Merge branch 'master' into fire
This commit is contained in:
Steve Plimpton
1
.github/CODEOWNERS
vendored
1
.github/CODEOWNERS
vendored
@ -111,6 +111,7 @@ src/exceptions.h @rbberger
|
||||
src/fix_nh.* @athomps
|
||||
src/info.* @akohlmey @rbberger
|
||||
src/timer.* @akohlmey
|
||||
src/min* @sjplimp @stanmoore1
|
||||
|
||||
# tools
|
||||
tools/msi2lmp/* @akohlmey
|
||||
|
||||
@ -46,10 +46,14 @@ endif()
|
||||
find_path (NETCDF_INCLUDE_DIR netcdf.h
|
||||
HINTS "${NETCDF_DIR}/include")
|
||||
mark_as_advanced (NETCDF_INCLUDE_DIR)
|
||||
|
||||
set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
|
||||
|
||||
string(REGEX REPLACE "/include/?$" ""
|
||||
NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
|
||||
|
||||
find_library (NETCDF_LIBRARY NAMES netcdf
|
||||
HINTS "${NETCDF_DIR}/lib")
|
||||
HINTS "${NETCDF_DIR}" "${NETCDF_LIB_HINT}" PATH_SUFFIXES lib lib64)
|
||||
mark_as_advanced (NETCDF_LIBRARY)
|
||||
|
||||
set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
|
||||
|
||||
55
cmake/Modules/FindPNetCDF.cmake
Normal file
55
cmake/Modules/FindPNetCDF.cmake
Normal file
@ -0,0 +1,55 @@
|
||||
# source: https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/CMake/FindPNetCDF.cmake
|
||||
# license: GPL v3 (https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/COPYING)
|
||||
#
|
||||
# - Find PNetCDF
|
||||
# Find the native PNetCDF includes and library
|
||||
#
|
||||
# PNETCDF_INCLUDES - where to find netcdf.h, etc
|
||||
# PNETCDF_LIBRARIES - Link these libraries when using NetCDF
|
||||
# PNETCDF_FOUND - True if PNetCDF was found
|
||||
#
|
||||
# Normal usage would be:
|
||||
# find_package (PNetCDF REQUIRED)
|
||||
# target_link_libraries (uses_pnetcdf ${PNETCDF_LIBRARIES})
|
||||
|
||||
if (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
|
||||
# Already in cache, be silent
|
||||
set (PNETCDF_FIND_QUIETLY TRUE)
|
||||
endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
|
||||
|
||||
find_path (PNETCDF_INCLUDES pnetcdf.h
|
||||
HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")
|
||||
|
||||
string(REGEX REPLACE "/include/?$" ""
|
||||
PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})
|
||||
|
||||
find_library (PNETCDF_LIBRARIES
|
||||
NAMES pnetcdf
|
||||
HINTS ${PNETCDF_LIB_HINT} PATH_SUFFIXES lib lib64)
|
||||
|
||||
if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
|
||||
message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")
|
||||
|
||||
file(TO_CMAKE_PATH "$ENV{LD_LIBRARY_PATH}" LD_LIBRARY_PATH)
|
||||
|
||||
find_library(PNETCDF_LIBRARIES
|
||||
NAMES pnetcdf
|
||||
HINTS ${LD_LIBRARY_PATH})
|
||||
|
||||
if (PNETCDF_LIBRARIES)
|
||||
get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)
|
||||
string(REGEX REPLACE "/(lib|lib64)/?$" "/include"
|
||||
PNETCDF_H_HINT ${PNETCDF_LIB_DIR})
|
||||
|
||||
find_path (PNETCDF_INCLUDES pnetcdf.h
|
||||
HINTS ${PNETCDF_H_HINT}
|
||||
DOC "Path to pnetcdf.h")
|
||||
endif()
|
||||
endif()
|
||||
|
||||
# handle the QUIETLY and REQUIRED arguments and set PNETCDF_FOUND to TRUE if
|
||||
# all listed variables are TRUE
|
||||
include (FindPackageHandleStandardArgs)
|
||||
find_package_handle_standard_args (PNetCDF DEFAULT_MSG PNETCDF_LIBRARIES PNETCDF_INCLUDES)
|
||||
|
||||
mark_as_advanced (PNETCDF_LIBRARIES PNETCDF_INCLUDES)
|
||||
@ -5,6 +5,16 @@ if(PKG_KIM)
|
||||
include_directories(${CURL_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
|
||||
add_definitions(-DLMP_KIM_CURL)
|
||||
set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
|
||||
mark_as_advanced(LMP_DEBUG_CURL)
|
||||
if(LMP_DEBUG_CURL)
|
||||
add_definitions(-DLMP_DEBUG_CURL)
|
||||
endif()
|
||||
set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
|
||||
mark_as_advanced(LMP_NO_SSL_CHECK)
|
||||
if(LMP_NO_SSL_CHECK)
|
||||
add_definitions(-DLMP_NO_SSL_CHECK)
|
||||
endif()
|
||||
endif()
|
||||
find_package(KIM-API QUIET)
|
||||
if(KIM-API_FOUND)
|
||||
|
||||
@ -1,6 +1,24 @@
|
||||
if(PKG_USER-NETCDF)
|
||||
find_package(NetCDF REQUIRED)
|
||||
include_directories(${NETCDF_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
|
||||
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
|
||||
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
|
||||
# NetCDF library enables dump sytle "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
|
||||
find_package(NetCDF)
|
||||
if(NETCDF_FOUND)
|
||||
find_package(PNetCDF)
|
||||
else(NETCDF_FOUND)
|
||||
find_package(PNetCDF REQUIRED)
|
||||
endif(NETCDF_FOUND)
|
||||
|
||||
if(NETCDF_FOUND)
|
||||
include_directories(${NETCDF_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
|
||||
add_definitions(-DLMP_HAS_NETCDF)
|
||||
endif(NETCDF_FOUND)
|
||||
|
||||
if(PNETCDF_FOUND)
|
||||
include_directories(${PNETCDF_INCLUDES})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${PNETCDF_LIBRARIES})
|
||||
add_definitions(-DLMP_HAS_PNETCDF)
|
||||
endif(PNETCDF_FOUND)
|
||||
|
||||
add_definitions(-DNC_64BIT_DATA=0x0020)
|
||||
endif()
|
||||
|
||||
46
doc/Makefile
46
doc/Makefile
@ -31,7 +31,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
|
||||
SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
|
||||
OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)
|
||||
|
||||
.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check
|
||||
.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check
|
||||
|
||||
# ------------------------------------------
|
||||
|
||||
@ -46,6 +46,7 @@ help:
|
||||
@echo " clean remove all intermediate RST files"
|
||||
@echo " clean-all reset the entire build environment"
|
||||
@echo " anchor_check scan for duplicate anchor labels"
|
||||
@echo " style_check check for complete and consistent style lists"
|
||||
@echo " spelling spell-check the manual"
|
||||
|
||||
# ------------------------------------------
|
||||
@ -69,6 +70,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
|
||||
echo "############################################" ;\
|
||||
rst_anchor_check src/*.rst ;\
|
||||
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
|
||||
python utils/check-styles.py -s ../src -d src ;\
|
||||
echo "############################################" ;\
|
||||
deactivate ;\
|
||||
)
|
||||
@ -122,24 +124,27 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
|
||||
cd ../../; \
|
||||
)
|
||||
@(\
|
||||
. $(VENV)/bin/activate ;\
|
||||
sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
|
||||
echo "############################################" ;\
|
||||
rst_anchor_check src/*.rst ;\
|
||||
echo "############################################" ;\
|
||||
deactivate ;\
|
||||
. $(VENV)/bin/activate ;\
|
||||
sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
|
||||
echo "############################################" ;\
|
||||
rst_anchor_check src/*.rst ;\
|
||||
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
|
||||
python utils/check-styles.py -s ../src -d src ;\
|
||||
echo "############################################" ;\
|
||||
deactivate ;\
|
||||
)
|
||||
@cd latex && \
|
||||
sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
|
||||
mv temp Makefile && \
|
||||
sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
|
||||
mv tmp.tex LAMMPS.tex && \
|
||||
sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
|
||||
mv tmp.tex LAMMPS.tex && \
|
||||
make && \
|
||||
make && \
|
||||
mv LAMMPS.pdf ../Manual.pdf && \
|
||||
cd ../;
|
||||
sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
|
||||
mv temp Makefile && \
|
||||
sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
|
||||
mv tmp.tex LAMMPS.tex && \
|
||||
sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
|
||||
mv tmp.tex LAMMPS.tex && \
|
||||
make && \
|
||||
make && \
|
||||
make && \
|
||||
mv LAMMPS.pdf ../Manual.pdf && \
|
||||
cd ../;
|
||||
@rm -rf latex/_sources
|
||||
@rm -rf latex/PDF
|
||||
@rm -rf latex/USER
|
||||
@ -166,6 +171,13 @@ anchor_check : $(ANCHORCHECK)
|
||||
deactivate ;\
|
||||
)
|
||||
|
||||
style_check :
|
||||
@(\
|
||||
. $(VENV)/bin/activate ;\
|
||||
python utils/check-styles.py -s ../src -d src ;\
|
||||
deactivate ;\
|
||||
)
|
||||
|
||||
# ------------------------------------------
|
||||
|
||||
$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
.TH LAMMPS "20 November 2019" "2019-11-20"
|
||||
.TH LAMMPS "9 January 2020" "2020-01-09"
|
||||
.SH NAME
|
||||
.B LAMMPS
|
||||
\- Molecular Dynamics Simulator.
|
||||
|
||||
5
doc/src/.gitignore
vendored
5
doc/src/.gitignore
vendored
@ -1,2 +1,3 @@
|
||||
Eqs
|
||||
JPG
|
||||
/Eqs
|
||||
/JPG
|
||||
/false_positives.txt
|
||||
|
||||
@ -195,12 +195,32 @@ minutes to hours) to build. Of course you only need to do that once.)
|
||||
.. parsed-literal::
|
||||
|
||||
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes
|
||||
-D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on
|
||||
-D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer, value = no (default) or yes
|
||||
|
||||
If DOWNLOAD\_KIM is set, the KIM library will be downloaded and built
|
||||
inside the CMake build directory. If the KIM library is already on
|
||||
your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH
|
||||
environment variable so that libkim-api can be found.
|
||||
|
||||
For using OpenKIM web queries in LAMMPS.
|
||||
|
||||
If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any
|
||||
libcurl calls within the KIM web query display a lot of information about
|
||||
libcurl operations. You hardly ever want this set in production use, you will
|
||||
almost always want this when you debug/report problems.
|
||||
|
||||
The libcurl performs peer SSL certificate verification by default. This
|
||||
verification is done using a CA certificate store that the SSL library can
|
||||
use to make sure the peer's server certificate is valid. If SSL reports an
|
||||
error ("certificate verify failed") during the handshake and thus refuses
|
||||
further communication with that server, you can set LMP\_NO\_SSL\_CHECK.
|
||||
If LMP\_NO\_SSL\_CHECK is set, libcurl does not verify the peer and connection
|
||||
succeeds regardless of the names in the certificate. This option is insecure.
|
||||
As an alternative, you can specify your own CA cert path by setting the
|
||||
environment variable CURL\_CA\_BUNDLE to the path of your choice. A call to the
|
||||
KIM web query would get this value from the environmental variable.
|
||||
|
||||
**Traditional make**\ :
|
||||
|
||||
You can download and build the KIM library manually if you prefer;
|
||||
|
||||
@ -27,8 +27,3 @@ commands in it are used to define a LAMMPS simulation.
|
||||
:maxdepth: 1
|
||||
|
||||
Commands_removed
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,59 +1,141 @@
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>` | :doc:`Compute styles <Commands_compute>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :doc:`Pair styles <Commands_pair>` | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :ref:`Dihedral styles <dihedral>` | :ref:`Improper styles <improper>` | :doc:`KSpace styles <Commands_kspace>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 3
|
||||
|
||||
* :doc:`General commands <Commands_all>`
|
||||
* :doc:`Fix styles <Commands_fix>`
|
||||
* :doc:`Compute styles <Commands_compute>`
|
||||
* :doc:`Pair styles <Commands_pair>`
|
||||
* :ref:`Bond styles <bond>`
|
||||
* :ref:`Angle styles <angle>`
|
||||
* :ref:`Dihedral styles <dihedral>`
|
||||
* :ref:`Improper styles <improper>`
|
||||
* :doc:`KSpace styles <Commands_kspace>`
|
||||
|
||||
General commands
|
||||
================
|
||||
|
||||
An alphabetic list of all general LAMMPS commands.
|
||||
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`angle\_coeff <angle_coeff>` | :doc:`angle\_style <angle_style>` | :doc:`atom\_modify <atom_modify>` | :doc:`atom\_style <atom_style>` | :doc:`balance <balance>` | :doc:`bond\_coeff <bond_coeff>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :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>` | :doc:`comm\_style <comm_style>` | :doc:`compute <compute>` | :doc:`compute\_modify <compute_modify>` | :doc:`create\_atoms <create_atoms>` | :doc:`create\_bonds <create_bonds>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`create\_box <create_box>` | :doc:`delete\_atoms <delete_atoms>` | :doc:`delete\_bonds <delete_bonds>` | :doc:`dielectric <dielectric>` | :doc:`dihedral\_coeff <dihedral_coeff>` | :doc:`dihedral\_style <dihedral_style>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`dimension <dimension>` | :doc:`displace\_atoms <displace_atoms>` | :doc:`dump <dump>` | :doc:`dump adios <dump_adios>` | :doc:`dump image <dump_image>` | :doc:`dump movie <dump_image>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`dump netcdf <dump_netcdf>` | :doc:`dump netcdf/mpiio <dump_netcdf>` | :doc:`dump vtk <dump_vtk>` | :doc:`dump\_modify <dump_modify>` | :doc:`dynamical\_matrix <dynamical_matrix>` | :doc:`echo <echo>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`fix <fix>` | :doc:`fix\_modify <fix_modify>` | :doc:`group <group>` | :doc:`group2ndx <group2ndx>` | :doc:`hyper <hyper>` | :doc:`if <if>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`info <info>` | :doc:`improper\_coeff <improper_coeff>` | :doc:`improper\_style <improper_style>` | :doc:`include <include>` | :doc:`jump <jump>` | :doc:`kim\_init <kim_commands>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`kim\_interactions <kim_commands>` | :doc:`kim\_query <kim_commands>` | :doc:`kspace\_modify <kspace_modify>` | :doc:`kspace\_style <kspace_style>` | :doc:`label <label>` | :doc:`lattice <lattice>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`log <log>` | :doc:`mass <mass>` | :doc:`message <message>` | :doc:`minimize <minimize>` | :doc:`min\_modify <min_modify>` | :doc:`min\_style <min_style>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`min\_style spin <min_spin>` | :doc:`molecule <molecule>` | :doc:`ndx2group <group2ndx>` | :doc:`neb <neb>` | :doc:`neb/spin <neb_spin>` | :doc:`neigh\_modify <neigh_modify>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`neighbor <neighbor>` | :doc:`newton <newton>` | :doc:`next <next>` | :doc:`package <package>` | :doc:`pair\_coeff <pair_coeff>` | :doc:`pair\_modify <pair_modify>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`pair\_style <pair_style>` | :doc:`pair\_write <pair_write>` | :doc:`partition <partition>` | :doc:`prd <prd>` | :doc:`print <print>` | :doc:`processors <processors>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`python <python>` | :doc:`quit <quit>` | :doc:`read\_data <read_data>` | :doc:`read\_dump <read_dump>` | :doc:`read\_restart <read_restart>` | :doc:`region <region>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`replicate <replicate>` | :doc:`rerun <rerun>` | :doc:`reset\_ids <reset_ids>` | :doc:`reset\_timestep <reset_timestep>` | :doc:`restart <restart>` | :doc:`run <run>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`run\_style <run_style>` | :doc:`server <server>` | :doc:`set <set>` | :doc:`shell <shell>` | :doc:`special\_bonds <special_bonds>` | :doc:`suffix <suffix>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`tad <tad>` | :doc:`temper <temper>` | :doc:`temper/grem <temper_grem>` | :doc:`temper/npt <temper_npt>` | :doc:`thermo <thermo>` | :doc:`thermo\_modify <thermo_modify>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`thermo\_style <thermo_style>` | :doc:`third\_order <third_order>` | :doc:`timer <timer>` | :doc:`timestep <timestep>` | :doc:`uncompute <uncompute>` | :doc:`undump <undump>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`unfix <unfix>` | :doc:`units <units>` | :doc:`variable <variable>` | :doc:`velocity <velocity>` | :doc:`write\_coeff <write_coeff>` | :doc:`write\_data <write_data>` |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
| :doc:`write\_dump <write_dump>` | :doc:`write\_restart <write_restart>` | | | | |
|
||||
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 6
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
* :doc:`angle_coeff <angle_coeff>`
|
||||
* :doc:`angle_style <angle_style>`
|
||||
* :doc:`atom_modify <atom_modify>`
|
||||
* :doc:`atom_style <atom_style>`
|
||||
* :doc:`balance <balance>`
|
||||
* :doc:`bond_coeff <bond_coeff>`
|
||||
* :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>`
|
||||
* :doc:`comm_style <comm_style>`
|
||||
* :doc:`compute <compute>`
|
||||
* :doc:`compute_modify <compute_modify>`
|
||||
* :doc:`create_atoms <create_atoms>`
|
||||
* :doc:`create_bonds <create_bonds>`
|
||||
* :doc:`create_box <create_box>`
|
||||
* :doc:`delete_atoms <delete_atoms>`
|
||||
* :doc:`delete_bonds <delete_bonds>`
|
||||
* :doc:`dielectric <dielectric>`
|
||||
* :doc:`dihedral_coeff <dihedral_coeff>`
|
||||
* :doc:`dihedral_style <dihedral_style>`
|
||||
* :doc:`dimension <dimension>`
|
||||
* :doc:`displace_atoms <displace_atoms>`
|
||||
* :doc:`dump <dump>`
|
||||
* :doc:`dump adios <dump_adios>`
|
||||
* :doc:`dump image <dump_image>`
|
||||
* :doc:`dump movie <dump_image>`
|
||||
* :doc:`dump netcdf <dump_netcdf>`
|
||||
* :doc:`dump netcdf/mpiio <dump_netcdf>`
|
||||
* :doc:`dump vtk <dump_vtk>`
|
||||
* :doc:`dump_modify <dump_modify>`
|
||||
* :doc:`dynamical_matrix <dynamical_matrix>`
|
||||
* :doc:`echo <echo>`
|
||||
* :doc:`fix <fix>`
|
||||
* :doc:`fix_modify <fix_modify>`
|
||||
* :doc:`group <group>`
|
||||
* :doc:`group2ndx <group2ndx>`
|
||||
* :doc:`hyper <hyper>`
|
||||
* :doc:`if <if>`
|
||||
* :doc:`improper_coeff <improper_coeff>`
|
||||
* :doc:`improper_style <improper_style>`
|
||||
* :doc:`include <include>`
|
||||
* :doc:`info <info>`
|
||||
* :doc:`jump <jump>`
|
||||
* :doc:`kim_init <kim_commands>`
|
||||
* :doc:`kim_interactions <kim_commands>`
|
||||
* :doc:`kim_param <kim_commands>`
|
||||
* :doc:`kim_query <kim_commands>`
|
||||
* :doc:`kspace_modify <kspace_modify>`
|
||||
* :doc:`kspace_style <kspace_style>`
|
||||
* :doc:`label <label>`
|
||||
* :doc:`lattice <lattice>`
|
||||
* :doc:`log <log>`
|
||||
* :doc:`mass <mass>`
|
||||
* :doc:`message <message>`
|
||||
* :doc:`minimize <minimize>`
|
||||
* :doc:`min_modify <min_modify>`
|
||||
* :doc:`min_style <min_style>`
|
||||
* :doc:`min_style spin <min_spin>`
|
||||
* :doc:`molecule <molecule>`
|
||||
* :doc:`ndx2group <group2ndx>`
|
||||
* :doc:`neb <neb>`
|
||||
* :doc:`neb/spin <neb_spin>`
|
||||
* :doc:`neigh_modify <neigh_modify>`
|
||||
* :doc:`neighbor <neighbor>`
|
||||
* :doc:`newton <newton>`
|
||||
* :doc:`next <next>`
|
||||
* :doc:`package <package>`
|
||||
* :doc:`pair_coeff <pair_coeff>`
|
||||
* :doc:`pair_modify <pair_modify>`
|
||||
* :doc:`pair_write <pair_write>`
|
||||
* :doc:`partition <partition>`
|
||||
* :doc:`prd <prd>`
|
||||
* :doc:`print <print>`
|
||||
* :doc:`processors <processors>`
|
||||
* :doc:`python <python>`
|
||||
* :doc:`quit <quit>`
|
||||
* :doc:`read_data <read_data>`
|
||||
* :doc:`read_dump <read_dump>`
|
||||
* :doc:`read_restart <read_restart>`
|
||||
* :doc:`region <region>`
|
||||
* :doc:`replicate <replicate>`
|
||||
* :doc:`rerun <rerun>`
|
||||
* :doc:`reset_ids <reset_ids>`
|
||||
* :doc:`reset_timestep <reset_timestep>`
|
||||
* :doc:`restart <restart>`
|
||||
* :doc:`run <run>`
|
||||
* :doc:`run_style <run_style>`
|
||||
* :doc:`server <server>`
|
||||
* :doc:`set <set>`
|
||||
* :doc:`shell <shell>`
|
||||
* :doc:`special_bonds <special_bonds>`
|
||||
* :doc:`suffix <suffix>`
|
||||
* :doc:`tad <tad>`
|
||||
* :doc:`temper <temper>`
|
||||
* :doc:`temper/grem <temper_grem>`
|
||||
* :doc:`temper/npt <temper_npt>`
|
||||
* :doc:`thermo <thermo>`
|
||||
* :doc:`thermo_modify <thermo_modify>`
|
||||
* :doc:`thermo_style <thermo_style>`
|
||||
* :doc:`third_order <third_order>`
|
||||
* :doc:`timer <timer>`
|
||||
* :doc:`timestep <timestep>`
|
||||
* :doc:`uncompute <uncompute>`
|
||||
* :doc:`undump <undump>`
|
||||
* :doc:`unfix <unfix>`
|
||||
* :doc:`units <units>`
|
||||
* :doc:`variable <variable>`
|
||||
* :doc:`velocity <velocity>`
|
||||
* :doc:`write_coeff <write_coeff>`
|
||||
* :doc:`write_data <write_data>`
|
||||
* :doc:`write_dump <write_dump>`
|
||||
* :doc:`write_restart <write_restart>`
|
||||
*
|
||||
*
|
||||
*
|
||||
*
|
||||
|
||||
@ -1,112 +1,165 @@
|
||||
.. table_from_list::
|
||||
:columns: 3
|
||||
|
||||
* :doc:`General commands <Commands_all>`
|
||||
* :doc:`Fix styles <Commands_fix>`
|
||||
* :doc:`Compute styles <Commands_compute>`
|
||||
* :doc:`Pair styles <Commands_pair>`
|
||||
* :ref:`Bond styles <bond>`
|
||||
* :ref:`Angle styles <angle>`
|
||||
* :ref:`Dihedral styles <dihedral>`
|
||||
* :ref:`Improper styles <improper>`
|
||||
* :doc:`KSpace styles <Commands_kspace>`
|
||||
|
||||
.. _bond:
|
||||
|
||||
Bond\_style potentials
|
||||
=================================
|
||||
Bond_style potentials
|
||||
=====================
|
||||
|
||||
All LAMMPS :doc:`bond\_style <bond_style>` commands. Some styles have
|
||||
All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles have
|
||||
accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
|
||||
| :doc:`none <bond_none>` | :doc:`zero <bond_zero>` | :doc:`hybrid <bond_hybrid>` | |
|
||||
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
|
||||
| | | | |
|
||||
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
|
||||
| :doc:`class2 (ko) <bond_class2>` | :doc:`fene (iko) <bond_fene>` | :doc:`fene/expand (o) <bond_fene_expand>` | :doc:`gromos (o) <bond_gromos>` |
|
||||
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
|
||||
| :doc:`harmonic (iko) <bond_harmonic>` | :doc:`harmonic/shift (o) <bond_harmonic_shift>` | :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>` | :doc:`mm3 <bond_mm3>` |
|
||||
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
|
||||
| :doc:`morse (o) <bond_morse>` | :doc:`nonlinear (o) <bond_nonlinear>` | :doc:`oxdna/fene <bond_oxdna>` | :doc:`oxdna2/fene <bond_oxdna>` |
|
||||
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
|
||||
| :doc:`quartic (o) <bond_quartic>` | :doc:`table (o) <bond_table>` | | |
|
||||
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
|
||||
|
||||
|
||||
----------
|
||||
.. table_from_list::
|
||||
:columns: 4
|
||||
|
||||
* :doc:`none <bond_none>`
|
||||
* :doc:`zero <bond_zero>`
|
||||
* :doc:`hybrid <bond_hybrid>`
|
||||
*
|
||||
*
|
||||
*
|
||||
*
|
||||
*
|
||||
* :doc:`class2 (ko) <bond_class2>`
|
||||
* :doc:`fene (iko) <bond_fene>`
|
||||
* :doc:`fene/expand (o) <bond_fene_expand>`
|
||||
* :doc:`gromos (o) <bond_gromos>`
|
||||
* :doc:`harmonic (iko) <bond_harmonic>`
|
||||
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
|
||||
* :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
|
||||
* :doc:`mm3 <bond_mm3>`
|
||||
* :doc:`morse (o) <bond_morse>`
|
||||
* :doc:`nonlinear (o) <bond_nonlinear>`
|
||||
* :doc:`oxdna/fene <bond_oxdna>`
|
||||
* :doc:`oxdna2/fene <bond_oxdna>`
|
||||
* :doc:`oxrna2/fene <bond_oxdna>`
|
||||
* :doc:`quartic (o) <bond_quartic>`
|
||||
* :doc:`table (o) <bond_table>`
|
||||
*
|
||||
|
||||
.. _angle:
|
||||
|
||||
Angle\_style potentials
|
||||
===================================
|
||||
Angle_style potentials
|
||||
======================
|
||||
|
||||
All LAMMPS :doc:`angle\_style <angle_style>` commands. Some styles have
|
||||
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have
|
||||
accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
|
||||
| :doc:`none <angle_none>` | :doc:`zero <angle_zero>` | :doc:`hybrid <angle_hybrid>` | |
|
||||
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
|
||||
| | | | |
|
||||
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
|
||||
| :doc:`charmm (iko) <angle_charmm>` | :doc:`class2 (ko) <angle_class2>` | :doc:`class2/p6 <angle_class2>` | :doc:`cosine (ko) <angle_cosine>` |
|
||||
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
|
||||
| :doc:`cosine/buck6d <angle_cosine_buck6d>` | :doc:`cosine/delta (o) <angle_cosine_delta>` | :doc:`cosine/periodic (o) <angle_cosine_periodic>` | :doc:`cosine/shift (o) <angle_cosine_shift>` |
|
||||
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
|
||||
| :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>` | :doc:`cosine/squared (o) <angle_cosine_squared>` | :doc:`cross <angle_cross>` | :doc:`dipole (o) <angle_dipole>` |
|
||||
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
|
||||
| :doc:`fourier (o) <angle_fourier>` | :doc:`fourier/simple (o) <angle_fourier_simple>` | :doc:`harmonic (iko) <angle_harmonic>` | :doc:`mm3 <angle_mm3>` |
|
||||
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
|
||||
| :doc:`quartic (o) <angle_quartic>` | :doc:`sdk (o) <angle_sdk>` | :doc:`table (o) <angle_table>` | |
|
||||
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
|
||||
|
||||
|
||||
----------
|
||||
.. table_from_list::
|
||||
:columns: 4
|
||||
|
||||
* :doc:`none <angle_none>`
|
||||
* :doc:`zero <angle_zero>`
|
||||
* :doc:`hybrid <angle_hybrid>`
|
||||
*
|
||||
*
|
||||
*
|
||||
*
|
||||
*
|
||||
* :doc:`charmm (iko) <angle_charmm>`
|
||||
* :doc:`class2 (ko) <angle_class2>`
|
||||
* :doc:`class2/p6 <angle_class2>`
|
||||
* :doc:`cosine (ko) <angle_cosine>`
|
||||
* :doc:`cosine/buck6d <angle_cosine_buck6d>`
|
||||
* :doc:`cosine/delta (o) <angle_cosine_delta>`
|
||||
* :doc:`cosine/periodic (o) <angle_cosine_periodic>`
|
||||
* :doc:`cosine/shift (o) <angle_cosine_shift>`
|
||||
* :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
|
||||
* :doc:`cosine/squared (o) <angle_cosine_squared>`
|
||||
* :doc:`cross <angle_cross>`
|
||||
* :doc:`dipole (o) <angle_dipole>`
|
||||
* :doc:`fourier (o) <angle_fourier>`
|
||||
* :doc:`fourier/simple (o) <angle_fourier_simple>`
|
||||
* :doc:`harmonic (iko) <angle_harmonic>`
|
||||
* :doc:`mm3 <angle_mm3>`
|
||||
* :doc:`quartic (o) <angle_quartic>`
|
||||
* :doc:`sdk (o) <angle_sdk>`
|
||||
* :doc:`table (o) <angle_table>`
|
||||
*
|
||||
|
||||
.. _dihedral:
|
||||
|
||||
Dihedral\_style potentials
|
||||
=========================================
|
||||
Dihedral_style potentials
|
||||
=========================
|
||||
|
||||
All LAMMPS :doc:`dihedral\_style <dihedral_style>` commands. Some styles
|
||||
All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles
|
||||
have accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| :doc:`none <dihedral_none>` | :doc:`zero <dihedral_zero>` | :doc:`hybrid <dihedral_hybrid>` | |
|
||||
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| | | | |
|
||||
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| :doc:`charmm (iko) <dihedral_charmm>` | :doc:`charmmfsw <dihedral_charmm>` | :doc:`class2 (ko) <dihedral_class2>` | :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>` |
|
||||
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| :doc:`fourier (io) <dihedral_fourier>` | :doc:`harmonic (iko) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>` | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>` |
|
||||
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| :doc:`nharmonic (o) <dihedral_nharmonic>` | :doc:`opls (iko) <dihedral_opls>` | :doc:`quadratic (o) <dihedral_quadratic>` | :doc:`spherical <dihedral_spherical>` |
|
||||
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| :doc:`table (o) <dihedral_table>` | :doc:`table/cut <dihedral_table_cut>` | | |
|
||||
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
|
||||
.. table_from_list::
|
||||
:columns: 4
|
||||
|
||||
----------
|
||||
|
||||
* :doc:`none <dihedral_none>`
|
||||
* :doc:`zero <dihedral_zero>`
|
||||
* :doc:`hybrid <dihedral_hybrid>`
|
||||
*
|
||||
*
|
||||
*
|
||||
*
|
||||
*
|
||||
* :doc:`charmm (iko) <dihedral_charmm>`
|
||||
* :doc:`charmmfsw <dihedral_charmm>`
|
||||
* :doc:`class2 (ko) <dihedral_class2>`
|
||||
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
|
||||
* :doc:`fourier (io) <dihedral_fourier>`
|
||||
* :doc:`harmonic (iko) <dihedral_harmonic>`
|
||||
* :doc:`helix (o) <dihedral_helix>`
|
||||
* :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
|
||||
* :doc:`nharmonic (o) <dihedral_nharmonic>`
|
||||
* :doc:`opls (iko) <dihedral_opls>`
|
||||
* :doc:`quadratic (o) <dihedral_quadratic>`
|
||||
* :doc:`spherical <dihedral_spherical>`
|
||||
* :doc:`table (o) <dihedral_table>`
|
||||
* :doc:`table/cut <dihedral_table_cut>`
|
||||
*
|
||||
*
|
||||
|
||||
.. _improper:
|
||||
|
||||
Improper\_style potentials
|
||||
=========================================
|
||||
Improper_style potentials
|
||||
=========================
|
||||
|
||||
All LAMMPS :doc:`improper\_style <improper_style>` commands. Some styles
|
||||
have accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| :doc:`none <improper_none>` | :doc:`zero <improper_zero>` | :doc:`hybrid <improper_hybrid>` | |
|
||||
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| | | | |
|
||||
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| :doc:`class2 (ko) <improper_class2>` | :doc:`cossq (o) <improper_cossq>` | :doc:`cvff (io) <improper_cvff>` | :doc:`distance <improper_distance>` |
|
||||
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| :doc:`distharm <improper_distharm>` | :doc:`fourier (o) <improper_fourier>` | :doc:`harmonic (iko) <improper_harmonic>` | :doc:`inversion/harmonic <improper_inversion_harmonic>` |
|
||||
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
| :doc:`ring (o) <improper_ring>` | :doc:`sqdistharm <improper_sqdistharm>` | :doc:`umbrella (o) <improper_umbrella>` | |
|
||||
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 4
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
* :doc:`none <improper_none>`
|
||||
* :doc:`zero <improper_zero>`
|
||||
* :doc:`hybrid <improper_hybrid>`
|
||||
*
|
||||
*
|
||||
*
|
||||
*
|
||||
*
|
||||
* :doc:`class2 (ko) <improper_class2>`
|
||||
* :doc:`cossq (o) <improper_cossq>`
|
||||
* :doc:`cvff (io) <improper_cvff>`
|
||||
* :doc:`distance <improper_distance>`
|
||||
* :doc:`distharm <improper_distharm>`
|
||||
* :doc:`fourier (o) <improper_fourier>`
|
||||
* :doc:`harmonic (iko) <improper_harmonic>`
|
||||
* :doc:`inversion/harmonic <improper_inversion_harmonic>`
|
||||
* :doc:`ring (o) <improper_ring>`
|
||||
* :doc:`sqdistharm <improper_sqdistharm>`
|
||||
* :doc:`umbrella (o) <improper_umbrella>`
|
||||
*
|
||||
|
||||
@ -130,8 +130,3 @@ Input script control:
|
||||
* :doc:`quit <quit>`,
|
||||
* :doc:`shell <shell>`,
|
||||
* :doc:`variable <variable>`
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,10 +1,15 @@
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>` | :doc:`Compute styles <Commands_compute>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :doc:`Pair styles <Commands_pair>` | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :ref:`Dihedral styles <dihedral>` | :ref:`Improper styles <improper>` | :doc:`KSpace styles <Commands_kspace>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 3
|
||||
|
||||
* :doc:`General commands <Commands_all>`
|
||||
* :doc:`Fix styles <Commands_fix>`
|
||||
* :doc:`Compute styles <Commands_compute>`
|
||||
* :doc:`Pair styles <Commands_pair>`
|
||||
* :ref:`Bond styles <bond>`
|
||||
* :ref:`Angle styles <angle>`
|
||||
* :ref:`Dihedral styles <dihedral>`
|
||||
* :ref:`Improper styles <improper>`
|
||||
* :doc:`KSpace styles <Commands_kspace>`
|
||||
|
||||
Compute commands
|
||||
================
|
||||
@ -14,57 +19,150 @@ Some styles have accelerated versions. This is indicated by
|
||||
additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`ackland/atom <compute_ackland_atom>` | :doc:`adf <compute_adf>` | :doc:`aggregate/atom <compute_cluster_atom>` | :doc:`angle <compute_angle>` | :doc:`angle/local <compute_angle_local>` | :doc:`angmom/chunk <compute_angmom_chunk>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`basal/atom <compute_basal_atom>` | :doc:`body/local <compute_body_local>` | :doc:`bond <compute_bond>` | :doc:`bond/local <compute_bond_local>` | :doc:`centro/atom <compute_centro_atom>` | :doc:`centroid/stress/atom <compute_stress_atom>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`chunk/atom <compute_chunk_atom>` | :doc:`chunk/spread/atom <compute_chunk_spread_atom>` | :doc:`cluster/atom <compute_cluster_atom>` | :doc:`cna/atom <compute_cna_atom>` | :doc:`cnp/atom <compute_cnp_atom>` | :doc:`com <compute_com>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`com/chunk <compute_com_chunk>` | :doc:`contact/atom <compute_contact_atom>` | :doc:`coord/atom <compute_coord_atom>` | :doc:`damage/atom <compute_damage_atom>` | :doc:`dihedral <compute_dihedral>` | :doc:`dihedral/local <compute_dihedral_local>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`dilatation/atom <compute_dilatation_atom>` | :doc:`dipole/chunk <compute_dipole_chunk>` | :doc:`displace/atom <compute_displace_atom>` | :doc:`dpd <compute_dpd>` | :doc:`dpd/atom <compute_dpd_atom>` | :doc:`edpd/temp/atom <compute_edpd_temp_atom>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`entropy/atom <compute_entropy_atom>` | :doc:`erotate/asphere <compute_erotate_asphere>` | :doc:`erotate/rigid <compute_erotate_rigid>` | :doc:`erotate/sphere <compute_erotate_sphere>` | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`fep <compute_fep>` | :doc:`force/tally <compute_tally>` | :doc:`fragment/atom <compute_cluster_atom>` | :doc:`global/atom <compute_global_atom>` | :doc:`group/group <compute_group_group>` | :doc:`gyration <compute_gyration>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`gyration/chunk <compute_gyration_chunk>` | :doc:`gyration/shape <compute_gyration_shape>` | :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>` | :doc:`heat/flux <compute_heat_flux>` | :doc:`heat/flux/tally <compute_tally>` | :doc:`hexorder/atom <compute_hexorder_atom>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`hma <compute_hma>` | :doc:`improper <compute_improper>` | :doc:`improper/local <compute_improper_local>` | :doc:`inertia/chunk <compute_inertia_chunk>` | :doc:`ke <compute_ke>` | :doc:`ke/atom <compute_ke_atom>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`ke/atom/eff <compute_ke_atom_eff>` | :doc:`ke/eff <compute_ke_eff>` | :doc:`ke/rigid <compute_ke_rigid>` | :doc:`meso/e/atom <compute_meso_e_atom>` | :doc:`meso/rho/atom <compute_meso_rho_atom>` | :doc:`meso/t/atom <compute_meso_t_atom>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`momentum <compute_momentum>` | :doc:`msd <compute_msd>` | :doc:`msd/chunk <compute_msd_chunk>` | :doc:`msd/nongauss <compute_msd_nongauss>` | :doc:`omega/chunk <compute_omega_chunk>` | :doc:`orientorder/atom <compute_orientorder_atom>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`pair <compute_pair>` | :doc:`pair/local <compute_pair_local>` | :doc:`pe <compute_pe>` | :doc:`pe/atom <compute_pe_atom>` | :doc:`pe/mol/tally <compute_tally>` | :doc:`pe/tally <compute_tally>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`plasticity/atom <compute_plasticity_atom>` | :doc:`pressure <compute_pressure>` | :doc:`pressure/cylinder <compute_pressure_cylinder>` | :doc:`pressure/uef <compute_pressure_uef>` | :doc:`property/atom <compute_property_atom>` | :doc:`property/chunk <compute_property_chunk>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`property/local <compute_property_local>` | :doc:`ptm/atom <compute_ptm_atom>` | :doc:`rdf <compute_rdf>` | :doc:`reduce <compute_reduce>` | :doc:`reduce/chunk <compute_reduce_chunk>` | :doc:`reduce/region <compute_reduce>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`rigid/local <compute_rigid_local>` | :doc:`saed <compute_saed>` | :doc:`slice <compute_slice>` | :doc:`smd/contact/radius <compute_smd_contact_radius>` | :doc:`smd/damage <compute_smd_damage>` | :doc:`smd/hourglass/error <compute_smd_hourglass_error>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`smd/internal/energy <compute_smd_internal_energy>` | :doc:`smd/plastic/strain <compute_smd_plastic_strain>` | :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>` | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>` | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` | :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>` | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>` | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>` | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` | :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` | :doc:`smd/vol <compute_smd_vol>` | :doc:`sna/atom <compute_sna_atom>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`snad/atom <compute_sna_atom>` | :doc:`snav/atom <compute_sna_atom>` | :doc:`spin <compute_spin>` | :doc:`stress/atom <compute_stress_atom>` | :doc:`stress/mop <compute_stress_mop>` | :doc:`stress/mop/profile <compute_stress_mop>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`stress/tally <compute_tally>` | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` | :doc:`temp (k) <compute_temp>` | :doc:`temp/asphere <compute_temp_asphere>` | :doc:`temp/body <compute_temp_body>` | :doc:`temp/chunk <compute_temp_chunk>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`temp/com <compute_temp_com>` | :doc:`temp/cs <compute_temp_cs>` | :doc:`temp/deform <compute_temp_deform>` | :doc:`temp/deform/eff <compute_temp_deform_eff>` | :doc:`temp/drude <compute_temp_drude>` | :doc:`temp/eff <compute_temp_eff>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`temp/partial <compute_temp_partial>` | :doc:`temp/profile <compute_temp_profile>` | :doc:`temp/ramp <compute_temp_ramp>` | :doc:`temp/region <compute_temp_region>` | :doc:`temp/region/eff <compute_temp_region_eff>` | :doc:`temp/rotate <compute_temp_rotate>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`temp/sphere <compute_temp_sphere>` | :doc:`temp/uef <compute_temp_uef>` | :doc:`ti <compute_ti>` | :doc:`torque/chunk <compute_torque_chunk>` | :doc:`vacf <compute_vacf>` | :doc:`vcm/chunk <compute_vcm_chunk>` |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
| :doc:`voronoi/atom <compute_voronoi_atom>` | :doc:`xrd <compute_xrd>` | | | | |
|
||||
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 6
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
* :doc:`ackland/atom <compute_ackland_atom>`
|
||||
* :doc:`adf <compute_adf>`
|
||||
* :doc:`aggregate/atom <compute_cluster_atom>`
|
||||
* :doc:`angle <compute_angle>`
|
||||
* :doc:`angle/local <compute_angle_local>`
|
||||
* :doc:`angmom/chunk <compute_angmom_chunk>`
|
||||
* :doc:`basal/atom <compute_basal_atom>`
|
||||
* :doc:`body/local <compute_body_local>`
|
||||
* :doc:`bond <compute_bond>`
|
||||
* :doc:`bond/local <compute_bond_local>`
|
||||
* :doc:`centro/atom <compute_centro_atom>`
|
||||
* :doc:`centroid/stress/atom <compute_stress_atom>`
|
||||
* :doc:`chunk/atom <compute_chunk_atom>`
|
||||
* :doc:`chunk/spread/atom <compute_chunk_spread_atom>`
|
||||
* :doc:`cluster/atom <compute_cluster_atom>`
|
||||
* :doc:`cna/atom <compute_cna_atom>`
|
||||
* :doc:`cnp/atom <compute_cnp_atom>`
|
||||
* :doc:`com <compute_com>`
|
||||
* :doc:`com/chunk <compute_com_chunk>`
|
||||
* :doc:`contact/atom <compute_contact_atom>`
|
||||
* :doc:`coord/atom <compute_coord_atom>`
|
||||
* :doc:`damage/atom <compute_damage_atom>`
|
||||
* :doc:`dihedral <compute_dihedral>`
|
||||
* :doc:`dihedral/local <compute_dihedral_local>`
|
||||
* :doc:`dilatation/atom <compute_dilatation_atom>`
|
||||
* :doc:`dipole/chunk <compute_dipole_chunk>`
|
||||
* :doc:`displace/atom <compute_displace_atom>`
|
||||
* :doc:`dpd <compute_dpd>`
|
||||
* :doc:`dpd/atom <compute_dpd_atom>`
|
||||
* :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
|
||||
* :doc:`entropy/atom <compute_entropy_atom>`
|
||||
* :doc:`erotate/asphere <compute_erotate_asphere>`
|
||||
* :doc:`erotate/rigid <compute_erotate_rigid>`
|
||||
* :doc:`erotate/sphere <compute_erotate_sphere>`
|
||||
* :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
|
||||
* :doc:`event/displace <compute_event_displace>`
|
||||
* :doc:`fep <compute_fep>`
|
||||
* :doc:`force/tally <compute_tally>`
|
||||
* :doc:`fragment/atom <compute_cluster_atom>`
|
||||
* :doc:`global/atom <compute_global_atom>`
|
||||
* :doc:`group/group <compute_group_group>`
|
||||
* :doc:`gyration <compute_gyration>`
|
||||
* :doc:`gyration/chunk <compute_gyration_chunk>`
|
||||
* :doc:`gyration/shape <compute_gyration_shape>`
|
||||
* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
|
||||
* :doc:`heat/flux <compute_heat_flux>`
|
||||
* :doc:`heat/flux/tally <compute_tally>`
|
||||
* :doc:`hexorder/atom <compute_hexorder_atom>`
|
||||
* :doc:`hma <compute_hma>`
|
||||
* :doc:`improper <compute_improper>`
|
||||
* :doc:`improper/local <compute_improper_local>`
|
||||
* :doc:`inertia/chunk <compute_inertia_chunk>`
|
||||
* :doc:`ke <compute_ke>`
|
||||
* :doc:`ke/atom <compute_ke_atom>`
|
||||
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
|
||||
* :doc:`ke/eff <compute_ke_eff>`
|
||||
* :doc:`ke/rigid <compute_ke_rigid>`
|
||||
* :doc:`meso/e/atom <compute_meso_e_atom>`
|
||||
* :doc:`meso/rho/atom <compute_meso_rho_atom>`
|
||||
* :doc:`meso/t/atom <compute_meso_t_atom>`
|
||||
* :doc:`momentum <compute_momentum>`
|
||||
* :doc:`msd <compute_msd>`
|
||||
* :doc:`msd/chunk <compute_msd_chunk>`
|
||||
* :doc:`msd/nongauss <compute_msd_nongauss>`
|
||||
* :doc:`omega/chunk <compute_omega_chunk>`
|
||||
* :doc:`orientorder/atom <compute_orientorder_atom>`
|
||||
* :doc:`pair <compute_pair>`
|
||||
* :doc:`pair/local <compute_pair_local>`
|
||||
* :doc:`pe <compute_pe>`
|
||||
* :doc:`pe/atom <compute_pe_atom>`
|
||||
* :doc:`pe/mol/tally <compute_tally>`
|
||||
* :doc:`pe/tally <compute_tally>`
|
||||
* :doc:`plasticity/atom <compute_plasticity_atom>`
|
||||
* :doc:`pressure <compute_pressure>`
|
||||
* :doc:`pressure/cylinder <compute_pressure_cylinder>`
|
||||
* :doc:`pressure/uef <compute_pressure_uef>`
|
||||
* :doc:`property/atom <compute_property_atom>`
|
||||
* :doc:`property/chunk <compute_property_chunk>`
|
||||
* :doc:`property/local <compute_property_local>`
|
||||
* :doc:`ptm/atom <compute_ptm_atom>`
|
||||
* :doc:`rdf <compute_rdf>`
|
||||
* :doc:`reduce <compute_reduce>`
|
||||
* :doc:`reduce/chunk <compute_reduce_chunk>`
|
||||
* :doc:`reduce/region <compute_reduce>`
|
||||
* :doc:`rigid/local <compute_rigid_local>`
|
||||
* :doc:`saed <compute_saed>`
|
||||
* :doc:`slice <compute_slice>`
|
||||
* :doc:`smd/contact/radius <compute_smd_contact_radius>`
|
||||
* :doc:`smd/damage <compute_smd_damage>`
|
||||
* :doc:`smd/hourglass/error <compute_smd_hourglass_error>`
|
||||
* :doc:`smd/internal/energy <compute_smd_internal_energy>`
|
||||
* :doc:`smd/plastic/strain <compute_smd_plastic_strain>`
|
||||
* :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>`
|
||||
* :doc:`smd/rho <compute_smd_rho>`
|
||||
* :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>`
|
||||
* :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`
|
||||
* :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>`
|
||||
* :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`
|
||||
* :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`
|
||||
* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
|
||||
* :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
|
||||
* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
|
||||
* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
|
||||
* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
|
||||
* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`
|
||||
* :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`
|
||||
* :doc:`smd/vol <compute_smd_vol>`
|
||||
* :doc:`snap <compute_sna_atom>`
|
||||
* :doc:`sna/atom <compute_sna_atom>`
|
||||
* :doc:`snad/atom <compute_sna_atom>`
|
||||
* :doc:`snav/atom <compute_sna_atom>`
|
||||
* :doc:`spin <compute_spin>`
|
||||
* :doc:`stress/atom <compute_stress_atom>`
|
||||
* :doc:`stress/mop <compute_stress_mop>`
|
||||
* :doc:`stress/mop/profile <compute_stress_mop>`
|
||||
* :doc:`stress/tally <compute_tally>`
|
||||
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
|
||||
* :doc:`temp (k) <compute_temp>`
|
||||
* :doc:`temp/asphere <compute_temp_asphere>`
|
||||
* :doc:`temp/body <compute_temp_body>`
|
||||
* :doc:`temp/chunk <compute_temp_chunk>`
|
||||
* :doc:`temp/com <compute_temp_com>`
|
||||
* :doc:`temp/cs <compute_temp_cs>`
|
||||
* :doc:`temp/deform <compute_temp_deform>`
|
||||
* :doc:`temp/deform/eff <compute_temp_deform_eff>`
|
||||
* :doc:`temp/drude <compute_temp_drude>`
|
||||
* :doc:`temp/eff <compute_temp_eff>`
|
||||
* :doc:`temp/partial <compute_temp_partial>`
|
||||
* :doc:`temp/profile <compute_temp_profile>`
|
||||
* :doc:`temp/ramp <compute_temp_ramp>`
|
||||
* :doc:`temp/region <compute_temp_region>`
|
||||
* :doc:`temp/region/eff <compute_temp_region_eff>`
