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Merge remote-tracking branch 'official/fix-pair-dump-skip' into feature/pace-al

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This commit is contained in:
Yury Lysogorskiy
2022-08-30 16:07:10 +02:00
parent 6e34856c77 ec4c458c7e
commit 4e5604daef
487 changed files with 123278 additions and 2382 deletions
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33
cmake/CMakeLists.txt
View File

@ -154,6 +154,19 @@ endif()
########################################################################
# User input options #
########################################################################
# set path to python interpreter and thus enforcing python version if
# when in a virtual environment and PYTHON_EXECUTABLE is not set on command line
if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
else()
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
endif()
set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
" Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
endif()
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
mark_as_advanced(LAMMPS_MACHINE)
if(LAMMPS_MACHINE)
@ -194,6 +207,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -202,7 +216,7 @@ set(STANDARD_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -358,6 +372,7 @@ pkg_depends(MPIIO MPI)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(SCAFACOS MPI)
pkg_depends(AMOEBA KSPACE)
pkg_depends(DIELECTRIC KSPACE)
pkg_depends(DIELECTRIC EXTRA-PAIR)
pkg_depends(CG-DNA MOLECULE)
@ -402,9 +417,11 @@ endif()
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
endif()
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
include(CheckGeneratorSupport)
if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
@ -633,7 +650,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -783,6 +800,10 @@ if(BUILD_SHARED_LIBS)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
if(BUILD_IS_MULTI_CONFIG)
@ -815,11 +836,17 @@ endif()
###############################################################################
if(BUILD_SHARED_LIBS OR PKG_PYTHON)
if(CMAKE_VERSION VERSION_LESS 3.12)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
if(Python_EXECUTABLE)

5
cmake/Modules/Packages/LATTE.cmake
View File

@ -23,8 +23,9 @@ if(DOWNLOAD_LATTE)
# CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1) AND NOT USE_INTERNAL_LINALG)
message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation. "
"Try to configure LAMMPS with '-D USE_INTERNAL_LINALG=on' added as a workaround.")
endif()
include(ExternalProject)

13
cmake/Modules/Packages/MDI.cmake
View File

@ -26,8 +26,21 @@ if(DOWNLOAD_MDI)
# detect if we have python development support and thus can enable python plugins
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# search for interpreter first, so we have a consistent library
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif()
# search for the library matching the selected interpreter
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs QUIET) # Deprecated since version 3.12
if(PYTHONLIBS_FOUND)
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
else()

13
cmake/Modules/Packages/MISC.cmake Normal file
View File

@ -0,0 +1,13 @@
# pair style and fix srp/react depend on the fixes bond/break and bond/create from the MC package
if(NOT PKG_MC)
get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.h)
set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.h)
set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.cpp)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

20
cmake/Modules/Packages/PYTHON.cmake
View File

@ -1,8 +1,28 @@
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# search for interpreter first, so we have a consistent library
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif()
# search for the library matching the selected interpreter
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
else()
if(NOT Python_INTERPRETER)
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
find_package(Python REQUIRED COMPONENTS Interpreter Development)
target_link_libraries(lammps PRIVATE Python::Python)
endif()

3
cmake/presets/all_off.cmake
View File

@ -3,6 +3,7 @@
set(ALL_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -11,7 +12,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

3
cmake/presets/all_on.cmake
View File

@ -5,6 +5,7 @@
set(ALL_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -13,7 +14,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

3
cmake/presets/mingw-cross.cmake
View File

@ -1,4 +1,5 @@
set(WIN_PACKAGES
AMOEBA
ASPHERE
ATC
AWPMD
@ -7,7 +8,7 @@ set(WIN_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

3
cmake/presets/most.cmake
View File

@ -3,13 +3,14 @@
# are removed. The resulting binary should be able to run most inputs.
set(ALL_PACKAGES
AMOEBA
ASPHERE
BOCS
BODY
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

3
cmake/presets/windows.cmake
View File

@ -1,11 +1,12 @@
set(WIN_PACKAGES
AMOEBA
ASPHERE
BOCS
BODY
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

