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Merge branch 'master' into doc-styles-check

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Axel Kohlmeyer 2020-01-11 17:05:16 -05:00
parent 87a04db02c 7b8498fab6
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1
.github/CODEOWNERS vendored
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@ -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

6
cmake/Modules/FindNetCDF.cmake
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@ -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
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@ -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)

10
cmake/Modules/Packages/KIM.cmake
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@ -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)

26
cmake/Modules/Packages/USER-NETCDF.cmake
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@ -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()

2
doc/lammps.1
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@ -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
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@ -1,2 +1,3 @@
Eqs
JPG
/Eqs
/JPG
/false_positives.txt

20
doc/src/Build_extras.rst
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@ -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 KIM web queries.
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;

5
doc/src/Commands.rst
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@ -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

180
doc/src/Commands_all.rst
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@ -1,59 +1,135 @@
+----------------------------------------+------------------------------------+------------------------------------------+
| :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:`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\_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>`

203
doc/src/Commands_bond.rst
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@ -1,112 +1,169 @@
.. 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:`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>`
*

5
doc/src/Commands_category.rst
View File

@ -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

218
doc/src/Commands_compute.rst
View File

@ -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>`
*
*
*

314
doc/src/Commands_fix.rst
View File

@ -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 (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>`
*
*

5
doc/src/Commands_input.rst
View File

@ -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

44
doc/src/Commands_kspace.rst
View File

@ -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 +19,18 @@ 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:`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>`
*

368
doc/src/Commands_pair.rst
View File

@ -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>`
Pair\_style potentials
======================
@ -14,123 +19,234 @@ 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 (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:`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>`
*
*

5
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@ -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

5
doc/src/Commands_structure.rst
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@ -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

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@ -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}

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@ -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}

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@ -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}

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@ -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}

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@ -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}

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@ -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}

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@ -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}

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@ -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}

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@ -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

11
doc/src/Howto_pylammps.rst
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@ -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

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@ -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

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@ -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,
}

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@ -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).

7
doc/src/compute.rst
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@ -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

54
doc/src/compute_sna_atom.rst
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@ -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

35
doc/src/compute_spin.rst
View File

@ -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

2
doc/src/fix_ave_atom.rst
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@ -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]

28
doc/src/fix_bond_react.rst
View File

@ -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:

16
doc/src/fix_nve_dot.rst
View File

@ -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).

21
doc/src/fix_nve_dotc_langevin.rst
View File

@ -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).

94
doc/src/fix_precession_spin.rst
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@ -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

8
doc/src/package.rst
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@ -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.
----------

7
doc/src/pair_agni.rst
View File

@ -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

2
doc/src/pair_granular.rst
View File

@ -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

3
doc/src/pair_lj.rst
View File

@ -102,6 +102,9 @@ pair\_style lj/cut/tip4p/long/omp command
pair\_style lj/cut/tip4p/long/opt command
=========================================
pair\_style lj/cut/tip4p/long/gpu command
=====================================
Syntax
""""""

13
doc/src/pair_meamc.rst
View File

@ -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

45
doc/src/pair_oxdna.rst
View File

@ -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

55
doc/src/pair_oxdna2.rst
View File

@ -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
View 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).

73
doc/src/pair_spin_exchange.rst
View File

@ -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

61
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@ -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

23
doc/txt/Build_extras.txt
View File

@ -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;

60
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@ -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 -->

139
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@ -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)

148
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@ -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)

141
doc/txt/Commands_category.txt
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@ -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

166
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@ -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)

240
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@ -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)

37
doc/txt/Commands_kspace.txt
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@ -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)

253
doc/txt/Commands_pair.txt
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@ -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)

66
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@ -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

95
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@ -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.

256
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@ -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

7
doc/txt/compute.txt
View File

@ -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

192
doc/txt/compute_heat_flux.txt
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@ -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

51
doc/txt/compute_sna_atom.txt
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@ -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

77
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@ -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)

2
doc/txt/fix_ave_atom.txt
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@ -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

116
doc/txt/fix_precession_spin.txt
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@ -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.

660
doc/txt/package.txt
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@ -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.

7
doc/txt/pair_agni.txt
View File

@ -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

2
doc/txt/pair_meamc.txt
View File

@ -139,6 +139,8 @@ potential parameters:
lat = lattice structure of reference configuration
z = number of nearest neighbors in the reference structure
This field is only read for compatibility, the correct
value is inferred from the lattice structure
ielement = atomic number
atwt = atomic weight
alat = lattice constant of reference structure

98
doc/txt/pair_spin_exchange.txt
View File

@ -1,98 +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
pair_style spin/exchange command :h3
[Syntax:]
pair_style spin/exchange cutoff :pre
cutoff = global cutoff pair (distance in metal units) :ulb,l
:ule
[Examples:]
pair_style spin/exchange 4.0
pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre
[Description:]
Style {spin/exchange} computes the exchange interaction between
pairs of magnetic spins:
:c,image(Eqs/pair_spin_exchange_interaction.jpg)
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
interaction for different neighboring shells. This function is defined as:
:c,image(Eqs/pair_spin_exchange_function.jpg)
where a, b and d are the three constant coefficients defined in the associated
"pair_coeff" command (see below for more explanations).
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.
Examples and more explanations about this function and its parameterization are reported
in "(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 "fix_nve_spin"_fix_nve_spin.html),
such as:
:c,image(Eqs/pair_spin_exchange_forces.jpg)
with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit
vector between sites i and j.
More details about the derivation of these torques/forces are reported in
"(Tranchida)"_#Tranchida3.
For the {spin/exchange} pair style, the following coefficients must be defined
for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in
the examples above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html commands, and
set in the following order:
rc (distance units)
a (energy units)
b (adim parameter)
d (distance units) :ul
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.
None of those coefficients is optional. If not specified, the
{spin/exchange} pair style cannot be used.
:line
[Restrictions:]
All the {pair/spin} styles are part of the SPIN package. These styles
are 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, "pair_coeff"_pair_coeff.html,
"pair_eam"_pair_eam.html,
[Default:] none
:line
:link(Tranchida3)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, 372, 406-425, (2018).

83
doc/txt/pair_spin_neel.txt
View File

@ -1,83 +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
pair_style spin/neel command :h3
[Syntax:]
pair_style spin/neel cutoff :pre
cutoff = global cutoff pair (distance in metal units) :ulb,l
:ule
[Examples:]
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 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0 :pre
[Description:]
Style {spin/neel} computes the Neel pair anisotropy model
between pairs of magnetic spins:
:c,image(Eqs/pair_spin_neel_interaction.jpg)
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
and quadrupolar contributions, with:
:c,image(Eqs/pair_spin_neel_functions.jpg)
With the functions g(rij) and q(rij) defined and fitted according to
the same Bethe-Slater function used to fit the exchange interaction:
:c,image(Eqs/pair_spin_exchange_function.jpg)
where a, b and 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
above matches with the values of the magneto-elastic constant of the
materials at stake.
Examples and more explanations about this function and its
parameterization are reported in "(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
calculations only).
More details about the derivation of these torques/forces are reported
in "(Tranchida)"_#Tranchida6.
:line
[Restrictions:]
All the {pair/spin} styles are part of the SPIN package. These styles
are 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, "pair_coeff"_pair_coeff.html,
"pair_eam"_pair_eam.html,
[Default:] none
:line
:link(Tranchida6)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, 372, 406-425, (2018).

8
doc/utils/sphinx-config/conf.py
View File

@ -20,6 +20,7 @@ import os
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#sys.path.insert(0, os.path.abspath('.'))
sys.path.append(os.path.join(os.path.dirname(__file__), '../../src/_ext'))
# -- General configuration ------------------------------------------------
@ -30,7 +31,10 @@ import os
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.mathjax', 'sphinx.ext.imgmath'
'sphinx.ext.mathjax',
'sphinx.ext.imgmath',
'sphinx.ext.autodoc',
'table_from_list',
]
# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
# yet we can no longer use Sphinx 15.x, since that breaks with
@ -323,3 +327,5 @@ import LAMMPSLexer
from sphinx.highlighting import lexers
lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)
sys.path.append(os.path.join(os.path.dirname(__file__), '../../../python'))

7
doc/utils/sphinx-config/false_positives.txt
View File

@ -213,6 +213,7 @@ Berne
Bertotti
Bessarab
Beutler
Bext
bgq
Bh
Biersack
@ -1042,6 +1043,7 @@ Gunsteren
Gunzenmuller
Guo
gw
gyromagnetic
gz
gzipped
Haak
@ -1061,6 +1063,7 @@ Haswell
Haugk
Hayoun
Hayre
hbar
hbcut
hbn
hbnewflag
@ -1403,6 +1406,7 @@ Lammps
LAMMPS
lammpsplot
Lamoureux
Lande
Landron
langevin
Langevin
@ -1775,6 +1779,7 @@ mtk
Mtotal
muB
Muccioli
mui
Mukherjee
Mulders
multi
@ -2074,7 +2079,9 @@ Ouyang
overlayed
Ovito
oxdna
oxrna
oxDNA
oxRNA
padua
Padua
palegoldenrod

16
examples/SPIN/README
View File

@ -1,20 +1,24 @@
This directory contains examples and applications of the SPIN package
=====================================================================
- the benchmark directory provides comparison between LAMMPS
results and a series of simple test problems (coded as python
scripts).
- the iron, cobalt_hcp, cobalt_fcc and nickel directories provide
examples of spin-lattice calculations.
examples of spin-lattice calculations.
- the bfo repository provides an example of spin dynamics calculation
performed on a fixed lattice, and applied to the multiferroic
material bismuth-oxide.
performed on a fixed lattice, and applied to the multiferroic
material bismuth-oxide.
- the read_restart directory provides examples allowing to write or
read data files, and restart magneto-mechanical simulations.
read data files, and restart magneto-mechanical simulations.
- vizualization of the dump files can be achieved using Ovito or
VMD. See the vmd repository for help vizualizing results with VMD.
VMD. See the vmd repository for help vizualizing results with VMD.
** Note, the aim of this repository is mainly to provide users with
examples. Better values and tuning of the magnetic and mechanical
interactions can be achieved for more accurate materials
interactions can (have to...) be achieved for more accurate materials
simulations. **

7
examples/SPIN/bfo/in.spin.bfo
View File

@ -1,9 +1,7 @@
# layer sc iron atoms (in the [001] plane) in bismuth oxide
clear
units metal
atom_style spin
dimension 3
boundary p p f
@ -18,7 +16,6 @@ create_atoms 1 box
# setting mass, mag. moments, and interactions for bfo
mass 1 1.0
set group all spin/random 11 2.50
#pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
@ -51,6 +48,6 @@ thermo_style custom step time v_magnorm pe ke v_emag temp etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
dump 1 all custom 100 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 2000
run 500