|
||||
* :doc:`temp/rotate <compute_temp_rotate>`
|
||||
* :doc:`temp/sphere <compute_temp_sphere>`
|
||||
* :doc:`temp/uef <compute_temp_uef>`
|
||||
* :doc:`ti <compute_ti>`
|
||||
* :doc:`torque/chunk <compute_torque_chunk>`
|
||||
* :doc:`vacf <compute_vacf>`
|
||||
* :doc:`vcm/chunk <compute_vcm_chunk>`
|
||||
* :doc:`voronoi/atom <compute_voronoi_atom>`
|
||||
* :doc:`xrd <compute_xrd>`
|
||||
*
|
||||
*
|
||||
*
|
||||
|
||||
@ -1,10 +1,15 @@
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>` | :doc:`Compute styles <Commands_compute>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :doc:`Pair styles <Commands_pair>` | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :ref:`Dihedral styles <dihedral>` | :ref:`Improper styles <improper>` | :doc:`KSpace styles <Commands_kspace>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 3
|
||||
|
||||
* :doc:`General commands <Commands_all>`
|
||||
* :doc:`Fix styles <Commands_fix>`
|
||||
* :doc:`Compute styles <Commands_compute>`
|
||||
* :doc:`Pair styles <Commands_pair>`
|
||||
* :ref:`Bond styles <bond>`
|
||||
* :ref:`Angle styles <angle>`
|
||||
* :ref:`Dihedral styles <dihedral>`
|
||||
* :ref:`Improper styles <improper>`
|
||||
* :doc:`KSpace styles <Commands_kspace>`
|
||||
|
||||
Fix commands
|
||||
============
|
||||
@ -14,81 +19,222 @@ have accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`adapt <fix_adapt>` | :doc:`adapt/fep <fix_adapt_fep>` | :doc:`addforce <fix_addforce>` | :doc:`addtorque <fix_addtorque>` | :doc:`append/atoms <fix_append_atoms>` | :doc:`atc <fix_atc>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`atom/swap <fix_atom_swap>` | :doc:`ave/atom <fix_ave_atom>` | :doc:`ave/chunk <fix_ave_chunk>` | :doc:`ave/correlate <fix_ave_correlate>` | :doc:`ave/correlate/long <fix_ave_correlate_long>` | :doc:`ave/histo <fix_ave_histo>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`ave/histo/weight <fix_ave_histo>` | :doc:`ave/time <fix_ave_time>` | :doc:`aveforce <fix_aveforce>` | :doc:`balance <fix_balance>` | :doc:`bocs <fix_bocs>` | :doc:`bond/break <fix_bond_break>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`bond/create <fix_bond_create>` | :doc:`bond/react <fix_bond_react>` | :doc:`bond/swap <fix_bond_swap>` | :doc:`box/relax <fix_box_relax>` | :doc:`client/md <fix_client_md>` | :doc:`cmap <fix_cmap>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`colvars <fix_colvars>` | :doc:`controller <fix_controller>` | :doc:`deform (k) <fix_deform>` | :doc:`deposit <fix_deposit>` | :doc:`dpd/energy (k) <fix_dpd_energy>` | :doc:`drag <fix_drag>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :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:`edpd/source <fix_dpd_source>` | :doc:`efield <fix_efield>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`ehex <fix_ehex>` | :doc:`electron/stopping <fix_electron_stopping>` | :doc:`enforce2d (k) <fix_enforce2d>` | :doc:`eos/cv <fix_eos_cv>` | :doc:`eos/table <fix_eos_table>` | :doc:`eos/table/rx (k) <fix_eos_table_rx>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`evaporate <fix_evaporate>` | :doc:`external <fix_external>` | :doc:`ffl <fix_ffl>` | :doc:`filter/corotate <fix_filter_corotate>` | :doc:`flow/gauss <fix_flow_gauss>` | :doc:`freeze (k) <fix_freeze>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`gcmc <fix_gcmc>` | :doc:`gld <fix_gld>` | :doc:`gle <fix_gle>` | :doc:`gravity (ko) <fix_gravity>` | :doc:`grem <fix_grem>` | :doc:`halt <fix_halt>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`heat <fix_heat>` | :doc:`hyper/global <fix_hyper_global>` | :doc:`hyper/local <fix_hyper_local>` | :doc:`imd <fix_imd>` | :doc:`indent <fix_indent>` | :doc:`ipi <fix_ipi>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`langevin (k) <fix_langevin>` | :doc:`langevin/drude <fix_langevin_drude>` | :doc:`langevin/eff <fix_langevin_eff>` | :doc:`langevin/spin <fix_langevin_spin>` | :doc:`latte <fix_latte>` | :doc:`lb/fluid <fix_lb_fluid>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`lb/momentum <fix_lb_momentum>` | :doc:`lb/pc <fix_lb_pc>` | :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` | :doc:`lb/viscous <fix_lb_viscous>` | :doc:`lineforce <fix_lineforce>` | :doc:`manifoldforce <fix_manifoldforce>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`meso <fix_meso>` | :doc:`meso/move <fix_meso_move>` | :doc:`meso/stationary <fix_meso_stationary>` | :doc:`momentum (k) <fix_momentum>` | :doc:`move <fix_move>` | :doc:`mscg <fix_mscg>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`msst <fix_msst>` | :doc:`mvv/dpd <fix_mvv_dpd>` | :doc:`mvv/edpd <fix_mvv_dpd>` | :doc:`mvv/tdpd <fix_mvv_dpd>` | :doc:`neb <fix_neb>` | :doc:`neb\_spin <fix_neb_spin>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`nph (ko) <fix_nh>` | :doc:`nph/asphere (o) <fix_nph_asphere>` | :doc:`nph/body <fix_nph_body>` | :doc:`nph/eff <fix_nh_eff>` | :doc:`nph/sphere (o) <fix_nph_sphere>` | :doc:`nphug (o) <fix_nphug>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`npt (iko) <fix_nh>` | :doc:`npt/asphere (o) <fix_npt_asphere>` | :doc:`npt/body <fix_npt_body>` | :doc:`npt/eff <fix_nh_eff>` | :doc:`npt/sphere (o) <fix_npt_sphere>` | :doc:`npt/uef <fix_nh_uef>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`nve (iko) <fix_nve>` | :doc:`nve/asphere (i) <fix_nve_asphere>` | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/awpmd <fix_nve_awpmd>` | :doc:`nve/body <fix_nve_body>` | :doc:`nve/dot <fix_nve_dot>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>` | :doc:`nve/eff <fix_nve_eff>` | :doc:`nve/limit <fix_nve_limit>` | :doc:`nve/line <fix_nve_line>` | :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>` | :doc:`nve/noforce <fix_nve_noforce>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`nve/sphere (ko) <fix_nve_sphere>` | :doc:`nve/spin <fix_nve_spin>` | :doc:`nve/tri <fix_nve_tri>` | :doc:`nvk <fix_nvk>` | :doc:`nvt (iko) <fix_nh>` | :doc:`nvt/asphere (o) <fix_nvt_asphere>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`nvt/body <fix_nvt_body>` | :doc:`nvt/eff <fix_nh_eff>` | :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>` | :doc:`nvt/sllod (io) <fix_nvt_sllod>` | :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>` | :doc:`nvt/sphere (o) <fix_nvt_sphere>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`nvt/uef <fix_nh_uef>` | :doc:`oneway <fix_oneway>` | :doc:`orient/bcc <fix_orient>` | :doc:`orient/fcc <fix_orient>` | :doc:`phonon <fix_phonon>` | :doc:`pimd <fix_pimd>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`planeforce <fix_planeforce>` | :doc:`plumed <fix_plumed>` | :doc:`poems <fix_poems>` | :doc:`pour <fix_pour>` | :doc:`precession/spin <fix_precession_spin>` | :doc:`press/berendsen <fix_press_berendsen>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`print <fix_print>` | :doc:`property/atom (k) <fix_property_atom>` | :doc:`python/invoke <fix_python_invoke>` | :doc:`python/move <fix_python_move>` | :doc:`qbmsst <fix_qbmsst>` | :doc:`qeq/comb (o) <fix_qeq_comb>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`qeq/dynamic <fix_qeq>` | :doc:`qeq/fire <fix_qeq>` | :doc:`qeq/point <fix_qeq>` | :doc:`qeq/reax (ko) <fix_qeq_reax>` | :doc:`qeq/shielded <fix_qeq>` | :doc:`qeq/slater <fix_qeq>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`qmmm <fix_qmmm>` | :doc:`qtb <fix_qtb>` | :doc:`rattle <fix_shake>` | :doc:`reax/c/bonds (k) <fix_reaxc_bonds>` | :doc:`reax/c/species (k) <fix_reaxc_species>` | :doc:`recenter <fix_recenter>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`restrain <fix_restrain>` | :doc:`rhok <fix_rhok>` | :doc:`rigid (o) <fix_rigid>` | :doc:`rigid/meso <fix_rigid_meso>` | :doc:`rigid/nph (o) <fix_rigid>` | :doc:`rigid/nph/small <fix_rigid>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`rigid/npt (o) <fix_rigid>` | :doc:`rigid/npt/small <fix_rigid>` | :doc:`rigid/nve (o) <fix_rigid>` | :doc:`rigid/nve/small <fix_rigid>` | :doc:`rigid/nvt (o) <fix_rigid>` | :doc:`rigid/nvt/small <fix_rigid>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`rigid/small (o) <fix_rigid>` | :doc:`rx (k) <fix_rx>` | :doc:`saed/vtk <fix_saed_vtk>` | :doc:`setforce (k) <fix_setforce>` | :doc:`shake <fix_shake>` | :doc:`shardlow (k) <fix_shardlow>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`smd <fix_smd>` | :doc:`smd/adjust\_dt <fix_smd_adjust_dt>` | :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` | :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>` | :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` | :doc:`smd/setvel <fix_smd_setvel>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`smd/wall\_surface <fix_smd_wall_surface>` | :doc:`spring <fix_spring>` | :doc:`spring/chunk <fix_spring_chunk>` | :doc:`spring/rg <fix_spring_rg>` | :doc:`spring/self <fix_spring_self>` | :doc:`srd <fix_srd>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`store/force <fix_store_force>` | :doc:`store/state <fix_store_state>` | :doc:`tdpd/source <fix_dpd_source>` | :doc:`temp/berendsen <fix_temp_berendsen>` | :doc:`temp/csld <fix_temp_csvr>` | :doc:`temp/csvr <fix_temp_csvr>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`temp/rescale <fix_temp_rescale>` | :doc:`temp/rescale/eff <fix_temp_rescale_eff>` | :doc:`tfmc <fix_tfmc>` | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`ti/spring <fix_ti_spring>` | :doc:`tmd <fix_tmd>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`ttm <fix_ttm>` | :doc:`ttm/mod <fix_ttm>` | :doc:`tune/kspace <fix_tune_kspace>` | :doc:`vector <fix_vector>` | :doc:`viscosity <fix_viscosity>` | :doc:`viscous <fix_viscous>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`wall/body/polygon <fix_wall_body_polygon>` | :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` | :doc:`wall/colloid <fix_wall>` | :doc:`wall/ees <fix_wall_ees>` | :doc:`wall/gran <fix_wall_gran>` | :doc:`wall/gran/region <fix_wall_gran_region>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`wall/harmonic <fix_wall>` | :doc:`wall/lj1043 <fix_wall>` | :doc:`wall/lj126 <fix_wall>` | :doc:`wall/lj93 (k) <fix_wall>` | :doc:`wall/morse <fix_wall>` | :doc:`wall/piston <fix_wall_piston>` |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>` | :doc:`wall/region/ees <fix_wall_ees>` | :doc:`wall/srd <fix_wall_srd>` | | |
|
||||
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 6
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
* :doc:`adapt <fix_adapt>`
|
||||
* :doc:`adapt/fep <fix_adapt_fep>`
|
||||
* :doc:`addforce <fix_addforce>`
|
||||
* :doc:`addtorque <fix_addtorque>`
|
||||
* :doc:`append/atoms <fix_append_atoms>`
|
||||
* :doc:`atc <fix_atc>`
|
||||
* :doc:`atom/swap <fix_atom_swap>`
|
||||
* :doc:`ave/atom <fix_ave_atom>`
|
||||
* :doc:`ave/chunk <fix_ave_chunk>`
|
||||
* :doc:`ave/correlate <fix_ave_correlate>`
|
||||
* :doc:`ave/correlate/long <fix_ave_correlate_long>`
|
||||
* :doc:`ave/histo <fix_ave_histo>`
|
||||
* :doc:`ave/histo/weight <fix_ave_histo>`
|
||||
* :doc:`ave/time <fix_ave_time>`
|
||||
* :doc:`aveforce <fix_aveforce>`
|
||||
* :doc:`balance <fix_balance>`
|
||||
* :doc:`bocs <fix_bocs>`
|
||||
* :doc:`bond/break <fix_bond_break>`
|
||||
* :doc:`bond/create <fix_bond_create>`
|
||||
* :doc:`bond/react <fix_bond_react>`
|
||||
* :doc:`bond/swap <fix_bond_swap>`
|
||||
* :doc:`box/relax <fix_box_relax>`
|
||||
* :doc:`client/md <fix_client_md>`
|
||||
* :doc:`cmap <fix_cmap>`
|
||||
* :doc:`colvars <fix_colvars>`
|
||||
* :doc:`controller <fix_controller>`
|
||||
* :doc:`deform (k) <fix_deform>`
|
||||
* :doc:`deposit <fix_deposit>`
|
||||
* :doc:`dpd/energy (k) <fix_dpd_energy>`
|
||||
* :doc:`drag <fix_drag>`
|
||||
* :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:`edpd/source <fix_dpd_source>`
|
||||
* :doc:`efield <fix_efield>`
|
||||
* :doc:`ehex <fix_ehex>`
|
||||
* :doc:`electron/stopping <fix_electron_stopping>`
|
||||
* :doc:`enforce2d (k) <fix_enforce2d>`
|
||||
* :doc:`eos/cv <fix_eos_cv>`
|
||||
* :doc:`eos/table <fix_eos_table>`
|
||||
* :doc:`eos/table/rx (k) <fix_eos_table_rx>`
|
||||
* :doc:`evaporate <fix_evaporate>`
|
||||
* :doc:`external <fix_external>`
|
||||
* :doc:`ffl <fix_ffl>`
|
||||
* :doc:`filter/corotate <fix_filter_corotate>`
|
||||
* :doc:`flow/gauss <fix_flow_gauss>`
|
||||
* :doc:`freeze (k) <fix_freeze>`
|
||||
* :doc:`gcmc <fix_gcmc>`
|
||||
* :doc:`gld <fix_gld>`
|
||||
* :doc:`gle <fix_gle>`
|
||||
* :doc:`gravity (ko) <fix_gravity>`
|
||||
* :doc:`grem <fix_grem>`
|
||||
* :doc:`halt <fix_halt>`
|
||||
* :doc:`heat <fix_heat>`
|
||||
* :doc:`hyper/global <fix_hyper_global>`
|
||||
* :doc:`hyper/local <fix_hyper_local>`
|
||||
* :doc:`imd <fix_imd>`
|
||||
* :doc:`indent <fix_indent>`
|
||||
* :doc:`ipi <fix_ipi>`
|
||||
* :doc:`langevin (k) <fix_langevin>`
|
||||
* :doc:`langevin/drude <fix_langevin_drude>`
|
||||
* :doc:`langevin/eff <fix_langevin_eff>`
|
||||
* :doc:`langevin/spin <fix_langevin_spin>`
|
||||
* :doc:`latte <fix_latte>`
|
||||
* :doc:`lb/fluid <fix_lb_fluid>`
|
||||
* :doc:`lb/momentum <fix_lb_momentum>`
|
||||
* :doc:`lb/pc <fix_lb_pc>`
|
||||
* :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
|
||||
* :doc:`lb/viscous <fix_lb_viscous>`
|
||||
* :doc:`lineforce <fix_lineforce>`
|
||||
* :doc:`manifoldforce <fix_manifoldforce>`
|
||||
* :doc:`meso <fix_meso>`
|
||||
* :doc:`meso/move <fix_meso_move>`
|
||||
* :doc:`meso/stationary <fix_meso_stationary>`
|
||||
* :doc:`momentum (k) <fix_momentum>`
|
||||
* :doc:`move <fix_move>`
|
||||
* :doc:`mscg <fix_mscg>`
|
||||
* :doc:`msst <fix_msst>`
|
||||
* :doc:`mvv/dpd <fix_mvv_dpd>`
|
||||
* :doc:`mvv/edpd <fix_mvv_dpd>`
|
||||
* :doc:`mvv/tdpd <fix_mvv_dpd>`
|
||||
* :doc:`neb <fix_neb>`
|
||||
* :doc:`neb/spin <fix_neb_spin>`
|
||||
* :doc:`nph (ko) <fix_nh>`
|
||||
* :doc:`nph/asphere (o) <fix_nph_asphere>`
|
||||
* :doc:`nph/body <fix_nph_body>`
|
||||
* :doc:`nph/eff <fix_nh_eff>`
|
||||
* :doc:`nph/sphere (o) <fix_nph_sphere>`
|
||||
* :doc:`nphug <fix_nphug>`
|
||||
* :doc:`npt (iko) <fix_nh>`
|
||||
* :doc:`npt/asphere (o) <fix_npt_asphere>`
|
||||
* :doc:`npt/body <fix_npt_body>`
|
||||
* :doc:`npt/eff <fix_nh_eff>`
|
||||
* :doc:`npt/sphere (o) <fix_npt_sphere>`
|
||||
* :doc:`npt/uef <fix_nh_uef>`
|
||||
* :doc:`nve (iko) <fix_nve>`
|
||||
* :doc:`nve/asphere (i) <fix_nve_asphere>`
|
||||
* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
|
||||
* :doc:`nve/awpmd <fix_nve_awpmd>`
|
||||
* :doc:`nve/body <fix_nve_body>`
|
||||
* :doc:`nve/dot <fix_nve_dot>`
|
||||
* :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
* :doc:`nve/eff <fix_nve_eff>`
|
||||
* :doc:`nve/limit <fix_nve_limit>`
|
||||
* :doc:`nve/line <fix_nve_line>`
|
||||
* :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
|
||||
* :doc:`nve/noforce <fix_nve_noforce>`
|
||||
* :doc:`nve/sphere (ko) <fix_nve_sphere>`
|
||||
* :doc:`nve/spin <fix_nve_spin>`
|
||||
* :doc:`nve/tri <fix_nve_tri>`
|
||||
* :doc:`nvk <fix_nvk>`
|
||||
* :doc:`nvt (iko) <fix_nh>`
|
||||
* :doc:`nvt/asphere (o) <fix_nvt_asphere>`
|
||||
* :doc:`nvt/body <fix_nvt_body>`
|
||||
* :doc:`nvt/eff <fix_nh_eff>`
|
||||
* :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`
|
||||
* :doc:`nvt/sllod (io) <fix_nvt_sllod>`
|
||||
* :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`
|
||||
* :doc:`nvt/sphere (o) <fix_nvt_sphere>`
|
||||
* :doc:`nvt/uef <fix_nh_uef>`
|
||||
* :doc:`oneway <fix_oneway>`
|
||||
* :doc:`orient/bcc <fix_orient>`
|
||||
* :doc:`orient/fcc <fix_orient>`
|
||||
* :doc:`phonon <fix_phonon>`
|
||||
* :doc:`pimd <fix_pimd>`
|
||||
* :doc:`planeforce <fix_planeforce>`
|
||||
* :doc:`plumed <fix_plumed>`
|
||||
* :doc:`poems <fix_poems>`
|
||||
* :doc:`pour <fix_pour>`
|
||||
* :doc:`precession/spin <fix_precession_spin>`
|
||||
* :doc:`press/berendsen <fix_press_berendsen>`
|
||||
* :doc:`print <fix_print>`
|
||||
* :doc:`property/atom (k) <fix_property_atom>`
|
||||
* :doc:`python/invoke <fix_python_invoke>`
|
||||
* :doc:`python/move <fix_python_move>`
|
||||
* :doc:`qbmsst <fix_qbmsst>`
|
||||
* :doc:`qeq/comb (o) <fix_qeq_comb>`
|
||||
* :doc:`qeq/dynamic <fix_qeq>`
|
||||
* :doc:`qeq/fire <fix_qeq>`
|
||||
* :doc:`qeq/point <fix_qeq>`
|
||||
* :doc:`qeq/reax (ko) <fix_qeq_reax>`
|
||||
* :doc:`qeq/shielded <fix_qeq>`
|
||||
* :doc:`qeq/slater <fix_qeq>`
|
||||
* :doc:`qmmm <fix_qmmm>`
|
||||
* :doc:`qtb <fix_qtb>`
|
||||
* :doc:`rattle <fix_shake>`
|
||||
* :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
|
||||
* :doc:`reax/c/species (k) <fix_reaxc_species>`
|
||||
* :doc:`recenter <fix_recenter>`
|
||||
* :doc:`restrain <fix_restrain>`
|
||||
* :doc:`rhok <fix_rhok>`
|
||||
* :doc:`rigid (o) <fix_rigid>`
|
||||
* :doc:`rigid/meso <fix_rigid_meso>`
|
||||
* :doc:`rigid/nph (o) <fix_rigid>`
|
||||
* :doc:`rigid/nph/small <fix_rigid>`
|
||||
* :doc:`rigid/npt (o) <fix_rigid>`
|
||||
* :doc:`rigid/npt/small <fix_rigid>`
|
||||
* :doc:`rigid/nve (o) <fix_rigid>`
|
||||
* :doc:`rigid/nve/small <fix_rigid>`
|
||||
* :doc:`rigid/nvt (o) <fix_rigid>`
|
||||
* :doc:`rigid/nvt/small <fix_rigid>`
|
||||
* :doc:`rigid/small (o) <fix_rigid>`
|
||||
* :doc:`rx (k) <fix_rx>`
|
||||
* :doc:`saed/vtk <fix_saed_vtk>`
|
||||
* :doc:`setforce (k) <fix_setforce>`
|
||||
* :doc:`setforce/spin <fix_setforce>`
|
||||
* :doc:`shake <fix_shake>`
|
||||
* :doc:`shardlow (k) <fix_shardlow>`
|
||||
* :doc:`smd <fix_smd>`
|
||||
* :doc:`smd/adjust_dt <fix_smd_adjust_dt>`
|
||||
* :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>`
|
||||
* :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>`
|
||||
* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
|
||||
* :doc:`smd/setvel <fix_smd_setvel>`
|
||||
* :doc:`smd/wall_surface <fix_smd_wall_surface>`
|
||||
* :doc:`spring <fix_spring>`
|
||||
* :doc:`spring/chunk <fix_spring_chunk>`
|
||||
* :doc:`spring/rg <fix_spring_rg>`
|
||||
* :doc:`spring/self <fix_spring_self>`
|
||||
* :doc:`srd <fix_srd>`
|
||||
* :doc:`store/force <fix_store_force>`
|
||||
* :doc:`store/state <fix_store_state>`
|
||||
* :doc:`tdpd/source <fix_dpd_source>`
|
||||
* :doc:`temp/berendsen <fix_temp_berendsen>`
|
||||
* :doc:`temp/csld <fix_temp_csvr>`
|
||||
* :doc:`temp/csvr <fix_temp_csvr>`
|
||||
* :doc:`temp/rescale <fix_temp_rescale>`
|
||||
* :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
|
||||
* :doc:`tfmc <fix_tfmc>`
|
||||
* :doc:`thermal/conductivity <fix_thermal_conductivity>`
|
||||
* :doc:`ti/spring <fix_ti_spring>`
|
||||
* :doc:`tmd <fix_tmd>`
|
||||
* :doc:`ttm <fix_ttm>`
|
||||
* :doc:`ttm/mod <fix_ttm>`
|
||||
* :doc:`tune/kspace <fix_tune_kspace>`
|
||||
* :doc:`vector <fix_vector>`
|
||||
* :doc:`viscosity <fix_viscosity>`
|
||||
* :doc:`viscous <fix_viscous>`
|
||||
* :doc:`wall/body/polygon <fix_wall_body_polygon>`
|
||||
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
|
||||
* :doc:`wall/colloid <fix_wall>`
|
||||
* :doc:`wall/ees <fix_wall_ees>`
|
||||
* :doc:`wall/gran <fix_wall_gran>`
|
||||
* :doc:`wall/gran/region <fix_wall_gran_region>`
|
||||
* :doc:`wall/harmonic <fix_wall>`
|
||||
* :doc:`wall/lj1043 <fix_wall>`
|
||||
* :doc:`wall/lj126 <fix_wall>`
|
||||
* :doc:`wall/lj93 (k) <fix_wall>`
|
||||
* :doc:`wall/morse <fix_wall>`
|
||||
* :doc:`wall/piston <fix_wall_piston>`
|
||||
* :doc:`wall/reflect (k) <fix_wall_reflect>`
|
||||
* :doc:`wall/region <fix_wall_region>`
|
||||
* :doc:`wall/region/ees <fix_wall_ees>`
|
||||
* :doc:`wall/srd <fix_wall_srd>`
|
||||
*
|
||||
|
||||
@ -55,8 +55,3 @@ Many input script errors are detected by LAMMPS and an ERROR or
|
||||
WARNING message is printed. The :doc:`Errors <Errors>` doc page gives
|
||||
more information on what errors mean. The documentation for each
|
||||
command lists restrictions on how the command can be used.
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,10 +1,15 @@
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>` | :doc:`Compute styles <Commands_compute>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :doc:`Pair styles <Commands_pair>` | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :ref:`Dihedral styles <dihedral>` | :ref:`Improper styles <improper>` | :doc:`KSpace styles <Commands_kspace>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 3
|
||||
|
||||
* :doc:`General commands <Commands_all>`
|
||||
* :doc:`Fix styles <Commands_fix>`
|
||||
* :doc:`Compute styles <Commands_compute>`
|
||||
* :doc:`Pair styles <Commands_pair>`
|
||||
* :ref:`Bond styles <bond>`
|
||||
* :ref:`Angle styles <angle>`
|
||||
* :ref:`Dihedral styles <dihedral>`
|
||||
* :ref:`Improper styles <improper>`
|
||||
* :doc:`KSpace styles <Commands_kspace>`
|
||||
|
||||
KSpace solvers
|
||||
==============
|
||||
@ -14,15 +19,22 @@ accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
|
||||
| :doc:`ewald (o) <kspace_style>` | :doc:`ewald/disp <kspace_style>` | :doc:`msm (o) <kspace_style>` | :doc:`msm/cg (o) <kspace_style>` |
|
||||
+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
|
||||
| :doc:`pppm (gok) <kspace_style>` | :doc:`pppm/cg (o) <kspace_style>` | :doc:`pppm/disp (i) <kspace_style>` | :doc:`pppm/disp/tip4p <kspace_style>` |
|
||||
+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
|
||||
| :doc:`pppm/stagger <kspace_style>` | :doc:`pppm/tip4p (o) <kspace_style>` | :doc:`scafacos <kspace_style>` | |
|
||||
+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 4
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
* :doc:`ewald (o) <kspace_style>`
|
||||
* :doc:`ewald/disp <kspace_style>`
|
||||
* :doc:`ewald/dipole <kspace_style>`
|
||||
* :doc:`ewald/dipole/spin <kspace_style>`
|
||||
* :doc:`msm (o) <kspace_style>`
|
||||
* :doc:`msm/cg (o) <kspace_style>`
|
||||
* :doc:`pppm (giko) <kspace_style>`
|
||||
* :doc:`pppm/cg (o) <kspace_style>`
|
||||
* :doc:`pppm/dipole <kspace_style>`
|
||||
* :doc:`pppm/dipole/spin <kspace_style>`
|
||||
* :doc:`pppm/disp (io) <kspace_style>`
|
||||
* :doc:`pppm/disp/tip4p (o) <kspace_style>`
|
||||
* :doc:`pppm/stagger <kspace_style>`
|
||||
* :doc:`pppm/tip4p (o) <kspace_style>`
|
||||
* :doc:`scafacos <kspace_style>`
|
||||
*
|
||||
|
||||
@ -1,136 +1,260 @@
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>` | :doc:`Compute styles <Commands_compute>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :doc:`Pair styles <Commands_pair>` | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
| :ref:`Dihedral styles <dihedral>` | :ref:`Improper styles <improper>` | :doc:`KSpace styles <Commands_kspace>` |
|
||||
+----------------------------------------+------------------------------------+------------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 3
|
||||
|
||||
Pair\_style potentials
|
||||
* :doc:`General commands <Commands_all>`
|
||||
* :doc:`Fix styles <Commands_fix>`
|
||||
* :doc:`Compute styles <Commands_compute>`
|
||||
* :doc:`Pair styles <Commands_pair>`
|
||||
* :ref:`Bond styles <bond>`
|
||||
* :ref:`Angle styles <angle>`
|
||||
* :ref:`Dihedral styles <dihedral>`
|
||||
* :ref:`Improper styles <improper>`
|
||||
* :doc:`KSpace styles <Commands_kspace>`
|
||||
|
||||
Pair_style potentials
|
||||
======================
|
||||
|
||||
All LAMMPS :doc:`pair\_style <pair_style>` commands. Some styles have
|
||||
All LAMMPS :doc:`pair_style <pair_style>` commands. Some styles have
|
||||
accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`none <pair_none>` | :doc:`zero <pair_zero>` | :doc:`hybrid (k) <pair_hybrid>` | :doc:`hybrid/overlay (k) <pair_hybrid>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| | | | |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`adp (o) <pair_adp>` | :doc:`agni (o) <pair_agni>` | :doc:`airebo (io) <pair_airebo>` | :doc:`airebo/morse (io) <pair_airebo>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`atm <pair_atm>` | :doc:`awpmd/cut <pair_awpmd>` | :doc:`beck (go) <pair_beck>` | :doc:`body/nparticle <pair_body_nparticle>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`body/rounded/polygon <pair_body_rounded_polygon>` | :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>` | :doc:`bop <pair_bop>` | :doc:`born (go) <pair_born>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`born/coul/dsf <pair_born>` | :doc:`born/coul/dsf/cs <pair_cs>` | :doc:`born/coul/long (go) <pair_born>` | :doc:`born/coul/long/cs (g) <pair_cs>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`born/coul/msm (o) <pair_born>` | :doc:`born/coul/wolf (go) <pair_born>` | :doc:`born/coul/wolf/cs (g) <pair_cs>` | :doc:`brownian (o) <pair_brownian>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`brownian/poly (o) <pair_brownian>` | :doc:`buck (giko) <pair_buck>` | :doc:`buck/coul/cut (giko) <pair_buck>` | :doc:`buck/coul/long (giko) <pair_buck>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`buck/coul/long/cs <pair_cs>` | :doc:`buck/coul/msm (o) <pair_buck>` | :doc:`buck/long/coul/long (o) <pair_buck_long>` | :doc:`buck/mdf <pair_mdf>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>` | :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>` | :doc:`colloid (go) <pair_colloid>` | :doc:`comb (o) <pair_comb>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`comb3 <pair_comb>` | :doc:`cosine/squared <pair_cosine_squared>` | :doc:`coul/cut (gko) <pair_coul>` | :doc:`coul/cut/soft (o) <pair_fep_soft>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`coul/debye (gko) <pair_coul>` | :doc:`coul/diel (o) <pair_coul_diel>` | :doc:`coul/dsf (gko) <pair_coul>` | :doc:`coul/long (gko) <pair_coul>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`coul/long/cs (g) <pair_cs>` | :doc:`coul/long/soft (o) <pair_fep_soft>` | :doc:`coul/msm (o) <pair_coul>` | :doc:`coul/shield <pair_coul_shield>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`coul/streitz <pair_coul>` | :doc:`coul/wolf (ko) <pair_coul>` | :doc:`coul/wolf/cs <pair_cs>` | :doc:`dpd (gio) <pair_dpd>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`dpd/fdt <pair_dpd_fdt>` | :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>` | :doc:`dpd/tstat (go) <pair_dpd>` | :doc:`dsmc <pair_dsmc>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`e3b <pair_e3b>` | :doc:`drip <pair_drip>` | :doc:`eam (gikot) <pair_eam>` | :doc:`eam/alloy (gikot) <pair_eam>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`eam/cd (o) <pair_eam>` | :doc:`eam/cd/old (o) <pair_eam>` | :doc:`eam/fs (gikot) <pair_eam>` | :doc:`edip (o) <pair_edip>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`edip/multi <pair_edip>` | :doc:`edpd <pair_meso>` | :doc:`eff/cut <pair_eff>` | :doc:`eim (o) <pair_eim>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`exp6/rx (k) <pair_exp6_rx>` | :doc:`extep <pair_extep>` | :doc:`gauss (go) <pair_gauss>` | :doc:`gauss/cut (o) <pair_gauss>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`gayberne (gio) <pair_gayberne>` | :doc:`gran/hertz/history (o) <pair_gran>` | :doc:`gran/hooke (o) <pair_gran>` | :doc:`gran/hooke/history (ko) <pair_gran>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`granular <pair_granular>` | :doc:`gw <pair_gw>` | :doc:`gw/zbl <pair_gw>` | :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>` | :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` | :doc:`kim <pair_kim>` | :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` | :doc:`lcbop <pair_lcbop>` | :doc:`lebedeva/z <pair_lebedeva_z>` | :doc:`lennard/mdf <pair_mdf>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`line/lj <pair_line_lj>` | :doc:`list <pair_list>` | :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>` | :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/charmm/coul/long (gikot) <pair_charmm>` | :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>` | :doc:`lj/charmm/coul/msm (o) <pair_charmm>` | :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/charmmfsw/coul/long <pair_charmm>` | :doc:`lj/class2 (gko) <pair_class2>` | :doc:`lj/class2/coul/cut (ko) <pair_class2>` | :doc:`lj/class2/coul/cut/soft <pair_fep_soft>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/class2/coul/long (gko) <pair_class2>` | :doc:`lj/class2/coul/long/soft <pair_fep_soft>` | :doc:`lj/class2/soft <pair_fep_soft>` | :doc:`lj/cubic (go) <pair_lj_cubic>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/cut (gikot) <pair_lj>` | :doc:`lj/cut/coul/cut (gko) <pair_lj>` | :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>` | :doc:`lj/cut/coul/debye (gko) <pair_lj>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/cut/coul/dsf (gko) <pair_lj>` | :doc:`lj/cut/coul/long (gikot) <pair_lj>` | :doc:`lj/cut/coul/long/cs <pair_cs>` | :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/cut/coul/msm (go) <pair_lj>` | :doc:`lj/cut/coul/wolf (o) <pair_lj>` | :doc:`lj/cut/dipole/cut (go) <pair_dipole>` | :doc:`lj/cut/dipole/long (g) <pair_dipole>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/cut/dipole/sf (go) <pair_dipole>` | :doc:`lj/cut/soft (o) <pair_fep_soft>` | :doc:`lj/cut/thole/long (o) <pair_thole>` | :doc:`lj/cut/tip4p/cut (o) <pair_lj>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/cut/tip4p/long (ot) <pair_lj>` | :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>` | :doc:`lj/expand (gko) <pair_lj_expand>` | :doc:`lj/expand/coul/long (g) <pair_lj_expand>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/gromacs (gko) <pair_gromacs>` | :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>` | :doc:`lj/long/coul/long (iot) <pair_lj_long>` | :doc:`lj/long/dipole/long <pair_dipole>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/long/tip4p/long (o) <pair_lj_long>` | :doc:`lj/mdf <pair_mdf>` | :doc:`lj/sdk (gko) <pair_sdk>` | :doc:`lj/sdk/coul/long (go) <pair_sdk>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/sdk/coul/msm (o) <pair_sdk>` | :doc:`lj/sf/dipole/sf (go) <pair_dipole>` | :doc:`lj/smooth (o) <pair_lj_smooth>` | :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>` | :doc:`lj96/cut (go) <pair_lj96>` | :doc:`local/density <pair_local_density>` | :doc:`lubricate (o) <pair_lubricate>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`lubricate/poly (o) <pair_lubricate>` | :doc:`lubricateU <pair_lubricateU>` | :doc:`lubricateU/poly <pair_lubricateU>` | :doc:`mdpd <pair_meso>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`mdpd/rhosum <pair_meso>` | :doc:`meam/c <pair_meamc>` | :doc:`meam/spline (o) <pair_meam_spline>` | :doc:`meam/sw/spline <pair_meam_sw_spline>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`mgpt <pair_mgpt>` | :doc:`mie/cut (g) <pair_mie>` | :doc:`momb <pair_momb>` | :doc:`morse (gkot) <pair_morse>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`morse/smooth/linear (o) <pair_morse>` | :doc:`morse/soft <pair_fep_soft>` | :doc:`multi/lucy <pair_multi_lucy>` | :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`nb3b/harmonic <pair_nb3b_harmonic>` | :doc:`nm/cut (o) <pair_nm>` | :doc:`nm/cut/coul/cut (o) <pair_nm>` | :doc:`nm/cut/coul/long (o) <pair_nm>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`oxdna/coaxstk <pair_oxdna>` | :doc:`oxdna/excv <pair_oxdna>` | :doc:`oxdna/hbond <pair_oxdna>` | :doc:`oxdna/stk <pair_oxdna>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`oxdna/xstk <pair_oxdna>` | :doc:`oxdna2/coaxstk <pair_oxdna2>` | :doc:`oxdna2/dh <pair_oxdna2>` | :doc:`oxdna2/excv <pair_oxdna2>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`oxdna2/hbond <pair_oxdna2>` | :doc:`oxdna2/stk <pair_oxdna2>` | :doc:`oxdna2/xstk <pair_oxdna2>` | :doc:`peri/eps <pair_peri>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`peri/lps (o) <pair_peri>` | :doc:`peri/pmb (o) <pair_peri>` | :doc:`peri/ves <pair_peri>` | :doc:`polymorphic <pair_polymorphic>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`python <pair_python>` | :doc:`quip <pair_quip>` | :doc:`reax/c (ko) <pair_reaxc>` | :doc:`rebo (io) <pair_airebo>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`resquared (go) <pair_resquared>` | :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | :doc:`smd/hertz <pair_smd_hertz>` | :doc:`smd/tlsph <pair_smd_tlsph>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`smd/tri\_surface <pair_smd_triangulated_surface>` | :doc:`smd/ulsph <pair_smd_ulsph>` | :doc:`smtbq <pair_smtbq>` | :doc:`snap (k) <pair_snap>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`snap (k) <pair_snap>` | :doc:`soft (go) <pair_soft>` | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`sph/lj <pair_sph_lj>` | :doc:`sph/rhosum <pair_sph_rhosum>` | :doc:`sph/taitwater <pair_sph_taitwater>` | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`spin/dipole/cut <pair_spin_dipole>` | :doc:`spin/dipole/long <pair_spin_dipole>` | :doc:`spin/dmi <pair_spin_dmi>` | :doc:`spin/exchange <pair_spin_exchange>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`spin/magelec <pair_spin_magelec>` | :doc:`spin/neel <pair_spin_neel>` | :doc:`srp <pair_srp>` | :doc:`sw (giko) <pair_sw>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`table (gko) <pair_table>` | :doc:`table/rx (k) <pair_table_rx>` | :doc:`tdpd <pair_meso>` | :doc:`tersoff (giko) <pair_tersoff>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`tersoff/mod (gko) <pair_tersoff_mod>` | :doc:`tersoff/mod/c (o) <pair_tersoff_mod>` | :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`thole <pair_thole>` | :doc:`tip4p/cut (o) <pair_coul>` | :doc:`tip4p/long (o) <pair_coul>` | :doc:`tip4p/long/soft (o) <pair_fep_soft>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`tri/lj <pair_tri_lj>` | :doc:`ufm (got) <pair_ufm>` | :doc:`vashishta (gko) <pair_vashishta>` | :doc:`vashishta/table (o) <pair_vashishta>` |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
| :doc:`yukawa (gko) <pair_yukawa>` | :doc:`yukawa/colloid (go) <pair_yukawa_colloid>` | :doc:`zbl (gko) <pair_zbl>` | |
|
||||
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
|
||||
.. table_from_list::
|
||||
:columns: 4
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
* :doc:`none <pair_none>`
|
||||
* :doc:`zero <pair_zero>`
|
||||
* :doc:`hybrid (k) <pair_hybrid>`
|
||||
* :doc:`hybrid/overlay (k) <pair_hybrid>`
|
||||
*
|
||||
*
|
||||
*
|
||||
*
|
||||
* :doc:`adp (o) <pair_adp>`
|
||||
* :doc:`agni (o) <pair_agni>`
|
||||
* :doc:`airebo (io) <pair_airebo>`
|
||||
* :doc:`airebo/morse (io) <pair_airebo>`
|
||||
* :doc:`atm <pair_atm>`
|
||||
* :doc:`awpmd/cut <pair_awpmd>`
|
||||
* :doc:`beck (go) <pair_beck>`
|
||||
* :doc:`body/nparticle <pair_body_nparticle>`
|
||||
* :doc:`body/rounded/polygon <pair_body_rounded_polygon>`
|
||||
* :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>`
|
||||
* :doc:`bop <pair_bop>`
|
||||
* :doc:`born (go) <pair_born>`
|
||||
* :doc:`born/coul/dsf <pair_born>`
|
||||
* :doc:`born/coul/dsf/cs <pair_cs>`
|
||||
* :doc:`born/coul/long (go) <pair_born>`
|
||||
* :doc:`born/coul/long/cs (g) <pair_cs>`
|
||||
* :doc:`born/coul/msm (o) <pair_born>`
|
||||
* :doc:`born/coul/wolf (go) <pair_born>`
|
||||
* :doc:`born/coul/wolf/cs (g) <pair_cs>`
|
||||
* :doc:`brownian (o) <pair_brownian>`
|
||||
* :doc:`brownian/poly (o) <pair_brownian>`
|
||||
* :doc:`buck (giko) <pair_buck>`
|
||||
* :doc:`buck/coul/cut (giko) <pair_buck>`
|
||||
* :doc:`buck/coul/long (giko) <pair_buck>`
|
||||
* :doc:`buck/coul/long/cs <pair_cs>`
|
||||
* :doc:`buck/coul/msm (o) <pair_buck>`
|
||||
* :doc:`buck/long/coul/long (o) <pair_buck_long>`
|
||||
* :doc:`buck/mdf <pair_mdf>`
|
||||
* :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`
|
||||
* :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`
|
||||
* :doc:`colloid (go) <pair_colloid>`
|
||||
* :doc:`comb (o) <pair_comb>`
|
||||
* :doc:`comb3 <pair_comb>`
|
||||
* :doc:`cosine/squared <pair_cosine_squared>`
|
||||
* :doc:`coul/cut (gko) <pair_coul>`
|
||||
* :doc:`coul/cut/soft (o) <pair_fep_soft>`
|
||||
* :doc:`coul/debye (gko) <pair_coul>`
|
||||
* :doc:`coul/diel (o) <pair_coul_diel>`
|
||||
* :doc:`coul/dsf (gko) <pair_coul>`
|
||||
* :doc:`coul/long (gko) <pair_coul>`
|
||||
* :doc:`coul/long/cs (g) <pair_cs>`
|
||||
* :doc:`coul/long/soft (o) <pair_fep_soft>`
|
||||
* :doc:`coul/msm (o) <pair_coul>`
|
||||
* :doc:`coul/shield <pair_coul_shield>`
|
||||
* :doc:`coul/streitz <pair_coul>`
|
||||
* :doc:`coul/wolf (ko) <pair_coul>`
|
||||
* :doc:`coul/wolf/cs <pair_cs>`
|
||||
* :doc:`dpd (gio) <pair_dpd>`
|
||||
* :doc:`dpd/fdt <pair_dpd_fdt>`
|
||||
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
|
||||
* :doc:`dpd/tstat (go) <pair_dpd>`
|
||||
* :doc:`dsmc <pair_dsmc>`
|
||||
* :doc:`e3b <pair_e3b>`
|
||||
* :doc:`drip <pair_drip>`
|
||||
* :doc:`eam (gikot) <pair_eam>`
|
||||
* :doc:`eam/alloy (gikot) <pair_eam>`
|
||||
* :doc:`eam/cd (o) <pair_eam>`
|
||||
* :doc:`eam/cd/old (o) <pair_eam>`
|
||||
* :doc:`eam/fs (gikot) <pair_eam>`
|
||||
* :doc:`edip (o) <pair_edip>`
|
||||
* :doc:`edip/multi <pair_edip>`
|
||||
* :doc:`edpd <pair_meso>`
|
||||
* :doc:`eff/cut <pair_eff>`
|
||||
* :doc:`eim (o) <pair_eim>`
|
||||
* :doc:`exp6/rx (k) <pair_exp6_rx>`
|
||||
* :doc:`extep <pair_extep>`
|
||||
* :doc:`gauss (go) <pair_gauss>`
|
||||
* :doc:`gauss/cut (o) <pair_gauss>`
|
||||
* :doc:`gayberne (gio) <pair_gayberne>`
|
||||
* :doc:`gran/hertz/history (o) <pair_gran>`
|
||||
* :doc:`gran/hooke (o) <pair_gran>`
|
||||
* :doc:`gran/hooke/history (ko) <pair_gran>`
|
||||
* :doc:`granular <pair_granular>`
|
||||
* :doc:`gw <pair_gw>`
|
||||
* :doc:`gw/zbl <pair_gw>`
|
||||
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
|
||||
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
|
||||
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
|
||||
* :doc:`kim <pair_kim>`
|
||||
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
|
||||
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
|
||||
* :doc:`lcbop <pair_lcbop>`
|
||||
* :doc:`lebedeva/z <pair_lebedeva_z>`
|
||||
* :doc:`lennard/mdf <pair_mdf>`
|
||||
* :doc:`line/lj <pair_line_lj>`
|
||||
* :doc:`list <pair_list>`
|
||||
* :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
|
||||
* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
|
||||
* :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
|
||||
* :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
|
||||
* :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
|
||||
* :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
|
||||
* :doc:`lj/charmmfsw/coul/long <pair_charmm>`
|
||||
* :doc:`lj/class2 (gko) <pair_class2>`
|
||||
* :doc:`lj/class2/coul/cut (ko) <pair_class2>`
|
||||
* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
|
||||
* :doc:`lj/class2/coul/long (gko) <pair_class2>`
|
||||
* :doc:`lj/class2/coul/long/soft <pair_fep_soft>`
|
||||
* :doc:`lj/class2/soft <pair_fep_soft>`
|
||||
* :doc:`lj/cubic (go) <pair_lj_cubic>`
|
||||
* :doc:`lj/cut (gikot) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/cut (gko) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
|
||||
* :doc:`lj/cut/coul/debye (gko) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/dsf (gko) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/long (gikot) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/long/cs <pair_cs>`
|
||||
* :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
|
||||
* :doc:`lj/cut/coul/msm (go) <pair_lj>`
|
||||
* :doc:`lj/cut/coul/wolf (o) <pair_lj>`
|
||||
* :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
|
||||
* :doc:`lj/cut/dipole/long (g) <pair_dipole>`
|
||||
* :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
|
||||
* :doc:`lj/cut/soft (o) <pair_fep_soft>`
|
||||
* :doc:`lj/cut/thole/long (o) <pair_thole>`
|
||||
* :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
|
||||
* :doc:`lj/cut/tip4p/long (got) <pair_lj>`
|
||||
* :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
|
||||
* :doc:`lj/expand (gko) <pair_lj_expand>`
|
||||
* :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
|
||||
* :doc:`lj/gromacs (gko) <pair_gromacs>`
|
||||
* :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
|
||||
* :doc:`lj/long/coul/long (iot) <pair_lj_long>`
|
||||
* :doc:`lj/long/dipole/long <pair_dipole>`
|
||||
* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
|
||||
* :doc:`lj/mdf <pair_mdf>`
|
||||
* :doc:`lj/sdk (gko) <pair_sdk>`
|
||||
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
|
||||
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
|
||||
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
|
||||
* :doc:`lj/smooth (o) <pair_lj_smooth>`
|
||||
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
|
||||
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
|
||||
* :doc:`lj96/cut (go) <pair_lj96>`
|
||||
* :doc:`local/density <pair_local_density>`
|
||||
* :doc:`lubricate (o) <pair_lubricate>`
|
||||
* :doc:`lubricate/poly (o) <pair_lubricate>`
|
||||
* :doc:`lubricateU <pair_lubricateU>`
|
||||
* :doc:`lubricateU/poly <pair_lubricateU>`
|
||||
* :doc:`mdpd <pair_meso>`
|
||||
* :doc:`mdpd/rhosum <pair_meso>`
|
||||
* :doc:`meam/c <pair_meamc>`
|
||||
* :doc:`meam/spline (o) <pair_meam_spline>`
|
||||
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
|
||||
* :doc:`mgpt <pair_mgpt>`
|
||||
* :doc:`mie/cut (g) <pair_mie>`
|
||||
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
|
||||
* :doc:`momb <pair_momb>`
|
||||
* :doc:`morse (gkot) <pair_morse>`
|
||||
* :doc:`morse/smooth/linear (o) <pair_morse>`
|
||||
* :doc:`morse/soft <pair_fep_soft>`
|
||||
* :doc:`multi/lucy <pair_multi_lucy>`
|
||||
* :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`
|
||||
* :doc:`nb3b/harmonic <pair_nb3b_harmonic>`
|
||||
* :doc:`nm/cut (o) <pair_nm>`
|
||||
* :doc:`nm/cut/coul/cut (o) <pair_nm>`
|
||||
* :doc:`nm/cut/coul/long (o) <pair_nm>`
|
||||
* :doc:`oxdna/coaxstk <pair_oxdna>`
|
||||
* :doc:`oxdna/excv <pair_oxdna>`
|
||||
* :doc:`oxdna/hbond <pair_oxdna>`
|
||||
* :doc:`oxdna/stk <pair_oxdna>`
|
||||
* :doc:`oxdna/xstk <pair_oxdna>`
|
||||
* :doc:`oxdna2/coaxstk <pair_oxdna2>`
|
||||
* :doc:`oxdna2/dh <pair_oxdna2>`
|
||||
* :doc:`oxdna2/excv <pair_oxdna2>`
|
||||
* :doc:`oxdna2/hbond <pair_oxdna2>`
|
||||
* :doc:`oxdna2/stk <pair_oxdna2>`
|
||||
* :doc:`oxdna2/xstk <pair_oxdna2>`
|
||||
* :doc:`oxrna2/excv <pair_oxrna2>`
|
||||
* :doc:`oxrna2/hbond <pair_oxrna2>`
|
||||
* :doc:`oxrna2/dh <pair_oxrna2>`
|
||||
* :doc:`oxrna2/stk <pair_oxrna2>`
|
||||
* :doc:`oxrna2/xstk <pair_oxrna2>`
|
||||
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
|
||||
* :doc:`peri/eps <pair_peri>`
|
||||
* :doc:`peri/lps (o) <pair_peri>`
|
||||
* :doc:`peri/pmb (o) <pair_peri>`
|
||||
* :doc:`peri/ves <pair_peri>`
|
||||
* :doc:`polymorphic <pair_polymorphic>`
|
||||
* :doc:`python <pair_python>`
|
||||
* :doc:`quip <pair_quip>`
|
||||
* :doc:`reax/c (ko) <pair_reaxc>`
|
||||
* :doc:`rebo (io) <pair_airebo>`
|
||||
* :doc:`resquared (go) <pair_resquared>`
|
||||
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
|
||||
* :doc:`smd/hertz <pair_smd_hertz>`
|
||||
* :doc:`smd/tlsph <pair_smd_tlsph>`
|
||||
* :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
|
||||
* :doc:`smd/ulsph <pair_smd_ulsph>`
|
||||
* :doc:`smtbq <pair_smtbq>`
|
||||
* :doc:`snap (k) <pair_snap>`
|
||||
* :doc:`snap (k) <pair_snap>`
|
||||
* :doc:`soft (go) <pair_soft>`
|
||||
* :doc:`sph/heatconduction <pair_sph_heatconduction>`
|
||||
* :doc:`sph/idealgas <pair_sph_idealgas>`
|
||||
* :doc:`sph/lj <pair_sph_lj>`
|
||||
* :doc:`sph/rhosum <pair_sph_rhosum>`
|
||||
* :doc:`sph/taitwater <pair_sph_taitwater>`
|
||||
* :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
|
||||
* :doc:`spin/dipole/cut <pair_spin_dipole>`
|
||||
* :doc:`spin/dipole/long <pair_spin_dipole>`
|
||||
* :doc:`spin/dmi <pair_spin_dmi>`
|
||||
* :doc:`spin/exchange <pair_spin_exchange>`
|
||||
* :doc:`spin/magelec <pair_spin_magelec>`
|
||||
* :doc:`spin/neel <pair_spin_neel>`
|
||||
* :doc:`srp <pair_srp>`
|
||||
* :doc:`sw (giko) <pair_sw>`
|
||||
* :doc:`table (gko) <pair_table>`
|
||||
* :doc:`table/rx (k) <pair_table_rx>`
|
||||
* :doc:`tdpd <pair_meso>`
|
||||
* :doc:`tersoff (giko) <pair_tersoff>`
|
||||
* :doc:`tersoff/mod (gko) <pair_tersoff_mod>`
|
||||
* :doc:`tersoff/mod/c (o) <pair_tersoff_mod>`
|
||||
* :doc:`tersoff/table (o) <pair_tersoff>`
|
||||
* :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`
|
||||
* :doc:`thole <pair_thole>`
|
||||
* :doc:`tip4p/cut (o) <pair_coul>`
|
||||
* :doc:`tip4p/long (o) <pair_coul>`
|
||||
* :doc:`tip4p/long/soft (o) <pair_fep_soft>`
|
||||
* :doc:`tri/lj <pair_tri_lj>`
|
||||
* :doc:`ufm (got) <pair_ufm>`
|
||||
* :doc:`vashishta (gko) <pair_vashishta>`
|
||||
* :doc:`vashishta/table (o) <pair_vashishta>`
|
||||
* :doc:`yukawa (gko) <pair_yukawa>`
|
||||
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
|
||||
* :doc:`zbl (gko) <pair_zbl>`
|
||||
*
|
||||
*
|
||||
|
||||
@ -146,8 +146,3 @@ comment indicator in (2) or substituted for as a variable in (3).
