factory function creating an instance of the ``PairLJCut``
class.
.. code-block:: C++
.. code-block:: c++
// from force.h
typedef Pair *(*PairCreator)(LAMMPS *);
@ -360,7 +360,7 @@ characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
argument type must be compatible or else the {fmt} formatting code will
throw an exception. Some format string examples are given below:
.. code-block:: C
.. code-block:: c++
auto mesg = fmt::format(" CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",

846
doc/src/Developer_grid.rst Normal file
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@ -0,0 +1,846 @@
Use of distributed grids within style classes
---------------------------------------------
.. versionadded:: 22Dec2022
The LAMMPS source code includes two classes which facilitate the
creation and use of distributed grids. These are the Grid2d and
Grid3d classes in the src/grid2d.cpp.h and src/grid3d.cpp.h files
respectively. As the names imply, they are used for 2d or 3d
simulations, as defined by the :doc:`dimension <dimension>` command.
The :doc:`Howto_grid <Howto_grid>` page gives an overview of how
distributed grids are defined from a user perspective, lists LAMMPS
commands which use them, and explains how grid cell data is referenced
from an input script. Please read that page first as it motivates the
coding details discussed here.
This doc page is for users who wish to write new styles (input script
commands) which use distributed grids. There are a variety of
material models and analysis methods which use atoms (or
coarse-grained particles) and grids in tandem.
A *distributed* grid means each processor owns a subset of the grid
cells. In LAMMPS, the subset for each processor will be a sub-block
of grid cells with low and high index bounds in each dimension of the
grid. The union of the sub-blocks across all processors is the global
grid.
More specifically, a grid point is defined for each cell (by default
the center point), and a processor owns a grid cell if its point is
within the processor's spatial sub-domain. The union of processor
sub-domains is the global simulation box. If a grid point is on the
boundary of two sub-domains, the lower processor owns the grid cell. A
processor may also store copies of ghost cells which surround its
owned cells.
----------
Style commands
^^^^^^^^^^^^^^
Style commands which can define and use distributed grids include the
:doc:`compute <compute>`, :doc:`fix <fix>`, :doc:`pair <pair_style>`,
and :doc:`kspace <kspace_style>` styles. If you wish grid cell data
to persist across timesteps, then use a fix. If you wish grid cell
data to be accessible by other commands, then use a fix or compute.
Currently in LAMMPS, the :doc:`pair_style amoeba <pair_amoeba>`,
:doc:`kspace_style pppm <kspace_style>`, and :doc:`kspace_style msm
<kspace_style>` commands use distributed grids but do not require
either of these capabilities; they thus create and use distributed
grids internally. Note that a pair style which needs grid cell data
to persist could be coded to work in tandem with a fix style which
provides that capability.
The *size* of a grid is specified by the number of grid cells in each
dimension of the simulation domain. In any dimension the size can be
any value >= 1. Thus a 10x10x1 grid for a 3d simulation is
effectively a 2d grid, where each grid cell spans the entire
z-dimension. A 1x100x1 grid for a 3d simulation is effectively a 1d
grid, where grid cells are a series of thin xz slabs in the
y-dimension. It is even possible to define a 1x1x1 3d grid, though it
may be inefficient to use it in a computational sense.
Note that the choice of grid size is independent of the number of
processors or their layout in a grid of processor sub-domains which
overlays the simulations domain. Depending on the distributed grid
size, a single processor may own many 1000s or no grid cells.
A command can define multiple grids, each of a different size. Each
grid is an instantiation of the Grid2d or Grid3d class.
The command also defines what data it will store for each grid it
creates and it allocates the multi-dimensional array(s) needed to
store the data. No grid cell data is stored within the Grid2d or
Grid3d classes.
If a single value per grid cell is needed, the data array will have
the same dimension as the grid, i.e. a 2d array for a 2d grid,
likewise for 3d. If multiple values per grid cell are needed, the
data array will have one more dimension than the grid, i.e. a 3d array
for a 2d grid, or 4d array for a 3d grid. A command can choose to
define multiple data arrays for each grid it defines.
----------
Grid data allocation and access
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The simplest way for a command to allocate and access grid cell data
is to use the *create_offset()* methods provided by the Memory class.
Arguments for these methods can be values returned by the
*setup_grid()* method (described below), which define the extent of
the grid cells (owned+ghost) the processor owns. These 4 methods
allocate memory for 2d (first two) and 3d (second two) grid data. The
two methods that end in "_one" allocate an array which stores a single
value per grid cell. The two that end in "_multi" allocate an array
which stores *Nvalues* per grid cell.
.. code-block:: c++
// single value per cell for a 2d grid = 2d array
memory->create2d_offset(data2d_one, nylo_out, nyhi_out,
nxlo_out, nxhi_out, "data2d_one");
// nvalues per cell for a 2d grid = 3d array
memory->create3d_offset_last(data2d_multi, nylo_out, nyhi_out,
nxlo_out, nxhi_out, nvalues, "data2d_multi");
// single value per cell for a 3d grid = 3d array
memory->create3d_offset(data3d_one, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out, "data3d_one");
// nvalues per cell for a 3d grid = 4d array
memory->create4d_offset_last(data3d_multi, nzlo_out, nzhi_out, nylo_out,
nyhi_out, nxlo_out, nxhi_out, nvalues,
"data3d_multi");
Note that these multi-dimensional arrays are allocated as contiguous
chunks of memory where the x-index of the grid varies fastest, then y,
and the z-index slowest. For multiple values per grid cell, the
Nvalues are contiguous, so their index varies even faster than the
x-index.
The key point is that the "offset" methods create arrays which are
indexed by the range of indices which are the bounds of the sub-block
of the global grid owned by this processor. This means loops like
these can be written in the caller code to loop over owned grid cells,
where the "i" loop bounds are the range of owned grid cells for the
processor. These are the bounds returned by the *setup_grid()*
method:
.. code-block:: c++
for (int iy = iylo; iy <= iyhi; iy++)
for (int ix = ixlo; ix <= ixhi; ix++)
data2d_one[iy][ix] = 0.0;
for (int iy = iylo; iy <= iyhi; iy++)
for (int ix = ixlo; ix <= ixhi; ix++)
for (int m = 0; m < nvalues; m++)
data2d_multi[iy][ix][m] = 0.0;
for (int iz = izlo; iz <= izhi; iz++)
for (int iy = iylo; iy <= iyhi; iy++)
for (int ix = ixlo; ix <= ixhi; ix++)
data3d_one[iz][iy][ix] = 0.0;
for (int iz = izlo; iz <= izhi; iz++)
for (int iy = iylo; iy <= iyhi; iy++)
for (int ix = ixlo; ix <= ixhi; ix++)
for (int m = 0; m < nvalues; m++)
data3d_multi[iz][iy][ix][m] = 0.0;
Simply replacing the "i" bounds with "o" bounds, also returned by the
*setup_grid()* method, would alter this code to loop over owned+ghost
cells (the entire allocated grid).
----------
Grid class constructors
^^^^^^^^^^^^^^^^^^^^^^^
The following sub-sections describe the public methods of the Grid3d
class which a style command can invoke. The Grid2d methods are
similar; simply remove arguments which refer to the z-dimension.
There are 2 constructors which can be used. They differ in the extra
i/o xyz lo/hi arguments:
.. code-block:: c++
Grid3d(class LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz)
Grid3d(class LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz,
int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi,
int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi)
Both constructors take the LAMMPS instance pointer and a communicator
over which the grid will be distributed. Typically this is the
*world* communicator the LAMMPS instance is using. The
:doc:`kspace_style msm <kspace_style>` command creates a series of
grids, each of different size, which are partitioned across different
sub-communicators of processors. Both constructors are also passed
the global grid size: *gnx* by *gny* by *gnz*.
The first constructor is used when the caller wants the Grid class to
partition the global grid across processors; the Grid class defines
which grid cells each processor owns and also which it stores as ghost
cells. A subsequent call to *setup_grid()*, discussed below, returns
this info to the caller.
The second constructor allows the caller to define the extent of owned
and ghost cells, and pass them to the Grid class. The 6 arguments
which start with "i" are the inclusive lower and upper index bounds of
the owned (inner) grid cells this processor owns in each of the 3
dimensions within the global grid. Owned grid cells are indexed from
0 to N-1 in each dimension.
The 6 arguments which start with "o" are the inclusive bounds of the
owned+ghost (outer) grid cells it stores. If the ghost cells are on
the other side of a periodic boundary, then these indices may be < 0
or >= N in any dimension, so that oxlo <= ixlo and ixhi >= ixhi is
always the case.
For example, if Nx = 100, then a processor might pass ixlo=50,
ixhi=60, oxlo=48, oxhi=62 to the Grid class. Or ixlo=0, ixhi=10,
oxlo=-2, oxhi=13. If a processor owns no grid cells in a dimension,
then the ihi value should be specified as one less than the ilo value.
Note that the only reason to use the second constructor is if the
logic for assigning ghost cells is too complex for the Grid class to
compute, using the various set() methods described next. Currently
only the kspace_style pppm/electrode and kspace_style msm commands use
the second constructor.
----------
Grid class set methods
^^^^^^^^^^^^^^^^^^^^^^
The following methods affect how the Grid class computes which owned
and ghost cells are assigned to each processor. *Set_shift_grid()* is
the only method which influences owned cell assignment; all the rest
influence ghost cell assignment. These methods are only used with the
first constructor; they are ignored if the second constructor is used.
These methods must be called before the *setup_grid()* method is
invoked, because they influence its operation.
.. code-block:: c++
void set_shift_grid(double shift);
void set_distance(double distance);
void set_stencil_atom(int lo, int hi);
void set_shift_atom(double shift_lo, double shift_hi);
void set_stencil_grid(int lo, int hi);
void set_zfactor(double factor);
Processors own a grid cell if a point within the grid cell is inside
the processor's sub-domain. By default this is the center point of the
grid cell. The *set_shift_grid()* method can change this. The *shift*
argument is a value from 0.0 to 1.0 (inclusive) which is the offset of
the point within the grid cell in each dimension. The default is 0.5
for the center of the cell. A value of 0.0 is the lower left corner
point; a value of 1.0 is the upper right corner point. There is
typically no need to change the default as it is optimal for
minimizing the number of ghost cells needed.
If a processor maps its particles to grid cells, it needs to allow for
its particles being outside its sub-domain between reneighboring. The
*distance* argument of the *set_distance()* method sets the furthest
distance outside a processor's sub-domain which a particle can move.
Typically this is half the neighbor skin distance, assuming
reneighboring is done appropriately. This distance is used in
determining how many ghost cells a processor needs to store to enable
its particles to be mapped to grid cells. The default value is 0.0.
Some commands, like the :doc:`kspace_style pppm <kspace_style>`
command, map values (charge in the case of PPPM) to a stencil of grid
cells beyond the grid cell the particle is in. The stencil extent may
be different in the low and high directions. The *set_stencil_atom()*
method defines the maximum values of those 2 extents, assumed to be
the same in each of the 3 dimensions. Both the lo and hi values are
specified as positive integers. The default values are both 0.
Some commands, like the :doc:`kspace_style pppm <kspace_style>`
command, shift the position of an atom when mapping it to a grid cell,
based on the size of the stencil used to map values to the grid
(charge in the case of PPPM). The lo and hi arguments of the
*set_shift_atom()* method are the minimum shift in the low direction
and the maximum shift in the high direction, assumed to be the same in
each of the 3 dimensions. The shifts should be fractions of a grid
cell size with values between 0.0 and 1.0 inclusive. The default
values are both 0.0. See the src/pppm.cpp file for examples of these
lo/hi values for regular and staggered grids.
Some methods like the :doc:`fix ttm/grid <fix_ttm>` command, perform
finite difference kinds of operations on the grid, to diffuse electron
heat in the case of the two-temperature model (TTM). This operation
uses ghost grid values beyond the owned grid values the processor
updates. The *set_stencil_grid()* method defines the extent of this
stencil in both directions, assumed to be the same in each of the 3
dimensions. Both the lo and hi values are specified as positive
integers. The default values are both 0.
The kspace_style pppm commands allow a grid to be defined which
overlays a volume which extends beyond the simulation box in the z
dimension. This is for the purpose of modeling a 2d-periodic slab
(non-periodic in z) as if it were a larger 3d periodic system,
extended (with empty space) in the z dimension. The
:doc:`kspace_modify slab <kspace_modify>` command is used to specify
the ratio of the larger volume to the simulation volume; a volume
ratio of ~3 is typical. For this kind of model, the PPPM caller sets
the global grid size *gnz* ~3x larger than it would be otherwise.
This same ratio is passed by the PPPM caller as the *factor* argument
to the Grid class via the *set_zfactor()* method (*set_yfactor()* for
2d grids). The Grid class will then assign ownership of the 1/3 of
grid cells that overlay the simulation box to the processors which
also overlay the simulation box. The remaining 2/3 of the grid cells
are assigned to processors whose sub-domains are adjacent to the upper
z boundary of the simulation box.
----------
Grid class setup_grid method
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The *setup_grid()* method is called after the first constructor
(above) to partition the grid across processors, which determines
which grid cells each processor owns. It also calculates how many
ghost grid cells in each dimension and each direction each processor
needs to store.
Note that this method is NOT called if the second constructor above is
used. In that case, the caller assigns owned and ghost cells to each
processor.
Also note that this method must be invoked after any *set_*()* methods have
been used, since they can influence the assignment of owned and ghost
cells.
.. code-block:: c++
void setup_grid(int &ixlo, int &ixhi, int &iylo, int &iyhi, int &izlo, int &izhi,
int &oxlo, int &oxhi, int &oylo, int &oyhi, int &ozlo, int &ozhi)
The 6 return arguments which start with "i" are the inclusive lower
and upper index bounds of the owned (inner) grid cells this processor
owns in each of the 3 dimensions within the global grid. Owned grid
cells are indexed from 0 to N-1 in each dimension.
The 6 return arguments which start with "o" are the inclusive bounds of
the owned+ghost cells it owns. If the ghost cells are on the other
side of a periodic boundary, then these indices may be < 0 or >= N in
any dimension, so that oxlo <= ixlo and ixhi >= ixhi is always the
case.
----------
More grid class set methods
^^^^^^^^^^^^^^^^^^^^^^^^^^^
The following 2 methods can be used to override settings made by the
constructors above. If used, they must be called called before the
*setup_comm()* method is invoked, since it uses the settings that
these methods override. In LAMMPS these methods are called by by the
:doc:`kspace_style msm <kspace_style>` command for the grids it
instantiates using the 2nd constructor above.
.. code-block:: c++
void set_proc_neighs(int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi)
void set_caller_grid(int fxlo, int fxhi, int fylo, int fyhi, int fzlo, int fzhi)
The *set_proc_neighs()* method sets the processor IDs of the 6
neighboring processors for each processor. Normally these would match
the processor grid neighbors which LAMMPS creates to overlay the
simulation box (the default). However, MSM excludes non-participating
processors from coarse grid communication when less processors are
used. This method allows MSM to override the default values.
The *set_caller_grid()* method species the size of the data arrays the
caller allocates. Normally these would match the extent of the ghost
grid cells (the default). However the MSM caller allocates a larger
data array (more ghost cells) for its finest-level grid, for use in
other operations besides owned/ghost cell communication. This method
allows MSM to override the default values.
----------
Grid class get methods
^^^^^^^^^^^^^^^^^^^^^^
The following methods allow the caller to query the settings for a
specific grid, whether it created the grid or another command created
it.
.. code-block:: c++
void get_size(int &nxgrid, int &nygrid, int &nzgrid);
void get_bounds_owned(int &xlo, int &xhi, int &ylo, int &yhi, int &zlo, int &zhi)
void get_bounds_ghost(int &xlo, int &xhi, int &ylo, int &yhi, int &zlo, int &zhi)
The *get_size()* method returns the size of the global grid in each dimension.
The *get_bounds_owned()* method return the inclusive index bounds of
the grid cells this processor owns. The values range from 0 to N-1 in
each dimension. These values are the same as the "i" values returned
by *setup_grid()*.
The *get_bounds_ghost()* method return the inclusive index bounds of
the owned+ghost grid cells this processor stores. The owned cell
indices range from 0 to N-1, so these indices may be less than 0 or
greater than or equal to N in each dimension. These values are the
same as the "o" values returned by *setup_grid()*.
----------
Grid class owned/ghost communication
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If needed by the command, the following methods setup and perform
communication of grid data to/from neighboring processors. The
*forward_comm()* method sends owned grid cell data to the
corresponding ghost grid cells on other processors. The
*reverse_comm()* method sends ghost grid cell data to the
corresponding owned grid cells on another processor. The caller can
choose to sum ghost grid cell data to the owned grid cell or simply
copy it.
.. code-block:: c++
void setup_comm(int &nbuf1, int &nbuf2)
void forward_comm(int caller, void *ptr, int which, int nper, int nbyte,
void *buf1, void *buf2, MPI_Datatype datatype);
void reverse_comm(int caller, void *ptr, int which, int nper, int nbyte,
void *buf1, void *buf2, MPI_Datatype datatype)
int ghost_adjacent();
The *setup_comm()* method must be called one time before performing
*forward* or *reverse* communication (multiple times if needed). It
returns two integers, which should be used to allocate two buffers.
The *nbuf1* and *nbuf2* values are the number of grid cells whose data
will be stored in two buffers by the Grid class when *forward* or
*reverse* communication is performed. The caller should thus allocate
them to a size large enough to hold all the data used in any single
forward or reverse communication operation it performs. Note that the
caller may allocate and communicate multiple data arrays for a grid it
instantiates. This size includes the bytes needed for the data type
of the grid data it stores, e.g. double precision values.
The *forward_comm()* and *reverse_comm()* methods send grid cell data
from owned to ghost cells, or ghost to owned cells, respectively, as
described above. The *caller* argument should be one of these values
-- Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
depending on the style of the caller class. The *ptr* argument is the
"this" pointer to the caller class. These 2 arguments are used to
call back to pack()/unpack() functions in the caller class, as
explained below.
The *which* argument is a flag the caller can set which is passed to
the caller's pack()/unpack() methods. This allows a single callback
method to pack/unpack data for several different flavors of
forward/reverse communication, e.g. operating on different grids or
grid data.
The *nper* argument is the number of values per grid cell to be
communicated. The *nbyte* argument is the number of bytes per value,
e.g. 8 for double-precision values. The *buf1* and *buf2* arguments
are the two allocated buffers described above. So long as they are
allocated for the maximum size communication, they can be re-used for
any *forward_comm()/reverse_comm()* call. The *datatype* argument is
the MPI_Datatype setting, which should match the buffer allocation and
the *nbyte* argument. E.g. MPI_DOUBLE for buffers storing double
precision values.
To use the *forward_grid()* method, the caller must provide two
callback functions; likewise for use of the *reverse_grid()* methods.
These are the 4 functions, their arguments are all the same.
.. code-block:: c++
void pack_forward_grid(int which, void *vbuf, int nlist, int *list);
void unpack_forward_grid(int which, void *vbuf, int nlist, int *list);
void pack_reverse_grid(int which, void *vbuf, int nlist, int *list);
void unpack_reverse_grid(int which, void *vbuf, int nlist, int *list);
The *which* argument is set to the *which* value of the
*forward_comm()* or *reverse_comm()* calls. It allows the pack/unpack
function to select what data values to pack/unpack. *Vbuf* is the
buffer to pack/unpack the data to/from. It is a void pointer so that
the caller can cast it to whatever data type it chooses, e.g. double
precision values. *Nlist* is the number of grid cells to pack/unpack
and *list* is a vector (nlist in length) of offsets to where the data
for each grid cell resides in the caller's data arrays, which is best
illustrated with an example from the src/EXTRA-FIX/fix_ttm_grid.cpp
class which stores the scalar electron temperature for 3d system in a
3d grid (one value per grid cell):
.. code-block:: c++
void FixTTMGrid::pack_forward_grid(int /*which*/, void *vbuf, int nlist, int *list)
{
auto buf = (double *) vbuf;
double *src = &T_electron[nzlo_out][nylo_out][nxlo_out];
for (int i = 0; i < nlist; i++) buf[i] = src[list[i]];
}
In this case, the *which* argument is not used, *vbuf* points to a
buffer of doubles, and the electron temperature is stored by the
FixTTMGrid class in a 3d array of owned+ghost cells called T_electron.
That array is allocated by the *memory->create_3d_offset()* method
described above so that the first grid cell it stores is indexed as
T_electron[nzlo_out][nylo_out][nxlo_out]. The *nlist* values in
*list* are integer offsets from that first grid cell. Setting *src*
to the address of the first cell allows those offsets to be used to
access the temperatures to pack into the buffer.
Here is a similar portion of code from the src/fix_ave_grid.cpp class
which can store two kinds of data, a scalar count of atoms in a grid
cell, and one or more grid-cell-averaged atom properties. The code
from its *unpack_reverse_grid()* function for 2d grids and multiple
per-atom properties per grid cell (*nvalues*) is shown here:
.. code-block:: c++
void FixAveGrid::unpack_reverse_grid(int /*which*/, void *vbuf, int nlist, int *list)
{
auto buf = (double *) vbuf;
double *count,*data,*values;
count = &count2d[nylo_out][nxlo_out];
data = &array2d[nylo_out][nxlo_out][0];
m = 0;
for (i = 0; i < nlist; i++) {
count[list[i]] += buf[m++];
values = &data[nvalues*list[i]];
for (j = 0; j < nvalues; j++)
values[j] += buf[m++];
}
}
Both the count and the multiple values per grid cell are communicated
in *vbuf*. Note that *data* is now a pointer to the first value in
the first grid cell. And *values* points to where the first value in
*data* is for an offset of grid cells, calculated by multiplying
*nvalues* by *list[i]*. Finally, because this is reverse
communication, the communicated buffer values are summed to the caller
values.
The *ghost_adjacent()* method returns a 1 if every processor can
perform the necessary owned/ghost communication with only its nearest
neighbor processors (4 in 2d, 6 in 3d). It returns a 0 if any
processor's ghost cells extend further than nearest neighbor
processors.
This can be checked by callers who have the option to change the
global grid size to insure more efficient nearest-neighbor-only
communication if they wish. In this case, they instantiate a grid of
a given size (resolution), then invoke *setup_comm()* followed by
*ghost_adjacent()*. If the ghost cells are not adjacent, they destroy
the grid instance and start over with a higher-resolution grid.
Several of the :doc:`kspace_style pppm <kspace_style>` command
variants have this option.
----------
Grid class remap methods for load balancing
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The following methods are used when a load-balancing operation,
triggered by the :doc:`balance <balance>` or :doc:`fix balance
<fix_balance>` commands, changes the partitioning of the simulation
domain into processor sub-domains.
In order to work with load-balancing, any style command (compute, fix,
pair, or kspace style) which allocates a grid and stores per-grid data
should define a *reset_grid()* method; it takes no arguments. It will
be called by the two balance commands after they have reset processor
sub-domains and migrated atoms (particles) to new owning processors.
The *reset_grid()* method will typically perform some or all of the
following operations. See the src/fix_ave_grid.cpp and
src/EXTRA_FIX/fix_ttm_grid.cpp files for examples of *reset_grid()*
methods, as well as the *pack_remap_grid()* and *unpack_remap_grid()*
functions.
First, the *reset_grid()* method can instantiate new grid(s) of the
same global size, then call *setup_grid()* to partition them via the
new processor sub-domains. At this point, it can invoke the
*identical()* method which compares the owned and ghost grid cell
index bounds between two grids, the old grid passed as a pointer
argument, and the new grid whose *identical()* method is being called.
It returns 1 if the indices match on all processors, otherwise 0. If
they all match, then the new grids can be deleted; the command can
continue to use the old grids.
If not, then the command should allocate new grid data array(s) which
depend on the new partitioning. If the command does not need to
persist its grid data from the old partitioning to the new one, then
the command can simply delete the old data array(s) and grid
instance(s). It can then return.
If the grid data does need to persist, then the data for each grid
needs to be "remapped" from the old grid partitioning to the new grid
partitioning. The *setup_remap()* and *remap()* methods are used for
that purpose.
.. code-block:: c++
int identical(Grid3d *old);
void setup_remap(Grid3d *old, int &nremap_buf1, int &nremap_buf2)
void remap(int caller, void *ptr, int which, int nper, int nbyte,
void *buf1, void *buf2, MPI_Datatype datatype)
The arguments to these methods are identical to those for
the *setup_comm()* and *forward_comm()* or *reverse_comm()* methods.
However the returned *nremap_buf1* and *nremap2_buf* values will be
different than the *nbuf1* and *nbuf2* values. They should be used to
allocate two different remap buffers, separate from the owned/ghost
communication buffers.
To use the *remap()* method, the caller must provide two
callback functions:
.. code-block:: c++
void pack_remap_grid(int which, void *vbuf, int nlist, int *list);
void unpack_remap_grid(int which, void *vbuf, int list, int *list);
Their arguments are identical to those for the *pack_forward_grid()*
and *unpack_forward_grid()* callback functions (or the reverse
variants) discussed above. Normally, both these methods pack/unpack
all the data arrays for a given grid. The *which* argument of the
*remap()* method sets the *which* value for the pack/unpack functions.
If the command instantiates multiple grids (of different sizes), it
can be used within the pack/unpack methods to select which grid's data
is being remapped.
Note that the *pack_remap_grid()* function must copy values from the
OLD grid data arrays into the *vbuf* buffer. The *unpack_remap_grid()*
function must copy values from the *vbuf* buffer into the NEW grid
data arrays.
After the remap operation for grid cell data has been performed, the
*reset_grid()* method can deallocate the two remap buffers it created,
and can then exit.
----------
Grid class I/O methods
^^^^^^^^^^^^^^^^^^^^^^
There are two I/O methods in the Grid classes which can be used to
read and write grid cell data to files. The caller can decide on the
precise format of each file, e.g. whether header lines are prepended
or comment lines are allowed. Fundamentally, the file should contain
one line per grid cell for the entire global grid. Each line should
contain identifying info as to which grid cell it is, e.g. a unique
grid cell ID or the ix,iy,iz indices of the cell within a 3d grid.
The line should also contain one or more data values which are stored
within the grid data arrays created by the command
For grid cell IDs, the LAMMPS convention is that the IDs run from 1 to
N, where N = Nx * Ny for 2d grids and N = Nx * Ny * Nz for 3d grids.
The x-index of the grid cell varies fastest, then y, and the z-index
varies slowest. So for a 10x10x10 grid the cell IDs from 901-1000
would be in the top xy layer of the z dimension.
The *read_file()* method does something simple. It reads a chunk of
consecutive lines from the file and passes them back to the caller to
process. The caller provides a *unpack_read_grid()* function for this
purpose. The function checks the grid cell ID or indices and only
stores grid cell data for the grid cells it owns.
The *write_file()* method does something slightly more complex. Each
processor packs the data for its owned grid cells into a buffer. The
caller provides a *pack_write_grid()* function for this purpose. The
*write_file()* method then loops over all processors and each sends
its buffer one at a time to processor 0, along with the 3d (or 2d)
index bounds of its grid cell data within the global grid. Processor
0 calls back to the *unpack_write_grid()* function provided by the
caller with the buffer. The function writes one line per grid cell to
the file.
See the src/EXTRA_FIX/fix_ttm_grid.cpp file for examples of now both
these methods are used to read/write electron temperature values
from/to a file, as well as for implementations of the the pack/unpack
functions described below.
Here are the details of the two I/O methods and the 3 callback
functions. See the src/fix_ave_grid.cpp file for examples of all of
them.
.. code-block:: c++
void read_file(int caller, void *ptr, FILE *fp, int nchunk, int maxline)
void write_file(int caller, void *ptr, int which,
int nper, int nbyte, MPI_Datatype datatype
The *caller* argument in both methods should be one of these values --
Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
depending on the style of the caller class. The *ptr* argument in
both methods is the "this" pointer to the caller class. These 2
arguments are used to call back to pack()/unpack() functions in the
caller class, as explained below.
For the *read_file()* method, the *fp* argument is a file pointer to
the file to be read from, opened on processor 0 by the caller.
*Nchunk* is the number of lines to read per chunk, and *maxline* is
the maximum number of characters per line. The Grid class will
allocate a buffer for storing chunks of lines based on these values.
For the *write_file()* method, the *which* argument is a flag the
caller can set which is passed back to the caller's pack()/unpack()
methods. If the command instantiates multiple grids (of different
sizes), this flag can be used within the pack/unpack methods to select
which grid's data is being written out (presumably to different
files). the *nper* argument is the number of values per grid cell to
be written out. The *nbyte* argument is the number of bytes per
value, e.g. 8 for double-precision values. The *datatype* argument is
the MPI_Datatype setting, which should match the *nbyte* argument.
E.g. MPI_DOUBLE for double precision values.
To use the *read_grid()* method, the caller must provide one callback
function. To use the *write_grid()* method, it provides two callback
functions:
.. code-block:: c++
int unpack_read_grid(int nlines, char *buffer)
void pack_write_grid(int which, void *vbuf)
void unpack_write_grid(int which, void *vbuf, int *bounds)
For *unpack_read_grid()* the *nlines* argument is the number of lines
of character data read from the file and contained in *buffer*. The
lines each include a newline character at the end. When the function
processes the lines, it may choose to skip some of them (header or
comment lines). It returns an integer count of the number of grid
cell lines it processed. This enables the Grid class *read_file()*
method to know when it has read the correct number of lines.
For *pack_write_grid()* and *unpack_write_grid()*, the *vbuf* argument
is the buffer to pack/unpack data to/from. It is a void pointer so
that the caller can cast it to whatever data type it chooses,
e.g. double precision values. the *which* argument is set to the
*which* value of the *write_file()* method. It allows the caller to
choose which grid data to operate on.
For *unpack_write_grid()*, the *bounds* argument is a vector of 4 or 6
integer grid indices (4 for 2d, 6 for 3d). They are the
xlo,xhi,ylo,yhi,zlo,zhi index bounds of the portion of the global grid
which the *vbuf* holds owned grid cell data values for. The caller
should loop over the values in *vbuf* with a double loop (2d) or
triple loop (3d), similar to the code snippets listed above. The
x-index varies fastest, then y, and the z-index slowest. If there are
multiple values per grid cell, the index for those values varies
fastest of all. The caller can add the x,y,z indices of the grid cell
(or the corresponding grid cell ID) to the data value(s) written as
one line to the output file.
----------
Style class grid access methods
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A style command can enable its grid cell data to be accessible from
other commands. For example :doc:`fix ave/grid <fix_ave_grid>` or
:doc:`dump grid <dump>` or :doc:`dump grid/vtk <dump>`. Those
commands access the grid cell data by using a *grid reference* in
their input script syntax, as described on the :doc:`Howto_grid
<Howto_grid>` doc page. They look like this:
* c_ID:gname:dname
* c_ID:gname:dname[I]
* f_ID:gname:dname
* f_ID:gname:dname[I]
Each grid a command instantiates has a unique *gname*, defined by the
command. Likewise each grid cell data structure (scalar or vector)
associated with a grid has a unique *dname*, also defined by the
command.
To provide access to its grid cell data, a style command needs to
implement the following 4 methods:
.. code-block:: c++
int get_grid_by_name(const std::string &name, int &dim);
void *get_grid_by_index(int index);
int get_griddata_by_name(int igrid, const std::string &name, int &ncol);
void *get_griddata_by_index(int index);
Currently only computes and fixes can implement these methods. If it
does so, the compute of fix should also set the variable
*pergrid_flag* to 1. See any of the compute or fix commands which set
"pergrid_flag = 1" for examples of how these 4 functions can be
implemented.
The *get_grid_by_name()* method takes a grid name as input and returns
two values. The *dim* argument is returned as 2 or 3 for the
dimensionality of the grid. The function return is a grid index from
0 to G-1 where *G* is the number of grids the command instantiates. A
value of -1 is returned if the grid name is not recognized.
The *get_grid_by_index()* method is called after the
*get_grid_by_name()* method, using the grid index it returned as its
argument. This method will return a pointer to the Grid2d or Grid3d
class. The caller can use this to query grid attributes, such as the
global size of the grid. The :doc:`dump grid <dump>` to insure each
its grid reference arguments are for grids of the same size.
The *get_griddata_by_name()* method takes a grid index *igrid* and a
data name as input. It returns two values. The *ncol* argument is
returned as a 0 if the grid data is a single value (scalar) per grid
cell, or an integer M > 0 if there are M values (vector) per grid
cell. Note that even if M = 1, it is still a 1-length vector, not a
scalar. The function return is a data index from 0 to D-1 where *D*
is the number of data sets associated with that grid by the command.
A value of -1 is returned if the data name is not recognized.
The *get_griddata_by_index()* method is called after the
*get_griddata_by_name()* method, using the data index it returned as
its argument. This method will return a pointer to the
multi-dimensional array which stores the requested data.
As in the discussion above of the Memory class *create_offset()*
methods, the dimensionality of the array associated with the returned
pointer depends on whether it is a 2d or 3d grid and whether there is
a single or multiple values stored for each grid cell:
* single value per cell for a 2d grid = 2d array pointer
* multiple values per cell for a 2d grid = 3d array pointer
* single value per cell for a 3d grid = 3d array pointer
* multiple values per cell for a 3d grid = 4d array pointer
The caller will typically access the data by casting the void pointer
to the corresponding array pointer and using nested loops in x,y,z
between owned or ghost index bounds returned by the
*get_bounds_owned()* or *get_bounds_ghost()* methods to index into the
array. Example code snippets with this logic were listed above,
----------
Final notes
^^^^^^^^^^^
Finally, here are some additional issues to pay attention to for
writing any style command which uses distributed grids via the Grid2d
or Grid3d class.
The command destructor should delete all instances of the Grid class,
any buffers it allocated for forward/reverse or remap communication,
and any data arrays it allocated to store grid cell data.
If a command is intended to work for either 2d or 3d simulations, then
it should have logic to instantiate either 2d or 3d grids and their
associated data arrays, depending on the dimension of the simulation
box. The :doc:`fix ave/grid <fix_ave_grid>` command is an example of
such a command.
When a command maps its particles to the grid and updates grid cell
values, it should check that it is not updating or accessing a grid
cell value outside the range of its owned+ghost cells, and generate an
error message if that is the case. This could happen, for example, if
a particle has moved further than half the neighbor skin distance,
because the neighbor list update criterion are not adequate to prevent
it from happening. See the src/KSPACE/pppm.cpp file and its
*particle_map()* method for an example of this kind of error check.