212
examples/SPIN/bfo/log.11May18.spin.bfo.g++.1
View File

@ -1,212 +0,0 @@
LAMMPS (11 May 2018)
# layer sc iron atoms (in the [001] plane) in bismuth oxide
clear
units metal
atom_style spin
dimension 3
boundary p p f
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice sc 3.96
Lattice spacing in x,y,z = 3.96 3.96 3.96
region box block 0.0 34.0 0.0 34.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 5780 atoms
Time spent = 0.0013566 secs
# setting mass, mag. moments, and interactions for bfo
mass 1 1.0
set group all spin/random 11 2.50
5780 settings made for spin/random
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.1 21
fix 3 all nve/spin lattice no
timestep 0.0002
compute out_mag all compute/spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_emag temp etotal
thermo 50
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 5000
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.1
ghost atom cutoff = 6.1
binsize = 3.05, bins = 45 45 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair spin/magelec, perpetual, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.272 | 7.272 | 7.272 Mbytes
Step Time v_magnorm v_emag Temp TotEng
0 0 0.010071723 -0.13298298 0 -0.12034311
50 0.01 0.0098643821 -1.3898985 0 -1.3772103
100 0.02 0.0096526211 -2.6381677 0 -2.6254222
150 0.03 0.0094342235 -3.8784006 0 -3.8656019
200 0.04 0.0092074832 -5.111441 0 -5.0986001
250 0.05 0.0089713115 -6.3380611 0 -6.3251904
300 0.06 0.0087256081 -7.5587787 0 -7.5458894
350 0.07 0.0084715548 -8.7738491 0 -8.7609521
400 0.08 0.008211486 -9.9833855 0 -9.9704932
450 0.09 0.0079483243 -11.18751 0 -11.174637
500 0.1 0.0076849713 -12.386462 0 -12.37362
550 0.11 0.007424064 -13.580633 0 -13.567832
600 0.12 0.0071680699 -14.770519 0 -14.757759
650 0.13 0.0069192726 -15.956579 0 -15.943853
700 0.14 0.0066793495 -17.139049 0 -17.126343
750 0.15 0.0064488038 -18.317803 0 -18.305099
800 0.16 0.0062267571 -19.492336 0 -19.479616
850 0.17 0.0060112235 -20.661925 0 -20.649176
900 0.18 0.0057995251 -21.825931 0 -21.813141
950 0.19 0.0055886511 -22.98413 0 -22.971297
1000 0.2 0.0053757923 -24.136967 0 -24.124095
1050 0.21 0.0051592263 -25.285621 0 -25.272717
1100 0.22 0.0049391661 -26.431928 0 -26.419004
1150 0.23 0.0047179149 -27.578212 0 -27.565281
1200 0.24 0.0044991004 -28.727051 0 -28.714128
1250 0.25 0.0042864034 -29.880967 0 -29.868062
1300 0.26 0.0040824475 -31.042054 0 -31.029173
1350 0.27 0.0038883007 -32.21165 0 -32.198795
1400 0.28 0.0037036595 -33.390159 0 -33.377326
1450 0.29 0.0035274815 -34.577121 0 -34.564302
1500 0.3 0.0033587207 -35.771483 0 -35.758672
1550 0.31 0.0031969501 -36.971996 0 -36.95919
1600 0.32 0.0030429081 -38.177601 0 -38.164801
1650 0.33 0.0028989804 -39.387757 0 -39.374962
1700 0.34 0.0027692024 -40.602665 0 -40.589873
1750 0.35 0.0026581403 -41.823341 0 -41.81054
1800 0.36 0.0025686991 -43.05145 0 -43.038628
1850 0.37 0.002500124 -44.288966 0 -44.276111
1900 0.38 0.0024477804 -45.537752 0 -45.52486
1950 0.39 0.0024050049 -46.799255 0 -46.786336
2000 0.4 0.0023657031 -48.074388 0 -48.061466
2050 0.41 0.0023260844 -49.363587 0 -49.350695
2100 0.42 0.0022848329 -50.666866 0 -50.654039
2150 0.43 0.0022419759 -51.983781 0 -51.971055
2200 0.44 0.0021972506 -53.31336 0 -53.300764
2250 0.45 0.0021488322 -54.654121 0 -54.641676
2300 0.46 0.0020929483 -56.004207 0 -55.991918
2350 0.47 0.0020244601 -57.361586 0 -57.349442
2400 0.48 0.001938225 -58.72428 0 -58.712247
2450 0.49 0.0018309419 -60.09064 0 -60.078671
2500 0.5 0.0017030436 -61.459658 0 -61.447705
2550 0.51 0.0015599449 -62.831213 0 -62.819237
2600 0.52 0.0014117554 -64.206088 0 -64.194074
2650 0.53 0.0012709942 -65.585701 0 -65.573657
2700 0.54 0.0011490452 -66.971565 0 -66.959515
2750 0.55 0.001053009 -68.364663 0 -68.352635
2800 0.56 0.00098415327 -69.765002 0 -69.753017
2850 0.57 0.00093809306 -71.171532 0 -71.159598
2900 0.58 0.00090656933 -72.58234 0 -72.570459
2950 0.59 0.00088069677 -73.994931 0 -73.983099
3000 0.6 0.00085472643 -75.406507 0 -75.39472
3050 0.61 0.00082842902 -76.814319 0 -76.802575
3100 0.62 0.00080642618 -78.216074 0 -78.204373
3150 0.63 0.00079463972 -79.610246 0 -79.598589
3200 0.64 0.0007962304 -80.996103 0 -80.984494
3250 0.65 0.00080980411 -82.37346 0 -82.361903
3300 0.66 0.00083070982 -83.742356 0 -83.730855
3350 0.67 0.00085389185 -85.102808 0 -85.091374
3400 0.68 0.00087624091 -86.454619 0 -86.443259
3450 0.69 0.00089741986 -87.797089 0 -87.785814
3500 0.7 0.00091910796 -89.12875 0 -89.117567
3550 0.71 0.00094318459 -90.447312 0 -90.436232
3600 0.72 0.00096989367 -91.750008 0 -91.739046
3650 0.73 0.00099713096 -93.034224 0 -93.023402
3700 0.74 0.0010212995 -94.298186 0 -94.287529
3750 0.75 0.0010391164 -95.5414 0 -95.530926
3800 0.76 0.0010491462 -96.764626 0 -96.754338
3850 0.77 0.0010521238 -97.969346 0 -97.95923
3900 0.78 0.0010500324 -99.156875 0 -99.146899
3950 0.79 0.0010447043 -100.32743 0 -100.31756
4000 0.8 0.0010368986 -101.4796 0 -101.46978
4050 0.81 0.0010263632 -102.61044 0 -102.60064
4100 0.82 0.0010126933 -103.71619 0 -103.70639
4150 0.83 0.00099631895 -104.79338 0 -104.78358
4200 0.84 0.0009789075 -105.8398 0 -105.82998
4250 0.85 0.00096287608 -106.85496 0 -106.84515
4300 0.86 0.00095034023 -107.84011 0 -107.83029
4350 0.87 0.00094219078 -108.7976 0 -108.78778
4400 0.88 0.00093779428 -109.73016 0 -109.72031
4450 0.89 0.0009354459 -110.63996 0 -110.63008
4500 0.9 0.00093342614 -111.52805 0 -111.51812
4550 0.91 0.0009311077 -112.39417 0 -112.38416
4600 0.92 0.00092926689 -113.23706 0 -113.22697
4650 0.93 0.00092921566 -114.05512 0 -114.04495
4700 0.94 0.00093142598 -114.84701 0 -114.83675
4750 0.95 0.00093479851 -115.61197 0 -115.60164
4800 0.96 0.0009369799 -116.3499 0 -116.33951
4850 0.97 0.00093516768 -117.06128 0 -117.05084
4900 0.98 0.00092684411 -117.74695 0 -117.73645
4950 0.99 0.00091046222 -118.40798 0 -118.39742
5000 1 0.00088619957 -119.04554 0 -119.03492
Loop time of 128.304 on 1 procs for 5000 steps with 5780 atoms
Performance: 0.673 ns/day, 35.640 hours/ns, 38.970 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 24.227 | 24.227 | 24.227 | 0.0 | 18.88
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.081048 | 0.081048 | 0.081048 | 0.0 | 0.06
Output | 39.796 | 39.796 | 39.796 | 0.0 | 31.02
Modify | 64.112 | 64.112 | 64.112 | 0.0 | 49.97
Other | | 0.08788 | | | 0.07
Nlocal: 5780 ave 5780 max 5780 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1065 ave 1065 max 1065 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 92480 ave 92480 max 92480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 92480
Ave neighs/atom = 16
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:02:08

212
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LAMMPS (11 May 2018)
# layer sc iron atoms (in the [001] plane) in bismuth oxide
clear
units metal
atom_style spin
dimension 3
boundary p p f
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice sc 3.96
Lattice spacing in x,y,z = 3.96 3.96 3.96
region box block 0.0 34.0 0.0 34.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 5780 atoms
Time spent = 0.000355959 secs
# setting mass, mag. moments, and interactions for bfo
mass 1 1.0
set group all spin/random 11 2.50
5780 settings made for spin/random
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.1 21
fix 3 all nve/spin lattice no
timestep 0.0002
compute out_mag all compute/spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_emag temp etotal
thermo 50
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 5000
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.1
ghost atom cutoff = 6.1
binsize = 3.05, bins = 45 45 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair spin/magelec, perpetual, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 6.862 | 6.862 | 6.862 Mbytes
Step Time v_magnorm v_emag Temp TotEng
0 0 0.010071723 -0.13298298 0 -0.12034311
50 0.01 0.0098643821 -1.3898985 0 -1.3772103
100 0.02 0.009652621 -2.6381677 0 -2.6254222
150 0.03 0.0094342234 -3.8784007 0 -3.8656019
200 0.04 0.009207483 -5.1114411 0 -5.0986001
250 0.05 0.0089713114 -6.3380611 0 -6.3251904
300 0.06 0.0087256079 -7.5587787 0 -7.5458894
350 0.07 0.0084715546 -8.7738491 0 -8.7609521
400 0.08 0.0082114858 -9.9833855 0 -9.9704932
450 0.09 0.0079483242 -11.18751 0 -11.174637
500 0.1 0.0076849711 -12.386462 0 -12.37362
550 0.11 0.0074240638 -13.580633 0 -13.567832
600 0.12 0.0071680697 -14.770519 0 -14.757759
650 0.13 0.0069192724 -15.956579 0 -15.943853
700 0.14 0.0066793493 -17.139049 0 -17.126343
750 0.15 0.0064488035 -18.317803 0 -18.305099
800 0.16 0.0062267569 -19.492336 0 -19.479616
850 0.17 0.0060112233 -20.661925 0 -20.649176
900 0.18 0.005799525 -21.825931 0 -21.813141
950 0.19 0.0055886511 -22.98413 0 -22.971297
1000 0.2 0.0053757923 -24.136967 0 -24.124095
1050 0.21 0.0051592265 -25.285621 0 -25.272717
1100 0.22 0.0049391664 -26.431928 0 -26.419004
1150 0.23 0.0047179153 -27.578212 0 -27.565281
1200 0.24 0.0044991009 -28.727051 0 -28.714128
1250 0.25 0.0042864039 -29.880967 0 -29.868062
1300 0.26 0.004082448 -31.042054 0 -31.029174
1350 0.27 0.0038883012 -32.21165 0 -32.198795
1400 0.28 0.0037036599 -33.390159 0 -33.377326
1450 0.29 0.0035274817 -34.577121 0 -34.564302
1500 0.3 0.0033587208 -35.771483 0 -35.758672
1550 0.31 0.0031969501 -36.971996 0 -36.95919
1600 0.32 0.0030429079 -38.177601 0 -38.164801
1650 0.33 0.0028989801 -39.387757 0 -39.374962
1700 0.34 0.0027692022 -40.602666 0 -40.589873
1750 0.35 0.0026581401 -41.823341 0 -41.81054
1800 0.36 0.002568699 -43.05145 0 -43.038628
1850 0.37 0.0025001242 -44.288966 0 -44.276111
1900 0.38 0.0024477808 -45.537752 0 -45.52486
1950 0.39 0.0024050056 -46.799255 0 -46.786336
2000 0.4 0.002365704 -48.074388 0 -48.061466
2050 0.41 0.0023260854 -49.363587 0 -49.350695
2100 0.42 0.002284834 -50.666866 0 -50.654039
2150 0.43 0.0022419771 -51.983781 0 -51.971055
2200 0.44 0.0021972518 -53.31336 0 -53.300764
2250 0.45 0.0021488333 -54.654121 0 -54.641676
2300 0.46 0.0020929494 -56.004207 0 -55.991918
2350 0.47 0.0020244612 -57.361586 0 -57.349441
2400 0.48 0.0019382262 -58.72428 0 -58.712247
2450 0.49 0.001830943 -60.090639 0 -60.078671
2500 0.5 0.0017030446 -61.459658 0 -61.447704
2550 0.51 0.0015599459 -62.831213 0 -62.819237
2600 0.52 0.0014117562 -64.206088 0 -64.194074
2650 0.53 0.001270995 -65.5857 0 -65.573657
2700 0.54 0.001149046 -66.971565 0 -66.959515
2750 0.55 0.0010530098 -68.364663 0 -68.352635
2800 0.56 0.00098415418 -69.765002 0 -69.753017
2850 0.57 0.00093809402 -71.171532 0 -71.159598
2900 0.58 0.00090657031 -72.58234 0 -72.570459
2950 0.59 0.00088069773 -73.994931 0 -73.983099
3000 0.6 0.00085472731 -75.406507 0 -75.39472
3050 0.61 0.00082842975 -76.814319 0 -76.802575
3100 0.62 0.00080642669 -78.216074 0 -78.204373
3150 0.63 0.00079464 -79.610246 0 -79.59859
3200 0.64 0.00079623049 -80.996103 0 -80.984494
3250 0.65 0.00080980416 -82.373461 0 -82.361903
3300 0.66 0.00083070997 -83.742356 0 -83.730856
3350 0.67 0.00085389223 -85.102809 0 -85.091374
3400 0.68 0.00087624159 -86.454619 0 -86.44326
3450 0.69 0.00089742086 -87.79709 0 -87.785815
3500 0.7 0.00091910931 -89.12875 0 -89.117568
3550 0.71 0.00094318635 -90.447312 0 -90.436233
3600 0.72 0.00096989594 -91.750008 0 -91.739047
3650 0.73 0.00099713386 -93.034224 0 -93.023403
3700 0.74 0.0010213031 -94.298186 0 -94.287529
3750 0.75 0.0010391209 -95.541401 0 -95.530926
3800 0.76 0.0010491514 -96.764626 0 -96.754339
3850 0.77 0.0010521296 -97.969347 0 -97.959231
3900 0.78 0.0010500386 -99.156876 0 -99.146899
3950 0.79 0.0010447106 -100.32743 0 -100.31756
4000 0.8 0.0010369046 -101.4796 0 -101.46978
4050 0.81 0.0010263688 -102.61044 0 -102.60064
4100 0.82 0.0010126985 -103.71619 0 -103.70639
4150 0.83 0.00099632366 -104.79338 0 -104.78358
4200 0.84 0.00097891183 -105.8398 0 -105.82998
4250 0.85 0.00096288003 -106.85496 0 -106.84515
4300 0.86 0.00095034371 -107.84011 0 -107.83029
4350 0.87 0.00094219371 -108.7976 0 -108.78778
4400 0.88 0.00093779663 -109.73016 0 -109.72031
4450 0.89 0.00093544766 -110.63996 0 -110.63008
4500 0.9 0.00093342739 -111.52805 0 -111.51812
4550 0.91 0.00093110855 -112.39417 0 -112.38416
4600 0.92 0.00092926746 -113.23706 0 -113.22697
4650 0.93 0.00092921608 -114.05512 0 -114.04495
4700 0.94 0.0009314263 -114.84701 0 -114.83675
4750 0.95 0.0009347987 -115.61197 0 -115.60164
4800 0.96 0.00093697985 -116.3499 0 -116.33951
4850 0.97 0.00093516726 -117.06128 0 -117.05084
4900 0.98 0.00092684316 -117.74695 0 -117.73645
4950 0.99 0.00091046061 -118.40798 0 -118.39742
5000 1 0.00088619727 -119.04554 0 -119.03492
Loop time of 37.142 on 4 procs for 5000 steps with 5780 atoms
Performance: 2.326 ns/day, 10.317 hours/ns, 134.619 timesteps/s
98.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.2804 | 6.3487 | 6.4569 | 2.7 | 17.09
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.15385 | 0.27957 | 0.36215 | 14.6 | 0.75
Output | 10.573 | 10.784 | 10.994 | 4.8 | 29.03
Modify | 19.48 | 19.707 | 19.925 | 3.7 | 53.06
Other | | 0.02255 | | | 0.06
Nlocal: 1445 ave 1445 max 1445 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 555 ave 555 max 555 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 23120 ave 23120 max 23120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 92480
Ave neighs/atom = 16
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:37