|
||||
triple quotes can be nested in the usual manner. See the doc pages
|
||||
for those commands for examples. Only one of level of nesting is
|
||||
allowed, but that should be sufficient for most use cases.
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -84,8 +84,3 @@ command. Energy minimization (molecular statics) is performed using
|
||||
the :doc:`minimize <minimize>` command. A parallel tempering
|
||||
(replica-exchange) simulation can be run using the
|
||||
:doc:`temper <temper>` command.
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 25 KiB |
@ -1,21 +0,0 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\bm{H}_{cubic} = -\sum_{{ i}=1}^{N} K_{1}
|
||||
\Big[
|
||||
\left(\vec{s}_{i} \cdot \vec{n1} \right)^2
|
||||
\left(\vec{s}_{i} \cdot \vec{n2} \right)^2 +
|
||||
\left(\vec{s}_{i} \cdot \vec{n2} \right)^2
|
||||
\left(\vec{s}_{i} \cdot \vec{n3} \right)^2 +
|
||||
\left(\vec{s}_{i} \cdot \vec{n1} \right)^2
|
||||
\left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \Big]
|
||||
+K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
|
||||
\left(\vec{s}_{i} \cdot \vec{n2} \right)^2
|
||||
\left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.9 KiB |
@ -1,11 +0,0 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\bm{H}_{aniso} = -\sum_{{ i}=1}^{N} K_{an}(\bm{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2, \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 6.4 KiB |
@ -1,11 +0,0 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\bm{H}_{zeeman} = -\mu_{B}\mu_0\sum_{i=0}^{N}g_{i} \vec{s}_{i} \cdot \vec{H}_{ext} \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 13 KiB |
@ -1,16 +0,0 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J}
|
||||
\left(r_{ij} \right)\,\vec{s}_{j}
|
||||
~~{\rm and}~~
|
||||
\vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
|
||||
\partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
|
||||
\nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 10 KiB |
@ -1,13 +0,0 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath, amssymb, graphics, setspace}
|
||||
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
{J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d}
|
||||
\right)^2 }\Theta (R_c - r_{ij}) \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.8 KiB |
@ -1,11 +0,0 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\bm{H}_{ex} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.8 KiB |
@ -1,13 +0,0 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{eqnarray}
|
||||
g_1(r_{ij}) &=& g(r_{ij}) + \frac{12}{35} q(r_{ij}) \nonumber \\
|
||||
q_1(r_{ij}) &=& \frac{9}{5} q(r_{ij}) \nonumber \\
|
||||
q_2(r_{ij}) &=& - \frac{2}{5} q(r_{ij}) \nonumber
|
||||
\end{eqnarray}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 11 KiB |
@ -1,16 +0,0 @@
|
||||
\documentclass[preview]{standalone}
|
||||
\usepackage{varwidth}
|
||||
\usepackage[utf8x]{inputenc}
|
||||
\usepackage{amsmath,amssymb,amsthm,bm}
|
||||
\begin{document}
|
||||
\begin{varwidth}{50in}
|
||||
\begin{equation}
|
||||
\mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\bm e}_{ij}\cdot {\bm s}_{i})({\bm e}_{ij}
|
||||
\cdot {\bm s}_{j})-\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
|
||||
+q_1(r_{ij})\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3}\right)
|
||||
\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
|
||||
+ q_2(r_{ij}) \Big( ({\bm e}_{ij}\cdot {\bm s}_{i}) ({\bm e}_{ij}\cdot {\bm s}_{j})^3 + ({\bm e}_{ij}\cdot
|
||||
{\bm s}_{j}) ({\bm e}_{ij}\cdot {\bm s}_{i})^3\Big) \nonumber
|
||||
\end{equation}
|
||||
\end{varwidth}
|
||||
\end{document}
|
||||
@ -518,6 +518,16 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
|
||||
*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
|
||||
Self-explanatory.
|
||||
|
||||
*Bond/react: First neighbors of chiral atoms must be of mutually different types*
|
||||
Self-explanatory.
|
||||
|
||||
*Bond/react: Chiral atoms must have exactly four first neighbors*
|
||||
Self-explanatory.
|
||||
|
||||
*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
|
||||
The coordinates of atoms in the pre-reacted template are used to determine
|
||||
chirality.
|
||||
|
||||
*Bond/react special bond generation overflow*
|
||||
The number of special bonds per-atom created by a reaction exceeds the
|
||||
system setting. See the read\_data or create\_box command for how to
|
||||
|
||||
@ -195,6 +195,12 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
|
||||
*Fix SRD walls overlap but fix srd overlap not set*
|
||||
You likely want to set this in your input script.
|
||||
|
||||
* Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
|
||||
When using fix bond/create multiple times or in combination with
|
||||
fix bond/break, the individual fix instances do not share information
|
||||
about changes they made at the same time step and thus it may result
|
||||
in unexpected behavior.
|
||||
|
||||
*Fix bond/swap will ignore defined angles*
|
||||
See the doc page for fix bond/swap for more info on this
|
||||
restriction.
|
||||
|
||||
@ -133,6 +133,8 @@ Lowercase directories
|
||||
+-------------+------------------------------------------------------------------+
|
||||
| reax | RDX and TATB models using the ReaxFF |
|
||||
+-------------+------------------------------------------------------------------+
|
||||
| rerun | use of rerun and read\_dump commands |
|
||||
+-------------+------------------------------------------------------------------+
|
||||
| rigid | rigid bodies modeled as independent or coupled |
|
||||
+-------------+------------------------------------------------------------------+
|
||||
| shear | sideways shear applied to 2d solid, with and without a void |
|
||||
|
||||
@ -362,18 +362,17 @@ accessible through its thermo name:
|
||||
|
||||
.. code-block:: Python
|
||||
|
||||
L.runs[0].step # list of time steps in first run
|
||||
L.runs[0].ke # list of kinetic energy values in first run
|
||||
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:
|
||||
|
||||
import matplotlib.plot as plt
|
||||
|
||||
|
||||
.. code-block:: Python
|
||||
|
||||
steps = L.runs[0].step
|
||||
ke = L.runs[0].ke
|
||||
import matplotlib.plot as plt
|
||||
steps = L.runs[0].thermo.Step
|
||||
ke = L.runs[0].thermo.Ke
|
||||
plt.plot(steps, ke)
|
||||
|
||||
Error handling with PyLammps
|
||||
|
||||
BIN
doc/src/JPG/zeeman_langevin.jpg
Normal file
BIN
doc/src/JPG/zeeman_langevin.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 170 KiB |
@ -55,9 +55,9 @@ the doc dir.
|
||||
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
|
||||
make clean # remove intermediate RST files created by HTML build
|
||||
make clean-all # remove entire build folder and any cached data
|
||||
|
||||
make anchor\_check # check for duplicate anchor labels
|
||||
make spelling # spell-check the manual
|
||||
make anchor_check # check for duplicate anchor labels
|
||||
style_check # check for complete and consistent style lists
|
||||
make spelling # spell-check the manual
|
||||
|
||||
|
||||
----------
|
||||
|
||||
@ -2438,8 +2438,8 @@ which discuss the `QuickFF <quickff_>`_ methodology.
|
||||
* :doc:`bond\_style mm3 <bond_mm3>`
|
||||
* :doc:`improper\_style distharm <improper_distharm>`
|
||||
* :doc:`improper\_style sqdistharm <improper_sqdistharm>`
|
||||
* :doc:`pair\_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss>`
|
||||
* :doc:`pair\_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>`
|
||||
* :doc:`pair\_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
|
||||
* :doc:`pair\_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
|
||||
* examples/USER/yaff
|
||||
|
||||
|
||||
|
||||
@ -9,7 +9,7 @@ below assumes you have first imported the "lammps" module in your
|
||||
Python script, as follows:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: Python
|
||||
|
||||
from lammps import lammps
|
||||
|
||||
@ -23,7 +23,7 @@ The python/examples directory has Python scripts which show how Python
|
||||
can run LAMMPS, grab data, change it, and put it back into LAMMPS.
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: Python
|
||||
|
||||
lmp = lammps() # create a LAMMPS object using the default liblammps.so library
|
||||
# 4 optional args are allowed: name, cmdargs, ptr, comm
|
||||
@ -100,7 +100,7 @@ can run LAMMPS, grab data, change it, and put it back into LAMMPS.
|
||||
The lines
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: Python
|
||||
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
@ -117,7 +117,7 @@ prompt.
|
||||
If the ptr argument is set like this:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: Python
|
||||
|
||||
lmp = lammps(ptr=lmpptr)
|
||||
|
||||
@ -134,7 +134,7 @@ Note that you can create multiple LAMMPS objects in your Python
|
||||
script, and coordinate and run multiple simulations, e.g.
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: Python
|
||||
|
||||
from lammps import lammps
|
||||
lmp1 = lammps()
|
||||
@ -230,7 +230,7 @@ ctypes vector of ints or doubles, allocated and initialized something
|
||||
like this:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: Python
|
||||
|
||||
from ctypes import \*
|
||||
natoms = lmp.get_natoms()
|
||||
@ -265,6 +265,15 @@ following steps:
|
||||
Python script.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
.. autoclass:: lammps.lammps
|
||||
:members:
|
||||
:no-undoc-members:
|
||||
|
||||
.. autoclass:: lammps.NeighList
|
||||
:members:
|
||||
:no-undoc-members:
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
|
||||
61
doc/src/_ext/table_from_list.py
Normal file
61
doc/src/_ext/table_from_list.py
Normal file
@ -0,0 +1,61 @@
|
||||
from docutils import nodes
|
||||
from sphinx.util.docutils import SphinxDirective
|
||||
from docutils.nodes import Element, Node
|
||||
from typing import Any, Dict, List
|
||||
from sphinx import addnodes
|
||||
from sphinx.util import logging
|
||||
from sphinx.errors import SphinxError
|
||||
|
||||
class TableFromList(SphinxDirective):
|
||||
has_content = True
|
||||
required_arguments = 0
|
||||
optional_arguments = 0
|
||||
final_argument_whitespace = False
|
||||
option_spec = {
|
||||
'columns': int,
|
||||
}
|
||||
|
||||
def run(self) -> List[Node]:
|
||||
ncolumns = self.options.get('columns', 2)
|
||||
node = addnodes.compact_paragraph()
|
||||
node.document = self.state.document
|
||||
self.state.nested_parse(self.content, self.content_offset, node)
|
||||
if len(node.children) != 1 or not isinstance(node.children[0],
|
||||
nodes.bullet_list):
|
||||
reporter = self.state.document.reporter
|
||||
raise SphinxError('table_from_list content is not a list')
|
||||
fulllist = node.children[0]
|
||||
|
||||
if (len(fulllist) % ncolumns) != 0:
|
||||
raise SphinxError('number of list elements not a multiple of column number')
|
||||
|
||||
table = nodes.table()
|
||||
tgroup = nodes.tgroup(cols=ncolumns)
|
||||
table += tgroup
|
||||
|
||||
for i in range(ncolumns):
|
||||
tgroup += nodes.colspec(colwidth=1)
|
||||
|
||||
tbody = nodes.tbody()
|
||||
tgroup += tbody
|
||||
current_row = nodes.row()
|
||||
|
||||
for idx, cell in enumerate(fulllist.children):
|
||||
if len(current_row.children) == ncolumns:
|
||||
tbody += current_row
|
||||
current_row = nodes.row()
|
||||
entry = nodes.entry()
|
||||
current_row += entry
|
||||
if len(cell.children) > 0:
|
||||
entry += cell.children[0]
|
||||
|
||||
tbody += current_row
|
||||
return [table]
|
||||
|
||||
def setup(app):
|
||||
app.add_directive("table_from_list", TableFromList)
|
||||
return {
|
||||
'version': '0.1',
|
||||
'parallel_read_safe': True,
|
||||
'parallel_write_safe': True,
|
||||
}
|
||||
@ -6,6 +6,9 @@ bond_style oxdna/fene command
|
||||
bond_style oxdna2/fene command
|
||||
==============================
|
||||
|
||||
bond_style oxrna2/fene command
|
||||
==============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -16,6 +19,8 @@ Syntax
|
||||
|
||||
bond_style oxdna2/fene
|
||||
|
||||
bond_style oxrna2/fene
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
@ -28,10 +33,13 @@ Examples
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
bond_style oxrna2/fene
|
||||
bond_coeff \* 2.0 0.25 0.76107
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *oxdna/fene* and *oxdna2/fene* bond styles use the potential
|
||||
The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential
|
||||
|
||||
.. math::
|
||||
|
||||
@ -39,9 +47,9 @@ The *oxdna/fene* and *oxdna2/fene* bond styles use the potential
|
||||
|
||||
|
||||
to define a modified finite extensible nonlinear elastic (FENE)
|
||||
potential :ref:`(Ouldridge) <oxdna_fene>` to model the connectivity of the
|
||||
phosphate backbone in the oxDNA force field for coarse-grained
|
||||
modelling of DNA.
|
||||
potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the
|
||||
phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
|
||||
modelling of DNA/RNA.
|
||||
|
||||
The following coefficients must be defined for the bond type via the
|
||||
:doc:`bond\_coeff <bond_coeff>` command as given in the above example, or
|
||||
@ -57,27 +65,36 @@ commands:
|
||||
|
||||
The oxDNA bond style has to be used together with the
|
||||
corresponding oxDNA pair styles for excluded volume interaction
|
||||
*oxdna/excv*\ , stacking *oxdna/stk*\ , cross-stacking *oxdna/xstk* and
|
||||
*oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and
|
||||
coaxial stacking interaction *oxdna/coaxstk* as well as
|
||||
hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
|
||||
:doc:`pair\_style oxdna/excv <pair_oxdna>`). For the oxDNA2
|
||||
:ref:`(Snodin) <oxdna2>` bond style the analogous pair styles and an
|
||||
additional Debye-Hueckel pair style *oxdna2/dh* have to be defined.
|
||||
:ref:`(Snodin) <Snodin0>` bond style the analogous pair styles
|
||||
*oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
|
||||
*oxdna2/hbond* and an additional Debye-Hueckel pair style
|
||||
*oxdna2/dh* have to be defined. The same applies to the oxRNA2
|
||||
:ref:`(Sulc1) <Sulc01>` styles.
|
||||
The coefficients in the above example have to be kept fixed and cannot
|
||||
be changed without reparameterizing the entire model.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in
|
||||
examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python
|
||||
setup tool which creates single straight or helical DNA strands, DNA
|
||||
duplexes or arrays of DNA duplexes can be found in
|
||||
Example input and data files for DNA and RNA duplexes can be found in
|
||||
examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python
|
||||
setup tool which creates single straight or helical DNA strands, DNA/RNA
|
||||
duplexes or arrays of DNA/RNA duplexes can be found in
|
||||
examples/USER/cgdna/util/.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich2>` and the relevant oxDNA articles in
|
||||
any publication that uses this implementation. The article contains
|
||||
more information on the model, the structure of the input file, the
|
||||
setup tool and the performance of the LAMMPS-implementation of oxDNA.
|
||||
The preprint version of the article can be found
|
||||
Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
|
||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
|
||||
`here <PDF/USER-CGDNA.pdf>`_.
|
||||
Please cite also the relevant oxDNA/oxRNA publications. These are
|
||||
:ref:`(Ouldridge) <Ouldridge0>` and
|
||||
:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA,
|
||||
:ref:`(Snodin) <Snodin0>` for oxDNA2,
|
||||
:ref:`(Sulc1) <Sulc01>` for oxRNA2
|
||||
and for sequence-specific hydrogen-bonding and stacking interactions
|
||||
:ref:`(Sulc2) <Sulc02>`.
|
||||
|
||||
|
||||
----------
|
||||
@ -94,32 +111,36 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`,
|
||||
:doc:`bond\_coeff <bond_coeff>`
|
||||
:doc:`pair\_style oxdna/excv <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
|
||||
:doc:`bond\_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
|
||||
**Default:** none
|
||||
**Default:**
|
||||
|
||||
none
|
||||
|
||||
|
||||
----------
|
||||
|
||||
.. _Henrich0:
|
||||
|
||||
.. _Henrich2:
|
||||
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
.. _Ouldridge-DPhil0:
|
||||
|
||||
**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
|
||||
|
||||
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
|
||||
T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
.. _Ouldridge0:
|
||||
|
||||
.. _oxdna\_fene:
|
||||
**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
|
||||
|
||||
.. _Snodin0:
|
||||
|
||||
**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
|
||||
|
||||
**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
|
||||
J. Chem. Phys. 134, 085101 (2011).
|
||||
.. _Sulc01:
|
||||
|
||||
.. _oxdna2:
|
||||
**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
|
||||
|
||||
.. _Sulc02:
|
||||
|
||||
|
||||
**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
|
||||
J. Chem. Phys. 142, 234901 (2015).
|
||||
**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
@ -100,6 +100,7 @@ accelerated styles exist.
|
||||
* :doc:`nonlinear <bond_nonlinear>` - nonlinear bond
|
||||
* :doc:`oxdna/fene <bond_oxdna>` - modified FENE bond suitable for DNA modeling
|
||||
* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
|
||||
* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
|
||||
* :doc:`quartic <bond_quartic>` - breakable quartic bond
|
||||
* :doc:`table <bond_table>` - tabulated by bond length
|
||||
|
||||
|
||||
@ -287,9 +287,10 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
|
||||
* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` -
|
||||
* :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
|
||||
* :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
|
||||
* :doc:`sna/atom <compute_sna_atom>` - calculate bispectrum coefficients for each atom
|
||||
* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum coefficients for each atom
|
||||
* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum coefficients for each atom
|
||||
* :doc:`snap <compute_sna_atom>` - bispectrum components and related quantities for a group of atoms
|
||||
* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
|
||||
* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
|
||||
* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
|
||||
* :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
|
||||
* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
|
||||
* :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
|
||||
|
||||
@ -9,6 +9,9 @@ compute snad/atom command
|
||||
compute snav/atom command
|
||||
=========================
|
||||
|
||||
compute snap command
|
||||
====================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -17,7 +20,8 @@ Syntax
|
||||
|
||||
compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
|
||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||
* sna/atom = style name of this compute command
|
||||
@ -53,12 +57,17 @@ Examples
|
||||
compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
|
||||
compute db all sna/atom 1.4 0.95 6 2.0 1.0
|
||||
compute vb all sna/atom 1.4 0.95 6 2.0 1.0
|
||||
compute snap all snap 1.4 0.95 6 2.0 1.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that calculates a set of bispectrum components
|
||||
for each atom in a group.
|
||||
Define a computation that calculates a set of quantities related to the
|
||||
bispectrum components of the atoms in a group. These computes are
|
||||
used primarily for calculating the dependence of energy, force, and
|
||||
stress components on the linear coefficients in the
|
||||
:doc:`snap pair\_style <pair_snap>`, which is useful when training a
|
||||
SNAP potential to match target data.
|
||||
|
||||
Bispectrum components of an atom are order parameters characterizing
|
||||
the radial and angular distribution of neighbor atoms. The detailed
|
||||
@ -148,6 +157,30 @@ Again, the sum is over all atoms *i'* of atom type *I*\ . For each atom
|
||||
virial components, each atom type, and each bispectrum component. See
|
||||
section below on output for a detailed explanation.
|
||||
|
||||
Compute *snap* calculates a global array contains information related
|
||||
to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ ,
|
||||
and *snav/atom*\ . The first row of the array contains the summation of
|
||||
*sna/atom* over all atoms, but broken out by type. The last six rows
|
||||
of the array contain the summation of *snav/atom* over all atoms, broken
|
||||
out by type. In between these are 3\*\ *N* rows containing the same values
|
||||
computed by *snad/atom* (these are already summed over all atoms and
|
||||
broken out by type). The element in the last column of each row contains
|
||||
the potential energy, force, or stress, according to the row.
|
||||
These quantities correspond to the user-specified reference potential
|
||||
that must be subtracted from the target data when fitting SNAP.
|
||||
The potential energy calculation uses the built in compute *thermo\_pe*.
|
||||
The stress calculation uses a compute called *snap\_press* that is
|
||||
automatically created behind the scenes, according to the following
|
||||
command:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
compute snap_press all pressure NULL virial
|
||||
|
||||
See section below on output for a detailed explanation of the data
|
||||
layout in the global array.
|
||||
|
||||
The value of all bispectrum components will be zero for atoms not in
|
||||
the group. Neighbor atoms not in the group do not contribute to the
|
||||
bispectrum of atoms in the group.
|
||||
@ -239,10 +272,25 @@ block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
|
||||
notation. Each of these sub-blocks contains one column for each
|
||||
bispectrum component, the same as for compute *sna/atom*
|
||||
|
||||
Compute *snap* evaluates a global array.
|
||||
The columns are arranged into
|
||||
*ntypes* blocks, listed in order of atom type *I*\ . Each block
|
||||
contains one column for each bispectrum component, the same as for compute
|
||||
*sna/atom*\ . A final column contains the corresponding energy, force component
|
||||
on an atom, or virial stress component. The rows of the array appear
|
||||
in the following order:
|
||||
|
||||
* 1 row: *sna/atom* quantities summed for all atoms of type *I*
|
||||
* 3\*\ *N* rows: *snad/atom* quantities, with derivatives w.r.t. x, y, and z coordinate of atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID.
|
||||
* 6 rows: *snav/atom* quantities summed for all atoms of type *I*
|
||||
|
||||
For example, if *K* =30 and ntypes=1, the number of columns in the per-atom
|
||||
arrays generated by *sna/atom*\ , *snad/atom*\ , and *snav/atom*
|
||||
are 30, 90, and 180, respectively. With *quadratic* value=1,
|
||||
the numbers of columns are 930, 2790, and 5580, respectively.
|
||||
The number of columns in the global array generated by *snap*
|
||||
are 31, and 931, respectively, while the number of rows is
|
||||
1+3\*\ *N*\ +6, where *N* is the total number of atoms.
|
||||
|
||||
If the *quadratic* keyword value is set to 1, then additional
|
||||
columns are generated, corresponding to
|
||||
|
||||
@ -7,7 +7,7 @@ Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute ID group-ID spin
|
||||
|
||||
@ -18,7 +18,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute out_mag all spin
|
||||
|
||||
@ -28,24 +28,22 @@ Description
|
||||
Define a computation that calculates magnetic quantities for a system
|
||||
of atoms having spins.
|
||||
|
||||
This compute calculates 6 magnetic quantities.
|
||||
This compute calculates the following 6 magnetic quantities:
|
||||
|
||||
The three first quantities are the x,y and z coordinates of the total
|
||||
magnetization.
|
||||
* the three first quantities are the x,y and z coordinates of the total
|
||||
magnetization,
|
||||
* the fourth quantity is the norm of the total magnetization,
|
||||
* The fifth quantity is the magnetic energy (in eV),
|
||||
* The sixth one is referred to as the spin temperature, according
|
||||
to the work of :ref:`(Nurdin) <Nurdin1>`.
|
||||
|
||||
The fourth quantity is the norm of the total magnetization.
|
||||
|
||||
The fifth quantity is the magnetic energy.
|
||||
|
||||
The sixth one is referred to as the spin temperature, according
|
||||
to the work of :ref:`(Nurdin) <Nurdin1>`.
|
||||
|
||||
The simplest way to output the results of the compute spin calculation
|
||||
is to define some of the quantities as variables, and to use the thermo and
|
||||
thermo\_style commands, for example:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
compute out_mag all spin
|
||||
|
||||
@ -74,9 +72,13 @@ The *spin* compute is part of the SPIN package. This compute is only
|
||||
enabled if LAMMPS was built with this package. See the :doc:`Build package <Build_package>` doc page for more info. The atom\_style
|
||||
has to be "spin" for this compute to be valid.
|
||||
|
||||
**Related commands:** none
|
||||
**Related commands:**
|
||||
|
||||
**Default:** none
|
||||
none
|
||||
|
||||
**Default:**
|
||||
|
||||
none
|
||||
|
||||
|
||||
----------
|
||||
@ -87,8 +89,3 @@ has to be "spin" for this compute to be valid.
|
||||
|
||||
|
||||
**(Nurdin)** Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000)
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -64,16 +64,16 @@ with new settings). This is the same as if an "unfix" command were
|
||||
first performed on the old fix, except that the new fix is kept in the
|
||||
same order relative to the existing fixes as the old one originally
|
||||
was. Note that this operation also wipes out any additional changes
|
||||
made to the old fix via the :doc:`fix\_modify <fix_modify>` command.
|
||||
made to the old fix via the :doc:`fix_modify <fix_modify>` command.
|
||||
|
||||
The :doc:`fix modify <fix_modify>` command allows settings for some
|
||||
fixes to be reset. See the doc page for individual fixes for details.
|
||||
|
||||
Some fixes store an internal "state" which is written to binary
|
||||
restart files via the :doc:`restart <restart>` or
|
||||
:doc:`write\_restart <write_restart>` commands. This allows the fix to
|
||||
:doc:`write_restart <write_restart>` commands. This allows the fix to
|
||||
continue on with its calculations in a restarted simulation. See the
|
||||
:doc:`read\_restart <read_restart>` command for info on how to re-specify
|
||||
:doc:`read_restart <read_restart>` command for info on how to re-specify
|
||||
a fix in an input script that reads a restart file. See the doc pages
|
||||
for individual fixes for info on which ones can be restarted.
|
||||
|
||||
@ -133,7 +133,7 @@ various commands explain the details.
|
||||
|
||||
In LAMMPS, the values generated by a fix can be used in several ways:
|
||||
|
||||
* Global values can be output via the :doc:`thermo\_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
|
||||
* Global values can be output via the :doc:`thermo_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
|
||||
Or the values can be referenced in a :doc:`variable equal <variable>` or
|
||||
:doc:`variable atom <variable>` command.
|
||||
* Per-atom values can be output via the :doc:`dump custom <dump>` command.
|
||||
@ -257,6 +257,7 @@ accelerated styles exist.
|
||||
* :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm
|
||||
* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
|
||||
* :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
|
||||
* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
|
||||
* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
|
||||
* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
|
||||
* :doc:`nph/body <fix_nph_body>` - NPH for body particles
|
||||
@ -339,15 +340,16 @@ accelerated styles exist.
|
||||
* :doc:`rx <fix_rx>` -
|
||||
* :doc:`saed/vtk <fix_saed_vtk>` -
|
||||
* :doc:`setforce <fix_setforce>` - set the force on each atom
|
||||
* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
|
||||
* :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
|
||||
* :doc:`smd/adjust\_dt <fix_smd_adjust_dt>` -
|
||||
* :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` -
|
||||
* :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>` -
|
||||
* :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` -
|
||||
* :doc:`smd/adjust_dt <fix_smd_adjust_dt>` -
|
||||
* :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>` -
|
||||
* :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>` -
|
||||
* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>` -
|
||||
* :doc:`smd/setvel <fix_smd_setvel>` -
|
||||
* :doc:`smd/wall\_surface <fix_smd_wall_surface>` -
|
||||
* :doc:`smd/wall_surface <fix_smd_wall_surface>` -
|
||||
* :doc:`spring <fix_spring>` - apply harmonic spring force to group of atoms
|
||||
* :doc:`spring/chunk <fix_spring_chunk>` - apply harmonic spring force to each chunk of atoms
|
||||
* :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of group of atoms
|
||||
@ -399,7 +401,7 @@ individual fixes tell if it is part of a package.