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@ -105,7 +105,7 @@ list, where each pair of atoms is listed only once (except when the
pairs straddling sub-domains or periodic boundaries will be listed twice).
Thus these are the default settings when a neighbor list request is created in:
.. code-block:: C++
.. code-block:: c++
void Pair::init_style()
{
@ -129,7 +129,7 @@ neighbor list request to the specific needs of a style an additional
request flag is needed. The :doc:`tersoff <pair_tersoff>` pair style,
for example, needs a "full" neighbor list:
.. code-block:: C++
.. code-block:: c++
void PairTersoff::init_style()
{
@ -141,7 +141,7 @@ When a pair style supports r-RESPA time integration with different cutoff region
the request flag may depend on the corresponding r-RESPA settings. Here an example
from pair style lj/cut:
.. code-block:: C++
.. code-block:: c++
void PairLJCut::init_style()
{
@ -160,7 +160,7 @@ Granular pair styles need neighbor lists based on particle sizes and not cutoff
and also may require to have the list of previous neighbors available ("history").
For example with:
.. code-block:: C++
.. code-block:: c++
if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY);
else neighbor->add_request(this, NeighConst::REQ_SIZE);
@ -170,7 +170,7 @@ settings each request can set an id which is then used in the corresponding
``init_list()`` function to assign it to the suitable pointer variable. This is
done for example by the :doc:`pair style meam <pair_meam>`:
.. code-block:: C++
.. code-block:: c++
void PairMEAM::init_style()
{
@ -189,7 +189,7 @@ just once) and this can also be indicated by a flag. As an example here
is the request from the ``FixPeriNeigh`` class which is created
internally by :doc:`Peridynamics pair styles <pair_peri>`:
.. code-block:: C++
.. code-block:: c++
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
@ -198,7 +198,7 @@ than what is usually inferred from the pair style settings (largest cutoff of
all pair styles plus neighbor list skin). The following is used in the
:doc:`compute rdf <compute_rdf>` command implementation:
.. code-block:: C++
.. code-block:: c++
if (cutflag)
neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
@ -212,7 +212,7 @@ for printing the neighbor list summary the name of the requesting command
should be set. Below is the request from the :doc:`delete atoms <delete_atoms>`
command:
.. code-block:: C++
.. code-block:: c++
neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);

6
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@ -95,7 +95,7 @@ a class ``PairMorse2`` in the files ``pair_morse2.h`` and
``pair_morse2.cpp`` with the factory function and initialization
function would look like this:
.. code-block:: C++
.. code-block:: c++
#include "lammpsplugin.h"
#include "version.h"
@ -141,7 +141,7 @@ list of argument strings), then the pointer type is ``lammpsplugin_factory2``
and it must be assigned to the *creator.v2* member of the plugin struct.
Below is an example for that:
.. code-block:: C++
.. code-block:: c++
#include "lammpsplugin.h"
#include "version.h"
@ -176,7 +176,7 @@ demonstrated in the following example, which also shows that the
implementation of the plugin class may be within the same source
file as the plugin interface code:
.. code-block:: C++
.. code-block:: c++
#include "lammpsplugin.h"

10
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@ -194,7 +194,7 @@ macro. These tests operate by capturing the screen output when executing
the failing command and then comparing that with a provided regular
expression string pattern. Example:
.. code-block:: C++
.. code-block:: c++
TEST_F(SimpleCommandsTest, UnknownCommand)
{
@ -226,9 +226,9 @@ The following test programs are currently available:
* - ``test_kim_commands.cpp``
- KimCommands
- Tests for several commands from the :ref:`KIM package <PKG-KIM>`
* - ``test_reset_ids.cpp``
- ResetIDs
- Tests to validate the :doc:`reset_atom_ids <reset_atom_ids>` and :doc:`reset_mol_ids <reset_mol_ids>` commands
* - ``test_reset_atoms.cpp``
- ResetAtoms
- Tests to validate the :doc:`reset_atoms <reset_atoms>` sub-commands
Tests for the C-style library interface
@ -249,7 +249,7 @@ MPI support. These include tests where LAMMPS is run in multi-partition
mode or only on a subset of the MPI world communicator. The CMake
script code for adding this kind of test looks like this:
.. code-block:: CMake
.. code-block:: cmake
if (BUILD_MPI)
add_executable(test_library_mpi test_library_mpi.cpp)

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@ -25,6 +25,7 @@ Available topics in mostly chronological order are:
- `Simplified and more compact neighbor list requests`_
- `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
- `Use Output::get_dump_by_id() instead of Output::find_dump()`_
- `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
----
@ -61,7 +62,7 @@ header file needs to be updated accordingly.
Old:
.. code-block:: C++
.. code-block:: c++
int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
@ -75,7 +76,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
@ -112,14 +113,14 @@ Example from a pair style:
Old:
.. code-block:: C++
.. code-block:: c++
if (eflag || vflag) ev_setup(eflag, vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
New:
.. code-block:: C++
.. code-block:: c++
ev_init(eflag, vflag);
@ -142,14 +143,14 @@ when they are called from only one or a subset of the MPI processes.
Old:
.. code-block:: C++
.. code-block:: c++
val = force->numeric(FLERR, arg[1]);
num = force->inumeric(FLERR, arg[2]);
New:
.. code-block:: C++
.. code-block:: c++
val = utils::numeric(FLERR, true, arg[1], lmp);
num = utils::inumeric(FLERR, false, arg[2], lmp);
@ -183,14 +184,14 @@ copy them around for simulations.
Old:
.. code-block:: C++
.. code-block:: c++
fp = force->open_potential(filename);
fp = fopen(filename, "r");
New:
.. code-block:: C++
.. code-block:: c++
fp = utils::open_potential(filename, lmp);
@ -207,7 +208,7 @@ Example:
Old:
.. code-block:: C++
.. code-block:: c++
if (fptr == NULL) {
char str[128];
@ -217,7 +218,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
if (fptr == nullptr)
error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror());
@ -237,7 +238,7 @@ an example from the ``FixWallReflect`` class:
Old:
.. code-block:: C++
.. code-block:: c++
FixWallReflect(class LAMMPS *, int, char **);
virtual ~FixWallReflect();
@ -247,7 +248,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
FixWallReflect(class LAMMPS *, int, char **);
~FixWallReflect() override;
@ -271,7 +272,7 @@ the type of the "this" pointer argument.
Old:
.. code-block:: C++
.. code-block:: c++
comm->forward_comm_pair(this);
comm->forward_comm_fix(this);
@ -284,7 +285,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
comm->forward_comm(this);
comm->reverse_comm(this);
@ -304,7 +305,7 @@ requests can be :doc:`found here <Developer_notes>`. Example from the
Old:
.. code-block:: C++
.. code-block:: c++
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
@ -317,7 +318,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
if (cutflag) req->set_cutoff(mycutneigh);
@ -340,7 +341,7 @@ these are internal fixes, there is no user visible change.
Old:
.. code-block:: C++
.. code-block:: c++
#include "fix_store.h"
@ -351,7 +352,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
#include "fix_store_peratom.h"
@ -362,7 +363,7 @@ New:
Old:
.. code-block:: C++
.. code-block:: c++
#include "fix_store.h"
@ -373,7 +374,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
#include "fix_store_global.h"
@ -396,7 +397,7 @@ the dump directly. Example:
Old:
.. code-block:: C++
.. code-block:: c++
int idump = output->find_dump(arg[iarg+1]);
if (idump < 0)
@ -412,7 +413,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
auto idump = output->get_dump_by_id(arg[iarg+1]);
if (!idump) error->all(FLERR,"Dump ID {} in hyper command does not exist", arg[iarg+1]);
@ -423,3 +424,56 @@ New:
if (dumpflag) for (auto idump : dumplist) idump->write();
This change is **required** or else the code will not compile.
Refactored grid communication using Grid3d/Grid2d classes instead of GridComm
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 22Dec2022
The ``GridComm`` class was for creating and communicating distributed
grids was replaced by the ``Grid3d`` class with added functionality.
A ``Grid2d`` class was also added for additional flexibility.
The new functionality and commands using the two grid classes are
discussed on the following documentation pages:
- :doc:`Howto_grid`
- :doc:`Developer_grid`
If you have custom LAMMPS code, which uses the GridComm class, here are some notes
on how to adapt it for using the Grid3d class.
(1) The constructor has changed to allow the ``Grid3d`` / ``Grid2d``
classes to partition the global grid across processors, both for
owned and ghost grid cells. Previously any class which called
``GridComm`` performed the partitioning itself and that information
was passed in the ``GridComm::GridComm()`` constructor. There are
several "set" functions which can be called to alter how ``Grid3d``
/ ``Grid2d`` perform the partitioning. They should be sufficient
for most use cases of the grid classes.
(2) The partitioning is triggered by the ``setup_grid()`` method.
(3) The ``setup()`` method of the ``GridComm`` class has been replaced
by the ``setup_comm()`` method in the new grid classes. The syntax
for the ``forward_comm()`` and ``reverse_comm()`` methods is
slightly altered as is the syntax of the associated pack/unpack
callback methods. But the functionality of these operations is the
same as before.
(4) The new ``Grid3d`` / ``Grid2d`` classes have additional
functionality for dynamic load-balancing of grids and their
associated data across processors. This did not exist in the
``GridComm`` class.
This and more is explained in detail on the :doc:`Developer_grid` page.
The following LAMMPS source files can be used as illustrative examples
for how the new grid classes are used by computes, fixes, and various
KSpace solvers which use distributed FFT grids:
- ``src/fix_ave_grid.cpp``
- ``src/compute_property_grid.cpp``
- ``src/EXTRA-FIX/fix_ttm_grid.cpp``
- ``src/KSPACE/pppm.cpp``
This change is **required** or else the code will not compile.

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@ -133,6 +133,9 @@ and parsing files or arguments.
.. doxygenfunction:: trim_comment
:project: progguide
.. doxygenfunction:: strip_style_suffix
:project: progguide
.. doxygenfunction:: star_subst
:project: progguide
@ -211,6 +214,9 @@ Argument processing
.. doxygenfunction:: expand_args
:project: progguide
.. doxygenfunction:: parse_grid_id
:project: progguide
.. doxygenfunction:: expand_type
:project: progguide
@ -317,7 +323,7 @@ are all "whitespace" characters, i.e. the space character, the tabulator
character, the carriage return character, the linefeed character, and
the form feed character.
.. code-block:: C++
.. code-block:: c++
:caption: Tokenizer class example listing entries of the PATH environment variable
#include "tokenizer.h"
@ -349,7 +355,7 @@ tokenizer into a ``try`` / ``catch`` block to handle errors. The
when a (type of) number is requested as next token that is not
compatible with the string representing the next word.
.. code-block:: C++
.. code-block:: c++
:caption: ValueTokenizer class example with exception handling
#include "tokenizer.h"
@ -427,7 +433,7 @@ one or two array indices "[<number>]" with numbers > 0.
A typical code segment would look like this:
.. code-block:: C++
.. code-block:: c++
:caption: Usage example for ArgInfo class
int nvalues = 0;
@ -476,7 +482,7 @@ open the file, and will call the :cpp:class:`LAMMPS_NS::Error` class in
case of failures to read or to convert numbers, so that LAMMPS will be
aborted.
.. code-block:: C++
.. code-block:: c++
:caption: Use of PotentialFileReader class in pair style coul/streitz
PotentialFileReader reader(lmp, file, "coul/streitz");
@ -555,7 +561,7 @@ chunk size needs to be known in advance, 2) with :cpp:func:`MyPage::vget()
its size is registered later with :cpp:func:`MyPage::vgot()
<LAMMPS_NS::MyPage::vgot>`.
.. code-block:: C++
.. code-block:: c++
:caption: Example of using :cpp:class:`MyPage <LAMMPS_NS::MyPage>`
#include "my_page.h"

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@ -26,7 +26,7 @@ constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
Every fix must be registered in LAMMPS by writing the following lines
of code in the header before include guards:
.. code-block:: c
.. code-block:: c++
#ifdef FIX_CLASS
// clang-format off
@ -47,7 +47,7 @@ keyword when it parses the input script.
Let's write a simple fix which will print the average velocity at the end
of each timestep. First of all, implement a constructor:
.. code-block:: C++
.. code-block:: c++
FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
: Fix(lmp, narg, arg)
@ -72,7 +72,7 @@ in the Fix class called ``nevery`` which specifies how often the method
The next method we need to implement is ``setmask()``:
.. code-block:: C++
.. code-block:: c++
int FixPrintVel::setmask()
{
@ -87,7 +87,7 @@ during execution. The constant ``END_OF_STEP`` corresponds to the
are called during a timestep and the order in which they are called
are shown in the previous section.
.. code-block:: C++
.. code-block:: c++
void FixPrintVel::end_of_step()
{
@ -143,7 +143,7 @@ The group membership information of an atom is contained in the *mask*
property of and atom and the bit corresponding to a given group is
stored in the groupbit variable which is defined in Fix base class:
.. code-block:: C++
.. code-block:: c++
for (int i = 0; i < nlocal; ++i) {
if (atom->mask[i] & groupbit) {
@ -174,7 +174,7 @@ to store positions of atoms from previous timestep, we need to add
``double** xold`` to the header file. Than add allocation code
to the constructor:
.. code-block:: C++
.. code-block:: c++
FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
{
@ -190,7 +190,7 @@ to the constructor:
Implement the aforementioned methods:
.. code-block:: C++
.. code-block:: c++
double FixSavePos::memory_usage()
{

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@ -51,6 +51,7 @@ Analysis howto
Howto_output
Howto_chunk
Howto_grid
Howto_temperature
Howto_elastic
Howto_kappa

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@ -0,0 +1,102 @@
Using distributed grids
=======================
.. versionadded:: 22Dec2022
LAMMPS has internal capabilities to create uniformly spaced grids
which overlay the simulation domain. For 2d and 3d simulations these
are 2d and 3d grids respectively. Conceptually a grid can be thought
of as a collection of grid cells. Each grid cell can store one or
more values (data).
The grid cells and data they store are distributed across processors.
Each processor owns the grid cells (and data) whose center points lie
within the spatial sub-domain of the processor. If needed for its
computations, a processor may also store ghost grid cells with their
data.
Distributed grids can overlay orthogonal or triclinic simulation
boxes; see the :doc:`Howto triclinic <Howto_triclinic>` doc page for
an explanation of the latter. For a triclinic box, the grid cell
shape conforms to the shape of the simulation domain,
e.g. parallelograms instead of rectangles in 2d.
If the box size or shape changes during a simulation, the grid changes
with it, so that it always overlays the entire simulation domain. For
non-periodic dimensions, the grid size in that dimension matches the
box size, as set by the :doc:`boundary <boundary>` command for fixed
or shrink-wrapped boundaries.
If load-balancing is invoked by the :doc:`balance <balance>` or
:doc:`fix balance <fix_balance>` commands, then the sub-domain owned
by a processor can change which may also change which grid cells they
own.
Post-processing and visualization of grid cell data can be enabled by
the :doc:`dump grid <dump>`, :doc:`dump grid/vtk <dump>`, and
:doc:`dump image <dump_image>` commands. The latter has an optional
*grid* keyword. The `OVITO visualization tool
<https://www.ovito.org>`_ also plans (as of Nov 2022) to add support
for visualizing grid cell data (along with atoms) using :doc:`dump
grid <dump>` output files as input.
.. note::
For developers, distributed grids are implemented within the code via
two classes: Grid2d and Grid3d. These partition the grid across
processors and have methods which allow forward and reverse
communication of ghost grid data as well as load balancing. If you
write a new compute or fix which needs a distributed grid, these are
the classes to look at. A new pair style could use a distributed
grid by having a fix define it. Please see the section on
:doc:`using distributed grids within style classes <Developer_grid>`
for a detailed description.
----------
These are the commands which currently define or use distributed
grids:
* :doc:`fix ttm/grid <fix_ttm>` - store electron temperature on grid
* :doc:`fix ave/grid <fix_ave_grid>` - time average per-atom or per-grid values
* :doc:`compute property/grid <compute_property_grid>` - generate grid IDs and coords
* :doc:`dump grid <dump>` - output per-grid values in LAMMPS format
* :doc:`dump grid/vtk <dump>` - output per-grid values in VTK format
* :doc:`dump image grid <dump_image>` - include colored grid in output images
* :doc:`pair_style amoeba <pair_amoeba>` - FFT grids
* :doc:`kspace_style pppm <kspace_style>` (and variants) - FFT grids
* :doc:`kspace_style msm <kspace_style>` (and variants) - MSM grids
The grids used by the :doc:`kspace_style <kspace_style>` can not be
referenced by an input script. However the grids and data created and
used by the other commands can be.
A compute or fix command may create one or more grids (of different
sizes). Each grid can store one or more data fields. A data field
can be a single value per grid point (per-grid vector) or multiple
values per grid point (per-grid array). See the :doc:`Howto output
<Howto_output>` doc page for an explanation of how per-grid data can
be generated by some commands and used by other commands.
A command accesses grid data from a compute or fix using a *grid
reference* with the following syntax:
* c_ID:gname:dname
* c_ID:gname:dname[I]
* f_ID:gname:dname
* f_ID:gname:dname[I]
The prefix "c\_" or "f\_" refers to the ID of the compute or fix; gname is
the name of the grid, which is assigned by the compute or fix; dname is
the name of the data field, which is also assigned by the compute or
fix.
If the data field is a per-grid vector (one value per grid point),
then no brackets are used to access the values. If the data field is
a per-grid array (multiple values per grid point), then brackets are
used to specify the column I of the array. I ranges from 1 to Ncol
inclusive, where Ncol is the number of columns in the array and is
defined by the compute or fix.
Currently, there are no per-grid variables implemented in LAMMPS. We
may add this feature at some point.

329
doc/src/Howto_output.rst
View File

@ -22,14 +22,17 @@ commands you specify.
As discussed below, LAMMPS gives you a variety of ways to determine
what quantities are computed and printed when the thermodynamics,
dump, or fix commands listed above perform output. Throughout this
discussion, note that users can also :doc:`add their own computes and fixes to LAMMPS <Modify>` which can then generate values that can then be
output with these commands.
discussion, note that users can also :doc:`add their own computes and
fixes to LAMMPS <Modify>` which can then generate values that can then
be output with these commands.
The following sub-sections discuss different LAMMPS command related
The following sub-sections discuss different LAMMPS commands related
to output and the kind of data they operate on and produce:
* :ref:`Global/per-atom/local data <global>`
* :ref:`Global/per-atom/local/per-grid data <global>`
* :ref:`Scalar/vector/array data <scalar>`
* :ref:`Per-grid data <grid>`
* :ref:`Disambiguation <disambiguation>`
* :ref:`Thermodynamic output <thermo>`
* :ref:`Dump file output <dump>`
* :ref:`Fixes that write output files <fixoutput>`
@ -42,27 +45,32 @@ to output and the kind of data they operate on and produce:
.. _global:
Global/per-atom/local data
--------------------------
Global/per-atom/local/per-grid data
-----------------------------------
Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more
system-wide values, e.g. the temperature of the system. A per-atom
datum is one or more values per atom, e.g. the kinetic energy of each
atom. Local datums are calculated by each processor based on the
atoms it owns, but there may be zero or more per atom, e.g. a list of
bond distances.
Various output-related commands work with four different styles of
data: global, per-atom, local, and per-grid. A global datum is one or
more system-wide values, e.g. the temperature of the system. A
per-atom datum is one or more values per atom, e.g. the kinetic energy
of each atom. Local datums are calculated by each processor based on
the atoms it owns, but there may be zero or more per atom, e.g. a list
of bond distances.
A per-grid datum is one or more values per grid cell, for a grid which
overlays the simulation domain. The grid cells and the data they
store are distributed across processors; each processor owns the grid
cells whose center point falls within its sub-domain.
.. _scalar:
Scalar/vector/array data
------------------------
Global, per-atom, and local datums can each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for a "compute" or "fix" or "variable" that generates data
will specify both the style and kind of data it produces, e.g. a
per-atom vector.
Global, per-atom, and local datums can come in three kinds: a single
scalar value, a vector of values, or a 2d array of values. The doc
page for a "compute" or "fix" or "variable" that generates data will
specify both the style and kind of data it produces, e.g. a per-atom
vector.
When a quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
@ -83,6 +91,18 @@ the dimension twice (array -> scalar). Thus a command that uses
scalar values as input can typically also process elements of a vector
or array.
.. _grid:
Per-grid data
------------------------
Per-grid data can come in two kinds: a vector of values (one per grid
cekk), or a 2d array of values (multiple values per grid ckk). The
doc page for a "compute" or "fix" that generates data will specify
names for both the grid(s) and datum(s) it produces, e.g. per-grid
vectors or arrays, which can be referenced by other commands. See the
:doc:`Howto grid <Howto_grid>` doc page for more details.
.. _disambiguation:
Disambiguation
@ -90,15 +110,15 @@ Disambiguation
Some computes and fixes produce data in multiple styles, e.g. a global
scalar and a per-atom vector. Usually the context in which the input
script references the data determines which style is meant. Example: if
a compute provides both a global scalar and a per-atom vector, the
script references the data determines which style is meant. Example:
if a compute provides both a global scalar and a per-atom vector, the
former will be accessed by using ``c_ID`` in an equal-style variable,
while the latter will be accessed by using ``c_ID`` in an atom-style
variable. Note that atom-style variable formulas can also access global
scalars, but in this case it is not possible to do directly because of
the ambiguity. Instead, an equal-style variable can be defined which
accesses the global scalar, and that variable used in the atom-style
variable formula in place of ``c_ID``.
variable. Note that atom-style variable formulas can also access
global scalars, but in this case it is not possible to do this
directly because of the ambiguity. Instead, an equal-style variable
can be defined which accesses the global scalar, and that variable can
be used in the atom-style variable formula in place of ``c_ID``.
.. _thermo:
@ -107,15 +127,14 @@ Thermodynamic output
The frequency and format of thermodynamic output is set by the
:doc:`thermo <thermo>`, :doc:`thermo_style <thermo_style>`, and
:doc:`thermo_modify <thermo_modify>` commands. The
:doc:`thermo_style <thermo_style>` command also specifies what values
are calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc). Three additional kinds of keywords can
also be specified (c_ID, f_ID, v_name), where a :doc:`compute <compute>`
or :doc:`fix <fix>` or :doc:`variable <variable>` provides the value to be
output. In each case, the compute, fix, or variable must generate
global values for input to the :doc:`thermo_style custom <dump>`
command.
:doc:`thermo_modify <thermo_modify>` commands. The :doc:`thermo_style
<thermo_style>` command also specifies what values are calculated and
written out. Pre-defined keywords can be specified (e.g. press, etotal,
etc). Three additional kinds of keywords can also be specified (c_ID,
f_ID, v_name), where a :doc:`compute <compute>` or :doc:`fix <fix>` or
:doc:`variable <variable>` provides the value to be output. In each
case, the compute, fix, or variable must generate global values for
input to the :doc:`thermo_style custom <dump>` command.
Note that thermodynamic output values can be "extensive" or
"intensive". The former scale with the number of atoms in the system
@ -141,9 +160,10 @@ There is also a :doc:`dump custom <dump>` format where the user
specifies what values are output with each atom. Pre-defined atom
attributes can be specified (id, x, fx, etc). Three additional kinds
of keywords can also be specified (c_ID, f_ID, v_name), where a
:doc:`compute <compute>` or :doc:`fix <fix>` or :doc:`variable <variable>`
provides the values to be output. In each case, the compute, fix, or
variable must generate per-atom values for input to the :doc:`dump custom <dump>` command.
:doc:`compute <compute>` or :doc:`fix <fix>` or :doc:`variable
<variable>` provides the values to be output. In each case, the
compute, fix, or variable must generate per-atom values for input to
the :doc:`dump custom <dump>` command.
There is also a :doc:`dump local <dump>` format where the user specifies
what local values to output. A pre-defined index keyword can be
@ -154,18 +174,23 @@ provides the values to be output. In each case, the compute or fix
must generate local values for input to the :doc:`dump local <dump>`
command.
There is also a :doc:`dump grid <dump>` format where the user
specifies what per-grid values to output from computes or fixes that
generate per-grid data.
.. _fixoutput:
Fixes that write output files
-----------------------------
Several fixes take various quantities as input and can write output
files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
:doc:`fix ave/correlate <fix_ave_correlate>`, and :doc:`fix print <fix_print>`.
files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk
<fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix
ave/correlate <fix_ave_correlate>`, and :doc:`fix print <fix_print>`.
The :doc:`fix ave/time <fix_ave_time>` command enables direct output to
a file and/or time-averaging of global scalars or vectors. The user
specifies one or more quantities as input. These can be global
The :doc:`fix ave/time <fix_ave_time>` command enables direct output
to a file and/or time-averaging of global scalars or vectors. The
user specifies one or more quantities as input. These can be global
:doc:`compute <compute>` values, global :doc:`fix <fix>` values, or
:doc:`variables <variable>` of any style except the atom style which
produces per-atom values. Since a variable can refer to keywords used
@ -184,8 +209,14 @@ atoms, e.g. individual molecules. The per-atom quantities can be atom
density (mass or number) or atom attributes such as position,
velocity, force. They can also be per-atom quantities calculated by a
:doc:`compute <compute>`, by a :doc:`fix <fix>`, or by an atom-style
:doc:`variable <variable>`. The chunk-averaged output of this fix can
also be used as input to other output commands.
:doc:`variable <variable>`. The chunk-averaged output of this fix is
global and can also be used as input to other output commands.
Note that the :doc:`fix ave/grid <fix_ave_grid>` command can also
average the same per-atom quantities within spatial bins, but it does
this for a distributed grid whose grid cells are owned by different
processors. It outputs per-grid data, not global data, so it is more
efficient for large numbers of averaging bins.
The :doc:`fix ave/histo <fix_ave_histo>` command enables direct output
to a file of histogrammed quantities, which can be global or per-atom
@ -202,38 +233,53 @@ written to the screen and log file or to a separate file, periodically
during a running simulation. The line can contain one or more
:doc:`variable <variable>` values for any style variable except the
vector or atom styles). As explained above, variables themselves can
contain references to global values generated by :doc:`thermodynamic keywords <thermo_style>`, :doc:`computes <compute>`,
:doc:`fixes <fix>`, or other :doc:`variables <variable>`, or to per-atom
values for a specific atom. Thus the :doc:`fix print <fix_print>`
command is a means to output a wide variety of quantities separate
from normal thermodynamic or dump file output.
contain references to global values generated by :doc:`thermodynamic
keywords <thermo_style>`, :doc:`computes <compute>`, :doc:`fixes
<fix>`, or other :doc:`variables <variable>`, or to per-atom values
for a specific atom. Thus the :doc:`fix print <fix_print>` command is
a means to output a wide variety of quantities separate from normal
thermodynamic or dump file output.
.. _computeoutput:
Computes that process output quantities
---------------------------------------
The :doc:`compute reduce <compute_reduce>` and :doc:`compute reduce/region <compute_reduce>` commands take one or more per-atom
or local vector quantities as inputs and "reduce" them (sum, min, max,
The :doc:`compute reduce <compute_reduce>` and :doc:`compute
reduce/region <compute_reduce>` commands take one or more per-atom or
local vector quantities as inputs and "reduce" them (sum, min, max,
ave) to scalar quantities. These are produced as output values which
can be used as input to other output commands.
The :doc:`compute slice <compute_slice>` command take one or more global
vector or array quantities as inputs and extracts a subset of their
values to create a new vector or array. These are produced as output
values which can be used as input to other output commands.
The :doc:`compute slice <compute_slice>` command take one or more
global vector or array quantities as inputs and extracts a subset of
their values to create a new vector or array. These are produced as
output values which can be used as input to other output commands.
The :doc:`compute property/atom <compute_property_atom>` command takes a
list of one or more pre-defined atom attributes (id, x, fx, etc) and
The :doc:`compute property/atom <compute_property_atom>` command takes
a list of one or more pre-defined atom attributes (id, x, fx, etc) and
stores the values in a per-atom vector or array. These are produced
as output values which can be used as input to other output commands.
The list of atom attributes is the same as for the :doc:`dump custom <dump>` command.
The list of atom attributes is the same as for the :doc:`dump custom
<dump>` command.
The :doc:`compute property/local <compute_property_local>` command takes
a list of one or more pre-defined local attributes (bond info, angle
info, etc) and stores the values in a local vector or array. These
are produced as output values which can be used as input to other
output commands.
The :doc:`compute property/local <compute_property_local>` command
takes a list of one or more pre-defined local attributes (bond info,
angle info, etc) and stores the values in a local vector or array.
These are produced as output values which can be used as input to
other output commands.
The :doc:`compute property/grid <compute_property_grid>` command takes
a list of one or more pre-defined per-grid attributes (id, grid cell
coords, etc) and stores the values in a per-grid vector or array.
These are produced as output values which can be used as input to the
:doc:`dump grid <dump>` command.
The :doc:`compute property/chunk <compute_property_chunk>` command
takes a list of one or more pre-defined chunk attributes (id, count,
coords for spatial bins) and stores the values in a global vector or
array. These are produced as output values which can be used as input
to other output commands.
.. _fixprocoutput:
@ -247,18 +293,42 @@ a time.
The :doc:`fix ave/atom <fix_ave_atom>` command performs time-averaging
of per-atom vectors. The per-atom quantities can be atom attributes
such as position, velocity, force. They can also be per-atom
quantities calculated by a :doc:`compute <compute>`, by a
:doc:`fix <fix>`, or by an atom-style :doc:`variable <variable>`. The
quantities calculated by a :doc:`compute <compute>`, by a :doc:`fix
<fix>`, or by an atom-style :doc:`variable <variable>`. The
time-averaged per-atom output of this fix can be used as input to
other output commands.
The :doc:`fix store/state <fix_store_state>` command can archive one or
more per-atom attributes at a particular time, so that the old values
can be used in a future calculation or output. The list of atom
attributes is the same as for the :doc:`dump custom <dump>` command,
including per-atom quantities calculated by a :doc:`compute <compute>`,
by a :doc:`fix <fix>`, or by an atom-style :doc:`variable <variable>`.
The output of this fix can be used as input to other output commands.
The :doc:`fix store/state <fix_store_state>` command can archive one
or more per-atom attributes at a particular time, so that the old
values can be used in a future calculation or output. The list of
atom attributes is the same as for the :doc:`dump custom <dump>`
command, including per-atom quantities calculated by a :doc:`compute
<compute>`, by a :doc:`fix <fix>`, or by an atom-style :doc:`variable
<variable>`. The output of this fix can be used as input to other
output commands.
The :doc:`fix ave/grid <fix_ave_grid>` command performs time-averaging
of either per-atom or per-grid data.
For per-atom data it performs averaging for the atoms within each grid
cell, similar to the :doc:`fix ave/chunk <fix_ave_chunk>` command when
its chunks are defined as regular 2d or 3d bins. The per-atom
quantities can be atom density (mass or number) or atom attributes
such as position, velocity, force. They can also be per-atom
quantities calculated by a :doc:`compute <compute>`, by a :doc:`fix
<fix>`, or by an atom-style :doc:`variable <variable>`.
The chief difference between the :doc:`fix ave/grid <fix_ave_grid>`
and :doc:`fix ave/chunk <fix_ave_chunk>` commands when used in this
context is that the former uses a distributed grid, while the latter
uses a global grid. Distributed means that each processor owns the
subset of grid cells within its sub-domain. Global means that each
processor owns a copy of the entire grid. The :doc:`fix ave/grid
<fix_ave_grid>` command is thus more efficient for large grids.
For per-grid data, the :doc:`fix ave/grid <fix_ave_grid>` command
takes inputs for grid data produced by other computes or fixes and
averages the values for each grid point over time.
.. _compute:
@ -266,24 +336,25 @@ Computes that generate values to output
---------------------------------------
Every :doc:`compute <compute>` in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors or
arrays of data. These values can be output using the other commands
described in this section. The page for each compute command
per-atom or local or per-grid values. The values can be scalars or
vectors or arrays of data. These values can be output using the other
commands described in this section. The page for each compute command
describes what it produces. Computes that produce per-atom or local
values have the word "atom" or "local" in their style name. Computes
without the word "atom" or "local" produce global values.
or per-grid values have the word "atom" or "local" or "grid as the
last word in their style name. Computes without the word "atom" or
"local" or "grid" produce global values.
.. _fix:
Fixes that generate values to output
------------------------------------
Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or
local values which can be accessed by other commands. The values can
be scalars or vectors or arrays of data. These values can be output
using the other commands described in this section. The page for
each fix command tells whether it produces any output quantities and
describes them.
Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom
or local or per-grid values which can be accessed by other commands.
The values can be scalars or vectors or arrays of data. These values
can be output using the other commands described in this section. The
page for each fix command tells whether it produces any output
quantities and describes them.
.. _variable:
@ -300,6 +371,8 @@ computes, fixes, and other variables. The values generated by
variables can be used as input to and thus output by the other
commands described in this section.
Per-grid variables have not (yet) been implemented.
.. _table:
Summary table of output options and data flow between commands
@ -319,44 +392,52 @@ Also note that, as described above, when a command takes a scalar as
input, that could be an element of a vector or array. Likewise a
vector input could be a column of an array.
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| Command | Input | Output |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`thermo_style custom <thermo_style>` | global scalars | screen, log file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`dump custom <dump>` | per-atom vectors | dump file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`dump local <dump>` | local vectors | dump file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fix print <fix_print>` | global scalar from variable | screen, file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`print <print>` | global scalar from variable | screen |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`computes <compute>` | N/A | global/per-atom/local scalar/vector/array |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fixes <fix>` | N/A | global/per-atom/local scalar/vector/array |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`variables <variable>` | global scalars and vectors, per-atom vectors | global scalar and vector, per-atom vector |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`compute reduce <compute_reduce>` | per-atom/local vectors | global scalar/vector |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`compute slice <compute_slice>` | global vectors/arrays | global vector/array |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`compute property/atom <compute_property_atom>` | per-atom vectors | per-atom vector/array |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`compute property/local <compute_property_local>` | local vectors | local vector/array |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fix vector <fix_vector>` | global scalars | global vector |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fix ave/atom <fix_ave_atom>` | per-atom vectors | per-atom vector/array |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fix ave/time <fix_ave_time>` | global scalars/vectors | global scalar/vector/array, file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fix ave/chunk <fix_ave_chunk>` | per-atom vectors | global array, file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fix ave/histo <fix_ave_histo>` | global/per-atom/local scalars and vectors | global array, file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fix ave/correlate <fix_ave_correlate>` | global scalars | global array, file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fix store/state <fix_store_state>` | per-atom vectors | per-atom vector/array |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| Command | Input | Output |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`thermo_style custom <thermo_style>` | global scalars | screen, log file |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`dump custom <dump>` | per-atom vectors | dump file |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`dump local <dump>` | local vectors | dump file |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`dump grid <dump>` | per-grid vectors | dump file |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`fix print <fix_print>` | global scalar from variable | screen, file |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`print <print>` | global scalar from variable | screen |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`computes <compute>` | N/A | global/per-atom/local/per-grid scalar/vector/array |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`fixes <fix>` | N/A | global/per-atom/local/per-grid scalar/vector/array |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`variables <variable>` | global scalars and vectors, per-atom vectors | global scalar and vector, per-atom vector |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`compute reduce <compute_reduce>` | per-atom/local vectors | global scalar/vector |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`compute slice <compute_slice>` | global vectors/arrays | global vector/array |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`compute property/atom <compute_property_atom>` | N/A | per-atom vector/array |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`compute property/local <compute_property_local>` | N/A | local vector/array |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`compute property/grid <compute_property_grid>` | N/A | per-grid vector/array |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`compute property/chunk <compute_property_chunk>` | N/A | global vector/array |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`fix vector <fix_vector>` | global scalars | global vector |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`fix ave/atom <fix_ave_atom>` | per-atom vectors | per-atom vector/array |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`fix ave/time <fix_ave_time>` | global scalars/vectors | global scalar/vector/array, file |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`fix ave/chunk <fix_ave_chunk>` | per-atom vectors | global array, file |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`fix ave/grid <fix_ave_grid>` | per-atom vectors or per-grid vectors | per-grid vector/array |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`fix ave/histo <fix_ave_histo>` | global/per-atom/local scalars and vectors | global array, file |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`fix ave/correlate <fix_ave_correlate>` | global scalars | global array, file |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
| :doc:`fix store/state <fix_store_state>` | per-atom vectors | per-atom vector/array |
+--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+

38
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View File

@ -152,14 +152,14 @@ Creating a new instance of PyLammps
To create a PyLammps object you need to first import the class from the lammps
module. By using the default constructor, a new *lammps* instance is created.
.. code-block:: Python
.. code-block:: python
from lammps import PyLammps
L = PyLammps()
You can also initialize PyLammps on top of this existing *lammps* object:
.. code-block:: Python
.. code-block:: python
from lammps import lammps, PyLammps
lmp = lammps()
@ -180,14 +180,14 @@ For instance, let's take the following LAMMPS command:
In the original interface this command can be executed with the following
Python code if *L* was a lammps instance:
.. code-block:: Python
.. code-block:: python
L.command("region box block 0 10 0 5 -0.5 0.5")
With the PyLammps interface, any command can be split up into arbitrary parts
separated by white-space, passed as individual arguments to a region method.
.. code-block:: Python
.. code-block:: python
L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
@ -199,14 +199,14 @@ The benefit of this approach is avoiding redundant command calls and easier
parameterization. In the original interface parameterization needed to be done
manually by creating formatted strings.
.. code-block:: Python
.. code-block:: python
L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
In contrast, methods of PyLammps accept parameters directly and will convert
them automatically to a final command string.
.. code-block:: Python
.. code-block:: python
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
@ -256,7 +256,7 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface.
To define a variable you can use the :doc:`variable <variable>` command:
.. code-block:: Python
.. code-block:: python
L.variable("a index 2")
@ -265,14 +265,14 @@ A dictionary of all variables is returned by L.variables
you can access an individual variable by retrieving a variable object from the
L.variables dictionary by name
.. code-block:: Python
.. code-block:: python
a = L.variables['a']
The variable value can then be easily read and written by accessing the value
property of this object.
.. code-block:: Python
.. code-block:: python
print(a.value)
a.value = 4
@ -284,7 +284,7 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The
passed string parameter can be any expression containing global thermo values,
variables, compute or fix data.
.. code-block:: Python
.. code-block:: python
result = L.eval("ke") # kinetic energy
result = L.eval("pe") # potential energy
@ -298,7 +298,7 @@ All atoms in the current simulation can be accessed by using the L.atoms list.
Each element of this list is an object which exposes its properties (id, type,
position, velocity, force, etc.).
.. code-block:: Python
.. code-block:: python
# access first atom
L.atoms[0].id
@ -311,7 +311,7 @@ position, velocity, force, etc.).
Some properties can also be used to set:
.. code-block:: Python
.. code-block:: python
# set position in 2D simulation
L.atoms[0].position = (1.0, 0.0)
@ -328,7 +328,7 @@ after a run via the L.runs list. This list contains a growing list of run data.
The first element is the output of the first run, the second element that of
the second run.
.. code-block:: Python
.. code-block:: python
L.run(1000)
L.runs[0] # data of first 1000 time steps
@ -339,14 +339,14 @@ the second run.
Each run contains a dictionary of all trajectories. Each trajectory is
accessible through its thermo name:
.. code-block:: Python
.. code-block:: python
L.runs[0].thermo.Step # list of time steps in first run
L.runs[0].thermo.Ke # list of kinetic energy values in first run
Together with matplotlib plotting data out of LAMMPS becomes simple:
.. code-block:: Python
.. code-block:: python
import matplotlib.plot as plt
steps = L.runs[0].thermo.Step
@ -406,7 +406,7 @@ Four atoms are placed in the simulation and the dihedral potential is applied on
them using a datafile. Then one of the atoms is rotated along the central axis by
setting its position from Python, which changes the dihedral angle.
.. code-block:: Python
.. code-block:: python
phi = [d \* math.pi / 180 for d in range(360)]
@ -439,7 +439,7 @@ Initially, a 2D system is created in a state with minimal energy.
It is then disordered by moving each atom by a random delta.
.. code-block:: Python
.. code-block:: python
random.seed(27848)
deltaperturb = 0.2
@ -458,7 +458,7 @@ It is then disordered by moving each atom by a random delta.
Finally, the Monte Carlo algorithm is implemented in Python. It continuously
moves random atoms by a random delta and only accepts certain moves.
.. code-block:: Python
.. code-block:: python
estart = L.eval("pe")
elast = estart
@ -517,7 +517,7 @@ PyLammps can be run in parallel using mpi4py. This python package can be install
The following is a short example which reads in an existing LAMMPS input file and
executes it in parallel. You can find in.melt in the examples/melt folder.
.. code-block:: Python
.. code-block:: python
from mpi4py import MPI
from lammps import PyLammps

2
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View File

@ -43,7 +43,7 @@ JSON
"ke": $(ke)
}""" file current_state.json screen no
.. code-block:: JSON
.. code-block:: json
:caption: current_state.json
{

5
doc/src/Howto_triclinic.rst
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@ -144,11 +144,6 @@ 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.
The limitation on not creating a simulation box with a tilt factor
skewing the box more than half the distance of the parallel box length
can be overridden via the :doc:`box <box>` command. Setting the *tilt*
keyword to *large* allows any tilt factors to be specified.
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.