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LAMMPS (30 Oct 2019)
# layer sc iron atoms (in the [001] plane) in bismuth oxide
units metal
atom_style spin
dimension 3
boundary p p f
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice sc 3.96
Lattice spacing in x,y,z = 3.96 3.96 3.96
region box block 0.0 34.0 0.0 34.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 5780 atoms
create_atoms CPU = 0.00226784 secs
# setting mass, mag. moments, and interactions for bfo
mass 1 1.0
set group all spin/random 11 2.50
5780 settings made for spin/random
#pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.1 21
fix 3 all nve/spin lattice frozen
timestep 0.0002
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
#thermo_style custom step time v_magnorm v_emag temp etotal
thermo_style custom step time v_magnorm pe ke v_emag temp etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 100 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 500
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.1
ghost atom cutoff = 6.1
binsize = 3.05, bins = 45 45 7
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair spin/magelec, perpetual, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(3) pair spin/dmi, perpetual, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.154 | 8.154 | 8.154 Mbytes
Step Time v_magnorm PotEng KinEng v_emag Temp TotEng
0 0 0.010071723 -0.059343109 0 -0.13132609 0 -0.059343109
10 0.002 0.01003044 -0.18537022 0 -0.38338861 0 -0.18537022
20 0.004 0.0099890716 -0.31121926 0 -0.63509581 0 -0.31121926
30 0.006 0.0099475919 -0.43689013 0 -0.88644739 0 -0.43689013
40 0.008 0.0099059782 -0.5623833 0 -1.1374442 0 -0.5623833
50 0.01 0.0098642085 -0.68769978 0 -1.388088 0 -0.68769978
60 0.012 0.0098222618 -0.81284106 0 -1.6383818 0 -0.81284106
70 0.014 0.0097801186 -0.93780907 0 -1.8883294 0 -0.93780907
80 0.016 0.0097377603 -1.0626062 0 -2.1379352 0 -1.0626062
90 0.018 0.0096951693 -1.187235 0 -2.3872045 0 -1.187235
100 0.02 0.0096523288 -1.3116986 0 -2.6361432 0 -1.3116986
110 0.022 0.0096092227 -1.4360002 0 -2.8847577 0 -1.4360002
120 0.024 0.009565836 -1.5601431 0 -3.1330547 0 -1.5601431
130 0.026 0.0095221542 -1.6841309 0 -3.3810411 0 -1.6841309
140 0.028 0.0094781635 -1.8079673 0 -3.6287241 0 -1.8079673
150 0.03 0.0094338509 -1.9316557 0 -3.8761109 0 -1.9316557
160 0.032 0.0093892044 -2.0551997 0 -4.1232085 0 -2.0551997
170 0.034 0.0093442126 -2.178603 0 -4.370024 0 -2.178603
180 0.036 0.0092988654 -2.3018687 0 -4.6165639 0 -2.3018687
190 0.038 0.0092531537 -2.4250002 0 -4.8628348 0 -2.4250002
200 0.04 0.0092070698 -2.5480003 0 -5.1088426 0 -2.5480003
210 0.042 0.0091606073 -2.670872 0 -5.3545929 0 -2.670872
220 0.044 0.0091137617 -2.7936178 0 -5.6000909 0 -2.7936178
230 0.046 0.0090665298 -2.9162399 0 -5.8453412 0 -2.9162399
240 0.048 0.0090189108 -3.0387405 0 -6.0903478 0 -3.0387405
250 0.05 0.0089709056 -3.1611214 0 -6.3351146 0 -3.1611214
260 0.052 0.0089225173 -3.2833841 0 -6.5796445 0 -3.2833841
270 0.054 0.0088737511 -3.4055299 0 -6.8239403 0 -3.4055299
280 0.056 0.0088246147 -3.52756 0 -7.0680043 0 -3.52756
290 0.058 0.0087751176 -3.6494754 0 -7.3118383 0 -3.6494754
300 0.06 0.008725272 -3.7712768 0 -7.5554438 0 -3.7712768
310 0.062 0.0086750916 -3.8929648 0 -7.7988222 0 -3.8929648
320 0.064 0.0086245927 -4.0145399 0 -8.0419744 0 -4.0145399
330 0.066 0.0085737928 -4.1360026 0 -8.2849013 0 -4.1360026
340 0.068 0.0085227116 -4.2573532 0 -8.5276035 0 -4.2573532
350 0.07 0.0084713698 -4.378592 0 -8.7700818 0 -4.378592
360 0.072 0.0084197895 -4.4997194 0 -9.0123367 0 -4.4997194
370 0.074 0.0083679936 -4.6207358 0 -9.2543688 0 -4.6207358
380 0.076 0.0083160058 -4.7416414 0 -9.496179 0 -4.7416414
390 0.078 0.0082638503 -4.8624367 0 -9.7377681 0 -4.8624367
400 0.08 0.0082115512 -4.9831222 0 -9.9791371 0 -4.9831222
410 0.082 0.0081591329 -5.1036986 0 -10.220287 0 -5.1036986
420 0.084 0.0081066195 -5.2241665 0 -10.46122 0 -5.2241665
430 0.086 0.0080540347 -5.3445267 0 -10.701936 0 -5.3445267
440 0.088 0.008001402 -5.4647802 0 -10.942439 0 -5.4647802
450 0.09 0.0079487439 -5.5849281 0 -11.18273 0 -5.5849281
460 0.092 0.0078960829 -5.7049716 0 -11.422811 0 -5.7049716
470 0.094 0.0078434404 -5.824912 0 -11.662686 0 -5.824912
480 0.096 0.0077908378 -5.9447508 0 -11.902357 0 -5.9447508
490 0.098 0.0077382955 -6.0644896 0 -12.141828 0 -6.0644896
500 0.1 0.0076858338 -6.1841301 0 -12.381101 0 -6.1841301
Loop time of 13.543 on 1 procs for 500 steps with 5780 atoms
Performance: 0.638 ns/day, 37.619 hours/ns, 36.919 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.8138 | 3.8138 | 3.8138 | 0.0 | 28.16
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.011875 | 0.011875 | 0.011875 | 0.0 | 0.09
Output | 0.049726 | 0.049726 | 0.049726 | 0.0 | 0.37
Modify | 9.655 | 9.655 | 9.655 | 0.0 | 71.29
Other | | 0.01262 | | | 0.09
Nlocal: 5780 ave 5780 max 5780 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1065 ave 1065 max 1065 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 92480 ave 92480 max 92480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 92480
Ave neighs/atom = 16
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:13

167
examples/SPIN/bfo/log.19Nov19.spin.bfo.g++.4 Normal file
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LAMMPS (30 Oct 2019)
# layer sc iron atoms (in the [001] plane) in bismuth oxide
units metal
atom_style spin
dimension 3
boundary p p f
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice sc 3.96
Lattice spacing in x,y,z = 3.96 3.96 3.96
region box block 0.0 34.0 0.0 34.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 5780 atoms
create_atoms CPU = 0.00149798 secs
# setting mass, mag. moments, and interactions for bfo
mass 1 1.0
set group all spin/random 11 2.50
5780 settings made for spin/random
#pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.1 21
fix 3 all nve/spin lattice frozen
timestep 0.0002
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
#thermo_style custom step time v_magnorm v_emag temp etotal
thermo_style custom step time v_magnorm pe ke v_emag temp etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 100 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 500
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.1
ghost atom cutoff = 6.1
binsize = 3.05, bins = 45 45 7
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair spin/magelec, perpetual, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(3) pair spin/dmi, perpetual, copy from (1)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.744 | 7.744 | 7.744 Mbytes
Step Time v_magnorm PotEng KinEng v_emag Temp TotEng
0 0 0.010071723 -0.11868622 0 -0.12966919 0 -0.11868622
10 0.002 0.010030399 -0.37068593 0 -0.38171598 0 -0.37068593
20 0.004 0.0099889925 -0.6223216 0 -0.6334048 0 -0.6223216
30 0.006 0.0099474775 -0.87359359 0 -0.8847354 0 -0.87359359
40 0.008 0.0099058307 -1.1245034 0 -1.1357086 0 -1.1245034
50 0.01 0.0098640297 -1.3750538 0 -1.3863265 0 -1.3750538
60 0.012 0.0098220535 -1.6252482 0 -1.6365919 0 -1.6252482
70 0.014 0.0097798823 -1.8750914 0 -1.8865086 0 -1.8750914
80 0.016 0.0097374973 -2.1245886 0 -2.1360814 0 -2.1245886
90 0.018 0.0096948808 -2.3737458 0 -2.3853155 0 -2.3737458
100 0.02 0.0096520159 -2.6225698 0 -2.6342168 0 -2.6225698
110 0.022 0.0096088866 -2.8710677 0 -2.8827919 0 -2.8710677
120 0.024 0.0095654776 -3.1192469 0 -3.1310475 0 -3.1192469
130 0.026 0.0095217746 -3.367115 0 -3.3789906 0 -3.367115
140 0.028 0.0094777638 -3.61468 0 -3.6266285 0 -3.61468
150 0.03 0.0094334323 -3.8619496 0 -3.8739683 0 -3.8619496
160 0.032 0.0093887679 -4.1089316 0 -4.1210173 0 -4.1089316
170 0.034 0.0093437596 -4.3556335 0 -4.3677824 0 -4.3556335
180 0.036 0.0092983972 -4.6020625 0 -4.6142704 0 -4.6020625
190 0.038 0.0092526717 -4.8482255 0 -4.8604877 0 -4.8482255
200 0.04 0.0092065755 -5.0941291 0 -5.1064403 0 -5.0941291
210 0.042 0.0091601024 -5.3397792 0 -5.3521339 0 -5.3397792
220 0.044 0.0091132478 -5.5851813 0 -5.5975736 0 -5.5851813
230 0.046 0.0090660089 -5.8303404 0 -5.842764 0 -5.8303404
240 0.048 0.0090183847 -6.0752609 0 -6.0877092 0 -6.0752609
250 0.05 0.0089703764 -6.3199467 0 -6.3324129 0 -6.3199467
260 0.052 0.0089219873 -6.5644011 0 -6.5768782 0 -6.5644011
270 0.054 0.0088732228 -6.808627 0 -6.8211078 0 -6.808627
280 0.056 0.0088240906 -7.0526266 0 -7.0651038 0 -7.0526266
290 0.058 0.0087746006 -7.296402 0 -7.3088682 0 -7.296402
300 0.06 0.0087247648 -7.5399545 0 -7.5524024 0 -7.5399545
310 0.062 0.0086745976 -7.7832854 0 -7.7957077 0 -7.7832854
320 0.064 0.0086241149 -8.0263956 0 -8.038785 0 -8.0263956
330 0.066 0.008573335 -8.2692858 0 -8.281635 0 -8.2692858
340 0.068 0.0085222772 -8.5119564 0 -8.5242586 0 -8.5119564
350 0.07 0.0084709627 -8.7544078 0 -8.7666562 0 -8.7544078
360 0.072 0.0084194136 -8.9966403 0 -9.0088285 0 -8.9966403
370 0.074 0.008367653 -9.2386543 0 -9.2507761 0 -9.2386543
380 0.076 0.0083157046 -9.4804501 0 -9.4924997 0 -9.4804501
390 0.078 0.0082635925 -9.7220281 0 -9.7340001 0 -9.7220281
400 0.08 0.0082113412 -9.9633888 0 -9.9752784 0 -9.9633888
410 0.082 0.0081589747 -10.204533 0 -10.216336 0 -10.204533
420 0.084 0.0081065173 -10.445462 0 -10.457173 0 -10.445462
430 0.086 0.0080539925 -10.686176 0 -10.697793 0 -10.686176
440 0.088 0.0080014235 -10.926676 0 -10.938197 0 -10.926676
450 0.09 0.0079488329 -11.166966 0 -11.178387 0 -11.166966
460 0.092 0.0078962427 -11.407045 0 -11.418366 0 -11.407045
470 0.094 0.0078436743 -11.646917 0 -11.658136 0 -11.646917
480 0.096 0.0077911486 -11.886583 0 -11.8977 0 -11.886583
490 0.098 0.007738686 -12.126047 0 -12.137063 0 -12.126047
500 0.1 0.0076863062 -12.365311 0 -12.376226 0 -12.365311
Loop time of 3.94852 on 4 procs for 500 steps with 5780 atoms
Performance: 2.188 ns/day, 10.968 hours/ns, 126.630 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.97416 | 0.98668 | 1.0022 | 1.0 | 24.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.032618 | 0.04948 | 0.062614 | 5.0 | 1.25
Output | 0.014166 | 0.014229 | 0.014374 | 0.1 | 0.36
Modify | 2.8947 | 2.8957 | 2.8965 | 0.0 | 73.34
Other | | 0.002385 | | | 0.06
Nlocal: 1445 ave 1445 max 1445 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 555 ave 555 max 555 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 23120 ave 23120 max 23120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 92480
Ave neighs/atom = 16
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