32
doc/src/Build_extras.rst
View File

@ -790,6 +790,8 @@ library.
-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
# value = no (default) or yes
If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
and built inside the CMake build directory. If the LATTE library
@ -797,6 +799,13 @@ library.
``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library
file, not the directory the library file is in.
The LATTE library requires LAPACK (and BLAS) and CMake can identify
their locations and pass that info to the LATTE build script. But
on some systems this triggers a (current) limitation of CMake and
the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
those cases to use the bundled linear algebra library and work around
the limitation.
.. tab:: Traditional make
You can download and build the LATTE library manually if you
@ -1913,14 +1922,25 @@ within CMake will download the non-commercial use version.
.. code-block:: bash
-D DOWNLOAD_QUIP=value # download OpenKIM API v2 for build, value = no (default) or yes
-D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
# value = no (default) or yes
CMake will try to download and build the QUIP library from GitHub, if it is not
found on the local machine. This requires to have git installed. It will use the same compilers
and flags as used for compiling LAMMPS. Currently this is only supported for the GNU and the
Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
and installed QUIP library and CMake cannot find it.
CMake will try to download and build the QUIP library from GitHub,
if it is not found on the local machine. This requires to have git
installed. It will use the same compilers and flags as used for
compiling LAMMPS. Currently this is only supported for the GNU
and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
want to use a previously compiled and installed QUIP library and
CMake cannot find it.
The QUIP library requires LAPACK (and BLAS) and CMake can identify
their locations and pass that info to the QUIP build script. But
on some systems this triggers a (current) limitation of CMake and
the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
those cases to use the bundled linear algebra library and work around
the limitation.
.. tab:: Traditional make

24
doc/src/Build_manual.rst
View File

@ -48,18 +48,15 @@ Build using GNU make
The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
can be translated to different output format using the `Sphinx
<sphinx_>`_ document generator tool. It also incorporates programmer
documentation extracted from the LAMMPS C++ sources through the `Doxygen
<https://doxygen.nl>`_ program. Currently the translation to HTML, PDF
(via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle
readers) are supported. For that to work a Python 3 interpreter, the
``doxygen`` tools and internet access to download additional files and
tools are required. This download is usually only required once or
after the documentation folder is returned to a pristine state with
``make clean-all``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _sphinx: https://www.sphinx-doc.org
<https://sphinx-doc.org>`_ document generator tool. It also
incorporates programmer documentation extracted from the LAMMPS C++
sources through the `Doxygen <https://doxygen.nl>`_ program. Currently
the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
and MOBI (for Amazon Kindle readers) are supported. For that to work a
Python 3 interpreter, the ``doxygen`` tools and internet access to
download additional files and tools are required. This download is
usually only required once or after the documentation folder is returned
to a pristine state with ``make clean-all``.
For the documentation build a python virtual environment is set up in
the folder ``doc/docenv`` and various python packages are installed into
@ -252,6 +249,5 @@ manual with ``make spelling``. This requires `a library called enchant
positives* (e.g. keywords, names, abbreviations) those can be added to
the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://www.lammps.org
.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html

1
doc/src/Commands.rst
View File

@ -21,6 +21,7 @@ commands in it are used to define a LAMMPS simulation.
Commands_pair
Commands_bond
Commands_kspace
Commands_dump
.. toctree::
:maxdepth: 1

5
doc/src/Commands_all.rst
View File

@ -10,11 +10,14 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
General commands
================
An alphabetic list of general LAMMPS commands.
An alphabetic list of general LAMMPS commands. Note that style
commands with many variants, can be more easily accessed via the small
table above.
.. table_from_list::
:columns: 5

5
doc/src/Commands_bond.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. _bond:
@ -74,6 +75,7 @@ OPT.
*
*
*
* :doc:`amoeba <angle_amoeba>`
* :doc:`charmm (iko) <angle_charmm>`
* :doc:`class2 (ko) <angle_class2>`
* :doc:`class2/p6 <angle_class2>`
@ -92,7 +94,7 @@ OPT.
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`sdk (o) <angle_sdk>`
* :doc:`spica (o) <angle_spica>`
* :doc:`table (o) <angle_table>`
.. _dihedral:
@ -152,6 +154,7 @@ OPT.
*
*
*
* :doc:`amoeba <improper_amoeba>`
* :doc:`class2 (ko) <improper_class2>`
* :doc:`cossq (o) <improper_cossq>`
* :doc:`cvff (io) <improper_cvff>`