2
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@ -39,7 +39,7 @@ crashes within LAMMPS may be recovered from by enabling
:ref:`exceptions <exceptions>`, avoiding them proactively is a safer
approach.
.. code-block:: C
.. code-block:: c
:caption: Example for using configuration settings functions
#include "library.h"

2
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@ -22,7 +22,7 @@ as the "handle" argument in subsequent function calls until that
instance is destroyed by calling :cpp:func:`lammps_close`. Here is a
simple example demonstrating its use:
.. code-block:: C
.. code-block:: c
#include "library.h"
#include <stdio.h>

2
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@ -30,7 +30,7 @@ be included in the file or strings, and expansion of variables with
``${name}`` or ``$(expression)`` syntax is performed.
Below is a short example using some of these functions.
.. code-block:: C
.. code-block:: c
/* define to make the otherwise hidden prototype for "lammps_open()" visible */
#define LAMMPS_LIB_MPI

2
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@ -32,7 +32,7 @@ indexed accordingly. Per-atom data can change sizes and ordering at
every neighbor list rebuild or atom sort event as atoms migrate between
sub-domains and processors.
.. code-block:: C
.. code-block:: c
#include "library.h"
#include <stdio.h>

6
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@ -7,6 +7,7 @@ functions. They do not directly call the LAMMPS library.
- :cpp:func:`lammps_encode_image_flags`
- :cpp:func:`lammps_decode_image_flags`
- :cpp:func:`lammps_set_fix_external_callback`
- :cpp:func:`lammps_fix_external_get_force`
- :cpp:func:`lammps_fix_external_set_energy_global`
- :cpp:func:`lammps_fix_external_set_energy_peratom`
- :cpp:func:`lammps_fix_external_set_virial_global`
@ -44,6 +45,11 @@ where such memory buffers were allocated that require the use of
-----------------------
.. doxygenfunction:: lammps_fix_external_get_force
:project: progguide
-----------------------
.. doxygenfunction:: lammps_fix_external_set_energy_global
:project: progguide

83
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@ -13,24 +13,65 @@ Here is a brief description of common methods you define in your
new derived class. See bond.h, angle.h, dihedral.h, and improper.h
for details and specific additional methods.
+-----------------------+---------------------------------------------------------------------------------------+
| init | check if all coefficients are set, calls *init_style* (optional) |
+-----------------------+---------------------------------------------------------------------------------------+
| init_style | check if style specific conditions are met (optional) |
+-----------------------+---------------------------------------------------------------------------------------+
| compute | compute the molecular interactions (required) |
+-----------------------+---------------------------------------------------------------------------------------+
| settings | apply global settings for all types (optional) |
+-----------------------+---------------------------------------------------------------------------------------+
| coeff | set coefficients for one type (required) |
+-----------------------+---------------------------------------------------------------------------------------+
| equilibrium_distance | length of bond, used by SHAKE (required, bond only) |
+-----------------------+---------------------------------------------------------------------------------------+
| equilibrium_angle | opening of angle, used by SHAKE (required, angle only) |
+-----------------------+---------------------------------------------------------------------------------------+
| write & read_restart | writes/reads coeffs to restart files (required) |
+-----------------------+---------------------------------------------------------------------------------------+
| single | force (bond only) and energy of a single bond or angle (required, bond or angle only) |
+-----------------------+---------------------------------------------------------------------------------------+
| memory_usage | tally memory allocated by the style (optional) |
+-----------------------+---------------------------------------------------------------------------------------+
+-----------------------+---------------------------------------------------------------------+
| Required | "pure" methods that *must* be overridden in a derived class |
+=======================+=====================================================================+
| compute | compute the molecular interactions for all listed items |
+-----------------------+---------------------------------------------------------------------+
| coeff | set coefficients for one type |
+-----------------------+---------------------------------------------------------------------+
| equilibrium_distance | length of bond, used by SHAKE (bond styles only) |
+-----------------------+---------------------------------------------------------------------+
| equilibrium_angle | opening of angle, used by SHAKE (angle styles only) |
+-----------------------+---------------------------------------------------------------------+
| write & read_restart | writes/reads coeffs to restart files |
+-----------------------+---------------------------------------------------------------------+
| single | force/r (bond styles only) and energy of a single bond or angle |
+-----------------------+---------------------------------------------------------------------+
+--------------------------------+----------------------------------------------------------------------+
| Optional | methods that have a default or dummy implementation |
+================================+======================================================================+
| init | check if all coefficients are set, calls init_style() |
+--------------------------------+----------------------------------------------------------------------+
| init_style | check if style specific conditions are met |
+--------------------------------+----------------------------------------------------------------------+
| settings | apply global settings for all types |
+--------------------------------+----------------------------------------------------------------------+
| write & read_restart_settings | writes/reads global style settings to restart files |
+--------------------------------+----------------------------------------------------------------------+
| write_data | write corresponding Coeffs section(s) in data file |
+--------------------------------+----------------------------------------------------------------------+
| memory_usage | tally memory allocated by the style |
+--------------------------------+----------------------------------------------------------------------+
| extract | provide access to internal data (bond or angle styles only) |
+--------------------------------+----------------------------------------------------------------------+
| reinit | reset all type-based parameters, called by fix adapt (bonds only) |
+--------------------------------+----------------------------------------------------------------------+
| pack & unpack_forward_comm | copy data to and from buffer in forward communication (bonds only) |
+--------------------------------+----------------------------------------------------------------------+
| pack & unpack_reverse_comm | copy data to and from buffer in reverse communication (bonds only) |
+--------------------------------+----------------------------------------------------------------------+
Here is a list of flags or settings that should be set in the
constructor of the derived class when they differ from the default
setting.
+---------------------------------+------------------------------------------------------------------------------+---------+
| Name of flag | Description | default |
+=================================+==============================================================================+=========+
| writedata | 1 if write_data() is implemented | 1 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| single_extra | number of extra single values calculated (bond styles only) | 0 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| partial_flag | 1 if bond type can be set to 0 and deleted (bond styles only) | 0 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| reinitflag | 1 if style has reinit() and is compatible with fix adapt | 1 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| comm_forward | size of buffer (in doubles) for forward communication (bond styles only) | 0 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| comm_reverse | size of buffer (in doubles) for reverse communication (bond styles only) | 0 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| comm_reverse_off | size of buffer for reverse communication with newton off (bond styles only) | 0 |
+---------------------------------+------------------------------------------------------------------------------+---------+

132
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@ -1,35 +1,121 @@
Pair styles
===========
Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include many-body potentials
such as EAM or Tersoff where particles interact without a static bond
topology. New styles can be created to add new pair potentials to
LAMMPS.
Classes that compute pairwise non-bonded interactions are derived from
the Pair class. In LAMMPS, pairwise calculation include many-body
potentials such as EAM, Tersoff, or ReaxFF where particles interact
without an explicit bond topology but include interactions beyond
pairwise non-bonded contributions. New styles can be created to add
support for additional pair potentials to LAMMPS. When the
modifications are small, sometimes it is more effective to derive from
an existing pair style class. This latter approach is also used by
:doc:`Accelerator packages <Speed_packages>` where the accelerated style
names differ from their base classes by an appended suffix.
Pair_lj_cut.cpp is a simple example of a Pair class, though it
includes some optional methods to enable its use with rRESPA.
The file ``src/pair_lj_cut.cpp`` is an example of a Pair class with a
very simple potential function. It includes several optional methods to
enable its use with :doc:`run_style respa <run_style>` and :doc:`compute
group/group <compute_group_group>`.
Here is a brief description of the class methods in pair.h:
Here is a brief list of some the class methods in the Pair class that
*must* be or *may* be overridden in a derived class.
+---------------------------------+---------------------------------------------------------------------+
| Required | "pure" methods that *must* be overridden in a derived class |
+=================================+=====================================================================+
| compute | workhorse routine that computes pairwise interactions |
+---------------------------------+---------------------------------------------------------------------+
| settings | reads the input script line with arguments you define |
| settings | processes the arguments to the pair_style command |
+---------------------------------+---------------------------------------------------------------------+
| coeff | set coefficients for one i,j type pair |
+---------------------------------+---------------------------------------------------------------------+
| init_one | perform initialization for one i,j type pair |
+---------------------------------+---------------------------------------------------------------------+
| init_style | initialization specific to this pair style |
+---------------------------------+---------------------------------------------------------------------+
| write & read_restart | write/read i,j pair coeffs to restart files |
+---------------------------------+---------------------------------------------------------------------+
| write & read_restart_settings | write/read global settings to restart files |
+---------------------------------+---------------------------------------------------------------------+
| single | force/r and energy of a single pairwise interaction between 2 atoms |
+---------------------------------+---------------------------------------------------------------------+
| compute_inner/middle/outer | versions of compute used by rRESPA |
| coeff | set coefficients for one i,j type pair, called from pair_coeff |
+---------------------------------+---------------------------------------------------------------------+
The inner/middle/outer routines are optional.
+---------------------------------+----------------------------------------------------------------------+
| Optional | methods that have a default or dummy implementation |
+=================================+======================================================================+
| init_one | perform initialization for one i,j type pair |
+---------------------------------+----------------------------------------------------------------------+
| init_style | style initialization: request neighbor list(s), error checks |
+---------------------------------+----------------------------------------------------------------------+
| init_list | Neighbor class callback function to pass neighbor list to pair style |
+---------------------------------+----------------------------------------------------------------------+
| single | force/r and energy of a single pairwise interaction between 2 atoms |
+---------------------------------+----------------------------------------------------------------------+
| compute_inner/middle/outer | versions of compute used by rRESPA |
+---------------------------------+----------------------------------------------------------------------+
| memory_usage | return estimated amount of memory used by the pair style |
+---------------------------------+----------------------------------------------------------------------+
| modify_params | process arguments to pair_modify command |
+---------------------------------+----------------------------------------------------------------------+
| extract | provide access to internal scalar or per-type data like cutoffs |
+---------------------------------+----------------------------------------------------------------------+
| extract_peratom | provide access to internal per-atom data |
+---------------------------------+----------------------------------------------------------------------+
| setup | initialization at the beginning of a run |
+---------------------------------+----------------------------------------------------------------------+
| finish | called at the end of a run, e.g. to print |
+---------------------------------+----------------------------------------------------------------------+
| write & read_restart | write/read i,j pair coeffs to restart files |
+---------------------------------+----------------------------------------------------------------------+
| write & read_restart_settings | write/read global settings to restart files |
+---------------------------------+----------------------------------------------------------------------+
| write_data | write Pair Coeffs section to data file |
+---------------------------------+----------------------------------------------------------------------+
| write_data_all | write PairIJ Coeffs section to data file |
+---------------------------------+----------------------------------------------------------------------+
| pack & unpack_forward_comm | copy data to and from buffer if style uses forward communication |
+---------------------------------+----------------------------------------------------------------------+
| pack & unpack_reverse_comm | copy data to and from buffer if style uses reverse communication |
+---------------------------------+----------------------------------------------------------------------+
| reinit | reset all type-based parameters, called by fix adapt for example |
+---------------------------------+----------------------------------------------------------------------+
| reset_dt | called when the time step is changed by timestep or fix reset/dt |
+---------------------------------+----------------------------------------------------------------------+
Here is a list of flags or settings that should be set in the
constructor of the derived pair class when they differ from the default
setting.
+---------------------------------+-------------------------------------------------------------+---------+
| Name of flag | Description | default |
+=================================+=============================================================+=========+
| single_enable | 1 if single() method is implemented, 0 if missing | 1 |
+---------------------------------+-------------------------------------------------------------+---------+
| respa_enable | 1 if pair style has compute_inner/middle/outer() | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| restartinfo | 1 if pair style writes its settings to a restart | 1 |
+---------------------------------+-------------------------------------------------------------+---------+
| one_coeff | 1 if only a pair_coeff * * command is allowed | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| manybody_flag | 1 if pair style is a manybody potential | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| unit_convert_flag | value != 0 indicates support for unit conversion | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| no_virial_fdotr_compute | 1 if pair style does not call virial_fdotr_compute() | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| writedata | 1 if write_data() and write_data_all() are implemented | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| comm_forward | size of buffer (in doubles) for forward communication | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| comm_reverse | size of buffer (in doubles) for reverse communication | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| ghostneigh | 1 if cutghost is set and style uses neighbors of ghosts | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| finitecutflag | 1 if cutoff depends on diameter of atoms | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| reinitflag | 1 if style has reinit() and is compatible with fix adapt | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| ewaldflag | 1 if compatible with kspace_style ewald | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| pppmflag | 1 if compatible with kspace_style pppm | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| msmflag | 1 if compatible with kspace_style msm | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| dispersionflag | 1 if compatible with ewald/disp or pppm/disp | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| tip4pflag | 1 if compatible with kspace_style pppm/tip4p | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| dipoleflag | 1 if compatible with dipole kspace_style | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| spinflag | 1 if compatible with spin kspace_style | 0 |
+---------------------------------+-------------------------------------------------------------+---------+

44
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@ -80,6 +80,7 @@ page gives those details.
* :ref:`ML-HDNNP <PKG-ML-HDNNP>`
* :ref:`ML-IAP <PKG-ML-IAP>`
* :ref:`ML-PACE <PKG-ML-PACE>`
* :ref:`ML-POD <PKG-ML-POD>`
* :ref:`ML-QUIP <PKG-ML-QUIP>`
* :ref:`ML-RANN <PKG-ML-RANN>`
* :ref:`ML-SNAP <PKG-ML-SNAP>`
@ -865,7 +866,7 @@ ELECTRODE package
The ELECTRODE package allows the user to enforce a constant potential method for
groups of atoms that interact with the remaining atoms as electrolyte.
**Authors:** The ELECTRODE library is written and maintained by Ludwig
**Authors:** The ELECTRODE package is written and maintained by Ludwig
Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
Robert Meissner (TUHH, Hamburg, Germany).
@ -878,7 +879,7 @@ This package has :ref:`specific installation instructions <electrode>` on the
**Supporting info:**
* :doc:`fix electrode/conp <fix_electrode_conp>`
* :doc:`fix electrode/conp <fix_electrode>`
----------
@ -1485,8 +1486,9 @@ MC package
Several fixes and a pair style that have Monte Carlo (MC) or MC-like
attributes. These include fixes for creating, breaking, and swapping
bonds, for performing atomic swaps, and performing grand-canonical MC
(GCMC) or similar processes in conjunction with dynamics.
bonds, for performing atomic swaps, and performing grand canonical
MC (GCMC), semi-grand canonical MC (SGCMC), or similar processes in
conjunction with molecular dynamics (MD).
**Supporting info:**
@ -1498,6 +1500,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
* :doc:`fix bond/swap <fix_bond_swap>`
* :doc:`fix charge/regulation <fix_charge_regulation>`
* :doc:`fix gcmc <fix_gcmc>`
* :doc:`fix sgcmc <fix_sgcmc>`
* :doc:`fix tfmc <fix_tfmc>`
* :doc:`fix widom <fix_widom>`
* :doc:`pair_style dsmc <pair_dsmc>`
@ -1796,6 +1799,39 @@ This package has :ref:`specific installation instructions <ml-pace>` on the
----------
.. _PKG-ML-POD:
ML-POD package
-------------------
**Contents:**
A pair style and fitpod style for Proper Orthogonal Descriptors
(POD). POD is a methodology for deriving descriptors based on the proper
orthogonal decomposition. The ML-POD package provides an efficient
implementation for running simulations with POD potentials, along with
fitting the potentials natively in LAMMPS.
**Authors:**
Ngoc Cuong Nguyen (MIT), Andrew Rohskopf (Sandia)
.. versionadded:: 22Dec2022
**Install:**
This package has :ref:`specific installation instructions <ml-pod>` on the
:doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/ML-POD: filenames -> commands
* :doc:`pair_style pod <pair_pod>`
* :doc:`command_style fitpod <fitpod_command>`
* examples/PACKAGES/pod
----------
.. _PKG-ML-QUIP:
ML-QUIP package

7
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@ -155,7 +155,7 @@ whether an extra library is needed to build and use the package:
- no
* - :ref:`ELECTRODE <PKG-ELECTRODE>`
- electrode charges to match potential
- :doc:`fix electrode/conp <fix_electrode_conp>`
- :doc:`fix electrode/conp <fix_electrode>`
- PACKAGES/electrode
- no
* - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
@ -298,6 +298,11 @@ whether an extra library is needed to build and use the package:
- :doc:`pair pace <pair_pace>`
- PACKAGES/pace
- ext
* - :ref:`ML-POD <PKG-ML-POD>`
- Proper orthogonal decomposition potentials
- :doc:`pair pod <pair_pod>`
- pod
- ext
* - :ref:`ML-QUIP <PKG-ML-QUIP>`
- QUIP/libatoms interface
- :doc:`pair_style quip <pair_quip>`

4
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@ -58,7 +58,7 @@ against invalid accesses.
Each element of this list is a :py:class:`Atom <lammps.Atom>` or :py:class:`Atom2D <lammps.Atom2D>` object. The attributes of
these objects provide access to their data (id, type, position, velocity, force, etc.):
.. code-block:: Python
.. code-block:: python
# access first atom
L.atoms[0].id
@ -71,7 +71,7 @@ against invalid accesses.
Some attributes can be changed:
.. code-block:: Python
.. code-block:: python
# set position in 2D simulation
L.atoms[0].position = (1.0, 0.0)

2
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@ -4,7 +4,7 @@ Configuration information
The following methods can be used to query the LAMMPS library
about compile time settings and included packages and styles.
.. code-block:: Python
.. code-block:: python
:caption: Example for using configuration settings functions
from lammps import lammps

6
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@ -74,7 +74,7 @@ Here are simple examples using all three Python interfaces:
:py:class:`PyLammps <lammps.PyLammps>` objects can also be created on top of an existing
:py:class:`lammps <lammps.lammps>` object:
.. code-block:: Python
.. code-block:: python
from lammps import lammps, PyLammps
...
@ -113,7 +113,7 @@ Here are simple examples using all three Python interfaces:
You can also initialize IPyLammps on top of an existing :py:class:`lammps` or :py:class:`PyLammps` object:
.. code-block:: Python
.. code-block:: python
from lammps import lammps, IPyLammps
...
@ -142,7 +142,7 @@ the MPI and/or Kokkos environment if enabled and active.
Note that you can create multiple LAMMPS objects in your Python
script, and coordinate and run multiple simulations, e.g.
.. code-block:: Python
.. code-block:: python
from lammps import lammps
lmp1 = lammps()

2
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@ -7,7 +7,7 @@ current Python process with an error message. C++ exceptions allow capturing
them on the C++ side and rethrowing them on the Python side. This way
LAMMPS errors can be handled through the Python exception handling mechanism.
.. code-block:: Python
.. code-block:: python
from lammps import lammps, MPIAbortException

8
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@ -60,7 +60,7 @@ it is possible to "compute" what the next LAMMPS command should be.
can be executed using with the lammps API with the following Python code if ``lmp`` is an
instance of :py:class:`lammps <lammps.lammps>`:
.. code-block:: Python
.. code-block:: python
from lammps import lammps
@ -73,7 +73,7 @@ it is possible to "compute" what the next LAMMPS command should be.
The arguments of the command can be passed as one string, or
individually.
.. code-block:: Python
.. code-block:: python
from lammps import PyLammps
@ -93,14 +93,14 @@ it is possible to "compute" what the next LAMMPS command should be.
parameterization. In the lammps API parameterization needed to be done
manually by creating formatted command strings.
.. code-block:: Python
.. code-block:: python
lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
In contrast, methods of PyLammps accept parameters directly and will convert
them automatically to a final command string.
.. code-block:: Python
.. code-block:: python
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)

2
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@ -56,7 +56,7 @@ and you should see the same output as if you had typed
Note that without the mpi4py specific lines from ``test.py``
.. code-block:: Python
.. code-block:: python
from lammps import lammps
lmp = lammps()

6
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@ -76,7 +76,7 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
To define a variable you can use the :doc:`variable <variable>` command:
.. code-block:: Python
.. code-block:: python
L.variable("a index 2")
@ -85,14 +85,14 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
you can access an individual variable by retrieving a variable object from the
``L.variables`` dictionary by name
.. code-block:: Python
.. code-block:: python
a = L.variables['a']
The variable value can then be easily read and written by accessing the value
property of this object.
.. code-block:: Python
.. code-block:: python
print(a.value)
a.value = 4

2
doc/src/Python_properties.rst
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@ -105,7 +105,7 @@ against invalid accesses.
variables, compute or fix data (see :doc:`Howto_output`):
.. code-block:: Python
.. code-block:: python
result = L.eval("ke") # kinetic energy
result = L.eval("pe") # potential energy

4
doc/src/Python_scatter.rst
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@ -1,7 +1,7 @@
Scatter/gather operations
=========================
.. code-block:: Python
.. code-block:: python
data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID
# name = "x", "charge", "type", etc
@ -42,7 +42,7 @@ For the scatter methods, the array of coordinates passed to must be a
ctypes vector of ints or doubles, allocated and initialized something
like this:
.. code-block:: Python
.. code-block:: python
from ctypes import c_double
natoms = lmp.get_natoms()

38
doc/src/Run_options.rst
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@ -262,6 +262,8 @@ Disable generating a citation reminder (see above) at all.
**-nonbuf**
.. versionadded:: 15Sep2022
Turn off buffering for screen and logfile output. For performance
reasons, output to the screen and logfile is usually buffered, i.e.
output is only written to a file if its buffer - typically 4096 bytes -
@ -442,7 +444,7 @@ the LAMMPS simulation domain.
.. _restart2data:
**-restart2data restartfile [remap] datafile keyword value ...**
**-restart2data restartfile datafile keyword value ...**
Convert the restart file into a data file and immediately exit. This
is the same operation as if the following 2-line input script were
@ -450,7 +452,7 @@ run:
.. code-block:: LAMMPS
read_restart restartfile [remap]
read_restart restartfile
write_data datafile keyword value ...
The specified restartfile and/or datafile name may contain the wild-card
@ -462,28 +464,21 @@ Note that a filename such as file.\* may need to be enclosed in quotes or
the "\*" character prefixed with a backslash ("\") to avoid shell
expansion of the "\*" character.
Following restartfile argument, the optional word "remap" may be used.
This has the same effect like adding it to a
:doc:`read_restart <read_restart>` command, and operates as explained on
its doc page. This is useful if reading the restart file triggers an
error that atoms have been lost. In that case, use of the remap flag
should allow the data file to still be produced.
The syntax following restartfile (or remap), namely
The syntax following restartfile, namely
.. parsed-literal::
datafile keyword value ...
is identical to the arguments of the :doc:`write_data <write_data>`
command. See its page for details. This includes its
command. See its documentation page for details. This includes its
optional keyword/value settings.
----------
.. _restart2dump:
**-restart2dump restartfile [remap] group-ID dumpstyle dumpfile arg1 arg2 ...**
**-restart2dump restartfile group-ID dumpstyle dumpfile arg1 arg2 ...**
Convert the restart file into a dump file and immediately exit. This
is the same operation as if the following 2-line input script were
@ -491,7 +486,7 @@ run:
.. code-block:: LAMMPS
read_restart restartfile [remap]
read_restart restartfile
write_dump group-ID dumpstyle dumpfile arg1 arg2 ...
Note that the specified restartfile and dumpfile names may contain
@ -503,24 +498,17 @@ such as file.\* may need to be enclosed in quotes or the "\*" character
prefixed with a backslash ("\") to avoid shell expansion of the "\*"
character.
Note that following the restartfile argument, the optional word "remap"
can be used. This has the effect as adding it to the
:doc:`read_restart <read_restart>` command, as explained on its doc page.
This is useful if reading the restart file triggers an error that atoms
have been lost. In that case, use of the remap flag should allow the
dump file to still be produced.
The syntax following restartfile (or remap), namely
The syntax following restartfile, namely
.. code-block:: LAMMPS
group-ID dumpstyle dumpfile arg1 arg2 ...
is identical to the arguments of the :doc:`write_dump <write_dump>`
command. See its page for details. This includes what per-atom
fields are written to the dump file and optional dump_modify settings,
including ones that affect how parallel dump files are written, e.g.
the *nfile* and *fileper* keywords. See the
command. See its documentation page for details. This includes what
per-atom fields are written to the dump file and optional dump_modify
settings, including ones that affect how parallel dump files are written,
e.g. the *nfile* and *fileper* keywords. See the
:doc:`dump_modify <dump_modify>` page for details.
----------

40
doc/src/Speed_kokkos.rst
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@ -212,14 +212,15 @@ threads/task as Nt. The product of these two values should be N, i.e.
.. note::
The default for the :doc:`package kokkos <package>` command when
running on KNL is to use "half" neighbor lists and set the Newton flag
to "on" for both pairwise and bonded interactions. This will typically
be best for many-body potentials. For simpler pairwise potentials, it
may be faster to use a "full" neighbor list with Newton flag to "off".
Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to change
the default :doc:`package kokkos <package>` options. See its page for
details and default settings. Experimenting with its options can provide
a speed-up for specific calculations. For example:
running on KNL is to use "half" neighbor lists and set the Newton
flag to "on" for both pairwise and bonded interactions. This will
typically be best for many-body potentials. For simpler pairwise
potentials, it may be faster to use a "full" neighbor list with
Newton flag to "off". Use the "-pk kokkos" :doc:`command-line switch
<Run_options>` to change the default :doc:`package kokkos <package>`
options. See its documentation page for details and default
settings. Experimenting with its options can provide a speed-up for
specific calculations. For example:
.. code-block:: bash
@ -271,17 +272,18 @@ one or more nodes, each with two GPUs:
.. note::
The default for the :doc:`package kokkos <package>` command when
running on GPUs is to use "full" neighbor lists and set the Newton flag
to "off" for both pairwise and bonded interactions, along with threaded
communication. When running on Maxwell or Kepler GPUs, this will
typically be best. For Pascal GPUs and beyond, using "half" neighbor lists and
setting the Newton flag to "on" may be faster. For many pair styles,
setting the neighbor binsize equal to twice the CPU default value will
give speedup, which is the default when running on GPUs. Use the "-pk
kokkos" :doc:`command-line switch <Run_options>` to change the default
:doc:`package kokkos <package>` options. See its page for details and
default settings. Experimenting with its options can provide a speed-up
for specific calculations. For example:
running on GPUs is to use "full" neighbor lists and set the Newton
flag to "off" for both pairwise and bonded interactions, along with
threaded communication. When running on Maxwell or Kepler GPUs, this
will typically be best. For Pascal GPUs and beyond, using "half"
neighbor lists and setting the Newton flag to "on" may be faster. For
many pair styles, setting the neighbor binsize equal to twice the CPU
default value will give speedup, which is the default when running on
GPUs. Use the "-pk kokkos" :doc:`command-line switch <Run_options>`
to change the default :doc:`package kokkos <package>` options. See
its documentation page for details and default
settings. Experimenting with its options can provide a speed-up for
specific calculations. For example:
.. code-block:: bash

20
doc/src/Tools.rst
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@ -57,7 +57,7 @@ Pre-processing tools
* :ref:`msi2lmp <msi>`
* :ref:`polybond <polybond>`
* :ref:`stl_bin2txt <stlconvert>`
* :ref:`tabulate <tabulate>`
Post-processing tools
=====================
@ -1159,13 +1159,27 @@ For illustration purposes below is a part of the Tcl example script.
----------
.. _tabulate:
tabulate tool
--------------
.. versionadded:: 22Dec2022
The ``tabulate`` folder contains Python scripts scripts to generate tabulated
potential files for LAMMPS. The bulk of the code is in the ``tabulate`` module
in the ``tabulate.py`` file. Some example files demonstrating its use are
included. See the README file for more information.
----------
.. _vim:
vim tool
------------------
The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
The files in the ``tools/vim`` directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the ``README.txt``
file for details.
These files were provided by Gerolf Ziegenhain (gerolf at

18
doc/src/angle_gaussian.rst
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@ -25,23 +25,25 @@ The *gaussian* angle style uses the potential:
.. math::
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(\theta-\theta_{i})^2}{w_i^2})\right) \right)
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(\theta-\theta_{i})^2}{w_i^2}\right) \right)
This analytical form is a suitable potential for obtaining mesoscale
effective force fields which can reproduce target atomistic
distributions :ref:`(Milano) <Milano1>`.
This analytical form is a suitable potential for obtaining
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano1>`
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:
* T temperature at which the potential was derived
* :math:`T` temperature at which the potential was derived
* :math:`n` (integer >=1)
* :math:`A_1` (-)
* :math:`w_1` (-)
* :math:`A_1` (> 0, radians)
* :math:`w_1` (> 0, radians)
* :math:`\theta_1` (degrees)
* ...
* :math:`A_n` (-)
* :math:`w_n` (-)
* :math:`A_n` (> 0, radians)
* :math:`w_n` (> 0, radians)
* :math:`\theta_n` (degrees)

4
doc/src/angle_table.rst
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@ -59,6 +59,10 @@ format of this file is described below.
----------
Suitable tables for use with this angle style can be created using the
Python code in the ``tools/tabulate`` folder of the LAMMPS source code
distribution.
The format of a tabulated file is as follows (without the
parenthesized comments):

2
doc/src/bond_bpm_rotational.rst
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@ -69,7 +69,7 @@ which is proportional to the tangential shear displacement with a
stiffness of :math:`k_s`. This tangential force also induces a torque.
In addition, bending and twisting torques are also applied to
particles which are proportional to angular bending and twisting
displacements with stiffnesses of :math`k_b` and :math:`k_t',
displacements with stiffnesses of :math:`k_b` and :math:`k_t`,
respectively. Details on the calculations of shear displacements and
angular displacements can be found in :ref:`(Wang) <Wang2009>` and
:ref:`(Wang and Mora) <Wang2009b>`.

25
doc/src/bond_gaussian.rst
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@ -25,33 +25,34 @@ The *gaussian* bond style uses the potential:
.. math::
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(r-r_{i})^2}{w_i^2})\right) \right)
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(r-r_{i})^2}{w_i^2}\right)\right)
This analytical form is a suitable potential for obtaining
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano0>`
This analytical form is a suitable potential for obtaining mesoscale
effective force fields which can reproduce target atomistic
distributions :ref:`(Milano) <Milano0>`
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* T temperature at which the potential was derived
* :math:`T` temperature at which the potential was derived
* :math:`n` (integer >=1)
* :math:`A_1` (-)
* :math:`w_1` (-)
* :math:`r_1` (length)
* :math:`A_1` (> 0, distance)
* :math:`w_1` (> 0, distance)
* :math:`r_1` (>= 0, distance)
* ...
* :math:`A_n` (-)
* :math:`w_n` (-)
* :math:`r_n` (length)
* :math:`A_n` (> 0, distance)
* :math:`w_n` (> 0, distance)
* :math:`r_n` (>= 0, distance)
Restrictions
""""""""""""
This bond 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.
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
doc page for more info.
Related commands
""""""""""""""""

10
doc/src/bond_table.rst
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@ -59,6 +59,13 @@ this file is described below.
----------
Suitable tables for use with this bond style can be created by LAMMPS
itself from existing bond styles using the :doc:`bond_write
<bond_write>` command. This can be useful to have a template file for
testing the bond style settings and to build a compatible custom file.
Another option to generate tables is the Python code in the
``tools/tabulate`` folder of the LAMMPS source code distribution.
The format of a tabulated file is as follows (without the
parenthesized comments):
@ -149,7 +156,8 @@ info.
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
:doc:`bond_write <bond_write>`
Default
"""""""

70
doc/src/box.rst
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@ -1,70 +0,0 @@
.. index:: box
box command
===========
Syntax
""""""
.. code-block:: LAMMPS
box keyword value ...
* one or more keyword/value pairs may be appended
* keyword = *tilt*
.. parsed-literal::
*tilt* value = *small* or *large*
Examples
""""""""
.. code-block:: LAMMPS
box tilt large
box tilt small
Description
"""""""""""
Set attributes of the simulation box.
For triclinic (non-orthogonal) simulation boxes, the *tilt* keyword
allows simulation domains to be created with arbitrary tilt factors,
e.g. via the :doc:`create_box <create_box>` or
:doc:`read_data <read_data>` commands. Tilt factors determine how
skewed the triclinic box is; see the :doc:`Howto triclinic <Howto_triclinic>` page for a discussion of triclinic
boxes in LAMMPS.
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). If *tilt* is set to
*small*, which is the default, then an error will be
generated if a box is created which exceeds this limit. If *tilt*
is set to *large*, then no limit is enforced. You can create
a box with any tilt factors you wish.
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 sub-domain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.
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.
Related commands
""""""""""""""""
none
Default
"""""""
The default value is tilt = small.