4
examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
View File

@ -57,7 +57,7 @@ variable tmag equal c_out_mag[6]
thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
thermo 50
#compute outsp all property/atom spx spy spz sp fmx fmy fmz
#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
# compute outsp all property/atom spx spy spz sp fmx fmy fmz
# dump 1 all custom 100 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 1000

142
examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1
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@ -1,142 +0,0 @@
LAMMPS (11 May 2018)
# fcc cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice fcc 3.54
Lattice spacing in x,y,z = 3.54 3.54 3.54
region box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000651121 secs
# setting mass, mag. moments, and interactions for fcc cobalt
mass 1 58.93
#set group all spin/random 31 1.72
set group all spin 1.72 0.0 0.0 1.0
500 settings made for spin
velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix_modify 1 energy yes
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
timestep 0.0001
# compute and output options
compute out_mag all compute/spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
thermo_style custom f_1
variable magx equal c_out_mag[1]
variable magy equal c_out_mag[2]
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
thermo 50
#compute outsp all property/atom spx spy spz sp fmx fmy fmz
#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 1000
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.59954
ghost atom cutoff = 6.59954
binsize = 3.29977, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.218 | 5.218 | 5.218 Mbytes
Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng
0 0 0.049785486 0 0 1 -187.94116 100.00543 -2372.4636
50 0.005 0.049785486 0 0 1 -187.94112 95.094679 -2372.4636
100 0.01 0.049785486 0 0 1 -187.94071 81.578321 -2372.4636
150 0.015 0.049785486 0 0 1 -187.93912 62.802727 -2372.4636
200 0.02 0.049785486 0 0 1 -187.93551 43.35108 -2372.4636
250 0.025 0.049785486 0 0 1 -187.92942 27.749821 -2372.4636
300 0.03 0.049785486 0 0 1 -187.92118 19.149389 -2372.4636
350 0.035 0.049785486 0 0 1 -187.91199 18.453387 -2372.4636
400 0.04 0.049785486 0 0 1 -187.90364 24.249423 -2372.4636
450 0.045 0.049785486 0 0 1 -187.89806 33.548008 -2372.4636
500 0.05 0.049785486 0 0 1 -187.89668 42.973172 -2372.4636
550 0.055 0.049785486 0 0 1 -187.9 49.902539 -2372.4636
600 0.06 0.049785486 0 0 1 -187.90735 53.166772 -2372.4636
650 0.065 0.049785486 0 0 1 -187.91706 53.153416 -2372.4636
700 0.07 0.049785486 0 0 1 -187.92692 51.377187 -2372.4636
750 0.075 0.049785486 0 0 1 -187.9348 49.725449 -2372.4636
800 0.08 0.049785486 0 0 1 -187.93921 49.663576 -2372.4636
850 0.085 0.049785486 0 0 1 -187.93974 51.681567 -2372.4636
900 0.09 0.049785486 0 0 1 -187.937 55.166554 -2372.4636
950 0.095 0.049785486 0 0 1 -187.93239 58.718232 -2372.4636
1000 0.1 0.049785486 0 0 1 -187.92755 60.75567 -2372.4636
Loop time of 4.1303 on 1 procs for 1000 steps with 500 atoms
Performance: 2.092 ns/day, 11.473 hours/ns, 242.113 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.142 | 2.142 | 2.142 | 0.0 | 51.86
Neigh | 0.0094573 | 0.0094573 | 0.0094573 | 0.0 | 0.23
Comm | 0.023293 | 0.023293 | 0.023293 | 0.0 | 0.56
Output | 0.00031972 | 0.00031972 | 0.00031972 | 0.0 | 0.01
Modify | 1.9488 | 1.9488 | 1.9488 | 0.0 | 47.18
Other | | 0.006488 | | | 0.16
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 24065 ave 24065 max 24065 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 48130 ave 48130 max 48130 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 48130
Ave neighs/atom = 96.26
Neighbor list builds = 6
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04

142
examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4
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@ -1,142 +0,0 @@
LAMMPS (11 May 2018)
# fcc cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice fcc 3.54
Lattice spacing in x,y,z = 3.54 3.54 3.54
region box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000240088 secs
# setting mass, mag. moments, and interactions for fcc cobalt
mass 1 58.93
#set group all spin/random 31 1.72
set group all spin 1.72 0.0 0.0 1.0
500 settings made for spin
velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix_modify 1 energy yes
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
timestep 0.0001
# compute and output options
compute out_mag all compute/spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
thermo_style custom f_1
variable magx equal c_out_mag[1]
variable magy equal c_out_mag[2]
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
thermo 50
#compute outsp all property/atom spx spy spz sp fmx fmy fmz
#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 1000
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.59954
ghost atom cutoff = 6.59954
binsize = 3.29977, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.163 | 5.163 | 5.163 Mbytes
Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng
0 0 0.049785486 0 0 1 -187.94116 100.00543 -2372.4636
50 0.005 0.049785486 0 0 1 -187.94101 95.174807 -2372.4636
100 0.01 0.049785486 0 0 1 -187.94029 81.854304 -2372.4636
150 0.015 0.049785486 0 0 1 -187.93834 63.270938 -2372.4636
200 0.02 0.049785486 0 0 1 -187.93446 43.867262 -2372.4636
250 0.025 0.049785486 0 0 1 -187.92831 28.075261 -2372.4636
300 0.03 0.049785486 0 0 1 -187.92031 19.046222 -2372.4636
350 0.035 0.049785486 0 0 1 -187.91161 17.79071 -2372.4636
400 0.04 0.049785486 0 0 1 -187.9039 23.079994 -2372.4636
450 0.045 0.049785486 0 0 1 -187.89895 32.127316 -2372.4636
500 0.05 0.049785486 0 0 1 -187.89801 41.709644 -2372.4636
550 0.055 0.049785486 0 0 1 -187.90146 49.246292 -2372.4636
600 0.06 0.049785486 0 0 1 -187.90859 53.465535 -2372.4636
650 0.065 0.049785486 0 0 1 -187.91778 54.522857 -2372.4636
700 0.07 0.049785486 0 0 1 -187.9269 53.635521 -2372.4636
750 0.075 0.049785486 0 0 1 -187.93396 52.419678 -2372.4636
800 0.08 0.049785486 0 0 1 -187.9376 52.176558 -2372.4636
850 0.085 0.049785486 0 0 1 -187.93744 53.380592 -2372.4636
900 0.09 0.049785486 0 0 1 -187.93412 55.551378 -2372.4636
950 0.095 0.049785486 0 0 1 -187.92902 57.540047 -2372.4636
1000 0.1 0.049785486 0 0 1 -187.92378 58.088674 -2372.4636
Loop time of 1.71411 on 4 procs for 1000 steps with 500 atoms
Performance: 5.041 ns/day, 4.761 hours/ns, 583.392 timesteps/s
97.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.54717 | 0.57392 | 0.58784 | 2.1 | 33.48
Neigh | 0.0023484 | 0.0025793 | 0.0026793 | 0.3 | 0.15
Comm | 0.058548 | 0.073335 | 0.10006 | 5.9 | 4.28
Output | 0.00042272 | 0.00079203 | 0.0018559 | 0.0 | 0.05
Modify | 1.0577 | 1.0611 | 1.0625 | 0.2 | 61.90
Other | | 0.00239 | | | 0.14
Nlocal: 125 ave 133 max 116 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 1099 ave 1108 max 1091 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Neighs: 6032.5 ave 6417 max 5489 min
Histogram: 1 0 0 0 0 0 1 1 0 1
FullNghs: 12065 ave 13062 max 10970 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 48260
Ave neighs/atom = 96.52
Neighbor list builds = 6
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01

142
examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.1 Normal file
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@ -0,0 +1,142 @@
LAMMPS (30 Oct 2019)
# fcc cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice fcc 3.54
Lattice spacing in x,y,z = 3.54 3.54 3.54
region box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
create_atoms CPU = 0.000470161 secs
# setting mass, mag. moments, and interactions for fcc cobalt
mass 1 58.93
#set group all spin/random 31 1.72
set group all spin 1.72 0.0 0.0 1.0
500 settings made for spin
velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix_modify 1 energy yes
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
thermo_style custom f_1
variable magx equal c_out_mag[1]
variable magy equal c_out_mag[2]
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
thermo 50
# compute outsp all property/atom spx spy spz sp fmx fmy fmz
# dump 1 all custom 100 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 1000
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.59954
ghost atom cutoff = 6.59954
binsize = 3.29977, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.718 | 5.718 | 5.718 Mbytes
Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng
0 0 -0.099570972 0 0 1 -188.09051 100.00543 -2278.6175
50 0.005 -0.099570972 0 0 1 -188.09048 95.094679 -2278.6175
100 0.01 -0.099570972 0 0 1 -188.09007 81.578321 -2278.6177
150 0.015 -0.099570972 0 0 1 -188.08848 62.802727 -2278.6185
200 0.02 -0.099570972 0 0 1 -188.08487 43.35108 -2278.6203
250 0.025 -0.099570972 0 0 1 -188.07877 27.749821 -2278.6233
300 0.03 -0.099570972 0 0 1 -188.07054 19.149389 -2278.6274
350 0.035 -0.099570972 0 0 1 -188.06135 18.453387 -2278.632
400 0.04 -0.099570972 0 0 1 -188.053 24.249423 -2278.6362
450 0.045 -0.099570972 0 0 1 -188.04742 33.548008 -2278.639
500 0.05 -0.099570972 0 0 1 -188.04604 42.973172 -2278.6397
550 0.055 -0.099570972 0 0 1 -188.04935 49.902539 -2278.638
600 0.06 -0.099570972 0 0 1 -188.0567 53.166772 -2278.6344
650 0.065 -0.099570972 0 0 1 -188.06642 53.153416 -2278.6295
700 0.07 -0.099570972 0 0 1 -188.07628 51.377187 -2278.6246
750 0.075 -0.099570972 0 0 1 -188.08415 49.725449 -2278.6206
800 0.08 -0.099570972 0 0 1 -188.08857 49.663576 -2278.6184
850 0.085 -0.099570972 0 0 1 -188.0891 51.681567 -2278.6182
900 0.09 -0.099570972 0 0 1 -188.08636 55.166554 -2278.6195
950 0.095 -0.099570972 0 0 1 -188.08174 58.718232 -2278.6218
1000 0.1 -0.099570972 0 0 1 -188.0769 60.75567 -2278.6243
Loop time of 4.6196 on 1 procs for 1000 steps with 500 atoms
Performance: 1.870 ns/day, 12.832 hours/ns, 216.469 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3116 | 2.3116 | 2.3116 | 0.0 | 50.04
Neigh | 0.011227 | 0.011227 | 0.011227 | 0.0 | 0.24
Comm | 0.032837 | 0.032837 | 0.032837 | 0.0 | 0.71
Output | 0.00039411 | 0.00039411 | 0.00039411 | 0.0 | 0.01
Modify | 2.2584 | 2.2584 | 2.2584 | 0.0 | 48.89
Other | | 0.005152 | | | 0.11
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 24065 ave 24065 max 24065 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 48130 ave 48130 max 48130 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 48130
Ave neighs/atom = 96.26
Neighbor list builds = 6
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04