1
doc/src/Commands_compute.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Compute commands
================

56
doc/src/Commands_dump.rst Normal file
View File

@ -0,0 +1,56 @@
.. 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>`
* :doc:`Dump styles <Commands_dump>`
Dump commands
=============
An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
.. table_from_list::
:columns: 5
* :doc:`atom <dump>`
* :doc:`atom/adios <dump_adios>`
* :doc:`atom/gz <dump>`
* :doc:`atom/mpiio <dump>`
* :doc:`atom/zstd <dump>`
* :doc:`cfg <dump>`
* :doc:`cfg/gz <dump>`
* :doc:`cfg/mpiio <dump>`
* :doc:`cfg/uef <dump_cfg_uef>`
* :doc:`cfg/zstd <dump>`
* :doc:`custom <dump>`
* :doc:`custom/adios <dump_adios>`
* :doc:`custom/gz <dump>`
* :doc:`custom/mpiio <dump>`
* :doc:`custom/zstd <dump>`
* :doc:`dcd <dump>`
* :doc:`deprecated <dump>`
* :doc:`h5md <dump_h5md>`
* :doc:`image <dump_image>`
* :doc:`local <dump>`
* :doc:`local/gz <dump>`
* :doc:`local/zstd <dump>`
* :doc:`molfile <dump_molfile>`
* :doc:`movie <dump_image>`
* :doc:`netcdf <dump_netcdf>`
* :doc:`netcdf/mpiio <dump>`
* :doc:`vtk <dump_vtk>`
* :doc:`xtc <dump>`
* :doc:`xyz <dump>`
* :doc:`xyz/gz <dump>`
* :doc:`xyz/mpiio <dump>`
* :doc:`xyz/zstd <dump>`
* :doc:`yaml <dump>`

4
doc/src/Commands_fix.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Fix commands
============
@ -28,6 +29,8 @@ OPT.
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
* :doc:`addtorque <fix_addtorque>`
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
* :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
* :doc:`append/atoms <fix_append_atoms>`
* :doc:`atc <fix_atc>`
* :doc:`atom/swap <fix_atom_swap>`
@ -162,6 +165,7 @@ OPT.
* :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>`
* :doc:`pafi <fix_pafi>`
* :doc:`pair <fix_pair>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`

1
doc/src/Commands_kspace.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
KSpace solvers
==============

10
doc/src/Commands_pair.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Pair_style potentials
======================
@ -38,6 +39,7 @@ OPT.
* :doc:`agni (o) <pair_agni>`
* :doc:`airebo (io) <pair_airebo>`
* :doc:`airebo/morse (io) <pair_airebo>`
* :doc:`amoeba <pair_amoeba>`
* :doc:`atm <pair_atm>`
* :doc:`awpmd/cut <pair_awpmd>`
* :doc:`beck (go) <pair_beck>`
@ -124,6 +126,7 @@ OPT.
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`hdnnp <pair_hdnnp>`
* :doc:`hippo <pair_amoeba>`
* :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`
* :doc:`ilp/tmd (t) <pair_ilp_tmd>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
@ -179,9 +182,9 @@ OPT.
* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/relres (o) <pair_lj_relres>`
* :doc:`lj/sdk (gko) <pair_sdk>`
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/spica (gko) <pair_spica>`
* :doc:`lj/spica/coul/long (go) <pair_spica>`
* :doc:`lj/spica/coul/msm (o) <pair_spica>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
@ -269,6 +272,7 @@ OPT.
* :doc:`spin/magelec <pair_spin_magelec>`
* :doc:`spin/neel <pair_spin_neel>`
* :doc:`srp <pair_srp>`
* :doc:`srp/react <pair_srp>`
* :doc:`sw (giko) <pair_sw>`
* :doc:`sw/angle/table <pair_sw_angle_table>`
* :doc:`sw/mod (o) <pair_sw>`

3
doc/src/Developer_utils.rst
View File

@ -154,6 +154,9 @@ and parsing files or arguments.
.. doxygenfunction:: trim_and_count_words
:project: progguide
.. doxygenfunction:: join_words
:project: progguide
.. doxygenfunction:: split_words
:project: progguide