5
doc/src/commands_list.rst
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@ -13,7 +13,6 @@ Commands
bond_style
bond_write
boundary
box
change_box
clear
comm_modify
@ -43,6 +42,7 @@ Commands
echo
fix
fix_modify
fitpod_command
group
group2ndx
hyper
@ -90,8 +90,7 @@ Commands
region
replicate
rerun
reset_atom_ids
reset_mol_ids
reset_atoms
reset_timestep
restart
run

54
doc/src/compute.rst
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@ -43,29 +43,38 @@ underscores.
----------
Computes calculate one of three styles of quantities: global,
per-atom, or local. A global quantity is one or more system-wide
values (e.g., the temperature of the system). A per-atom quantity is
one or more values per atom (e.g., the kinetic energy of each atom).
Per-atom values are set to 0.0 for atoms not in the specified compute
group. Local quantities are calculated by each processor based on the
atoms it owns, but there may be zero or more per atom (e.g., a list of
bond distances). Computes that produce per-atom quantities have the
word "atom" in their style (e.g., *ke/atom*\ ). Computes that produce
local quantities have the word "local" in their style
(e.g., *bond/local*\ ). Styles with neither "atom" or "local" in their
style produce global quantities.
Computes calculate one or more of four styles of quantities: global,
per-atom, local, or per-atom. A global quantity is one or more
system-wide values, e.g. the temperature of the system. A per-atom
quantity is one or more values per atom, e.g. the kinetic energy of
each atom. Per-atom values are set to 0.0 for atoms not in the
specified compute group. Local quantities are calculated by each
processor based on the atoms it owns, but there may be zero or more
per atom, e.g. a list of bond distances. Per-grid quantities are
calculated on a regular 2d or 3d grid which overlays a 2d or 3d
simulation domain. The grid points and the data they store are
distributed across processors; each processor owns the grid points
which fall within its sub-domain.
Note that a single compute can produce either global or per-atom or
local quantities, but not both global and per-atom. It can produce
local quantities in tandem with global or per-atom quantities. The
compute page will explain.
Computes that produce per-atom quantities have the word "atom" at the
end of their style, e.g. *ke/atom*\ . Computes that produce local
quantities have the word "local" at the end of their style,
e.g. *bond/local*\ . Computes that produce per-grid quantities have
the word "grid" at the end of their style, e.g. *property/grid*\ .
Styles with neither "atom" or "local" or "grid" at the end of their
style name produce global quantities.
Global, per-atom, and local quantities each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for each compute describes the style and kind of values it
produces (e.g., a per-atom vector). Some computes produce more than one
kind of a single style (e.g., a global scalar and a global vector).
Note that a single compute typically produces either global or
per-atom or local or per-grid values. It does not compute both global
and per-atom values. It can produce local values or per-grid values
in tandem with global or per-atom quantities. The compute doc page
will explain the details.
Global, per-atom, local, and per-grid quantities come in three kinds:
a single scalar value, a vector of values, or a 2d array of values.
The doc page for each compute describes the style and kind of values
it produces, e.g. a per-atom vector. Some computes produce more than
one kind of a single style, e.g. a global scalar and a global vector.
When a compute quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
@ -252,7 +261,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
* :doc:`property/atom <compute_property_atom>` - convert atom attributes to per-atom vectors/arrays
* :doc:`property/chunk <compute_property_chunk>` - extract various per-chunk attributes
* :doc:`property/local <compute_property_local>` - convert local attributes to localvectors/arrays
* :doc:`property/grid <compute_property_grid>` - convert per-grid attributes to per-grid vectors/arrays
* :doc:`property/local <compute_property_local>` - convert local attributes to local vectors/arrays
* :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
* :doc:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value

38
doc/src/compute_modify.rst
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@ -37,27 +37,29 @@ Description
Modify one or more parameters of a previously defined compute. Not
all compute styles support all parameters.
The *extra/dof* or *extra* keyword refers to how many degrees of freedom are
subtracted (typically from :math:`3N`) as a normalizing
The *extra/dof* or *extra* keyword refers to how many degrees of
freedom are subtracted (typically from :math:`3N`) as a normalizing
factor in a temperature computation. Only computes that compute a
temperature use this option. The default is 2 or 3 for
:doc:`2d or 3d systems <dimension>`, which is a correction factor for an
ensemble of velocities with zero total linear momentum. For compute
temp/partial, if one or more velocity components are excluded, the
value used for *extra* is scaled accordingly. You can use a negative
number for the *extra* parameter if you need to add
degrees-of-freedom. See the :doc:`compute temp/asphere <compute_temp_asphere>` command for an example.
temperature use this option. The default is 2 or 3 for :doc:`2d or 3d
systems <dimension>` which is a correction factor for an ensemble of
velocities with zero total linear momentum. For compute temp/partial,
if one or more velocity components are excluded, the value used for
*extra* is scaled accordingly. You can use a negative number for the
*extra* parameter if you need to add degrees-of-freedom. See the
:doc:`compute temp/asphere <compute_temp_asphere>` command for an
example.
The *dynamic/dof* or *dynamic* keyword determines whether the number
of atoms :math:`N` in the compute group and their associated degrees of
freedom (DOF) are re-computed each time a temperature is computed. Only
compute styles that calculate a temperature use this option. By
default, :math:`N` and their DOF are assumed to be constant. If you are
adding atoms or molecules to the system (see the :doc:`fix pour <fix_pour>`,
:doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or
expect atoms or molecules to be lost (e.g., due to exiting the simulation box
or via :doc:`fix evaporate <fix_evaporate>`), then this option should be used
to ensure the temperature is correctly normalized.
of atoms :math:`N` in the compute group and their associated degrees
of freedom (DOF) are re-computed each time a temperature is computed.
Only compute styles that calculate a temperature use this option. By
default, :math:`N` and their DOF are assumed to be constant. If you
are adding atoms or molecules to the system (see the :doc:`fix pour
<fix_pour>`, :doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc
<fix_gcmc>` commands) or expect atoms or molecules to be lost
(e.g. due to exiting the simulation box or via :doc:`fix evaporate
<fix_evaporate>`), then this option should be used to insure the
temperature is correctly normalized.
.. note::

2
doc/src/compute_pair_local.rst
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@ -59,7 +59,7 @@ commands.
The value *dist* is the distance between the pair of atoms.
The values *dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the
*distance* between the pair of atoms. This value is always the
distance from the atom of lower to the one with the higher id.
distance from the atom of higher to the one with the lower atom ID.
The value *eng* is the interaction energy for the pair of atoms.

71
doc/src/compute_property_chunk.rst
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@ -12,7 +12,8 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command
* property/chunk = style name of this compute command
* input = one or more attributes
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command that defines the chunks
* input1,etc = one or more attributes
.. parsed-literal::
@ -26,8 +27,8 @@ Examples
.. code-block:: LAMMPS
compute 1 all property/chunk count
compute 1 all property/chunk ID coord1
compute 1 all property/chunk bin2d id count
compute 1 all property/chunk myChunks id coord1
Description
"""""""""""
@ -35,29 +36,28 @@ Description
Define a computation that stores the specified attributes of chunks of
atoms.
In LAMMPS, chunks are collections of atoms defined by a
:doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a molecule or
atoms in a spatial bin. See the :doc:`compute chunk/atom <compute_chunk_atom>`
and :doc:`Howto chunk <Howto_chunk>` doc pages for details of how chunks can be
defined and examples of how they can be used to measure properties of a system.
In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
single chunk (or no chunk). The ID for this command is specified as
chunkID. For example, a single chunk could be the atoms in a molecule
or atoms in a spatial bin. See the :doc:`compute chunk/atom
<compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>` doc pages
for details of how chunks can be defined and examples of how they can
be used to measure properties of a system.
This compute calculates and stores the specified attributes of chunks
as global data so they can be accessed by other
:doc:`output commands <Howto_output>` and used in conjunction with other
commands that generate per-chunk data, such as
:doc:`compute com/chunk <compute_com_chunk>` or
:doc:`compute msd/chunk <compute_msd_chunk>`.
as global data so they can be accessed by other :doc:`output commands
<Howto_output>` and used in conjunction with other commands that
generate per-chunk data, such as :doc:`compute com/chunk
<compute_com_chunk>` or :doc:`compute msd/chunk <compute_msd_chunk>`.
Note that only atoms in the specified group contribute to the
calculation of the *count* attribute. The
:doc:`compute chunk/atom <compute_chunk_atom>` command defines its own group;
atoms will have a chunk ID = 0 if they are not in that group,
signifying they are not assigned to a chunk, and will thus also not
contribute to this calculation. You can specify the "all" group for
this command if you simply want to include atoms with non-zero chunk
IDs.
calculation of the *count* attribute. The :doc:`compute chunk/atom
<compute_chunk_atom>` command defines its own group; atoms will have a
chunk ID = 0 if they are not in that group, signifying they are not
assigned to a chunk, and will thus also not contribute to this
calculation. You can specify the "all" group for this command if you
simply want to include atoms with non-zero chunk IDs.
The *count* attribute is the number of atoms in the chunk.
@ -66,21 +66,24 @@ can only be used if the *compress* keyword was set to *yes* for the
:doc:`compute chunk/atom <compute_chunk_atom>` command referenced by
chunkID. This means that the original chunk IDs (e.g., molecule IDs)
will have been compressed to remove chunk IDs with no atoms assigned
to them. Thus a compressed chunk ID of 3 may correspond to an original
chunk ID (molecule ID in this case) of 415. The *id* attribute will
then be 415 for the third chunk.
to them. Thus a compressed chunk ID of 3 may correspond to an
original chunk ID (molecule ID in this case) of 415. The *id*
attribute will then be 415 for the third chunk.
The *coordN* attributes can only be used if a *binning* style was used
in the :doc:`compute chunk/atom <compute_chunk_atom>` command referenced
by chunkID. For *bin/1d*, *bin/2d*, and *bin/3d* styles the attribute
is the center point of the bin in the corresponding dimension. Style
*bin/1d* only defines a *coord1* attribute. Style *bin/2d* adds a
*coord2* attribute. Style *bin/3d* adds a *coord3* attribute.
Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or *lattice*, the
*coordN* attributes will be in distance :doc:`units <units>`. If the
value of the *units* keyword is *reduced*, the *coordN* attributes
will be in unitless reduced units (0--1).
in the :doc:`compute chunk/atom <compute_chunk_atom>` command
referenced by chunkID. For *bin/1d*, *bin/2d*, and *bin/3d* styles
the attribute is the center point of the bin in the corresponding
dimension. Style *bin/1d* only defines a *coord1* attribute. Style
*bin/2d* adds a *coord2* attribute. Style *bin/3d* adds a *coord3*
attribute.
Note that if the value of the *units* keyword used in the
:doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or
*lattice*, the *coordN* attributes will be in distance :doc:`units
<units>`. If the value of the *units* keyword is *reduced*, the
*coordN* attributes will be in unitless reduced units (0-1).
The simplest way to output the results of the compute property/chunk
calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`

114
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@ -0,0 +1,114 @@
.. index:: compute property/grid
compute property/grid command
=============================
Syntax
""""""
.. parsed-literal::
compute ID group-ID property/grid Nx Ny Nz input1 input2 ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* property/grid = style name of this compute command
* Nx, Ny, Nz = grid size in each dimension
* input1,etc = one or more attributes
.. parsed-literal::
attributes = id, ix, iy, iz, x, y, z, xs, ys, zs, xc, yc, zc, xsc, ysc, zsc
id = ID of grid cell, x fastest, y next, z slowest
ix,iy,iz = grid indices in each dimension (1 to N inclusive)
x,y,z = coords of lower left corner of grid cell
xs,ys,zs = scaled coords of lower left corner of grid cell (0.0 to 1.0)
xc,yc,zc = coords of center point of grid cell
xsc,ysc,zsc = scaled coords of center point of grid cell (0.0 to 1.0)
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all property/grid id ix iy iz
compute 1 all property/grid id xc yc zc
Description
"""""""""""
Define a computation that stores the specified attributes of a
distributed grid. In LAMMPS, distributed grids are regular 2d or 3d
grids which overlay a 2d or 3d simulation domain. Each processor owns
the grid cells whose center points lie within its sub-domain. See the
:doc:`Howto grid <Howto_grid>` doc page for details of how distributed
grids can be defined by various commands and referenced.
This compute stores the specified attributes of grids as per-grid data
so they can be accessed by other :doc:`output commands <Howto_output>`
such as :doc:`dump grid <dump>`.
*Nx*, *Ny*, and *Nz* define the size of the grid. For a 2d simulation
*Nz* must be 1. When this compute is used by :doc:`dump grid <dump>`,
to output per-grid values from other computes of fixes, the grid size
specified for this command must be consistent with the grid sizes
used by the other commands.
The *id* attribute stores the grid ID for each grid cell. For a
global grid of size Nx by Ny by Nz (in 3d simulations) the grid IDs
range from 1 to Nx*Ny*Nz. They are ordered with the X index of the 3d
grid varying fastest, then Y, then Z slowest. For 2d grids (in 2d
simulations), the grid IDs range from 1 to Nx*Ny, with X varying
fastest and Y slowest.
The *ix*, *iy*, *iz* attributes are the indices of a grid cell in
each dimension. They range from 1 to Nx inclusive in the X dimension,
and similar for Y and Z.
The *x*, *y*, *z* attributes are the coordinates of the lower left
corner point of each grid cell.
The *xs*, *ys*, *zs* attributes are also coordinates of the lower left
corner point of each grid cell, except in scaled coordinates, where
the lower-left corner of the entire simulation box is (0,0,0) and the
upper right corner is (1,1,1).
The *xc*, *yc*, *zc* attributes are the coordinates of the center
point of each grid cell.
The *xsc*, *ysc*, *zsc* attributes are also coordinates of the center
point each grid cell, except in scaled coordinates, where the
lower-left corner of the entire simulation box is (0,0,0) and the upper
right corner is (1,1,1).
For :doc:`triclinic simulation boxes <Howto_triclinic>`, the grid
point coordinates for (x,y,z) and (xc,yc,zc) will reflect the
triclinic geometry. For (xs,yz,zs) and (xsc,ysc,zsc), the coordinates
are the same for orthogonal versus triclinic boxes.
Output info
"""""""""""
This compute calculates a per-grid vector or array depending on the
number of input values. The length of the vector or number of array
rows (distributed across all processors) is Nx * Ny * Nz. For access
by other commands, the name of the single grid produced by this
command is "grid". The name of its per-grid data is "data".
The (x,y,z) and (xc,yc,zc) coordinates are in distance :doc:`units
<units>`.
Restrictions
""""""""""""
For 2d simulations, the attributes which refer to
the Z dimension cannot be used.
Related commands
""""""""""""""""
:doc:`dump grid <dump>`
Default
"""""""
none

27
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@ -85,10 +85,11 @@ Description
"""""""""""
Define a computation that stores the specified attributes as local
data so it can be accessed by other :doc:`output commands <Howto_output>`. If the input attributes refer to bond
information, then the number of datums generated, aggregated across
all processors, equals the number of bonds in the system. Ditto for
pairs, angles, etc.
data so it can be accessed by other :doc:`output commands
<Howto_output>`. If the input attributes refer to bond information,
then the number of datums generated, aggregated across all processors,
equals the number of bonds in the system. Ditto for pairs, angles,
etc.
If multiple attributes are specified then they must all generate the
same amount of information, so that the resulting local array has the
@ -129,17 +130,20 @@ specified compute group. Likewise for angles, dihedrals, etc.
For bonds and angles, a bonds/angles that have been broken by setting
their bond/angle type to 0 will not be included. Bonds/angles that
have been turned off (see the :doc:`fix shake <fix_shake>` or
:doc:`delete_bonds <delete_bonds>` commands) by setting their bond/angle
type negative are written into the file. This is consistent with the
:doc:`compute bond/local <compute_bond_local>` and :doc:`compute angle/local <compute_angle_local>` commands
:doc:`delete_bonds <delete_bonds>` commands) by setting their
bond/angle type negative are written into the file. This is
consistent with the :doc:`compute bond/local <compute_bond_local>` and
:doc:`compute angle/local <compute_angle_local>` commands
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, output from the :doc:`compute bond/local <compute_bond_local>` command can be combined with bond
atom indices from this command and output by the :doc:`dump local <dump>` command in a consistent way.
For example, output from the :doc:`compute bond/local
<compute_bond_local>` command can be combined with bond atom indices
from this command and output by the :doc:`dump local <dump>` command
in a consistent way.
The *natom1* and *natom2* or *patom1* and *patom2* attributes refer
to the atom IDs of the 2 atoms in each pairwise interaction computed
@ -177,9 +181,8 @@ the array is the number of bonds, angles, etc. If a single input is
specified, a local vector is produced. If two or more inputs are
specified, a local array is produced where the number of columns = the
number of inputs. The vector or array can be accessed by any command
that uses local values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
that uses local values from a compute as input. See the :doc:`Howto
output <Howto_output>` page for an overview of LAMMPS output options.
The vector or array values will be integers that correspond to the
specified attribute.

32
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@ -29,8 +29,9 @@ Description
Define a computation that calculates the temperature of a group of
atoms. A compute of this style can be used by any command that
computes a temperature (e.g., :doc:`thermo_modify <thermo_modify>`,
:doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`)
computes a temperature, e.g. :doc:`thermo_modify <thermo_modify>`,
:doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`,
etc.
The temperature is calculated by the formula
@ -39,17 +40,17 @@ The temperature is calculated by the formula
\text{KE} = \frac{\text{dim}}{2} N k_B T,
where KE = total kinetic energy of the group of atoms (sum of
:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
constant, and :math:`T` is the absolute temperature.
:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the
simulation, :math:`N` is the number of atoms in the group, :math:`k_B`
is the Boltzmann constant, and :math:`T` is the absolute temperature.
A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that :math:`v^2` is replaced by
:math:`v_x v_y` for the :math:`xy` component, and so on.
The six components of the vector are ordered :math:`xx`, :math:`yy`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
the above formula, except that :math:`v^2` is replaced by :math:`v_x
v_y` for the :math:`xy` component, and so on. The six components of
the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`,
:math:`xz`, :math:`yz`.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the *dynamic* option of the
@ -85,11 +86,10 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length six (KE tensor), which can be accessed by indices 1--6.
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.
vector of length six (KE tensor), which can be accessed by indices
1--6. 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 value calculated by this compute is "intensive". The
vector values are "extensive".
@ -104,7 +104,9 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute temp/partial <compute_temp_partial>`, :doc:`compute temp/region <compute_temp_region>`, :doc:`compute pressure <compute_pressure>`
:doc:`compute temp/partial <compute_temp_partial>`,
:doc:`compute temp/region <compute_temp_region>`,
:doc:`compute pressure <compute_pressure>`
Default
"""""""

25
doc/src/create_box.rst
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@ -66,20 +66,21 @@ 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.
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
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 :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. If you wish to define a box with tilt
factors that exceed these limits, you can use the :doc:`box tilt <box>`
command, with a setting of *large*\ ; a setting of *small* is the
default.
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.
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
geometric description of triclinic boxes, as defined by LAMMPS, and

4
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@ -135,7 +135,7 @@ number of atoms in the system. Note that this is not done for
molecular systems (see the :doc:`atom_style <atom_style>` command),
regardless of the *compress* setting, since it would foul up the bond
connectivity that has already been assigned. However, the
:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this
:doc:`reset_atoms id <reset_atoms>` command can be used after this
command to accomplish the same thing.
Note that the re-assignment of IDs is not really a compression, where
@ -203,7 +203,7 @@ using molecule template files via the :doc:`molecule <molecule>` and
Related commands
""""""""""""""""
:doc:`create_atoms <create_atoms>`, :doc:`reset_atom_ids <reset_atom_ids>`
:doc:`create_atoms <create_atoms>`, :doc:`reset_atoms id <reset_atoms>`
Default
"""""""

4
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@ -114,6 +114,10 @@ below.
----------
Suitable tables for use with this dihedral style can be created using
the Python code in the ``tools/tabulate`` folder of the LAMMPS source
code distribution.
The format of a tabulated file is as follows (without the
parenthesized comments). It can begin with one or more comment
or blank lines.