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`unfix <unfix>`, :doc:`fix\_modify <fix_modify>`
|
||||
:doc:`unfix <unfix>`, :doc:`fix_modify <fix_modify>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
@ -88,7 +88,7 @@ command creates a per-atom array with 6 columns:
|
||||
|
||||
compute my_stress all stress/atom NULL
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress[\*]
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[2] &
|
||||
c_my_stress[3] c_my_stress[4] &
|
||||
c_my_stress[5] c_my_stress[6]
|
||||
|
||||
|
||||
@ -20,9 +20,9 @@ Syntax
|
||||
* the common keyword/values may be appended directly after 'bond/react'
|
||||
* this applies to all reaction specifications (below)
|
||||
* common\_keyword = *stabilization*
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
|
||||
*stabilization* values = *no* or *yes* *group-ID* *xmax*
|
||||
*no* = no reaction site stabilization
|
||||
*yes* = perform reaction site stabilization
|
||||
@ -40,9 +40,9 @@ Syntax
|
||||
* map\_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
|
||||
* zero or more individual keyword/value pairs may be appended to each react argument
|
||||
* individual\_keyword = *prob* or *max\_rxn* or *stabilize\_steps* or *update\_edges*
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
|
||||
*prob* values = fraction seed
|
||||
fraction = initiate reaction with this probability if otherwise eligible
|
||||
seed = random number seed (positive integer)
|
||||
@ -253,7 +253,7 @@ A discussion of correctly handling this is also provided on the
|
||||
The map file is a text document with the following format:
|
||||
|
||||
A map file has a header and a body. The header of map file the
|
||||
contains one mandatory keyword and four optional keywords. The
|
||||
contains one mandatory keyword and five optional keywords. The
|
||||
mandatory keyword is 'equivalences':
|
||||
|
||||
|
||||
@ -269,10 +269,11 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'customIDs' and
|
||||
|
||||
N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template
|
||||
N *deleteIDs* = # of atoms N that are specified for deletion
|
||||
N *chiralIDs* = # of specified chiral centers N
|
||||
N *customIDs* = # of atoms N that are specified for a custom update
|
||||
N *constraints* = # of specified reaction constraints N
|
||||
|
||||
The body of the map file contains two mandatory sections and four
|
||||
The body of the map file contains two mandatory sections and five
|
||||
optional sections. The first mandatory section begins with the keyword
|
||||
'BondingIDs' and lists the atom IDs of the bonding atom pair in the
|
||||
pre-reacted molecule template. The second mandatory section begins
|
||||
@ -284,12 +285,14 @@ molecule template. The first optional section begins with the keyword
|
||||
'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
|
||||
molecule template. The second optional section begins with the keyword
|
||||
'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
|
||||
delete. The third optional section begins with the keyword 'Custom
|
||||
delete. The third optional section begins with the keyword 'ChiralIDs'
|
||||
lists the atom IDs of chiral atoms whose handedness should be
|
||||
enforced. The fourth optional section begins with the keyword 'Custom
|
||||
Edges' and allows for forcing the update of a specific atom's atomic
|
||||
charge. The first column is the ID of an atom near the edge of the
|
||||
pre-reacted molecule template, and the value of the second column is
|
||||
either 'none' or 'charges.' Further details are provided in the
|
||||
discussion of the 'update\_edges' keyword. The fourth optional section
|
||||
discussion of the 'update\_edges' keyword. The fifth optional section
|
||||
begins with the keyword 'Constraints' and lists additional criteria
|
||||
that must be satisfied in order for the reaction to occur. Currently,
|
||||
there are three types of constraints available, as discussed below.
|
||||
@ -332,6 +335,15 @@ A sample map file is given below:
|
||||
----------
|
||||
|
||||
|
||||
The handedness of atoms that are chiral centers can be enforced by
|
||||
listing their IDs in the ChiralIDs section. A chiral atom must be
|
||||
bonded to four atoms with mutually different atom types. This feature
|
||||
uses the coordinates and types of the involved atoms in the
|
||||
pre-reaction template to determine handedness. Three atoms bonded to
|
||||
the chiral center are arbitrarily chosen, to define an oriented plane,
|
||||
and the relative position of the fourth bonded atom determines the
|
||||
chiral center's handedness.
|
||||
|
||||
Any number of additional constraints may be specified in the
|
||||
Constraints section of the map file. The constraint of type 'distance'
|
||||
has syntax as follows:
|
||||
|
||||
@ -57,6 +57,8 @@ Syntax
|
||||
fix-ID = ID of :doc:`fix rigid/small <fix_rigid>` command
|
||||
*shake* value = fix-ID
|
||||
fix-ID = ID of :doc:`fix shake <fix_shake>` command
|
||||
*orient* values = rx ry rz
|
||||
rx,ry,rz = vector to randomly rotate an inserted molecule around
|
||||
*units* value = *lattice* or *box*
|
||||
lattice = the geometry is defined in lattice units
|
||||
box = the geometry is defined in simulation box units
|
||||
@ -236,6 +238,13 @@ sputtering process. E.g. the target point can be far away, so that
|
||||
all incident particles strike the surface as if they are in an
|
||||
incident beam of particles at a prescribed angle.
|
||||
|
||||
The *orient* keyword is only used when molecules are deposited. By
|
||||
default, each molecule is inserted at a random orientation. If this
|
||||
keyword is specified, then (rx,ry,rz) is used as an orientation
|
||||
vector, and each inserted molecule is rotated around that vector with
|
||||
a random value from zero to 2*PI. For a 2d simulation, rx = ry = 0.0
|
||||
is required, since rotations can only be performed around the z axis.
|
||||
|
||||
The *id* keyword determines how atom IDs and molecule IDs are assigned
|
||||
to newly deposited particles. Molecule IDs are only assigned if
|
||||
molecules are being inserted. For the *max* setting, the atom and
|
||||
|
||||
@ -26,11 +26,11 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack1>`
|
||||
Apply a rigid-body integrator as described in :ref:`(Davidchack) <Davidchack4>`
|
||||
to a group of atoms, but without Langevin dynamics.
|
||||
This command performs Molecular dynamics (MD)
|
||||
via a velocity-Verlet algorithm and an evolution operator that rotates
|
||||
the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller1>`.
|
||||
the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) <Miller4>`.
|
||||
|
||||
This command is the equivalent of the :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
without damping and noise and can be used to determine the stability range
|
||||
@ -40,7 +40,7 @@ The command is equivalent to the :doc:`fix nve <fix_nve>`.
|
||||
The particles are always considered to have a finite size.
|
||||
|
||||
An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
|
||||
Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich3>`.
|
||||
Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich4>`.
|
||||
The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
|
||||
|
||||
|
||||
@ -66,19 +66,15 @@ Related commands
|
||||
----------
|
||||
|
||||
|
||||
.. _Davidchack1:
|
||||
|
||||
|
||||
|
||||
.. _Miller1:
|
||||
.. _Davidchack4:
|
||||
|
||||
**(Davidchack)** R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
|
||||
|
||||
|
||||
.. _Henrich3:
|
||||
.. _Miller4:
|
||||
|
||||
**(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
|
||||
|
||||
.. _Henrich4:
|
||||
|
||||
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
|
||||
@ -38,14 +38,14 @@ Description
|
||||
"""""""""""
|
||||
|
||||
Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
|
||||
as described in :ref:`(Davidchack) <Davidchack2>`
|
||||
as described in :ref:`(Davidchack) <Davidchack5>`
|
||||
to a group of atoms, which models an interaction with an implicit background
|
||||
solvent. This command performs Brownian dynamics (BD)
|
||||
via a technique that splits the integration into a deterministic Hamiltonian
|
||||
part and the Ornstein-Uhlenbeck process for noise and damping.
|
||||
The quaternion degrees of freedom are updated though an evolution
|
||||
operator which performs a rotation in quaternion space, preserves
|
||||
the quaternion norm and is akin to :ref:`(Miller) <Miller2>`.
|
||||
the quaternion norm and is akin to :ref:`(Miller) <Miller5>`.
|
||||
|
||||
In terms of syntax this command has been closely modelled on the
|
||||
:doc:`fix langevin <fix_langevin>` and its *angmom* option. But it combines
|
||||
@ -86,7 +86,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired
|
||||
temperature, m is the mass of the particle, dt is the timestep size,
|
||||
and damp is the damping factor. Random numbers are used to randomize
|
||||
the direction and magnitude of this force as described in
|
||||
:ref:`(Dunweg) <Dunweg3>`, where a uniform random number is used (instead of
|
||||
:ref:`(Dunweg) <Dunweg5>`, where a uniform random number is used (instead of
|
||||
a Gaussian random number) for speed.
|
||||
|
||||
|
||||
@ -128,7 +128,7 @@ The scale factor after the *angmom* keyword gives the ratio of the rotational to
|
||||
the translational friction coefficient.
|
||||
|
||||
An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
|
||||
Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich4>`.
|
||||
Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich5>`.
|
||||
The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
|
||||
|
||||
|
||||
@ -154,24 +154,19 @@ Related commands
|
||||
----------
|
||||
|
||||
|
||||
.. _Davidchack2:
|
||||
|
||||
|
||||
|
||||
.. _Miller2:
|
||||
.. _Davidchack5:
|
||||
|
||||
**(Davidchack)** R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
|
||||
|
||||
|
||||
.. _Dunweg3:
|
||||
.. _Miller5:
|
||||
|
||||
**(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
|
||||
|
||||
|
||||
.. _Henrich4:
|
||||
.. _Dunweg5:
|
||||
|
||||
**(Dunweg)** B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
|
||||
|
||||
.. _Henrich5:
|
||||
|
||||
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
|
||||
@ -7,7 +7,7 @@ Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix ID group precession/spin style args
|
||||
|
||||
@ -37,7 +37,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
|
||||
fix 1 3 precession/spin anisotropy 0.001 0.0 0.0 1.0
|
||||
@ -53,42 +53,83 @@ Style *zeeman* is used for the simulation of the interaction
|
||||
between the magnetic spins in the defined group and an external
|
||||
magnetic field:
|
||||
|
||||
.. image:: Eqs/force_spin_zeeman.jpg
|
||||
.. math::
|
||||
|
||||
H_{Zeeman} = -g \sum_{i=0}^{N}\mu_{i}\, \vec{s}_{i} \cdot\vec{B}_{ext}
|
||||
|
||||
with:
|
||||
|
||||
* :math:`\vec{B}_{ext}` the external magnetic field (in T)
|
||||
* :math:`g` the Lande factor (hard-coded as :math:`g=2.0`)
|
||||
* :math:`\vec{s}_i` the unitary vector describing the orientation of spin :math:`i`
|
||||
* :math:`\mu_i` the atomic moment of spin :math:`i` given as a multiple of the
|
||||
Bohr magneton :math:`\mu_B` (for example, :math:`\mu_i \approx 2.2` in bulk iron).
|
||||
|
||||
|
||||
The field value in Tesla is multiplied by the gyromagnetic
|
||||
ratio, :math:`g \cdot \mu_B/\hbar`, converting it into a precession frequency in
|
||||
rad.THz (in metal units and with :math:`\mu_B = 5.788 eV/T`).
|
||||
|
||||
As a comparison, the figure below displays the simulation of a
|
||||
single spin (of norm :math:`\mu_i = 1.0`) submitted to an external
|
||||
magnetic field of :math:`\vert B_{ext}\vert = 10.0\; \mathrm{Tesla}` (and oriented along the z
|
||||
axis).
|
||||
The upper plot shows the average magnetization along the
|
||||
external magnetic field axis and the lower plot the Zeeman
|
||||
energy, both as a function of temperature.
|
||||
The reference result is provided by the plot of the Langevin
|
||||
function for the same parameters.
|
||||
|
||||
.. image:: JPG/zeeman_langevin.jpg
|
||||
:align: center
|
||||
|
||||
with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T
|
||||
in metal units).
|
||||
The temperature effects are accounted for by connecting the spin
|
||||
:math:`i` to a thermal bath using a Langevin thermostat (see
|
||||
:doc:`fix\_langevin\_spin <fix_langevin_spin>` for the definition of
|
||||
this thermostat).
|
||||
|
||||
Style *anisotropy* is used to simulate an easy axis or an easy plane
|
||||
for the magnetic spins in the defined group:
|
||||
|
||||
.. image:: Eqs/force_spin_aniso.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
with n defining the direction of the anisotropy, and K (in eV) its intensity.
|
||||
If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
|
||||
H_{aniso} = -\sum_{{ i}=1}^{N} K_{an}(\mathbf{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2
|
||||
|
||||
with :math:`n` defining the direction of the anisotropy, and :math:`K` (in eV) its intensity.
|
||||
If :math:`K > 0`, an easy axis is defined, and if :math:`K < 0`, an easy plane is defined.
|
||||
|
||||
Style *cubic* is used to simulate a cubic anisotropy, with three
|
||||
possible easy axis for the magnetic spins in the defined group:
|
||||
|
||||
.. image:: Eqs/fix_spin_cubic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
with K1 and K2c (in eV) the intensity coefficients and
|
||||
n1, n2 and n3 defining the three anisotropic directions
|
||||
defined by the command (from n1x to n3z).
|
||||
For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an
|
||||
iron type anisotropy (easy axis along the (001)-type cube
|
||||
edges), and K1 > 0 defines a nickel type anisotropy (easy axis
|
||||
along the (111)-type cube diagonals).
|
||||
K2\^c > 0 also defines easy axis along the (111)-type cube
|
||||
H_{cubic} = -\sum_{{ i}=1}^{N} K_{1}
|
||||
\Big[
|
||||
\left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
|
||||
\left(\vec{s}_{i} \cdot \vec{n_2} \right)^2 +
|
||||
\left(\vec{s}_{i} \cdot \vec{n_2} \right)^2
|
||||
\left(\vec{s}_{i} \cdot \vec{n_3} \right)^2 +
|
||||
\left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
|
||||
\left(\vec{s}_{i} \cdot \vec{n_3} \right)^2 \Big]
|
||||
+K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
|
||||
\left(\vec{s}_{i} \cdot \vec{n_2} \right)^2
|
||||
\left(\vec{s}_{i} \cdot \vec{n_3} \right)^2
|
||||
|
||||
with :math:`K_1` and :math:`K_{2c}` (in eV) the intensity coefficients and
|
||||
:math:`\vec{n}_1`, :math:`\vec{n}_2` and :math:`\vec{n}_3` defining the three anisotropic directions
|
||||
defined by the command (from *n1x* to *n3z*).
|
||||
For :math:`\vec{n}_1 = (1 0 0)`, :math:`\vec{n}_2 = (0 1 0)`, and :math:`\vec{n}_3 = (0 0 1)`, :math:`K_1 < 0` defines an
|
||||
iron type anisotropy (easy axis along the :math:`(0 0 1)`-type cube
|
||||
edges), and :math:`K_1 > 0` defines a nickel type anisotropy (easy axis
|
||||
along the :math:`(1 1 1)`-type cube diagonals).
|
||||
:math:`K_2^c > 0` also defines easy axis along the :math:`(1 1 1)`-type cube
|
||||
diagonals.
|
||||
See chapter 2 of :ref:`(Skomski) <Skomski1>` for more details on cubic
|
||||
anisotropies.
|
||||
|
||||
In all cases, the choice of (x y z) only imposes the vector
|
||||
In all cases, the choice of :math:`(x y z)` only imposes the vector
|
||||
directions for the forces. Only the direction of the vector is
|
||||
important; it's length is ignored (the entered vectors are
|
||||
important; its length is ignored (the entered vectors are
|
||||
normalized).
|
||||
|
||||
Those styles can be combined within one single command line.
|
||||
@ -105,7 +146,7 @@ The :doc:`fix\_modify <fix_modify>` *energy* option is supported by this fix
|
||||
to add this magnetic potential energy to the potential energy of the system,
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
@ -128,7 +169,9 @@ Related commands
|
||||
|
||||
:doc:`atom\_style spin <atom_style>`
|
||||
|
||||
**Default:** none
|
||||
**Default:**
|
||||
|
||||
none
|
||||
|
||||
|
||||
----------
|
||||
@ -140,8 +183,3 @@ Related commands
|
||||
|
||||
**(Skomski)** Skomski, R. (2008). Simple models of magnetism.
|
||||
Oxford University Press.
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -11,26 +11,30 @@ Syntax
|
||||
|
||||
kspace_style style value
|
||||
|
||||
* style = *none* or *ewald* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
|
||||
|
||||
* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
|
||||
*none* value = none
|
||||
*ewald* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*ewald/disp* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*ewald/omp* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*ewald/dipole* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*ewald/dipole/spin* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*ewald/disp* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*ewald/omp* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/cg* values = accuracy (smallq)
|
||||
accuracy = desired relative error in forces
|
||||
smallq = cutoff for charges to be considered (optional) (charge units)
|
||||
*pppm/dipole* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/dipole/spin* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/disp* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/tip4p* value = accuracy
|
||||
@ -41,22 +45,23 @@ Syntax
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/intel* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/disp/intel* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/kk* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/omp* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/cg/omp* value = accuracy
|
||||
*pppm/cg/omp* values = accuracy (smallq)
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/disp/intel* value = accuracy
|
||||
smallq = cutoff for charges to be considered (optional) (charge units)
|
||||
*pppm/disp/omp* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/tip4p/omp* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/disp/tip4p/omp* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/stagger* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/dipole* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*pppm/dipole/spin* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*msm* value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
*msm/cg* value = accuracy (smallq)
|
||||
|
||||
@ -547,10 +547,10 @@ the *cuda/aware* keyword is automatically set to *off* by default. When
|
||||
the *cuda/aware* keyword is set to *off* while any of the *comm*
|
||||
keywords are set to *device*\ , the value for these *comm* keywords will
|
||||
be automatically changed to *host*\ . This setting has no effect if not
|
||||
running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later
|
||||
versions), Mvapich2 1.9 (or later) when the "MV2\_USE\_CUDA" environment
|
||||
variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu"
|
||||
flag is used.
|
||||
running on GPUs or if using only one MPI rank. CUDA-aware MPI is available
|
||||
for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the
|
||||
"MV2\_USE\_CUDA" environment variable is set to "1", CrayMPI, and IBM
|
||||
Spectrum MPI when the "-gpu" flag is used.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
@ -105,8 +105,11 @@ Restrictions
|
||||
|
||||
|
||||
Currently, only elemental systems are implemented. Also, the method
|
||||
only provides access to the forces and not energies or
|
||||
stresses. However, one can access the energy via thermodynamic
|
||||
only provides access to the forces and not energies or stresses.
|
||||
The lack of potential energy data makes this pair style incompatible with
|
||||
several of the :doc:`minimizer algorthms <min_style>` like *cg* or *sd*\ .
|
||||
It should work with damped dynamics based minimizers like *fire* or
|
||||
*quickmin*\ . However, one can access the energy via thermodynamic
|
||||
integration of the forces as discussed in
|
||||
:ref:`(Botu3) <Botu2016construct>`. This pair style is part of the
|
||||
USER-MISC package. It is only enabled if LAMMPS was built with that
|
||||
|
||||
@ -432,7 +432,7 @@ option by an additional factor of *a*\ , the radius of the contact region. The t
|
||||
Here, *a* is the radius of the contact region, given by :math:`a =\sqrt{R\delta}`
|
||||
for all normal contact models, except for *jkr*\ , where it is given
|
||||
implicitly by :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`, see
|
||||
discussion above. To match the Mindlin solution, one should set :math:`k_t = 8G`, where :math:`G` is the shear modulus, related to Young's modulus
|
||||
discussion above. To match the Mindlin solution, one should set :math:`k_t = 4G/(2-\nu)`, where :math:`G` is the shear modulus, related to Young's modulus
|
||||
:math:`E` by :math:`G = E/(2(1+\nu))`, where :math:`\nu` is Poisson's ratio. This
|
||||
can also be achieved by specifying *NULL* for :math:`k_t`, in which case a
|
||||
normal contact model that specifies material parameters :math:`E` and
|
||||
|
||||
@ -90,6 +90,9 @@ pair\_style lj/cut/coul/wolf/omp command
|
||||
pair\_style lj/cut/tip4p/cut command
|
||||
====================================
|
||||
|
||||
pair\_style lj/cut/tip4p/cut/gpu command
|
||||
========================================
|
||||
|
||||
pair\_style lj/cut/tip4p/cut/omp command
|
||||
========================================
|
||||
|
||||
|
||||
@ -233,15 +233,20 @@ where
|
||||
Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
|
||||
by K (I<=J); default = 2.0
|
||||
lattce(I,J) = lattice structure of I-J reference structure:
|
||||
dia = diamond (interlaced fcc for alloy)
|
||||
fcc = face centered cubic
|
||||
bcc = body centered cubic
|
||||
dim = dimer
|
||||
b1 = rock salt (NaCl structure)
|
||||
hcp = hexagonal close-packed
|
||||
dim = dimer
|
||||
dia = diamond (interlaced fcc for alloy)
|
||||
dia3= diamond structure with primary 1NN and secondary 3NN interation
|
||||
b1 = rock salt (NaCl structure)
|
||||
c11 = MoSi2 structure
|
||||
l12 = Cu3Au structure (lower case L, followed by 12)
|
||||
b2 = CsCl structure (interpenetrating simple cubic)
|
||||
ch4 = methane-like structure, only for binary system
|
||||
lin = linear structure (180 degree angle)
|
||||
zig = zigzag structure with a uniform angle
|
||||
tri = H2O-like structure that has an angle
|
||||
nn2(I,J) = turn on second-nearest neighbor MEAM formulation for
|
||||
I-J pair (see for example :ref:`(Lee) <Lee>`).
|
||||
0 = second-nearest neighbor formulation off
|
||||
@ -254,6 +259,8 @@ where
|
||||
zbl(I,J) = blend the MEAM I-J pair potential with the ZBL potential for small
|
||||
atom separations :ref:`(ZBL) <ZBL>`
|
||||
default = 1
|
||||
theta(I,J) = angle between three atoms in line, zigzag, and trimer reference structures in degrees
|
||||
default = 180
|
||||
gsmooth_factor = factor determining the length of the G-function smoothing
|
||||
region; only significant for ibar=0 or ibar=4.
|
||||
99.0 = short smoothing region, sharp step
|
||||
|
||||
@ -37,7 +37,7 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *mm3/switch3/coulgauss* style evaluates the MM3
|
||||
The *mm3/switch3/coulgauss/long* style evaluates the MM3
|
||||
vdW potential :ref:`(Allinger) <mm3-allinger1989>`
|
||||
|
||||
.. image:: Eqs/pair_mm3_switch3.jpg
|
||||
@ -247,7 +247,9 @@ or *lj/coul* to change both to the same set of 3 values. The wt1,wt2,wt3
|
||||
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
|
||||
1-3, and 1-4 bond topology neighbors, respectively. The *special*
|
||||
keyword can only be used in conjunction with the *pair* keyword
|
||||
and has to directly follow it.
|
||||
and has to directly follow it. This option is not compatible with
|
||||
pair styles from the GPU or the USER-INTEL package and attempting
|
||||
it will cause an error.
|
||||
|
||||
.. note::
|
||||
|
||||
@ -278,10 +280,11 @@ and allows to selectively disable or enable processing of the various
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
You cannot use *shift* yes with *tail* yes, since those are
|
||||
conflicting options. You cannot use *tail* yes with 2d simulations.
|
||||
You cannot use *special* with pair styles from the GPU or
|
||||
USER-INTEL package.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
@ -36,8 +36,8 @@ Syntax
|
||||
*oxdna/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
xi = temperature-independent coefficient in stacking strength
|
||||
kappa = coefficient of linear temperature dependence in stacking strength
|
||||
xi = 1.3448 (temperature-independent coefficient in stacking strength)
|
||||
kappa = 2.6568 (coefficient of linear temperature dependence in stacking strength)
|
||||
*oxdna/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs)
|
||||
@ -94,11 +94,15 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich1>` and the relevant oxDNA articles in any publication that uses this implementation.
|
||||
The article contains more information on the model, the structure of the input file, the setup tool
|
||||
and the performance of the LAMMPS-implementation of oxDNA.
|
||||
The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich1>` in any publication that uses
|
||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
|
||||
`here <PDF/USER-CGDNA.pdf>`_.
|
||||
Please cite also the relevant oxDNA publications
|
||||
:ref:`(Ouldridge) <Ouldridge1>`,
|
||||
:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>`
|
||||
and :ref:`(Sulc) <Sulc1>`.
|
||||
|
||||
----------
|
||||
|
||||
@ -114,39 +118,32 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`pair\_coeff <pair_coeff>`,
|
||||
:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`
|
||||
|
||||
:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
|
||||
:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
|
||||
:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
|
||||
:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
.. _Henrich1:
|
||||
|
||||
|
||||
|
||||
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
.. _Sulc1:
|
||||
|
||||
|
||||
|
||||
**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
.. _Ouldridge-DPhil1:
|
||||
|
||||
|
||||
|
||||
**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
|
||||
**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
|
||||
|
||||
.. _Ouldridge1:
|
||||
|
||||
|
||||
|
||||
**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
|
||||
|
||||
.. _Sulc1:
|
||||
|
||||
**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
|
||||
@ -39,15 +39,15 @@ Syntax
|
||||
*oxdna2/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
xi = temperature-independent coefficient in stacking strength
|
||||
kappa = coefficient of linear temperature dependence in stacking strength
|
||||
xi = 1.3523 (temperature-independent coefficient in stacking strength)
|
||||
kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength)
|
||||
*oxdna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
|
||||
*oxdna2/dh* args = T rhos qeff
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
rhos = salt concentration (mole per litre)
|
||||
qeff = effective charge (elementary charges)
|
||||
qeff = 0.815 (effective charge in elementary charges)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -63,7 +63,7 @@ Examples
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff \* \* oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff \* \* oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff \* \* oxdna2/dh 0.1 1.0 0.815
|
||||
pair_coeff \* \* oxdna2/dh 0.1 0.5 0.815
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -83,7 +83,7 @@ The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to :ref:`(Snodin) <Snodin>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
|
||||
We refer to :ref:`(Snodin) <Snodin2>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil2>`
|
||||
and :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 force field.
|
||||
|
||||
.. note::
|
||||
@ -94,7 +94,7 @@ and :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 fo
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
|
||||
the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients
|
||||
after *oxdna2/dh* (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
|
||||
after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat
|
||||
e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
||||
@ -102,11 +102,13 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich>` and the relevant oxDNA articles in any publication that uses this implementation.
|
||||
The article contains more information on the model, the structure of the input file, the setup tool
|
||||
and the performance of the LAMMPS-implementation of oxDNA.
|
||||
The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
|
||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
|
||||
`here <PDF/USER-CGDNA.pdf>`_.
|
||||
Please cite also the relevant oxDNA2 publications
|
||||
:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
|
||||
|
||||
----------
|
||||
|
||||
@ -122,43 +124,34 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`, :doc:`pair\_coeff <pair_coeff>`,
|
||||
:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`
|
||||
:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
|
||||
:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`,
|
||||
:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
|
||||
:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
.. _Henrich:
|
||||
|
||||
|
||||
.. _Henrich2:
|
||||
|
||||
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
.. _Sulc2:
|
||||
|
||||
|
||||
|
||||
**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
.. _Snodin:
|
||||
|
||||
|
||||
.. _Snodin2:
|
||||
|
||||
**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
|
||||
|
||||
.. _Sulc2:
|
||||
|
||||
**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
.. _Ouldridge-DPhil2:
|
||||
|
||||
|
||||
|
||||
**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
|
||||
**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
|
||||
|
||||
.. _Ouldridge2:
|
||||
|
||||
|
||||
|
||||
**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
|
||||
|
||||
|
||||
|
||||
158
doc/src/pair_oxrna2.rst
Normal file
158
doc/src/pair_oxrna2.rst
Normal file
@ -0,0 +1,158 @@
|
||||
.. index:: pair_style oxrna2/excv
|
||||
|
||||
pair_style oxrna2/excv command
|
||||
==============================
|
||||
|
||||
pair_style oxrna2/stk command
|
||||
=============================
|
||||
|
||||
pair_style oxrna2/hbond command
|
||||
===============================
|
||||
|
||||
pair_style oxrna2/xstk command
|
||||
==============================
|
||||
|
||||
pair_style oxrna2/coaxstk command
|
||||
=================================
|
||||
|
||||
pair_style oxrna2/dh command
|
||||
============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style style1
|
||||
|
||||
pair_coeff * * style2 args
|
||||
|
||||
* style1 = *hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh*
|
||||
|
||||
* style2 = *oxrna2/excv* or *oxrna2/stk* or *oxrna2/hbond* or *oxrna2/xstk* or *oxrna2/coaxstk* or *oxrna2/dh*
|
||||
* args = list of arguments for these particular styles
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
xi = 1.40206 (temperature-independent coefficient in stacking strength)
|
||||
kappa = 2.77 (coefficient of linear temperature dependence in stacking strength)
|
||||
*oxrna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 0.870439 (between base pairs A-T, C-G and G-T) or 0 (all other pairs)
|
||||
*oxrna2/dh* args = T rhos qeff
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
rhos = salt concentration (mole per litre)
|
||||
qeff = 1.02455 (effective charge in elementary charges)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
|
||||
pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxrna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 3 4 oxrna2/hbond seqdep 0.870439 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
|
||||
pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
|
||||
pair_coeff * * oxrna2/dh 0.1 0.5 1.02455
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction *oxrna2/excv*\ , the stacking *oxrna2/stk*\ , cross-stacking *oxrna2/xstk*
|
||||
and coaxial stacking interaction *oxrna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxrna2/dh*
|
||||
as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on
|
||||
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
|
||||
are supported :ref:`(Sulc2) <Sulc32>`. Quasi-unique base-pairing between nucleotides can be achieved by using
|
||||
more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc.
|
||||
This prevents the hybridization of in principle complementary bases within Ntypes/4 bases
|
||||
up and down along the backbone.
|
||||
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to :ref:`(Sulc1) <Sulc31>` and the original oxDNA publications :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil3>`
|
||||
and :ref:`(Ouldridge) <Ouldridge3>` for a detailed description of the oxRNA2 force field.
|
||||
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used together with the related oxDNA2 bond style
|
||||
*oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of
|
||||
:doc:`bond\_style oxrna2/fene <bond_oxdna>`). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
Exceptions are the first four coefficients after *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 in the above example),
|
||||
the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients
|
||||
after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 in the above example). When using a Langevin thermostat
|
||||
e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich3>` in any publication that uses
|
||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
|
||||
`here <PDF/USER-CGDNA.pdf>`_.
|
||||
Please cite also the relevant oxRNA2 publications
|
||||
:ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
|
||||
These pair styles can only be used if LAMMPS was built with the
|
||||
USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
:doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`bond\_style oxrna2/fene <bond_oxdna>`, :doc:`pair\_coeff <pair_coeff>`,
|
||||
:doc:`bond\_style oxdna/fene <bond_oxdna>`, :doc:`pair\_style oxdna/excv <pair_oxdna>`,
|
||||
:doc:`bond\_style oxdna2/fene <bond_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`,
|
||||
:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
|
||||
**Default:**
|
||||
|
||||
none
|
||||
|
||||
|
||||
----------
|
||||
|
||||
.. _Henrich3:
|
||||
|
||||
**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
.. _Sulc31:
|
||||
|
||||
**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
|
||||
|
||||
.. _Sulc32:
|
||||
|
||||
**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
|
||||
|
||||
.. _Ouldridge-DPhil3:
|
||||
|
||||
**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
|
||||
|
||||
.. _Ouldridge3:
|
||||
|
||||
**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
|
||||
@ -7,7 +7,7 @@ Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style spin/exchange cutoff
|
||||
|
||||
@ -18,10 +18,10 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style spin/exchange 4.0
|
||||
pair_coeff \* \* exchange 4.0 0.0446928 0.003496 1.4885
|
||||
pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
|
||||
pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965
|
||||
|
||||
Description
|
||||
@ -30,35 +30,43 @@ Description
|
||||
Style *spin/exchange* computes the exchange interaction between
|
||||
pairs of magnetic spins:
|
||||
|
||||
.. image:: Eqs/pair_spin_exchange_interaction.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where si and sj are two neighboring magnetic spins of two particles,
|
||||
rij = ri - rj is the inter-atomic distance between the two particles,
|
||||
and J(rij) is a function defining the intensity and the sign of the exchange
|
||||
H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,\vec{s}_i \cdot \vec{s}_j
|
||||
|
||||
where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two neighboring magnetic spins of two particles,
|
||||
:math:`r_{ij} = \vert \vec{r}_i - \vec{r}_j \vert` is the inter-atomic distance between the two
|
||||
particles. The summation is over pairs of nearest neighbors.
|
||||
:math:`J(r_{ij})` is a function defining the intensity and the sign of the exchange
|
||||
interaction for different neighboring shells. This function is defined as:
|
||||
|
||||
.. image:: Eqs/pair_spin_exchange_function.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where a, b and d are the three constant coefficients defined in the associated
|
||||
"pair\_coeff" command (see below for more explanations).
|
||||
{J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
|
||||
|
||||
The coefficients a, b, and d need to be fitted so that the function above matches with
|
||||
the value of the exchange interaction for the N neighbor shells taken into account.
|
||||
where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the associated
|
||||
"pair\_coeff" command, and :math:`R_c` is the radius cutoff associated to
|
||||
the pair interaction (see below for more explanations).
|
||||
|
||||
The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function above matches with
|
||||
the value of the exchange interaction for the :math:`N` neighbor shells taken into account.
|
||||
Examples and more explanations about this function and its parameterization are reported
|
||||
in :ref:`(Tranchida) <Tranchida3>`.
|
||||
|
||||
From this exchange interaction, each spin i will be submitted
|
||||
to a magnetic torque omega, and its associated atom can be submitted to a
|
||||
force F for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
|
||||
From this exchange interaction, each spin :math:`i` will be submitted
|
||||
to a magnetic torque :math:`\vec{\omega}`, and its associated atom can be submitted to a
|
||||
force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
|
||||
such as:
|
||||
|
||||
.. image:: Eqs/pair_spin_exchange_forces.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
with h the Planck constant (in metal units), and eij = (ri - rj)/\|ri-rj\| the unit
|
||||
vector between sites i and j.
|
||||
\vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J}
|
||||
\left(r_{ij} \right)\,\vec{s}_{j}
|
||||
~~{\rm and}~~
|
||||
\vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
|
||||
|
||||
with :math:`\hbar` the Planck constant (in metal units), and :math:`\vec{e}_{ij} = \frac{\vec{r}_i - \vec{r}_j}{\vert \vec{r}_i-\vec{r}_j \vert}` the unit
|
||||
vector between sites :math:`i` and :math:`j`.
|
||||
|
||||
More details about the derivation of these torques/forces are reported in
|
||||
:ref:`(Tranchida) <Tranchida3>`.
|
||||
@ -69,14 +77,14 @@ the examples above, or in the data file or restart files read by the
|
||||
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` commands, and
|
||||
set in the following order:
|
||||
|
||||
* rc (distance units)
|
||||
* a (energy units)
|
||||
* b (adim parameter)
|
||||
* d (distance units)
|
||||
* :math:`R_c` (distance units)
|
||||
* :math:`a` (energy units)
|
||||
* :math:`b` (adim parameter)
|
||||
* :math:`d` (distance units)
|
||||
|
||||
Note that rc is the radius cutoff of the considered exchange interaction,
|
||||
and a, b and d are the three coefficients performing the parameterization
|
||||
of the function J(rij) defined above.
|
||||
Note that :math:`R_c` is the radius cutoff of the considered exchange interaction,
|
||||
and :math:`a`, :math:`b` and :math:`d` are the three coefficients performing the parameterization
|
||||
of the function :math:`J(r_{ij})` defined above.
|
||||
|
||||
None of those coefficients is optional. If not specified, the
|
||||
*spin/exchange* pair style cannot be used.
|
||||
@ -99,7 +107,9 @@ Related commands
|
||||
:doc:`atom\_style spin <atom_style>`, :doc:`pair\_coeff <pair_coeff>`,
|
||||
:doc:`pair\_eam <pair_eam>`,
|
||||
|
||||
**Default:** none
|
||||
**Default:**
|
||||
|
||||
none
|
||||
|
||||
|
||||
----------
|
||||
@ -111,8 +121,3 @@ Related commands
|
||||
|
||||
**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
|
||||
Journal of Computational Physics, 372, 406-425, (2018).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: pair\_style spin/neel
|
||||
.. index:: pair_style spin/neel
|
||||
|
||||
pair\_style spin/neel command
|
||||
=============================
|
||||
pair_style spin/neel command
|
||||
============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style spin/neel cutoff
|
||||
|
||||
@ -18,10 +18,10 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style spin/neel 4.0
|
||||
pair_coeff \* \* neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
|
||||
pair_coeff * * neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
|
||||
pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0
|
||||
|
||||
Description
|
||||
@ -30,28 +30,38 @@ Description
|
||||
Style *spin/neel* computes the Neel pair anisotropy model
|
||||
between pairs of magnetic spins:
|
||||
|
||||
.. image:: Eqs/pair_spin_neel_interaction.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where si and sj are two neighboring magnetic spins of two particles,
|
||||
rij = ri - rj is the inter-atomic distance between the two particles,
|
||||
eij = (ri - rj)/\|ri-rj\| is their normalized separation vector and g1,
|
||||
q1 and q2 are three functions defining the intensity of the dipolar
|
||||
\mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})({\mathbf{e}}_{ij}
|
||||
\cdot {\mathbf{s}}_{j})-\frac{{\mathbf{s}}_{i}\cdot{\mathbf{s}}_{j}}{3} \right)
|
||||
+q_1(r_{ij})\left( ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})^2 -\frac{{\mathbf{s}}_{i}\cdot{\mathbf{s}}_{j}}{3}\right)
|
||||
\left( ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})^2 -\frac{{\mathbf{s}}_{i}\cdot{\mathbf{s}}_{j}}{3} \right)
|
||||
+ q_2(r_{ij}) \Big( ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i}) ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{j})^3 + ({\mathbf{e}}_{ij}\cdot
|
||||
{\mathbf{s}}_{j}) ({\mathbf{e}}_{ij}\cdot {\mathbf{s}}_{i})^3\Big)
|
||||
|
||||
where :math:`\mathbf{s}_i` and :math:`\mathbf{s}_j` are two neighboring magnetic spins of two particles,
|
||||
:math:`r_{ij} = \vert \mathbf{r}_i - \mathbf{r}_j \vert` is the inter-atomic distance between the two particles,
|
||||
:math:`\mathbf{e}_{ij} = \frac{\mathbf{r}_i - \mathbf{r}_j}{\vert \mathbf{r}_i - \mathbf{r}_j\vert}` is their normalized separation vector and :math:`g_1`,
|
||||
:math:`q_1` and :math:`q_2` are three functions defining the intensity of the dipolar
|
||||
and quadrupolar contributions, with:
|
||||
|
||||
.. image:: Eqs/pair_spin_neel_functions.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
With the functions g(rij) and q(rij) defined and fitted according to
|
||||
g_1(r_{ij}) &= g(r_{ij}) + \frac{12}{35} q(r_{ij}) \\
|
||||
q_1(r_{ij}) &= \frac{9}{5} q(r_{ij}) \\
|
||||
q_2(r_{ij}) &= - \frac{2}{5} q(r_{ij})
|
||||
|
||||
With the functions :math:`g(r_{ij})` and :math:`q(r_{ij})` defined and fitted according to
|
||||
the same Bethe-Slater function used to fit the exchange interaction:
|
||||
|
||||
.. image:: Eqs/pair_spin_exchange_function.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where a, b and d are the three constant coefficients defined in the
|
||||
{J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
|
||||
|
||||
where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the
|
||||
associated "pair\_coeff" command.
|
||||
|
||||
The coefficients a, b, and d need to be fitted so that the function
|
||||
The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function
|
||||
above matches with the values of the magneto-elastic constant of the
|
||||
materials at stake.
|
||||
|
||||
@ -59,8 +69,8 @@ Examples and more explanations about this function and its
|
||||
parameterization are reported in :ref:`(Tranchida) <Tranchida6>`. More
|
||||
examples of parameterization will be provided in future work.
|
||||
|
||||
From this DM interaction, each spin i will be submitted to a magnetic
|
||||
torque omega and its associated atom to a force F (for spin-lattice
|
||||
From this DM interaction, each spin :math:`i` will be submitted to a magnetic
|
||||
torque :math:`\mathbf{\omega}` and its associated atom to a force :math:`\mathbf{F}` (for spin-lattice
|
||||
calculations only).
|
||||
|
||||
More details about the derivation of these torques/forces are reported
|
||||
@ -84,7 +94,9 @@ Related commands
|
||||
:doc:`atom\_style spin <atom_style>`, :doc:`pair\_coeff <pair_coeff>`,
|
||||
:doc:`pair\_eam <pair_eam>`,
|
||||
|
||||
**Default:** none
|
||||
**Default:**
|
||||
|
||||
none
|
||||
|
||||
|
||||
----------
|
||||
@ -96,8 +108,3 @@ Related commands
|
||||
|
||||
**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
|
||||
Journal of Computational Physics, 372, 406-425, (2018).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -32,7 +32,7 @@ Description
|
||||
Set the formula(s) LAMMPS uses to compute pairwise interactions. In
|
||||
LAMMPS, pair potentials are defined between pairs of atoms that are
|
||||
within a cutoff distance and the set of active interactions typically
|
||||
changes over time. See the :doc:`bond\_style <bond_style>` command to
|
||||
changes over time. See the :doc:`bond_style <bond_style>` command to
|
||||
define potentials between pairs of bonded atoms, which typically
|
||||
remain in place for the duration of a simulation.
|
||||
|
||||
@ -48,11 +48,11 @@ different pair potentials can be setup using the *hybrid* pair style.
|
||||
|
||||
The coefficients associated with a pair style are typically set for
|
||||
each pair of atom types, and are specified by the
|
||||
:doc:`pair\_coeff <pair_coeff>` command or read from a file by the
|
||||
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
|
||||
:doc:`pair_coeff <pair_coeff>` command or read from a file by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands.
|
||||
|
||||
The :doc:`pair\_modify <pair_modify>` command sets options for mixing of
|
||||
The :doc:`pair_modify <pair_modify>` command sets options for mixing of
|
||||
type I-J interaction coefficients and adding energy offsets or tail
|
||||
corrections to Lennard-Jones potentials. Details on these options as
|
||||
they pertain to individual potentials are described on the doc page
|
||||
@ -70,11 +70,11 @@ cutoffs for all pairs of atom types. The distance(s) can be smaller
|
||||
or larger than the dimensions of the simulation box.
|
||||
|
||||
Typically, the global cutoff value can be overridden for a specific
|
||||
pair of atom types by the :doc:`pair\_coeff <pair_coeff>` command. The
|
||||
pair of atom types by the :doc:`pair_coeff <pair_coeff>` command. The
|
||||
pair style settings (including global cutoffs) can be changed by a
|
||||
subsequent pair\_style command using the same style. This will reset
|
||||
the cutoffs for all atom type pairs, including those previously set
|
||||
explicitly by a :doc:`pair\_coeff <pair_coeff>` command. The exceptions
|
||||
explicitly by a :doc:`pair_coeff <pair_coeff>` command. The exceptions
|
||||
to this are that pair\_style *table* and *hybrid* settings cannot be
|
||||
reset. A new pair\_style command for these styles will wipe out all
|
||||
previously specified pair\_coeff values.
|
||||
@ -88,7 +88,7 @@ also listed in more compact form on the :doc:`Commands pair <Commands_pair>` doc
|
||||
|
||||
Click on the style to display the formula it computes, any additional
|
||||
arguments specified in the pair\_style command, and coefficients
|
||||
specified by the associated :doc:`pair\_coeff <pair_coeff>` command.
|
||||
specified by the associated :doc:`pair_coeff <pair_coeff>` command.
|
||||
|
||||
There are also additional accelerated pair styles included in the
|
||||
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
|
||||
@ -170,6 +170,7 @@ accelerated styles exist.
|
||||
* :doc:`gauss <pair_gauss>` - Gaussian potential
|
||||
* :doc:`gauss/cut <pair_gauss>` - generalized Gaussian potential
|
||||
* :doc:`gayberne <pair_gayberne>` - Gay-Berne ellipsoidal potential
|
||||
* :doc:`granular <pair_granular>` - Generalized granular potential
|
||||
* :doc:`gran/hertz/history <pair_gran>` - granular potential with Hertzian interactions
|
||||
* :doc:`gran/hooke <pair_gran>` - granular potential with history effects
|
||||
* :doc:`gran/hooke/history <pair_gran>` - granular potential without history effects
|
||||
@ -231,7 +232,7 @@ accelerated styles exist.
|
||||
* :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces
|
||||
* :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential
|
||||
* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
|
||||
* `lj/switch3/coulgauss <pair_lj_switch3_coulgauss>`_ - smoothed LJ vdW potential with Gaussian electrostatics
|
||||
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed LJ vdW potential with Gaussian electrostatics
|
||||
* :doc:`lj96/cut <pair_lj96>` - Lennard-Jones 9/6 potential
|
||||
* :doc:`local/density <pair_local_density>` - generalized basic local density potential
|
||||
* :doc:`lubricate <pair_lubricate>` - hydrodynamic lubrication forces
|
||||
@ -245,7 +246,7 @@ accelerated styles exist.
|
||||
* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
|
||||
* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
|
||||
* :doc:`mie/cut <pair_mie>` - Mie potential
|
||||
* `mm3/switch3/coulgauss <pair_mm3_switch3_coulgauss>`_ - smoothed MM3 vdW potential with Gaussian electrostatics
|
||||
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
|
||||
* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
|
||||
* :doc:`morse <pair_morse>` - Morse potential
|
||||
* :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential
|
||||
@ -267,6 +268,12 @@ accelerated styles exist.
|
||||
* :doc:`oxdna2/hbond <pair_oxdna2>` -
|
||||
* :doc:`oxdna2/stk <pair_oxdna2>` -
|
||||
* :doc:`oxdna2/xstk <pair_oxdna2>` -
|
||||
* :doc:`oxrna2/coaxstk <pair_oxrna2>` -
|
||||
* :doc:`oxrna2/dh <pair_oxrna2>` -
|
||||
* :doc:`oxrna2/excv <pair_oxrna2>` -
|
||||
* :doc:`oxrna2/hbond <pair_oxrna2>` -
|
||||
* :doc:`oxrna2/stk <pair_oxrna2>` -
|
||||
* :doc:`oxrna2/xstk <pair_oxrna2>` -
|
||||
* :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
|
||||
* :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
|
||||
* :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
|
||||
@ -280,7 +287,7 @@ accelerated styles exist.
|
||||
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
|
||||
* :doc:`smd/hertz <pair_smd_hertz>` -
|
||||
* :doc:`smd/tlsph <pair_smd_tlsph>` -
|
||||
* :doc:`smd/tri\_surface <pair_smd_triangulated_surface>` -
|
||||
* :doc:`smd/tri_surface <pair_smd_triangulated_surface>` -
|
||||
* :doc:`smd/ulsph <pair_smd_ulsph>` -
|
||||
* :doc:`smtbq <pair_smtbq>` -
|
||||
* :doc:`snap <pair_snap>` - SNAP quantum-accurate potential
|
||||
@ -328,8 +335,8 @@ Restrictions
|
||||
|
||||
|
||||
This command must be used before any coefficients are set by the
|
||||
:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`, or
|
||||
:doc:`read\_restart <read_restart>` commands.
|
||||
:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`, or
|
||||
:doc:`read_restart <read_restart>` commands.
|
||||
|
||||
Some pair styles are part of specific packages. They are only enabled
|
||||
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. The doc pages for
|
||||
@ -338,9 +345,9 @@ individual pair potentials tell if it is part of a package.