126
doc/src/Errors_messages.rst
View File

@ -476,65 +476,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Bonds defined but no bond types*
The data file header lists bonds but no bond types.
*Bond/react: Cannot use fix bond/react with non-molecular systems*
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
*Bond/react: Invalid template atom ID in map file*
Atom IDs in molecule templates range from 1 to the number of atoms in the template.
*Bond/react: Rmax cutoff is longer than pairwise cutoff*
This is not allowed because bond creation is done using the pairwise
neighbor list.
*Bond/react: Molecule template ID for fix bond/react does not exist*
A valid molecule template must have been created with the molecule
command.
*Bond/react: Reaction templates must contain the same number of atoms*
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file.
*Bond/react: Unknown section in map file*
Please ensure reaction map files are properly formatted.
*Bond/react: Atom/Bond type affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Bond/react: Fix bond/react needs ghost atoms from farther away*
This is because a processor needs to map the entire unreacted
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
*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
specify this value.
*Bond/react topology/atom exceed system topology/atom*
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value.
*Both restart files must use % or neither*
Self-explanatory.
@ -1291,7 +1232,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Cannot use chosen neighbor list style with lj/gromacs/kk*
Self-explanatory.
*Cannot use chosen neighbor list style with lj/sdk/kk*
*Cannot use chosen neighbor list style with lj/spica/kk*
That style is not supported by Kokkos.
*Cannot use chosen neighbor list style with pair eam/kk*
@ -1659,10 +1600,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Cannot use newton pair with lj/gromacs/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj/sdk/coul/long/gpu pair style*
*Cannot use newton pair with lj/spica/coul/long/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj/sdk/gpu pair style*
*Cannot use newton pair with lj/spica/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj96/cut/gpu pair style*
@ -3521,6 +3462,65 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
acquire needed info, The comm_modify cutoff command can be used to
extend the communication range.
*Fix bond/react: Cannot use fix bond/react with non-molecular systems*
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
*Fix bond/react: Invalid template atom ID in map file*
Atom IDs in molecule templates range from 1 to the number of atoms in the template.
*Fix bond/react: Rmax cutoff is longer than pairwise cutoff*
This is not allowed because bond creation is done using the pairwise
neighbor list.
*Fix bond/react: Molecule template ID for fix bond/react does not exist*
A valid molecule template must have been created with the molecule
command.
*Fix bond/react: Reaction templates must contain the same number of atoms*
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file.
*Fix bond/react: Unknown section in map file*
Please ensure reaction map files are properly formatted.
*Fix bond/react: Atom/Bond type affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Fix bond/react: Fix bond/react needs ghost atoms from farther away*
This is because a processor needs to map the entire unreacted
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
*Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
Self-explanatory.
*Fix bond/react: First neighbors of chiral atoms must be of mutually different types*
Self-explanatory.
*Fix bond/react: Chiral atoms must have exactly four first neighbors*
Self-explanatory.
*Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
The coordinates of atoms in the pre-reacted template are used to determine
chirality.
*Fix 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
specify this value.
*Fix bond/react topology/atom exceed system topology/atom*
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value.
*Fix bond/swap cannot use dihedral or improper styles*
These styles cannot be defined when using this fix.
@ -6782,7 +6782,7 @@ keyword to allow for additional bonds to be formed
This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors.
*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
*Pair style lj/spica/coul/long/gpu requires atom attribute q*
The atom style defined does not have this attribute.
*Pair style nb3b/harmonic requires atom IDs*

19
doc/src/Errors_warnings.rst
View File

@ -68,14 +68,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
length, multiplying by the number of bonds in the interaction (e.g. 3
for a dihedral) and adding a small amount of stretch.
*Bond/react: Atom affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
Self-explanatory.
@ -206,12 +198,20 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Fix SRD walls overlap but fix srd overlap not set*
You likely want to set this in your input script.
* Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
*Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
When using fix bond/create multiple times or in combination with
fix bond/break, the individual fix instances do not share information
about changes they made at the same time step and thus it may result
in unexpected behavior.
*Fix bond/react: Atom affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Fix bond/swap will ignore defined angles*
See the page for fix bond/swap for more info on this
restriction.
@ -810,4 +810,3 @@ This will most likely cause errors in kinetic fluctuations.
*Using pair tail corrections with pair_modify compute no*
The tail corrections will thus not be computed.