649
doc/src/dump.rst
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@ -3,6 +3,8 @@
.. index:: dump cfg
.. index:: dump custom
.. index:: dump dcd
.. index:: dump grid
.. index:: dump grid/vtk
.. index:: dump local
.. index:: dump xtc
.. index:: dump yaml
@ -57,46 +59,48 @@ Syntax
.. code-block:: LAMMPS
dump ID group-ID style N file args
dump ID group-ID style N file attribute1 attribute2 ...
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped
* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
* N = dump on timesteps which are multiples of N
* file = name of file to write dump info to
* args = list of arguments for a particular style
* attribute1,attribute2,... = list of attributes for a particular style
.. parsed-literal::
*atom* args = none
*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` page
*atom/gz* args = none
*atom/zstd* args = none
*atom/mpiio* args = none
*cfg* args = same as *custom* args, see below
*cfg/gz* args = same as *custom* args, see below
*cfg/zstd* args = same as *custom* args, see below
*cfg/mpiio* args = same as *custom* args, see below
*cfg/uef* args = same as *custom* args, discussed on :doc:`dump cfg/uef <dump_cfg_uef>` page
*custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* args = see below
*custom/adios* args = same as *custom* args, discussed on :doc:`dump custom/adios <dump_adios>` page
*dcd* args = none
*h5md* args = discussed on :doc:`dump h5md <dump_h5md>` page
*image* args = discussed on :doc:`dump image <dump_image>` page
*local*, *local/gz*, *local/zstd* args = see below
*molfile* args = discussed on :doc:`dump molfile <dump_molfile>` page
*movie* args = discussed on :doc:`dump image <dump_image>` page
*netcdf* args = discussed on :doc:`dump netcdf <dump_netcdf>` page
*netcdf/mpiio* args = discussed on :doc:`dump netcdf <dump_netcdf>` page
*vtk* args = same as *custom* args, see below, also :doc:`dump vtk <dump_vtk>` page
*xtc* args = none
*xyz* args = none
*xyz/gz* args = none
*xyz/zstd* args = none
*xyz/mpiio* args = none
*yaml* args = same as *custom* args, see below
*atom* attributes = none
*atom/adios* attributes = none, discussed on :doc:`dump atom/adios <dump_adios>` page
*atom/gz* attributes = none
*atom/zstd* attributes = none
*atom/mpiio* attributes = none
*cfg* attributes = same as *custom* attributes, see below
*cfg/gz* attributes = same as *custom* attributes, see below
*cfg/zstd* attributes = same as *custom* attributes, see below
*cfg/mpiio* attributes = same as *custom* attributes, see below
*cfg/uef* attributes = same as *custom* attributes, discussed on :doc:`dump cfg/uef <dump_cfg_uef>` page
*custom*, *custom/gz*, *custom/zstd*, *custom/mpiio* attributes = see below
*custom/adios* attributes = same as *custom* attributes, discussed on :doc:`dump custom/adios <dump_adios>` page
*dcd* attributes = none
*h5md* attributes = discussed on :doc:`dump h5md <dump_h5md>` page
*grid* attributes = see below
*grid/vtk* attributes = see below
*image* attributes = discussed on :doc:`dump image <dump_image>` page
*local*, *local/gz*, *local/zstd* attributes = see below
*molfile* attributes = discussed on :doc:`dump molfile <dump_molfile>` page
*movie* attributes = discussed on :doc:`dump image <dump_image>` page
*netcdf* attributes = discussed on :doc:`dump netcdf <dump_netcdf>` page
*netcdf/mpiio* attributes = discussed on :doc:`dump netcdf <dump_netcdf>` page
*vtk* attributes = same as *custom* attributes, see below, also :doc:`dump vtk <dump_vtk>` page
*xtc* attributes = none
*xyz* attributes = none
*xyz/gz* attributes = none
*xyz/zstd* attributes = none
*xyz/mpiio* attributes = none
*yaml* attributes = same as *custom* attributes, see below
* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *netcdf* or *netcdf/mpiio* or *yaml* args = list of atom attributes
* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *netcdf* or *netcdf/mpiio* or *yaml* attributes:
.. parsed-literal::
@ -143,7 +147,7 @@ Syntax
i2_name[I] = Ith column of custom integer array with name, I can include wildcard (see below)
d2_name[I] = Ith column of custom floating point vector with name, I can include wildcard (see below)
* *local* or *local/gz* or *local/zstd* args = list of local attributes
* *local* or *local/gz* or *local/zstd* attributes:
.. parsed-literal::
@ -154,6 +158,18 @@ Syntax
f_ID = local vector calculated by a fix with ID
f_ID[I] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below)
* *grid* or *grid/vtk* attributes:
.. parsed-literal::
possible attributes = c_ID:gname:dname, c_ID:gname:dname[I], f_ID:gname:dname, f_ID:gname:dname[I]
gname = name of grid defined by compute or fix
dname = name of data field defined by compute or fix
c_ID = per-grid vector calculated by a compute with ID
c_ID[I] = Ith column of per-grid array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-grid vector calculated by a fix with ID
f_ID[I] = Ith column of per-grid array calculated by a fix with ID, I can include wildcard (see below)
Examples
""""""""
@ -176,24 +192,32 @@ Examples
Description
"""""""""""
Dump a snapshot of atom quantities to one or more files once every
:math:`N` timesteps in one of several styles. The *image* and *movie*
styles are the exception: the *image* style renders a JPG, PNG, or PPM
image file of the atom configuration every :math:`N` timesteps while
the *movie* style combines and compresses them into a movie file; both
are discussed in detail on the :doc:`dump image <dump_image>` page.
The timesteps on which dump output is written can also be controlled
by a variable. See the :doc:`dump_modify every <dump_modify>`
command.
Dump a snapshot of quantities to one or more files once every
:math:`N` timesteps in one of several styles. The timesteps on which
dump output is written can also be controlled by a variable. See the
:doc:`dump_modify every <dump_modify>` command.
Almost all the styles output per-atom data, i.e. one or more values
per atom. The exceptions are as follows. The *local* styles output
one or more values per bond (angle, dihedral, improper) or per pair of
interacting atoms (force or neighbor interactions). The *grid* styles
output one or more values per grid cell, which are produced by other
commands which overlay the simulation domain with a regular grid. See
the :doc:`Howto grid <Howto_grid>` doc page for details. The *image*
style renders a JPG, PNG, or PPM image file of the system for each
snapshot, while the *movie* style combines and compresses the series
of images into a movie file; both styles are discussed in detail on
the :doc:`dump image <dump_image>` page.
Only information for atoms in the specified group is dumped. The
:doc:`dump_modify thresh and region and refresh <dump_modify>` commands
can also alter what atoms are included. Not all styles support
these options; see details on the :doc:`dump_modify <dump_modify>` doc page.
:doc:`dump_modify thresh and region and refresh <dump_modify>`
commands can also alter what atoms are included. Not all styles
support these options; see details on the :doc:`dump_modify
<dump_modify>` doc page.
As described below, the filename determines the kind of output (text
or binary or gzipped, one big file or one per timestep, one big file
or multiple smaller files).
As described below, the filename determines the kind of output: text
or binary or gzipped, one big file or one per timestep, one file for
all the processors or multiple smaller files.
.. note::
@ -207,74 +231,54 @@ or multiple smaller files).
.. note::
Unless the :doc:`dump_modify sort <dump_modify>` option is
invoked, the lines of atom information written to dump files
(typically one line per atom) will be in an indeterminate order for
each snapshot. This is even true when running on a single processor,
if the :doc:`atom_modify sort <atom_modify>` option is on, which it is
by default. In this case atoms are re-ordered periodically during a
simulation, due to spatial sorting. It is also true when running in
parallel, because data for a single snapshot is collected from
multiple processors, each of which owns a subset of the atoms.
Unless the :doc:`dump_modify sort <dump_modify>` option is invoked,
the lines of atom or grid information written to dump files
(typically one line per atom or grid cell) will be in an
indeterminate order for each snapshot. This is even true when
running on a single processor, if the :doc:`atom_modify sort
<atom_modify>` option is on, which it is by default. In this case
atoms are re-ordered periodically during a simulation, due to
spatial sorting. It is also true when running in parallel, because
data for a single snapshot is collected from multiple processors,
each of which owns a subset of the atoms.
For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by
default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting
by atom ID is on by default. See the :doc:`dump_modify <dump_modify>`
page for details.
For the *atom*, *custom*, *cfg*, *grid*, and *local* styles, sorting
is off by default. For the *dcd*, *grid/vtk*, *xtc*, *xyz*, and
*molfile* styles, sorting by atom ID or grid ID is on by default. See
the :doc:`dump_modify <dump_modify>` page for details.
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
are identical in command syntax to the corresponding styles without
"gz", however, they generate compressed files using the zlib
library. Thus the filename suffix ".gz" is mandatory. This is an
alternative approach to writing compressed files via a pipe, as done by
the regular dump styles, which may be required on clusters where the
interface to the high-speed network disallows using the fork() library
call (which is needed for a pipe). For the remainder of this page, you
should thus consider the *atom* and *atom/gz* styles (etc.) to be
inter-changeable, with the exception of the required filename suffix.
The *style* keyword determines what kind of data is written to the
dump file(s) and in what format.
Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*, and
*xyz/zstd* styles are identical to the gz styles, but use the Zstd
compression library instead and require the ".zst" suffix. See the
:doc:`dump_modify <dump_modify>` page for details on how to control the
compression level in both variants.
Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files
can be read directly by `VMD <https://www.ks.uiuc.edu/Research/vmd>`_,
a popular tool for viewing molecular system.
As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and
*xyz/mpiio* styles are identical in command syntax and in the format of
the dump files they create, to the corresponding styles without "mpiio",
except the single dump file they produce is written in parallel via the
MPI-IO library. For the remainder of this page, you should thus
consider the *atom* and *atom/mpiio* styles (etc.) to be
inter-changeable. The one exception is how the filename is specified
for the MPI-IO styles, as explained below.
Likewise the `OVITO visualization tool <https://www.ovito.org>`_,
popular for materials modeling, can read the *atom*, *custom*, and
*grid* style dump files.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
The precision of values output to text-based dump files can be
controlled by the :doc:`dump_modify format <dump_modify>` command and
its options.
Note that settings made via the :doc:`dump_modify <dump_modify>`
command can also alter the format of individual values and content of
the dump file itself. This includes the precision of values output to
text-based dump files which is controlled by the :doc:`dump_modify
format <dump_modify>` command and its options.
----------
The *style* keyword determines what atom quantities are written to the
file and in what format. Settings made via the
:doc:`dump_modify <dump_modify>` command can also alter the format of
individual values and the file itself.
Format of native LAMMPS format dump files:
The *atom*, *local*, and *custom* styles create files in a simple text
format that is self-explanatory when viewing a dump file. Some of the
LAMMPS post-processing tools described on the :doc:`Tools <Tools>` doc
page, including `Pizza.py <https://lammps.github.io/pizza>`_,
work with this format, as does the :doc:`rerun <rerun>` command.
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
: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 post-processing purposes the *atom*, *local*, and *custom* text
files are self-describing in the following sense.
The dimensions of the simulation box are included in each snapshot.
For an orthogonal simulation box this information is formatted as:
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:
.. parsed-literal::
@ -316,10 +320,13 @@ 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.
The "ITEM: ATOMS" line in each snapshot lists column descriptors for
the per-atom lines that follow. For example, the descriptors would be
"id type xs ys zs" for the default *atom* style, and would be the atom
attributes you specify in the dump command for the *custom* style.
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
lines that follow. For example, the descriptors would be "id type xs
ys zs" for the default *atom* style, and would be the atom attributes
you specify in the dump command for the *custom* style. Each
subsequent line will list the data for a single atom.
For style *atom*, atom coordinates are written to the file, along with
the atom ID and atom type. By default, atom coords are written in a
@ -332,12 +339,31 @@ added for each atom via dump_modify.
Style *custom* allows you to specify a list of atom attributes to be
written to the dump file for each atom. Possible attributes are
listed above and will appear in the order specified. You cannot
specify a quantity that is not defined for a particular simulation---such as
*q* for atom style *bond*, since that atom style does not
assign charges. Dumps occur at the very end of a timestep, so atom
attributes will include effects due to fixes that are applied during
the timestep. An explanation of the possible dump custom attributes
is given below.
specify a quantity that is not defined for a particular
simulation---such as *q* for atom style *bond*, since that atom style
does not assign charges. Dumps occur at the very end of a timestep,
so atom attributes will include effects due to fixes that are applied
during the timestep. An explanation of the possible dump custom
attributes is given below.
.. versionadded:: 22Dec2022
For style *grid* the extent of the Nx by Ny by Nz grid that overlays
the simulation domain is output with each snapshot:
.. parsed-literal::
ITEM: GRID EXTENT
nx ny nz
For 2d simulations, nz will be 1. There will also be an "ITEM: GRID
DATA" line which includes column descriptors for the per grid cell
data. Each subsequent line (Nx * Ny * Nz lines) will list the data
for a single grid cell. If grid cell IDs are included in the output
via the :doc:`compute property/grid <compute_property_grid>` command,
then the IDs will range from 1 to N = Nx*Ny*Nz. The ordering of IDs
is with the x index varying fastest, then the y index, and the z index
varying slowest.
For style *local*, local output generated by :doc:`computes <compute>`
and :doc:`fixes <fix>` is used to generate lines of output that is
@ -351,6 +377,17 @@ generate information on bonds, angles, etc. that can be cut and pasted
directly into a data file read by the :doc:`read_data <read_data>`
command.
----------
Dump files in other popular formats:
.. note::
This section only discusses file formats relevant to this doc page.
The top of this page has links to other dump commands (with their
own pages) which write files in additional popular formats.
Style *cfg* has the same command syntax as style *custom* and writes
extended CFG format files, as used by the `AtomEye
<http://li.mit.edu/Archive/Graphics/A/>`_ visualization package.
@ -387,15 +424,15 @@ periodic box. Note that these coordinates may thus be far outside
the box size stored with the snapshot.
The *xtc* style writes XTC files, a compressed trajectory format used
by the GROMACS molecular dynamics package, and described
`here <https://manual.gromacs.org/current/reference-manual/file-formats.html#xtc>`_.
by the GROMACS molecular dynamics package, and described `here
<https://manual.gromacs.org/current/reference-manual/file-formats.html#xtc>`_.
The precision used in XTC files can be adjusted via the
:doc:`dump_modify <dump_modify>` command. The default value of 1000
means that coordinates are stored to 1/1000 nanometer accuracy. XTC
files are portable binary files written in the NFS XDR data format,
so that any machine which supports XDR should be able to read them.
The number of atoms per snapshot cannot change with the *xtc* style.
The *unwrap* option of the :doc:`dump_modify <dump_modify>` command allows
files are portable binary files written in the NFS XDR data format, so
that any machine which supports XDR should be able to read them. The
number of atoms per snapshot cannot change with the *xtc* style. The
*unwrap* option of the :doc:`dump_modify <dump_modify>` command allows
XTC coordinates to be written "unwrapped" by the image flags for each
atom. Unwrapped means that if the atom has passed through a periodic
boundary one or more times, the value is printed for what the
@ -404,27 +441,41 @@ box. Note that these coordinates may thus be far outside the box size
stored with the snapshot.
The *xyz* style writes XYZ files, which is a simple text-based
coordinate format that many codes can read. Specifically it has
a line with the number of atoms, then a comment line that is
usually ignored followed by one line per atom with the atom type
and the :math:`x`-, :math:`y`-, and :math:`z`-coordinate of that atom.
You can use the :doc:`dump_modify element <dump_modify>` option to change the
output from using the (numerical) atom type to an element name (or some other
label). This will help many visualization programs to guess bonds and colors.
coordinate format that many codes can read. Specifically it has a line
with the number of atoms, then a comment line that is usually ignored
followed by one line per atom with the atom type and the :math:`x`-,
:math:`y`-, and :math:`z`-coordinate of that atom. You can use the
:doc:`dump_modify element <dump_modify>` option to change the output
from using the (numerical) atom type to an element name (or some other
label). This will help many visualization programs to guess bonds and
colors.
.. versionadded:: 22Dec2022
The *grid/vtk* style writes VTK files for grid data on a regular
rectilinear grid. Its content is conceptually similar to that of the
text file produced by the *grid* style, except that it in an XML-based
format which visualization programs which support the VTK format can
read, e.g. the `ParaView tool <https://www.paraview.org>`_. For this
style, there can only be 1 or 3 per grid cell attributes specified.
If it is a single value, it is a scalar quantity. If 3 values are
specified it is encoded in the VTK file as a vector quantity (for each
grid cell). The filename for this style must include a "\*" wildcard
character to produce one file per snapshot; see details below.
.. versionadded:: 4May2022
Dump style *yaml* has the same command syntax as style *custom* and
writes YAML format files that can be easily parsed by a variety of data
processing tools and programming languages. Each timestep will be
written as a YAML "document" (i.e., starts with "---" and ends with
writes YAML format files that can be easily parsed by a variety of
data processing tools and programming languages. Each timestep will
be written as a YAML "document" (i.e., starts with "---" and ends with
"..."). The style supports writing one file per timestep through the
"\*" wildcard but not multi-processor outputs with the "%" token in the
filename. In addition to per-atom data, :doc:`thermo <thermo>` data can
be included in the *yaml* style dump file using the :doc:`dump_modify
thermo yes <dump_modify>`. The data included in the dump file uses the
"thermo" tag and is otherwise identical to data specified by the
:doc:`thermo_style <thermo_style>` command.
"\*" wildcard but not multi-processor outputs with the "%" token in
the filename. In addition to per-atom data, :doc:`thermo <thermo>`
data can be included in the *yaml* style dump file using the
:doc:`dump_modify thermo yes <dump_modify>`. The data included in the
dump file uses the "thermo" tag and is otherwise identical to data
specified by the :doc:`thermo_style <thermo_style>` command.
Below is an example for a YAML format dump created by the following commands.
@ -435,13 +486,13 @@ Below is an example for a YAML format dump created by the following commands.
The tags "time", "units", and "thermo" are optional and enabled by the
dump_modify command. The list under the "box" tag has three lines for
orthogonal boxes and four lines for triclinic boxes, where the first three are
the box boundaries and the fourth the three tilt factors (:math:`xy`,
:math:`xz`, :math:`yz`). The "thermo" data follows the format of the *yaml*
thermo style. The "keywords" tag lists the per-atom properties contained in
the "data" columns, which contain a list with one line per atom. The keywords
may be renamed using the dump_modify command same as for the *custom* dump
style.
orthogonal boxes and four lines for triclinic boxes, where the first
three are the box boundaries and the fourth the three tilt factors
(:math:`xy`, :math:`xz`, :math:`yz`). The "thermo" data follows the
format of the *yaml* thermo style. The "keywords" tag lists the
per-atom properties contained in the "data" columns, which contain a
list with one line per atom. The keywords may be renamed using the
dump_modify command same as for the *custom* dump style.
.. code-block:: yaml
@ -479,11 +530,7 @@ style.
----------
Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files
can be read directly by `VMD <https://www.ks.uiuc.edu/Research/vmd>`_, a
popular molecular viewing program.
----------
Frequency of dump output:
Dumps are performed on timesteps that are a multiple of :math:`N`
(including timestep 0) and on the last timestep of a minimization if
@ -508,29 +555,35 @@ every/time <dump_modify>` command can be used. This can be useful
when the timestep size varies during a simulation run, e.g. by use of
the :doc:`fix dt/reset <fix_dt_reset>` command.
The specified filename determines how the dump file(s) is written.
The default is to write one large text file, which is opened when the
dump command is invoked and closed when an :doc:`undump <undump>`
command is used or when LAMMPS exits. For the *dcd* and *xtc* styles,
this is a single large binary file.
----------
Dump filenames can contain two wildcard characters. If a "\*"
character appears in the filename, then one file per snapshot is
written and the "\*" character is replaced with the timestep value.
For example, tmp.dump.\* becomes tmp.dump.0, tmp.dump.10000,
tmp.dump.20000, etc. This option is not available for the *dcd* and
*xtc* styles. Note that the :doc:`dump_modify pad <dump_modify>`
command can be used to insure all timestep numbers are the same length
(e.g., 00010), which can make it easier to read a series of dump files
in order with some post-processing tools.
Dump filenames:
The specified dump filename determines how the dump file(s) is
written. The default is to write one large text file, which is opened
when the dump command is invoked and closed when an :doc:`undump
<undump>` command is used or when LAMMPS exits. For the *dcd* and
*xtc* styles, this is a single large binary file.
Many of the styles allow dump filenames to contain either or both of
two wildcard characters. If a "\*" character appears in the filename,
then one file per snapshot is written and the "\*" character is
replaced with the timestep value. For example, tmp.dump.\* becomes
tmp.dump.0, tmp.dump.10000, tmp.dump.20000, etc. This option is not
available for the *dcd* and *xtc* styles. Note that the
:doc:`dump_modify pad <dump_modify>` command can be used to insure all
timestep numbers are the same length (e.g., 00010), which can make it
easier to read a series of dump files in order with some
post-processing tools.
If a "%" character appears in the filename, then each of P processors
writes a portion of the dump file, and the "%" character is replaced
with the processor ID from :math:`0` to :math:`P-1`. For example, tmp.dump.%
becomes tmp.dump.0, tmp.dump.1, ... tmp.dump.:math:`P-1`, etc. This creates
smaller files and can be a fast mode of output on parallel machines that
support parallel I/O for output. This option is **not** available for the
*dcd*, *xtc*, *xyz*, and *yaml* styles.
with the processor ID from :math:`0` to :math:`P-1`. For example,
tmp.dump.% becomes tmp.dump.0, tmp.dump.1, ... tmp.dump.:math:`P-1`,
etc. This creates smaller files and can be a fast mode of output on
parallel machines that support parallel I/O for output. This option is
**not** available for the *dcd*, *xtc*, *xyz*, *grid/vtk*, and *yaml*
styles.
By default, :math:`P` is the the number of processors, meaning one file per
processor, but :math:`P` can be set to a smaller value via the *nfile* or
@ -541,47 +594,41 @@ when running on large numbers of processors.
Note that using the "\*" and "%" characters together can produce a
large number of small dump files!
For the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio*
styles, a single dump file is written in parallel via the MPI-IO
library, which is part of the MPI standard for versions 2.0 and above.
Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
package installed, viz.,
.. code-block:: bash
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform
Second, use a dump filename which contains ".mpiio". Note that it does
not have to end in ".mpiio", just contain those characters. Unlike
MPI-IO restart files, which must be both written and read using MPI-IO,
the dump files produced by these MPI-IO styles are identical in format
to the files produced by their non-MPI-IO style counterparts. This
means you can write a dump file using MPI-IO and use the :doc:`read_dump
For styles that end with *mpiio* an ".mpiio" must appear somewhere in
the specified filename. These styles write their dump file in
parallel via the MPI-IO library, which is part of the MPI standard for
versions 2.0 and above. Note these styles are identical in command
syntax to the corresponding styles without "mpiio". Likewise, the
dump files produced by these MPI-IO styles are identical in format to
the files produced by their non-MPI-IO style counterparts. This means
you can write a dump file using MPI-IO and use the :doc:`read_dump
<read_dump>` command or perform other post-processing, just as if the
dump file was not written using MPI-IO.
Because MPI-IO dump files are one large file which all processors
write to, you cannot use the "%" wildcard character described above in
the filename. However you can use the ".bin" or ".lammpsbin" suffix
described below. Again, this file will be written in parallel and
have the same binary format as if it were written without MPI-IO.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
The MPIIO package within LAMMPS is currently unmaintained and has
become unreliable. Use with caution.
Note that MPI-IO dump files are one large file which all processors
write to. You thus cannot use the "%" wildcard character described
above in the filename since that specifies generation of multiple files.
You can use the ".bin" or ".lammpsbin" suffix described below in an
MPI-IO dump file; again this file will be written in parallel and have
the same binary format as if it were written without MPI-IO.
----------
If the filename ends with ".bin" or ".lammpsbin", the dump file (or
files, if "\*" or "%" is also used) is written in binary format. A
binary dump file will be about the same size as a text version, but will
typically write out much faster. Of course, when post-processing, you
will need to convert it back to text format (see the :ref:`binary2txt
tool <binary>`) or write your own code to read the binary file. The
format of the binary file can be understood by looking at the
:file:`tools/binary2txt.cpp` file. This option is only available for
the *atom* and *custom* styles.
Compression of dump file data:
If the specified filename ends with ".bin" or ".lammpsbin", the dump
file (or files, if "\*" or "%" is also used) is written in binary
format. A binary dump file will be about the same size as a text
version, but will typically write out much faster. Of course, when
post-processing, you will need to convert it back to text format (see
the :ref:`binary2txt tool <binary>`) or write your own code to read
the binary file. The format of the binary file can be understood by
looking at the :file:`tools/binary2txt.cpp` file. This option is only
available for the *atom* and *custom* styles.
If the filename ends with ".gz", the dump file (or files, if "\*" or "%"
is also used) is written in gzipped format. A gzipped dump file will be
@ -589,19 +636,40 @@ about :math:`3\times` smaller than the text version, but will also take
longer to write. This option is not available for the *dcd* and *xtc*
styles.
Note that styles that end with *gz* are identical in command syntax to
the corresponding styles without "gz", however, they generate
compressed files using the zlib library. Thus the filename suffix
".gz" is mandatory. This is an alternative approach to writing
compressed files via a pipe, as done by the regular dump styles, which
may be required on clusters where the interface to the high-speed
network disallows using the fork() library call (which is needed for a
pipe). For the remainder of this page, you should thus consider the
*atom* and *atom/gz* styles (etc.) to be inter-changeable, with the
exception of the required filename suffix.
Similarly, styles that end with *zstd* are identical to the gz styles,
but use the Zstd compression library instead and require a ".zst"
suffix. See the :doc:`dump_modify <dump_modify>` page for details on
how to control the compression level in both variants.
----------
Note that in the discussion which follows, for styles which can
reference values from a compute or fix or custom atom property, like the
*custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i`
can be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
"m\*n". If :math:`N` is the number of columns in the array, then an
asterisk with no numeric values means all column indices from 1 to
:math:`N`. A leading asterisk means all indices from 1 to n
(inclusive). A trailing asterisk means all indices from m to :math:`N`
(inclusive). A middle asterisk means all indices from m to n
(inclusive).
Arguments for different styles:
The sections below describe per-atom, local, and per grid cell
attributes which can be used as arguments to the various styles.
Note that in the discussion below, for styles which can reference
values from a compute or fix or custom atom property, like the
*custom*\ , *cfg*\ , *grid* or *local* styles, the bracketed index
:math:`i` can be specified using a wildcard asterisk with the index to
effectively specify multiple values. This takes the form "\*" or
"\*n" or "m\*" or "m\*n". If :math:`N` is the number of columns in
the array, then an asterisk with no numeric values means all column
indices from 1 to :math:`N`. A leading asterisk means all indices
from 1 to n (inclusive). A trailing asterisk means all indices from m
to :math:`N` (inclusive). A middle asterisk means all indices from m
to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. For example, these two dump commands are
@ -617,63 +685,7 @@ command creates a per-atom array with six columns:
----------
This section explains the local attributes that can be specified as
part of the *local* style.
The *index* attribute can be used to generate an index number from 1
to :math:`N` for each line written into the dump file, where :math:`N` is the
total number of local datums from all processors, or lines of output that
will appear in the snapshot. Note that because data from different
processors depend on what atoms they currently own, and atoms migrate
between processor, there is no guarantee that the same index will be
used for the same info (e.g., a particular bond) in successive snapshots.
The *c_ID* and *c_ID[I]* attributes allow local vectors or arrays
calculated by a :doc:`compute <compute>` to be output. The ID in the
attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script. See the
:doc:`compute <compute>` command for details. There are computes for
calculating local information such as indices, types, and energies for
bonds and angles.
Note that computes which calculate global or per-atom quantities, as
opposed to local quantities, cannot be output in a dump local command.
Instead, global quantities can be output by the :doc:`thermo_style
custom <thermo_style>` command, and per-atom quantities can be output
by the dump custom command.
If *c_ID* is used as a attribute, then the local vector calculated by
the compute is printed. If *c_ID[i]* is used, then :math:`i` must be in the
range from :math:`1-M`, which will print the Ith column of the local array
with :math:`M` columns calculated by the compute. See the discussion above
for how :math:`i` can be specified with a wildcard asterisk to effectively
specify multiple values.
The *f_ID* and *f_ID[I]* attributes allow local vectors or arrays
calculated by a :doc:`fix <fix>` to be output. The ID in the attribute
should be replaced by the actual ID of the fix that has been defined
previously in the input script.
If *f_ID* is used as a attribute, then the local vector calculated by
the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the
range :math:`1`--:math:`M`, which will print the :math:`i`\ th column of the
local with :math:`M` columns calculated by the fix. See the discussion above
for how :math:`i` can be specified with a wildcard asterisk to effectively
specify multiple values.
Here is an example of how to dump bond info for a system, including
the distance and energy of each bond:
.. code-block:: LAMMPS
compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local dist eng
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
----------
This section explains the atom attributes that can be specified as
part of the *custom* and *cfg* styles.
Per-atom attributes used as arguments to the *custom* and *cfg* styles:
The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*,
*vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory.
@ -808,6 +820,97 @@ which could then be output into dump files.
----------
Attributes used as arguments to the *local* style:
The *index* attribute can be used to generate an index number from 1
to N for each line written into the dump file, where N is the total
number of local datums from all processors, or lines of output that
will appear in the snapshot. Note that because data from different
processors depend on what atoms they currently own, and atoms migrate
between processor, there is no guarantee that the same index will be
used for the same info (e.g. a particular bond) in successive
snapshots.
The *c_ID* and *c_ID[I]* attributes allow local vectors or arrays
calculated by a :doc:`compute <compute>` to be output. The ID in the
attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script. See the
:doc:`compute <compute>` command for details. There are computes for
calculating local information such as indices, types, and energies for
bonds and angles.
Note that computes which calculate global or per-atom quantities, as
opposed to local quantities, cannot be output in a dump local command.
Instead, global quantities can be output by the :doc:`thermo_style
custom <thermo_style>` command, and per-atom quantities can be output
by the dump custom command.
If *c_ID* is used as a attribute, then the local vector calculated by
the compute is printed. If *c_ID[I]* is used, then I must be in the
range from 1-M, which will print the Ith column of the local array
with M columns calculated by the compute. See the discussion above
for how I can be specified with a wildcard asterisk to effectively
specify multiple values.
The *f_ID* and *f_ID[I]* attributes allow local vectors or arrays
calculated by a :doc:`fix <fix>` to be output. The ID in the attribute
should be replaced by the actual ID of the fix that has been defined
previously in the input script.
If *f_ID* is used as a attribute, then the local vector calculated by
the fix is printed. If *f_ID[I]* is used, then I must be in the
range from 1-M, which will print the Ith column of the local with M
columns calculated by the fix. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.
Here is an example of how to dump bond info for a system, including
the distance and energy of each bond:
.. code-block:: LAMMPS
compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local dist eng
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
----------
Attributes used as arguments to the *grid* and *grid/vtk* styles:
The attributes that begin with *c_ID* and *f_ID* both take
colon-separated fields *gname* and *dname*. These refer to a grid
name and data field name which is defined by the compute or fix. Note
that a compute or fix can define one or more grids (of different
sizes) and one or more data fields for each of those grids. The sizes
of all grids output in a single dump grid command must be the same.
The *c_ID:gname:dname* and *c_ID:gname:dname[I]* attributes allow
per-grid vectors or arrays calculated by a :doc:`compute <compute>` to
be output. The ID in the attribute should be replaced by the actual
ID of the compute that has been defined previously in the input
script.
If *c_ID:gname:dname* is used as a attribute, then the per-grid vector
calculated by the compute is printed. If *c_ID:gname:dname[I]* is
used, then I must be in the range from 1-M, which will print the Ith
column of the per-grid array with M columns calculated by the compute.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
The *f_ID:gname:dname* and *f_ID:gname:dname[I]* attributes allow
per-grid vectors or arrays calculated by a :doc:`fix <fix>` to be
output. The ID in the attribute should be replaced by the actual ID
of the fix that has been defined previously in the input script.
If *f_ID:gname:dname* is used as a attribute, then the per-grid vector
calculated by the fix is printed. If *f_ID:gname:dname[I]* is used,
then I must be in the range from 1-M, which will print the Ith column
of the per-grid with M columns calculated by the fix. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
----------
Restrictions
""""""""""""
@ -816,9 +919,9 @@ To write gzipped dump files, you must either compile LAMMPS with the
See the :doc:`Build settings <Build_settings>` page for details.
While a dump command is active (i.e., has not been stopped by using
the :doc:`undump command <undump>`), no commands may be used that will change
the timestep (e.g., :doc:`reset_timestep <reset_timestep>`). LAMMPS
will terminate with an error otherwise.
the :doc:`undump command <undump>`), no commands may be used that will
change the timestep (e.g., :doc:`reset_timestep <reset_timestep>`).
LAMMPS will terminate with an error otherwise.
The *atom/gz*, *cfg/gz*, *custom/gz*, and *xyz/gz* styles are part of
the COMPRESS package. They are only enabled if LAMMPS was built with

47
doc/src/dump_image.rst
View File

@ -24,7 +24,7 @@ Syntax
* color = atom attribute that determines color of each atom
* diameter = atom attribute that determines size of each atom
* zero or more keyword/value pairs may be appended
* keyword = *atom* or *adiam* or *bond* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *box* or *axes* or *subbox* or *shiny* or *ssao*
* keyword = *atom* or *adiam* or *bond* or *grid* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *box* or *axes* or *subbox* or *shiny* or *ssao*
.. parsed-literal::
@ -34,6 +34,14 @@ Syntax
color = *atom* or *type* or *none*
width = number or *atom* or *type* or *none*
number = numeric value for bond width (distance units)
*grid* = per-grid value to use when coloring each grid cell
per-grid value = c_ID:gname:dname, c_ID:gname:dname[I], f_ID:gname:dname, f_ID:gname:dname[I]
gname = name of grid defined by compute or fix
dname = name of data field defined by compute or fix
c_ID = per-grid vector calculated by a compute with ID
c_ID[I] = Ith column of per-grid array calculated by a compute with ID
f_ID = per-grid vector calculated by a fix with ID
f_ID[I] = Ith column of per-grid array calculated by a fix with ID
*line* = color width
color = *type*
width = numeric value for line width (distance units)
@ -69,7 +77,7 @@ Syntax
yes/no = do or do not draw simulation box lines
diam = diameter of box lines as fraction of shortest box length
*axes* values = axes length diam = draw xyz axes
axes = *yes* or *no = do or do not draw xyz axes lines next to simulation box
axes = *yes* or *no* = do or do not draw xyz axes lines next to simulation box
length = length of axes lines as fraction of respective box lengths
diam = diameter of axes lines as fraction of shortest box length
*subbox* values = lines diam = draw outline of processor sub-domains
@ -95,7 +103,7 @@ Syntax
dump_modify dump-ID keyword values ...
* these keywords apply only to the *image* and *movie* styles and are documented on this page
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
* keyword = *acolor* or *adiam* or *amap* or *gmap* or *backcolor* or *bcolor* or *bdiam* or *bitrate* or *boxcolor* or *color* or *framerate* or *gmap*
* see the :doc:`dump modify <dump_modify>` doc page for more general keywords
.. parsed-literal::
@ -134,15 +142,16 @@ Syntax
*bdiam* args = type diam
type = bond type or range of types (see below)
diam = diameter of bonds of that type (distance units)
*bitrate* arg = rate
rate = target bitrate for movie in kbps
*boxcolor* arg = color
color = name of color for simulation box lines and processor sub-domain lines
*color* args = name R G B
name = name of color
R,G,B = red/green/blue numeric values from 0.0 to 1.0
*bitrate* arg = rate
rate = target bitrate for movie in kbps
*framerate* arg = fps
fps = frames per second for movie
*gmap* args = identical to *amap* args
Examples
""""""""
@ -214,7 +223,7 @@ Similarly, the format of the resulting movie is chosen with the
and thus details have to be looked up in the `FFmpeg documentation
<https://ffmpeg.org/ffmpeg.html>`_. Typical examples are: .avi, .mpg,
.m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie
compression like bitrate and framerate can be set using the
compression like *bitrate* and *framerate* can be set using the
dump_modify command as described below.
To write out JPEG and PNG format files, you must build LAMMPS with
@ -300,13 +309,13 @@ settings, they are interpreted in the following way.
If "vx", for example, is used as the *color* setting, then the color
of the atom will depend on the x-component of its velocity. The
association of a per-atom value with a specific color is determined by
a "color map", which can be specified via the dump_modify command, as
described below. The basic idea is that the atom-attribute will be
within a range of values, and every value within the range is mapped
to a specific color. Depending on how the color map is defined, that
mapping can take place via interpolation so that a value of -3.2 is
halfway between "red" and "blue", or discretely so that the value of
-3.2 is "orange".
a "color map", which can be specified via the dump_modify amap
command, as described below. The basic idea is that the
atom-attribute will be within a range of values, and every value
within the range is mapped to a specific color. Depending on how the
color map is defined, that mapping can take place via interpolation so
that a value of -3.2 is halfway between "red" and "blue", or
discretely so that the value of -3.2 is "orange".
If "vx", for example, is used as the *diameter* setting, then the atom
will be rendered using the x-component of its velocity as the
@ -948,6 +957,17 @@ frequently.
----------
The *gmap* keyword can be used with the dump image command, with its
*grid* keyword, to setup a color map. The color map is used to assign
a specific RGB (red/green/blue) color value to an individual grid cell
when it is drawn, based on the grid cell value, which is a numeric
quantity specified with the *grid* keyword.
The arguments for the *gmap* keyword are identical to those for the
*amap* keyword (for atom coloring) described above.
----------
Restrictions
""""""""""""
@ -1031,6 +1051,7 @@ The defaults for the dump_modify keywords specific to dump image and dump movie
* boxcolor = yellow
* color = 140 color names are pre-defined as listed below
* framerate = 24
* gmap = min max cf 0.0 2 min blue max red
----------

4
doc/src/dump_vtk.rst
View File

@ -90,8 +90,8 @@ hexahedrons in either legacy .vtk or .vtu XML format.
Style *vtk* allows you to specify a list of atom attributes to be
written to the dump file for each atom. The list of possible attributes
is the same as for the :doc:`dump_style custom <dump>` command; see
its page for a listing and an explanation of each attribute.
is the same as for the :doc:`dump_style custom <dump>` command; see its
documentation page for a listing and an explanation of each attribute.
.. note::