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`,
|
||||
:doc:`pair\_modify <pair_modify>`, :doc:`kspace\_style <kspace_style>`,
|
||||
:doc:`dielectric <dielectric>`, :doc:`pair\_write <pair_write>`
|
||||
:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`,
|
||||
:doc:`pair_modify <pair_modify>`, :doc:`kspace_style <kspace_style>`,
|
||||
:doc:`dielectric <dielectric>`, :doc:`pair_write <pair_write>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -186,13 +186,34 @@ minutes to hours) to build. Of course you only need to do that once.)
|
||||
|
||||
[CMake build]:
|
||||
|
||||
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes :pre
|
||||
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes
|
||||
-D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on
|
||||
-D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer, value = no (default) or yes
|
||||
:pre
|
||||
|
||||
If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
|
||||
inside the CMake build directory. If the KIM library is already on
|
||||
your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
|
||||
environment variable so that libkim-api can be found.
|
||||
|
||||
For using OpenKIM web queries in LAMMPS.
|
||||
|
||||
If LMP_DEBUG_CURL is set, the libcurl verbose mode will be on, and any
|
||||
libcurl calls within the KIM web query display a lot of information about
|
||||
libcurl operations. You hardly ever want this set in production use, you will
|
||||
almost always want this when you debug/report problems.
|
||||
|
||||
The libcurl performs peer SSL certificate verification by default. This
|
||||
verification is done using a CA certificate store that the SSL library can
|
||||
use to make sure the peer's server certificate is valid. If SSL reports an
|
||||
error ("certificate verify failed") during the handshake and thus refuses
|
||||
further communication with that server, you can set LMP_NO_SSL_CHECK.
|
||||
If LMP_NO_SSL_CHECK is set, libcurl does not verify the peer and connection
|
||||
succeeds regardless of the names in the certificate. This option is insecure.
|
||||
As an alternative, you can specify your own CA cert path by setting the
|
||||
environment variable CURL_CA_BUNDLE to the path of your choice. A call to the
|
||||
KIM web query would get this value from the environmental variable.
|
||||
|
||||
[Traditional make]:
|
||||
|
||||
You can download and build the KIM library manually if you prefer;
|
||||
|
||||
@ -1,60 +0,0 @@
|
||||
"Previous Section"_Run_head.html - "LAMMPS WWW Site"_lws -
|
||||
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
|
||||
Section"_Packages.html :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
Commands :h2
|
||||
|
||||
These pages describe how a LAMMPS input script is formatted and the
|
||||
commands in it are used to define a LAMMPS simulation.
|
||||
|
||||
<!-- RST
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
Commands_input
|
||||
Commands_parse
|
||||
Commands_structure
|
||||
Commands_category
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
Commands_all
|
||||
Commands_fix
|
||||
Commands_compute
|
||||
Commands_pair
|
||||
Commands_bond
|
||||
Commands_kspace
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
Commands_removed
|
||||
|
||||
END_RST -->
|
||||
|
||||
<!-- HTML_ONLY -->
|
||||
|
||||
"LAMMPS input scripts"_Commands_input.html
|
||||
"Parsing rules for input scripts"_Commands_parse.html
|
||||
"Input script structure"_Commands_structure.html
|
||||
"Commands by category"_Commands_category.html :all(b)
|
||||
|
||||
"General commands"_Commands_all.html
|
||||
"Fix commands"_Commands_fix.html
|
||||
"Compute commands"_Commands_compute.html
|
||||
"Pair commands"_Commands_pair.html
|
||||
"Bond, angle, dihedral, improper commands"_Commands_bond.html
|
||||
"KSpace solvers"_Commands_kspace.html :all(b)
|
||||
|
||||
"Removed commands and packages"_Commands_removed.html :all(b)
|
||||
|
||||
<!-- END_HTML_ONLY -->
|
||||
|
||||
@ -1,139 +0,0 @@
|
||||
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
"General commands"_Commands_all.html,
|
||||
"Fix styles"_Commands_fix.html,
|
||||
"Compute styles"_Commands_compute.html,
|
||||
"Pair styles"_Commands_pair.html,
|
||||
"Bond styles"_Commands_bond.html,
|
||||
"Angle styles"_Commands_bond.html#angle,
|
||||
"Dihedral styles"_Commands_bond.html#dihedral,
|
||||
"Improper styles"_Commands_bond.html#improper,
|
||||
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
|
||||
|
||||
General commands :h3
|
||||
|
||||
An alphabetic list of all general LAMMPS commands.
|
||||
|
||||
"angle_coeff"_angle_coeff.html,
|
||||
"angle_style"_angle_style.html,
|
||||
"atom_modify"_atom_modify.html,
|
||||
"atom_style"_atom_style.html,
|
||||
"balance"_balance.html,
|
||||
"bond_coeff"_bond_coeff.html,
|
||||
"bond_style"_bond_style.html,
|
||||
"bond_write"_bond_write.html,
|
||||
"boundary"_boundary.html,
|
||||
"box"_box.html,
|
||||
"change_box"_change_box.html,
|
||||
"clear"_clear.html,
|
||||
"comm_modify"_comm_modify.html,
|
||||
"comm_style"_comm_style.html,
|
||||
"compute"_compute.html,
|
||||
"compute_modify"_compute_modify.html,
|
||||
"create_atoms"_create_atoms.html,
|
||||
"create_bonds"_create_bonds.html,
|
||||
"create_box"_create_box.html,
|
||||
"delete_atoms"_delete_atoms.html,
|
||||
"delete_bonds"_delete_bonds.html,
|
||||
"dielectric"_dielectric.html,
|
||||
"dihedral_coeff"_dihedral_coeff.html,
|
||||
"dihedral_style"_dihedral_style.html,
|
||||
"dimension"_dimension.html,
|
||||
"displace_atoms"_displace_atoms.html,
|
||||
"dump"_dump.html,
|
||||
"dump adios"_dump_adios.html,
|
||||
"dump image"_dump_image.html,
|
||||
"dump movie"_dump_image.html,
|
||||
"dump netcdf"_dump_netcdf.html,
|
||||
"dump netcdf/mpiio"_dump_netcdf.html,
|
||||
"dump vtk"_dump_vtk.html,
|
||||
"dump_modify"_dump_modify.html,
|
||||
"dynamical_matrix"_dynamical_matrix.html,
|
||||
"echo"_echo.html,
|
||||
"fix"_fix.html,
|
||||
"fix_modify"_fix_modify.html,
|
||||
"group"_group.html,
|
||||
"group2ndx"_group2ndx.html,
|
||||
"hyper"_hyper.html,
|
||||
"if"_if.html,
|
||||
"info"_info.html,
|
||||
"improper_coeff"_improper_coeff.html,
|
||||
"improper_style"_improper_style.html,
|
||||
"include"_include.html,
|
||||
"jump"_jump.html,
|
||||
"kim_init"_kim_commands.html,
|
||||
"kim_interactions"_kim_commands.html,
|
||||
"kim_query"_kim_commands.html,
|
||||
"kspace_modify"_kspace_modify.html,
|
||||
"kspace_style"_kspace_style.html,
|
||||
"label"_label.html,
|
||||
"lattice"_lattice.html,
|
||||
"log"_log.html,
|
||||
"mass"_mass.html,
|
||||
"message"_message.html,
|
||||
"minimize"_minimize.html,
|
||||
"min_modify"_min_modify.html,
|
||||
"min_style"_min_style.html,
|
||||
"min_style spin"_min_spin.html,
|
||||
"molecule"_molecule.html,
|
||||
"ndx2group"_group2ndx.html,
|
||||
"neb"_neb.html,
|
||||
"neb/spin"_neb_spin.html,
|
||||
"neigh_modify"_neigh_modify.html,
|
||||
"neighbor"_neighbor.html,
|
||||
"newton"_newton.html,
|
||||
"next"_next.html,
|
||||
"package"_package.html,
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_modify"_pair_modify.html,
|
||||
"pair_style"_pair_style.html,
|
||||
"pair_write"_pair_write.html,
|
||||
"partition"_partition.html,
|
||||
"prd"_prd.html,
|
||||
"print"_print.html,
|
||||
"processors"_processors.html,
|
||||
"python"_python.html,
|
||||
"quit"_quit.html,
|
||||
"read_data"_read_data.html,
|
||||
"read_dump"_read_dump.html,
|
||||
"read_restart"_read_restart.html,
|
||||
"region"_region.html,
|
||||
"replicate"_replicate.html,
|
||||
"rerun"_rerun.html,
|
||||
"reset_ids"_reset_ids.html,
|
||||
"reset_timestep"_reset_timestep.html,
|
||||
"restart"_restart.html,
|
||||
"run"_run.html,
|
||||
"run_style"_run_style.html,
|
||||
"server"_server.html,
|
||||
"set"_set.html,
|
||||
"shell"_shell.html,
|
||||
"special_bonds"_special_bonds.html,
|
||||
"suffix"_suffix.html,
|
||||
"tad"_tad.html,
|
||||
"temper"_temper.html,
|
||||
"temper/grem"_temper_grem.html,
|
||||
"temper/npt"_temper_npt.html,
|
||||
"thermo"_thermo.html,
|
||||
"thermo_modify"_thermo_modify.html,
|
||||
"thermo_style"_thermo_style.html,
|
||||
"third_order"_third_order.html,
|
||||
"timer"_timer.html,
|
||||
"timestep"_timestep.html,
|
||||
"uncompute"_uncompute.html,
|
||||
"undump"_undump.html,
|
||||
"unfix"_unfix.html,
|
||||
"units"_units.html,
|
||||
"variable"_variable.html,
|
||||
"velocity"_velocity.html,
|
||||
"write_coeff"_write_coeff.html,
|
||||
"write_data"_write_data.html,
|
||||
"write_dump"_write_dump.html,
|
||||
"write_restart"_write_restart.html :tb(c=6,ea=c)
|
||||
@ -1,148 +0,0 @@
|
||||
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
"General commands"_Commands_all.html,
|
||||
"Fix styles"_Commands_fix.html,
|
||||
"Compute styles"_Commands_compute.html,
|
||||
"Pair styles"_Commands_pair.html,
|
||||
"Bond styles"_Commands_bond.html#bond,
|
||||
"Angle styles"_Commands_bond.html#angle,
|
||||
"Dihedral styles"_Commands_bond.html#dihedral,
|
||||
"Improper styles"_Commands_bond.html#improper,
|
||||
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
|
||||
|
||||
Bond, angle, dihedral, and improper commands :h3
|
||||
|
||||
:line
|
||||
|
||||
Bond_style potentials :h3,link(bond)
|
||||
|
||||
All LAMMPS "bond_style"_bond_style.html commands. Some styles have
|
||||
accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
"none"_bond_none.html,
|
||||
"zero"_bond_zero.html,
|
||||
"hybrid"_bond_hybrid.html,
|
||||
,
|
||||
,
|
||||
,
|
||||
,
|
||||
,
|
||||
"class2 (ko)"_bond_class2.html,
|
||||
"fene (iko)"_bond_fene.html,
|
||||
"fene/expand (o)"_bond_fene_expand.html,
|
||||
"gromos (o)"_bond_gromos.html,
|
||||
"harmonic (iko)"_bond_harmonic.html,
|
||||
"harmonic/shift (o)"_bond_harmonic_shift.html,
|
||||
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
|
||||
"mm3"_bond_mm3.html,
|
||||
"morse (o)"_bond_morse.html,
|
||||
"nonlinear (o)"_bond_nonlinear.html,
|
||||
"oxdna/fene"_bond_oxdna.html,
|
||||
"oxdna2/fene"_bond_oxdna.html,
|
||||
"quartic (o)"_bond_quartic.html,
|
||||
"table (o)"_bond_table.html :tb(c=4,ea=c)
|
||||
|
||||
:line
|
||||
|
||||
Angle_style potentials :h3,link(angle)
|
||||
|
||||
All LAMMPS "angle_style"_angle_style.html commands. Some styles have
|
||||
accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
"none"_angle_none.html,
|
||||
"zero"_angle_zero.html,
|
||||
"hybrid"_angle_hybrid.html,
|
||||
,
|
||||
,
|
||||
,
|
||||
,
|
||||
,
|
||||
"charmm (iko)"_angle_charmm.html,
|
||||
"class2 (ko)"_angle_class2.html,
|
||||
"class2/p6"_angle_class2.html,
|
||||
"cosine (ko)"_angle_cosine.html,
|
||||
"cosine/buck6d"_angle_cosine_buck6d.html,
|
||||
"cosine/delta (o)"_angle_cosine_delta.html,
|
||||
"cosine/periodic (o)"_angle_cosine_periodic.html,
|
||||
"cosine/shift (o)"_angle_cosine_shift.html,
|
||||
"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
|
||||
"cosine/squared (o)"_angle_cosine_squared.html,
|
||||
"cross"_angle_cross.html,
|
||||
"dipole (o)"_angle_dipole.html,
|
||||
"fourier (o)"_angle_fourier.html,
|
||||
"fourier/simple (o)"_angle_fourier_simple.html,
|
||||
"harmonic (iko)"_angle_harmonic.html,
|
||||
"mm3"_angle_mm3.html,
|
||||
"quartic (o)"_angle_quartic.html,
|
||||
"sdk (o)"_angle_sdk.html,
|
||||
"table (o)"_angle_table.html :tb(c=4,ea=c)
|
||||
|
||||
:line
|
||||
|
||||
Dihedral_style potentials :h3,link(dihedral)
|
||||
|
||||
All LAMMPS "dihedral_style"_dihedral_style.html commands. Some styles
|
||||
have accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
"none"_dihedral_none.html,
|
||||
"zero"_dihedral_zero.html,
|
||||
"hybrid"_dihedral_hybrid.html,
|
||||
,
|
||||
,
|
||||
,
|
||||
,
|
||||
,
|
||||
"charmm (iko)"_dihedral_charmm.html,
|
||||
"charmmfsw"_dihedral_charmm.html,
|
||||
"class2 (ko)"_dihedral_class2.html,
|
||||
"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
|
||||
"fourier (io)"_dihedral_fourier.html,
|
||||
"harmonic (iko)"_dihedral_harmonic.html,
|
||||
"helix (o)"_dihedral_helix.html,
|
||||
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
|
||||
"nharmonic (o)"_dihedral_nharmonic.html,
|
||||
"opls (iko)"_dihedral_opls.html,
|
||||
"quadratic (o)"_dihedral_quadratic.html,
|
||||
"spherical"_dihedral_spherical.html,
|
||||
"table (o)"_dihedral_table.html,
|
||||
"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
|
||||
|
||||
:line
|
||||
|
||||
Improper_style potentials :h3,link(improper)
|
||||
|
||||
All LAMMPS "improper_style"_improper_style.html commands. Some styles
|
||||
have accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
"none"_improper_none.html,
|
||||
"zero"_improper_zero.html,
|
||||
"hybrid"_improper_hybrid.html,
|
||||
,
|
||||
,
|
||||
,
|
||||
,
|
||||
,
|
||||
"class2 (ko)"_improper_class2.html,
|
||||
"cossq (o)"_improper_cossq.html,
|
||||
"cvff (io)"_improper_cvff.html,
|
||||
"distance"_improper_distance.html,
|
||||
"distharm"_improper_distharm.html,
|
||||
"fourier (o)"_improper_fourier.html,
|
||||
"harmonic (iko)"_improper_harmonic.html,
|
||||
"inversion/harmonic"_improper_inversion_harmonic.html,
|
||||
"ring (o)"_improper_ring.html,
|
||||
"sqdistharm"_improper_sqdistharm.html,
|
||||
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
|
||||
@ -1,141 +0,0 @@
|
||||
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
Commands by category :h3
|
||||
|
||||
This page lists most of the LAMMPS commands, grouped by category. The
|
||||
"General commands"_Commands_all.html doc page lists all general commands
|
||||
alphabetically. Style options for entries like fix, compute, pair etc.
|
||||
have their own pages where they are listed alphabetically.
|
||||
|
||||
Initialization:
|
||||
|
||||
"newton"_newton.html,
|
||||
"package"_package.html,
|
||||
"processors"_processors.html,
|
||||
"suffix"_suffix.html,
|
||||
"units"_units.html :ul
|
||||
|
||||
Setup simulation box:
|
||||
|
||||
"boundary"_boundary.html,
|
||||
"box"_box.html,
|
||||
"change_box"_change_box.html,
|
||||
"create_box"_create_box.html,
|
||||
"dimension"_dimension.html,
|
||||
"lattice"_lattice.html,
|
||||
"region"_region.html :ul
|
||||
|
||||
Setup atoms:
|
||||
|
||||
"atom_modify"_atom_modify.html,
|
||||
"atom_style"_atom_style.html,
|
||||
"balance"_balance.html,
|
||||
"create_atoms"_create_atoms.html,
|
||||
"create_bonds"_create_bonds.html,
|
||||
"delete_atoms"_delete_atoms.html,
|
||||
"delete_bonds"_delete_bonds.html,
|
||||
"displace_atoms"_displace_atoms.html,
|
||||
"group"_group.html,
|
||||
"mass"_mass.html,
|
||||
"molecule"_molecule.html,
|
||||
"read_data"_read_data.html,
|
||||
"read_dump"_read_dump.html,
|
||||
"read_restart"_read_restart.html,
|
||||
"replicate"_replicate.html,
|
||||
"set"_set.html,
|
||||
"velocity"_velocity.html :ul
|
||||
|
||||
Force fields:
|
||||
|
||||
"angle_coeff"_angle_coeff.html,
|
||||
"angle_style"_angle_style.html,
|
||||
"bond_coeff"_bond_coeff.html,
|
||||
"bond_style"_bond_style.html,
|
||||
"bond_write"_bond_write.html,
|
||||
"dielectric"_dielectric.html,
|
||||
"dihedral_coeff"_dihedral_coeff.html,
|
||||
"dihedral_style"_dihedral_style.html,
|
||||
"improper_coeff"_improper_coeff.html,
|
||||
"improper_style"_improper_style.html,
|
||||
"kspace_modify"_kspace_modify.html,
|
||||
"kspace_style"_kspace_style.html,
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_modify"_pair_modify.html,
|
||||
"pair_style"_pair_style.html,
|
||||
"pair_write"_pair_write.html,
|
||||
"special_bonds"_special_bonds.html :ul
|
||||
|
||||
Settings:
|
||||
|
||||
"comm_modify"_comm_modify.html,
|
||||
"comm_style"_comm_style.html,
|
||||
"info"_info.html,
|
||||
"min_modify"_min_modify.html,
|
||||
"min_style"_min_style.html,
|
||||
"neigh_modify"_neigh_modify.html,
|
||||
"neighbor"_neighbor.html,
|
||||
"partition"_partition.html,
|
||||
"reset_timestep"_reset_timestep.html,
|
||||
"run_style"_run_style.html,
|
||||
"timer"_timer.html,
|
||||
"timestep"_timestep.html :ul
|
||||
|
||||
Operations within timestepping (fixes) and diagnostics (computes):
|
||||
|
||||
"compute"_compute.html,
|
||||
"compute_modify"_compute_modify.html,
|
||||
"fix"_fix.html,
|
||||
"fix_modify"_fix_modify.html,
|
||||
"uncompute"_uncompute.html,
|
||||
"unfix"_unfix.html :ul
|
||||
|
||||
Output:
|
||||
|
||||
"dump image"_dump_image.html,
|
||||
"dump movie"_dump_image.html,
|
||||
"dump"_dump.html,
|
||||
"dump_modify"_dump_modify.html,
|
||||
"restart"_restart.html,
|
||||
"thermo"_thermo.html,
|
||||
"thermo_modify"_thermo_modify.html,
|
||||
"thermo_style"_thermo_style.html,
|
||||
"undump"_undump.html,
|
||||
"write_coeff"_write_coeff.html,
|
||||
"write_data"_write_data.html,
|
||||
"write_dump"_write_dump.html,
|
||||
"write_restart"_write_restart.html :ul
|
||||
|
||||
Actions:
|
||||
|
||||
"minimize"_minimize.html,
|
||||
"neb"_neb.html,
|
||||
"neb_spin"_neb_spin.html,
|
||||
"prd"_prd.html,
|
||||
"rerun"_rerun.html,
|
||||
"run"_run.html,
|
||||
"tad"_tad.html,
|
||||
"temper"_temper.html :ul
|
||||
|
||||
Input script control:
|
||||
|
||||
"clear"_clear.html,
|
||||
"echo"_echo.html,
|
||||
"if"_if.html,
|
||||
"include"_include.html,
|
||||
"jump"_jump.html,
|
||||
"label"_label.html,
|
||||
"log"_log.html,
|
||||
"next"_next.html,
|
||||
"print"_print.html,
|
||||
"python"_python.html,
|
||||
"quit"_quit.html,
|
||||
"shell"_shell.html,
|
||||
"variable"_variable.html :ul
|
||||
|
||||
@ -1,166 +0,0 @@
|
||||
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
"General commands"_Commands_all.html,
|
||||
"Fix styles"_Commands_fix.html,
|
||||
"Compute styles"_Commands_compute.html,
|
||||
"Pair styles"_Commands_pair.html,
|
||||
"Bond styles"_Commands_bond.html,
|
||||
"Angle styles"_Commands_bond.html#angle,
|
||||
"Dihedral styles"_Commands_bond.html#dihedral,
|
||||
"Improper styles"_Commands_bond.html#improper,
|
||||
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
|
||||
|
||||
Compute commands :h3
|
||||
|
||||
An alphabetic list of all LAMMPS "compute"_compute.html commands.
|
||||
Some styles have accelerated versions. This is indicated by
|
||||
additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
"ackland/atom"_compute_ackland_atom.html,
|
||||
"adf"_compute_adf.html,
|
||||
"aggregate/atom"_compute_cluster_atom.html,
|
||||
"angle"_compute_angle.html,
|
||||
"angle/local"_compute_angle_local.html,
|
||||
"angmom/chunk"_compute_angmom_chunk.html,
|
||||
"basal/atom"_compute_basal_atom.html,
|
||||
"body/local"_compute_body_local.html,
|
||||
"bond"_compute_bond.html,
|
||||
"bond/local"_compute_bond_local.html,
|
||||
"centro/atom"_compute_centro_atom.html,
|
||||
"centroid/stress/atom"_compute_stress_atom.html,
|
||||
"chunk/atom"_compute_chunk_atom.html,
|
||||
"chunk/spread/atom"_compute_chunk_spread_atom.html,
|
||||
"cluster/atom"_compute_cluster_atom.html,
|
||||
"cna/atom"_compute_cna_atom.html,
|
||||
"cnp/atom"_compute_cnp_atom.html,
|
||||
"com"_compute_com.html,
|
||||
"com/chunk"_compute_com_chunk.html,
|
||||
"contact/atom"_compute_contact_atom.html,
|
||||
"coord/atom"_compute_coord_atom.html,
|
||||
"damage/atom"_compute_damage_atom.html,
|
||||
"dihedral"_compute_dihedral.html,
|
||||
"dihedral/local"_compute_dihedral_local.html,
|
||||
"dilatation/atom"_compute_dilatation_atom.html,
|
||||
"dipole/chunk"_compute_dipole_chunk.html,
|
||||
"displace/atom"_compute_displace_atom.html,
|
||||
"dpd"_compute_dpd.html,
|
||||
"dpd/atom"_compute_dpd_atom.html,
|
||||
"edpd/temp/atom"_compute_edpd_temp_atom.html,
|
||||
"entropy/atom"_compute_entropy_atom.html,
|
||||
"erotate/asphere"_compute_erotate_asphere.html,
|
||||
"erotate/rigid"_compute_erotate_rigid.html,
|
||||
"erotate/sphere"_compute_erotate_sphere.html,
|
||||
"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
|
||||
"event/displace"_compute_event_displace.html,
|
||||
"fep"_compute_fep.html,
|
||||
"force/tally"_compute_tally.html,
|
||||
"fragment/atom"_compute_cluster_atom.html,
|
||||
"global/atom"_compute_global_atom.html,
|
||||
"group/group"_compute_group_group.html,
|
||||
"gyration"_compute_gyration.html,
|
||||
"gyration/chunk"_compute_gyration_chunk.html,
|
||||
"gyration/shape"_compute_gyration_shape.html,
|
||||
"gyration/shape/chunk"_compute_gyration_shape_chunk.html,
|
||||
"heat/flux"_compute_heat_flux.html,
|
||||
"heat/flux/tally"_compute_tally.html,
|
||||
"hexorder/atom"_compute_hexorder_atom.html,
|
||||
"hma"_compute_hma.html,
|
||||
"improper"_compute_improper.html,
|
||||
"improper/local"_compute_improper_local.html,
|
||||
"inertia/chunk"_compute_inertia_chunk.html,
|
||||
"ke"_compute_ke.html,
|
||||
"ke/atom"_compute_ke_atom.html,
|
||||
"ke/atom/eff"_compute_ke_atom_eff.html,
|
||||
"ke/eff"_compute_ke_eff.html,
|
||||
"ke/rigid"_compute_ke_rigid.html,
|
||||
"meso/e/atom"_compute_meso_e_atom.html,
|
||||
"meso/rho/atom"_compute_meso_rho_atom.html,
|
||||
"meso/t/atom"_compute_meso_t_atom.html,
|
||||
"momentum"_compute_momentum.html,
|
||||
"msd"_compute_msd.html,
|
||||
"msd/chunk"_compute_msd_chunk.html,
|
||||
"msd/nongauss"_compute_msd_nongauss.html,
|
||||
"omega/chunk"_compute_omega_chunk.html,
|
||||
"orientorder/atom"_compute_orientorder_atom.html,
|
||||
"pair"_compute_pair.html,
|
||||
"pair/local"_compute_pair_local.html,
|
||||
"pe"_compute_pe.html,
|
||||
"pe/atom"_compute_pe_atom.html,
|
||||
"pe/mol/tally"_compute_tally.html,
|
||||
"pe/tally"_compute_tally.html,
|
||||
"plasticity/atom"_compute_plasticity_atom.html,
|
||||
"pressure"_compute_pressure.html,
|
||||
"pressure/cylinder"_compute_pressure_cylinder.html,
|
||||
"pressure/uef"_compute_pressure_uef.html,
|
||||
"property/atom"_compute_property_atom.html,
|
||||
"property/chunk"_compute_property_chunk.html,
|
||||
"property/local"_compute_property_local.html,
|
||||
"ptm/atom"_compute_ptm_atom.html,
|
||||
"rdf"_compute_rdf.html,
|
||||
"reduce"_compute_reduce.html,
|
||||
"reduce/chunk"_compute_reduce_chunk.html,
|
||||
"reduce/region"_compute_reduce.html,
|
||||
"rigid/local"_compute_rigid_local.html,
|
||||
"saed"_compute_saed.html,
|
||||
"slice"_compute_slice.html,
|
||||
"smd/contact/radius"_compute_smd_contact_radius.html,
|
||||
"smd/damage"_compute_smd_damage.html,
|
||||
"smd/hourglass/error"_compute_smd_hourglass_error.html,
|
||||
"smd/internal/energy"_compute_smd_internal_energy.html,
|
||||
"smd/plastic/strain"_compute_smd_plastic_strain.html,
|
||||
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
|
||||
"smd/rho"_compute_smd_rho.html,
|
||||
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
|
||||
"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
|
||||
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
|
||||
"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
|
||||
"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
|
||||
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
|
||||
"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
|
||||
"smd/triangle/vertices"_compute_smd_triangle_vertices.html,
|
||||
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
|
||||
"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
|
||||
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
|
||||
"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
|
||||
"smd/vol"_compute_smd_vol.html,
|
||||
"sna/atom"_compute_sna_atom.html,
|
||||
"snad/atom"_compute_sna_atom.html,
|
||||
"snav/atom"_compute_sna_atom.html,
|
||||
"spin"_compute_spin.html,
|
||||
"stress/atom"_compute_stress_atom.html,
|
||||
"stress/mop"_compute_stress_mop.html,
|
||||
"stress/mop/profile"_compute_stress_mop.html,
|
||||
"stress/tally"_compute_tally.html,
|
||||
"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
|
||||
"temp (k)"_compute_temp.html,
|
||||
"temp/asphere"_compute_temp_asphere.html,
|
||||
"temp/body"_compute_temp_body.html,
|
||||
"temp/chunk"_compute_temp_chunk.html,
|
||||
"temp/com"_compute_temp_com.html,
|
||||
"temp/cs"_compute_temp_cs.html,
|
||||
"temp/deform"_compute_temp_deform.html,
|
||||
"temp/deform/eff"_compute_temp_deform_eff.html,
|
||||
"temp/drude"_compute_temp_drude.html,
|
||||
"temp/eff"_compute_temp_eff.html,
|
||||
"temp/partial"_compute_temp_partial.html,
|
||||
"temp/profile"_compute_temp_profile.html,
|
||||
"temp/ramp"_compute_temp_ramp.html,
|
||||
"temp/region"_compute_temp_region.html,
|
||||
"temp/region/eff"_compute_temp_region_eff.html,
|
||||
"temp/rotate"_compute_temp_rotate.html,
|
||||
"temp/sphere"_compute_temp_sphere.html,
|
||||
"temp/uef"_compute_temp_uef.html,
|
||||
"ti"_compute_ti.html,
|
||||
"torque/chunk"_compute_torque_chunk.html,
|
||||
"vacf"_compute_vacf.html,
|
||||
"vcm/chunk"_compute_vcm_chunk.html,
|
||||
"voronoi/atom"_compute_voronoi_atom.html,
|
||||
"xrd"_compute_xrd.html :tb(c=6,ea=c)
|
||||
@ -1,240 +0,0 @@
|
||||
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
"General commands"_Commands_all.html,
|
||||
"Fix styles"_Commands_fix.html,
|
||||
"Compute styles"_Commands_compute.html,
|
||||
"Pair styles"_Commands_pair.html,
|
||||
"Bond styles"_Commands_bond.html,
|
||||
"Angle styles"_Commands_bond.html#angle,
|
||||
"Dihedral styles"_Commands_bond.html#dihedral,
|
||||
"Improper styles"_Commands_bond.html#improper,
|
||||
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
|
||||
|
||||
Fix commands :h3
|
||||
|
||||
An alphabetic list of all LAMMPS "fix"_fix.html commands. Some styles
|
||||
have accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
"adapt"_fix_adapt.html,
|
||||
"adapt/fep"_fix_adapt_fep.html,
|
||||
"addforce"_fix_addforce.html,
|
||||
"addtorque"_fix_addtorque.html,
|
||||
"append/atoms"_fix_append_atoms.html,
|
||||
"atc"_fix_atc.html,
|
||||
"atom/swap"_fix_atom_swap.html,
|
||||
"ave/atom"_fix_ave_atom.html,
|
||||
"ave/chunk"_fix_ave_chunk.html,
|
||||
"ave/correlate"_fix_ave_correlate.html,
|
||||
"ave/correlate/long"_fix_ave_correlate_long.html,
|
||||
"ave/histo"_fix_ave_histo.html,
|
||||
"ave/histo/weight"_fix_ave_histo.html,
|
||||
"ave/time"_fix_ave_time.html,
|
||||
"aveforce"_fix_aveforce.html,
|
||||
"balance"_fix_balance.html,
|
||||
"bocs"_fix_bocs.html,
|
||||
"bond/break"_fix_bond_break.html,
|
||||
"bond/create"_fix_bond_create.html,
|
||||
"bond/react"_fix_bond_react.html,
|
||||
"bond/swap"_fix_bond_swap.html,
|
||||
"box/relax"_fix_box_relax.html,
|
||||
"client/md"_fix_client_md.html,
|
||||
"cmap"_fix_cmap.html,
|
||||
"colvars"_fix_colvars.html,
|
||||
"controller"_fix_controller.html,
|
||||
"deform (k)"_fix_deform.html,
|
||||
"deposit"_fix_deposit.html,
|
||||
"dpd/energy (k)"_fix_dpd_energy.html,
|
||||
"drag"_fix_drag.html,
|
||||
"drude"_fix_drude.html,
|
||||
"drude/transform/direct"_fix_drude_transform.html,
|
||||
"drude/transform/inverse"_fix_drude_transform.html,
|
||||
"dt/reset"_fix_dt_reset.html,
|
||||
"edpd/source"_fix_dpd_source.html,
|
||||
"efield"_fix_efield.html,
|
||||
"ehex"_fix_ehex.html,
|
||||
"electron/stopping"_fix_electron_stopping.html,
|
||||
"enforce2d (k)"_fix_enforce2d.html,
|
||||
"eos/cv"_fix_eos_cv.html,
|
||||
"eos/table"_fix_eos_table.html,
|
||||
"eos/table/rx (k)"_fix_eos_table_rx.html,
|
||||
"evaporate"_fix_evaporate.html,
|
||||
"external"_fix_external.html,
|
||||
"ffl"_fix_ffl.html,
|
||||
"filter/corotate"_fix_filter_corotate.html,
|
||||
"flow/gauss"_fix_flow_gauss.html,
|
||||
"freeze (k)"_fix_freeze.html,
|
||||
"gcmc"_fix_gcmc.html,
|
||||
"gld"_fix_gld.html,
|
||||
"gle"_fix_gle.html,
|
||||
"gravity (ko)"_fix_gravity.html,
|
||||
"grem"_fix_grem.html,
|
||||
"halt"_fix_halt.html,
|
||||
"heat"_fix_heat.html,
|
||||
"hyper/global"_fix_hyper_global.html,
|
||||
"hyper/local"_fix_hyper_local.html,
|
||||
"imd"_fix_imd.html,
|
||||
"indent"_fix_indent.html,
|
||||
"ipi"_fix_ipi.html,
|
||||
"langevin (k)"_fix_langevin.html,
|
||||
"langevin/drude"_fix_langevin_drude.html,
|
||||
"langevin/eff"_fix_langevin_eff.html,
|
||||
"langevin/spin"_fix_langevin_spin.html,
|
||||
"latte"_fix_latte.html,
|
||||
"lb/fluid"_fix_lb_fluid.html,
|
||||
"lb/momentum"_fix_lb_momentum.html,
|
||||
"lb/pc"_fix_lb_pc.html,
|
||||
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
|
||||
"lb/viscous"_fix_lb_viscous.html,
|
||||
"lineforce"_fix_lineforce.html,
|
||||
"manifoldforce"_fix_manifoldforce.html,
|
||||
"meso"_fix_meso.html,
|
||||
"meso/move"_fix_meso_move.html,
|
||||
"meso/stationary"_fix_meso_stationary.html,
|
||||
"momentum (k)"_fix_momentum.html,
|
||||
"move"_fix_move.html,
|
||||
"mscg"_fix_mscg.html,
|
||||
"msst"_fix_msst.html,
|
||||
"mvv/dpd"_fix_mvv_dpd.html,
|
||||
"mvv/edpd"_fix_mvv_dpd.html,
|
||||
"mvv/tdpd"_fix_mvv_dpd.html,
|
||||
"neb"_fix_neb.html,
|
||||
"neb_spin"_fix_neb_spin.html,
|
||||
"nph (ko)"_fix_nh.html,
|
||||
"nph/asphere (o)"_fix_nph_asphere.html,
|
||||
"nph/body"_fix_nph_body.html,
|
||||
"nph/eff"_fix_nh_eff.html,
|
||||
"nph/sphere (o)"_fix_nph_sphere.html,
|
||||
"nphug (o)"_fix_nphug.html,
|
||||
"npt (iko)"_fix_nh.html,
|
||||
"npt/asphere (o)"_fix_npt_asphere.html,
|
||||
"npt/body"_fix_npt_body.html,
|
||||
"npt/eff"_fix_nh_eff.html,
|
||||
"npt/sphere (o)"_fix_npt_sphere.html,
|
||||
"npt/uef"_fix_nh_uef.html,
|
||||
"nve (iko)"_fix_nve.html,
|
||||
"nve/asphere (i)"_fix_nve_asphere.html,
|
||||
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
|
||||
"nve/awpmd"_fix_nve_awpmd.html,
|
||||
"nve/body"_fix_nve_body.html,
|
||||
"nve/dot"_fix_nve_dot.html,
|
||||
"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
|
||||
"nve/eff"_fix_nve_eff.html,
|
||||
"nve/limit"_fix_nve_limit.html,
|
||||
"nve/line"_fix_nve_line.html,
|
||||
"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
|
||||
"nve/noforce"_fix_nve_noforce.html,
|
||||
"nve/sphere (ko)"_fix_nve_sphere.html,
|
||||
"nve/spin"_fix_nve_spin.html,
|
||||
"nve/tri"_fix_nve_tri.html,
|
||||
"nvk"_fix_nvk.html,
|
||||
"nvt (iko)"_fix_nh.html,
|
||||
"nvt/asphere (o)"_fix_nvt_asphere.html,
|
||||
"nvt/body"_fix_nvt_body.html,
|
||||
"nvt/eff"_fix_nh_eff.html,
|
||||
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
|
||||
"nvt/sllod (io)"_fix_nvt_sllod.html,
|
||||
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
|
||||
"nvt/sphere (o)"_fix_nvt_sphere.html,
|
||||
"nvt/uef"_fix_nh_uef.html,
|
||||
"oneway"_fix_oneway.html,
|
||||
"orient/bcc"_fix_orient.html,
|
||||
"orient/fcc"_fix_orient.html,
|
||||
"phonon"_fix_phonon.html,
|
||||
"pimd"_fix_pimd.html,
|
||||
"planeforce"_fix_planeforce.html,
|
||||
"plumed"_fix_plumed.html,
|
||||
"poems"_fix_poems.html,
|
||||
"pour"_fix_pour.html,
|
||||
"precession/spin"_fix_precession_spin.html,
|
||||
"press/berendsen"_fix_press_berendsen.html,
|
||||
"print"_fix_print.html,
|
||||
"property/atom (k)"_fix_property_atom.html,
|
||||
"python/invoke"_fix_python_invoke.html,
|
||||
"python/move"_fix_python_move.html,
|
||||
"qbmsst"_fix_qbmsst.html,
|
||||
"qeq/comb (o)"_fix_qeq_comb.html,
|
||||
"qeq/dynamic"_fix_qeq.html,
|
||||
"qeq/fire"_fix_qeq.html,
|
||||
"qeq/point"_fix_qeq.html,
|
||||
"qeq/reax (ko)"_fix_qeq_reax.html,
|
||||
"qeq/shielded"_fix_qeq.html,
|
||||
"qeq/slater"_fix_qeq.html,
|
||||
"qmmm"_fix_qmmm.html,
|
||||
"qtb"_fix_qtb.html,
|
||||
"rattle"_fix_shake.html,
|
||||
"reax/c/bonds (k)"_fix_reaxc_bonds.html,
|
||||
"reax/c/species (k)"_fix_reaxc_species.html,
|
||||
"recenter"_fix_recenter.html,
|
||||
"restrain"_fix_restrain.html,
|
||||
"rhok"_fix_rhok.html,
|
||||
"rigid (o)"_fix_rigid.html,
|
||||
"rigid/meso"_fix_rigid_meso.html,
|
||||
"rigid/nph (o)"_fix_rigid.html,
|
||||
"rigid/nph/small"_fix_rigid.html,
|
||||
"rigid/npt (o)"_fix_rigid.html,
|
||||
"rigid/npt/small"_fix_rigid.html,
|
||||
"rigid/nve (o)"_fix_rigid.html,
|
||||
"rigid/nve/small"_fix_rigid.html,
|
||||
"rigid/nvt (o)"_fix_rigid.html,
|
||||
"rigid/nvt/small"_fix_rigid.html,
|
||||
"rigid/small (o)"_fix_rigid.html,
|
||||
"rx (k)"_fix_rx.html,
|
||||
"saed/vtk"_fix_saed_vtk.html,
|
||||
"setforce (k)"_fix_setforce.html,
|
||||
"shake"_fix_shake.html,
|
||||
"shardlow (k)"_fix_shardlow.html,
|
||||
"smd"_fix_smd.html,
|
||||
"smd/adjust_dt"_fix_smd_adjust_dt.html,
|
||||
"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html,
|
||||
"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html,
|
||||
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
|
||||
"smd/setvel"_fix_smd_setvel.html,
|
||||
"smd/wall_surface"_fix_smd_wall_surface.html,
|
||||
"spring"_fix_spring.html,
|
||||
"spring/chunk"_fix_spring_chunk.html,
|
||||
"spring/rg"_fix_spring_rg.html,
|
||||
"spring/self"_fix_spring_self.html,
|
||||
"srd"_fix_srd.html,
|
||||
"store/force"_fix_store_force.html,
|
||||
"store/state"_fix_store_state.html,
|
||||
"tdpd/source"_fix_dpd_source.html,
|
||||
"temp/berendsen"_fix_temp_berendsen.html,
|
||||
"temp/csld"_fix_temp_csvr.html,
|
||||
"temp/csvr"_fix_temp_csvr.html,
|
||||
"temp/rescale"_fix_temp_rescale.html,
|
||||
"temp/rescale/eff"_fix_temp_rescale_eff.html,
|
||||
"tfmc"_fix_tfmc.html,
|
||||
"thermal/conductivity"_fix_thermal_conductivity.html,
|
||||
"ti/spring"_fix_ti_spring.html,
|
||||
"tmd"_fix_tmd.html,
|
||||
"ttm"_fix_ttm.html,
|
||||
"ttm/mod"_fix_ttm.html,
|
||||
"tune/kspace"_fix_tune_kspace.html,
|
||||
"vector"_fix_vector.html,
|
||||
"viscosity"_fix_viscosity.html,
|
||||
"viscous"_fix_viscous.html,
|
||||
"wall/body/polygon"_fix_wall_body_polygon.html,
|
||||
"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
|
||||
"wall/colloid"_fix_wall.html,
|
||||
"wall/ees"_fix_wall_ees.html,
|
||||
"wall/gran"_fix_wall_gran.html,
|
||||
"wall/gran/region"_fix_wall_gran_region.html,
|
||||
"wall/harmonic"_fix_wall.html,
|
||||
"wall/lj1043"_fix_wall.html,
|
||||
"wall/lj126"_fix_wall.html,
|
||||
"wall/lj93 (k)"_fix_wall.html,
|
||||
"wall/morse"_fix_wall.html,
|
||||
"wall/piston"_fix_wall_piston.html,
|
||||
"wall/reflect (k)"_fix_wall_reflect.html,
|
||||
"wall/region"_fix_wall_region.html,
|
||||
"wall/region/ees"_fix_wall_ees.html,
|
||||
"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c)
|
||||
@ -1,37 +0,0 @@
|
||||
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands.html)
|
||||
|
||||
:line
|
||||
|
||||
"General commands"_Commands_all.html,
|
||||
"Fix styles"_Commands_fix.html,
|
||||
"Compute styles"_Commands_compute.html,
|
||||
"Pair styles"_Commands_pair.html,
|
||||
"Bond styles"_Commands_bond.html,
|
||||
"Angle styles"_Commands_bond.html#angle,
|
||||
"Dihedral styles"_Commands_bond.html#dihedral,
|
||||
"Improper styles"_Commands_bond.html#improper,
|
||||
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
|
||||
|
||||
KSpace solvers :h3
|
||||
|
||||
All LAMMPS "kspace_style"_kspace_style.html solvers. Some styles have
|
||||
accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
"ewald (o)"_kspace_style.html,
|
||||
"ewald/disp"_kspace_style.html,
|
||||
"msm (o)"_kspace_style.html,
|
||||
"msm/cg (o)"_kspace_style.html,
|
||||
"pppm (gok)"_kspace_style.html,
|
||||
"pppm/cg (o)"_kspace_style.html,
|
||||
"pppm/disp (i)"_kspace_style.html,
|
||||
"pppm/disp/tip4p"_kspace_style.html,
|
||||
"pppm/stagger"_kspace_style.html,
|
||||
"pppm/tip4p (o)"_kspace_style.html,
|
||||
"scafacos"_kspace_style.html :tb(c=4,ea=c)
|
||||
@ -1,253 +0,0 @@
|
||||
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
"General commands"_Commands_all.html,
|
||||
"Fix styles"_Commands_fix.html,
|
||||
"Compute styles"_Commands_compute.html,
|
||||
"Pair styles"_Commands_pair.html,
|
||||
"Bond styles"_Commands_bond.html,
|
||||
"Angle styles"_Commands_bond.html#angle,
|
||||
"Dihedral styles"_Commands_bond.html#dihedral,
|
||||
"Improper styles"_Commands_bond.html#improper,
|
||||
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
|
||||
|
||||
Pair_style potentials :h3
|
||||
|
||||
All LAMMPS "pair_style"_pair_style.html commands. Some styles have
|
||||
accelerated versions. This is indicated by additional letters in
|
||||
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
|
||||
OPT.