1
doc/src/Howto.rst
View File

@ -65,6 +65,7 @@ Force fields howto
:maxdepth: 1
Howto_bioFF
Howto_amoeba
Howto_tip3p
Howto_tip4p
Howto_spc

324
doc/src/Howto_amoeba.rst Normal file
View File

@ -0,0 +1,324 @@
AMOEBA and HIPPO force fields
=============================
The AMOEBA and HIPPO polarizable force fields were developed by Jay
Ponder's group at the U Washington at St Louis. Their implementation
in LAMMPS was done using F90 code provided by the Ponder group from
their `Tinker MD code <https://dasher.wustl.edu/tinker/>`_.
The current implementation (July 2022) of AMOEBA in LAMMPS matches the
version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren)
<amoeba-Ren>`, and :ref:`(Shi) <amoeba-Shi>`. Likewise the current
implementation of HIPPO in LAMMPS matches the version discussed in
:ref:`(Rackers) <amoeba-Rackers>`.
These force fields can be used when polarization effects are desired
in simulations of water, organic molecules, and biomolecules including
proteins, provided that parameterizations (Tinker PRM force field
files) are available for the systems you are interested in. Files in
the LAMMPS potentials directory with a "amoeba" or "hippo" suffix can
be used. The Tinker distribution and website have additional force
field files as well:
`https://github.com/TinkerTools/tinker/tree/release/params
<https://github.com/TinkerTools/tinker/tree/release/params>`_.
Note that currently, HIPPO can only be used for water systems, but
HIPPO files for a variety of small organic and biomolecules are in
preparation by the Ponder group. Those force field files will be
included in the LAMMPS distribution when available.
To use the AMOEBA or HIPPO force fields, a simulation must be 3d, and
fully periodic or fully non-periodic, and use an orthogonal (not
triclinic) simulation box.
----------
The AMOEBA and HIPPO force fields contain the following terms in their
energy (U) computation. Further details for AMOEBA equations are in
:ref:`(Ponder) <amoeba-Ponder>`, further details for the HIPPO
equations are in :ref:`(Rackers) <amoeba-Rackers>`.
.. math::
U & = U_{intermolecular} + U_{intramolecular} \\
U_{intermolecular} & = U_{hal} + U_{repulsion} + U_{dispersion} + U_{multipole} + U_{polar} + U_{qxfer} \\
U_{intramolecular} & = U_{bond} + U_{angle} + U_{torsion} + U_{oop} + U_{b\theta} + U_{UB} + U_{pitorsion} + U_{bitorsion}
For intermolecular terms, the AMOEBA force field includes only the
:math:`U_{hal}`, :math:`U_{multipole}`, :math:`U_{polar}` terms. The
HIPPO force field includes all but the :math:`U_{hal}` term. In
LAMMPS, these are all computed by the :doc:`pair_style amoeba or hippo
<pair_style>` command. Note that the :math:`U_{multipole}` and
:math:`U_{polar}` terms in this formula are not the same for the
AMOEBA and HIPPO force fields.
For intramolecular terms, the :math:`U_{bond}`, :math:`U_{angle}`,
:math:`U_{torsion}`, :math:`U_{oop}` terms are computed by the
:doc:`bond_style class2 <bond_class2>` :doc:`angle_style amoeba
<angle_amoeba>`, :doc:`dihedral_style fourier <dihedral_fourier>`, and
:doc:`improper_style amoeba <improper_amoeba>` commands respectively.
The :doc:`angle_style amoeba <angle_amoeba>` command includes the
:math:`U_{b\theta}` bond-angle cross term, and the :math:`U_{UB}` term
for a Urey-Bradley bond contribution between the I,K atoms in the IJK
angle.
The :math:`U_{pitorsion}` term is computed by the :doc:`fix
amoeba/pitorsion <fix_amoeba_pitorsion>` command. It computes 6-body
interaction between a pair of bonded atoms which each have 2
additional bond partners.
The :math:`U_{bitorsion}` term is computed by the :doc:`fix
amoeba/bitorsion <fix_amoeba_bitorsion>` command. It computes 5-body
interaction between two 4-body torsions (dihedrals) which overlap,
having 3 atoms in common.
These command doc pages have additional details on the terms they
compute:
* :doc:`pair_style amoeba or hippo <pair_amoeba>`
* :doc:`bond_style class2 <bond_class2>`