142
examples/SPIN/cobalt_fcc/log.19Nov19.spin.cobalt_fcc.g++.4 Normal file
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@ -0,0 +1,142 @@
LAMMPS (30 Oct 2019)
# fcc cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice fcc 3.54
Lattice spacing in x,y,z = 3.54 3.54 3.54
region box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
create_atoms CPU = 0.000808001 secs
# setting mass, mag. moments, and interactions for fcc cobalt
mass 1 58.93
#set group all spin/random 31 1.72
set group all spin 1.72 0.0 0.0 1.0
500 settings made for spin
velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix_modify 1 energy yes
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
thermo_style custom f_1
variable magx equal c_out_mag[1]
variable magy equal c_out_mag[2]
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
thermo 50
# compute outsp all property/atom spx spy spz sp fmx fmy fmz
# dump 1 all custom 100 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 1000
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.59954
ghost atom cutoff = 6.59954
binsize = 3.29977, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.664 | 5.664 | 5.664 Mbytes
Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng
0 0 -0.099570972 0 0 1 -188.09051 100.00543 -2372.6129
50 0.005 -0.099570972 0 0 1 -188.09036 95.174807 -2372.6129
100 0.01 -0.099570972 0 0 1 -188.08965 81.854304 -2372.6129
150 0.015 -0.099570972 0 0 1 -188.0877 63.270938 -2372.6129
200 0.02 -0.099570972 0 0 1 -188.08381 43.867262 -2372.6129
250 0.025 -0.099570972 0 0 1 -188.07767 28.075261 -2372.6129
300 0.03 -0.099570972 0 0 1 -188.06966 19.046222 -2372.6129
350 0.035 -0.099570972 0 0 1 -188.06096 17.79071 -2372.6129
400 0.04 -0.099570972 0 0 1 -188.05326 23.079994 -2372.6129
450 0.045 -0.099570972 0 0 1 -188.04831 32.127316 -2372.6129
500 0.05 -0.099570972 0 0 1 -188.04737 41.709644 -2372.6129
550 0.055 -0.099570972 0 0 1 -188.05082 49.246292 -2372.6129
600 0.06 -0.099570972 0 0 1 -188.05795 53.465535 -2372.6129
650 0.065 -0.099570972 0 0 1 -188.06713 54.522857 -2372.6129
700 0.07 -0.099570972 0 0 1 -188.07626 53.635521 -2372.6129
750 0.075 -0.099570972 0 0 1 -188.08332 52.419678 -2372.6129
800 0.08 -0.099570972 0 0 1 -188.08696 52.176558 -2372.6129
850 0.085 -0.099570972 0 0 1 -188.0868 53.380592 -2372.6129
900 0.09 -0.099570972 0 0 1 -188.08348 55.551378 -2372.6129
950 0.095 -0.099570972 0 0 1 -188.07838 57.540047 -2372.6129
1000 0.1 -0.099570972 0 0 1 -188.07314 58.088674 -2372.6129
Loop time of 2.54753 on 4 procs for 1000 steps with 500 atoms
Performance: 3.392 ns/day, 7.076 hours/ns, 392.538 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.62017 | 0.6485 | 0.66275 | 2.1 | 25.46
Neigh | 0.0027115 | 0.0029724 | 0.0030868 | 0.3 | 0.12
Comm | 0.095047 | 0.1102 | 0.13819 | 5.0 | 4.33
Output | 0.00039029 | 0.00042999 | 0.00049996 | 0.0 | 0.02
Modify | 1.7801 | 1.7834 | 1.7852 | 0.1 | 70.01
Other | | 0.002028 | | | 0.08
Nlocal: 125 ave 133 max 116 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 1099 ave 1108 max 1091 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Neighs: 6032.5 ave 6417 max 5489 min
Histogram: 1 0 0 0 0 0 1 1 0 1
FullNghs: 12065 ave 13062 max 10970 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 48260
Ave neighs/atom = 96.52
Neighbor list builds = 6
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

9
examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
View File

@ -25,8 +25,7 @@ velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy ../examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy Co
#pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
@ -52,10 +51,10 @@ variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_emag temp etotal
thermo_style custom step time v_magnorm v_emag temp press etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
dump 1 all custom 100 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 20000
run 1000

318
examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1
View File

@ -1,318 +0,0 @@
LAMMPS (11 May 2018)
# hcp cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice hcp 2.5071
Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
region box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000801802 secs
# setting mass, mag. moments, and interactions for hcp cobalt
mass 1 58.93
#set group all spin/random 31 1.72
set group all spin 1.72 0.0 0.0 1.0
500 settings made for spin
velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
timestep 0.0001
compute out_mag all compute/spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_emag temp etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 2000
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.59954
ghost atom cutoff = 6.59954
binsize = 3.29977, bins = 4 7 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.401 | 7.401 | 7.401 Mbytes
Step Time v_magnorm v_emag Temp TotEng
0 0 1 -187.29499 100.00543 -2375.8943
10 0.001 1 -187.29714 99.845593 -2375.8943
20 0.002 1 -187.30356 99.367234 -2375.8943
30 0.003 1 -187.31419 98.573996 -2375.8943
40 0.004 1 -187.32896 97.472027 -2375.8943
50 0.005 1 -187.34772 96.069944 -2375.8943
60 0.006 1 -187.37032 94.378764 -2375.8943
70 0.007 1 -187.39656 92.411827 -2375.8943
80 0.008 1 -187.4262 90.184697 -2375.8943
90 0.009 1 -187.459 87.715037 -2375.8943
100 0.01 1 -187.49466 85.022479 -2375.8943
110 0.011 1 -187.53289 82.128462 -2375.8943
120 0.012 1 -187.57334 79.05606 -2375.8943
130 0.013 1 -187.61568 75.82979 -2375.8943
140 0.014 1 -187.65953 72.475403 -2375.8943
150 0.015 1 -187.70453 69.019658 -2375.8943
160 0.016 1 -187.75028 65.490086 -2375.8943
170 0.017 1 -187.79642 61.914735 -2375.8943
180 0.018 1 -187.84254 58.321911 -2375.8943
190 0.019 1 -187.88828 54.739907 -2375.8943
200 0.02 1 -187.93324 51.196728 -2375.8943
210 0.021 1 -187.97708 47.719812 -2375.8943
220 0.022 1 -188.01947 44.335762 -2375.8943
230 0.023 1 -188.06003 41.07007 -2375.8943
240 0.024 1 -188.09853 37.946852 -2375.8944
250 0.025 1 -188.13457 34.988599 -2375.8944
260 0.026 1 -188.16795 32.215943 -2375.8944
270 0.027 1 -188.19851 29.647465 -2375.8944
280 0.028 1 -188.22593 27.299481 -2375.8944
290 0.029 1 -188.25011 25.185896 -2375.8944
300 0.03 1 -188.27095 23.318075 -2375.8945
310 0.031 1 -188.2883 21.70475 -2375.8945
320 0.032 1 -188.30213 20.35194 -2375.8945
330 0.033 1 -188.31251 19.262946 -2375.8945
340 0.034 1 -188.31928 18.438347 -2375.8945
350 0.035 1 -188.32258 17.876036 -2375.8945
360 0.036 1 -188.32249 17.571322 -2375.8945
370 0.037 1 -188.31913 17.517032 -2375.8945
380 0.038 1 -188.31264 17.703653 -2375.8945
390 0.039 1 -188.30321 18.119513 -2375.8945
400 0.04 1 -188.29102 18.750969 -2375.8945
410 0.041 1 -188.2763 19.582631 -2375.8945
420 0.042 1 -188.25929 20.597597 -2375.8945
430 0.043 1 -188.24025 21.777699 -2375.8945
440 0.044 1 -188.21945 23.103765 -2375.8945
450 0.045 1 -188.19719 24.555878 -2375.8946
460 0.046 1 -188.17368 26.113643 -2375.8946
470 0.047 1 -188.1493 27.756439 -2375.8946
480 0.048 1 -188.12429 29.463677 -2375.8946
490 0.049 1 -188.09895 31.21504 -2375.8946
500 0.05 1 -188.07354 32.990713 -2375.8946
510 0.051 1 -188.04832 34.771601 -2375.8945
520 0.052 1 -188.02358 36.539517 -2375.8945
530 0.053 1 -187.99951 38.27736 -2375.8945
540 0.054 1 -187.97636 39.969275 -2375.8945
550 0.055 1 -187.95437 41.600775 -2375.8945
560 0.056 1 -187.93364 43.158863 -2375.8944
570 0.057 1 -187.9144 44.632119 -2375.8944
580 0.058 1 -187.89669 46.010765 -2375.8944
590 0.059 1 -187.88074 47.286714 -2375.8944
600 0.06 1 -187.86658 48.453573 -2375.8944
610 0.061 1 -187.85422 49.506668 -2375.8943
620 0.062 1 -187.84377 50.443021 -2375.8943
630 0.063 1 -187.8352 51.261297 -2375.8943
640 0.064 1 -187.8285 51.961764 -2375.8943
650 0.065 1 -187.8236 52.54622 -2375.8943
660 0.066 1 -187.8205 53.017899 -2375.8943
670 0.067 1 -187.81909 53.381374 -2375.8943
680 0.068 1 -187.81926 53.64244 -2375.8943
690 0.069 1 -187.82092 53.807997 -2375.8943
700 0.07 1 -187.82391 53.885909 -2375.8943
710 0.071 1 -187.82814 53.884865 -2375.8943
720 0.072 1 -187.83339 53.814238 -2375.8943
730 0.073 1 -187.83952 53.68392 -2375.8943
740 0.074 1 -187.84635 53.504185 -2375.8943
750 0.075 1 -187.85375 53.285525 -2375.8943
760 0.076 1 -187.86153 53.038494 -2375.8943
770 0.077 1 -187.86952 52.773567 -2375.8943
780 0.078 1 -187.87758 52.500994 -2375.8943
790 0.079 1 -187.88549 52.230655 -2375.8943
800 0.08 1 -187.89313 51.971933 -2375.8943
810 0.081 1 -187.90035 51.733593 -2375.8943
820 0.082 1 -187.90702 51.523671 -2375.8943
830 0.083 1 -187.91302 51.349376 -2375.8943
840 0.084 1 -187.91824 51.217006 -2375.8943
850 0.085 1 -187.9226 51.131875 -2375.8943
860 0.086 1 -187.92602 51.098259 -2375.8943
870 0.087 1 -187.92844 51.119356 -2375.8943
880 0.088 1 -187.92979 51.197261 -2375.8943
890 0.089 1 -187.93011 51.332955 -2375.8943
900 0.09 1 -187.92937 51.526314 -2375.8943
910 0.091 1 -187.92757 51.77613 -2375.8943
920 0.092 1 -187.92475 52.080145 -2375.8943
930 0.093 1 -187.92096 52.435106 -2375.8943
940 0.094 1 -187.91624 52.836825 -2375.8943
950 0.095 1 -187.91068 53.280251 -2375.8943
960 0.096 1 -187.90435 53.759559 -2375.8943
970 0.097 1 -187.89734 54.268246 -2375.8943
980 0.098 1 -187.88981 54.799223 -2375.8943
990 0.099 1 -187.88185 55.344928 -2375.8943
1000 0.1 1 -187.87357 55.897438 -2375.8943
1010 0.101 1 -187.86511 56.448585 -2375.8943
1020 0.102 1 -187.8566 56.990069 -2375.8943
1030 0.103 1 -187.84817 57.513575 -2375.8943
1040 0.104 1 -187.83995 58.010887 -2375.8943
1050 0.105 1 -187.83208 58.474004 -2375.8943
1060 0.106 1 -187.8247 58.89524 -2375.8943
1070 0.107 1 -187.81789 59.267328 -2375.8943
1080 0.108 1 -187.81177 59.583518 -2375.8943
1090 0.109 1 -187.80646 59.837665 -2375.8943
1100 0.11 1 -187.80204 60.024306 -2375.8943
1110 0.111 1 -187.79861 60.138734 -2375.8943
1120 0.112 1 -187.79625 60.177056 -2375.8943
1130 0.113 1 -187.79497 60.136244 -2375.8943
1140 0.114 1 -187.79485 60.014176 -2375.8943
1150 0.115 1 -187.7959 59.809665 -2375.8943
1160 0.116 1 -187.79811 59.52248 -2375.8943
1170 0.117 1 -187.80157 59.153353 -2375.8943
1180 0.118 1 -187.80618 58.703971 -2375.8943
1190 0.119 1 -187.81193 58.176956 -2375.8943
1200 0.12 1 -187.81879 57.575849 -2375.8943
1210 0.121 1 -187.82668 56.905072 -2375.8943
1220 0.122 1 -187.83554 56.169878 -2375.8943
1230 0.123 1 -187.84528 55.376297 -2375.8943
1240 0.124 1 -187.85581 54.53107 -2375.8943
1250 0.125 1 -187.86702 53.641573 -2375.8943
1260 0.126 1 -187.8788 52.715739 -2375.8943
1270 0.127 1 -187.89103 51.761969 -2375.8943
1280 0.128 1 -187.90358 50.789036 -2375.8943
1290 0.129 1 -187.91632 49.805988 -2375.8943
1300 0.13 1 -187.92911 48.822045 -2375.8943
1310 0.131 1 -187.94182 47.846491 -2375.8943
1320 0.132 1 -187.95428 46.888574 -2375.8943
1330 0.133 1 -187.96643 45.957394 -2375.8943
1340 0.134 1 -187.9781 45.061794 -2375.8943
1350 0.135 1 -187.9892 44.210263 -2375.8943
1360 0.136 1 -187.99955 43.410832 -2375.8943
1370 0.137 1 -188.00907 42.670979 -2375.8943
1380 0.138 1 -188.01767 41.997547 -2375.8943
1390 0.139 1 -188.02525 41.396655 -2375.8943
1400 0.14 1 -188.03177 40.873631 -2375.8944
1410 0.141 1 -188.03711 40.432952 -2375.8944
1420 0.142 1 -188.04124 40.078172 -2375.8944
1430 0.143 1 -188.04413 39.811902 -2375.8944
1440 0.144 1 -188.04575 39.635775 -2375.8944
1450 0.145 1 -188.04607 39.550435 -2375.8943
1460 0.146 1 -188.04515 39.555512 -2375.8943
1470 0.147 1 -188.04298 39.649651 -2375.8943
1480 0.148 1 -188.03961 39.830523 -2375.8943
1490 0.149 1 -188.03508 40.094865 -2375.8943
1500 0.15 1 -188.02944 40.438519 -2375.8943
1510 0.151 1 -188.02275 40.856491 -2375.8943
1520 0.152 1 -188.01515 41.343019 -2375.8943
1530 0.153 1 -188.00671 41.891643 -2375.8943
1540 0.154 1 -187.99753 42.495295 -2375.8943
1550 0.155 1 -187.98772 43.14639 -2375.8943
1560 0.156 1 -187.9774 43.836918 -2375.8943
1570 0.157 1 -187.9667 44.558553 -2375.8943
1580 0.158 1 -187.95576 45.302751 -2375.8943
1590 0.159 1 -187.94466 46.060862 -2375.8943
1600 0.16 1 -187.93356 46.824226 -2375.8943
1610 0.161 1 -187.92257 47.584289 -2375.8943
1620 0.162 1 -187.91183 48.332703 -2375.8943
1630 0.163 1 -187.90145 49.061422 -2375.8943
1640 0.164 1 -187.89155 49.762798 -2375.8943
1650 0.165 1 -187.88222 50.429671 -2375.8943
1660 0.166 1 -187.87357 51.055445 -2375.8943
1670 0.167 1 -187.86569 51.634167 -2375.8943
1680 0.168 1 -187.85864 52.160588 -2375.8943
1690 0.169 1 -187.85249 52.630219 -2375.8943
1700 0.17 1 -187.8473 53.039377 -2375.8943
1710 0.171 1 -187.84311 53.385221 -2375.8943
1720 0.172 1 -187.83994 53.665778 -2375.8943
1730 0.173 1 -187.83781 53.879954 -2375.8943
1740 0.174 1 -187.83671 54.027539 -2375.8943
1750 0.175 1 -187.83663 54.109201 -2375.8943
1760 0.176 1 -187.83753 54.126472 -2375.8943
1770 0.177 1 -187.83941 54.081708 -2375.8943
1780 0.178 1 -187.8422 53.97806 -2375.8943
1790 0.179 1 -187.84584 53.819424 -2375.8943
1800 0.18 1 -187.85025 53.610389 -2375.8943
1810 0.181 1 -187.85535 53.356163 -2375.8943
1820 0.182 1 -187.86105 53.06251 -2375.8943
1830 0.183 1 -187.86723 52.735671 -2375.8943
1840 0.184 1 -187.87384 52.382262 -2375.8943
1850 0.185 1 -187.88075 52.009201 -2375.8943
1860 0.186 1 -187.88784 51.623613 -2375.8943
1870 0.187 1 -187.89501 51.232726 -2375.8943
1880 0.188 1 -187.90214 50.843782 -2375.8943
1890 0.189 1 -187.90912 50.463929 -2375.8943
1900 0.19 1 -187.91585 50.100133 -2375.8943
1910 0.191 1 -187.92222 49.759075 -2375.8943
1920 0.192 1 -187.92814 49.447064 -2375.8943
1930 0.193 1 -187.93351 49.169949 -2375.8943
1940 0.194 1 -187.93826 48.933036 -2375.8943
1950 0.195 1 -187.94232 48.741013 -2375.8943
1960 0.196 1 -187.94561 48.597888 -2375.8943
1970 0.197 1 -187.94809 48.506926 -2375.8943
1980 0.198 1 -187.94972 48.470605 -2375.8943
1990 0.199 1 -187.95047 48.490576 -2375.8943
2000 0.2 1 -187.95033 48.567643 -2375.8943
Loop time of 10.5391 on 1 procs for 2000 steps with 500 atoms
Performance: 1.640 ns/day, 14.638 hours/ns, 189.770 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.9958 | 4.9958 | 4.9958 | 0.0 | 47.40
Neigh | 0.020741 | 0.020741 | 0.020741 | 0.0 | 0.20
Comm | 0.05899 | 0.05899 | 0.05899 | 0.0 | 0.56
Output | 1.1598 | 1.1598 | 1.1598 | 0.0 | 11.00
Modify | 4.2885 | 4.2885 | 4.2885 | 0.0 | 40.69
Other | | 0.01522 | | | 0.14
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2444 ave 2444 max 2444 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 27041 ave 27041 max 27041 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 54082 ave 54082 max 54082 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 54082
Ave neighs/atom = 108.164
Neighbor list builds = 12
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:10