|
||||
|
||||
"none"_pair_none.html,
|
||||
"zero"_pair_zero.html,
|
||||
"hybrid (k)"_pair_hybrid.html,
|
||||
"hybrid/overlay (k)"_pair_hybrid.html,
|
||||
,
|
||||
,
|
||||
,
|
||||
,
|
||||
"adp (o)"_pair_adp.html,
|
||||
"agni (o)"_pair_agni.html,
|
||||
"airebo (io)"_pair_airebo.html,
|
||||
"airebo/morse (io)"_pair_airebo.html,
|
||||
"atm"_pair_atm.html,
|
||||
"awpmd/cut"_pair_awpmd.html,
|
||||
"beck (go)"_pair_beck.html,
|
||||
"body/nparticle"_pair_body_nparticle.html,
|
||||
"body/rounded/polygon"_pair_body_rounded_polygon.html,
|
||||
"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html,
|
||||
"bop"_pair_bop.html,
|
||||
"born (go)"_pair_born.html,
|
||||
"born/coul/dsf"_pair_born.html,
|
||||
"born/coul/dsf/cs"_pair_cs.html,
|
||||
"born/coul/long (go)"_pair_born.html,
|
||||
"born/coul/long/cs (g)"_pair_cs.html,
|
||||
"born/coul/msm (o)"_pair_born.html,
|
||||
"born/coul/wolf (go)"_pair_born.html,
|
||||
"born/coul/wolf/cs (g)"_pair_cs.html,
|
||||
"brownian (o)"_pair_brownian.html,
|
||||
"brownian/poly (o)"_pair_brownian.html,
|
||||
"buck (giko)"_pair_buck.html,
|
||||
"buck/coul/cut (giko)"_pair_buck.html,
|
||||
"buck/coul/long (giko)"_pair_buck.html,
|
||||
"buck/coul/long/cs"_pair_cs.html,
|
||||
"buck/coul/msm (o)"_pair_buck.html,
|
||||
"buck/long/coul/long (o)"_pair_buck_long.html,
|
||||
"buck/mdf"_pair_mdf.html,
|
||||
"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html,
|
||||
"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html,
|
||||
"colloid (go)"_pair_colloid.html,
|
||||
"comb (o)"_pair_comb.html,
|
||||
"comb3"_pair_comb.html,
|
||||
"cosine/squared"_pair_cosine_squared.html,
|
||||
"coul/cut (gko)"_pair_coul.html,
|
||||
"coul/cut/soft (o)"_pair_fep_soft.html,
|
||||
"coul/debye (gko)"_pair_coul.html,
|
||||
"coul/diel (o)"_pair_coul_diel.html,
|
||||
"coul/dsf (gko)"_pair_coul.html,
|
||||
"coul/long (gko)"_pair_coul.html,
|
||||
"coul/long/cs (g)"_pair_cs.html,
|
||||
"coul/long/soft (o)"_pair_fep_soft.html,
|
||||
"coul/msm (o)"_pair_coul.html,
|
||||
"coul/shield"_pair_coul_shield.html,
|
||||
"coul/streitz"_pair_coul.html,
|
||||
"coul/wolf (ko)"_pair_coul.html,
|
||||
"coul/wolf/cs"_pair_cs.html,
|
||||
"dpd (gio)"_pair_dpd.html,
|
||||
"dpd/fdt"_pair_dpd_fdt.html,
|
||||
"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
|
||||
"dpd/tstat (go)"_pair_dpd.html,
|
||||
"dsmc"_pair_dsmc.html,
|
||||
"e3b"_pair_e3b.html,
|
||||
"drip"_pair_drip.html,
|
||||
"eam (gikot)"_pair_eam.html,
|
||||
"eam/alloy (gikot)"_pair_eam.html,
|
||||
"eam/cd (o)"_pair_eam.html,
|
||||
"eam/cd/old (o)"_pair_eam.html,
|
||||
"eam/fs (gikot)"_pair_eam.html,
|
||||
"edip (o)"_pair_edip.html,
|
||||
"edip/multi"_pair_edip.html,
|
||||
"edpd"_pair_meso.html,
|
||||
"eff/cut"_pair_eff.html,
|
||||
"eim (o)"_pair_eim.html,
|
||||
"exp6/rx (k)"_pair_exp6_rx.html,
|
||||
"extep"_pair_extep.html,
|
||||
"gauss (go)"_pair_gauss.html,
|
||||
"gauss/cut (o)"_pair_gauss.html,
|
||||
"gayberne (gio)"_pair_gayberne.html,
|
||||
"gran/hertz/history (o)"_pair_gran.html,
|
||||
"gran/hooke (o)"_pair_gran.html,
|
||||
"gran/hooke/history (ko)"_pair_gran.html,
|
||||
"granular"_pair_granular.html,
|
||||
"gw"_pair_gw.html,
|
||||
"gw/zbl"_pair_gw.html,
|
||||
"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
|
||||
"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
|
||||
"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
|
||||
"kim"_pair_kim.html,
|
||||
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
|
||||
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
|
||||
"lcbop"_pair_lcbop.html,
|
||||
"lebedeva/z"_pair_lebedeva_z.html,
|
||||
"lennard/mdf"_pair_mdf.html,
|
||||
"line/lj"_pair_line_lj.html,
|
||||
"list"_pair_list.html,
|
||||
"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
|
||||
"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
|
||||
"lj/charmm/coul/long (gikot)"_pair_charmm.html,
|
||||
"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html,
|
||||
"lj/charmm/coul/msm (o)"_pair_charmm.html,
|
||||
"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
|
||||
"lj/charmmfsw/coul/long"_pair_charmm.html,
|
||||
"lj/class2 (gko)"_pair_class2.html,
|
||||
"lj/class2/coul/cut (ko)"_pair_class2.html,
|
||||
"lj/class2/coul/cut/soft"_pair_fep_soft.html,
|
||||
"lj/class2/coul/long (gko)"_pair_class2.html,
|
||||
"lj/class2/coul/long/soft"_pair_fep_soft.html,
|
||||
"lj/class2/soft"_pair_fep_soft.html,
|
||||
"lj/cubic (go)"_pair_lj_cubic.html,
|
||||
"lj/cut (gikot)"_pair_lj.html,
|
||||
"lj/cut/coul/cut (gko)"_pair_lj.html,
|
||||
"lj/cut/coul/cut/soft (o)"_pair_fep_soft.html,
|
||||
"lj/cut/coul/debye (gko)"_pair_lj.html,
|
||||
"lj/cut/coul/dsf (gko)"_pair_lj.html,
|
||||
"lj/cut/coul/long (gikot)"_pair_lj.html,
|
||||
"lj/cut/coul/long/cs"_pair_cs.html,
|
||||
"lj/cut/coul/long/soft (o)"_pair_fep_soft.html,
|
||||
"lj/cut/coul/msm (go)"_pair_lj.html,
|
||||
"lj/cut/coul/wolf (o)"_pair_lj.html,
|
||||
"lj/cut/dipole/cut (go)"_pair_dipole.html,
|
||||
"lj/cut/dipole/long (g)"_pair_dipole.html,
|
||||
"lj/cut/dipole/sf (go)"_pair_dipole.html,
|
||||
"lj/cut/soft (o)"_pair_fep_soft.html,
|
||||
"lj/cut/thole/long (o)"_pair_thole.html,
|
||||
"lj/cut/tip4p/cut (o)"_pair_lj.html,
|
||||
"lj/cut/tip4p/long (ot)"_pair_lj.html,
|
||||
"lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html,
|
||||
"lj/expand (gko)"_pair_lj_expand.html,
|
||||
"lj/expand/coul/long (g)"_pair_lj_expand.html,
|
||||
"lj/gromacs (gko)"_pair_gromacs.html,
|
||||
"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
|
||||
"lj/long/coul/long (iot)"_pair_lj_long.html,
|
||||
"lj/long/dipole/long"_pair_dipole.html,
|
||||
"lj/long/tip4p/long (o)"_pair_lj_long.html,
|
||||
"lj/mdf"_pair_mdf.html,
|
||||
"lj/sdk (gko)"_pair_sdk.html,
|
||||
"lj/sdk/coul/long (go)"_pair_sdk.html,
|
||||
"lj/sdk/coul/msm (o)"_pair_sdk.html,
|
||||
"lj/sf/dipole/sf (go)"_pair_dipole.html,
|
||||
"lj/smooth (o)"_pair_lj_smooth.html,
|
||||
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
|
||||
"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
|
||||
"lj96/cut (go)"_pair_lj96.html,
|
||||
"local/density"_pair_local_density.html,
|
||||
"lubricate (o)"_pair_lubricate.html,
|
||||
"lubricate/poly (o)"_pair_lubricate.html,
|
||||
"lubricateU"_pair_lubricateU.html,
|
||||
"lubricateU/poly"_pair_lubricateU.html,
|
||||
"mdpd"_pair_meso.html,
|
||||
"mdpd/rhosum"_pair_meso.html,
|
||||
"meam/c"_pair_meamc.html,
|
||||
"meam/spline (o)"_pair_meam_spline.html,
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html,
|
||||
"mgpt"_pair_mgpt.html,
|
||||
"mie/cut (g)"_pair_mie.html,
|
||||
"momb"_pair_momb.html,
|
||||
"morse (gkot)"_pair_morse.html,
|
||||
"morse/smooth/linear (o)"_pair_morse.html,
|
||||
"morse/soft"_pair_fep_soft.html,
|
||||
"multi/lucy"_pair_multi_lucy.html,
|
||||
"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
|
||||
"nb3b/harmonic"_pair_nb3b_harmonic.html,
|
||||
"nm/cut (o)"_pair_nm.html,
|
||||
"nm/cut/coul/cut (o)"_pair_nm.html,
|
||||
"nm/cut/coul/long (o)"_pair_nm.html,
|
||||
"oxdna/coaxstk"_pair_oxdna.html,
|
||||
"oxdna/excv"_pair_oxdna.html,
|
||||
"oxdna/hbond"_pair_oxdna.html,
|
||||
"oxdna/stk"_pair_oxdna.html,
|
||||
"oxdna/xstk"_pair_oxdna.html,
|
||||
"oxdna2/coaxstk"_pair_oxdna2.html,
|
||||
"oxdna2/dh"_pair_oxdna2.html,
|
||||
"oxdna2/excv"_pair_oxdna2.html,
|
||||
"oxdna2/hbond"_pair_oxdna2.html,
|
||||
"oxdna2/stk"_pair_oxdna2.html,
|
||||
"oxdna2/xstk"_pair_oxdna2.html,
|
||||
"peri/eps"_pair_peri.html,
|
||||
"peri/lps (o)"_pair_peri.html,
|
||||
"peri/pmb (o)"_pair_peri.html,
|
||||
"peri/ves"_pair_peri.html,
|
||||
"polymorphic"_pair_polymorphic.html,
|
||||
"python"_pair_python.html,
|
||||
"quip"_pair_quip.html,
|
||||
"reax/c (ko)"_pair_reaxc.html,
|
||||
"rebo (io)"_pair_airebo.html,
|
||||
"resquared (go)"_pair_resquared.html,
|
||||
"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
|
||||
"smd/hertz"_pair_smd_hertz.html,
|
||||
"smd/tlsph"_pair_smd_tlsph.html,
|
||||
"smd/tri_surface"_pair_smd_triangulated_surface.html,
|
||||
"smd/ulsph"_pair_smd_ulsph.html,
|
||||
"smtbq"_pair_smtbq.html,
|
||||
"snap (k)"_pair_snap.html,
|
||||
"snap (k)"_pair_snap.html,
|
||||
"soft (go)"_pair_soft.html,
|
||||
"sph/heatconduction"_pair_sph_heatconduction.html,
|
||||
"sph/idealgas"_pair_sph_idealgas.html,
|
||||
"sph/lj"_pair_sph_lj.html,
|
||||
"sph/rhosum"_pair_sph_rhosum.html,
|
||||
"sph/taitwater"_pair_sph_taitwater.html,
|
||||
"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
|
||||
"spin/dipole/cut"_pair_spin_dipole.html,
|
||||
"spin/dipole/long"_pair_spin_dipole.html,
|
||||
"spin/dmi"_pair_spin_dmi.html,
|
||||
"spin/exchange"_pair_spin_exchange.html,
|
||||
"spin/magelec"_pair_spin_magelec.html,
|
||||
"spin/neel"_pair_spin_neel.html,
|
||||
"srp"_pair_srp.html,
|
||||
"sw (giko)"_pair_sw.html,
|
||||
"table (gko)"_pair_table.html,
|
||||
"table/rx (k)"_pair_table_rx.html,
|
||||
"tdpd"_pair_meso.html,
|
||||
"tersoff (giko)"_pair_tersoff.html,
|
||||
"tersoff/mod (gko)"_pair_tersoff_mod.html,
|
||||
"tersoff/mod/c (o)"_pair_tersoff_mod.html,
|
||||
"tersoff/table (o)"_pair_tersoff.html,
|
||||
"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
|
||||
"thole"_pair_thole.html,
|
||||
"tip4p/cut (o)"_pair_coul.html,
|
||||
"tip4p/long (o)"_pair_coul.html,
|
||||
"tip4p/long/soft (o)"_pair_fep_soft.html,
|
||||
"tri/lj"_pair_tri_lj.html,
|
||||
"ufm (got)"_pair_ufm.html,
|
||||
"vashishta (gko)"_pair_vashishta.html,
|
||||
"vashishta/table (o)"_pair_vashishta.html,
|
||||
"yukawa (gko)"_pair_yukawa.html,
|
||||
"yukawa/colloid (go)"_pair_yukawa_colloid.html,
|
||||
"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c)
|
||||
@ -1,66 +0,0 @@
|
||||
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands.html)
|
||||
|
||||
:line
|
||||
|
||||
Removed commands and packages :h3
|
||||
|
||||
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.
|
||||
|
||||
Fix ave/spatial and fix ave/spatial/sphere :h4
|
||||
|
||||
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
|
||||
ways through the "compute chunk/atom"_compute_chunk_atom.html command
|
||||
and then averaging is done using "fix ave/chunk"_fix_ave_chunk.html.
|
||||
Please refer to the "chunk HOWTO"_Howto_chunk.html section for an overview.
|
||||
|
||||
MEAM package :h4
|
||||
|
||||
The MEAM package has been removed since it was superseded by the
|
||||
"USER-MEAMC package"_Package_details.html#PKG-USER-MEAMC. The code in
|
||||
the USER-MEAMC package 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 new pair style "meam/c"_pair_meamc.html has
|
||||
the exact same syntax as the old "meam" pair style and thus pair style
|
||||
"meam"_pair_meamc.html is an alias to the new style and backward
|
||||
compatibility of old inputs is preserved.
|
||||
|
||||
REAX package :h4
|
||||
|
||||
The REAX package has been removed since it was superseded by the
|
||||
"USER-REAXC package"_Package_details.html#PKG-USER-REAXC. The USER-REAXC
|
||||
package has been tested to yield equivalent results to the REAX package,
|
||||
offers better performance, supports OpenMP multi-threading via USER-OMP,
|
||||
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.
|
||||
|
||||
USER-CUDA package :h4
|
||||
|
||||
The USER-CUDA package had been removed, since it had been unmaintained
|
||||
for a long time and had known bugs and problems. Significant parts of
|
||||
the design were transferred to the
|
||||
"KOKKOS package"_Package_details.html#PKG-KOKKOS, which has similar
|
||||
performance characteristics on Nvidia GPUs. Both, the KOKKOS
|
||||
and the "GPU package"_Package_details.html#PKG-GPU are maintained
|
||||
and allow running LAMMPS with GPU acceleration.
|
||||
|
||||
restart2data tool :h4
|
||||
|
||||
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 "read_restart"_read_restart.html and
|
||||
"write_data"_write_data.html can be used to the same effect. For added
|
||||
convenience this conversion can also be triggered by "command line
|
||||
flags"_Run_options.html
|
||||
@ -1,95 +0,0 @@
|
||||
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
Input script structure :h3
|
||||
|
||||
This page describes the structure of a typical LAMMPS input script.
|
||||
The examples directory in the LAMMPS distribution contains many sample
|
||||
input scripts; it is discussed on the "Examples"_Examples.html doc
|
||||
page.
|
||||
|
||||
A LAMMPS input script typically has 4 parts:
|
||||
|
||||
Initialization
|
||||
Atom definition
|
||||
Settings
|
||||
Run a simulation :ol
|
||||
|
||||
The last 2 parts can be repeated as many times as desired. I.e. run a
|
||||
simulation, change some settings, run some more, etc. Each of the 4
|
||||
parts is now described in more detail. Remember that almost all
|
||||
commands need only be used if a non-default value is desired.
|
||||
|
||||
(1) Initialization
|
||||
|
||||
Set parameters that need to be defined before atoms are created or
|
||||
read-in from a file.
|
||||
|
||||
The relevant commands are "units"_units.html,
|
||||
"dimension"_dimension.html, "newton"_newton.html,
|
||||
"processors"_processors.html, "boundary"_boundary.html,
|
||||
"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
|
||||
|
||||
If force-field parameters appear in the files that will be read, these
|
||||
commands tell LAMMPS what kinds of force fields are being used:
|
||||
"pair_style"_pair_style.html, "bond_style"_bond_style.html,
|
||||
"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
|
||||
"improper_style"_improper_style.html.
|
||||
|
||||
(2) Atom definition
|
||||
|
||||
There are 3 ways to define atoms in LAMMPS. Read them in from a data
|
||||
or restart file via the "read_data"_read_data.html or
|
||||
"read_restart"_read_restart.html commands. These files can contain
|
||||
molecular topology information. Or create atoms on a lattice (with no
|
||||
molecular topology), using these commands: "lattice"_lattice.html,
|
||||
"region"_region.html, "create_box"_create_box.html,
|
||||
"create_atoms"_create_atoms.html. The entire set of atoms can be
|
||||
duplicated to make a larger simulation using the
|
||||
"replicate"_replicate.html command.
|
||||
|
||||
(3) Settings
|
||||
|
||||
Once atoms and molecular topology are defined, a variety of settings
|
||||
can be specified: force field coefficients, simulation parameters,
|
||||
output options, etc.
|
||||
|
||||
Force field coefficients are set by these commands (they can also be
|
||||
set in the read-in files): "pair_coeff"_pair_coeff.html,
|
||||
"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
|
||||
"dihedral_coeff"_dihedral_coeff.html,
|
||||
"improper_coeff"_improper_coeff.html,
|
||||
"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
|
||||
"special_bonds"_special_bonds.html.
|
||||
|
||||
Various simulation parameters are set by these commands:
|
||||
"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
|
||||
"group"_group.html, "timestep"_timestep.html,
|
||||
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
|
||||
"min_style"_min_style.html, "min_modify"_min_modify.html.
|
||||
|
||||
Fixes impose a variety of boundary conditions, time integration, and
|
||||
diagnostic options. The "fix"_fix.html command comes in many flavors.
|
||||
|
||||
Various computations can be specified for execution during a
|
||||
simulation using the "compute"_compute.html,
|
||||
"compute_modify"_compute_modify.html, and "variable"_variable.html
|
||||
commands.
|
||||
|
||||
Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
|
||||
and "restart"_restart.html commands.
|
||||
|
||||
(4) Run a simulation
|
||||
|
||||
A molecular dynamics simulation is run using the "run"_run.html
|
||||
command. Energy minimization (molecular statics) is performed using
|
||||
the "minimize"_minimize.html command. A parallel tempering
|
||||
(replica-exchange) simulation can be run using the
|
||||
"temper"_temper.html command.
|
||||
|
||||
@ -239,6 +239,13 @@ will be truncated to attempt to prevent the bond from blowing up. :dd
|
||||
|
||||
You likely want to set this in your input script. :dd
|
||||
|
||||
{ Fix bond/create is used multiple times or with fix bond/break - may not work as expected} :dt
|
||||
|
||||
When using fix bond/create multiple times or in combination with
|
||||
fix bond/break, the individual fix instances do not share information
|
||||
about changes they made at the same time step and thus it may result
|
||||
in unexpected behavior. :dd
|
||||
|
||||
{Fix bond/swap will ignore defined angles} :dt
|
||||
|
||||
See the doc page for fix bond/swap for more info on this
|
||||
|
||||
@ -94,6 +94,7 @@ python: using embedded Python in a LAMMPS input script
|
||||
qeq: use of the QEQ package for charge equilibration
|
||||
rdf-adf: computing radial and angle distribution functions for water
|
||||
reax: RDX and TATB models using the ReaxFF
|
||||
rerun: use of rerun and read_dump commands
|
||||
rigid: rigid bodies modeled as independent or coupled
|
||||
shear: sideways shear applied to 2d solid, with and without a void
|
||||
snap: NVE dynamics for BCC tantalum crystal using SNAP potential
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,256 +0,0 @@
|
||||
"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws -
|
||||
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
Python library interface :h3
|
||||
|
||||
As described previously, the Python interface to LAMMPS consists of a
|
||||
Python "lammps" module, the source code for which is in
|
||||
python/lammps.py, which creates a "lammps" object, with a set of
|
||||
methods that can be invoked on that object. The sample Python code
|
||||
below assumes you have first imported the "lammps" module in your
|
||||
Python script, as follows:
|
||||
|
||||
from lammps import lammps :pre
|
||||
|
||||
These are the methods defined by the lammps module. If you look at
|
||||
the files src/library.cpp and src/library.h you will see they
|
||||
correspond one-to-one with calls you can make to the LAMMPS library
|
||||
from a C++ or C or Fortran program, and which are described on the
|
||||
"Howto library"_Howto_library.html doc page.
|
||||
|
||||
The python/examples directory has Python scripts which show how Python
|
||||
can run LAMMPS, grab data, change it, and put it back into LAMMPS.
|
||||
|
||||
lmp = lammps() # create a LAMMPS object using the default liblammps.so library
|
||||
# 4 optional args are allowed: name, cmdargs, ptr, comm
|
||||
lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
|
||||
lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
|
||||
lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library
|
||||
lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre
|
||||
|
||||
lmp.close() # destroy a LAMMPS object :pre
|
||||
|
||||
version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 :pre
|
||||
|
||||
lmp.file(file) # run an entire input script, file = "in.lj"
|
||||
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100"
|
||||
lmp.commands_list(cmdlist) # invoke commands in cmdlist = ["run 10", "run 20"]
|
||||
lmp.commands_string(multicmd) # invoke commands in multicmd = "run 10\nrun 20" :pre
|
||||
|
||||
size = lmp.extract_setting(name) # return data type info :pre
|
||||
|
||||
xlo = lmp.extract_global(name,type) # extract a global quantity
|
||||
# name = "boxxlo", "nlocal", etc
|
||||
# type = 0 = int
|
||||
# 1 = double :pre
|
||||
|
||||
boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box() # extract box info :pre
|
||||
|
||||
coords = lmp.extract_atom(name,type) # extract a per-atom quantity
|
||||
# name = "x", "type", etc
|
||||
# type = 0 = vector of ints
|
||||
# 1 = array of ints
|
||||
# 2 = vector of doubles
|
||||
# 3 = array of doubles :pre
|
||||
|
||||
eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
|
||||
v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
|
||||
# id = ID of compute or fix
|
||||
# style = 0 = global data
|
||||
# 1 = per-atom data
|
||||
# 2 = local data
|
||||
# type = 0 = scalar
|
||||
# 1 = vector
|
||||
# 2 = array
|
||||
# i,j = indices of value in global vector or array :pre
|
||||
|
||||
var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
|
||||
# name = name of variable
|
||||
# group = group ID (ignored for equal-style variables)
|
||||
# flag = 0 = equal-style variable
|
||||
# 1 = atom-style variable :pre
|
||||
|
||||
value = lmp.get_thermo(name) # return current value of a thermo keyword
|
||||
natoms = lmp.get_natoms() # total # of atoms as int :pre
|
||||
|
||||
flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
|
||||
lmp.reset_box(boxlo,boxhi,xy,yz,xz) # reset the simulation box size :pre
|
||||
|
||||
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
|
||||
data = lmp.gather_atoms_concat(name,type,count) # ditto, but concatenated atom values from each proc (unordered)
|
||||
data = lmp.gather_atoms_subset(name,type,count,ndata,ids) # ditto, but for subset of Ndata atoms with IDs :pre
|
||||
|
||||
lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID
|
||||
# name = "x", "charge", "type", etc
|
||||
# count = # of per-atom values, 1 or 3, etc :pre
|
||||
lmp.scatter_atoms_subset(name,type,count,ndata,ids,data) # ditto, but for subset of Ndata atoms with IDs :pre
|
||||
|
||||
lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed) # create N atoms with IDs, types, x, v, and image flags :pre
|
||||
|
||||
:line
|
||||
|
||||
The lines
|
||||
|
||||
from lammps import lammps
|
||||
lmp = lammps() :pre
|
||||
|
||||
create an instance of LAMMPS, wrapped in a Python class by the lammps
|
||||
Python module, and return an instance of the Python class as lmp. It
|
||||
is used to make all subsequent calls to the LAMMPS library.
|
||||
|
||||
Additional arguments to lammps() can be used to tell Python the name
|
||||
of the shared library to load or to pass arguments to the LAMMPS
|
||||
instance, the same as if LAMMPS were launched from a command-line
|
||||
prompt.
|
||||
|
||||
If the ptr argument is set like this:
|
||||
|
||||
lmp = lammps(ptr=lmpptr) :pre
|
||||
|
||||
then lmpptr must be an argument passed to Python via the LAMMPS
|
||||
"python"_python.html command, when it is used to define a Python
|
||||
function that is invoked by the LAMMPS input script. This mode of
|
||||
calling Python from LAMMPS is described in the "Python
|
||||
call"_Python_call.html doc page. The variable lmpptr refers to the
|
||||
instance of LAMMPS that called the embedded Python interpreter. Using
|
||||
it as an argument to lammps() allows the returned Python class
|
||||
instance "lmp" to make calls to that instance of LAMMPS. See the
|
||||
"python"_python.html command doc page for examples using this syntax.
|
||||
|
||||
Note that you can create multiple LAMMPS objects in your Python
|
||||
script, and coordinate and run multiple simulations, e.g.
|
||||
|
||||
from lammps import lammps
|
||||
lmp1 = lammps()
|
||||
lmp2 = lammps()
|
||||
lmp1.file("in.file1")
|
||||
lmp2.file("in.file2") :pre
|
||||
|
||||
The file(), command(), commands_list(), commands_string() methods
|
||||
allow an input script, a single command, or multiple commands to be
|
||||
invoked.
|
||||
|
||||
The extract_setting(), extract_global(), extract_box(),
|
||||
extract_atom(), extract_compute(), extract_fix(), and
|
||||
extract_variable() methods return values or pointers to data
|
||||
structures internal to LAMMPS.
|
||||
|
||||
For extract_global() see the src/library.cpp file for the list of
|
||||
valid names. New names could easily be added. A double or integer is
|
||||
returned. You need to specify the appropriate data type via the type
|
||||
argument.
|
||||
|
||||
For extract_atom(), a pointer to internal LAMMPS atom-based data is
|
||||
returned, which you can use via normal Python subscripting. See the
|
||||
extract() method in the src/atom.cpp file for a list of valid names.
|
||||
Again, new names could easily be added if the property you want is not
|
||||
listed. A pointer to a vector of doubles or integers, or a pointer to
|
||||
an array of doubles (double **) or integers (int **) is returned. You
|
||||
need to specify the appropriate data type via the type argument.
|
||||
|
||||
For extract_compute() and extract_fix(), the global, per-atom, or
|
||||
local data calculated by the compute or fix can be accessed. What is
|
||||
returned depends on whether the compute or fix calculates a scalar or
|
||||
vector or array. For a scalar, a single double value is returned. If
|
||||
the compute or fix calculates a vector or array, a pointer to the
|
||||
internal LAMMPS data is returned, which you can use via normal Python
|
||||
subscripting. The one exception is that for a fix that calculates a
|
||||
global vector or array, a single double value from the vector or array
|
||||
is returned, indexed by I (vector) or I and J (array). I,J are
|
||||
zero-based indices. The I,J arguments can be left out if not needed.
|
||||
See the "Howto output"_Howto_output.html doc page for a discussion of
|
||||
global, per-atom, and local data, and of scalar, vector, and array
|
||||
data types. See the doc pages for individual "computes"_compute.html
|
||||
and "fixes"_fix.html for a description of what they calculate and
|
||||
store.
|
||||
|
||||
For extract_variable(), an "equal-style or atom-style
|
||||
variable"_variable.html is evaluated and its result returned.
|
||||
|
||||
For equal-style variables a single double value is returned and the
|
||||
group argument is ignored. For atom-style variables, a vector of
|
||||
doubles is returned, one value per atom, which you can use via normal
|
||||
Python subscripting. The values will be zero for atoms not in the
|
||||
specified group.
|
||||
|
||||
The get_thermo() method returns the current value of a thermo
|
||||
keyword as a float.
|
||||
|
||||
The get_natoms() method returns the total number of atoms in the
|
||||
simulation, as an int.
|
||||
|
||||
The set_variable() method sets an existing string-style variable to a
|
||||
new string value, so that subsequent LAMMPS commands can access the
|
||||
variable.
|
||||
|
||||
The reset_box() method resets the size and shape of the simulation
|
||||
box, e.g. as part of restoring a previously extracted and saved state
|
||||
of a simulation.
|
||||
|
||||
The gather methods collect peratom info of the requested type (atom
|
||||
coords, atom types, forces, etc) from all processors, and returns the
|
||||
same vector of values to each calling processor. The scatter
|
||||
functions do the inverse. They distribute a vector of peratom values,
|
||||
passed by all calling processors, to individual atoms, which may be
|
||||
owned by different processors.
|
||||
|
||||
Note that the data returned by the gather methods,
|
||||
e.g. gather_atoms("x"), is different from the data structure returned
|
||||
by extract_atom("x") in four ways. (1) Gather_atoms() returns a
|
||||
vector which you index as x\[i\]; extract_atom() returns an array
|
||||
which you index as x\[i\]\[j\]. (2) Gather_atoms() orders the atoms
|
||||
by atom ID while extract_atom() does not. (3) Gather_atoms() returns
|
||||
a list of all atoms in the simulation; extract_atoms() returns just
|
||||
the atoms local to each processor. (4) Finally, the gather_atoms()
|
||||
data structure is a copy of the atom coords stored internally in
|
||||
LAMMPS, whereas extract_atom() returns an array that effectively
|
||||
points directly to the internal data. This means you can change
|
||||
values inside LAMMPS from Python by assigning a new values to the
|
||||
extract_atom() array. To do this with the gather_atoms() vector, you
|
||||
need to change values in the vector, then invoke the scatter_atoms()
|
||||
method.
|
||||
|
||||
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:
|
||||
|
||||
from ctypes import *
|
||||
natoms = lmp.get_natoms()
|
||||
n3 = 3*natoms
|
||||
x = (n3*c_double)()
|
||||
x\[0\] = x coord of atom with ID 1
|
||||
x\[1\] = y coord of atom with ID 1
|
||||
x\[2\] = z coord of atom with ID 1
|
||||
x\[3\] = x coord of atom with ID 2
|
||||
...
|
||||
x\[n3-1\] = z coord of atom with ID natoms
|
||||
lmp.scatter_atoms("x",1,3,x) :pre
|
||||
|
||||
Alternatively, you can just change values in the vector returned by
|
||||
the gather methods, since they are also ctypes vectors.
|
||||
|
||||
:line
|
||||
|
||||
As noted above, these Python class methods correspond one-to-one with
|
||||
the functions in the LAMMPS library interface in src/library.cpp and
|
||||
library.h. This means you can extend the Python wrapper via the
|
||||
following steps:
|
||||
|
||||
Add a new interface function to src/library.cpp and
|
||||
src/library.h. :ulb,l
|
||||
|
||||
Rebuild LAMMPS as a shared library. :l
|
||||
|
||||
Add a wrapper method to python/lammps.py for this interface
|
||||
function. :l
|
||||
|
||||
You should now be able to invoke the new interface function from a
|
||||
Python script. :l
|
||||
:ule
|
||||
@ -278,9 +278,10 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
||||
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
|
||||
"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
|
||||
"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics
|
||||
"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
|
||||
"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
|
||||
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
|
||||
"snap"_compute_sna_atom.html - bispectrum components and related quantities for a group of atoms
|
||||
"sna/atom"_compute_sna_atom.html - bispectrum components for each atom
|
||||
"snad/atom"_compute_sna_atom.html - derivative of bispectrum components for each atom
|
||||
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum components for each atom
|
||||
"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins
|
||||
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
|
||||
"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
|
||||
|
||||
@ -1,192 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
compute heat/flux command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID heat/flux ke-ID pe-ID stress-ID :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
heat/flux = style name of this compute command
|
||||
ke-ID = ID of a compute that calculates per-atom kinetic energy
|
||||
pe-ID = ID of a compute that calculates per-atom potential energy
|
||||
stress-ID = ID of a compute that calculates per-atom stress :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute myFlux all heat/flux myKE myPE myStress :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the heat flux vector based on
|
||||
contributions from atoms in the specified group. This can be used by
|
||||
itself to measure the heat flux through a set of atoms (e.g. a region
|
||||
between two thermostatted reservoirs held at different temperatures),
|
||||
or to calculate a thermal conductivity using the equilibrium
|
||||
Green-Kubo formalism.
|
||||
|
||||
For other non-equilibrium ways to compute a thermal conductivity, see
|
||||
the "Howto kappa"_Howto_kappa.html doc page.. These include use of
|
||||
the "fix thermal/conductivity"_fix_thermal_conductivity.html command
|
||||
for the Muller-Plathe method. Or the "fix heat"_fix_heat.html command
|
||||
which can add or subtract heat from groups of atoms.
|
||||
|
||||
The compute takes three arguments which are IDs of other
|
||||
"computes"_compute.html. One calculates per-atom kinetic energy
|
||||
({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the
|
||||
third calculates per-atom stress ({stress-ID}).
|
||||
|
||||
NOTE: These other computes should provide values for all the atoms in
|
||||
the group this compute specifies. That means the other computes could
|
||||
use the same group as this compute, or they can just use group "all"
|
||||
(or any group whose atoms are superset of the atoms in this compute's
|
||||
group). LAMMPS does not check for this.
|
||||
|
||||
The Green-Kubo formulas relate the ensemble average of the
|
||||
auto-correlation of the heat flux J to the thermal conductivity kappa:
|
||||
|
||||
:c,image(Eqs/heat_flux_J.jpg)
|
||||
|
||||
:c,image(Eqs/heat_flux_k.jpg)
|
||||
|
||||
Ei in the first term of the equation for J is the per-atom energy
|
||||
(potential and kinetic). This is calculated by the computes {ke-ID}
|
||||
and {pe-ID}. Si in the second term of the equation for J is the
|
||||
per-atom stress tensor calculated by the compute {stress-ID}. The
|
||||
tensor multiplies Vi as a 3x3 matrix-vector multiply to yield a
|
||||
vector. Note that as discussed below, the 1/V scaling factor in the
|
||||
equation for J is NOT included in the calculation performed by this
|
||||
compute; you need to add it for a volume appropriate to the atoms
|
||||
included in the calculation.
|
||||
|
||||
NOTE: The "compute pe/atom"_compute_pe_atom.html and "compute
|
||||
stress/atom"_compute_stress_atom.html commands have options for which
|
||||
terms to include in their calculation (pair, bond, etc). The heat
|
||||
flux calculation will thus include exactly the same terms. Normally
|
||||
you should use "compute stress/atom virial"_compute_stress_atom.html
|
||||
so as not to include a kinetic energy term in the heat flux.
|
||||
|
||||
This compute calculates 6 quantities and stores them in a 6-component
|
||||
vector. The first 3 components are the x, y, z components of the full
|
||||
heat flux vector, i.e. (Jx, Jy, Jz). The next 3 components are the x,
|
||||
y, z components of just the convective portion of the flux, i.e. the
|
||||
first term in the equation for J above.
|
||||
|
||||
:line
|
||||
|
||||
The heat flux can be output every so many timesteps (e.g. via the
|
||||
"thermo_style custom"_thermo_style.html command). Then as a
|
||||
post-processing operation, an auto-correlation can be performed, its
|
||||
integral estimated, and the Green-Kubo formula above evaluated.
|
||||
|
||||
The "fix ave/correlate"_fix_ave_correlate.html command can calculate
|
||||
the auto-correlation. The trap() function in the
|
||||
"variable"_variable.html command can calculate the integral.
|
||||
|
||||
An example LAMMPS input script for solid Ar is appended below. The
|
||||
result should be: average conductivity ~0.29 in W/mK.
|
||||
|
||||
:line
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global vector of length 6 (total heat flux
|
||||
vector, followed by convective heat flux vector), which can be
|
||||
accessed by indices 1-6. These values can be used by any command that
|
||||
uses global vector values from a compute as input. See the "Howto
|
||||
output"_Howto_output.html doc page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The vector values calculated by this compute are "extensive", meaning
|
||||
they scale with the number of atoms in the simulation. They can be
|
||||
divided by the appropriate volume to get a flux, which would then be
|
||||
an "intensive" value, meaning independent of the number of atoms in
|
||||
the simulation. Note that if the compute is "all", then the
|
||||
appropriate volume to divide by is the simulation box volume.
|
||||
However, if a sub-group is used, it should be the volume containing
|
||||
those atoms.
|
||||
|
||||
The vector values will be in energy*velocity "units"_units.html. Once
|
||||
divided by a volume the units will be that of flux, namely
|
||||
energy/area/time "units"_units.html
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix thermal/conductivity"_fix_thermal_conductivity.html,
|
||||
"fix ave/correlate"_fix_ave_correlate.html,
|
||||
"variable"_variable.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
# Sample LAMMPS input script for thermal conductivity of solid Ar :pre
|
||||
|
||||
units real
|
||||
variable T equal 70
|
||||
variable V equal vol
|
||||
variable dt equal 4.0
|
||||
variable p equal 200 # correlation length
|
||||
variable s equal 10 # sample interval
|
||||
variable d equal $p*$s # dump interval :pre
|
||||
|
||||
# convert from LAMMPS real units to SI :pre
|
||||
|
||||
variable kB equal 1.3806504e-23 # \[J/K\] Boltzmann
|
||||
variable kCal2J equal 4186.0/6.02214e23
|
||||
variable A2m equal 1.0e-10
|
||||
variable fs2s equal 1.0e-15
|
||||
variable convert equal $\{kCal2J\}*$\{kCal2J\}/$\{fs2s\}/$\{A2m\} :pre
|
||||
|
||||
# setup problem :pre
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 39.948
|
||||
pair_style lj/cut 13.0
|
||||
pair_coeff * * 0.2381 3.405
|
||||
timestep $\{dt\}
|
||||
thermo $d :pre
|
||||
|
||||
# equilibration and thermalization :pre
|
||||
|
||||
velocity all create $T 102486 mom yes rot yes dist gaussian
|
||||
fix NVT all nvt temp $T $T 10 drag 0.2
|
||||
run 8000 :pre
|
||||
|
||||
# thermal conductivity calculation, switch to NVE if desired :pre
|
||||
|
||||
#unfix NVT
|
||||
#fix NVE all nve :pre
|
||||
|
||||
reset_timestep 0
|
||||
compute myKE all ke/atom
|
||||
compute myPE all pe/atom
|
||||
compute myStress all stress/atom NULL virial
|
||||
compute flux all heat/flux myKE myPE myStress
|
||||
variable Jx equal c_flux\[1\]/vol
|
||||
variable Jy equal c_flux\[2\]/vol
|
||||
variable Jz equal c_flux\[3\]/vol
|
||||
fix JJ all ave/correlate $s $p $d &
|
||||
c_flux\[1\] c_flux\[2\] c_flux\[3\] type auto file J0Jt.dat ave running
|
||||
variable scale equal $\{convert\}/$\{kB\}/$T/$T/$V*$s*$\{dt\}
|
||||
variable k11 equal trap(f_JJ\[3\])*$\{scale\}
|
||||
variable k22 equal trap(f_JJ\[4\])*$\{scale\}
|
||||
variable k33 equal trap(f_JJ\[5\])*$\{scale\}
|
||||
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
|
||||
run 100000
|
||||
variable k equal (v_k11+v_k22+v_k33)/3.0
|
||||
variable ndens equal count(all)/vol
|
||||
print "average conductivity: $k\[W/mK\] @ $T K, $\{ndens\} /A^3" :pre
|
||||
@ -9,12 +9,14 @@
|
||||
compute sna/atom command :h3
|
||||
compute snad/atom command :h3
|
||||
compute snav/atom command :h3
|
||||
compute snap command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre
|
||||
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
sna/atom = style name of this compute command :l
|
||||
@ -41,12 +43,17 @@ keyword = {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
|
||||
|
||||
compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
|
||||
compute db all sna/atom 1.4 0.95 6 2.0 1.0
|
||||
compute vb all sna/atom 1.4 0.95 6 2.0 1.0 :pre
|
||||
compute vb all sna/atom 1.4 0.95 6 2.0 1.0
|
||||
compute snap all snap 1.4 0.95 6 2.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates a set of bispectrum components
|
||||
for each atom in a group.
|
||||
Define a computation that calculates a set of quantities related to the
|
||||
bispectrum components of the atoms in a group. These computes are
|
||||
used primarily for calculating the dependence of energy, force, and
|
||||
stress components on the linear coefficients in the
|
||||
"snap pair_style"_pair_snap.html, which is useful when training a
|
||||
SNAP potential to match target data.
|
||||
|
||||
Bispectrum components of an atom are order parameters characterizing
|
||||
the radial and angular distribution of neighbor atoms. The detailed
|
||||
@ -130,6 +137,27 @@ Again, the sum is over all atoms {i'} of atom type {I}. For each atom
|
||||
virial components, each atom type, and each bispectrum component. See
|
||||
section below on output for a detailed explanation.
|
||||
|
||||
Compute {snap} calculates a global array contains information related
|
||||
to all three of the above per-atom computes {sna/atom}, {snad/atom},
|
||||
and {snav/atom}. The first row of the array contains the summation of
|
||||
{sna/atom} over all atoms, but broken out by type. The last six rows
|
||||
of the array contain the summation of {snav/atom} over all atoms, broken
|
||||
out by type. In between these are 3*{N} rows containing the same values
|
||||
computed by {snad/atom} (these are already summed over all atoms and
|
||||
broken out by type). The element in the last column of each row contains
|
||||
the potential energy, force, or stress, according to the row.
|
||||
These quantities correspond to the user-specified reference potential
|
||||
that must be subtracted from the target data when fitting SNAP.
|
||||
The potential energy calculation uses the built in compute {thermo_pe}.
|
||||
The stress calculation uses a compute called {snap_press} that is
|
||||
automatically created behind the scenes, according to the following
|
||||
command:
|
||||
|
||||
compute snap_press all pressure NULL virial :pre
|
||||
|
||||
See section below on output for a detailed explanation of the data
|
||||
layout in the global array.
|
||||
|
||||
The value of all bispectrum components will be zero for atoms not in
|
||||
the group. Neighbor atoms not in the group do not contribute to the
|
||||
bispectrum of atoms in the group.
|
||||
@ -214,10 +242,25 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz},
|
||||
notation. Each of these sub-blocks contains one column for each
|
||||
bispectrum component, the same as for compute {sna/atom}
|
||||
|
||||
Compute {snap} evaluates a global array.
|
||||
The columns are arranged into
|
||||
{ntypes} blocks, listed in order of atom type {I}. Each block
|
||||
contains one column for each bispectrum component, the same as for compute
|
||||
{sna/atom}. A final column contains the corresponding energy, force component
|
||||
on an atom, or virial stress component. The rows of the array appear
|
||||
in the following order:
|
||||
|
||||
1 row: {sna/atom} quantities summed for all atoms of type {I}
|
||||
3*{N} rows: {snad/atom} quantities, with derivatives w.r.t. x, y, and z coordinate of atom {i} appearing in consecutive rows. The atoms are sorted based on atom ID.
|
||||
6 rows: {snav/atom} quantities summed for all atoms of type {I} :ul
|
||||
|
||||
For example, if {K} =30 and ntypes=1, the number of columns in the per-atom
|
||||
arrays generated by {sna/atom}, {snad/atom}, and {snav/atom}
|
||||
are 30, 90, and 180, respectively. With {quadratic} value=1,
|
||||
the numbers of columns are 930, 2790, and 5580, respectively.
|
||||
The number of columns in the global array generated by {snap}
|
||||
are 31, and 931, respectively, while the number of rows is
|
||||
1+3*{N}+6, where {N} is the total number of atoms.
|
||||
|
||||
If the {quadratic} keyword value is set to 1, then additional
|
||||
columns are generated, corresponding to
|
||||
|
||||
@ -1,77 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
compute spin command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID spin :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
spin = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute out_mag all spin :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates magnetic quantities for a system
|
||||
of atoms having spins.
|
||||
|
||||
This compute calculates 6 magnetic quantities.
|
||||
|
||||
The three first quantities are the x,y and z coordinates of the total
|
||||
magnetization.
|
||||
|
||||
The fourth quantity is the norm of the total magnetization.
|
||||
|
||||
The fifth quantity is the magnetic energy.
|
||||
|
||||
The sixth one is referred to as the spin temperature, according
|
||||
to the work of "(Nurdin)"_#Nurdin1.
|
||||
|
||||
The simplest way to output the results of the compute spin calculation
|
||||
is to define some of the quantities as variables, and to use the thermo and
|
||||
thermo_style commands, for example:
|
||||
|
||||
compute out_mag all spin :pre
|
||||
|
||||
variable mag_z equal c_out_mag\[3\]
|
||||
variable mag_norm equal c_out_mag\[4\]
|
||||
variable temp_mag equal c_out_mag\[6\] :pre
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre
|
||||
|
||||
This series of commands evaluates the total magnetization along z, the norm of
|
||||
the total magnetization, and the magnetic temperature. Three variables are
|
||||
assigned to those quantities. The thermo and thermo_style commands print them
|
||||
every 10 timesteps.
|
||||
|
||||
[Output info:]
|
||||
|
||||
The array values are "intensive". The array values will be in
|
||||
metal units ("units"_units.html).
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The {spin} compute is part of the SPIN package. This compute is only
|
||||
enabled if LAMMPS was built with this package. See the "Build
|
||||
package"_Build_package.html doc page for more info. The atom_style
|
||||
has to be "spin" for this compute to be valid.