745
doc/src/fitpod_command.rst Normal file
View File

@ -0,0 +1,745 @@
.. index:: fitpod
fitpod command
======================
Syntax
""""""
.. parsed-literal::
fitpod Ta_param.pod Ta_data.pod
* fitpod = style name of this command
* Ta_param.pod = an input file that describes proper orthogonal descriptors (PODs)
* Ta_data.pod = an input file that specifies DFT data used to fit a POD potential
Examples
""""""""
.. code-block:: LAMMPS
fitpod Ta_param.pod Ta_data.pod
Description
"""""""""""
.. versionadded:: 22Dec2022
Fit a machine-learning interatomic potential (ML-IAP) based on proper
orthogonal descriptors (POD). Two input files are required for this
command. The first input file describes a POD potential parameter
settings, while the second input file specifies the DFT data used for
the fitting procedure.
The table below has one-line descriptions of all the keywords that can
be used in the first input file (i.e. ``Ta_param.pod`` in the example
above):
.. list-table::
:header-rows: 1
:widths: auto
* - Keyword
- Default
- Type
- Description
* - species
- (none)
- STRING
- Chemical symbols for all elements in the system and have to match XYZ training files.
* - pbc
- 1 1 1
- INT
- three integer constants specify boundary conditions
* - rin
- 1.0
- REAL
- a real number specifies the inner cut-off radius
* - rcut
- 5.0
- REAL
- a real number specifies the outer cut-off radius
* - bessel_polynomial_degree
- 3
- INT
- the maximum degree of Bessel polynomials
* - inverse_polynomial_degree
- 6
- INT
- the maximum degree of inverse radial basis functions
* - onebody
- 1
- BOOL
- turns on/off one-body potential
* - twobody_number_radial_basis_functions
- 6
- INT
- number of radial basis functions for two-body potential
* - threebody_number_radial_basis_functions
- 5
- INT
- number of radial basis functions for three-body potential
* - threebody_number_angular_basis_functions
- 5
- INT
- number of angular basis functions for three-body potential
* - fourbody_snap_twojmax
- 0
- INT
- band limit for SNAP bispectrum components (0,2,4,6,8... allowed)
* - fourbody_snap_chemflag
- 0
- BOOL
- turns on/off the explicit multi-element variant of the SNAP bispectrum components
* - quadratic_pod_potential
- 0
- BOOL
- turns on/off quadratic POD potential
All keywords except *species* have default values. If a keyword is not
set in the input file, its default value is used. The next table
describes all keywords that can be used in the second input file
(i.e. ``Ta_data.pod`` in the example above):
.. list-table::
:header-rows: 1
:widths: auto
* - Keyword
- Default
- Type
- Description
* - file_format
- extxyz
- STRING
- only the extended xyz format (extxyz) is currently supported
* - file_extension
- xyz
- STRING
- extension of the data files
* - path_to_training_data_set
- (none)
- STRING
- specifies the path to training data files in double quotes
* - path_to_test_data_set
- ""
- STRING
- specifies the path to test data files in double quotes
* - fraction_training_data_set
- 1.0
- REAL
- a real number (<= 1.0) specifies the fraction of the training set used to fit POD
* - randomize_training_data_set
- 0
- BOOL
- turns on/off randomization of the training set
* - fitting_weight_energy
- 100.0
- REAL
- a real constant specifies the weight for energy in the least-squares fit
* - fitting_weight_force
- 1.0
- REAL
- a real constant specifies the weight for force in the least-squares fit
* - fitting_regularization_parameter
- 1.0e-10
- REAL
- a real constant specifies the regularization parameter in the least-squares fit
* - error_analysis_for_training_data_set
- 0
- BOOL
- turns on/off error analysis for the training data set
* - error_analysis_for_test_data_set
- 0
- BOOL
- turns on/off error analysis for the test data set
* - basename_for_output_files
- pod
- STRING
- a basename string added to the output files
* - precision_for_pod_coefficients
- 8
- INT
- number of digits after the decimal points for numbers in the coefficient file
All keywords except *path_to_training_data_set* have default values. If
a keyword is not set in the input file, its default value is used. After
successful training, a number of output files are produced, if enabled:
* ``<basename>_training_errors.pod`` reports the errors in energy and forces for the training data set
* ``<basename>_training_analysis.pod`` reports detailed errors for all training configurations
* ``<basename>_test_errors.pod`` reports errors for the test data set
* ``<basename>_test_analysis.pod`` reports detailed errors for all test configurations
* ``<basename>_coefficients.pod`` contains the coefficients of the POD potential
After training the POD potential, ``Ta_param.pod`` and ``<basename>_coefficients.pod``
are the two files needed to use the POD potential in LAMMPS. See
:doc:`pair_style pod <pair_pod>` for using the POD potential. Examples
about training and using POD potentials are found in the directory
lammps/examples/PACKAGES/pod.
Parameterized Potential Energy Surface
""""""""""""""""""""""""""""""""""""""
We consider a multi-element system of *N* atoms with :math:`N_{\rm e}`
unique elements. We denote by :math:`\boldsymbol r_n` and :math:`Z_n`
position vector and type of an atom *n* in the system,
respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e}
\}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots,
\boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1,
Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The potential energy surface
(PES) of the system can be expressed as a many-body expansion of the
form
.. math::
E(\boldsymbol R, \boldsymbol Z, \boldsymbol{\eta}, \boldsymbol{\mu}) \ = \ & \sum_{i} V^{(1)}(\boldsymbol r_i, Z_i, \boldsymbol \mu^{(1)} ) + \frac12 \sum_{i,j} V^{(2)}(\boldsymbol r_i, \boldsymbol r_j, Z_i, Z_j, \boldsymbol \eta, \boldsymbol \mu^{(2)}) \\
& + \frac16 \sum_{i,j,k} V^{(3)}(\boldsymbol r_i, \boldsymbol r_j, \boldsymbol r_k, Z_i, Z_j, Z_k, \boldsymbol \eta, \boldsymbol \mu^{(3)}) + \ldots
where :math:`V^{(1)}` is the one-body potential often used for
representing external field or energy of isolated elements, and the
higher-body potentials :math:`V^{(2)}, V^{(3)}, \ldots` are symmetric,
uniquely defined, and zero if two or more indices take identical values.
The superscript on each potential denotes its body order. Each *q*-body
potential :math:`V^{(q)}` depends on :math:`\boldsymbol \mu^{(q)}` which
are sets of parameters to fit the PES. Note that :math:`\boldsymbol \mu`
is a collection of all potential parameters :math:`\boldsymbol
\mu^{(1)}`, :math:`\boldsymbol \mu^{(2)}`, :math:`\boldsymbol
\mu^{(3)}`, etc, and that :math:`\boldsymbol \eta` is a set of
hyper-parameters such as inner cut-off radius :math:`r_{\rm in}` and
outer cut-off radius :math:`r_{\rm cut}`.
Interatomic potentials rely on parameters to learn relationship between
atomic environments and interactions. Since interatomic potentials are
approximations by nature, their parameters need to be set to some
reference values or fitted against data by necessity. Typically,
potential fitting finds optimal parameters, :math:`\boldsymbol \mu^*`,
to minimize a certain loss function of the predicted quantities and
data. Since the fitted potential depends on the data set used to fit it,
different data sets will yield different optimal parameters and thus
different fitted potentials. When fitting the same functional form on
*Q* different data sets, we would obtain *Q* different optimized
potentials, :math:`E(\boldsymbol R,\boldsymbol Z, \boldsymbol \eta,
\boldsymbol \mu_q^*), 1 \le q \le Q`. Consequently, there exist many
different sets of optimized parameters for empirical interatomic
potentials.
Instead of optimizing the potential parameters, inspired by the reduced
basis method :ref:`(Grepl) <Grepl20072>` for parameterized partial
differential equations, we view the parameterized PES as a parametric
manifold of potential energies
.. math::
\mathcal{M} = \{E(\boldsymbol R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu) \ | \ \boldsymbol \mu \in \Omega^{\boldsymbol \mu} \}
where :math:`\Omega^{\boldsymbol \mu}` is a parameter domain in which
:math:`\boldsymbol \mu` resides. The parametric manifold
:math:`\mathcal{M}` contains potential energy surfaces for all values of
:math:`\boldsymbol \mu \in \Omega^{\boldsymbol \mu}`. Therefore, the
parametric manifold yields a much richer and more transferable atomic
representation than any particular individual PES :math:`E(\boldsymbol
R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu^*)`.
We propose specific forms of the parameterized potentials for one-body,
two-body, and three-body interactions. We apply the Karhunen-Loeve
expansion to snapshots of the parameterized potentials to obtain sets of
orthogonal basis functions. These basis functions are aggregated
according to the chemical elements of atoms, thus leading to
multi-element proper orthogonal descriptors.
Proper Orthogonal Descriptors
"""""""""""""""""""""""""""""
Proper orthogonal descriptors are finger prints characterizing the
radial and angular distribution of a system of atoms. The detailed
mathematical definition is given in the paper by Nguyen and Rohskopf
:ref:`(Nguyen) <Nguyen20222>`.
The descriptors for the one-body interaction are used to capture energy
of isolated elements and defined as follows
.. math::
D_{ip}^{(1)} = \left\{
\begin{array}{ll}
1, & \mbox{if } Z_i = p \\
0, & \mbox{if } Z_i \neq p
\end{array}
\right.
for :math:`1 \le i \le N, 1 \le p \le N_{\rm e}`. The number of one-body
descriptors per atom is equal to the number of elements. The one-body
descriptors are independent of atom positions, but dependent on atom
types. The one-body descriptors are active only when the keyword
*onebody* is set to 1.
We adopt the usual assumption that the direct interaction between two
atoms vanishes smoothly when their distance is greater than the outer
cutoff distance :math:`r_{\rm cut}`. Furthermore, we assume that two
atoms can not get closer than the inner cutoff distance :math:`r_{\rm
in}` due to the Pauli repulsion principle. Let :math:`r \in (r_{\rm in},
r_{\rm cut})`, we introduce the following parameterized radial functions
.. math::
\phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) = \frac{\sin (\alpha \pi x) }{r - r_{\rm in}}, \qquad \varphi(r, \gamma) = \frac{1}{r^\gamma} ,
where the scaled distance function :math:`x` is defined below to enrich the two-body manifold
.. math::
x(r, r_{\rm in}, r_{\rm cut}, \beta) = \frac{e^{-\beta(r - r_{\rm in})/(r_{\rm cut} - r_{\rm in})} - 1}{e^{-\beta} - 1} .
We introduce the following function as a convex combination of the two functions
.. math::
\psi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta, \gamma, \kappa) = \kappa \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) + (1- \kappa) \varphi(r, \gamma) .
We see that :math:`\psi` is a function of distance :math:`r`, cut-off
distances :math:`r_{\rm in}` and :math:`r_{\rm cut}`, and parameters
:math:`\alpha, \beta, \gamma, \kappa`. Together these parameters allow
the function :math:`\psi` to characterize a diverse spectrum of two-body
interactions within the cut-off interval :math:`(r_{\rm in}, r_{\rm
cut})`.
Next, we introduce the following parameterized potential
.. math::
W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}) = f_{\rm c}(r_{ij}, \boldsymbol \eta) \psi(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)})
where :math:`\eta_1 = r_{\rm in}, \eta_2 = r_{\rm cut}, \mu_1^{(2)} =
\alpha, \mu_2^{(2)} = \beta, \mu_3^{(2)} = \gamma`, and
:math:`\mu_4^{(2)} = \kappa`. Here the cut-off function :math:`f_{\rm
c}(r_{ij}, \boldsymbol \eta)` proposed in [refs] is used to ensure the
smooth vanishing of the potential and its derivative for :math:`r_{ij}
\ge r_{\rm cut}`:
.. math::
f_{\rm c}(r_{ij}, r_{\rm in}, r_{\rm cut}) = \exp \left(1 -\frac{1}{\sqrt{\left(1 - \frac{(r-r_{\rm in})^3}{(r_{\rm cut} - r_{\rm in})^3} \right)^2 + 10^{-6}}} \right)
Based on the parameterized potential, we form a set of snapshots as
follows. We assume that we are given :math:`N_{\rm s}` parameter tuples
:math:`\boldsymbol \mu^{(2)}_\ell, 1 \le \ell \le N_{\rm s}`. We
introduce the following set of snapshots on :math:`(r_{\rm in}, r_{\rm
cut})`:
.. math::
\xi_\ell(r_{ij}, \boldsymbol \eta) = W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}_\ell), \quad \ell = 1, \ldots, N_{\rm s} .
To ensure adequate sampling of the PES for different parameters, we
choose :math:`N_{\rm s}` parameter points :math:`\boldsymbol
\mu^{(2)}_\ell = (\alpha_\ell, \beta_\ell, \gamma_\ell, \kappa_\ell), 1
\le \ell \le N_{\rm s}` as follows. The parameters :math:`\alpha \in [1,
N_\alpha]` and :math:`\gamma \in [1, N_\gamma]` are integers, where
:math:`N_\alpha` and :math:`N_\gamma` are the highest degrees for
:math:`\alpha` and :math:`\gamma`, respectively. We next choose
:math:`N_\beta` different values of :math:`\beta` in the interval
:math:`[\beta_{\min}, \beta_{\max}]`, where :math:`\beta_{\min} = 0` and
:math:`\beta_{\max} = 4`. The parameter :math:`\kappa` can be set either
0 or 1. Hence, the total number of parameter points is :math:`N_{\rm s}
= N_\alpha N_\beta + N_\gamma`. Although :math:`N_\alpha, N_\beta,
N_\gamma` can be chosen conservatively large, we find that
:math:`N_\alpha = 6, N_\beta = 3, N_\gamma = 8` are adequate for most
problems. Note that :math:`N_\alpha` and :math:`N_\gamma` correspond to
*bessel_polynomial_degree* and *inverse_polynomial_degree*,
respectively.
We employ the Karhunen-Loeve (KL) expansion to generate an orthogonal
basis set which is known to be optimal for representation of the
snapshot family :math:`\{\xi_\ell\}_{\ell=1}^{N_{\rm s}}`. The two-body
orthogonal basis functions are computed as follows
.. math::
U^{(2)}_m(r_{ij}, \boldsymbol \eta) = \sum_{\ell = 1}^{N_{\rm s}} A_{\ell m}(\boldsymbol \eta) \, \xi_\ell(r_{ij}, \boldsymbol \eta), \qquad m = 1, \ldots, N_{\rm 2b} ,
where the matrix :math:`\boldsymbol A \in \mathbb{R}^{N_{\rm s} \times
N_{\rm s}}` consists of eigenvectors of the eigenvalue problem
.. math::
\boldsymbol C \boldsymbol a = \lambda \boldsymbol a
with the entries of :math:`\boldsymbol C \in \mathbb{R}^{N_{\rm s} \times N_{\rm s}}` being given by
.. math::
C_{ij} = \frac{1}{N_{\rm s}} \int_{r_{\rm in}}^{r_{\rm cut}} \xi_i(x, \boldsymbol \eta) \xi_j(x, \boldsymbol \eta) dx, \quad 1 \le i, j \le N_{\rm s}
Note that the eigenvalues :math:`\lambda_\ell, 1 \le \ell \le N_{\rm
s}`, are ordered such that :math:`\lambda_1 \ge \lambda_2 \ge \ldots \ge
\lambda_{N_{\rm s}}`, and that the matrix :math:`\boldsymbol A` is
pe-computed and stored for any given :math:`\boldsymbol \eta`. Owing to
the rapid convergence of the KL expansion, only a small number of
orthogonal basis functions is needed to obtain accurate
approximation. The value of :math:`N_{\rm 2b}` corresponds to
*twobody_number_radial_basis_functions*.
The two-body proper orthogonal descriptors at each atom *i* are computed
by summing the orthogonal basis functions over the neighbors of atom *i*
and numerating on the atom types as follows
.. math::
D^{(2)}_{im l(p, q) }(\boldsymbol \eta) = \left\{
\begin{array}{ll}
\displaystyle \sum_{\{j | Z_j = q\}} U^{(2)}_m(r_{ij}, \boldsymbol \eta), & \mbox{if } Z_i = p \\
0, & \mbox{if } Z_i \neq p
\end{array}
\right.
for :math:`1 \le i \le N, 1 \le m \le N_{\rm 2b}, 1 \le q, p \le N_{\rm
e}`. Here :math:`l(p,q)` is a symmetric index mapping such that
.. math::
l(p,q) = \left\{
\begin{array}{ll}
q + (p-1) N_{\rm e} - p(p-1)/2, & \mbox{if } q \ge p \\
p + (q-1) N_{\rm e} - q(q-1)/2, & \mbox{if } q < p .
\end{array}
\right.
The number of two-body descriptors per atom is thus :math:`N_{\rm 2b}
N_{\rm e}(N_{\rm e}+1)/2`.
It is important to note that the orthogonal basis functions do not
depend on the atomic numbers :math:`Z_i` and :math:`Z_j`. Therefore, the
cost of evaluating the basis functions and their derivatives with
respect to :math:`r_{ij}` is independent of the number of elements
:math:`N_{\rm e}`. Consequently, even though the two-body proper
orthogonal descriptors depend on :math:`\boldsymbol Z`, their
computational complexity is independent of :math:`N_{\rm e}`.
In order to provide proper orthogonal descriptors for three-body
interactions, we need to introduce a three-body parameterized
potential. In particular, the three-body potential is defined as a
product of radial and angular functions as follows
.. math::
W^{(3)}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta, \boldsymbol \mu^{(3)}) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}) \\
\psi(r_{ik}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ik}, r_{\rm min}, r_{\rm max}) \\
\cos (\sigma \theta_{ijk} + \zeta)
where :math:`\sigma` is the periodic multiplicity, :math:`\zeta` is the
equilibrium angle, :math:`\boldsymbol \mu^{(3)} = (\alpha, \beta,
\gamma, \kappa, \sigma, \zeta)`. The three-body potential provides an
angular fingerprint of the atomic environment through the bond angles
:math:`\theta_{ijk}` formed with each pair of neighbors :math:`j` and
:math:`k`. Compared to the two-body potential, the three-body potential
has two extra parameters :math:`(\sigma, \zeta)` associated with the
angular component.
Let :math:`\boldsymbol \varrho = (\alpha, \beta, \gamma, \kappa)`. We
assume that we are given :math:`L_{\rm r}` parameter tuples
:math:`\boldsymbol \varrho_\ell, 1 \le \ell \le L_{\rm r}`. We
introduce the following set of snapshots on :math:`(r_{\min},
r_{\max})`:
.. math::
\zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \boldsymbol \varrho_\ell) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}), \quad 1 \le \ell \le L_{\rm r} .
We apply the Karhunen-Loeve (KL) expansion to this set of snapshots to
obtain orthogonal basis functions as follows
.. math::
U^{r}_m(r_{ij}, r_{\rm min}, r_{\rm max} ) = \sum_{\ell = 1}^{L_{\rm r}} A_{\ell m} \, \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ), \qquad m = 1, \ldots, N_{\rm r} ,
where the matrix :math:`\boldsymbol A \in \mathbb{R}^{L_{\rm r} \times L_{\rm r}}` consists
of eigenvectors of the eigenvalue problem. For the parameterized angular function,
we consider angular basis functions
.. math::
U^{a}_n(\theta_{ijk}) = \cos ((n-1) \theta_{ijk}), \qquad n = 1,\ldots, N_{\rm a},
where :math:`N_{\rm a}` is the number of angular basis functions. The orthogonal
basis functions for the parameterized potential are computed as follows
.. math::
U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta) = U^{r}_m(r_{ij}, \boldsymbol \eta) U^{r}_m(r_{ik}, \boldsymbol \eta) U^{a}_n(\theta_{ijk}),
for :math:`1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}`. The number of three-body
orthogonal basis functions is equal to :math:`N_{\rm 3b} = N_{\rm r} N_{\rm a}` and
independent of the number of elements. The value of :math:`N_{\rm r}` corresponds to
*threebody_number_radial_basis_functions*, while that of :math:`N_{\rm a}` to
*threebody_number_angular_basis_functions*.
The three-body proper orthogonal descriptors at each atom *i*
are obtained by summing over the neighbors *j* and *k* of atom *i* as
.. math::
D^{(3)}_{imn \ell(p, q, s)}(\boldsymbol \eta) = \left\{
\begin{array}{ll}
\displaystyle \sum_{\{j | Z_j = q\}} \sum_{\{k | Z_k = s\}} U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta), & \mbox{if } Z_i = p \\
0, & \mbox{if } Z_i \neq p
\end{array}
\right.
for :math:`1 \le i \le N, 1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}, 1 \le q, p, s \le N_{\rm e}`,
where
.. math::
\ell(p,q,s) = \left\{
\begin{array}{ll}
s + (q-1) N_{\rm e} - q(q-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2 , & \mbox{if } s \ge q \\
q + (s-1) N_{\rm e} - s(s-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2, & \mbox{if } s < q .
\end{array}
\right.
The number of three-body descriptors per atom is thus :math:`N_{\rm 3b} N_{\rm e}^2(N_{\rm e}+1)/2`.
While the number of three-body PODs is cubic function of the number of elements,
the computational complexity of the three-body PODs is independent of the number of elements.
Four-Body SNAP Descriptors
""""""""""""""""""""""""""
In addition to the proper orthogonal descriptors described above, we also employ
the spectral neighbor analysis potential (SNAP) descriptors. SNAP uses bispectrum components
to characterize the local neighborhood of each atom in a very general way. The mathematical definition
of the bispectrum calculation and its derivatives w.r.t. atom positions is described in
:doc:`compute snap <compute_sna_atom>`. In SNAP, the
total energy is decomposed into a sum over atom energies. The energy of
atom *i* is expressed as a weighted sum over bispectrum components.
.. math::
E_i^{\rm SNAP} = \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}
where the SNAP descriptors are related to the bispectrum components by
.. math::
D^{(4)}_{ikp} = \left\{
\begin{array}{ll}
\displaystyle B_{ik}, & \mbox{if } Z_i = p \\
0, & \mbox{if } Z_i \neq p
\end{array}
\right.
Here :math:`B_{ik}` is the *k*\ -th bispectrum component of atom *i*. The number of
bispectrum components :math:`N_{\rm 4b}` depends on the value of *fourbody_snap_twojmax* :math:`= 2 J_{\rm max}`
and *fourbody_snap_chemflag*. If *fourbody_snap_chemflag* = 0
then :math:`N_{\rm 4b} = (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`.
If *fourbody_snap_chemflag* = 1 then :math:`N_{\rm 4b} = N_{\rm e}^3 (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`.
The bispectrum calculation is described in more detail in :doc:`compute sna/atom <compute_sna_atom>`.
Linear Proper Orthogonal Descriptor Potentials
""""""""""""""""""""""""""""""""""""""""""""""
The proper orthogonal descriptors and SNAP descriptors are used to define the atomic energies
in the following expansion
.. math::
E_{i}(\boldsymbol \eta) = \sum_{p=1}^{N_{\rm e}} c^{(1)}_p D^{(1)}_{ip} + \sum_{m=1}^{N_{\rm 2b}} \sum_{l=1}^{N_{\rm e}(N_{\rm e}+1)/2} c^{(2)}_{ml} D^{(2)}_{iml}(\boldsymbol \eta) + \sum_{m=1}^{N_{\rm r}} \sum_{n=1}^{N_{\rm a}} \sum_{\ell=1}^{N_{\rm e}^2(N_{\rm e}+1)/2} c^{(3)}_{mn\ell} D^{(3)}_{imn\ell}(\boldsymbol \eta) + \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}(\boldsymbol \eta),
where :math:`D^{(1)}_{ip}, D^{(2)}_{iml}, D^{(3)}_{imn\ell}, D^{(4)}_{ikp}` are the one-body, two-body, three-body, four-body descriptors,
respectively, and :math:`c^{(1)}_p, c^{(2)}_{ml}, c^{(3)}_{mn\ell}, c^{(4)}_{kp}` are their respective expansion
coefficients. In a more compact notation that implies summation over descriptor indices
the atomic energies can be written as
.. math::
E_i(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m D^{(1)}_{im} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_k D^{(2)}_{im} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m D^{(3)}_{im} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m D^{(4)}_{im}
where :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2`,
:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2`, and
:math:`N_{\rm d}^{(4)} = N_{\rm 4b} N_{\rm e}` are
the number of two-body, three-body, and four-body descriptors, respectively.
The potential energy is then obtained by summing local atomic energies :math:`E_i`
for all atoms :math:`i` in the system
.. math::
E(\boldsymbol \eta) = \sum_{i}^N E_{i}(\boldsymbol \eta)
Because the descriptors are one-body, two-body, and three-body terms,
the resulting POD potential is a three-body PES. We can express the potential
energy as a linear combination of the global descriptors as follows
.. math::
E(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m d^{(1)}_{m} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m d^{(2)}_{m} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m d^{(3)}_{m} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m d^{(4)}_{m}
where the global descriptors are given by
.. math::
d_{m}^{(1)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(1)}(\boldsymbol \eta), \quad d_{m}^{(2)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(2)}(\boldsymbol \eta), \quad d_{m}^{(3)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(3)}(\boldsymbol \eta), \quad d_{m}^{(4)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(4)}(\boldsymbol \eta)
Hence, we obtain the atomic forces as
.. math::
\boldsymbol F = -\nabla E(\boldsymbol \eta) = - \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m \nabla d_m^{(2)} - \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m \nabla d_m^{(3)} - \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m \nabla d_m^{(4)}
where :math:`\nabla d_m^{(2)}`, :math:`\nabla d_m^{(3)}` and :math:`\nabla d_m^{(4)}` are derivatives of the two-body
three-body, and four-body global descriptors with respect to atom positions, respectively.
Note that since the first-body global descriptors are constant, their derivatives are zero.
Quadratic Proper Orthogonal Descriptor Potentials
"""""""""""""""""""""""""""""""""""""""""""""""""
We recall two-body PODs :math:`D^{(2)}_{ik}, 1 \le k \le N_{\rm d}^{(2)}`,
and three-body PODs :math:`D^{(3)}_{im}, 1 \le m \le N_{\rm d}^{(3)}`,
with :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2` and
:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2` being
the number of descriptors per atom for the two-body PODs and three-body PODs,
respectively. We employ them to define a new set of atomic descriptors as follows
.. math::
D^{(2*3)}_{ikm} = \frac{1}{2N}\left( D^{(2)}_{ik} \sum_{j=1}^N D^{(3)}_{jm} + D^{(3)}_{im} \sum_{j=1}^N D^{(2)}_{jk} \right)
for :math:`1 \le i \le N, 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`.
The new descriptors are four-body because they involve central atom :math:`i` together
with three neighbors :math:`j, k` and :math:`l`. The total number of new descriptors per atom is equal to
.. math::
N_{\rm d}^{(2*3)} = N_{\rm d}^{(2)} * N_{\rm d}^{(3)} = N_{\rm 2b} N_{\rm 3b} N_{\rm e}^3 (N_{\rm e}+1)^2/4 .
The new global descriptors are calculated as
.. math::
d^{(2*3)}_{km} = \sum_{i=1}^N D^{(2*3)}_{ikm} = \left( \sum_{i=1}^N D^{(2)}_{ik} \right) \left( \sum_{i=1}^N D^{(3)}_{im} \right) = d^{(2)}_{k} d^{(3)}_m,
for :math:`1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. Hence, the gradient
of the new global descriptors with respect to atom positions is calculated as
.. math::
\nabla d^{(2*3)}_{km} = d^{(3)}_m \nabla d^{(2)}_{k} + d^{(2)}_{k} \nabla d^{(3)}_m, \quad 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)} .
The quadratic POD potential is defined as a linear combination of the
original and new global descriptors as follows
.. math::
E^{(2*3)} = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d^{(2*3)}_{km} .
It thus follows that
.. math::
E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \left( \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)} \right) d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} \left( \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)} \right) d_m^{(3)} ,
which is simplified to
.. math::
E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b_k^{(2)} d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b_m^{(3)} d_m^{(3)}
where
.. math::
b_k^{(2)} & = \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)}, \quad k = 1,\ldots, N_{\rm 2d}^{(2*3)}, \\
b_m^{(3)} & = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)}, \quad m = 1,\ldots, N_{\rm 3d}^{(2*3)} .
The quadratic POD potential results in the following atomic forces
.. math::
\boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} \nabla d^{(2*3)}_{km} .
It can be shown that
.. math::
\boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b^{(2)}_k \nabla d_k^{(2)} - \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b^{(3)}_m \nabla d_m^{(3)} .
The calculation of the atomic forces for the quadratic POD potential
only requires the extra calculation of :math:`b_k^{(2)}` and :math:`b_m^{(3)}` which can be negligible.
As a result, the quadratic POD potential does not increase the computational complexity.
Training
""""""""
POD potentials are trained using the least-squares regression against
density functional theory (DFT) data. Let :math:`J` be the number of
training configurations, with :math:`N_j` being the number of atoms in
the j-th configuration. Let :math:`\{E^{\star}_j\}_{j=1}^{J}` and
:math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` be the DFT energies and
forces for :math:`J` configurations. Next, we calculate the global
descriptors and their derivatives for all training configurations. Let
:math:`d_{jm}, 1 \le m \le M`, be the global descriptors associated with
the j-th configuration, where :math:`M` is the number of global
descriptors. We then form a matrix :math:`\boldsymbol A \in
\mathbb{R}^{J \times M}` with entries :math:`A_{jm} = d_{jm}/ N_j` for
:math:`j=1,\ldots,J` and :math:`m=1,\ldots,M`. Moreover, we form a
matrix :math:`\boldsymbol B \in \mathbb{R}^{\mathcal{N} \times M}` by
stacking the derivatives of the global descriptors for all training
configurations from top to bottom, where :math:`\mathcal{N} =
3\sum_{j=1}^{J} N_j`.
The coefficient vector :math:`\boldsymbol c` of the POD potential is
found by solving the following least-squares problem
.. math::
{\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A(\boldsymbol \eta) \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B(\boldsymbol \eta) \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2,
where :math:`w_E` and :math:`w_F` are weights for the energy
(*fitting_weight_energy*) and force (*fitting_weight_force*),
respectively; and :math:`w_R` is the regularization parameter (*fitting_regularization_parameter*). Here :math:`\bar{\boldsymbol E}^{\star} \in
\mathbb{R}^{J}` is a vector of with entries :math:`\bar{E}^{\star}_j =
E^{\star}_j/N_j` and :math:`\boldsymbol F^{\star}` is a vector of
:math:`\mathcal{N}` entries obtained by stacking :math:`\{\boldsymbol
F^{\star}_j\}_{j=1}^{J}` from top to bottom.
The training procedure is the same for both the linear and quadratic POD
potentials. However, since the quadratic POD potential has a
significantly larger number of the global descriptors, it is more
expensive to train the linear POD potential. This is because the
training of the quadratic POD potential still requires us to calculate
and store the quadratic global descriptors and their
gradient. Furthermore, the quadratic POD potential may require more
training data in order to prevent over-fitting. In order to reduce the
computational cost of fitting the quadratic POD potential and avoid
over-fitting, we can use subsets of two-body and three-body PODs for
constructing the new descriptors.
Restrictions
""""""""""""
This command is part of the ML-POD package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`pair_style pod <pair_pod>`
Default
"""""""
The keyword defaults are also given in the description of the input files.
----------
.. _Grepl20072:
**(Grepl)** Grepl, Maday, Nguyen, and Patera, ESAIM: Mathematical Modelling and Numerical Analysis 41(3), 575-605, (2007).
.. _Nguyen20222:
**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022).

49
doc/src/fix.rst
View File

@ -77,26 +77,31 @@ for individual fixes for info on which ones can be restarted.
----------
Some fixes calculate one of three styles of quantities: global,
per-atom, or local, which can be used by other commands or output as
described below. A global quantity is one or more system-wide values
(e.g., the energy of a wall interacting with particles). A per-atom
quantity is one or more values per atom (e.g., the displacement vector
for each atom since time 0). Per-atom values are set to 0.0 for atoms
not in the specified fix group. Local quantities are calculated by
each processor based on the atoms it owns, but there may be zero or
more per atoms.
Some fixes calculate one or more of four styles of quantities: global,
per-atom, local, or per-grid, which can be used by other commands or
output as described below. A global quantity is one or more
system-wide values, e.g. the energy of a wall interacting with
particles. A per-atom quantity is one or more values per atom,
e.g. the displacement vector for each atom since time 0. Per-atom
values are set to 0.0 for atoms not in the specified fix group. Local
quantities are calculated by each processor based on the atoms it
owns, but there may be zero or more per atoms. Per-grid quantities
are calculated on a regular 2d or 3d grid which overlays a 2d or 3d
simulation domain. The grid points and the data they store are
distributed across processors; each processor owns the grid points
which fall within its sub-domain.
Note that a single fix can produce either global or per-atom or local
quantities (or none at all), but not both global and per-atom. It can
produce local quantities in tandem with global or per-atom quantities.
The fix page will explain.
Note that a single fix typically produces either global or per-atom or
local or per-grid values (or none at all). It does not produce both
global and per-atom. It can produce local or per-grid values in
tandem with global or per-atom values. The fix doc page will explain
the details.
Global, per-atom, and local quantities each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
doc page for each fix describes the style and kind of values it
produces (e.g., a per-atom vector). Some fixes produce more than one
kind of a single style (e.g., a global scalar and a global vector).
Global, per-atom, local, and per-grid quantities come in three kinds:
a single scalar value, a vector of values, or a 2d array of values.
The doc page for each fix describes the style and kind of values it
produces, e.g. a per-atom vector. Some fixes produce more than one
kind of a single style, e.g. a global scalar and a global vector.
When a fix quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket
@ -185,6 +190,7 @@ accelerated styles exist.
* :doc:`ave/chunk <fix_ave_chunk>` - compute per-chunk time-averaged quantities
* :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
* :doc:`ave/correlate/long <fix_ave_correlate_long>` - alternative to :doc:`ave/correlate <fix_ave_correlate>` that allows efficient calculation over long time windows
* :doc:`ave/grid <fix_ave_grid>` - compute per-grid time-averaged quantities
* :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
* :doc:`ave/histo/weight <fix_ave_histo>` - weighted version of fix ave/histo
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
@ -216,9 +222,9 @@ accelerated styles exist.
* :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
* :doc:`efield <fix_efield>` - impose electric field on system
* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
* :doc:`electrode/conp <fix_electrode_conp>` - impose electric potential
* :doc:`electrode/conq <fix_electrode_conp>` - impose total electric charge
* :doc:`electrode/thermo <fix_electrode_conp>` - apply thermo-potentiostat
* :doc:`electrode/conp <fix_electrode>` - impose electric potential
* :doc:`electrode/conq <fix_electrode>` - impose total electric charge
* :doc:`electrode/thermo <fix_electrode>` - apply thermo-potentiostat
* :doc:`electron/stopping <fix_electron_stopping>` - electronic stopping power as a friction force
* :doc:`electron/stopping/fit <fix_electron_stopping>` - electronic stopping power as a friction force
* :doc:`enforce2d <fix_enforce2d>` - zero out *z*-dimension velocity and force
@ -360,6 +366,7 @@ accelerated styles exist.
* :doc:`saed/vtk <fix_saed_vtk>` - time-average the intensities from :doc:`compute saed <compute_saed>`
* :doc:`setforce <fix_setforce>` - set the force on each atom
* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
* :doc:`sgcmc <fix_sgcmc>` - fix for hybrid semi-grand canonical MD/MC simulations
* :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
* :doc:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting
* :doc:`smd <fix_smd>` - applied a steered MD force to a group

3
doc/src/fix_atom_swap.rst
View File

@ -63,7 +63,8 @@ be needed when running such a hybrid simulation, especially if the
swapped atoms are not well equilibrated.
The *types* keyword is required. At least two atom types must be
specified.
specified. If not using *semi-grand*, exactly two atom types
are required.
The *ke* keyword can be set to *no* to turn off kinetic energy
conservation for swaps. The default is *yes*, which means that swapped

38
doc/src/fix_ave_chunk.rst
View File

@ -112,6 +112,17 @@ or atoms in a spatial bin. See the :doc:`compute chunk/atom
page for details of how chunks can be defined and examples of how they
can be used to measure properties of a system.
Note that if the :doc:`compute chunk/atom <compute_chunk_atom>`
command defines spatial bins, the fix ave/chunk command performs a
similar computation as the :doc:`fix ave/grid <fix_ave_grid>` command.
However, the per-bin outputs from the fix ave/chunk command are
global; each processor stores a copy of the entire set of bin data.
By contrast, the :doc:`fix ave/grid <fix_ave_grid>` command uses a
distributed grid where each processor owns a subset of the bins. Thus
it is more efficient to use the :doc:`fix ave/grid <fix_ave_grid>`
command when the grid is large and a simulation is run on many
processors.
Note that only atoms in the specified group contribute to the summing
and averaging calculations. The :doc:`compute chunk/atom
<compute_chunk_atom>` command defines its own group as well as an
@ -141,10 +152,11 @@ quantities. :doc:`Variables <variable>` of style *atom* are the only
ones that can be used with this fix since all other styles of variable
produce global quantities.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or the
Note that for values from a compute or fix that produces a per-atom
array (multiple values per atom), the bracketed index I can be
specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "n\*"
or "m\*n". If :math:`N` = the size of the vector (for *mode* = scalar) or the
number of columns in the array (for *mode* = vector), then an asterisk
with no numeric values means all indices from 1 to :math:`N`. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
@ -359,6 +371,8 @@ For the *density/number* and *density/mass* values, the
volume (bin volume or system volume) used in the per-sample sum
normalization will be the current volume at each sampling step.
----------
The *ave* keyword determines how the per-chunk values produced every
:math:`N_\text{freq}` steps are averaged with values produced on previous steps
that were multiples of :math:`N_\text{freq}`, before they are accessed by
@ -385,6 +399,8 @@ of the individual chunk values on time steps 8000, 9000, and 10000. Outputs on
early steps will average over less than :math:`M` values if they are not
available.
----------
The *bias* keyword specifies the ID of a temperature compute that
removes a "bias" velocity from each atom, specified as *bias-ID*\ .
It is only used when the *temp* value is calculated, to compute the
@ -415,6 +431,8 @@ set to the remaining degrees of freedom for the entire molecule
(entire chunk in this case), that is, 6 for 3d or 3 for 2d for a rigid
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
@ -523,12 +541,14 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`,
:doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`
:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, `fix
:doc:ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`variable <variable>`, :doc:`fix ave/correlate
:doc:<fix_ave_correlate>`, `fix ave/atogrid <fix_ave_grid>`
Default
"""""""
The option defaults are norm = all, ave = one, bias = none, no file output, and
title 1,2,3 = strings as described above.
The option defaults are norm = all, ave = one, bias = none, no file
output, and title 1,2,3 = strings as described above.

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.. index:: fix ave/grid
fix ave/grid command
=====================
Syntax
""""""
.. parsed-literal::
fix ID group-ID ave/grid Nevery Nrepeat Nfreq Nx Ny Nz value1 value2 ... keyword args ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* ave/grid = style name of this fix command
* Nevery = use input values every this many timesteps
* Nrepeat = # of times to use input values for calculating averages
* Nfreq = calculate averages every this many timesteps
* Nx, Ny, Nz = grid size in each dimension
* one or more per-atom or per-grid input values can be listed
* per-atom value = vx, vy, vz, fx, fy, fz, density/mass, density/number, mass, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
.. parsed-literal::
vx,vy,vz,fx,fy,fz,mass = atom attribute (velocity, force component, mass)
density/number, density/mass = number or mass density (per volume)
temp = temperature
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
f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
v_name = per-atom vector calculated by an atom-style variable with name
* per-grid value = c_ID:gname:dname, c_ID:gname:dname[I], f_ID:gname:dname, f_ID:gname:dname[I]
.. parsed-literal::
gname = name of grid defined by compute or fix
dname = name of data field defined by compute or fix
c_ID = per-grid vector calculated by a compute with ID
c_ID[I] = Ith column of per-grid array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-grid vector calculated by a fix with ID
f_ID[I] = Ith column of per-grid array calculated by a fix with ID, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *discard* or *norm* or *ave* or *bias* or *adof* or *cdof*
.. parsed-literal::
*discard* arg = *yes* or *no*
yes = discard an atom outside grid in a non-periodic dimension
no = remap an atom outside grid in a non-periodic dimension to first or last grid cell
*norm* arg = *all* or *sample* or *none* = how output on *Nfreq* steps is normalized
all = output is sum of atoms across all *Nrepeat* samples, divided by atom count
sample = output is sum of *Nrepeat* sample averages, divided by *Nrepeat*
none = output is sum of *Nrepeat* sample sums, divided by *Nrepeat*
*ave* args = *one* or *running* or *window M*
one = output new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
*bias* arg = bias-ID
bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
*adof* value = dof_per_atom
dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
*cdof* value = dof_per_grid_cell
dof_per_grid_cell = add this many degrees-of-freedom per grid_cell for temperature calculation
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all ave/grid 10000 1 10000 10 10 10 fx fy fz c_myMSD[*]
fix 1 flow ave/grid 100 10 1000 20 20 30 f_TTM:grid:data
Description
"""""""""""
Overlay the 2d or 3d simulation box with a uniformly spaced 2d or 3d
grid and use it to either (a) time-average per-atom quantities for the
atoms in each grid cell, or to (b) time-average per-grid quantities
produced by other computes or fixes. This fix operates in either
"per-atom mode" (all input values are per-atom) or in "per-grid mode"
(all input values are per-grid). You cannot use both per-atom and
per-grid inputs in the same command.
The grid created by this command is distributed; each processor owns
the grid points that are within its sub-domain. This is similar to
the :doc:`fix ave/chunk <fix_ave_chunk>` command when it uses chunks
from the :doc:`compute chunk/atom <compute_chunk_atom>` command which
are 2d or 3d regular bins. However, the per-bin outputs in that case
are global; each processor stores a copy of the entire set of bin
data. Thus it more efficient to use the fix ave/grid command when the
grid is large and a simulation is run on many processors.
For per-atom mode, only atoms in the specified group contribute to the
summing and averaging calculations. For per-grid mode, the specified
group is ignored.
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
timesteps the input values will be accessed and contribute to the
average. The final averaged quantities are generated on timesteps
that are a multiples of *Nfreq*\ . The average is over *Nrepeat*
quantities, computed in the preceding portion of the simulation every
*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and
*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nrepeat\*Nevery
can not exceed Nfreq.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps
100,200,etc.
In per-atom mode, each input value can also be averaged over the atoms
in each grid cell. The way the averaging is done across the *Nrepeat*
timesteps to produce output on the *Nfreq* timesteps, and across
multiple *Nfreq* outputs, is determined by the *norm* and *ave*
keyword settings, as discussed below.
----------
The *Nx*, *Ny*, and *Nz* arguments specify the size of the grid that
overlays the simulation box. For 2d simulations, *Nz* must be 1. The
*Nx*, *Ny*, *Nz* values can be any positive integer. The grid can be
very coarse compared to the particle count, or very fine. If one or
more of the values = 1, then bins are 2d planes or 1d slices of the
simulation domain. Note that if the total number of grid cells is
small, it may be more efficient to use the doc:`fix ave/chunk
<fix_ave_chunk>` command which can treat a grid defined by the
:doc:`compute chunk/atom <compute_chunk_atom>` command as a global
grid where each processor owns a copy of all the grid cells. If *Nx*
= *Ny* = *Nz* = 1 is used, the same calculation would be more
efficiently performed by the doc:`fix ave/atom <fix_ave_atom>`
command.
If the simulation box size or shape changes during a simulation, the
grid always conforms to the size/shape of the current simulation box.
If one more dimensions have non-periodic shrink-wrapped boundary
conditions, as defined by the :doc:`boundary <boundary>` command, then
the grid will extend over the (dynamic) shrink-wrapped extent in each
dimension. If the box shape is triclinic, as explained in :doc:`Howto
triclinic <Howto_triclinic>`, then the grid is also triclinic; each
grid cell is a small triclinic cell with the same shape as the
simulation box.
----------
In both per-atom and per-grid mode, input values from a compute or fix
that produces an array of values (multiple values per atom or per grid
point), the bracketed index I can be specified using a wildcard
asterisk with the index to effectively specify multiple values. This
takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of
columns in the array (for *mode* = vector), then an asterisk with no
numeric values means all indices from 1 to N. A leading asterisk
means all indices from 1 to n (inclusive). A trailing asterisk means
all indices from n to N (inclusive). A middle asterisk means all
indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. if there were a compute fft/grid
command which produced 3 values for each grid point, these two fix
ave/grid commands would be equivalent:
.. code-block:: LAMMPS
compute myFFT all fft/grid 10 10 10 ...
fix 1 all ave/grid 100 1 100 10 10 10 c_myFFT:grid:data[*]
fix 2 all ave/grid 100 1 100 10 10 10 c_myFFT:grid:data[*][1] c_myFFT:grid:data[*][2] c_myFFT:grid:data[3]
----------
*Per-atom mode*:
Each specified per-atom value can be an atom attribute (velocity,
force component), a number or mass density, a mass or temperature, or
the result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the
evaluation of an atom-style :doc:`variable <variable>`. In the latter
cases, the compute, fix, or variable must produce a per-atom quantity,
not a global quantity. Note that the :doc:`compute property/atom
<compute_property_atom>` command provides access to any attribute
defined and stored by atoms.
The per-atom values of each input vector are summed and averaged
independently of the per-atom values in other input vectors.
:doc:`Computes <compute>` that produce per-atom quantities are those
which have the word *atom* in their style name. See the doc pages for
individual :doc:`fixes <fix>` to determine which ones produce per-atom
quantities. :doc:`Variables <variable>` of style *atom* are the only
ones that can be used with this fix since all other styles of variable
produce global quantities.
----------
The atom attribute values (vx,vy,vz,fx,fy,fz,mass) are
self-explanatory. As noted above, any other atom attributes can be
used as input values to this fix by using the :doc:`compute
property/atom <compute_property_atom>` command and then specifying an
input value from that compute.
The *density/number* value means the number density is computed for
each grid cell, i.e. number/volume. The *density/mass* value means
the mass density is computed for each grid/cell,
i.e. total-mass/volume. The output values are in units of 1/volume or
density (mass/volume). See the :doc:`units <units>` command page for
the definition of density for each choice of units, e.g. gram/cm\^3.
The *temp* value computes the temperature for each grid cell, by the
formula
.. math::
\text{KE} = \frac{\text{DOF}}{2} k_B T,
where KE = total kinetic energy of the atoms in the grid cell (
:math:`\frac{1}{2} m v^2`), DOF = the total number of degrees of
freedom for all atoms in the grid cell, :math:`k_B` = Boltzmann
constant, and :math:`T` = temperature.
The DOF is calculated as N\*adof + cdof, where N = number of atoms in
the grid cell, adof = degrees of freedom per atom, and cdof = degrees
of freedom per grid cell. By default adof = 2 or 3 = dimensionality
of system, as set via the :doc:`dimension <dimension>` command, and
cdof = 0.0. This gives the usual formula for temperature.
Note that currently this temperature only includes translational
degrees of freedom for each atom. No rotational degrees of freedom
are included for finite-size particles. Also no degrees of freedom
are subtracted for any velocity bias or constraints that are applied,
such as :doc:`compute temp/partial <compute_temp_partial>`, or
:doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`. This is
because those degrees of freedom (e.g. a constrained bond) could apply
to sets of atoms that are both inside and outside a specific grid
cell, and hence the concept is somewhat ill-defined. In some cases,
you can use the *adof* and *cdof* keywords to adjust the calculated
degrees of freedom appropriately, as explained below.
Also note that a bias can be subtracted from atom velocities before
they are used in the above formula for KE, by using the *bias*
keyword. This allows, for example, a thermal temperature to be
computed after removal of a flow velocity profile.
Note that the per-grid-cell temperature calculated by this fix and the
:doc:`compute temp/chunk <compute_temp_chunk>` command (using bins)
can be different. The compute calculates the temperature for each
chunk for a single snapshot. This fix can do that but can also time
average those values over many snapshots, or it can compute a
temperature as if the atoms in the grid cell on different timesteps
were collected together as one set of atoms to calculate their
temperature. The compute allows the center-of-mass velocity of each
chunk to be subtracted before calculating the temperature; this fix
does not.
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the compute is used. Users can also write code for
their own compute styles and :doc:`add them to LAMMPS <Modify>`. See
the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the fix is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the fix is used. Note that some fixes only produce
their values on certain timesteps, which must be compatible with
*Nevery*, else an error results. Users can also write code for their
own fix styles and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. Variables of style
*atom* can reference thermodynamic keywords and various per-atom
attributes, or invoke other computes, fixes, or variables when they
are evaluated, so this is a very general means of generating per-atom
quantities to average within grid cells.
----------
*Per-grid mode*:
The attributes that begin with *c_ID* and *f_ID* both take
colon-separated fields *gname* and *dname*. These refer to a grid
name and data field name which is defined by the compute or fix. Note
that a compute or fix can define one or more grids (of different
sizes) and one or more data fields for each of those grids. The sizes
of all grids used as values for one instance of this fix must be the
same.
The *c_ID:gname:dname* and *c_ID:gname:dname[I]* attributes allow
per-grid vectors or arrays calculated by a :doc:`compute <compute>` to
be accessed. The ID in the attribute should be replaced by the actual
ID of the compute that has been defined previously in the input
script.
If *c_ID:gname:dname* is used as a attribute, then the per-grid vector
calculated by the compute is accessed. If *c_ID:gname:dname[I]* is
used, then I must be in the range from 1-M, which will access the Ith
column of the per-grid array with M columns calculated by the compute.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
The *f_ID:gname:dname* and *f_ID:gname:dname[I]* attributes allow
per-grid vectors or arrays calculated by a :doc:`fix <fix>` to be
output. The ID in the attribute should be replaced by the actual ID
of the fix that has been defined previously in the input script.
If *f_ID:gname:dname* is used as a attribute, then the per-grid vector
calculated by the fix is printed. If *f_ID:gname:dname[I]* is used,
then I must be in the range from 1-M, which will print the Ith column
of the per-grid with M columns calculated by the fix. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
----------
Additional optional keywords also affect the operation of this fix and
its outputs. Some are only applicable to per-atom mode. Some are
applicable to both per-atom and per-grid mode.
The *discard* keyword is only applicable to per-atom mode. If a
dimension of the system is non-periodic, then grid cells will only
span the box dimension (fixed or shrink-wrap boundaries as set by the
:doc:`boundary` command). An atom may thus be slightly outside the
range of grid cells on a particular timestep. If *discard* is set to
*yes* (the default), then the atom will be assigned to the closest
grid cell (lowest or highest) in that dimension. If *discard* is set
to *no* the atom will be ignored.
----------
The *norm* keyword is only applicable to per-atom mode. In per-grid
mode, the *norm* keyword setting is ignored. The output grid value on
an *Nfreq* timestep is the sum of the grid values in each of the
*Nrepeat* samples, divided by *Nrepeat*.
In per-atom mode, the *norm" keywod affects how averaging is done for
the per-grid values that are output on an *Nfreq* timestep. *Nrepeat*
samples contribute to the output. The *norm* keyword has 3 possible
settings: *all* or *sample* or *none*. *All* is the default.
In the formulas that follow, SumI is the sum of a per-atom property
over the CountI atoms in a grid cell for a single sample I, where I
varies from 1 to N, and N = Nrepeat. These formulas are used for any
per-atom input value listed above, except *density/number*,
*density/mass*, and *temp*. Those input values are discussed below.
In per-atom mode, for *norm all* the output grid value on the *Nfreq*
timestep is an average over atoms across the entire *Nfreq* timescale:
Output = (Sum1 + Sum2 + ... + SumN) / (Count1 + Count2 + ... + CountN)
In per-atom mode, for *norm sample* the output grid value on the
*Nfreq* timestep is an average of an average:
Output = (Sum1/Count1 + Sum2/Count2 + ... + SumN/CountN) / Nrepeat
In per-atom mode, for *norm none* the output grid value on the
*Nfreq* timestep is not normalized by the atom counts:
Output = (Sum1 + Sum2 + ... SumN) / Nrepeat
For *density/number* and *density/mass*, the output value is the same
as in the formulas above for *norm all* and *norm sample*, except that
the result is also divided by the grid cell volume. For *norm all*,
this will be the volume at the final *Nfreq* timestep. For *norm
sample*, the divide-by-volume is done for each sample, using the grid
cell volume at the sample timestep. For *norm none*, the output is
the same as for *norm all*.
For *temp*, the output temperature uses the formula for kinetic energy
KE listed above, and is normalized similarly to the formulas above for
*norm all* and *norm sample*, except for the way the degrees of
freedom (DOF) are calculated. For *norm none*, the output is the same
as for *norm all*.
For *norm all*, the DOF = *Nrepeat* times *cdof* plus *Count* times
*adof*, where *Count* = (Count1 + Count2 + ... + CountN). The *cdof*
and *adof* keywords are discussed below. The output temperature is
computed with all atoms across all samples contributing.
For *norm sample*, the DOF for a single sample = *cdof* plus *Count*
times *adof*, where *Count* = CountI for a single sample. The output
temperature is the average of *Nsample* temperatures calculated for
each sample.
Finally, for all 3 *norm* settings the output count of atoms per grid
cell is:
Output count = (Count1 + Count2 + ... CountN) / Nrepeat
This count is the same for all per-atom input values, including
*density/number*, *density/mass*, and *temp*.
----------
The *ave* keyword is applied to both per-atom and per-grid mode. It
determines how the per-grid values produced once every *Nfreq* steps
are averaged with values produced on previous steps that were
multiples of *Nfreq*, before they are accessed by another output
command.
If the *ave* setting is *one*, which is the default, then the grid
values produced on *Nfreq* timesteps are independent of each other;
they are output as-is without further averaging.
If the *ave* setting is *running*, then the grid values produced on
*Nfreq* timesteps are summed and averaged in a cumulative sense before
being output. Each output grid value is thus the average of the grid
value produced on that timestep with all preceding values for the same
grid value. This running average begins when the fix is defined; it
can only be restarted by deleting the fix via the :doc:`unfix <unfix>`
command, or re-defining the fix by re-specifying it.
If the *ave* setting is *window*, then the grid values produced on
*Nfreq* timesteps are summed and averaged within a moving "window" of
time, so that the last M values for the same grid are used to produce
the output. E.g. if M = 3 and Nfreq = 1000, then the grid value
output on step 10000 will be the average of the grid values on steps
8000,9000,10000. Outputs on early steps will average over less than M
values if they are not available.
----------
The *bias*, *adof*, and *cdof* keywords are only applicable to
per-atom mode.
The *bias* keyword specifies the ID of a temperature compute that
removes a "bias" velocity from each atom, specified as *bias-ID*\ .
It is only used when the *temp* value is calculated, to compute the
thermal temperature of each grid cell after the translational kinetic
energy components have been altered in a prescribed way, e.g. to
remove a flow velocity profile. See the doc pages for individual
computes that calculate a temperature to see which ones implement a
bias.
The *adof* and *cdof* keywords define the values used in the degree of
freedom (DOF) formula described above for temperature calculation for
each grid cell. They are only used when the *temp* value is
calculated. They can be used to calculate a more appropriate
temperature in some cases. Here are 3 examples:
If grid cells contain some number of water molecules and :doc:`fix
shake <fix_shake>` is used to make each molecule rigid, then you could
calculate a temperature with 6 degrees of freedom (DOF) (3
translational, 3 rotational) per molecule by setting *adof* to 2.0.
If :doc:`compute temp/partial <compute_temp_partial>` is used with the
*bias* keyword to only allow the x component of velocity to contribute
to the temperature, then *adof* = 1.0 would be appropriate.
Using *cdof* = -2 or -3 (for 2d or 3d simulations) will subtract out 2
or 3 degrees of freedom for each grid cell, similar to how the
:doc:`compute temp <compute_temp>` command subtracts out 3 DOF for the
entire system.
----------
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.
This fix calculates a per-grid array which has one column for each of
the specified input values. The units for each column with be in the
:doc:`units <units>` for the per-atom or per-grid quantity for the
corresponding input value. If the fix is used in per-atom mode, it
also calculates a per-grid vector with the count of atoms in each grid
cell. The number of rows in the per-grid array and number of values
in the per-grid vector (distributed across all processors) is Nx *
Ny * Nz.
For access by other commands, the name of the single grid produced by
this fix is "grid". The names of its two per-grid datums are "data"
for the per-grid array and "count" for the per-grid vector (if using
per-atom values). Both datums can be accessed by various :doc:`output
commands <Howto_output>`.
In per-atom mode, the per-grid array values calculated by this fix are
treated as "intensive", since they are typically already normalized by
the count of atoms in each grid cell.
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
""""""""""""
none
Related commands
""""""""""""""""
:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`
Default
"""""""
The option defaults are discard = yes, norm = all, ave = one, and bias
= none.