318
examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4
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LAMMPS (11 May 2018)
# hcp cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice hcp 2.5071
Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
region box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
Time spent = 0.000241518 secs
# setting mass, mag. moments, and interactions for hcp cobalt
mass 1 58.93
#set group all spin/random 31 1.72
set group all spin 1.72 0.0 0.0 1.0
500 settings made for spin
velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
timestep 0.0001
compute out_mag all compute/spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_emag temp etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 2000
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.59954
ghost atom cutoff = 6.59954
binsize = 3.29977, bins = 4 7 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.314 | 7.314 Mbytes
Step Time v_magnorm v_emag Temp TotEng
0 0 1 -187.29499 100.00543 -2375.8943
10 0.001 1 -187.29721 99.841045 -2375.8943
20 0.002 1 -187.30385 99.349208 -2375.8943
30 0.003 1 -187.31485 98.533905 -2375.8943
40 0.004 1 -187.33011 97.401749 -2375.8943
50 0.005 1 -187.34949 95.961938 -2375.8943
60 0.006 1 -187.37283 94.22618 -2375.8943
70 0.007 1 -187.39992 92.208606 -2375.8943
80 0.008 1 -187.43051 89.92566 -2375.8943
90 0.009 1 -187.46434 87.39597 -2375.8943
100 0.01 1 -187.5011 84.640195 -2375.8943
110 0.011 1 -187.54047 81.680862 -2375.8943
120 0.012 1 -187.5821 78.542172 -2375.8943
130 0.013 1 -187.62564 75.249797 -2375.8943
140 0.014 1 -187.67069 71.830656 -2375.8943
150 0.015 1 -187.71686 68.312673 -2375.8943
160 0.016 1 -187.76377 64.724523 -2375.8943
170 0.017 1 -187.81099 61.095365 -2375.8943
180 0.018 1 -187.85814 57.454566 -2375.8943
190 0.019 1 -187.90481 53.831412 -2375.8943
200 0.02 1 -187.95061 50.254822 -2375.8943
210 0.021 1 -187.99517 46.753056 -2375.8943
220 0.022 1 -188.03812 43.353428 -2375.8943
230 0.023 1 -188.07913 40.082023 -2375.8943
240 0.024 1 -188.11787 36.963429 -2375.8943
250 0.025 1 -188.15409 34.020481 -2375.8943
260 0.026 1 -188.1875 31.27403 -2375.8943
270 0.027 1 -188.21782 28.74271 -2375.8943
280 0.028 1 -188.2449 26.44276 -2375.8943
290 0.029 1 -188.26857 24.387875 -2375.8943
300 0.03 1 -188.28877 22.589076 -2375.8944
310 0.031 1 -188.30529 21.054615 -2375.8944
320 0.032 1 -188.31814 19.789913 -2375.8944
330 0.033 1 -188.3273 18.797563 -2375.8944
340 0.034 1 -188.33284 18.077336 -2375.8944
350 0.035 1 -188.33478 17.626237 -2375.8945
360 0.036 1 -188.33319 17.438611 -2375.8945
370 0.037 1 -188.32824 17.506247 -2375.8945
380 0.038 1 -188.32007 17.818564 -2375.8945
390 0.039 1 -188.30888 18.362769 -2375.8945
400 0.04 1 -188.2949 19.124086 -2375.8945
410 0.041 1 -188.27837 20.085983 -2375.8945
420 0.042 1 -188.25957 21.230423 -2375.8945
430 0.043 1 -188.23868 22.538112 -2375.8945
440 0.044 1 -188.21604 23.988778 -2375.8945
450 0.045 1 -188.19195 25.561447 -2375.8945
460 0.046 1 -188.16672 27.234703 -2375.8945
470 0.047 1 -188.14064 28.986964 -2375.8946
480 0.048 1 -188.11402 30.796738 -2375.8946
490 0.049 1 -188.08713 32.642869 -2375.8945
500 0.05 1 -188.06032 34.504776 -2375.8945
510 0.051 1 -188.03383 36.362662 -2375.8945
520 0.052 1 -188.00793 38.197721 -2375.8945
530 0.053 1 -187.98284 39.992314 -2375.8945
540 0.054 1 -187.95884 41.730127 -2375.8945
550 0.055 1 -187.93612 43.396298 -2375.8945
560 0.056 1 -187.91489 44.97754 -2375.8945
570 0.057 1 -187.89524 46.462224 -2375.8945
580 0.058 1 -187.87735 47.840443 -2375.8945
590 0.059 1 -187.8613 49.104064 -2375.8945
600 0.06 1 -187.84719 50.246744 -2375.8945
610 0.061 1 -187.83509 51.26393 -2375.8944
620 0.062 1 -187.82506 52.152839 -2375.8944
630 0.063 1 -187.81706 52.912413 -2375.8944
640 0.064 1 -187.81109 53.543272 -2375.8944
650 0.065 1 -187.80708 54.047636 -2375.8944
660 0.066 1 -187.80499 54.429234 -2375.8944
670 0.067 1 -187.8047 54.693202 -2375.8944
680 0.068 1 -187.80613 54.845965 -2375.8944
690 0.069 1 -187.80914 54.895106 -2375.8944
700 0.07 1 -187.81356 54.849238 -2375.8944
710 0.071 1 -187.81923 54.71786 -2375.8943
720 0.072 1 -187.82608 54.511181 -2375.8943
730 0.073 1 -187.83388 54.239987 -2375.8943
740 0.074 1 -187.84244 53.91548 -2375.8943
750 0.075 1 -187.85158 53.549112 -2375.8943
760 0.076 1 -187.86112 53.152433 -2375.8943
770 0.077 1 -187.87086 52.736925 -2375.8943
780 0.078 1 -187.88063 52.313858 -2375.8943
790 0.079 1 -187.89026 51.894138 -2375.8943
800 0.08 1 -187.89958 51.488169 -2375.8943
810 0.081 1 -187.90842 51.105725 -2375.8943
820 0.082 1 -187.91663 50.755829 -2375.8943
830 0.083 1 -187.92411 50.446651 -2375.8943
840 0.084 1 -187.93071 50.185404 -2375.8943
850 0.085 1 -187.93637 49.978262 -2375.8943
860 0.086 1 -187.94099 49.830307 -2375.8943
870 0.087 1 -187.9445 49.745473 -2375.8943
880 0.088 1 -187.94685 49.726517 -2375.8943
890 0.089 1 -187.94802 49.774999 -2375.8943
900 0.09 1 -187.94799 49.891282 -2375.8943
910 0.091 1 -187.94678 50.074549 -2375.8943
920 0.092 1 -187.94441 50.322833 -2375.8943
930 0.093 1 -187.94093 50.633063 -2375.8943
940 0.094 1 -187.93639 51.001126 -2375.8943
950 0.095 1 -187.93089 51.421938 -2375.8943
960 0.096 1 -187.9245 51.889531 -2375.8943
970 0.097 1 -187.91733 52.397148 -2375.8943
980 0.098 1 -187.9095 52.937345 -2375.8943
990 0.099 1 -187.90113 53.502108 -2375.8943
1000 0.1 1 -187.89236 54.082966 -2375.8943
1010 0.101 1 -187.88332 54.671115 -2375.8943
1020 0.102 1 -187.87415 55.257545 -2375.8943
1030 0.103 1 -187.86501 55.833162 -2375.8943
1040 0.104 1 -187.85602 56.388915 -2375.8943
1050 0.105 1 -187.84734 56.915918 -2375.8943
1060 0.106 1 -187.83909 57.405575 -2375.8943
1070 0.107 1 -187.83143 57.849686 -2375.8943
1080 0.108 1 -187.82446 58.240564 -2375.8943
1090 0.109 1 -187.8183 58.571132 -2375.8943
1100 0.11 1 -187.81306 58.835016 -2375.8943
1110 0.111 1 -187.80883 59.026633 -2375.8943
1120 0.112 1 -187.8057 59.141258 -2375.8943
1130 0.113 1 -187.80372 59.17509 -2375.8943
1140 0.114 1 -187.80295 59.125305 -2375.8943
1150 0.115 1 -187.80341 58.990092 -2375.8943
1160 0.116 1 -187.80515 58.76868 -2375.8943
1170 0.117 1 -187.80814 58.461352 -2375.8943
1180 0.118 1 -187.81244 58.069457 -2375.8943
1190 0.119 1 -187.81794 57.595377 -2375.8944
1200 0.12 1 -187.82458 57.042514 -2375.8944
1210 0.121 1 -187.83233 56.415256 -2375.8944
1220 0.122 1 -187.84112 55.718931 -2375.8944
1230 0.123 1 -187.85086 54.959744 -2375.8944
1240 0.124 1 -187.86145 54.144707 -2375.8944
1250 0.125 1 -187.87277 53.281562 -2375.8944
1260 0.126 1 -187.88471 52.378686 -2375.8944
1270 0.127 1 -187.89713 51.445 -2375.8944
1280 0.128 1 -187.9099 50.489858 -2375.8944
1290 0.129 1 -187.92288 49.522943 -2375.8944
1300 0.13 1 -187.93591 48.554147 -2375.8944
1310 0.131 1 -187.94886 47.593456 -2375.8944
1320 0.132 1 -187.96157 46.650829 -2375.8944
1330 0.133 1 -187.97391 45.736073 -2375.8944
1340 0.134 1 -187.98573 44.858733 -2375.8944
1350 0.135 1 -187.99691 44.027964 -2375.8944
1360 0.136 1 -188.00731 43.252426 -2375.8944
1370 0.137 1 -188.01678 42.540178 -2375.8943
1380 0.138 1 -188.02529 41.898568 -2375.8943
1390 0.139 1 -188.0327 41.334152 -2375.8943
1400 0.14 1 -188.03894 40.852606 -2375.8943
1410 0.141 1 -188.04396 40.45866 -2375.8944
1420 0.142 1 -188.04768 40.156041 -2375.8944
1430 0.143 1 -188.05007 39.947416 -2375.8944
1440 0.144 1 -188.05107 39.834367 -2375.8944
1450 0.145 1 -188.0507 39.817378 -2375.8944
1460 0.146 1 -188.04898 39.895828 -2375.8944
1470 0.147 1 -188.04595 40.068005 -2375.8945
1480 0.148 1 -188.04164 40.331129 -2375.8945
1490 0.149 1 -188.03603 40.681394 -2375.8945
1500 0.15 1 -188.02929 41.114003 -2375.8945
1510 0.151 1 -188.02148 41.623259 -2375.8945
1520 0.152 1 -188.0127 42.20263 -2375.8945
1530 0.153 1 -188.00302 42.844846 -2375.8945
1540 0.154 1 -187.99255 43.541977 -2375.8945
1550 0.155 1 -187.98148 44.285554 -2375.8945
1560 0.156 1 -187.96989 45.066666 -2375.8945
1570 0.157 1 -187.95793 45.876084 -2375.8945
1580 0.158 1 -187.94574 46.704378 -2375.8945
1590 0.159 1 -187.93346 47.542032 -2375.8945
1600 0.16 1 -187.92122 48.379564 -2375.8945
1610 0.161 1 -187.90916 49.207642 -2375.8945
1620 0.162 1 -187.89742 50.0172 -2375.8945
1630 0.163 1 -187.88613 50.799541 -2375.8945
1640 0.164 1 -187.87536 51.546446 -2375.8944
1650 0.165 1 -187.86531 52.250265 -2375.8944
1660 0.166 1 -187.85604 52.904001 -2375.8944
1670 0.167 1 -187.84765 53.501394 -2375.8944
1680 0.168 1 -187.84021 54.036987 -2375.8944
1690 0.169 1 -187.83379 54.506178 -2375.8944
1700 0.17 1 -187.82846 54.905273 -2375.8944
1710 0.171 1 -187.82424 55.231514 -2375.8944
1720 0.172 1 -187.82117 55.483104 -2375.8944
1730 0.173 1 -187.81922 55.659221 -2375.8944
1740 0.174 1 -187.81843 55.760007 -2375.8944
1750 0.175 1 -187.81881 55.786556 -2375.8944
1760 0.176 1 -187.82029 55.740888 -2375.8944
1770 0.177 1 -187.82284 55.625916 -2375.8944
1780 0.178 1 -187.82639 55.445397 -2375.8944
1790 0.179 1 -187.83088 55.203871 -2375.8944
1800 0.18 1 -187.83623 54.906597 -2375.8944
1810 0.181 1 -187.84235 54.559471 -2375.8944
1820 0.182 1 -187.84913 54.168949 -2375.8944
1830 0.183 1 -187.85646 53.741952 -2375.8943
1840 0.184 1 -187.86424 53.28578 -2375.8943
1850 0.185 1 -187.87239 52.807988 -2375.8943
1860 0.186 1 -187.88077 52.3163 -2375.8943
1870 0.187 1 -187.88925 51.81851 -2375.8943
1880 0.188 1 -187.89772 51.322368 -2375.8943
1890 0.189 1 -187.90605 50.835483 -2375.8943
1900 0.19 1 -187.91415 50.365218 -2375.8943
1910 0.191 1 -187.92189 49.9186 -2375.8943
1920 0.192 1 -187.92917 49.502222 -2375.8943
1930 0.193 1 -187.93591 49.122167 -2375.8943
1940 0.194 1 -187.94198 48.783928 -2375.8943
1950 0.195 1 -187.94737 48.492348 -2375.8943
1960 0.196 1 -187.95199 48.25154 -2375.8943
1970 0.197 1 -187.95576 48.064862 -2375.8943
1980 0.198 1 -187.95866 47.934875 -2375.8943
1990 0.199 1 -187.96065 47.863314 -2375.8943
2000 0.2 1 -187.96171 47.851079 -2375.8943
Loop time of 4.40076 on 4 procs for 2000 steps with 500 atoms
Performance: 3.927 ns/day, 6.112 hours/ns, 454.467 timesteps/s
96.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2934 | 1.3683 | 1.432 | 4.2 | 31.09
Neigh | 0.005039 | 0.0053418 | 0.0054908 | 0.2 | 0.12
Comm | 0.12642 | 0.1922 | 0.26891 | 11.6 | 4.37
Output | 0.39256 | 0.40875 | 0.43431 | 2.5 | 9.29
Modify | 2.395 | 2.4202 | 2.4352 | 1.0 | 54.99
Other | | 0.006007 | | | 0.14
Nlocal: 125 ave 130 max 122 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 1324 ave 1330 max 1316 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 6747 ave 6959 max 6652 min
Histogram: 2 1 0 0 0 0 0 0 0 1
FullNghs: 13494 ave 14060 max 13186 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 53976
Ave neighs/atom = 107.952
Neighbor list builds = 12
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04