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Nurdin1)
|
||||
[(Nurdin)] Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000)
|
||||
|
||||
392
doc/txt/fix.txt
392
doc/txt/fix.txt
@ -1,392 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
fix command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID style args :pre
|
||||
|
||||
ID = user-assigned name for the fix
|
||||
group-ID = ID of the group of atoms to apply the fix to
|
||||
style = one of a long list of possible style names (see below)
|
||||
args = arguments used by a particular style :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all nve
|
||||
fix 3 all nvt temp 300.0 300.0 0.01
|
||||
fix mine top setforce 0.0 NULL 0.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Set a fix that will be applied to a group of atoms. In LAMMPS, a
|
||||
"fix" is any operation that is applied to the system during
|
||||
timestepping or minimization. Examples include updating of atom
|
||||
positions and velocities due to time integration, controlling
|
||||
temperature, applying constraint forces to atoms, enforcing boundary
|
||||
conditions, computing diagnostics, etc. There are hundreds of fixes
|
||||
defined in LAMMPS and new ones can be added; see the
|
||||
"Modify"_Modify.html doc page for details.
|
||||
|
||||
Fixes perform their operations at different stages of the timestep.
|
||||
If 2 or more fixes operate at the same stage of the timestep, they are
|
||||
invoked in the order they were specified in the input script.
|
||||
|
||||
The ID of a fix can only contain alphanumeric characters and
|
||||
underscores.
|
||||
|
||||
Fixes can be deleted with the "unfix"_unfix.html command.
|
||||
|
||||
NOTE: The "unfix"_unfix.html command is the only way to turn off a
|
||||
fix; simply specifying a new fix with a similar style will not turn
|
||||
off the first one. This is especially important to realize for
|
||||
integration fixes. For example, using a "fix nve"_fix_nve.html
|
||||
command for a second run after using a "fix nvt"_fix_nh.html command
|
||||
for the first run, will not cancel out the NVT time integration
|
||||
invoked by the "fix nvt" command. Thus two time integrators would be
|
||||
in place!
|
||||
|
||||
If you specify a new fix with the same ID and style as an existing
|
||||
fix, the old fix is deleted and the new one is created (presumably
|
||||
with new settings). This is the same as if an "unfix" command were
|
||||
first performed on the old fix, except that the new fix is kept in the
|
||||
same order relative to the existing fixes as the old one originally
|
||||
was. Note that this operation also wipes out any additional changes
|
||||
made to the old fix via the "fix_modify"_fix_modify.html command.
|
||||
|
||||
The "fix modify"_fix_modify.html command allows settings for some
|
||||
fixes to be reset. See the doc page for individual fixes for details.
|
||||
|
||||
Some fixes store an internal "state" which is written to binary
|
||||
restart files via the "restart"_restart.html or
|
||||
"write_restart"_write_restart.html commands. This allows the fix to
|
||||
continue on with its calculations in a restarted simulation. See the
|
||||
"read_restart"_read_restart.html command for info on how to re-specify
|
||||
a fix in an input script that reads a restart file. See the doc pages
|
||||
for individual fixes for info on which ones can be restarted.
|
||||
|
||||
:line
|
||||
|
||||
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.
|
||||
|
||||
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 doc page will explain.
|
||||
|
||||
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.
|
||||
|
||||
When a fix quantity is accessed, as in many of the output commands
|
||||
discussed below, it can be referenced via the following bracket
|
||||
notation, where ID is the ID of the fix:
|
||||
|
||||
f_ID | entire scalar, vector, or array
|
||||
f_ID\[I\] | one element of vector, one column of array
|
||||
f_ID\[I\]\[J\] | one element of array :tb(s=|)
|
||||
|
||||
In other words, using one bracket reduces the dimension of the
|
||||
quantity once (vector -> scalar, array -> vector). Using two brackets
|
||||
reduces the dimension twice (array -> scalar). Thus a command that
|
||||
uses scalar fix values as input can also process elements of a vector
|
||||
or array.
|
||||
|
||||
Note that commands and "variables"_variable.html which use fix
|
||||
quantities typically do not allow for all kinds, e.g. a command may
|
||||
require a vector of values, not a scalar. This means there is no
|
||||
ambiguity about referring to a fix quantity as f_ID even if it
|
||||
produces, for example, both a scalar and vector. The doc pages for
|
||||
various commands explain the details.
|
||||
|
||||
:line
|
||||
|
||||
In LAMMPS, the values generated by a fix can be used in several ways:
|
||||
|
||||
Global values can be output via the "thermo_style
|
||||
custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command.
|
||||
Or the values can be referenced in a "variable equal"_variable.html or
|
||||
"variable atom"_variable.html command. :ulb,l
|
||||
|
||||
Per-atom values can be output via the "dump custom"_dump.html command.
|
||||
Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html
|
||||
command or reduced by the "compute reduce"_compute_reduce.html
|
||||
command. Or the per-atom values can be referenced in an "atom-style
|
||||
variable"_variable.html. :l
|
||||
|
||||
Local values can be reduced by the "compute
|
||||
reduce"_compute_reduce.html command, or histogrammed by the "fix
|
||||
ave/histo"_fix_ave_histo.html command. :l
|
||||
:ule
|
||||
|
||||
See the "Howto output"_Howto_output.html doc page for a summary of
|
||||
various LAMMPS output options, many of which involve fixes.
|
||||
|
||||
The results of fixes that calculate global quantities can be either
|
||||
"intensive" or "extensive" values. Intensive means the value is
|
||||
independent of the number of atoms in the simulation,
|
||||
e.g. temperature. Extensive means the value scales with the number of
|
||||
atoms in the simulation, e.g. total rotational kinetic energy.
|
||||
"Thermodynamic output"_thermo_style.html will normalize extensive
|
||||
values by the number of atoms in the system, depending on the
|
||||
"thermo_modify norm" setting. It will not normalize intensive values.
|
||||
If a fix value is accessed in another way, e.g. by a
|
||||
"variable"_variable.html, you may want to know whether it is an
|
||||
intensive or extensive value. See the doc page for individual fixes
|
||||
for further info.
|
||||
|
||||
:line
|
||||
|
||||
Each fix style has its own doc page which describes its arguments and
|
||||
what it does, as listed below. Here is an alphabetic list of fix
|
||||
styles available in LAMMPS. They are also listed in more compact form
|
||||
on the "Commands fix"_Commands_fix.html doc page.
|
||||
|
||||
There are also additional accelerated fix styles included in the
|
||||
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
|
||||
The individual style names on the "Commands fix"_Commands_fix.html doc
|
||||
page are followed by one or more of (g,i,k,o,t) to indicate which
|
||||
accelerated styles exist.
|
||||
|
||||
"adapt"_fix_adapt.html - change a simulation parameter over time
|
||||
"adapt/fep"_fix_adapt_fep.html - enhanced version of fix adapt
|
||||
"addforce"_fix_addforce.html - add a force to each atom
|
||||
"addtorque"_fix_addtorque.html - add a torque to a group of atoms
|
||||
"append/atoms"_fix_append_atoms.html - append atoms to a running simulation
|
||||
"atc"_fix_atc.html - initiates a coupled MD/FE simulation
|
||||
"atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
|
||||
"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
|
||||
"ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
|
||||
"ave/correlate"_fix_ave_correlate.html - compute/output time correlations
|
||||
"ave/correlate/long"_fix_ave_correlate_long.html -
|
||||
"ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
|
||||
"ave/histo/weight"_fix_ave_histo.html - weighted version of fix ave/histo
|
||||
"ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
|
||||
"aveforce"_fix_aveforce.html - add an averaged force to each atom
|
||||
"balance"_fix_balance.html - perform dynamic load-balancing
|
||||
"bocs"_fix_bocs.html - NPT style time integration with pressure correction
|
||||
"bond/break"_fix_bond_break.html - break bonds on the fly
|
||||
"bond/create"_fix_bond_create.html - create bonds on the fly
|
||||
"bond/react"_fix_bond_react.html - apply topology changes to model reactions
|
||||
"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
|
||||
"box/relax"_fix_box_relax.html - relax box size during energy minimization
|
||||
"client/md"_fix_client_md.html - MD client for client/server simulations
|
||||
"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
|
||||
"colvars"_fix_colvars.html - interface to the collective variables "Colvars" library
|
||||
"controller"_fix_controller.html - apply control loop feedback mechanism
|
||||
"deform"_fix_deform.html - change the simulation box size/shape
|
||||
"deposit"_fix_deposit.html - add new atoms above a surface
|
||||
"dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics
|
||||
"drag"_fix_drag.html - drag atoms towards a defined coordinate
|
||||
"drude"_fix_drude.html - part of Drude oscillator polarization model
|
||||
"drude/transform/direct"_fix_drude_transform.html - part of Drude oscillator polarization model
|
||||
"drude/transform/inverse"_fix_drude_transform.html - part of Drude oscillator polarization model
|
||||
"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
|
||||
"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations
|
||||
"efield"_fix_efield.html - impose electric field on system
|
||||
"ehex"_fix_ehex.html - enhanced heat exchange algorithm
|
||||
"electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
|
||||
"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
|
||||
"eos/cv"_fix_eos_cv.html -
|
||||
"eos/table"_fix_eos_table.html -
|
||||
"eos/table/rx"_fix_eos_table_rx.html -
|
||||
"evaporate"_fix_evaporate.html - remove atoms from simulation periodically
|
||||
"external"_fix_external.html - callback to an external driver program
|
||||
"ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat
|
||||
"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA
|
||||
"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux
|
||||
"freeze"_fix_freeze.html - freeze atoms in a granular simulation
|
||||
"gcmc"_fix_gcmc.html - grand canonical insertions/deletions
|
||||
"gld"_fix_gld.html - generalized Langevin dynamics integrator
|
||||
"gle"_fix_gle.html - generalized Langevin equation thermostat
|
||||
"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
|
||||
"grem"_fix_grem.html - implements the generalized replica exchange method
|
||||
"halt"_fix_halt.html - terminate a dynamics run or minimization
|
||||
"heat"_fix_heat.html - add/subtract momentum-conserving heat
|
||||
"hyper/global"_fix_hyper_global.html - global hyperdynamics
|
||||
"hyper/local"_fix_hyper_local.html - local hyperdynamics
|
||||
"imd"_fix_imd.html - implements the "Interactive MD" (IMD) protocol
|
||||
"indent"_fix_indent.html - impose force due to an indenter
|
||||
"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
|
||||
"langevin"_fix_langevin.html - Langevin temperature control
|
||||
"langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators
|
||||
"langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model
|
||||
"langevin/spin"_fix_langevin_spin.html - Langevin temperature control for a spin or spin-lattice system
|
||||
"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
|
||||
"lb/fluid"_fix_lb_fluid.html -
|
||||
"lb/momentum"_fix_lb_momentum.html -
|
||||
"lb/pc"_fix_lb_pc.html -
|
||||
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html -
|
||||
"lb/viscous"_fix_lb_viscous.html -
|
||||
"lineforce"_fix_lineforce.html - constrain atoms to move in a line
|
||||
"manifoldforce"_fix_manifoldforce.html - restrain atoms to a manifold during minimization
|
||||
"meso"_fix_meso.html - time integration for SPH/DPDE particles
|
||||
"meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
|
||||
"meso/stationary"_fix_meso_stationary.html -
|
||||
"momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
|
||||
"move"_fix_move.html - move atoms in a prescribed fashion
|
||||
"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
|
||||
"msst"_fix_msst.html - multi-scale shock technique (MSST) integration
|
||||
"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
|
||||
"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm
|
||||
"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
|
||||
"neb"_fix_neb.html - nudged elastic band (NEB) spring forces
|
||||
"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
|
||||
"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
|
||||
"nph/body"_fix_nph_body.html - NPH for body particles
|
||||
"nph/eff"_fix_nh_eff.html - NPH for nuclei and electrons in the electron force field model
|
||||
"nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
|
||||
"nphug"_fix_nphug.html - constant-stress Hugoniostat integration
|
||||
"npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
|
||||
"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
|
||||
"npt/body"_fix_npt_body.html - NPT for body particles
|
||||
"npt/eff"_fix_nh_eff.html - NPT for nuclei and electrons in the electron force field model
|
||||
"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
|
||||
"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow
|
||||
"nve"_fix_nve.html - constant NVE time integration
|
||||
"nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
|
||||
"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces
|
||||
"nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model
|
||||
"nve/body"_fix_nve_body.html - NVE for body particles
|
||||
"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models
|
||||
"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models
|
||||
"nve/eff"_fix_nve_eff.html - NVE for nuclei and electrons in the electron force field model
|
||||
"nve/limit"_fix_nve_limit.html - NVE with limited step length
|
||||
"nve/line"_fix_nve_line.html - NVE for line segments
|
||||
"nve/manifold/rattle"_fix_nve_manifold_rattle.html -
|
||||
"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
|
||||
"nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
|
||||
"nve/spin"_fix_nve_spin.html - NVE for a spin or spin-lattice system
|
||||
"nve/tri"_fix_nve_tri.html - NVE for triangles
|
||||
"nvk"_fix_nvk.html - constant kinetic energy time integration
|
||||
"nvt"_fix_nh.html - NVT time integration via Nose/Hoover
|
||||
"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
|
||||
"nvt/body"_fix_nvt_body.html - NVT for body particles
|
||||
"nvt/eff"_fix_nh_eff.html - NVE for nuclei and electrons in the electron force field model
|
||||
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -
|
||||
"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
|
||||
"nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model
|
||||
"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
|
||||
"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow
|
||||
"oneway"_fix_oneway.html - constrain particles on move in one direction
|
||||
"orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
|
||||
"orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
|
||||
"phonon"_fix_phonon.html - calculate dynamical matrix from MD simulations
|
||||
"pimd"_fix_pimd.html - Feynman path integral molecular dynamics
|
||||
"planeforce"_fix_planeforce.html - constrain atoms to move in a plane
|
||||
"plumed"_fix_plumed.html - wrapper on PLUMED free energy library
|
||||
"poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies
|
||||
"pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain
|
||||
"precession/spin"_fix_precession_spin.html -
|
||||
"press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat
|
||||
"print"_fix_print.html - print text and variables during a simulation
|
||||
"property/atom"_fix_property_atom.html - add customized per-atom values
|
||||
"python/invoke"_fix_python_invoke.html - call a Python function during a simulation
|
||||
"python/move"_fix_python_move.html - call a Python function during a simulation run
|
||||
"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator
|
||||
"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential
|
||||
"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method
|
||||
"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer
|
||||
"qeq/point"_fix_qeq.html - charge equilibration via point method
|
||||
"qeq/reax"_fix_qeq_reax.html - charge equilibration for ReaxFF potential
|
||||
"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
|
||||
"qeq/slater"_fix_qeq.html - charge equilibration via Slater method
|
||||
"qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling
|
||||
"qtb"_fix_qtb.html - implement quantum thermal bath scheme
|
||||
"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
|
||||
"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
|
||||
"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
|
||||
"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
|
||||
"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
|
||||
"rhok"_fix_rhok.html - add bias potential for long-range ordered systems
|
||||
"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
|
||||
"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
|
||||
"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
|
||||
"rigid/nph/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration
|
||||
"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration
|
||||
"rigid/npt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
|
||||
"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
|
||||
"rigid/nve/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
|
||||
"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration
|
||||
"rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
|
||||
"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
|
||||
"rx"_fix_rx.html -
|
||||
"saed/vtk"_fix_saed_vtk.html -
|
||||
"setforce"_fix_setforce.html - set the force on each atom
|
||||
"shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
|
||||
"shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting
|
||||
"smd"_fix_smd.html - applied a steered MD force to a group
|
||||
"smd/adjust_dt"_fix_smd_adjust_dt.html -
|
||||
"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html -
|
||||
"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html -
|
||||
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html -
|
||||
"smd/setvel"_fix_smd_setvel.html -
|
||||
"smd/wall_surface"_fix_smd_wall_surface.html -
|
||||
"spring"_fix_spring.html - apply harmonic spring force to group of atoms
|
||||
"spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms
|
||||
"spring/rg"_fix_spring_rg.html - spring on radius of gyration of group of atoms
|
||||
"spring/self"_fix_spring_self.html - spring from each atom to its origin
|
||||
"srd"_fix_srd.html - stochastic rotation dynamics (SRD)
|
||||
"store/force"_fix_store_force.html - store force on each atom
|
||||
"store/state"_fix_store_state.html - store attributes for each atom
|
||||
"tdpd/source"_fix_dpd_source.html -
|
||||
"temp/berendsen"_fix_temp_berendsen.html - temperature control by Berendsen thermostat
|
||||
"temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
|
||||
"temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
|
||||
"temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling
|
||||
"temp/rescale/eff"_fix_temp_rescale_eff.html - temperature control by velocity rescaling in the electron force field model
|
||||
"tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
|
||||
"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
|
||||
"ti/spring"_fix_ti_spring.html -
|
||||
"tmd"_fix_tmd.html - guide a group of atoms to a new configuration
|
||||
"ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
|
||||
"ttm/mod"_fix_ttm.html - enhanced two-temperature model with additional options
|
||||
"tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters
|
||||
"vector"_fix_vector.html - accumulate a global vector every N timesteps
|
||||
"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation
|
||||
"viscous"_fix_viscous.html - viscous damping for granular simulations
|
||||
"wall/body/polygon"_fix_wall_body_polygon.html -
|
||||
"wall/body/polyhedron"_fix_wall_body_polyhedron.html -
|
||||
"wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
|
||||
"wall/ees"_fix_wall_ees.html - wall for ellipsoidal particles
|
||||
"wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
|
||||
"wall/gran/region"_fix_wall_gran_region.html -
|
||||
"wall/harmonic"_fix_wall.html - harmonic spring wall
|
||||
"wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall
|
||||
"wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
|
||||
"wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall
|
||||
"wall/morse"_fix_wall.html - Morse potential wall
|
||||
"wall/piston"_fix_wall_piston.html - moving reflective piston wall
|
||||
"wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
|
||||
"wall/region"_fix_wall_region.html - use region surface as wall
|
||||
"wall/region/ees"_fix_wall_ees.html - use region surface as wall for ellipsoidal particles
|
||||
"wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Some fix styles are part of specific packages. They are only enabled
|
||||
if LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info. The doc pages for
|
||||
individual fixes tell if it is part of a package.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"unfix"_unfix.html, "fix_modify"_fix_modify.html
|
||||
|
||||
[Default:] none
|
||||
@ -80,7 +80,7 @@ command creates a per-atom array with 6 columns:
|
||||
|
||||
compute my_stress all stress/atom NULL
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress\[*\]
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[1\] &
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[2\] &
|
||||
c_my_stress\[3\] c_my_stress\[4\] &
|
||||
c_my_stress\[5\] c_my_stress\[6\] :pre
|
||||
|
||||
|
||||
@ -1,295 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
fix deposit command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID deposit N type M seed keyword values ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
deposit = style name of this fix command :l
|
||||
N = # of atoms or molecules to insert :l
|
||||
type = atom type to assign to inserted atoms (offset for molecule insertion) :l
|
||||
M = insert a single atom or molecule every M steps :l
|
||||
seed = random # seed (positive integer) :l
|
||||
one or more keyword/value pairs may be appended to args :l
|
||||
keyword = {region} or {id} or {global} or {local} or {near} or {gaussian} or {attempt} or {rate} or {vx} or {vy} or {vz} or {mol} or {rigid} or {shake} or {units} :l
|
||||
{region} value = region-ID
|
||||
region-ID = ID of region to use as insertion volume
|
||||
{id} value = {max} or {next}
|
||||
max = atom ID for new atom(s) is max ID of all current atoms plus one
|
||||
next = atom ID for new atom(s) increments by one for every deposition
|
||||
{global} values = lo hi
|
||||
lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
|
||||
{local} values = lo hi delta
|
||||
lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
|
||||
delta = lateral distance within which a neighbor is considered "nearby" (distance units)
|
||||
{near} value = R
|
||||
R = only insert atom/molecule if further than R from existing particles (distance units)
|
||||
{gaussian} values = xmid ymid zmid sigma
|
||||
xmid,ymid,zmid = center of the gaussian distribution (distance units)
|
||||
sigma = width of gaussian distribution (distance units)
|
||||
{attempt} value = Q
|
||||
Q = attempt a single insertion up to Q times
|
||||
{rate} value = V
|
||||
V = z velocity (y in 2d) at which insertion volume moves (velocity units)
|
||||
{vx} values = vxlo vxhi
|
||||
vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
|
||||
{vy} values = vylo vyhi
|
||||
vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
|
||||
{vz} values = vzlo vzhi
|
||||
vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
|
||||
{target} values = tx ty tz
|
||||
tx,ty,tz = location of target point (distance units)
|
||||
{mol} value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
|
||||
{molfrac} values = f1 f2 ... fN
|
||||
f1 to fN = relative probability of creating each of N molecules in template-ID
|
||||
{rigid} value = fix-ID
|
||||
fix-ID = ID of "fix rigid/small"_fix_rigid.html command
|
||||
{shake} value = fix-ID
|
||||
fix-ID = ID of "fix shake"_fix_shake.html command
|
||||
{units} value = {lattice} or {box}
|
||||
lattice = the geometry is defined in lattice units
|
||||
box = the geometry is defined in simulation box units :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
|
||||
fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
|
||||
fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice
|
||||
fix 5 insert deposit 200 2 100 777 region disk gaussian 5.0 5.0 9.0 1.0 units box :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Insert a single atom or molecule into the simulation domain every M
|
||||
timesteps until N atoms or molecules have been inserted. This is
|
||||
useful for simulating deposition onto a surface. For the remainder of
|
||||
this doc page, a single inserted atom or molecule is referred to as a
|
||||
"particle".
|
||||
|
||||
If inserted particles are individual atoms, they are assigned the
|
||||
specified atom type. If they are molecules, the type of each atom in
|
||||
the inserted molecule is specified in the file read by the
|
||||
"molecule"_molecule.html command, and those values are added to the
|
||||
specified atom type. E.g. if the file specifies atom types 1,2,3, and
|
||||
those are the atom types you want for inserted molecules, then specify
|
||||
{type} = 0. If you specify {type} = 2, the in the inserted molecule
|
||||
will have atom types 3,4,5.
|
||||
|
||||
All atoms in the inserted particle are assigned to two groups: the
|
||||
default group "all" and the group specified in the fix deposit command
|
||||
(which can also be "all").
|
||||
|
||||
If you are computing temperature values which include inserted
|
||||
particles, you will want to use the
|
||||
"compute_modify"_compute_modify.html dynamic option, which insures the
|
||||
current number of atoms is used as a normalizing factor each time the
|
||||
temperature is computed.
|
||||
|
||||
Care must be taken that inserted particles are not too near existing
|
||||
atoms, using the options described below. When inserting particles
|
||||
above a surface in a non-periodic box (see the
|
||||
"boundary"_boundary.html command), the possibility of a particle
|
||||
escaping the surface and flying upward should be considered, since the
|
||||
particle may be lost or the box size may grow infinitely large. A
|
||||
"fix wall/reflect"_fix_wall_reflect.html command can be used to
|
||||
prevent this behavior. Note that if a shrink-wrap boundary is used,
|
||||
it is OK to insert the new particle outside the box, however the box
|
||||
will immediately be expanded to include the new particle. When
|
||||
simulating a sputtering experiment it is probably more realistic to
|
||||
ignore those atoms using the "thermo_modify"_thermo_modify.html
|
||||
command with the {lost ignore} option and a fixed
|
||||
"boundary"_boundary.html.
|
||||
|
||||
The fix deposit command must use the {region} keyword to define an
|
||||
insertion volume. The specified region must have been previously
|
||||
defined with a "region"_region.html command. It must be defined with
|
||||
side = {in}.
|
||||
|
||||
NOTE: LAMMPS checks that the specified region is wholly inside the
|
||||
simulation box. It can do this correctly for orthonormal simulation
|
||||
boxes. However for "triclinic boxes"_Howto_triclinic.html, it only
|
||||
tests against the larger orthonormal box that bounds the tilted
|
||||
simulation box. If the specified region includes volume outside the
|
||||
tilted box, then an insertion will likely fail, leading to a "lost
|
||||
atoms" error. Thus for triclinic boxes you should insure the
|
||||
specified region is wholly inside the simulation box.
|
||||
|
||||
The locations of inserted particles are taken from uniform distributed
|
||||
random numbers, unless the {gaussian} keyword is used. Then the
|
||||
individual coordinates are taken from a gaussian distribution of
|
||||
width {sigma} centered on {xmid,ymid,zmid}.
|
||||
|
||||
Individual atoms are inserted, unless the {mol} keyword is used. It
|
||||
specifies a {template-ID} previously defined using the
|
||||
"molecule"_molecule.html command, which reads files that define one or
|
||||
more molecules. The coordinates, atom types, charges, etc, as well as
|
||||
any bond/angle/etc and special neighbor information for the molecule
|
||||
can be specified in the molecule file. See the
|
||||
"molecule"_molecule.html command for details. The only settings
|
||||
required to be in each file are the coordinates and types of atoms in
|
||||
the molecule.
|
||||
|
||||
If the molecule template contains more than one molecule, the relative
|
||||
probability of depositing each molecule can be specified by the
|
||||
{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are
|
||||
specified, where N is the number of molecules in the template. Each
|
||||
time a molecule is deposited, a random number is used to sample from
|
||||
the list of relative probabilities. The N values must sum to 1.0.
|
||||
|
||||
If you wish to insert molecules via the {mol} keyword, that will be
|
||||
treated as rigid bodies, use the {rigid} keyword, specifying as its
|
||||
value the ID of a separate "fix rigid/small"_fix_rigid.html
|
||||
command which also appears in your input script.
|
||||
|
||||
NOTE: If you wish the new rigid molecules (and other rigid molecules)
|
||||
to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
|
||||
or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
|
||||
"fix_modify dynamic/dof yes" command for the rigid fix. This is to
|
||||
inform that fix that the molecule count will vary dynamically.
|
||||
|
||||
If you wish to insert molecules via the {mol} keyword, that will have
|
||||
their bonds or angles constrained via SHAKE, use the {shake} keyword,
|
||||
specifying as its value the ID of a separate "fix
|
||||
shake"_fix_shake.html command which also appears in your input script.
|
||||
|
||||
Each timestep a particle is inserted, the coordinates for its atoms
|
||||
are chosen as follows. For insertion of individual atoms, the
|
||||
"position" referred to in the following description is the coordinate
|
||||
of the atom. For insertion of molecule, the "position" is the
|
||||
geometric center of the molecule; see the "molecule"_molecule.html doc
|
||||
page for details. A random rotation of the molecule around its center
|
||||
point is performed, which determines the coordinates all the
|
||||
individual atoms.
|
||||
|
||||
A random position within the region insertion volume is generated. If
|
||||
neither the {global} or {local} keyword is used, the random position
|
||||
is the trial position. If the {global} keyword is used, the random
|
||||
x,y values are used, but the z position of the new particle is set
|
||||
above the highest current atom in the simulation by a distance
|
||||
randomly chosen between lo/hi. (For a 2d simulation, this is done for
|
||||
the y position.) If the {local} keyword is used, the z position is
|
||||
set a distance between lo/hi above the highest current atom in the
|
||||
simulation that is "nearby" the chosen x,y position. In this context,
|
||||
"nearby" means the lateral distance (in x,y) between the new and old
|
||||
particles is less than the {delta} setting.
|
||||
|
||||
Once a trial x,y,z position has been selected, the insertion is only
|
||||
performed if no current atom in the simulation is within a distance R
|
||||
of any atom in the new particle, including the effect of periodic
|
||||
boundary conditions if applicable. R is defined by the {near}
|
||||
keyword. Note that the default value for R is 0.0, which will allow
|
||||
atoms to strongly overlap if you are inserting where other atoms are
|
||||
present. This distance test is performed independently for each atom
|
||||
in an inserted molecule, based on the randomly rotated configuration
|
||||
of the molecule. If this test fails, a new random position within the
|
||||
insertion volume is chosen and another trial is made. Up to Q
|
||||
attempts are made. If the particle is not successfully inserted,
|
||||
LAMMPS prints a warning message.
|
||||
|
||||
NOTE: If you are inserting finite size particles or a molecule or
|
||||
rigid body consisting of finite-size particles, then you should
|
||||
typically set R larger than the distance at which any inserted
|
||||
particle may overlap with either a previously inserted particle or an
|
||||
existing particle. LAMMPS will issue a warning if R is smaller than
|
||||
this value, based on the radii of existing and inserted particles.
|
||||
|
||||
The {rate} option moves the insertion volume in the z direction (3d)
|
||||
or y direction (2d). This enables particles to be inserted from a
|
||||
successively higher height over time. Note that this parameter is
|
||||
ignored if the {global} or {local} keywords are used, since those
|
||||
options choose a z-coordinate for insertion independently.
|
||||
|
||||
The vx, vy, and vz components of velocity for the inserted particle
|
||||
are set using the values specified for the {vx}, {vy}, and {vz}
|
||||
keywords. Note that normally, new particles should be a assigned a
|
||||
negative vertical velocity so that they move towards the surface. For
|
||||
molecules, the same velocity is given to every particle (no rotation
|
||||
or bond vibration).
|
||||
|
||||
If the {target} option is used, the velocity vector of the inserted
|
||||
particle is changed so that it points from the insertion position
|
||||
towards the specified target point. The magnitude of the velocity is
|
||||
unchanged. This can be useful, for example, for simulating a
|
||||
sputtering process. E.g. the target point can be far away, so that
|
||||
all incident particles strike the surface as if they are in an
|
||||
incident beam of particles at a prescribed angle.
|
||||
|
||||
The {id} keyword determines how atom IDs and molecule IDs are assigned
|
||||
to newly deposited particles. Molecule IDs are only assigned if
|
||||
molecules are being inserted. For the {max} setting, the atom and
|
||||
molecule IDs of all current atoms are checked. Atoms in the new
|
||||
particle are assigned IDs starting with the current maximum plus one.
|
||||
If a molecule is inserted it is assigned an ID = current maximum plus
|
||||
one. This means that if particles leave the system, the new IDs may
|
||||
replace the lost ones. For the {next} setting, the maximum ID of any
|
||||
atom and molecule is stored at the time the fix is defined. Each time
|
||||
a new particle is added, this value is incremented to assign IDs to
|
||||
the new atom(s) or molecule. Thus atom and molecule IDs for deposited
|
||||
particles will be consecutive even if particles leave the system over
|
||||
time.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
for the other deposition parameters. A {box} value selects standard
|
||||
distance units as defined by the "units"_units.html command,
|
||||
e.g. Angstroms for units = real or metal. A {lattice} value means the
|
||||
distance units are in lattice spacings. The "lattice"_lattice.html
|
||||
command must have been previously used to define the lattice spacing.
|
||||
Note that the units choice affects all the keyword values that have
|
||||
units of distance or velocity.
|
||||
|
||||
NOTE: If you are monitoring the temperature of a system where the atom
|
||||
count is changing due to adding particles, you typically should use
|
||||
the "compute_modify dynamic yes"_compute_modify.html command for the
|
||||
temperature compute you are using.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
This fix writes the state of the deposition to "binary restart
|
||||
files"_restart.html. This includes information about how many
|
||||
particles have been deposited, the random number generator seed, the
|
||||
next timestep for deposition, etc. See the
|
||||
"read_restart"_read_restart.html 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: For this to work correctly, the timestep must [not] be changed
|
||||
after reading the restart with "reset_timestep"_reset_timestep.html.
|
||||
The fix will try to detect it and stop with an error.
|
||||
|
||||
None of the "fix_modify"_fix_modify.html options are relevant to this
|
||||
fix. No global or per-atom quantities are stored by this fix for
|
||||
access by various "output commands"_Howto_output.html. No parameter
|
||||
of this fix can be used with the {start/stop} keywords of the
|
||||
"run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the MISC package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
The specified insertion region cannot be a "dynamic" region, as
|
||||
defined by the "region"_region.html command.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix pour"_fix_pour.html, "region"_region.html
|
||||
|
||||
[Default:]
|
||||
|
||||
Insertions are performed for individual atoms, i.e. no {mol} setting
|
||||
is defined. If the {mol} keyword is used, the default for {molfrac}
|
||||
is an equal probabilities for all molecules in the template.
|
||||
Additional option defaults are id = max, delta = 0.0, near = 0.0,
|
||||
attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0,
|
||||
and units = lattice.
|
||||
@ -1,63 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
fix nve/dot command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID nve/dot :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
nve/dot = style name of this fix command :l
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all nve/dot :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
|
||||
to a group of atoms, but without Langevin dynamics.
|
||||
This command performs Molecular dynamics (MD)
|
||||
via a velocity-Verlet algorithm and an evolution operator that rotates
|
||||
the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
|
||||
|
||||
This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
without damping and noise and can be used to determine the stability range
|
||||
in a NVE ensemble prior to using the Langevin-type DOTC-integrator
|
||||
(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
|
||||
The command is equivalent to the "fix nve"_fix_nve.html.
|
||||
The particles are always considered to have a finite size.
|
||||
|
||||
An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
|
||||
Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3.
|
||||
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
These pair styles can only be used if LAMMPS was built with the
|
||||
"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
|
||||
See the "Build package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "fix nve"_fix_nve.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Davidchack1)
|
||||
[(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
|
||||
:link(Miller1)
|
||||
[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
|
||||
:link(Henrich3)
|
||||
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
@ -1,143 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
fix nve/dotc/langevin command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
nve/dotc/langevin = style name of this fix command :l
|
||||
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
|
||||
damp = damping parameter (time units) :l
|
||||
seed = random number seed to use for white noise (positive integer) :l
|
||||
keyword = {angmom} :l
|
||||
{angmom} value = factor
|
||||
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
|
||||
as described in "(Davidchack)"_#Davidchack2
|
||||
to a group of atoms, which models an interaction with an implicit background
|
||||
solvent. This command performs Brownian dynamics (BD)
|
||||
via a technique that splits the integration into a deterministic Hamiltonian
|
||||
part and the Ornstein-Uhlenbeck process for noise and damping.
|
||||
The quaternion degrees of freedom are updated though an evolution
|
||||
operator which performs a rotation in quaternion space, preserves
|
||||
the quaternion norm and is akin to "(Miller)"_#Miller2.
|
||||
|
||||
In terms of syntax this command has been closely modelled on the
|
||||
"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
|
||||
the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
|
||||
one single command. The main feature is improved stability
|
||||
over the standard integrator, permitting slightly larger timestep sizes.
|
||||
|
||||
NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
|
||||
also time integration of the translational and quaternion degrees of freedom.
|
||||
|
||||
The total force on each atom will have the form:
|
||||
|
||||
F = Fc + Ff + Fr
|
||||
Ff = - (m / damp) v
|
||||
Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
|
||||
|
||||
Fc is the conservative force computed via the usual inter-particle
|
||||
interactions ("pair_style"_pair_style.html,
|
||||
"bond_style"_bond_style.html, etc).
|
||||
|
||||
The Ff and Fr terms are implicitly taken into account by this fix
|
||||
on a per-particle basis.
|
||||
|
||||
Ff is a frictional drag or viscous damping term proportional to the
|
||||
particle's velocity. The proportionality constant for each atom is
|
||||
computed as m/damp, where m is the mass of the particle and damp is
|
||||
the damping factor specified by the user.
|
||||
|
||||
Fr is a force due to solvent atoms at a temperature T randomly bumping
|
||||
into the particle. As derived from the fluctuation/dissipation
|
||||
theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
|
||||
dt damp), where Kb is the Boltzmann constant, T is the desired
|
||||
temperature, m is the mass of the particle, dt is the timestep size,
|
||||
and damp is the damping factor. Random numbers are used to randomize
|
||||
the direction and magnitude of this force as described in
|
||||
"(Dunweg)"_#Dunweg3, where a uniform random number is used (instead of
|
||||
a Gaussian random number) for speed.
|
||||
|
||||
:line
|
||||
|
||||
{Tstart} and {Tstop} have to be constant values, i.e. they cannot
|
||||
be variables. If used together with the oxDNA force field for
|
||||
coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
|
||||
corresponds to T = 300 K.
|
||||
|
||||
The {damp} parameter is specified in time units and determines how
|
||||
rapidly the temperature is relaxed. For example, a value of 0.03
|
||||
means to relax the temperature in a timespan of (roughly) 0.03 time
|
||||
units tau (see the "units"_units.html command).
|
||||
The damp factor can be thought of as inversely related to the
|
||||
viscosity of the solvent, i.e. a small relaxation time implies a
|
||||
hi-viscosity solvent and vice versa. See the discussion about gamma
|
||||
and viscosity in the documentation for the "fix
|
||||
viscous"_fix_viscous.html command for more details.
|
||||
Note that the value 78.9375 in the second example above corresponds
|
||||
to a diffusion constant, which is about an order of magnitude larger
|
||||
than realistic ones. This has been used to sample configurations faster
|
||||
in Brownian dynamics simulations.
|
||||
|
||||
The random # {seed} must be a positive integer. A Marsaglia random
|
||||
number generator is used. Each processor uses the input seed to
|
||||
generate its own unique seed and its own stream of random numbers.
|
||||
Thus the dynamics of the system will not be identical on two runs on
|
||||
different numbers of processors.
|
||||
|
||||
The keyword/value option has to be used in the following way:
|
||||
|
||||
This fix has to be used together with the {angmom} keyword. The
|
||||
particles are always considered to have a finite size.
|
||||
The keyword {angmom} enables thermostatting of the rotational degrees of
|
||||
freedom in addition to the usual translational degrees of freedom.
|
||||
|
||||
The scale factor after the {angmom} keyword gives the ratio of the rotational to
|
||||
the translational friction coefficient.
|
||||
|
||||
An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
|
||||
Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4.
|
||||
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
These pair styles can only be used if LAMMPS was built with the
|
||||
"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
|
||||
See the "Build package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Davidchack2)
|
||||
[(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
|
||||
:link(Miller2)
|
||||
[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
|
||||
:link(Dunweg3)
|
||||
[(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
|
||||
:link(Henrich4)
|
||||
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
@ -1,116 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
fix precession/spin command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group precession/spin style args :pre
|
||||
|
||||
ID, group are documented in "fix"_fix.html command :ulb,l
|
||||
precession/spin = style name of this fix command :l
|
||||
style = {zeeman} or {anisotropy} or {cubic} :l
|
||||
{zeeman} args = H x y z
|
||||
H = intensity of the magnetic field (in Tesla)
|
||||
x y z = vector direction of the field
|
||||
{anisotropy} args = K x y z
|
||||
K = intensity of the magnetic anisotropy (in eV)
|
||||
x y z = vector direction of the anisotropy :pre
|
||||
{cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z
|
||||
K1 and K2c = intensity of the magnetic anisotropy (in eV)
|
||||
n1x to n3z = three direction vectors of the cubic anisotropy :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
|
||||
fix 1 3 precession/spin anisotropy 0.001 0.0 0.0 1.0
|
||||
fix 1 iron precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
|
||||
fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix applies a precession torque to each magnetic spin in the group.
|
||||
|
||||
Style {zeeman} is used for the simulation of the interaction
|
||||
between the magnetic spins in the defined group and an external
|
||||
magnetic field:
|
||||
|
||||
:c,image(Eqs/force_spin_zeeman.jpg)
|
||||
|
||||
with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T
|
||||
in metal units).
|
||||
|
||||
Style {anisotropy} is used to simulate an easy axis or an easy plane
|
||||
for the magnetic spins in the defined group:
|
||||
|
||||
:c,image(Eqs/force_spin_aniso.jpg)
|
||||
|
||||
with n defining the direction of the anisotropy, and K (in eV) its intensity.
|
||||
If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
|
||||
|
||||
Style {cubic} is used to simulate a cubic anisotropy, with three
|
||||
possible easy axis for the magnetic spins in the defined group:
|
||||
|
||||
:c,image(Eqs/fix_spin_cubic.jpg)
|
||||
|
||||
with K1 and K2c (in eV) the intensity coefficients and
|
||||
n1, n2 and n3 defining the three anisotropic directions
|
||||
defined by the command (from n1x to n3z).
|
||||
For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an
|
||||
iron type anisotropy (easy axis along the (001)-type cube
|
||||
edges), and K1 > 0 defines a nickel type anisotropy (easy axis
|
||||
along the (111)-type cube diagonals).
|
||||
K2^c > 0 also defines easy axis along the (111)-type cube
|
||||
diagonals.
|
||||
See chapter 2 of "(Skomski)"_#Skomski1 for more details on cubic
|
||||
anisotropies.
|
||||
|
||||
In all cases, the choice of (x y z) only imposes the vector
|
||||
directions for the forces. Only the direction of the vector is
|
||||
important; it's length is ignored (the entered vectors are
|
||||
normalized).
|
||||
|
||||
Those styles can be combined within one single command line.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
By default, the energy associated to this fix is not added to the potential
|
||||
energy of the system.
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this fix
|
||||
to add this magnetic potential energy to the potential energy of the system,
|
||||
|
||||
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes :pre
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
"output commands"_Howto_output.html.
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The {precession/spin} style is part of the SPIN package. This style
|
||||
is only enabled if LAMMPS was built with this package, and if the
|
||||
atom_style "spin" was declared. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"atom_style spin"_atom_style.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Skomski1)
|
||||
[(Skomski)] Skomski, R. (2008). Simple models of magnetism.
|
||||
Oxford University Press.
|
||||
@ -1,495 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
kspace_style command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
kspace_style style value :pre
|
||||
|
||||
style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} or {scafacos} :ulb,l
|
||||
{none} value = none
|
||||
{ewald} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{ewald/disp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{ewald/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{ewald/dipole} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{ewald/dipole/spin} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/cg} values = accuracy (smallq)
|
||||
accuracy = desired relative error in forces
|
||||
smallq = cutoff for charges to be considered (optional) (charge units)
|
||||
{pppm/disp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/tip4p} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/disp/tip4p} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/gpu} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/intel} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/kk} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/cg/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/disp/intel} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/tip4p/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/stagger} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/dipole} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/dipole/spin} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{msm} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{msm/cg} value = accuracy (smallq)
|
||||
accuracy = desired relative error in forces
|
||||
smallq = cutoff for charges to be considered (optional) (charge units)
|
||||
{msm/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{msm/cg/omp} value = accuracy (smallq)
|
||||
accuracy = desired relative error in forces
|
||||
smallq = cutoff for charges to be considered (optional) (charge units)
|
||||
{scafacos} values = method accuracy
|
||||
method = fmm or p2nfft or p3m or ewald or direct
|
||||
accuracy = desired relative error in forces :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
kspace_style pppm 1.0e-4
|
||||
kspace_style pppm/cg 1.0e-5 1.0e-6
|
||||
kspace style msm 1.0e-4
|
||||
kspace style scafacos fmm 1.0e-4
|
||||
kspace_style none :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a long-range solver for LAMMPS to use each timestep to compute
|
||||
long-range Coulombic interactions or long-range 1/r^6 interactions.
|
||||
Most of the long-range solvers perform their computation in K-space,
|
||||
hence the name of this command.
|
||||
|
||||
When such a solver is used in conjunction with an appropriate pair
|
||||
style, the cutoff for Coulombic or 1/r^N interactions is effectively
|
||||
infinite. If the Coulombic case, this means each charge in the system
|
||||
interacts with charges in an infinite array of periodic images of the
|
||||
simulation domain.
|
||||
|
||||
Note that using a long-range solver requires use of a matching "pair
|
||||
style"_pair_style.html to perform consistent short-range pairwise
|
||||
calculations. This means that the name of the pair style contains a
|
||||
matching keyword to the name of the KSpace style, as in this table:
|
||||
|
||||
Pair style : KSpace style
|
||||
coul/long : ewald or pppm
|
||||
coul/msm : msm
|
||||
lj/long or buck/long : disp (for dispersion)
|
||||
tip4p/long : tip4p :tb(s=:,ea=c)
|
||||
|
||||
:line
|
||||
|
||||
The {ewald} style performs a standard Ewald summation as described in
|
||||
any solid-state physics text.
|
||||
|
||||
The {ewald/disp} style adds a long-range dispersion sum option for
|
||||
1/r^6 potentials and is useful for simulation of interfaces
|
||||
"(Veld)"_#Veld. It also performs standard Coulombic Ewald summations,
|
||||
but in a more efficient manner than the {ewald} style. The 1/r^6
|
||||
capability means that Lennard-Jones or Buckingham potentials can be
|
||||
used without a cutoff, i.e. they become full long-range potentials.
|
||||
The {ewald/disp} style can also be used with point-dipoles, see
|
||||
"(Toukmaji)"_#Toukmaji.
|
||||
|
||||
The {ewald/dipole} style adds long-range standard Ewald summations
|
||||
for dipole-dipole interactions, see "(Toukmaji)"_#Toukmaji.
|
||||
|
||||
The {ewald/dipole/spin} style adds long-range standard Ewald
|
||||
summations for magnetic dipole-dipole interactions between
|
||||
magnetic spins.
|
||||
|
||||
:line
|
||||
|
||||
The {pppm} style invokes a particle-particle particle-mesh solver
|
||||
"(Hockney)"_#Hockney which maps atom charge to a 3d mesh, uses 3d FFTs
|
||||
to solve Poisson's equation on the mesh, then interpolates electric
|
||||
fields on the mesh points back to the atoms. It is closely related to
|
||||
the particle-mesh Ewald technique (PME) "(Darden)"_#Darden used in
|
||||
AMBER and CHARMM. The cost of traditional Ewald summation scales as
|
||||
N^(3/2) where N is the number of atoms in the system. The PPPM solver
|
||||
scales as Nlog(N) due to the FFTs, so it is almost always a faster
|
||||
choice "(Pollock)"_#Pollock.
|
||||
|
||||
The {pppm/cg} style is identical to the {pppm} style except that it
|
||||
has an optimization for systems where most particles are uncharged.
|
||||
Similarly the {msm/cg} style implements the same optimization for {msm}.
|
||||
The optional {smallq} argument defines the cutoff for the absolute
|
||||
charge value which determines whether a particle is considered charged
|
||||
or not. Its default value is 1.0e-5.
|
||||
|
||||
The {pppm/dipole} style invokes a particle-particle particle-mesh solver
|
||||
for dipole-dipole interactions, following the method of "(Cerda)"_#Cerda2008.
|
||||
|
||||
The {pppm/dipole/spin} style invokes a particle-particle particle-mesh solver
|
||||
for magnetic dipole-dipole interactions between magnetic spins.
|
||||
|
||||
The {pppm/tip4p} style is identical to the {pppm} style except that it
|
||||
adds a charge at the massless 4th site in each TIP4P water molecule.
|
||||
It should be used with "pair styles"_pair_style.html with a
|
||||
{tip4p/long} in their style name.
|
||||
|
||||
The {pppm/stagger} style performs calculations using two different
|
||||
meshes, one shifted slightly with respect to the other. This can
|
||||
reduce force aliasing errors and increase the accuracy of the method
|
||||
for a given mesh size. Or a coarser mesh can be used for the same
|
||||
target accuracy, which saves CPU time. However, there is a trade-off
|
||||
since FFTs on two meshes are now performed which increases the
|
||||
computation required. See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov,
|
||||
and "(Hockney)"_#Hockney for details of the method.
|
||||
|
||||
For high relative accuracy, using staggered PPPM allows the mesh size
|
||||
to be reduced by a factor of 2 in each dimension as compared to
|
||||
regular PPPM (for the same target accuracy). This can give up to a 4x
|
||||
speedup in the KSpace time (8x less mesh points, 2x more expensive).
|
||||
However, for low relative accuracy, the staggered PPPM mesh size may
|
||||
be essentially the same as for regular PPPM, which means the method
|
||||
will be up to 2x slower in the KSpace time (simply 2x more expensive).
|
||||
For more details and timings, see the "Speed tips"_Speed_tips.html doc
|
||||
page.
|
||||
|
||||
NOTE: Using {pppm/stagger} may not give the same increase in the
|
||||
accuracy of energy and pressure as it does in forces, so some caution
|
||||
must be used if energy and/or pressure are quantities of interest,
|
||||
such as when using a barostat.
|
||||
|
||||
:line
|
||||
|
||||
The {pppm/disp} and {pppm/disp/tip4p} styles add a mesh-based long-range
|
||||
dispersion sum option for 1/r^6 potentials "(Isele-Holder)"_#Isele-Holder2012,
|
||||
similar to the {ewald/disp} style. The 1/r^6 capability means
|
||||
that Lennard-Jones or Buckingham potentials can be used without a cutoff,
|
||||
i.e. they become full long-range potentials.
|
||||
|
||||
For these styles, you will possibly want to adjust the default choice
|
||||
of parameters by using the "kspace_modify"_kspace_modify.html command.
|
||||
This can be done by either choosing the Ewald and grid parameters, or
|
||||
by specifying separate accuracies for the real and kspace
|
||||
calculations. When not making any settings, the simulation will stop
|
||||
with an error message. Further information on the influence of the
|
||||
parameters and how to choose them is described in
|
||||
"(Isele-Holder)"_#Isele-Holder2012,
|
||||
"(Isele-Holder2)"_#Isele-Holder2013 and the "Howto
|
||||
dispersion"_Howto_dispersion.html doc page.
|
||||
|
||||
:line
|
||||
|
||||
NOTE: All of the PPPM styles can be used with single-precision FFTs by
|
||||
using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
|
||||
lo-level Makefile. This setting also changes some of the PPPM
|
||||
operations (e.g. mapping charge to mesh and interpolating electric
|
||||
fields to particles) to be performed in single precision. This option
|
||||
can speed-up long-range calculations, particularly in parallel or on
|
||||
GPUs. The use of the -DFFT_SINGLE flag is discussed on the "Build
|
||||
settings"_Build_settings.html doc page. MSM does not currently support
|
||||
the -DFFT_SINGLE compiler switch.
|
||||
|
||||
:line
|
||||
|
||||
The {msm} style invokes a multi-level summation method MSM solver,
|
||||
"(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge
|
||||
to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser
|
||||
meshes on which direct Coulomb solvers are done. This method does not
|
||||
use FFTs and scales as N. It may therefore be faster than the other
|
||||
K-space solvers for relatively large problems when running on large
|
||||
core counts. MSM can also be used for non-periodic boundary conditions
|
||||
and for mixed periodic and non-periodic boundaries.
|
||||
|
||||
MSM is most competitive versus Ewald and PPPM when only relatively
|
||||
low accuracy forces, about 1e-4 relative error or less accurate,
|
||||
are needed. Note that use of a larger Coulombic cutoff (i.e. 15
|
||||
angstroms instead of 10 angstroms) provides better MSM accuracy for
|
||||
both the real space and grid computed forces.
|
||||
|
||||
Currently calculation of the full pressure tensor in MSM is expensive.
|
||||
Using the "kspace_modify"_kspace_modify.html {pressure/scalar yes}
|
||||
command provides a less expensive way to compute the scalar pressure
|
||||
(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
|
||||
to run an isotropic barostat. If the full pressure tensor is needed,
|
||||
then calculating the pressure at every timestep or using a fixed
|
||||
pressure simulation with MSM will cause the code to run slower.
|
||||
|
||||
:line
|
||||
|
||||
The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver
|
||||
library"_http://www.scafacos.de which provides a variety of solver
|
||||
methods which can be used with LAMMPS. The paper by "(Who)"_#Who2012
|
||||
gives an overview of ScaFaCoS.
|
||||
|
||||
ScaFaCoS was developed by a consortium of German research facilities
|
||||
with a BMBF (German Ministry of Science and Education) funded project
|
||||
in 2009-2012. Participants of the consortium were the Universities of
|
||||
Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
|
||||
Forschungszentrum Juelich.
|
||||
|
||||
The library is available for download at "http://scafacos.de" or can
|
||||
be cloned from the git-repository
|
||||
"git://github.com/scafacos/scafacos.git".
|
||||
|
||||
In order to use this KSpace style, you must download and build the
|
||||
ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package
|
||||
installed package which links LAMMPS to the ScaFaCoS library.
|
||||
See details on "this page"_Section_packages.html#USER-SCAFACOS.