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@ -0,0 +1,9 @@
Fix ave/spatial command
=======================
.. meta::
:http-equiv=Refresh: 5; url='https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere'
.. deprecated:: 11Dec2015
The `fix ave/spatial` command has been superseded by :doc:`fix ave/chunk <fix_ave_chunk>`.

9
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@ -0,0 +1,9 @@
Fix ave/spatial command
=======================
.. meta::
:http-equiv=Refresh: 5; url='https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere'
.. deprecated:: 11Dec2015
The `fix ave/spatial/sphere` command has been superseded by :doc:`fix ave/chunk <fix_ave_chunk>`.

20
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@ -177,12 +177,12 @@ due to the internal dynamic grouping performed by fix bond/react.
If the group-ID is an existing static group, react-group-IDs
should also be specified as this static group or a subset.
The *reset_mol_ids* keyword invokes the :doc:`reset_mol_ids <reset_mol_ids>`
command after a reaction occurs, to ensure that molecule IDs are
consistent with the new bond topology. The group-ID used for
:doc:`reset_mol_ids <reset_mol_ids>` is the group-ID for this fix.
Resetting molecule IDs is necessarily a global operation, so it can
be slow for very large systems.
The *reset_mol_ids* keyword invokes the :doc:`reset_atoms mol
<reset_atoms>` command after a reaction occurs, to ensure that
molecule IDs are consistent with the new bond topology. The group-ID
used for :doc:`reset_atoms mol <reset_atoms>` is the group-ID for this
fix. Resetting molecule IDs is necessarily a global operation, so it
can be slow for very large systems.
The following comments pertain to each *react* argument (in other
words, they can be customized for each reaction, or reaction step):
@ -520,7 +520,7 @@ example, the molecule fragment could consist of only the backbone
atoms of a polymer chain. This constraint can be used to enforce a
specific relative position and orientation between reacting molecules.
.. versionchanged:: TBD
.. versionchanged:: 22Dec2022
The constraint of type "custom" has the following syntax:
@ -637,10 +637,10 @@ eligible reaction only occurs if the random number is less than the
fraction. Up to :math:`N` reactions are permitted to occur, as optionally
specified by the *max_rxn* keyword.
.. versionadded:: TBD
.. versionadded:: 22Dec2022
The *rate_limit* keyword can enforce an upper limit on the overall
rate of the reaction. The number of reaction occurences is limited to
rate of the reaction. The number of reaction occurrences is limited to
Nlimit within an interval of Nsteps timesteps. No reactions are
permitted to occur within the first Nsteps timesteps of the first run
after reading a data file. Nlimit can be specified with an equal-style
@ -664,7 +664,7 @@ charges are updated to those specified by the post-reaction template
fragment defined in the pre-reaction molecule template. In this case,
only the atomic charges of atoms in the molecule fragment are updated.
.. versionadded:: TBD
.. versionadded:: 22Dec2022
The *rescale_charges* keyword can be used to ensure the total charge
of the system does not change as reactions occur. When the argument is

70
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@ -94,12 +94,9 @@ insert (delete) a proton (atom type 2). Besides, the fix implements
self-ionization reaction of water :math:`\emptyset \rightleftharpoons
\mathrm{H}^++\mathrm{OH}^-`.
However, this approach is highly
inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of
both protons and hydroxyl ions is low, resulting in a relatively low
acceptance rate of MC moves.
However, this approach is highly inefficient at :math:`\mathrm{pH}
\approx 7` when the concentration of both protons and hydroxyl ions is
low, resulting in a relatively low acceptance rate of MC moves.
A more efficient way is to allow salt ions to participate in ionization
reactions, which can be easily achieved via
@ -108,10 +105,13 @@ reactions, which can be easily achieved via
fix acid_reaction2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
where particles of atom type 4 and 5 are the salt cations and anions, both at activity (effective concentration) of :math:`10^{-2}` mol/l, see :ref:`(Curk1) <Curk1>` and
:ref:`(Landsgesell) <Landsgesell>` for more details.
where particles of atom type 4 and 5 are the salt cations and anions,
both at activity (effective concentration) of :math:`10^{-2}` mol/l, see
:ref:`(Curk1) <Curk1>` and :ref:`(Landsgesell) <Landsgesell>` for more
details.
We could have simultaneously added a base ionization reaction (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
We could have simultaneously added a base ionization reaction
(:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
.. code-block:: LAMMPS
@ -122,7 +122,18 @@ where the fix will attempt to charge :math:`\mathrm{B}` (discharge
insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3.
Dissociated ions and salt ions can be combined into a single particle type, which reduces the number of necessary MC moves and increases sampling performance, see :ref:`(Curk1) <Curk1>`. The :math:`\mathrm{H}^+` and monovalent salt cation (:math:`\mathrm{S}^+`) are combined into a single particle type, :math:`\mathrm{X}^+ = \{\mathrm{H}^+, \mathrm{S}^+\}`. In this case "pIp" refers to the effective concentration of the combined cation type :math:`\mathrm{X}^+` and its value is determined by :math:`10^{-\mathrm{pIp}} = 10^{-\mathrm{pH}} + 10^{-\mathrm{pSp}}`, where :math:`10^{-\mathrm{pSp}}` is the effective concentration of salt cations. For example, at pH=7 and pSp=6 we would find pIp~5.958 and the command that performs reactions with combined ions could read,
Dissociated ions and salt ions can be combined into a single particle
type, which reduces the number of necessary MC moves and increases
sampling performance, see :ref:`(Curk1) <Curk1>`. The
:math:`\mathrm{H}^+` and monovalent salt cation (:math:`\mathrm{S}^+`)
are combined into a single particle type, :math:`\mathrm{X}^+ =
\{\mathrm{H}^+, \mathrm{S}^+\}`. In this case "pIp" refers to the
effective concentration of the combined cation type :math:`\mathrm{X}^+`
and its value is determined by :math:`10^{-\mathrm{pIp}} =
10^{-\mathrm{pH}} + 10^{-\mathrm{pSp}}`, where
:math:`10^{-\mathrm{pSp}}` is the effective concentration of salt
cations. For example, at pH=7 and pSp=6 we would find pIp~5.958 and the
command that performs reactions with combined ions could read,
.. code-block:: LAMMPS
@ -138,16 +149,16 @@ If neither the acid or the base type is specified, for example,
the fix simply inserts or deletes an ion pair of a free cation (atom
type 4) and a free anion (atom type 5) as done in a conventional
grand-canonical MC simulation. Multivalent ions can be inserted (deleted) by using the *onlysalt* keyword.
grand-canonical MC simulation. Multivalent ions can be inserted
(deleted) by using the *onlysalt* keyword.
The fix is compatible with LAMMPS sub-packages such as *molecule* or
*rigid*. The acid and base particles can be part of larger
molecules or rigid bodies. Free ions that are inserted to or deleted
from the system must be defined as single particles (no bonded
interactions allowed) and cannot be part of larger molecules or rigid
bodies. If *molecule* package is used, all inserted ions have a molecule
ID equal to zero.
This fix is compatible with LAMMPS packages such as MOLECULE or
RIGID. The acid and base particles can be part of larger molecules or
rigid bodies. Free ions that are inserted to or deleted from the system
must be defined as single particles (no bonded interactions allowed) and
cannot be part of larger molecules or rigid bodies. If an atom style
with molecule IDs is used, all inserted ions have a molecule ID equal to
zero.
Note that LAMMPS implicitly assumes a constant number of particles
(degrees of freedom). Since using this fix alters the total number of
@ -164,14 +175,15 @@ Langevin thermostat:
fix fT all langevin 1.0 1.0 1.0 123
fix_modify fT temp dtemp
The units of pH, pKa, pKb, pIp, pIm are considered to be in the standard -log10
representation assuming reference concentration :math:`\rho_0 =
\mathrm{mol}/\mathrm{l}`. For example, in the dilute
The units of pH, pKa, pKb, pIp, pIm are considered to be in the
standard -log10 representation assuming reference concentration
:math:`\rho_0 = \mathrm{mol}/\mathrm{l}`. For example, in the dilute
ideal solution limit, the concentration of free cations will be
:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. To perform the internal unit
conversion, the the value of the LAMMPS unit length must be
specified in nanometers via *lunit_nm*. The default value is set to the Bjerrum length in water
at room temperature (0.71 nm), *lunit_nm* = 0.71.
:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. To
perform the internal unit conversion, the the value of the LAMMPS unit
length must be specified in nanometers via *lunit_nm*. The default value
is set to the Bjerrum length in water at room temperature (0.71 nm),
*lunit_nm* = 0.71.
The temperature used in MC acceptance probability is set by *temp*. This
temperature should be the same as the temperature set by the molecular
@ -236,9 +248,9 @@ quantities:
Restrictions
""""""""""""
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 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.
The :doc:`atom_style <atom_style>`, used must contain the charge
property, for example, the style could be *charge* or *full*. Only

7
doc/src/fix_dt_reset.rst
View File

@ -1,8 +1,11 @@
.. index:: fix dt/reset
.. index:: fix dt/reset/kk
fix dt/reset command
====================
Accelerator Variants: *dt/reset/kk*
Syntax
""""""
@ -86,6 +89,10 @@ allows dump files to be written at intervals specified by simulation
time, rather than by timesteps. Simulation time is in time units;
see the :doc:`units <units>` doc page for details.
----------
.. include:: accel_styles.rst
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

421
doc/src/fix_electrode.rst Normal file
View File

@ -0,0 +1,421 @@
.. index:: fix electrode/conp
.. index:: fix electrode/conq
.. index:: fix electrode/thermo
.. index:: fix electrode/conp/intel
.. index:: fix electrode/conq/intel
.. index:: fix electrode/thermo/intel
fix electrode/conp command
==========================
Accelerator Variant: *electrode/conp/intel*
fix electrode/conq command
==========================
Accelerator Variant: *electrode/conq/intel*
fix electrode/thermo command
============================
Accelerator Variant: *electrode/thermo/intel*
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID style args keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* style = *electrode/conp* or *electrode/conq* or *electrode/thermo*
* args = arguments used by a particular style
.. parsed-literal::
*electrode/conp* args = potential eta
*electrode/conq* args = charge eta
*electrode/thermo* args = potential eta *temp* values
potential = electrode potential
charge = electrode charge
eta = reciprocal width of electrode charge smearing
*temp* values = T_v tau_v rng_v
T_v = temperature of thermo-potentiostat
tau_v = time constant of thermo-potentiostat
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*
.. parsed-literal::
*algo* values = *mat_inv* or *mat_cg* tol or *cg* tol
specify the algorithm used to compute the electrode charges
*symm* value = *on* or *off*
turn on/off charge neutrality constraint for the electrodes
*couple* values = group-ID val
group-ID = group of atoms treated as additional electrode
val = electric potential or charge on this electrode
*etypes* value = *on* or *off*
turn on/off type-based optimized neighbor lists (electrode and electrolyte types may not overlap)
*ffield* value = *on* or *off*
turn on/off finite-field implementation
*write_mat* value = filename
filename = file to which to write elastance matrix
*write_inv* value = filename
filename = file to which to write inverted matrix
*read_mat* value = filename
filename = file from which to read elastance matrix
*read_inv* value = filename
filename = file from which to read inverted matrix
Examples
""""""""
.. code-block:: LAMMPS
fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on
fix fxconp electrodes electrode/conq 0.0 1.805 algo cg 1e-5
fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0
Description
"""""""""""
The *electrode* fixes implement the constant potential method (CPM)
(:ref:`Siepmann <Siepmann>`, :ref:`Reed <Reed3>`), and modern variants,
to accurately model electrified, conductive electrodes. This is
primarily useful for studying electrode-electrolyte interfaces,
especially at high potential differences or ionicities, with non-planar
electrodes such as nanostructures or nanopores, and to study dynamic
phenomena such as charging or discharging time scales or conductivity or
ionic diffusivities.
Each *electrode* fix allows users to set additional electrostatic
relationships between the specified groups which model useful
electrostatic configurations:
* *electrode/conp* sets potentials or potential differences between electrodes
* (resulting in changing electrode total charges)
* *electrode/conq* sets the total charge on each electrode
* (resulting in changing electrode potentials)
* *electrode/thermo* sets a thermopotentiostat
:ref:`(Deissenbeck)<Deissenbeck>` between two electrodes
* (resulting in changing charges and potentials with appropriate
average potential difference and thermal variance)
The first group-ID provided to each fix specifies the first electrode
group, and more group(s) are added using the *couple* keyword for each
additional group. While *electrode/thermo* only accepts two groups,
*electrode/conp* and *electrode/conq* accept any number of groups, up to
LAMMPS's internal restrictions (see Restrictions below). Electrode
groups must not overlap, i.e. the fix will issue an error if any
particle is detected to belong to at least two electrode groups.
CPM involves updating charges on groups of electrode particles, per time
step, so that the system's total energy is minimized with respect to
those charges. From basic electrostatics, this is equivalent to making
each group conductive, or imposing an equal electrostatic potential on
every particle in the same group (hence the name CPM). The charges are
usually modelled as a Gaussian distribution to make the charge-charge
interaction matrix invertible (:ref:`Gingrich <Gingrich>`). The keyword
*eta* specifies the distribution's width in units of inverse length.
.. versionadded:: 22Dec2022
Three algorithms are available to minimize the energy, varying in how
matrices are pre-calculated before a run to provide computational
speedup. These algorithms can be selected using the keyword *algo*:
* *algo mat_inv* pre-calculates the capacitance matrix and obtains the
charge configuration in one matrix-vector calculation per time step
* *algo mat_cg* pre-calculates the elastance matrix (inverse of
capacitance matrix) and obtains the charge configuration using a
conjugate gradient solver in multiple matrix-vector calculations per
time step
* *algo cg* does not perform any pre-calculation and obtains the charge
configuration using a conjugate gradient solver and multiple
calculations of the electric potential per time step.
For both *cg* methods, the command must specify the conjugate gradient
tolerance. *fix electrode/thermo* currently only supports the *mat_inv*
algorithm.
The keyword *symm* can be set *on* (or *off*) to turn on (or turn off)
the capacitance matrix constraint that sets total electrode charge to be
zero. This has slightly different effects for each *fix electrode*
variant. For *fix electrode/conp*, with *symm off*, the potentials
specified are absolute potentials, but the charge configurations
satisfying them may add up to an overall non-zero, varying charge for
the electrodes (and thus the simulation box). With *symm on*, the total
charge over all electrode groups is constrained to zero, and potential
differences rather than absolute potentials are the physically relevant
quantities.
For *fix electrode/conq*, with *symm off*, overall neutrality is
explicitly obeyed or violated by the user input (which is not
checked!). With *symm on*, overall neutrality is ensured by ignoring the
user-input charge for the last listed electrode (instead, its charge
will always be minus the total sum of all other electrode charges). For
*fix electrode/thermo*, overall neutrality is always automatically
imposed for any setting of *symm*, but *symm on* allows finite-field
mode (*ffield on*, described below) for faster simulations.
For all three fixes, any potential (or charge for *conq*) can be
specified as an equal-style variable prefixed with "v\_". For example,
the following code will ramp the potential difference between electrodes
from 0.0V to 2.0V over the course of the simulation:
.. code-block:: LAMMPS
fix fxconp bot electrode/conp 0.0 1.805 couple top v_v symm on
variable v equal ramp(0.0, 2.0)
Note that these fixes only parse their supplied variable name when
starting a run, and so these fixes will accept equal-style variables
defined *after* the fix definition, including variables dependent on the
fix's own output. This is useful, for example, in the fix's internal
finite-field commands (see below). For an advanced example of this see
the in.conq2 input file in the directory
``examples/PACKAGES/electrode/graph-il``.
This fix necessitates the use of a long range solver that calculates and
provides the matrix of electrode-electrode interactions and a vector of
electrode-electrolyte interactions. The Kspace styles
*ewald/electrode*, *pppm/electrode* and *pppm/electrode/intel* are
created specifically for this task :ref:`(Ahrens-Iwers) <Ahrens-Iwers>`.
For systems with non-periodic boundaries in one or two directions dipole
corrections are available with the :doc:`kspace_modify <kspace_modify>`.
For ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) <Hu>`
can be used by setting "slab ew2d":
.. code-block:: LAMMPS
kspace_modify slab <slab_factor>
kspace_modify wire <wire_factor>
kspace_modify slab ew2d
Two implementations for the calculation of the elastance matrix are
available with pppm and can be selected using the *amat onestep/twostep*
keyword. *onestep* is the default; *twostep* can be faster for large
electrodes and a moderate mesh size but requires more memory.
.. code-block:: LAMMPS
kspace_modify amat onestep/twostep
For all versions of the fix, the keyword-value *ffield on* enables the
finite-field mode (:ref:`Dufils <Dufils>`, :ref:`Tee <Tee>`), which uses
an electric field across a periodic cell instead of non-periodic
boundary conditions to impose a potential difference between the two
electrodes bounding the cell. The fix (with name *fix-ID*) detects which
of the two electrodes is "on top" (has the larger maximum *z*-coordinate
among all particles). Assuming the first electrode group is on top, it
then issues the following commands internally:
.. code-block:: LAMMPS
variable fix-ID_ffield_zfield equal (f_fix-ID[2]-f_fix-ID[1])/lz
efield fix-ID_efield all efield 0.0 0.0 v_fix-ID_ffield_zfield
which implements the required electric field as the potential difference
divided by cell length. The internal commands use variable so that the
electric field will correctly vary with changing potentials in the
correct way (for example with equal-style potential difference or with
*fix electrode/conq*). This keyword requires two electrodes and will
issue an error with any other number of electrodes. This keyword
requires electroneutrality to be imposed (*symm on*) and will issue an
error otherwise.
.. versionchanged:: 22Dec2022
For all versions of the fix, the keyword-value *etypes on* enables
type-based optimized neighbor lists. With this feature enabled, LAMMPS
provides the fix with an occasional neighbor list restricted to
electrode-electrode interactions for calculating the electrode matrix,
and a perpetual neighbor list restricted to electrode-electrolyte
interactions for calculating the electrode potentials, using particle
types to list only desired interactions, and typically resulting in
5--10\% less computational time. Without this feature the fix will
simply use the active pair style's neighbor list. This feature cannot
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.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix currently does not write any information to restart files.
The *fix_modify tf* option enables the Thomas-Fermi metallicity model
(:ref:`Scalfi <Scalfi>`) and allows parameters to be set for each atom type.
.. code-block:: LAMMPS
fix_modify ID tf type length voronoi
If this option is used parameters must be set for all atom types of the
electrode.
The *fix_modify timer* option turns on (off) additional timer outputs in the log
file, for code developers to track optimization.
.. code-block:: LAMMPS
fix_modify ID timer on/off
----------
These fixes compute a global (extensive) scalar, a global (intensive)
vector, and a global array, which can be accessed by various
:doc:`output commands <Howto_output>`.
The global scalar outputs the energy added to the system by this fix,
which is the negative of the total charge on each electrode multiplied
by that electrode's potential.
The global vector outputs the potential on each electrode (and thus has
*N* entries if the fix manages *N* electrode groups), in :doc:`units
<units>` of electric field multiplied by distance (thus volts for *real*
and *metal* units). The electrode groups' ordering follows the order in
which they were input in the fix command using *couple*. The global
vector output is useful for *fix electrode/conq* and *fix
electrode/thermo*, where potential is dynamically updated based on
electrolyte configuration instead of being directly set.
The global array has *N* rows and *2N+1* columns, where the fix manages
*N* electrode groups managed by the fix. For the *I*-th row of the
array, the elements are:
* array[I][1] = total charge that group *I* would have had *if it were
at 0 V applied potential* * array[I][2 to *N* + 1] = the *N* entries
of the *I*-th row of the electrode capacitance matrix (definition
follows) * array[I][*N* + 2 to *2N* + 1] = the *N* entries of the
*I*-th row of the electrode elastance matrix (the inverse of the
electrode capacitance matrix)
The :math:`N \times N` electrode capacitance matrix, denoted :math:`\mathbf{C}`
in the following equation, summarizes how the total charge induced on each
electrode (:math:`\mathbf{Q}` as an *N*-vector) is related to the potential on
each electrode, :math:`\mathbf{V}`, and the charge-at-0V :math:`\mathbf{Q}_{0V}`
(which is influenced by the local electrolyte structure):
.. math::
\mathbf{Q} = \mathbf{Q}_{0V} + \mathbf{C} \cdot \mathbf{V}
The charge-at-0V, electrode capacitance and elastance matrices are internally
used to calculate the potentials required to induce the specified total
electrode charges in *fix electrode/conq* and *fix electrode/thermo*. With the
*symm on* option, the electrode capacitance matrix would be singular, and thus
its last row is replaced with *N* copies of its top-left entry
(:math:`\mathbf{C}_{11}`) for invertibility.
The global array output is mainly useful for quickly determining the 'vacuum
capacitance' of the system (capacitance with only electrodes, no electrolyte),
and can also be used for advanced simulations setting the potential as some
function of the charge-at-0V (such as the ``in.conq2`` example mentioned above).
Please cite :ref:`(Ahrens-Iwers2022) <Ahrens-Iwers2>` in any publication that
uses this implementation. Please cite also the publication on the combination
of the CPM with PPPM if you use *pppm/electrode* :ref:`(Ahrens-Iwers)
<Ahrens-Iwers>`.
----------
Restrictions
""""""""""""
For algorithms that use a matrix for the electrode-electrode
interactions, positions of electrode particles have to be immobilized at
all times.
With *ffield off* (i.e. the default), the box geometry is expected to be
*z*-non-periodic (i.e. *boundary p p f*), and this fix will issue an
error if the box is *z*-periodic. With *ffield on*, the box geometry is
expected to be *z*-periodic, and this fix will issue an error if the box
is *z*-non-periodic.
The parallelization for the fix works best if electrode atoms are evenly
distributed across processors. For a system with two electrodes at the bottom
and top of the cell this can be achieved with *processors * * 2*, or with the
line
.. code-block:: LAMMPS
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
which avoids an error if the script is run on an odd number of
processors (such as on just one processor for testing).
The fix creates an additional group named *[fix-ID]_group* which is the
union of all electrode groups supplied to LAMMPS. This additional group
counts towards LAMMPS's limitation on the total number of groups
(currently 32), which may not allow scripts that use that many groups to
run with this fix.
The matrix-based algorithms (*algo mat_inv* and *algo mat_cg*) currently
store an interaction matrix (either elastance or capacitance) of *N* by
*N* doubles for each MPI process. This memory requirement may be
prohibitive for large electrode groups. The fix will issue a warning if
it expects to use more than 0.5 GiB of memory.
Default
"""""""
The default keyword-option settings are *algo mat_inv*, *symm off*,
*etypes off* and *ffield off*.
----------
.. include:: accel_styles.rst
----------
.. _Siepmann:
**(Siepmann)** Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).
.. _Reed3:
**(Reed)** Reed *et al.*, J. Chem. Phys. 126, 084704 (2007).
.. _Deissenbeck:
**(Deissenbeck)** Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021).
.. _Gingrich:
**(Gingrich)** Gingrich, `MSc thesis` <https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf>` (2010).
.. _Ahrens-Iwers:
**(Ahrens-Iwers)** Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
.. _Hu:
**(Hu)** Hu, J. Chem. Theory Comput. 10, 5254 (2014).
.. _Dufils:
**(Dufils)** Dufils *et al.*, Phys. Rev. Letters 123, 195501 (2019).
.. _Tee:
**(Tee)** Tee and Searles, J. Chem. Phys. 156, 184101 (2022).
.. _Scalfi:
**(Scalfi)** Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020).
.. _Ahrens-Iwers2:
**(Ahrens-Iwers2022)** Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022).

230
doc/src/fix_electrode_conp.rst
View File

@ -1,230 +0,0 @@
.. index:: fix electrode/conp
.. index:: fix electrode/conq
.. index:: fix electrode/thermo
.. index:: fix electrode/conp/intel
.. index:: fix electrode/conq/intel
.. index:: fix electrode/thermo/intel
fix electrode/conp command
==========================
Accelerator Variant: *electrode/conp/intel*
fix electrode/conq command
==========================
Accelerator Variant: *electrode/conq/intel*
fix electrode/thermo command
============================
Accelerator Variant: *electrode/thermo/intel*
Syntax
""""""
.. parsed-literal::
fix ID group-ID style args keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* style = *electrode/conp* or *electrode/conq* or *electrode/thermo*
* args = arguments used by a particular style
.. parsed-literal::
*electrode/conp* args = potential eta
*electrode/conq* args = charge eta
*electrode/thermo* args = potential eta *temp* values
potential = electrode potential
charge = electrode charge
eta = reciprocal width of electrode charge smearing
*temp* values = T_v tau_v rng_v
T_v = temperature of thermo-potentiostat
tau_v = time constant of thermo-potentiostat
rng_v = integer used to initialize random number generator
* zero or more keyword/value pairs may be appended
* keyword = *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv*
.. parsed-literal::
*symm* value = *on* or *off*
turn on/off charge neutrality constraint for the electrodes
*couple* values = group-ID val
group-ID = group of atoms treated as additional electrode
val = electric potential or charge on this electrode
*etypes* values = type
type = atom type (can be a range) exclusive to the electrode for optimized neighbor lists
*ffield* value = *on* or *off*
turn on/off finite-field implementation
*write_mat* value = filename
filename = file to which to write elastance matrix
*write_inv* value = filename
filename = file to which to write inverted matrix
*read_mat* value = filename
filename = file from which to read elastance matrix
*read_inv* value = filename
filename = file from which to read inverted matrix
Examples
""""""""
.. code-block:: LAMMPS
fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on
fix fxconp electrodes electrode/conq 0.0 1.805
fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0
Description
"""""""""""
fix electrode/conp mode implements a constant potential method (CPM)
(:ref:`Siepmann <Siepmann>`, :ref:`Reed <Reed3>`). Charges of groups specified
via group-ID and optionally with the `couple` keyword are adapted to meet their respective
potential at every time step. An arbitrary number of electrodes can be set but
the respective groups may not overlap. Electrode charges have a Gaussian charge
distribution with reciprocal width eta. The energy minimization is achieved via
matrix inversion :ref:`(Wang) <Wang5>`.
fix electrode/conq enforces a total charge specified in the input on each electrode. The energy is
minimized w.r.t. the charge distribution within the electrode.
fix electrode/thermo implements a thermo-potentiostat :ref:`(Deissenbeck)
<Deissenbeck>`. Temperature and time constant of the thermo-potentiostat need
to be specified using the temp keyword. Currently, only two electrodes are possible with
this style.
This fix necessitates the use of a long range solver that calculates and provides the matrix
of electrode-electrode interactions and a vector of electrode-electrolyte
interactions. The Kspace styles *ewald/electrode*, *pppm/electrode* and
*pppm/electrode/intel* are created specifically for this task
:ref:`(Ahrens-Iwers) <Ahrens-Iwers>`.
For systems with non-periodic boundaries in one or two directions dipole
corrections are available with the :doc:`kspace_modify <kspace_modify>`. For
ewald/electrode a two-dimensional Ewald summation :ref:`(Hu) <Hu>` can be used
by setting "slab ew2d":
.. code-block:: LAMMPS
kspace_modify slab <slab_factor>
kspace_modify wire <wire_factor>
kspace_modify slab ew2d
Two implementations for the calculation of the elastance matrix are available
with pppm and can be selected using the *amat onestep/twostep* keyword.
*onestep* is the default; *twostep* can be faster for large electrodes and a
moderate mesh size but requires more memory.
.. code-block:: LAMMPS
kspace_modify amat onestep/twostep
The *fix_modify tf* option enables the Thomas-Fermi metallicity model
(:ref:`Scalfi <Scalfi>`) and allows parameters to be set for each atom type.
.. code-block:: LAMMPS
fix_modify ID tf type length voronoi
If this option is used parameters must be set for all atom types of the electrode.
The *fix_modify timer* option turns on (off) additional timer outputs in the log
file, for code developers to track optimization.
.. code-block:: LAMMPS
fix_modify ID timer on/off
The *fix_modify set* options allow calculated quantities to be accessed via
internal variables. Currently four types of quantities can be accessed:
.. code-block:: LAMMPS
fix-modify ID set v group-ID variablename
fix-modify ID set qsb group-ID variablename
fix-modify ID set mc group-ID1 group-ID2 variablename
fix-modify ID set me group-ID1 group-ID2 variablename
One use case is to output the potential that is internally calculated and
applied to each electrode group by *fix electrode/conq* or *fix electrode/thermo*.
For that case the *v* option makes *fix electrode* update the variable
*variablename* with the potential applied to group *group-ID*, where *group-ID*
must be a group whose charges are updated by *fix electrode* and *variablename*
must be an internal-style variable:
.. code-block:: LAMMPS
fix conq bot electrode/conq -1.0 1.979 couple top 1.0
variable vbot internal 0.0
fix_modify conq set v bot vbot
The *qsb* option similarly outputs the total updated charge of the group if its
potential were 0.0V. The *mc* option requires two *group-IDs*, and outputs the
entry \{*group-ID1*, *group-ID2*\} of the (symmetric) *macro-capacitance* matrix
(MC) which relates the electrodes' applied potentials (V), total charges (Q), and
total charges at 0.0 V (Qsb):
.. math::
\mathbf{Q} = \mathbf{Q}_{SB} + \mathbf{MC} \cdot \mathbf{V}
Lastly, the *me* option also requires two *group-IDs* and outputs the entry
\{*group-ID1*, *group-ID2*\} of the *macro-elastance* matrix, which is the
inverse of the macro-capacitance matrix. (As the names denote, the
macro-capacitance matrix gives electrode charges from potentials, and the
macro-elastance matrix gives electrode potentials from charges).
.. warning::
Positions of electrode particles have to be immobilized at all times.
The parallelization for the fix works best if electrode atoms are evenly
distributed across processors. For a system with two electrodes at the bottom
and top of the cell this can be achieved with *processors * * 2*, or with the
line
.. code-block:: LAMMPS
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
which avoids an error if the script is run on an odd number of processors (such
as on just one processor for testing).
----------
.. include:: accel_styles.rst
----------
.. _Siepmann:
**(Siepmann)** Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).
.. _Reed3:
**(Reed)** Reed *et al.*, J. Chem. Phys. 126, 084704 (2007).
.. _Wang5:
**(Wang)** Wang *et al.*, J. Chem. Phys. 141, 184102 (2014).
.. _Deissenbeck:
**(Deissenbeck)** Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021).
.. _Ahrens-Iwers:
**(Ahrens-Iwers)** Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
.. _Hu:
**(Hu)** Hu, J. Chem. Theory Comput. 10, 5254 (2014).
.. _Scalfi:
**(Scalfi)** Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020).