219
examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.1 Normal file
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LAMMPS (30 Oct 2019)
# hcp cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice hcp 2.5071
Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
region box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
create_atoms CPU = 0.00105 secs
# setting mass, mag. moments, and interactions for hcp cobalt
mass 1 58.93
set group all spin/random 31 1.72
500 settings made for spin/random
#set group all spin 1.72 0.0 0.0 1.0
velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix 1 all precession/spin anisotropy 0.01 0.0 0.0 1.0
#fix 2 all langevin/spin 0.0 0.0 21
fix 2 all langevin/spin 0.0 0.1 21
fix 3 all nve/spin lattice moving
timestep 0.0001
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_emag temp press etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 100 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 1000
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.59954
ghost atom cutoff = 6.59954
binsize = 3.29977, bins = 4 7 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.902 | 7.902 | 7.902 Mbytes
Step Time v_magnorm v_emag Temp Press TotEng
0 0 0.076558814 -5.1073764 100.00543 -552.75983 -2189.4486
10 0.001 0.074494403 -6.2746901 100.01038 -1571.7966 -2190.0317
20 0.002 0.072366265 -7.4280779 99.885587 -2535.9845 -2190.5874
30 0.003 0.070127018 -8.5667999 99.611653 -3445.9872 -2191.1169
40 0.004 0.067755946 -9.6899272 99.164813 -4302.5715 -2191.6215
50 0.005 0.065261592 -10.79648 98.520535 -5107.2841 -2192.103
60 0.006 0.062676613 -11.885341 97.657148 -5862.7198 -2192.5638
70 0.007 0.060046709 -12.955115 96.558718 -6572.0571 -2193.0064
80 0.008 0.057417313 -14.004096 95.216748 -7238.1396 -2193.4327
90 0.009 0.054822275 -15.030416 93.630634 -7862.5226 -2193.8437
100 0.01 0.052277835 -16.032345 91.80711 -8445.2646 -2194.2391
110 0.011 0.049783153 -17.008652 89.759163 -8985.5937 -2194.6181
120 0.012 0.047326373 -17.958895 87.504922 -9483.1141 -2194.98
130 0.013 0.044893289 -18.883574 85.066818 -9938.8838 -2195.3247
140 0.014 0.042474822 -19.784052 82.471014 -10355.911 -2195.6533
150 0.015 0.040070404 -20.662271 79.746901 -10739.081 -2195.9677
160 0.016 0.037686856 -21.520294 76.926428 -11094.793 -2196.2709
170 0.017 0.035334961 -22.359822 74.043181 -11430.247 -2196.5659
180 0.018 0.033026799 -23.181822 71.131269 -11752.268 -2196.8556
190 0.019 0.030775544 -23.986406 68.224204 -12065.774 -2197.1412
200 0.02 0.028597121 -24.773013 65.353995 -12372.712 -2197.4226
210 0.021 0.026511775 -25.540835 62.55053 -12672.055 -2197.6975
220 0.022 0.02454383 -26.289327 59.841288 -12961.112 -2197.9631
230 0.023 0.02271918 -27.018625 57.251361 -13237.544 -2198.2165
240 0.024 0.021061271 -27.729714 54.80373 -13501.028 -2198.4564
250 0.025 0.019587072 -28.42449 52.519717 -13754.325 -2198.6833
260 0.026 0.018304494 -29.105398 50.419388 -14002.718 -2198.8994
270 0.027 0.017211977 -29.775134 48.521812 -14253.089 -2199.1079
280 0.028 0.016300002 -30.436204 46.845075 -14512.437 -2199.3119
290 0.029 0.015553519 -31.090499 45.405985 -14786.53 -2199.5143
300 0.03 0.014954102 -31.739026 44.219544 -15079.165 -2199.7168
310 0.031 0.014481189 -32.381585 43.298175 -15391.531 -2199.9198
320 0.032 0.014112494 -33.016984 42.650874 -15722.828 -2200.1226
330 0.033 0.013824206 -33.643289 42.282535 -16070.874 -2200.324
340 0.034 0.013591568 -34.258323 42.19365 -16433.065 -2200.5226
350 0.035 0.013390035 -34.860184 42.380506 -16807.186 -2200.7174
360 0.036 0.01319679 -35.447655 42.835832 -17191.816 -2200.9077
370 0.037 0.012992271 -36.020512 43.549656 -17586.676 -2201.0935
380 0.038 0.012761486 -36.579332 44.510078 -17991.857 -2201.2754
390 0.039 0.012494918 -37.125414 45.703757 -18407.738 -2201.4538
400 0.04 0.0121888 -37.660321 47.115967 -18834.276 -2201.6292
410 0.041 0.011844474 -38.185489 48.730291 -19270.674 -2201.8019
420 0.042 0.011466715 -38.70192 50.528119 -19715.276 -2201.9716
430 0.043 0.011061388 -39.21005 52.488204 -20165.66 -2202.1377
440 0.044 0.010633241 -39.709778 54.586528 -20618.997 -2202.2998
450 0.045 0.010184696 -40.200724 56.79654 -21072.538 -2202.4571
460 0.046 0.0097161044 -40.682449 59.089699 -21523.873 -2202.6094
470 0.047 0.0092271788 -41.154614 61.436133 -21970.922 -2202.7565
480 0.048 0.0087187266 -41.617256 63.805414 -22412.32 -2202.8989
490 0.049 0.0081937768 -42.070708 66.167399 -22847.061 -2203.037
500 0.05 0.0076576327 -42.51563 68.493235 -23274.619 -2203.172
510 0.051 0.0071170477 -42.952841 70.756444 -23694.559 -2203.3046
520 0.052 0.006579078 -43.383338 72.933996 -24106.717 -2203.4358
530 0.053 0.006050144 -43.807962 75.007131 -24510.338 -2203.5662
540 0.054 0.0055354475 -44.227552 76.961803 -24904.495 -2203.6957
550 0.055 0.0050386503 -44.64268 78.788647 -25287.341 -2203.8241
560 0.056 0.0045617699 -45.053996 80.4825 -25657.11 -2203.9504
570 0.057 0.0041054334 -45.461923 82.041527 -26011.443 -2204.0737
580 0.058 0.003669689 -45.866895 83.466142 -26348.265 -2204.1931
590 0.059 0.0032553824 -46.269219 84.757926 -26665.834 -2204.3077
600 0.06 0.0028655752 -46.669125 85.918711 -26963.24 -2204.4173
610 0.061 0.0025060765 -47.066641 86.95 -27240.331 -2204.5218
620 0.062 0.0021839971 -47.461566 87.852838 -27497.728 -2204.6218
630 0.063 0.0019039581 -47.853462 88.628142 -27736.503 -2204.7177
640 0.064 0.0016633855 -48.241747 89.277364 -27957.91 -2204.81
650 0.065 0.0014502904 -48.625803 89.803307 -28163.11 -2204.899
660 0.066 0.0012463786 -49.005026 90.210807 -28352.881 -2204.9847
670 0.067 0.0010345087 -49.378935 90.507107 -28527.721 -2205.0668
680 0.068 0.00080788134 -49.747325 90.701795 -28688.395 -2205.1453
690 0.069 0.000586442 -50.110227 90.80636 -28836.094 -2205.22
700 0.07 0.00046855102 -50.467799 90.833539 -28972.361 -2205.2911
710 0.071 0.00061091693 -50.82044 90.796649 -29099.44 -2205.3592
720 0.072 0.00094960177 -51.168606 90.709122 -29219.676 -2205.4249
730 0.073 0.0013742455 -51.512913 90.584346 -29335.643 -2205.4887
740 0.074 0.0018397629 -51.853957 90.435783 -29449.521 -2205.5511
750 0.075 0.0023216474 -52.192407 90.277231 -29563.316 -2205.6124
760 0.076 0.0028000512 -52.528883 90.123061 -29678.726 -2205.6729
770 0.077 0.0032569295 -52.863859 89.98824 -29797.079 -2205.7329
780 0.078 0.0036765431 -53.197843 89.888047 -29919.964 -2205.7925
790 0.079 0.0040467094 -53.530921 89.837568 -30048.271 -2205.8521
800 0.08 0.0043597837 -53.862938 89.850978 -30182.622 -2205.9119
810 0.081 0.0046129296 -54.193489 89.940884 -30323.293 -2205.9718
820 0.082 0.0048076151 -54.522077 90.117797 -30470.468 -2206.0321
830 0.083 0.004948533 -54.84813 90.389814 -30624.056 -2206.0926
840 0.084 0.0050423324 -55.171024 90.762454 -30783.658 -2206.1532
850 0.085 0.0050965581 -55.490357 91.238681 -30949.141 -2206.2139
860 0.086 0.0051190641 -55.805904 91.818973 -31120.5 -2206.2745
870 0.087 0.0051180301 -56.117429 92.501449 -31297.412 -2206.3349
880 0.088 0.0051024116 -56.424751 93.281992 -31479.436 -2206.3949
890 0.089 0.005082454 -56.727832 94.154367 -31666.293 -2206.4544
900 0.09 0.0050697645 -57.026442 95.110386 -31857.043 -2206.513
910 0.091 0.0050765431 -57.320291 96.140056 -32050.436 -2206.5703
920 0.092 0.0051139309 -57.609075 97.231838 -32245.079 -2206.6257
930 0.093 0.0051899535 -57.89236 98.372982 -32439.141 -2206.6788
940 0.094 0.0053078572 -58.169742 99.54995 -32630.727 -2206.7288
950 0.095 0.0054654923 -58.44083 100.74893 -32817.882 -2206.7752
960 0.096 0.0056558757 -58.705483 101.95638 -32999.116 -2206.8176
970 0.097 0.0058685513 -58.963698 103.15953 -33173.159 -2206.8557
980 0.098 0.0060912487 -59.215624 104.34681 -33338.961 -2206.8893
990 0.099 0.0063114886 -59.461806 105.50819 -33496.345 -2206.9188
1000 0.1 0.0065179843 -59.702883 106.63524 -33645.259 -2206.9444
Loop time of 5.20295 on 1 procs for 1000 steps with 500 atoms
Performance: 1.661 ns/day, 14.453 hours/ns, 192.199 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6241 | 2.6241 | 2.6241 | 0.0 | 50.43
Neigh | 0.01424 | 0.01424 | 0.01424 | 0.0 | 0.27
Comm | 0.041207 | 0.041207 | 0.041207 | 0.0 | 0.79
Output | 0.0090086 | 0.0090086 | 0.0090086 | 0.0 | 0.17
Modify | 2.5084 | 2.5084 | 2.5084 | 0.0 | 48.21
Other | | 0.006008 | | | 0.12
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2442 ave 2442 max 2442 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 27581 ave 27581 max 27581 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 55162 ave 55162 max 55162 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 55162
Ave neighs/atom = 110.324
Neighbor list builds = 7
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:05