|
||||
|
||||
NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
|
||||
Coulombic interactions, both short- and long-range. Thus you should
|
||||
NOT use a Coulombic pair style when using kspace_style scafacos. This
|
||||
also means the total Coulombic energy (short- and long-range) will be
|
||||
tallied for "thermodynamic output"_thermo_style.html command as part
|
||||
of the {elong} keyword; the {ecoul} keyword will be zero.
|
||||
|
||||
NOTE: See the current restriction below about use of ScaFaCoS in
|
||||
LAMMPS with molecular charged systems or the TIP4P water model.
|
||||
|
||||
The specified {method} determines which ScaFaCoS algorithm is used.
|
||||
These are the ScaFaCoS methods currently available from LAMMPS:
|
||||
|
||||
{fmm} = Fast Multi-Pole method
|
||||
{p2nfft} = FFT-based Coulomb solver
|
||||
{ewald} = Ewald summation
|
||||
{direct} = direct O(N^2) summation
|
||||
{p3m} = PPPM :ul
|
||||
|
||||
We plan to support additional ScaFaCoS solvers from LAMMPS in the
|
||||
future. For an overview of the included solvers, refer to
|
||||
"(Sutmann)"_#Sutmann2013
|
||||
|
||||
The specified {accuracy} is similar to the accuracy setting for other
|
||||
LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret
|
||||
it in different ways for different methods it supports. Within the
|
||||
ScaFaCoS library the {accuracy} is treated as a tolerance level
|
||||
(either absolute or relative) for the chosen quantity, where the
|
||||
quantity can be either the Columic field values, the per-atom Columic
|
||||
energy or the total Columic energy. To select from these options, see
|
||||
the "kspace_modify scafacos accuracy"_kspace_modify.html doc page.
|
||||
|
||||
The "kspace_modify scafacos"_kspace_modify.html command also explains
|
||||
other ScaFaCoS options currently exposed to LAMMPS.
|
||||
|
||||
:line
|
||||
|
||||
The specified {accuracy} determines the relative RMS error in per-atom
|
||||
forces calculated by the long-range solver. It is set as a
|
||||
dimensionless number, relative to the force that two unit point
|
||||
charges (e.g. 2 monovalent ions) exert on each other at a distance of
|
||||
1 Angstrom. This reference value was chosen as representative of the
|
||||
magnitude of electrostatic forces in atomic systems. Thus an accuracy
|
||||
value of 1.0e-4 means that the RMS error will be a factor of 10000
|
||||
smaller than the reference force.
|
||||
|
||||
The accuracy setting is used in conjunction with the pairwise cutoff
|
||||
to determine the number of K-space vectors for style {ewald} or the
|
||||
grid size for style {pppm} or {msm}.
|
||||
|
||||
Note that style {pppm} only computes the grid size at the beginning of
|
||||
a simulation, so if the length or triclinic tilt of the simulation
|
||||
cell increases dramatically during the course of the simulation, the
|
||||
accuracy of the simulation may degrade. Likewise, if the
|
||||
"kspace_modify slab"_kspace_modify.html option is used with
|
||||
shrink-wrap boundaries in the z-dimension, and the box size changes
|
||||
dramatically in z. For example, for a triclinic system with all three
|
||||
tilt factors set to the maximum limit, the PPPM grid should be
|
||||
increased roughly by a factor of 1.5 in the y direction and 2.0 in the
|
||||
z direction as compared to the same system using a cubic orthogonal
|
||||
simulation cell. One way to handle this issue if you have a long
|
||||
simulation where the box size changes dramatically, is to break it
|
||||
into shorter simulations (multiple "run"_run.html commands). This
|
||||
works because the grid size is re-computed at the beginning of each
|
||||
run. Another way to ensure the described accuracy requirement is met
|
||||
is to run a short simulation at the maximum expected tilt or length,
|
||||
note the required grid size, and then use the
|
||||
"kspace_modify"_kspace_modify.html {mesh} command to manually set the
|
||||
PPPM grid size to this value for the long run. The simulation then
|
||||
will be "too accurate" for some portion of the run.
|
||||
|
||||
RMS force errors in real space for {ewald} and {pppm} are estimated
|
||||
using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as
|
||||
equation 9 of "(Petersen)"_#Petersen. RMS force errors in K-space for
|
||||
{ewald} are estimated using equation 11 of "(Petersen)"_#Petersen,
|
||||
which is similar to equation 32 of "(Kolafa)"_#Kolafa. RMS force
|
||||
errors in K-space for {pppm} are estimated using equation 38 of
|
||||
"(Deserno)"_#Deserno. RMS force errors for {msm} are estimated
|
||||
using ideas from chapter 3 of "(Hardy)"_#Hardy2006, with equation 3.197
|
||||
of particular note. When using {msm} with non-periodic boundary
|
||||
conditions, it is expected that the error estimation will be too
|
||||
pessimistic. RMS force errors for dipoles when using {ewald/disp}
|
||||
or {ewald/dipole} are estimated using equations 33 and 46 of
|
||||
"(Wang)"_#Wang. The RMS force errors for {pppm/dipole} are estimated
|
||||
using the equations in "(Cerda)"_#Cerda2008.
|
||||
|
||||
|
||||
See the "kspace_modify"_kspace_modify.html command for additional
|
||||
options of the K-space solvers that can be set, including a {force}
|
||||
option for setting an absolute RMS error in forces, as opposed to a
|
||||
relative RMS error.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
More specifically, the {pppm/gpu} style performs charge assignment and
|
||||
force interpolation calculations on the GPU. These processes are
|
||||
performed either in single or double precision, depending on whether
|
||||
the -DFFT_SINGLE setting was specified in your lo-level Makefile, as
|
||||
discussed above. The FFTs themselves are still calculated on the CPU.
|
||||
If {pppm/gpu} is used with a GPU-enabled pair style, part of the PPPM
|
||||
calculation can be performed concurrently on the GPU while other
|
||||
calculations for non-bonded and bonded force calculation are performed
|
||||
on the CPU.
|
||||
|
||||
The {pppm/kk} style also performs charge assignment and force
|
||||
interpolation calculations on the GPU while the FFTs themselves are
|
||||
calculated on the CPU in non-threaded mode.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP, and OPT packages respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Note that the long-range electrostatic solvers in LAMMPS assume conducting
|
||||
metal (tinfoil) boundary conditions for both charge and dipole
|
||||
interactions. Vacuum boundary conditions are not currently supported.
|
||||
|
||||
The {ewald/disp}, {ewald}, {pppm}, and {msm} styles support
|
||||
non-orthogonal (triclinic symmetry) simulation boxes. However,
|
||||
triclinic simulation cells may not yet be supported by suffix versions
|
||||
of these styles.
|
||||
|
||||
All of the kspace styles are part of the KSPACE package. They are
|
||||
only enabled if LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
For MSM, a simulation must be 3d and one can use any combination of
|
||||
periodic, non-periodic, or shrink-wrapped boundaries (specified using
|
||||
the "boundary"_boundary.html command).
|
||||
|
||||
For Ewald and PPPM, a simulation must be 3d and periodic in all
|
||||
dimensions. The only exception is if the slab option is set with
|
||||
"kspace_modify"_kspace_modify.html, in which case the xy dimensions
|
||||
must be periodic and the z dimension must be non-periodic.
|
||||
|
||||
The scafacos KSpace style will only be enabled if LAMMPS is built with
|
||||
the USER-SCAFACOS package. See the "Build package"_Build_package.html
|
||||
doc page for more info.
|
||||
|
||||
The use of ScaFaCos in LAMMPS does not yet support molecular charged
|
||||
systems where the short-range Coulombic interactions between atoms in
|
||||
the same bond/angle/dihedral are weighted by the
|
||||
"special_bonds"_special_bonds.html command. Likewise it does not
|
||||
support the "TIP4P water style" where a fictitious charge site is
|
||||
introduced in each water molecule.
|
||||
Finally, the methods {p3m} and {ewald} do not support computing the
|
||||
virial, so this contribution is not included.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"kspace_modify"_kspace_modify.html, "pair_style
|
||||
lj/cut/coul/long"_pair_lj.html, "pair_style
|
||||
lj/charmm/coul/long"_pair_charmm.html, "pair_style
|
||||
lj/long/coul/long"_pair_lj_long.html, "pair_style
|
||||
buck/coul/long"_pair_buck.html
|
||||
|
||||
[Default:]
|
||||
|
||||
kspace_style none :pre
|
||||
|
||||
:line
|
||||
|
||||
:link(Darden)
|
||||
[(Darden)] Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
|
||||
|
||||
:link(Deserno)
|
||||
[(Deserno)] Deserno and Holm, J Chem Phys, 109, 7694 (1998).
|
||||
|
||||
:link(Hockney)
|
||||
[(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles,
|
||||
Adam Hilger, NY (1989).
|
||||
|
||||
:link(Kolafa)
|
||||
[(Kolafa)] Kolafa and Perram, Molecular Simulation, 9, 351 (1992).
|
||||
|
||||
:link(Petersen)
|
||||
[(Petersen)] Petersen, J Chem Phys, 103, 3668 (1995).
|
||||
|
||||
:link(Wang)
|
||||
[(Wang)] Wang and Holm, J Chem Phys, 115, 6277 (2001).
|
||||
|
||||
:link(Pollock)
|
||||
[(Pollock)] Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
|
||||
|
||||
:link(Cerutti)
|
||||
[(Cerutti)] Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory
|
||||
and Computation 5, 2322 (2009)
|
||||
|
||||
:link(Neelov)
|
||||
[(Neelov)] Neelov, Holm, J Chem Phys 132, 234103 (2010)
|
||||
|
||||
:link(Veld)
|
||||
[(Veld)] In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
|
||||
|
||||
:link(Toukmaji)
|
||||
[(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
|
||||
10913 (2000).
|
||||
|
||||
:link(Isele-Holder2012)
|
||||
[(Isele-Holder)] Isele-Holder, Mitchell, Ismail, J Chem Phys, 137,
|
||||
174107 (2012).
|
||||
|
||||
:link(Isele-Holder2013)
|
||||
[(Isele-Holder2)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail,
|
||||
J Chem Theory Comput 9, 5412 (2013).
|
||||
|
||||
:link(Hardy2006)
|
||||
[(Hardy)] David Hardy thesis: Multilevel Summation for the Fast
|
||||
Evaluation of Forces for the Simulation of Biomolecules, University of
|
||||
Illinois at Urbana-Champaign, (2006).
|
||||
|
||||
:link(Hardy2009)
|
||||
[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177
|
||||
(2009).
|
||||
|
||||
:link(Sutmann2013)
|
||||
[(Sutmann)] Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
|
||||
|
||||
:link(Cerda2008)
|
||||
[(Cerda)] Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
|
||||
|
||||
:link(Who2012)
|
||||
[(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177
|
||||
(2012).
|
||||
@ -1,660 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
package command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
package style args :pre
|
||||
|
||||
style = {gpu} or {intel} or {kokkos} or {omp} :ulb,l
|
||||
args = arguments specific to the style :l
|
||||
{gpu} args = Ngpu keyword value ...
|
||||
Ngpu = # of GPUs per node
|
||||
zero or more keyword/value pairs may be appended
|
||||
keywords = {neigh} or {newton} or {binsize} or {split} or {gpuID} or {tpa} or {device} or {blocksize}
|
||||
{neigh} value = {yes} or {no}
|
||||
yes = neighbor list build on GPU (default)
|
||||
no = neighbor list build on CPU
|
||||
{newton} = {off} or {on}
|
||||
off = set Newton pairwise flag off (default and required)
|
||||
on = set Newton pairwise flag on (currently not allowed)
|
||||
{binsize} value = size
|
||||
size = bin size for neighbor list construction (distance units)
|
||||
{split} = fraction
|
||||
fraction = fraction of atoms assigned to GPU (default = 1.0)
|
||||
{gpuID} values = first last
|
||||
first = ID of first GPU to be used on each node
|
||||
last = ID of last GPU to be used on each node
|
||||
{tpa} value = Nthreads
|
||||
Nthreads = # of GPU threads used per atom
|
||||
{device} value = device_type or platform_id:device_type or platform_id:custom,val1,val2,val3,..,val13
|
||||
platform_id = numerical OpenCL platform id (default: -1)
|
||||
device_type = {kepler} or {fermi} or {cypress} or {intel} or {phi} or {generic} or {custom}
|
||||
val1,val2,... = custom OpenCL tune parameters (see below for details)
|
||||
{blocksize} value = size
|
||||
size = thread block size for pair force computation
|
||||
{intel} args = NPhi keyword value ...
|
||||
Nphi = # of co-processors per node
|
||||
zero or more keyword/value pairs may be appended
|
||||
keywords = {mode} or {omp} or {lrt} or {balance} or {ghost} or {tpc} or {tptask} or {no_affinity}
|
||||
{mode} value = {single} or {mixed} or {double}
|
||||
single = perform force calculations in single precision
|
||||
mixed = perform force calculations in mixed precision
|
||||
double = perform force calculations in double precision
|
||||
{omp} value = Nthreads
|
||||
Nthreads = number of OpenMP threads to use on CPU (default = 0)
|
||||
{lrt} value = {yes} or {no}
|
||||
yes = use additional thread dedicated for some PPPM calculations
|
||||
no = do not dedicate an extra thread for some PPPM calculations
|
||||
{balance} value = split
|
||||
split = fraction of work to offload to co-processor, -1 for dynamic
|
||||
{ghost} value = {yes} or {no}
|
||||
yes = include ghost atoms for offload
|
||||
no = do not include ghost atoms for offload
|
||||
{tpc} value = Ntpc
|
||||
Ntpc = max number of co-processor threads per co-processor core (default = 4)
|
||||
{tptask} value = Ntptask
|
||||
Ntptask = max number of co-processor threads per MPI task (default = 240)
|
||||
{no_affinity} values = none
|
||||
{kokkos} args = keyword value ...
|
||||
zero or more keyword/value pairs may be appended
|
||||
keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {cuda/aware}
|
||||
{neigh} value = {full} or {half}
|
||||
full = full neighbor list
|
||||
half = half neighbor list built in thread-safe manner
|
||||
{neigh/qeq} value = {full} or {half}
|
||||
full = full neighbor list
|
||||
half = half neighbor list built in thread-safe manner
|
||||
{neigh/thread} value = {off} or {on}
|
||||
off = thread only over atoms
|
||||
on = thread over both atoms and neighbors
|
||||
{newton} = {off} or {on}
|
||||
off = set Newton pairwise and bonded flags off
|
||||
on = set Newton pairwise and bonded flags on
|
||||
{binsize} value = size
|
||||
size = bin size for neighbor list construction (distance units)
|
||||
{comm} value = {no} or {host} or {device}
|
||||
use value for comm/exchange and comm/forward and comm/reverse
|
||||
{comm/exchange} value = {no} or {host} or {device}
|
||||
{comm/forward} value = {no} or {host} or {device}
|
||||
{comm/reverse} value = {no} or {host} or {device}
|
||||
no = perform communication pack/unpack in non-KOKKOS mode
|
||||
host = perform pack/unpack on host (e.g. with OpenMP threading)
|
||||
device = perform pack/unpack on device (e.g. on GPU)
|
||||
{cuda/aware} = {off} or {on}
|
||||
off = do not use CUDA-aware MPI
|
||||
on = use CUDA-aware MPI (default)
|
||||
{omp} args = Nthreads keyword value ...
|
||||
Nthread = # of OpenMP threads to associate with each MPI process
|
||||
zero or more keyword/value pairs may be appended
|
||||
keywords = {neigh}
|
||||
{neigh} value = {yes} or {no}
|
||||
yes = threaded neighbor list build (default)
|
||||
no = non-threaded neighbor list build :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
package gpu 1
|
||||
package gpu 1 split 0.75
|
||||
package gpu 2 split -1.0
|
||||
package gpu 1 device kepler
|
||||
package gpu 1 device 2:generic
|
||||
package gpu 1 device custom,32,4,8,256,11,128,256,128,32,64,8,128,128
|
||||
package kokkos neigh half comm device
|
||||
package omp 0 neigh no
|
||||
package omp 4
|
||||
package intel 1
|
||||
package intel 2 omp 4 mode mixed balance 0.5 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This command invokes package-specific settings for the various
|
||||
accelerator packages available in LAMMPS. Currently the following
|
||||
packages use settings from this command: GPU, USER-INTEL, KOKKOS, and
|
||||
USER-OMP.
|
||||
|
||||
If this command is specified in an input script, it must be near the
|
||||
top of the script, before the simulation box has been defined. This
|
||||
is because it specifies settings that the accelerator packages use in
|
||||
their initialization, before a simulation is defined.
|
||||
|
||||
This command can also be specified from the command-line when
|
||||
launching LAMMPS, using the "-pk" "command-line
|
||||
switch"_Run_options.html. The syntax is exactly the same as when used
|
||||
in an input script.
|
||||
|
||||
Note that all of the accelerator packages require the package command
|
||||
to be specified (except the OPT package), if the package is to be used
|
||||
in a simulation (LAMMPS can be built with an accelerator package
|
||||
without using it in a particular simulation). However, in all cases,
|
||||
a default version of the command is typically invoked by other
|
||||
accelerator settings.
|
||||
|
||||
The KOKKOS package requires a "-k on" "command-line
|
||||
switch"_Run_options.html respectively, which invokes a "package
|
||||
kokkos" command with default settings.
|
||||
|
||||
For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf
|
||||
intel" or "-sf omp" "command-line switch"_Run_options.html is used to
|
||||
auto-append accelerator suffixes to various styles in the input
|
||||
script, then those switches also invoke a "package gpu", "package
|
||||
intel", or "package omp" command with default settings.
|
||||
|
||||
NOTE: A package command for a particular style can be invoked multiple
|
||||
times when a simulation is setup, e.g. by the "-c on, -k on, -sf, and
|
||||
-pk command-line switches"_Run_options.html, and by using this command
|
||||
in an input script. Each time it is used all of the style options are
|
||||
set, either to default values or to specified settings. I.e. settings
|
||||
from previous invocations do not persist across multiple invocations.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more details
|
||||
about using the various accelerator packages for speeding up LAMMPS
|
||||
simulations.
|
||||
|
||||
:line
|
||||
|
||||
The {gpu} style invokes settings associated with the use of the GPU
|
||||
package.
|
||||
|
||||
The {Ngpu} argument sets the number of GPUs per node. There must be
|
||||
at least as many MPI tasks per node as GPUs, as set by the mpirun or
|
||||
mpiexec command. If there are more MPI tasks (per node)
|
||||
than GPUs, multiple MPI tasks will share each GPU.
|
||||
|
||||
Optional keyword/value pairs can also be specified. Each has a
|
||||
default value as listed below.
|
||||
|
||||
The {neigh} keyword specifies where neighbor lists for pair style
|
||||
computation will be built. If {neigh} is {yes}, which is the default,
|
||||
neighbor list building is performed on the GPU. If {neigh} is {no},
|
||||
neighbor list building is performed on the CPU. GPU neighbor list
|
||||
building currently cannot be used with a triclinic box. GPU neighbor
|
||||
lists are not compatible with commands that are not GPU-enabled. When
|
||||
a non-GPU enabled command requires a neighbor list, it will also be
|
||||
built on the CPU. In these cases, it will typically be more efficient
|
||||
to only use CPU neighbor list builds.
|
||||
|
||||
The {newton} keyword sets the Newton flags for pairwise (not bonded)
|
||||
interactions to {off} or {on}, the same as the "newton"_newton.html
|
||||
command allows. Currently, only an {off} value is allowed, since all
|
||||
the GPU package pair styles require this setting. This means more
|
||||
computation is done, but less communication. In the future a value of
|
||||
{on} may be allowed, so the {newton} keyword is included as an option
|
||||
for compatibility with the package command for other accelerator
|
||||
styles. Note that the newton setting for bonded interactions is not
|
||||
affected by this keyword.
|
||||
|
||||
The {binsize} keyword sets the size of bins used to bin atoms in
|
||||
neighbor list builds performed on the GPU, if {neigh} = {yes} is set.
|
||||
If {binsize} is set to 0.0 (the default), then bins = the size of the
|
||||
pairwise cutoff + neighbor skin distance. This is 2x larger than the
|
||||
LAMMPS default used for neighbor list building on the CPU. This will
|
||||
be close to optimal for the GPU, so you do not normally need to use
|
||||
this keyword. Note that if you use a longer-than-usual pairwise
|
||||
cutoff, e.g. to allow for a smaller fraction of KSpace work with a
|
||||
"long-range Coulombic solver"_kspace_style.html because the GPU is
|
||||
faster at performing pairwise interactions, then it may be optimal to
|
||||
make the {binsize} smaller than the default. For example, with a
|
||||
cutoff of 20*sigma in LJ "units"_units.html and a neighbor skin
|
||||
distance of sigma, a {binsize} = 5.25*sigma can be more efficient than
|
||||
the default.
|
||||
|
||||
The {split} keyword can be used for load balancing force calculations
|
||||
between CPU and GPU cores in GPU-enabled pair styles. If 0 < {split} <
|
||||
1.0, a fixed fraction of particles is offloaded to the GPU while force
|
||||
calculation for the other particles occurs simultaneously on the CPU.
|
||||
If {split} < 0.0, the optimal fraction (based on CPU and GPU timings)
|
||||
is calculated every 25 timesteps, i.e. dynamic load-balancing across
|
||||
the CPU and GPU is performed. If {split} = 1.0, all force
|
||||
calculations for GPU accelerated pair styles are performed on the GPU.
|
||||
In this case, other "hybrid"_pair_hybrid.html pair interactions,
|
||||
"bond"_bond_style.html, "angle"_angle_style.html,
|
||||
"dihedral"_dihedral_style.html, "improper"_improper_style.html, and
|
||||
"long-range"_kspace_style.html calculations can be performed on the
|
||||
CPU while the GPU is performing force calculations for the GPU-enabled
|
||||
pair style. If all CPU force computations complete before the GPU
|
||||
completes, LAMMPS will block until the GPU has finished before
|
||||
continuing the timestep.
|
||||
|
||||
As an example, if you have two GPUs per node and 8 CPU cores per node,
|
||||
and would like to run on 4 nodes (32 cores) with dynamic balancing of
|
||||
force calculation across CPU and GPU cores, you could specify
|
||||
|
||||
mpirun -np 32 -sf gpu -in in.script # launch command
|
||||
package gpu 2 split -1 # input script command :pre
|
||||
|
||||
In this case, all CPU cores and GPU devices on the nodes would be
|
||||
utilized. Each GPU device would be shared by 4 CPU cores. The CPU
|
||||
cores would perform force calculations for some fraction of the
|
||||
particles at the same time the GPUs performed force calculation for
|
||||
the other particles.
|
||||
|
||||
The {gpuID} keyword allows selection of which GPUs on each node will
|
||||
be used for a simulation. The {first} and {last} values specify the
|
||||
GPU IDs to use (from 0 to Ngpu-1). By default, first = 0 and last =
|
||||
Ngpu-1, so that all GPUs are used, assuming Ngpu is set to the number
|
||||
of physical GPUs. If you only wish to use a subset, set Ngpu to a
|
||||
smaller number and first/last to a sub-range of the available GPUs.
|
||||
|
||||
The {tpa} keyword sets the number of GPU thread per atom used to
|
||||
perform force calculations. With a default value of 1, the number of
|
||||
threads will be chosen based on the pair style, however, the value can
|
||||
be set explicitly with this keyword to fine-tune performance. For
|
||||
large cutoffs or with a small number of particles per GPU, increasing
|
||||
the value can improve performance. The number of threads per atom must
|
||||
be a power of 2 and currently cannot be greater than 32.
|
||||
|
||||
The {device} keyword can be used to tune parameters optimized for a
|
||||
specific accelerator and platform when using OpenCL. OpenCL supports
|
||||
the concept of a [platform], which represents one or more devices that
|
||||
share the same driver (e.g. there would be a different platform for
|
||||
GPUs from different vendors or for CPU based accelerator support).
|
||||
In LAMMPS only one platform can be active at a time and by default
|
||||
the first platform with an accelerator is selected. This is equivalent
|
||||
to using a platform ID of -1. The platform ID is a number corresponding
|
||||
to the output of the ocl_get_devices tool. The platform ID is passed
|
||||
to the GPU library, by prefixing the {device} keyword with that number
|
||||
separated by a colon. For CUDA, the {device} keyword is ignored.
|
||||
Currently, the device tuning support is limited to NVIDIA Kepler, NVIDIA
|
||||
Fermi, AMD Cypress, Intel x86_64 CPU, Intel Xeon Phi, or a generic device.
|
||||
More devices may be added later. The default device type can be
|
||||
specified when building LAMMPS with the GPU library, via setting a
|
||||
variable in the lib/gpu/Makefile that is used.
|
||||
|
||||
In addition, a device type {custom} is available, which is followed by
|
||||
13 comma separated numbers, which allows to set those tweakable parameters
|
||||
from the package command. It can be combined with the (colon separated)
|
||||
platform id. The individual settings are:
|
||||
|
||||
MEM_THREADS
|
||||
THREADS_PER_ATOM
|
||||
THREADS_PER_CHARGE
|
||||
BLOCK_PAIR
|
||||
MAX_SHARED_TYPES
|
||||
BLOCK_NBOR_BUILD
|
||||
BLOCK_BIO_PAIR
|
||||
BLOCK_ELLIPSE
|
||||
WARP_SIZE
|
||||
PPPM_BLOCK_1D
|
||||
BLOCK_CELL_2D
|
||||
BLOCK_CELL_ID
|
||||
MAX_BIO_SHARED_TYPES :ul
|
||||
|
||||
The {blocksize} keyword allows you to tweak the number of threads used
|
||||
per thread block. This number should be a multiple of 32 (for GPUs)
|
||||
and its maximum depends on the specific GPU hardware. Typical choices
|
||||
are 64, 128, or 256. A larger block size increases occupancy of
|
||||
individual GPU cores, but reduces the total number of thread blocks,
|
||||
thus may lead to load imbalance.
|
||||
|
||||
:line
|
||||
|
||||
The {intel} style invokes settings associated with the use of the
|
||||
USER-INTEL package. All of its settings, except the {omp} and {mode}
|
||||
keywords, are ignored if LAMMPS was not built with Xeon Phi
|
||||
co-processor support. All of its settings, including the {omp} and
|
||||
{mode} keyword are applicable if LAMMPS was built with co-processor
|
||||
support.
|
||||
|
||||
The {Nphi} argument sets the number of co-processors per node.
|
||||
This can be set to any value, including 0, if LAMMPS was not
|
||||
built with co-processor support.
|
||||
|
||||
Optional keyword/value pairs can also be specified. Each has a
|
||||
default value as listed below.
|
||||
|
||||
The {omp} keyword determines the number of OpenMP threads allocated
|
||||
for each MPI task when any portion of the interactions computed by a
|
||||
USER-INTEL pair style are run on the CPU. This can be the case even
|
||||
if LAMMPS was built with co-processor support; see the {balance}
|
||||
keyword discussion below. If you are running with less MPI tasks/node
|
||||
than there are CPUs, it can be advantageous to use OpenMP threading on
|
||||
the CPUs.
|
||||
|
||||
NOTE: The {omp} keyword has nothing to do with co-processor threads on
|
||||
the Xeon Phi; see the {tpc} and {tptask} keywords below for a
|
||||
discussion of co-processor threads.
|
||||
|
||||
The {Nthread} value for the {omp} keyword sets the number of OpenMP
|
||||
threads allocated for each MPI task. Setting {Nthread} = 0 (the
|
||||
default) instructs LAMMPS to use whatever value is the default for the
|
||||
given OpenMP environment. This is usually determined via the
|
||||
{OMP_NUM_THREADS} environment variable or the compiler runtime, which
|
||||
is usually a value of 1.
|
||||
|
||||
For more details, including examples of how to set the OMP_NUM_THREADS
|
||||
environment variable, see the discussion of the {Nthreads} setting on
|
||||
this doc page for the "package omp" command. Nthreads is a required
|
||||
argument for the USER-OMP package. Its meaning is exactly the same
|
||||
for the USER-INTEL package.
|
||||
|
||||
NOTE: If you build LAMMPS with both the USER-INTEL and USER-OMP
|
||||
packages, be aware that both packages allow setting of the {Nthreads}
|
||||
value via their package commands, but there is only a single global
|
||||
{Nthreads} value used by OpenMP. Thus if both package commands are
|
||||
invoked, you should insure the two values are consistent. If they are
|
||||
not, the last one invoked will take precedence, for both packages.
|
||||
Also note that if the "-sf hybrid intel omp command-line
|
||||
switch"_Run_options.html is used, it invokes a "package intel"
|
||||
command, followed by a "package omp" command, both with a setting of
|
||||
{Nthreads} = 0.
|
||||
|
||||
The {mode} keyword determines the precision mode to use for
|
||||
computing pair style forces, either on the CPU or on the co-processor,
|
||||
when using a USER-INTEL supported "pair style"_pair_style.html. It
|
||||
can take a value of {single}, {mixed} which is the default, or
|
||||
{double}. {Single} means single precision is used for the entire
|
||||
force calculation. {Mixed} means forces between a pair of atoms are
|
||||
computed in single precision, but accumulated and stored in double
|
||||
precision, including storage of forces, torques, energies, and virial
|
||||
quantities. {Double} means double precision is used for the entire
|
||||
force calculation.
|
||||
|
||||
The {lrt} keyword can be used to enable "Long Range Thread (LRT)"
|
||||
mode. It can take a value of {yes} to enable and {no} to disable.
|
||||
LRT mode generates an extra thread (in addition to any OpenMP threads
|
||||
specified with the OMP_NUM_THREADS environment variable or the {omp}
|
||||
keyword). The extra thread is dedicated for performing part of the
|
||||
"PPPM solver"_kspace_style.html computations and communications. This
|
||||
can improve parallel performance on processors supporting
|
||||
Simultaneous Multithreading (SMT) such as Hyper-Threading (HT) on Intel
|
||||
processors. In this mode, one additional thread is generated per MPI
|
||||
process. LAMMPS will generate a warning in the case that more threads
|
||||
are used than available in SMT hardware on a node. If the PPPM solver
|
||||
from the USER-INTEL package is not used, then the LRT setting is
|
||||
ignored and no extra threads are generated. Enabling LRT will replace
|
||||
the "run_style"_run_style.html with the {verlet/lrt/intel} style that
|
||||
is identical to the default {verlet} style aside from supporting the
|
||||
LRT feature. This feature requires setting the pre-processor flag
|
||||
-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS.
|
||||
|
||||
The {balance} keyword sets the fraction of "pair
|
||||
style"_pair_style.html work offloaded to the co-processor for split
|
||||
values between 0.0 and 1.0 inclusive. While this fraction of work is
|
||||
running on the co-processor, other calculations will run on the host,
|
||||
including neighbor and pair calculations that are not offloaded, as
|
||||
well as angle, bond, dihedral, kspace, and some MPI communications.
|
||||
If {split} is set to -1, the fraction of work is dynamically adjusted
|
||||
automatically throughout the run. This typically give performance
|
||||
within 5 to 10 percent of the optimal fixed fraction.
|
||||
|
||||
The {ghost} keyword determines whether or not ghost atoms, i.e. atoms
|
||||
at the boundaries of processor sub-domains, are offloaded for neighbor
|
||||
and force calculations. When the value = "no", ghost atoms are not
|
||||
offloaded. This option can reduce the amount of data transfer with
|
||||
the co-processor and can also overlap MPI communication of forces with
|
||||
computation on the co-processor when the "newton pair"_newton.html
|
||||
setting is "on". When the value = "yes", ghost atoms are offloaded.
|
||||
In some cases this can provide better performance, especially if the
|
||||
{balance} fraction is high.
|
||||
|
||||
The {tpc} keyword sets the max # of co-processor threads {Ntpc} that
|
||||
will run on each core of the co-processor. The default value = 4,
|
||||
which is the number of hardware threads per core supported by the
|
||||
current generation Xeon Phi chips.
|
||||
|
||||
The {tptask} keyword sets the max # of co-processor threads (Ntptask}
|
||||
assigned to each MPI task. The default value = 240, which is the
|
||||
total # of threads an entire current generation Xeon Phi chip can run
|
||||
(240 = 60 cores * 4 threads/core). This means each MPI task assigned
|
||||
to the Phi will enough threads for the chip to run the max allowed,
|
||||
even if only 1 MPI task is assigned. If 8 MPI tasks are assigned to
|
||||
the Phi, each will run with 30 threads. If you wish to limit the
|
||||
number of threads per MPI task, set {tptask} to a smaller value.
|
||||
E.g. for {tptask} = 16, if 8 MPI tasks are assigned, each will run
|
||||
with 16 threads, for a total of 128.
|
||||
|
||||
Note that the default settings for {tpc} and {tptask} are fine for
|
||||
most problems, regardless of how many MPI tasks you assign to a Phi.
|
||||
|
||||
The {no_affinity} keyword will turn off automatic setting of core
|
||||
affinity for MPI tasks and OpenMP threads on the host when using
|
||||
offload to a co-processor. Affinity settings are used when possible
|
||||
to prevent MPI tasks and OpenMP threads from being on separate NUMA
|
||||
domains and to prevent offload threads from interfering with other
|
||||
processes/threads used for LAMMPS.
|
||||
|
||||
:line
|
||||
|
||||
The {kokkos} style invokes settings associated with the use of the
|
||||
KOKKOS package.
|
||||
|
||||
All of the settings are optional keyword/value pairs. Each has a default
|
||||
value as listed below.
|
||||
|
||||
The {neigh} keyword determines how neighbor lists are built. A value of
|
||||
{half} uses a thread-safe variant of half-neighbor lists, the same as
|
||||
used by most pair styles in LAMMPS, which is the default when running on
|
||||
CPUs (i.e. the Kokkos CUDA back end is not enabled).
|
||||
|
||||
A value of {full} uses a full neighbor lists and is the default when
|
||||
running on GPUs. This performs twice as much computation as the {half}
|
||||
option, however that is often a win because it is thread-safe and
|
||||
doesn't require atomic operations in the calculation of pair forces. For
|
||||
that reason, {full} is the default setting for GPUs. However, when
|
||||
running on CPUs, a {half} neighbor list is the default because it are
|
||||
often faster, just as it is for non-accelerated pair styles. Similarly,
|
||||
the {neigh/qeq} keyword determines how neighbor lists are built for "fix
|
||||
qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of
|
||||
{neigh/qeq} will match {neigh}.
|
||||
|
||||
If the {neigh/thread} keyword is set to {off}, then the KOKKOS package
|
||||
threads only over atoms. However, for small systems, this may not expose
|
||||
enough parallelism to keep a GPU busy. When this keyword is set to {on},
|
||||
the KOKKOS package threads over both atoms and neighbors of atoms. When
|
||||
using {neigh/thread} {on}, a full neighbor list must also be used. Using
|
||||
{neigh/thread} {on} may be slower for large systems, so this this option
|
||||
is turned on by default only when there are 16K atoms or less owned by
|
||||
an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled
|
||||
potentials support this keyword yet, and only thread over atoms. Many
|
||||
simple pair-wise potentials such as Lennard-Jones do support threading
|
||||
over both atoms and neighbors.
|
||||
|
||||
The {newton} keyword sets the Newton flags for pairwise and bonded
|
||||
interactions to {off} or {on}, the same as the "newton"_newton.html
|
||||
command allows. The default for GPUs is {off} because this will almost
|
||||
always give better performance for the KOKKOS package. This means more
|
||||
computation is done, but less communication. However, when running on
|
||||
CPUs a value of {on} is the default since it can often be faster, just
|
||||
as it is for non-accelerated pair styles
|
||||
|
||||
The {binsize} keyword sets the size of bins used to bin atoms in
|
||||
neighbor list builds. The same value can be set by the "neigh_modify
|
||||
binsize"_neigh_modify.html command. Making it an option in the package
|
||||
kokkos command allows it to be set from the command line. The default
|
||||
value for CPUs is 0.0, which means the LAMMPS default will be used,
|
||||
which is bins = 1/2 the size of the pairwise cutoff + neighbor skin
|
||||
distance. This is fine when neighbor lists are built on the CPU. For GPU
|
||||
builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin
|
||||
is often faster, which is the default. Note that if you use a
|
||||
longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction
|
||||
of KSpace work with a "long-range Coulombic solver"_kspace_style.html
|
||||
because the GPU is faster at performing pairwise interactions, then this
|
||||
rule of thumb may give too large a binsize and the default should be
|
||||
overridden with a smaller value.
|
||||
|
||||
The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse}
|
||||
keywords determine whether the host or device performs the packing and
|
||||
unpacking of data when communicating per-atom data between processors.
|
||||
"Exchange" communication happens only on timesteps that neighbor lists
|
||||
are rebuilt. The data is only for atoms that migrate to new processors.
|
||||
"Forward" communication happens every timestep. "Reverse" communication
|
||||
happens every timestep if the {newton} option is on. The data is for
|
||||
atom coordinates and any other atom properties that needs to be updated
|
||||
for ghost atoms owned by each processor.
|
||||
|
||||
The {comm} keyword is simply a short-cut to set the same value for both
|
||||
the {comm/exchange} and {comm/forward} and {comm/reverse} keywords.
|
||||
|
||||
The value options for all 3 keywords are {no} or {host} or {device}. A
|
||||
value of {no} means to use the standard non-KOKKOS method of
|
||||
packing/unpacking data for the communication. A value of {host} means to
|
||||
use the host, typically a multi-core CPU, and perform the
|
||||
packing/unpacking in parallel with threads. A value of {device} means to
|
||||
use the device, typically a GPU, to perform the packing/unpacking
|
||||
operation.
|
||||
|
||||
The optimal choice for these keywords depends on the input script and
|
||||
the hardware used. The {no} value is useful for verifying that the
|
||||
Kokkos-based {host} and {device} values are working correctly. It is the
|
||||
default when running on CPUs since it is usually the fastest.
|
||||
|
||||
When running on CPUs or Xeon Phi, the {host} and {device} values work
|
||||
identically. When using GPUs, the {device} value is the default since it
|
||||
will typically be optimal if all of your styles used in your input
|
||||
script are supported by the KOKKOS package. In this case data can stay
|
||||
on the GPU for many timesteps without being moved between the host and
|
||||
GPU, if you use the {device} value. If your script uses styles (e.g.
|
||||
fixes) which are not yet supported by the KOKKOS package, then data has
|
||||
to be move between the host and device anyway, so it is typically faster
|
||||
to let the host handle communication, by using the {host} value. Using
|
||||
{host} instead of {no} will enable use of multiple threads to
|
||||
pack/unpack communicated data. When running small systems on a GPU,
|
||||
performing the exchange pack/unpack on the host CPU can give speedup
|
||||
since it reduces the number of CUDA kernel launches.
|
||||
|
||||
The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When
|
||||
this keyword is set to {on}, buffers in GPU memory are passed directly
|
||||
through MPI send/receive calls. This reduces overhead of first copying
|
||||
the data to the host CPU. However CUDA-aware MPI is not supported on all
|
||||
systems, which can lead to segmentation faults and would require using a
|
||||
value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not
|
||||
available (currently only possible with OpenMPI v2.0.0 or later), then
|
||||
the {cuda/aware} keyword is automatically set to {off} by default. When
|
||||
the {cuda/aware} keyword is set to {off} while any of the {comm}
|
||||
keywords are set to {device}, the value for these {comm} keywords will
|
||||
be automatically changed to {host}. This setting has no effect if not
|
||||
running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later
|
||||
versions), Mvapich2 1.9 (or later) when the "MV2_USE_CUDA" environment
|
||||
variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu"
|
||||
flag is used.
|
||||
|
||||
:line
|
||||
|
||||
The {omp} style invokes settings associated with the use of the
|
||||
USER-OMP package.
|
||||
|
||||
The {Nthread} argument sets the number of OpenMP threads allocated for
|
||||
each MPI task. For example, if your system has nodes with dual
|
||||
quad-core processors, it has a total of 8 cores per node. You could
|
||||
use two MPI tasks per node (e.g. using the -ppn option of the mpirun
|
||||
command in MPICH or -npernode in OpenMPI), and set {Nthreads} = 4.
|
||||
This would use all 8 cores on each node. Note that the product of MPI
|
||||
tasks * threads/task should not exceed the physical number of cores
|
||||
(on a node), otherwise performance will suffer.
|
||||
|
||||
Setting {Nthread} = 0 instructs LAMMPS to use whatever value is the
|
||||
default for the given OpenMP environment. This is usually determined
|
||||
via the {OMP_NUM_THREADS} environment variable or the compiler
|
||||
runtime. Note that in most cases the default for OpenMP capable
|
||||
compilers is to use one thread for each available CPU core when
|
||||
{OMP_NUM_THREADS} is not explicitly set, which can lead to poor
|
||||
performance.
|
||||
|
||||
Here are examples of how to set the environment variable when
|
||||
launching LAMMPS:
|
||||
|
||||
env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
|
||||
env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
|
||||
mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script :pre
|
||||
|
||||
or you can set it permanently in your shell's start-up script.
|
||||
All three of these examples use a total of 4 CPU cores.
|
||||
|
||||
Note that different MPI implementations have different ways of passing
|
||||
the OMP_NUM_THREADS environment variable to all MPI processes. The
|
||||
2nd example line above is for MPICH; the 3rd example line with -x is
|
||||
for OpenMPI. Check your MPI documentation for additional details.
|
||||
|
||||
What combination of threads and MPI tasks gives the best performance
|
||||
is difficult to predict and can depend on many components of your
|
||||
input. Not all features of LAMMPS support OpenMP threading via the
|
||||
USER-OMP package and the parallel efficiency can be very different,
|
||||
too.
|
||||
|
||||
Optional keyword/value pairs can also be specified. Each has a
|
||||
default value as listed below.
|
||||
|
||||
The {neigh} keyword specifies whether neighbor list building will be
|
||||
multi-threaded in addition to force calculations. If {neigh} is set
|
||||
to {no} then neighbor list calculation is performed only by MPI tasks
|
||||
with no OpenMP threading. If {mode} is {yes} (the default), a
|
||||
multi-threaded neighbor list build is used. Using {neigh} = {yes} is
|
||||
almost always faster and should produce identical neighbor lists at the
|
||||
expense of using more memory. Specifically, neighbor list pages are
|
||||
allocated for all threads at the same time and each thread works
|
||||
within its own pages.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command cannot be used after the simulation box is defined by a
|
||||
"read_data"_read_data.html or "create_box"_create_box.html command.
|
||||
|
||||
The gpu style of this command can only be invoked if LAMMPS was built
|
||||
with the GPU package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
The intel style of this command can only be invoked if LAMMPS was
|
||||
built with the USER-INTEL package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
The kk style of this command can only be invoked if LAMMPS was built
|
||||
with the KOKKOS package. See the "Build package"_Build_package.html
|
||||
doc page for more info.
|
||||
|
||||
The omp style of this command can only be invoked if LAMMPS was built
|
||||
with the USER-OMP package. See the "Build package"_Build_package.html
|
||||
doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"suffix"_suffix.html, "-pk command-line switch"_Run_options.html
|
||||
|
||||
[Default:]
|
||||
|
||||
For the GPU package, the default is Ngpu = 1 and the option defaults
|
||||
are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
|
||||
to Ngpu-1, tpa = 1, and device = not used. These settings are made
|
||||
automatically if the "-sf gpu" "command-line switch"_Run_options.html
|
||||
is used. If it is not used, you must invoke the package gpu command
|
||||
in your input script or via the "-pk gpu" "command-line
|
||||
switch"_Run_options.html.
|
||||
|
||||
For the USER-INTEL package, the default is Nphi = 1 and the option
|
||||
defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4,
|
||||
tptask = 240. The default ghost option is determined by the pair
|
||||
style being used. This value is output to the screen in the offload
|
||||
report at the end of each run. Note that all of these settings,
|
||||
except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
|
||||
Phi co-processor support. These settings are made automatically if the
|
||||
"-sf intel" "command-line switch"_Run_options.html is used. If it is
|
||||
not used, you must invoke the package intel command in your input
|
||||
script or via the "-pk intel" "command-line
|
||||
switch"_Run_options.html.
|
||||
|
||||
For the KOKKOS package, the option defaults for GPUs are neigh = full,
|
||||
neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default
|
||||
value, comm = device, cuda/aware = on. When LAMMPS can safely detect
|
||||
that CUDA-aware MPI is not available, the default value of cuda/aware
|
||||
becomes "off". For CPUs or Xeon Phis, the option defaults are neigh =
|
||||
half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The
|
||||
option neigh/thread = on when there are 16K atoms or less on an MPI
|
||||
rank, otherwise it is "off". These settings are made automatically by
|
||||
the required "-k on" "command-line switch"_Run_options.html. You can
|
||||
change them by using the package kokkos command in your input script or
|
||||
via the "-pk kokkos command-line switch"_Run_options.html.
|
||||
|
||||
For the OMP package, the default is Nthreads = 0 and the option
|
||||
defaults are neigh = yes. These settings are made automatically if
|
||||
the "-sf omp" "command-line switch"_Run_options.html is used. If it
|
||||
is not used, you must invoke the package omp command in your input
|
||||
script or via the "-pk omp" "command-line switch"_Run_options.html.
|
||||
@ -97,8 +97,11 @@ This pair style can only be used via the {pair} keyword of the
|
||||
[Restrictions:]
|
||||
|
||||
Currently, only elemental systems are implemented. Also, the method
|
||||
only provides access to the forces and not energies or
|
||||
stresses. However, one can access the energy via thermodynamic
|
||||
only provides access to the forces and not energies or stresses.
|
||||
The lack of potential energy data makes this pair style incompatible with
|
||||
several of the "minimizer algorthms"_min_style.html like {cg} or {sd}.
|
||||
It should work with damped dynamics based minimizers like {fire} or
|
||||
{quickmin}. However, one can access the energy via thermodynamic
|
||||
integration of the forces as discussed in
|
||||
"(Botu3)"_#Botu2016construct. This pair style is part of the
|
||||
USER-MISC package. It is only enabled if LAMMPS was built with that
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user