6
doc/src/fix_ipi.rst
View File

@ -90,6 +90,12 @@ coordinates are transferred. However, one could use this strategy to
define an external potential acting on the atoms that are moved by
i-PI.
Since the i-PI code uses atomic units internally, this fix needs to
convert LAMMPS data to and from its :doc:`specified units <units>`
accordingly when communicating with i-PI. This is not possible for
reduced units ("units lj") and thus *fix ipi* will stop with an error in
this case.
This fix is part of the MISC package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.

97
doc/src/fix_nh_uef.rst
View File

@ -44,19 +44,23 @@ Examples
Description
"""""""""""
This fix can be used to simulate non-equilibrium molecular dynamics
(NEMD) under diagonal flow fields, including uniaxial and bi-axial
flow. Simulations under continuous extensional flow may be carried
out for an indefinite amount of time. It is an implementation of the
boundary conditions from :ref:`(Dobson) <Dobson>`, and also uses numerical
These fixes can be used to simulate non-equilibrium molecular dynamics
(NEMD) under diagonal flow fields, including uniaxial and bi-axial flow.
Simulations under continuous extensional flow may be carried out for an
indefinite amount of time. It is an implementation of the boundary
conditions from :ref:`(Dobson) <Dobson>`, and also uses numerical
lattice reduction as was proposed by :ref:`(Hunt) <Hunt>`. The lattice
reduction algorithm is from :ref:`(Semaev) <Semaev>`. The fix is intended for
simulations of homogeneous flows, and integrates the SLLOD equations
of motion, originally proposed by Hoover and Ladd (see :ref:`(Evans and Morriss) <Sllod>`). Additional detail about this implementation can be
found in :ref:`(Nicholson and Rutledge) <Nicholson>`.
reduction algorithm is from :ref:`(Semaev) <Semaev>`. The fix is
intended for simulations of homogeneous flows, and integrates the SLLOD
equations of motion, originally proposed by Hoover and Ladd (see
:ref:`(Evans and Morriss) <Sllod>`). Additional detail about this
implementation can be found in :ref:`(Nicholson and Rutledge)
<Nicholson>`.
Note that NEMD simulations of a continuously strained system can be
performed using the :doc:`fix deform <fix_deform>`, :doc:`fix nvt/sllod <fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>` commands.
performed using the :doc:`fix deform <fix_deform>`, :doc:`fix nvt/sllod
<fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>`
commands.
The applied flow field is set by the *eps* keyword. The values
*edot_x* and *edot_y* correspond to the strain rates in the xx and yy
@ -73,11 +77,11 @@ to -(*edot_x* + *edot_y*).
The boundary conditions require a simulation box that does not have a
consistent alignment relative to the applied flow field. Since LAMMPS
utilizes an upper-triangular simulation box, it is not possible to
express the evolving simulation box in the same coordinate system as
the flow field. This fix keeps track of two coordinate systems: the
flow frame, and the upper triangular LAMMPS frame. The coordinate
systems are related to each other through the QR decomposition, as is
illustrated in the image below.
express the evolving simulation box in the same coordinate system as the
flow field. These fixes keep track of two coordinate systems: the flow
frame, and the upper triangular LAMMPS frame. The coordinate systems are
related to each other through the QR decomposition, as is illustrated in
the image below.
.. image:: JPG/uef_frames.jpg
:align: center
@ -99,12 +103,12 @@ using the dump command will be in the LAMMPS frame unless the
----------
Temperature control is achieved with the default Nose-Hoover style
thermostat documented in :doc:`fix npt <fix_nh>`. When this fix is
thermostat documented in :doc:`fix nvt <fix_nh>`. When this fix is
active, only the peculiar velocity of each atom is stored, defined as
the velocity relative to the streaming velocity. This is in contrast
to :doc:`fix nvt/sllod <fix_nvt_sllod>`, which uses a lab-frame
velocity, and removes the contribution from the streaming velocity in
order to compute the temperature.
the velocity relative to the streaming velocity. This is in contrast to
:doc:`fix nvt/sllod <fix_nvt_sllod>`, which uses a lab-frame velocity,
and removes the contribution from the streaming velocity in order to
compute the temperature.
Pressure control is achieved using the default Nose-Hoover barostat
documented in :doc:`fix npt <fix_nh>`. There are two ways to control the
@ -156,8 +160,8 @@ The following commands will not work:
----------
These fix computes a temperature and pressure each timestep. To do
this, it creates its own computes of style "temp/uef" and
These fixes compute a temperature and pressure each timestep. To do
this, they create their own computes of style "temp/uef" and
"pressure/uef", as if one of these two sets of commands had been
issued:
@ -169,18 +173,19 @@ issued:
compute fix-ID_temp all temp/uef
compute fix-ID_press all pressure/uef fix-ID_temp
See the :doc:`compute temp/uef <compute_temp_uef>` and :doc:`compute pressure/uef <compute_pressure_uef>` commands for details. Note
that the IDs of the new computes are the fix-ID + underscore + "temp"
or fix_ID + underscore + "press".
See the :doc:`compute temp/uef <compute_temp_uef>` and :doc:`compute
pressure/uef <compute_pressure_uef>` commands for details. Note that
the IDs of the new computes are the fix-ID + underscore + "temp" or
fix_ID + underscore + "press".
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The fix writes the state of all the thermostat and barostat variables,
as well as the cumulative strain applied, to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>` command
for info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion.
as well as the cumulative strain applied, to :doc:`binary restart files
<restart>`. See the :doc:`read_restart <read_restart>` command for info
on how to re-specify a fix in an input script that reads a restart file,
so that the operation of the fix continues in an uninterrupted fashion.
.. note::
@ -189,43 +194,41 @@ uninterrupted fashion.
not contain the cumulative applied strain, will this keyword be
necessary.
This fix can be used with the :doc:`fix_modify <fix_modify>` *temp* and
*press* options. The temperature and pressure computes used must be of
type *temp/uef* and *pressure/uef*\ .
These fixes can be used with the :doc:`fix_modify <fix_modify>` *temp*
and *press* options. The temperature and pressure computes used must be
of type *temp/uef* and *pressure/uef*\ .
This fix computes the same global scalar and vector quantities as :doc:`fix npt <fix_nh>`.
These fixes compute the same global scalar and vector quantities as
:doc:`fix nvt andnpt <fix_nh>`.
The fix is not invoked during :doc:`energy minimization <minimize>`.
These fixes are not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the UEF package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
These fixes are part of the UEF package. They are only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Due to requirements of the boundary conditions, when the *strain*
keyword is set to zero (or unset), the initial simulation box must be
cubic and have style triclinic. If the box is initially of type ortho,
use :doc:`change_box <change_box>` before invoking the fix.
.. note::
When resuming from restart files, you may need to use :doc:`box tilt
large <box>` since LAMMPS has internal criteria from lattice
reduction that are not the same as the criteria in the numerical
lattice reduction algorithm.
Related commands
""""""""""""""""
:doc:`fix nvt <fix_nh>`, :doc:`fix nvt/sllod <fix_nvt_sllod>`, :doc:`compute temp/uef <compute_temp_uef>`, :doc:`compute pressure/uef <compute_pressure_uef>`, :doc:`dump cfg/uef <dump_cfg_uef>`
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, `fix nvt/sllod
:doc:<fix_nvt_sllod>`, `compute temp/uef <compute_temp_uef>`,
:doc::doc:`compute pressure/uef <compute_pressure_uef>`, `dump cfg/uef
:doc:<dump_cfg_uef>`
Default
"""""""
The default keyword values specific to this fix are exy = xyz, strain
= 0 0. The remaining defaults are the same as for :doc:`fix npt <fix_nh>`
except tchain = 1. The reason for this change is given in
The default keyword values specific to these fixes are exy = xyz, strain
= 0 0. The remaining defaults are the same as for :doc:`fix nvt or npt
<fix_nh>` except tchain = 1. The reason for this change is given in
:doc:`fix nvt/sllod <fix_nvt_sllod>`.
----------

2
doc/src/fix_pimd.rst
View File

@ -156,6 +156,8 @@ This fix is part of the REPLICA package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
Fix pid cannot be used with :doc:`lj units <units>`.
A PIMD simulation can be initialized with a single data file read via
the :doc:`read_data <read_data>` command. However, this means all
quasi-beads in a ring polymer will have identical positions and

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

@ -0,0 +1,188 @@
.. index:: fix sgcmc
fix sgcmc command
=================
Syntax
""""""
.. parsed-literal::
fix ID group-ID sgcmc every_nsteps swap_fraction temperature deltamu ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* sgcmc = style name of this fix command
* every_nsteps = number of MD steps between MC cycles
* swap_fraction = fraction of a full MC cycle carried out at each call (a value of 1.0 will perform as many trial moves as there are atoms)
* temperature = temperature that enters Boltzmann factor in Metropolis criterion (usually the same as MD temperature)
* deltamu = chemical potential difference(s) (`N-1` values must be provided, with `N` being the number of elements)
* Zero or more keyword/value pairs may be appended to fix definition line:
.. parsed-literal::
keyword = *variance* or *randseed* or *window_moves* or *window_size*
*variance* kappa conc1 [conc2] ... [concN]
kappa = variance constraint parameter
conc1,conc2,... = target concentration(s) in the range 0.0-1.0 (*N-1* values must be provided, with *N* being the number of elements)
*randseed* N
N = seed for pseudo random number generator
*window_moves* N
N = number of times sampling window is moved during one MC cycle
*window_size* frac
frac = size of sampling window (must be between 0.5 and 1.0)
Examples
""""""""
.. code-block:: LAMMPS
fix mc all sgcmc 50 0.1 400.0 -0.55
fix vc all sgcmc 20 0.2 700.0 -0.7 randseed 324234 variance 2000.0 0.05
fix 2 all sgcmc 20 0.1 700.0 -0.7 window_moves 20
Description
"""""""""""
.. versionadded:: 22Dec2022
This command allows to carry out parallel hybrid molecular
dynamics/Monte Carlo (MD/MC) simulations using the algorithms described
in :ref:`(Sadigh1) <Sadigh1>`. Simulations can be carried out in either
the semi-grand canonical (SGC) or variance constrained semi-grand
canonical (VC-SGC) ensemble :ref:`(Sadigh2) <Sadigh2>`. Only atom type
swaps are performed by the SGCMC fix. Relaxations are accounted for by
the molecular dynamics integration steps.
This fix can be used with standard multi-element EAM potentials
(:doc:`pair styles eam/alloy or eam/fs <pair_eam>`)
The SGCMC fix can handle Finnis/Sinclair type EAM potentials where
:math:`\rho(r)` is atom-type specific, such that different elements can
contribute differently to the total electron density at an atomic site
depending on the identity of the element at that atomic site.
------------
If this fix is applied, the regular MD simulation will be interrupted in
defined intervals to carry out a fraction of a Monte Carlo (MC)
cycle. The interval is set using the parameter *every_nsteps* which
determines how many MD integrator steps are taken between subsequent
calls to the MC routine.
It is possible to carry out pure lattice MC simulations by setting
*every_nsteps* to 1 and not defining an integration fix such as NVE,
NPT etc. In that case, the particles will not move and only the MC
routine will be called to perform atom type swaps.
The parameter *swap_fraction* determines how many MC trial steps are carried
out every time the MC routine is entered. It is measured in units of full MC
cycles where one full cycle, *swap_fraction=1*, corresponds to as many MC
trial steps as there are atoms.
------------
The parameter *temperature* specifies the temperature that is used
to evaluate the Metropolis acceptance criterion. While it usually
should be set to the same value as the MD temperature there are cases
when it can be useful to use two different values for at least part of
the simulation, e.g., to speed up equilibration at low temperatures.
------------
The parameter *deltamu* is used to set the chemical potential difference
in the SGC MC algorithm (see Eq. 16 in :ref:`Sadigh1 <Sadigh1>`). By
convention it is the difference of the chemical potentials of elements
`B`, `C` ..., with respect to element A. When the simulation includes
`N` elements, `N-1` values must be specified.
------------
The variance-constrained SGC MC algorithm is activated if the keyword
*variance* is used. In that case the fix parameter *deltamu* determines
the effective average constraint in the parallel VC-SGC MC algorithm
(parameter :math:`\delta\mu_0` in Eq. (20) of :ref:`Sadigh1
<Sadigh1>`). The parameter *kappa* specifies the variance constraint
(see Eqs. (20-21) in :ref:`Sadigh1 <Sadigh1>`).
The parameter *conc* sets the target concentration (parameter
:math:`c_0` in Eqs. (20-21) of :ref:`Sadigh1 <Sadigh1>`). The atomic
concentrations refer to components `B`, `C` ..., with `A` being set
automatically. When the simulation includes `N` elements, `N-1`
concentration values must be specified.
------------
There are several technical parameters that can be set via optional flags.
*randseed* is expected to be a positive integer number and is used
to initialize the random number generator on each processor.
*window_size* controls the size of the sampling window in a parallel MC
simulation. The size has to lie between 0.5 and 1.0. Normally, this
parameter should be left unspecified which instructs the code to choose
the optimal window size automatically (see Sect. III.B and Figure 6 in
:ref:`Sadigh1 <Sadigh1>` for details).
The number of times the window is moved during a MC cycle is set using
the parameter *window_moves* (see Sect. III.B in :ref:`Sadigh1
<Sadigh1>` for details).
------------
Restart, fix_modify, output, run start/stop, minimize info
==========================================================
No information about this fix is written to restart files.
The MC routine keeps track of the global concentration(s) as well as the
number of accepted and rejected trial swaps during each MC step. These
values are provided by the sgcmc fix in the form of a global vector that
can be accessed by various :doc:`output commands <Howto_output>`
components of the vector represent the following quantities:
* 1 = The absolute number of accepted trial swaps during the last MC step
* 2 = The absolute number of rejected trial swaps during the last MC step
* 3 = The current global concentration of species *A* (= number of atoms of type 1 / total number of atoms)
* 4 = The current global concentration of species *B* (= number of atoms of type 2 / total number of atoms)
* ...
* N+2: The current global concentration of species *X* (= number of atoms of type *N* / total number of atoms)
Restrictions
============
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.
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
supported by using the generic potential functions. This, however, will
lead to exceedingly slow simulations since it implies that the
energy of the *entire* system is recomputed at each MC trial step. If
other potentials are to be used it is strongly recommended to modify and
optimize the existing generic potential functions for this purpose.
Also, the generic energy calculation can not be used for parallel
execution i.e. it only works with a single MPI process.
------------
Default
=======
The optional parameters default to the following values:
* *randseed* = 324234
* *window_moves* = 8
* *window_size* = automatic
------------
.. _Sadigh1:
**(Sadigh1)** B. Sadigh, P. Erhart, A. Stukowski, A. Caro, E. Martinez, and L. Zepeda-Ruiz, Phys. Rev. B **85**, 184203 (2012)
.. _Sadigh2:
**(Sadigh2)** B. Sadigh and P. Erhart, Phys. Rev. B **86**, 134204 (2012)

112
doc/src/fix_ttm.rst
View File

@ -183,29 +183,32 @@ embedded within a larger continuum representation of the electronic
subsystem.
The *set* keyword specifies a *Tinit* temperature value to initialize
the value stored on all grid points.
the value stored on all grid points. By default the temperatures
are all zero when the grid is created.
The *infile* keyword specifies an input file of electronic temperatures
for each grid point to be read in to initialize the grid. By default
the temperatures are all zero when the grid is created. The input file
is a text file which may have comments starting with the '#' character.
Each line contains four numeric columns: ix,iy,iz,Temperature. Empty
or comment-only lines will be ignored. The
number of lines must be equal to the number of user-specified grid
points (Nx by Ny by Nz). The ix,iy,iz are grid point indices ranging
from 0 to nxnodes-1 inclusive in each dimension. The lines can appear
in any order. For example, the initial electronic temperatures on a 1
by 2 by 3 grid could be specified in the file as follows:
for each grid point to be read in to initialize the grid, as an alternative
to using the *set* keyword.
The input file is a text file which may have comments starting with
the '#' character. Each line contains four numeric columns:
ix,iy,iz,Temperature. Empty or comment-only lines will be
ignored. The number of lines must be equal to the number of
user-specified grid points (Nx by Ny by Nz). The ix,iy,iz are grid
point indices ranging from 1 to Nxyz inclusive in each dimension. The
lines can appear in any order. For example, the initial electronic
temperatures on a 1 by 2 by 3 grid could be specified in the file as
follows:
.. parsed-literal::
# UNITS: metal COMMENT: initial electron temperature
0 0 0 1.0
0 0 1 1.0
0 0 2 1.0
0 1 0 2.0
0 1 1 2.0
0 1 2 2.0
1 1 1 1.0
1 1 2 1.0
1 1 3 1.0
1 2 1 2.0
1 2 2 2.0
1 2 3 2.0
where the electronic temperatures along the y=0 plane have been set to
1.0, and the electronic temperatures along the y=1 plane have been set
@ -223,17 +226,31 @@ units used.
The *outfile* keyword has 2 values. The first value *Nout* triggers
output of the electronic temperatures for each grid point every Nout
timesteps. The second value is the filename for output which will
be suffixed by the timestep. The format of each output file is exactly
timesteps. The second value is the filename for output, which will be
suffixed by the timestep. The format of each output file is exactly
the same as the input temperature file. It will contain a comment in
the first line reporting the date the file was created, the LAMMPS
units setting in use, grid size and the current timestep.
Note that the atomic temperature for atoms in each grid cell can also
be computed and output by the :doc:`fix ave/chunk <fix_ave_chunk>`
command using the :doc:`compute chunk/atom <compute_chunk_atom>`
command to create a 3d array of chunks consistent with the grid used
by this fix.
.. note::
The fix ttm/grid command does not support the *outfile* keyword.
Instead you can use the :doc:`dump grid <dump>` command to output
the electronic temperature on the distributed grid to a dump file or
the :doc:`restart <restart>` command which creates a file specific
to this fix which the :doc:`read restart <read_restart>` command
reads. The file has the same format as the file the *infile* option
reads.
For the fix ttm and fix ttm/mod commands, the corresponding atomic
temperature for atoms in each grid cell can be computed and output by
the :doc:`fix ave/chunk <fix_ave_chunk>` command using the
:doc:`compute chunk/atom <compute_chunk_atom>` command to create a 3d
array of chunks consistent with the grid used by this fix.
For the fix ttm/grid command the same thing can be done using the
:doc:`fix ave/grid <fix_ave_grid>` command and its per-grid values can
be output via the :doc:`dump grid <dump>` command.
----------
@ -339,19 +356,25 @@ ignored. The lines with the even numbers are treated as follows:
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
These fixes write the state of the electronic subsystem and the energy
exchange between the subsystems to :doc:`binary restart files
<restart>`. See the :doc:`read_restart <read_restart>` command for
info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion. Note that the restart script must define the
same size grid as the original script.
The fix ttm and fix ttm/mod commands write the state of the electronic
subsystem and the energy exchange between the subsystems to
:doc:`binary restart files <restart>`. The fix ttm/grid command does
not yet support writing of its distributed grid to a restart file.
Because the state of the random number generator is not saved in the
restart files, this means you cannot do "exact" restarts with this
fix, where the simulation continues on the same as if no restart had
taken place. However, in a statistical sense, a restarted simulation
should produce the same behavior.
See the :doc:`read_restart <read_restart>` command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion. Note
that the restart script must define the same size grid as the original
script.
The fix ttm/grid command also outputs an auxiliary file each time a
restart file is written, with the electron temperatures for each grid
cell. The format of this file is the same as that read by the
*infile* option explained above. The filename is the same as the
restart filename with ".ttm" appended. This auxiliary file can be
read in for a restarted run by using the *infile* option for the fix
ttm/grid command, following the :doc:`read_restart <read_restart>`
command.
None of the :doc:`fix_modify <fix_modify>` options are relevant to
these fixes.
@ -371,6 +394,14 @@ electronic subsystem energies reported at the end of the timestep.
The vector values calculated are "extensive".
The fix ttm/grid command also outputs a per-grid vector which stores
the electron temperature for each grid cell in temperature :doc:`units
<units>`. which can be accessed by various :doc:`output commands
<Howto_output>`. The length of the vector (distributed across all
processors) is Nx * Ny * Nz. For access by other commands, the name
of the single grid produced by fix ttm/grid is "grid". The name of
its per-grid data is "data".
No parameter of the fixes can be used with the *start/stop* keywords
of the :doc:`run <run>` command. The fixes are not invoked during
:doc:`energy minimization <minimize>`.
@ -385,6 +416,15 @@ package <Build_package>` page for more info.
As mentioned above, these fixes require 3d simulations and orthogonal
simulation boxes periodic in all 3 dimensions.
These fixes used a random number generator to Langevin thermostat the
electron temperature. This means you will not get identical answers
when running on different numbers of processors or when restarting a
simulation (even on the same number of processors). However, in a
statistical sense, simulations on different processor counts and
restarted simulation should produce results which are statistically
the same.
Related commands
""""""""""""""""

7
doc/src/fix_viscous.rst
View File

@ -1,8 +1,11 @@
.. index:: fix viscous
.. index:: fix viscous/kk
fix viscous command
===================
Accelerator Variants: *viscous/kk*
Syntax
""""""
@ -84,6 +87,10 @@ more easily be used as a thermostat.
----------
.. include:: accel_styles.rst
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

30
doc/src/kim_commands.rst
View File

@ -1333,13 +1333,13 @@ For example,
Citation of OpenKIM IMs
"""""""""""""""""""""""
When publishing results obtained using OpenKIM IMs researchers are requested
to cite the OpenKIM project :ref:`(Tadmor) <kim-mainpaper>`, KIM API
:ref:`(Elliott) <kim-api>`, and the specific IM codes used in the simulations,
in addition to the relevant scientific references for the IM. The citation
format for an IM is displayed on its page on
`OpenKIM <https://openkim.org>`_ along with the corresponding BibTex file, and
is automatically added to the LAMMPS citation reminder.
When publishing results obtained using OpenKIM IMs researchers are
requested to cite the OpenKIM project :ref:`(Tadmor) <kim-mainpaper>`,
KIM API :ref:`(Elliott) <kim-api>`, and the specific IM codes used in
the simulations, in addition to the relevant scientific references for
the IM. The citation format for an IM is displayed on its page on
`OpenKIM <https://openkim.org>`_ along with the corresponding BibTex
file, and is automatically added to the LAMMPS citation reminder.
Citing the IM software (KIM infrastructure and specific PM or SM codes) used in
the simulation gives credit to the researchers who developed them and enables
@ -1348,15 +1348,15 @@ open source efforts like OpenKIM to function.
Restrictions
""""""""""""
The *kim* command is part of the KIM package. It is only enabled if LAMMPS is
built with that package. A requirement for the KIM package, is the KIM API
library that must be downloaded from the
`OpenKIM website <https://openkim.org/kim-api/>`_ and installed before LAMMPS is
The *kim* command is part of the KIM package. It is only enabled if
LAMMPS is built with that package. A requirement for the KIM package,
is the KIM API library that must be downloaded from the `OpenKIM website
<https://openkim.org/kim-api/>`_ and installed before LAMMPS is
compiled. When installing LAMMPS from binary, the kim-api package is a
dependency that is automatically downloaded and installed. The *kim query*
command requires the *libcurl* library to be installed. The *kim property*
command requires *Python* 3.6 or later and the *kim-property* python package to
be installed. See the KIM section of the
dependency that is automatically downloaded and installed. The *kim
query* command requires the *libcurl* library to be installed. The *kim
property* command requires *Python* 3.6 or later and the *kim-property*
python package to be installed. See the KIM section of the
:doc:`Packages details <Packages_details>` for details.
Furthermore, when using *kim* command to run KIM SMs, any packages required by

62
doc/src/kspace_modify.rst
View File

@ -51,7 +51,6 @@ Syntax
*slab* value = volfactor or *nozforce*
volfactor = ratio of the total extended volume used in the
2d approximation compared with the volume of the simulation domain
*ew2d* EW2D correction (available with ELECTRODE package)
*nozforce* turns off kspace forces in the z direction
*splittol* value = tol
tol = relative size of two eigenvalues (see discussion below)
@ -381,18 +380,22 @@ solver is set up.
The *slab* keyword allows an Ewald or PPPM solver to be used for a
systems that are periodic in x,y but non-periodic in z - a
:doc:`boundary <boundary>` setting of "boundary p p f". This is done by
treating the system as if it were periodic in z, but inserting empty
volume between atom slabs and removing dipole inter-slab interactions
so that slab-slab interactions are effectively turned off. The
volfactor value sets the ratio of the extended dimension in z divided
by the actual dimension in z. The recommended value is 3.0. A larger
value is inefficient; a smaller value introduces unwanted slab-slab
:doc:`boundary <boundary>` setting of "boundary p p f". This is done
by treating the system as if it were periodic in z, but inserting
empty volume between atom slabs and removing dipole inter-slab
interactions so that slab-slab interactions are effectively turned
off. The volfactor value sets the ratio of the extended dimension in
z divided by the actual dimension in z. It must be a value >= 1.0. A
value of 1.0 (the default) means the slab approximation is not used.
The recommended value for volfactor is 3.0. A larger value is
inefficient; a smaller value introduces unwanted slab-slab
interactions. The use of fixed boundaries in z means that the user
must prevent particle migration beyond the initial z-bounds, typically
by providing a wall-style fix. The methodology behind the *slab*
option is explained in the paper by :ref:`(Yeh) <Yeh>`. The *slab* option
is also extended to non-neutral systems :ref:`(Ballenegger) <Ballenegger>`.
option is explained in the paper by :ref:`(Yeh) <Yeh>`. The *slab*
option is also extended to non-neutral systems :ref:`(Ballenegger)
<Ballenegger>`.
An alternative slab option can be invoked with the *nozforce* keyword
in lieu of the volfactor. This turns off all kspace forces in the z
@ -402,8 +405,8 @@ boundaries can be set using :doc:`boundary <boundary>` (the slab
approximation in not needed). The *slab* keyword is not currently
supported by Ewald or PPPM when using a triclinic simulation cell. The
slab correction has also been extended to point dipole interactions
:ref:`(Klapp) <Klapp>` in :doc:`kspace_style <kspace_style>` *ewald/disp*,
*ewald/dipole*, and *pppm/dipole*\ .
:ref:`(Klapp) <Klapp>` in :doc:`kspace_style <kspace_style>`
*ewald/disp*, *ewald/dipole*, and *pppm/dipole*\ .
.. note::
@ -448,15 +451,32 @@ Related commands
Default
"""""""
The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff =
ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace
= -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel,
order = order/disp = 7. For scafacos settings, the scafacos tolerance
option depends on the method chosen, as documented above. The
scafacos fmm_tuning default = 0.
The option defaults are as follows:
* compute = yes
* cutoff/adjust = yes (MSM)
* diff = ik (PPPM)
* disp/auto = no
* fftbench = no (PPPM)
* force = -1.0,
* force/disp/kspace = -1.0
* force/disp/real = -1.0
* gewald = gewald/disp = 0.0
* mesh = mesh/disp = 0 0 0
* minorder = 2
* mix/disp = pair
* order = 10 (MSM)
* order = order/disp = 5 (PPPM)
* order = order/disp = 7 (PPPM/intel)
* overlap = yes
* pressure/scalar = yes (MSM)
* slab = 1.0
* split = 0
* tol = 1.0e-6
For scafacos settings, the scafacos tolerance option depends on the
method chosen, as documented above. The scafacos fmm_tuning default
= 0.
----------

2
doc/src/kspace_style.rst
View File

@ -283,7 +283,7 @@ parameters and how to choose them is described in
----------
The *electrode* styles add methods that are required for the constant potential
method implemented in :doc:`fix electrode/* <fix_electrode_conp>`. The styles
method implemented in :doc:`fix electrode/* <fix_electrode>`. The styles
*ewald/electrode*, *pppm/electrode* and *pppm/electrode/intel* are available.
These styles do not support the `kspace_modify slab nozforce` command.

44
doc/src/pair_coul.rst
View File

@ -174,11 +174,11 @@ shifted force model described in :ref:`Fennell <Fennell1>`, given by:
E = q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
where :math:`\alpha` is the damping parameter and erfc() is the
complementary error-function. The potential corrects issues in the
Wolf model (described below) to provide consistent forces and energies
(the Wolf potential is not differentiable at the cutoff) and smooth
decay to zero.
where :math:`\alpha` is the damping parameter and *erfc()* is the
complementary error-function. The potential corrects issues in the Wolf
model (described below) to provide consistent forces and energies (the
Wolf potential is not differentiable at the cutoff) and smooth decay to
zero.
----------
@ -192,30 +192,32 @@ summation method, described in :ref:`Wolf <Wolf1>`, given by:
\frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
where :math:`\alpha` is the damping parameter, and erc() and erfc() are
error-function and complementary error-function terms. This potential
is essentially a short-range, spherically-truncated,
where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()*
are error-function and complementary error-function terms. This
potential is essentially a short-range, spherically-truncated,
charge-neutralized, shifted, pairwise *1/r* summation. With a
manipulation of adding and subtracting a self term (for i = j) to the
first and second term on the right-hand-side, respectively, and a
small enough :math:`\alpha` damping parameter, the second term shrinks and
the potential becomes a rapidly-converging real-space summation. With
a long enough cutoff and small enough :math:`\alpha` parameter, the energy and
forces calculated by the Wolf summation method approach those of the
first and second term on the right-hand-side, respectively, and a small
enough :math:`\alpha` damping parameter, the second term shrinks and the
potential becomes a rapidly-converging real-space summation. With a
long enough cutoff and small enough :math:`\alpha` parameter, the energy
and forces calculated by the Wolf summation method approach those of the
Ewald sum. So it is a means of getting effective long-range
interactions with a short-range potential.
----------
Style *coul/streitz* is the Coulomb pair interaction defined as part
of the Streitz-Mintmire potential, as described in :ref:`this paper <Streitz2>`, in which charge distribution about an atom is modeled
as a Slater 1\ *s* orbital. More details can be found in the referenced
Style *coul/streitz* is the Coulomb pair interaction defined as part of
the Streitz-Mintmire potential, as described in :ref:`this paper
<Streitz2>`, in which charge distribution about an atom is modeled as a
Slater 1\ *s* orbital. More details can be found in the referenced
paper. To fully reproduce the published Streitz-Mintmire potential,
which is a variable charge potential, style *coul/streitz* must be
used with :doc:`pair_style eam/alloy <pair_eam>` (or some other
short-range potential that has been parameterized appropriately) via
the :doc:`pair_style hybrid/overlay <pair_hybrid>` command. Likewise,
charge equilibration must be performed via the :doc:`fix qeq/slater <fix_qeq>` command. For example:
which is a variable charge potential, style *coul/streitz* must be used
with :doc:`pair_style eam/alloy <pair_eam>` (or some other short-range
potential that has been parameterized appropriately) via the
:doc:`pair_style hybrid/overlay <pair_hybrid>` command. Likewise,
charge equilibration must be performed via the :doc:`fix qeq/slater
<fix_qeq>` command. For example:
.. code-block:: LAMMPS

10
doc/src/pair_dpd_ext.rst
View File

@ -1,17 +1,19 @@
.. index:: pair_style dpd/ext
.. index:: pair_style dpd/ext/kk
.. index:: pair_style dpd/ext/omp
.. index:: pair_style dpd/ext/tstat
.. index:: pair_style dpd/ext/tstat/kk
.. index:: pair_style dpd/ext/tstat/omp
pair_style dpd/ext command
==========================
Accelerator Variants: dpd/ext/kk
Accelerator Variants: dpd/ext/kk dpd/ext/omp
pair_style dpd/ext/tstat command
================================
Accelerator Variants: dpd/ext/tstat/kk
Accelerator Variants: dpd/ext/tstat/kk dpd/ext/tstat/omp
Syntax
""""""
@ -113,10 +115,10 @@ each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command
as in the examples above:
* A (force units)
* :math:`\gamma_{\perp}` (force/velocity units)
* :math:`\gamma_{\parallel}` (force/velocity units)
* :math:`s_{\perp}` (unitless)
* :math:`\gamma_{\perp}` (force/velocity units)
* :math:`s_{\parallel}` (unitless)
* :math:`s_{\perp}` (unitless)
* :math:`r_c` (distance units)
The last coefficient is optional. If not specified, the global DPD

97
doc/src/pair_pod.rst Normal file
View File

@ -0,0 +1,97 @@
.. index:: pair_style pod
pair_style pod command
========================
Syntax
""""""
.. code-block:: LAMMPS
pair_style pod
Examples
""""""""
.. code-block:: LAMMPS
pair_style pod
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
Description
"""""""""""
.. versionadded:: 22Dec2022
Pair style *pod* defines the proper orthogonal descriptor (POD)
potential :ref:`(Nguyen) <Nguyen20221>`. The mathematical definition of
the POD potential is described from :doc:`fitpod <fitpod_command>`, which is
used to fit the POD potential to *ab initio* energy and force data.
Only a single pair_coeff command is used with the *pod* style which
specifies a POD parameter file followed by a coefficient file.
The coefficient file (``Ta_coefficients.pod``) contains coefficients for the
POD potential. The top of the coefficient file can contain any number of
blank and comment lines (start with #), but follows a strict format
after that. The first non-blank non-comment line must contain:
* POD_coefficients: *ncoeff*
This is followed by *ncoeff* coefficients, one per line. The coefficient
file is generated after training the POD potential using :doc:`fitpod
<fitpod_command>`.
The POD parameter file (``Ta_param.pod``) can contain blank and comment lines
(start with #) anywhere. Each non-blank non-comment line must contain
one keyword/value pair. See :doc:`fitpod <fitpod_command>` for the description
of all the keywords that can be assigned in the parameter file.
As an example, if a LAMMPS indium phosphide simulation has 4 atoms
types, with the first two being indium and the third and fourth being
phophorous, the pair_coeff command would look like this:
.. code-block:: LAMMPS
pair_coeff * * pod InP_param.pod InP_coefficients.pod In In P P
The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
The two filenames are for the parameter and coefficient files, respectively.
The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
POD 'In' element. The two trailing 'P' arguments map LAMMPS atom types
3 and 4 to the POD 'P' element.
If a POD mapping value is specified as NULL, the mapping is not
performed. This can be used when a *pod* 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.
Examples about training and using POD potentials are found in the
directory lammps/examples/PACKAGES/pod.
----------
Restrictions
""""""""""""
This style is part of the ML-POD package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This pair style does not compute per-atom energies and per-atom stresses.
Related commands
""""""""""""""""
:doc:`fitpod <fitpod_command>`,
Default
"""""""
none
----------
.. _Nguyen20221:
**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022).

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