219
examples/SPIN/cobalt_hcp/log.19Nov19.spin.cobalt_hcp.g++.4 Normal file
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LAMMPS (30 Oct 2019)
# hcp cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice hcp 2.5071
Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
region box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 1 box
Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
create_atoms CPU = 0.00101995 secs
# setting mass, mag. moments, and interactions for hcp cobalt
mass 1 58.93
set group all spin/random 31 1.72
500 settings made for spin/random
#set group all spin 1.72 0.0 0.0 1.0
velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
pair_style hybrid/overlay eam/alloy spin/exchange 4.0
pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix 1 all precession/spin anisotropy 0.01 0.0 0.0 1.0
#fix 2 all langevin/spin 0.0 0.0 21
fix 2 all langevin/spin 0.0 0.1 21
fix 3 all nve/spin lattice moving
timestep 0.0001
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_emag temp press etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 100 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 1000
Neighbor list info ...
update every 10 steps, delay 20 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.59954
ghost atom cutoff = 6.59954
binsize = 3.29977, bins = 4 7 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.814 | 7.814 | 7.815 Mbytes
Step Time v_magnorm v_emag Temp Press TotEng
0 0 0.076558814 -5.1073764 100.00543 -552.75983 -2190.3478
10 0.001 0.074494512 -6.2728301 99.980769 -1570.0726 -2191.5261
20 0.002 0.072367013 -7.4259977 99.847801 -2531.5119 -2192.6655
30 0.003 0.070129365 -8.566306 99.586282 -3438.1309 -2193.7672
40 0.004 0.067761178 -9.6929189 99.171132 -4291.017 -2194.8323
50 0.005 0.065270916 -10.8048 98.575397 -5091.9111 -2195.8628
60 0.006 0.062690557 -11.900573 97.773618 -5843.4528 -2196.8612
70 0.007 0.060064592 -12.978381 96.745047 -6548.726 -2197.8306
80 0.008 0.05743694 -14.035923 95.476292 -7210.2954 -2198.773
90 0.009 0.054839883 -15.07074 93.963026 -7829.4252 -2199.689
100 0.01 0.052288504 -16.08066 92.210482 -8405.9983 -2200.5773
110 0.011 0.049782155 -17.064251 90.232741 -8939.3051 -2201.4357
120 0.012 0.047311759 -18.021135 88.051042 -9429.1353 -2202.2626
130 0.013 0.044869196 -18.952065 85.691573 -9876.5628 -2203.0575
140 0.014 0.042453961 -19.858739 83.18315 -10284.249 -2203.8215
150 0.015 0.040074171 -20.743348 80.555177 -10656.417 -2204.5569
160 0.016 0.037742459 -21.608 77.836156 -10998.818 -2205.2677
170 0.017 0.035470168 -22.454209 75.052994 -11318.525 -2205.9587
180 0.018 0.033263447 -23.282658 72.231211 -11623.118 -2206.6354
190 0.019 0.031122821 -24.093311 69.395936 -11919.248 -2207.3023
200 0.02 0.029045634 -24.88579 66.573223 -12211.306 -2207.9613
210 0.021 0.027029857 -25.659817 63.791041 -12500.812 -2208.6115
220 0.022 0.025077742 -26.415541 61.079413 -12787.018 -2209.2498
230 0.023 0.023198048 -27.153652 58.469604 -13068.277 -2209.8722
240 0.024 0.02140599 -27.875313 55.992687 -13343.621 -2210.4756
250 0.025 0.019720922 -28.581973 53.678031 -13613.86 -2211.0588
260 0.026 0.018162738 -29.275283 51.552191 -13882.15 -2211.6232
270 0.027 0.016748514 -29.956802 49.638467 -14153.137 -2212.1718
280 0.028 0.01549075 -30.628043 47.957071 -14432.246 -2212.7087
290 0.029 0.014397611 -31.290177 46.525552 -14724.005 -2213.2371
300 0.03 0.013474315 -31.943984 45.359085 -15031.315 -2213.759
310 0.031 0.012723957 -32.589853 44.47023 -15355.595 -2214.275
320 0.032 0.012146358 -33.227585 43.868153 -15696.845 -2214.7851
330 0.033 0.011734827 -33.856656 43.557623 -16054.887 -2215.289
340 0.034 0.011472508 -34.476313 43.538346 -16429.77 -2215.7871
350 0.035 0.011330772 -35.085716 43.805034 -16821.627 -2216.2802
360 0.036 0.011271169 -35.684147 44.348312 -17230.21 -2216.7687
370 0.037 0.01125027 -36.271215 45.156046 -17654.485 -2217.2524
380 0.038 0.011225354 -36.847053 46.214576 -18092.623 -2217.7301
390 0.039 0.011159026 -37.412284 47.509345 -18542.156 -2218.2003
400 0.04 0.011022073 -37.967916 49.024843 -19000.554 -2218.6614
410 0.041 0.01079477 -38.515123 50.744046 -19465.713 -2219.1128
420 0.042 0.010467095 -39.054921 52.647653 -19935.873 -2219.5544
430 0.043 0.010038219 -39.588034 54.713405 -20409.666 -2219.9869
440 0.044 0.0095155267 -40.114703 56.915658 -20885.556 -2220.4109
450 0.045 0.0089134996 -40.634722 59.225397 -21361.621 -2220.8268
460 0.046 0.0082528918 -41.147681 61.610799 -21835.762 -2221.2347
470 0.047 0.0075606723 -41.653088 64.038349 -22305.687 -2221.6343
480 0.048 0.0068707613 -42.150486 66.474377 -22768.948 -2222.0253
490 0.049 0.0062249854 -42.639704 68.886721 -23223.418 -2222.4076
500 0.05 0.0056723593 -43.120772 71.24617 -23667.077 -2222.7814
510 0.051 0.00526312 -43.59404 73.527392 -24098.459 -2223.147
520 0.052 0.0050342241 -44.059917 75.709206 -24516.163 -2223.5051
530 0.053 0.0049906301 -44.518898 77.774314 -24919.192 -2223.8564
540 0.054 0.0050976586 -44.971364 79.708763 -25306.611 -2224.2014
550 0.055 0.0052941974 -45.417577 81.501347 -25677.67 -2224.5405
560 0.056 0.0055157717 -45.857628 83.143173 -26031.673 -2224.8736
570 0.057 0.0057113414 -46.291426 84.627457 -26367.904 -2225.2003
580 0.058 0.0058493207 -46.718709 85.949497 -26685.6 -2225.52
590 0.059 0.0059162201 -47.139052 87.10679 -26984.124 -2225.8316
600 0.06 0.0059118584 -47.551892 88.099176 -27263.145 -2226.1347
610 0.061 0.005843747 -47.956571 88.928929 -27522.773 -2226.4287
620 0.062 0.0057222223 -48.352422 89.600763 -27763.549 -2226.7139
630 0.063 0.0055570967 -48.738876 90.12173 -27986.321 -2226.9905
640 0.064 0.0053558993 -49.115723 90.501081 -28192.238 -2227.2593
650 0.065 0.0051233209 -49.483122 90.750056 -28382.3 -2227.5205
660 0.066 0.0048614512 -49.841791 90.881635 -28557.623 -2227.7746
670 0.067 0.0045706003 -50.192974 90.910245 -28719.422 -2228.0219
680 0.068 0.0042506564 -50.538196 90.851397 -28868.809 -2228.2627
690 0.069 0.0039028575 -50.879364 90.721317 -29007.619 -2228.4973
700 0.07 0.0035319814 -51.218193 90.536521 -29137.623 -2228.7265
710 0.071 0.0031491486 -51.556251 90.313501 -29261.193 -2228.9511
720 0.072 0.0027758205 -51.894643 90.068503 -29380.924 -2229.1724
730 0.073 0.002449449 -52.233987 89.817462 -29499.606 -2229.3917
740 0.074 0.0022276613 -52.574465 89.57612 -29620.196 -2229.6103
750 0.075 0.0021767124 -52.915641 89.360246 -29744.882 -2229.829
760 0.076 0.0023310362 -53.256843 89.185838 -29875.573 -2230.0485
770 0.077 0.0026637349 -53.597197 89.069228 -30013.477 -2230.2685
780 0.078 0.0031129938 -53.93565 89.026943 -30158.812 -2230.4882
790 0.079 0.0036204667 -54.271339 89.075322 -30311.602 -2230.7066
800 0.08 0.0041448552 -54.603455 89.229912 -30471.244 -2230.9226
810 0.081 0.0046613106 -54.931421 89.504766 -30636.938 -2231.1352
820 0.082 0.0051580947 -55.255056 89.911726 -30808.087 -2231.3434
830 0.083 0.0056329652 -55.574491 90.459766 -30984.153 -2231.5469
840 0.084 0.0060893356 -55.890024 91.154456 -31164.372 -2231.7452
850 0.085 0.0065324419 -56.202052 91.997528 -31347.792 -2231.9379
860 0.086 0.0069661977 -56.511206 92.986622 -31533.977 -2232.1249
870 0.087 0.0073913051 -56.817814 94.115192 -31721.92 -2232.306
880 0.088 0.0078048547 -57.122061 95.372548 -31910.795 -2232.4809
890 0.089 0.008201165 -57.423984 96.744135 -32100.108 -2232.65
900 0.09 0.0085732702 -57.723377 98.212046 -32289.532 -2232.8136
910 0.091 0.0089144724 -58.019938 99.755667 -32479.154 -2232.9728
920 0.092 0.0092194916 -58.313266 101.35254 -32669.227 -2233.1285
930 0.093 0.0094849872 -58.602956 102.97932 -32860.091 -2233.2822
940 0.094 0.0097093572 -58.888668 104.61271 -33051.981 -2233.4348
950 0.095 0.0098920175 -59.169925 106.23045 -33244.279 -2233.5871
960 0.096 0.01003244 -59.44662 107.81212 -33436.562 -2233.7396
970 0.097 0.010129313 -59.718668 109.33976 -33627.714 -2233.8925
980 0.098 0.010180127 -59.986126 110.79823 -33816.218 -2234.0455
990 0.099 0.010181304 -60.24929 112.17528 -34000.522 -2234.1984
1000 0.1 0.01012881 -60.508632 113.46137 -34179.052 -2234.3508
Loop time of 2.93788 on 4 procs for 1000 steps with 500 atoms
Performance: 2.941 ns/day, 8.161 hours/ns, 340.381 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.72349 | 0.73783 | 0.7554 | 1.3 | 25.11
Neigh | 0.00353 | 0.0036981 | 0.0038559 | 0.2 | 0.13
Comm | 0.12285 | 0.14476 | 0.16041 | 3.6 | 4.93
Output | 0.0046515 | 0.0047909 | 0.0050418 | 0.2 | 0.16
Modify | 2.0407 | 2.0439 | 2.0482 | 0.2 | 69.57
Other | | 0.00288 | | | 0.10
Nlocal: 125 ave 136 max 119 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 1324 ave 1331 max 1310 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 6897.25 ave 7552 max 6604 min
Histogram: 2 1 0 0 0 0 0 0 0 1
FullNghs: 13794.5 ave 15117 max 13164 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 55178
Ave neighs/atom = 110.356
Neighbor list builds = 7
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

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