* :doc:`angle_style amoeba <angle_amoeba>`
* :doc:`dihedral_style fourier <dihedral_fourier>`
* :doc:`improper_style amoeba <improper_amoeba>`
* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
----------
To use the AMOEBA or HIPPO force fields in LAMMPS, use commands like
the following appropriately in your input script. The only change
needed for AMOEBA vs HIPPO simulation is for the :doc:`pair_style
<pair_style>` and :doc:`pair_coeff <pair_coeff>` commands, as shown
below. See examples/amoeba for example input scripts for both AMOEBA
and HIPPO.
.. code-block:: LAMMPS
units real # required
atom_style amoeba
bond_style class2 # CLASS2 package
angle_style amoeba
dihedral_style fourier # EXTRA-MOLECULE package
improper_style amoeba
# required per-atom data
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
fix polaxe all property/atom i_polaxe
fix pit all amoeba/pitorsion # PiTorsion terms in FF
fix_modify pit energy yes
# Bitorsion terms in FF
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pit "pitorsion types" "PiTorsion Coeffs" &
fix pit pitorsions PiTorsions &
fix bit bitorsions BiTorsions
pair_style amoeba # AMOEBA FF
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
pair_style hippo # HIPPO FF
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes # 1-5 neighbors
The data file read by the :doc:`read_data <read_data>` command should
be created by the tools/tinker/tinker2lmp.py conversion program
described below. It will create a section in the data file with the
header "Tinker Types". A :doc:`fix property/atom <fix_property_atom>`
command for the data must be specified before the read_data command.
In the example above the fix ID is *amtype*.
Similarly, if the system you are simulating defines AMOEBA/HIPPO
pitorsion or bitorsion interactions, there will be entries in the data
file for those interactions. They require a :doc:`fix
amoeba/pitortion <fix_amoeba_pitorsion>` and :doc:`fix
amoeba/bitorsion <fix_amoeba_bitorsion>` command be defined. In the
example above, the IDs for these two fixes are *pit* and *bit*.
Of course, if the system being modeled does not have one or more of
the following -- bond, angle, dihedral, improper, pitorsion,
bitorsion interactions -- then the corresponding style and fix
commands above do not need to be used. See the example scripts in
examples/amoeba for water systems as examples; they are simpler than
what is listed above.
The two :doc:`fix property/atom <fix_property_atom>` commands with IDs
(in the example above) *extra* and *polaxe* are also needed to define
internal per-atom quantities used by the AMOEBA and HIPPO force
fields.
The :doc:`pair_coeff <pair_coeff>` command used for either the AMOEBA
or HIPPO force field takes two arguments for Tinker force field files,
namely a PRM and KEY file. The keyfile can be specified as NULL and
default values for a various settings will be used. Note that these 2
files are meant to allow use of native Tinker files as-is. However
LAMMPS does not support all the options which can be included
in a Tinker PRM or KEY file. See specifics below.
A :doc:`special_bonds <special_bonds>` command with the *one/five*
option is required, since the AMOEBA/HIPPO force fields define
weighting factors for not only 1-2, 1-3, 1-4 interactions, but also
1-5 interactions. This command will trigger a per-atom list of 1-5
neighbors to be generated. The AMOEBA and HIPPO force fields define
their own custom weighting factors for all the 1-2, 1-3, 1-4, 1-5
terms which in the Tinker PRM and KEY files; they can be different for
different terms in the force field.
In addition to the list above, these command doc pages have additional
details:
* :doc:`atom_style amoeba <atom_style>`
* :doc:`fix property/atom <fix_property_atom>`
* :doc:`special_bonds <special_bonds>`
----------
Tinker PRM and KEY files
A Tinker PRM file is composed of sections, each of which has multiple
lines. This is the list of PRM sections LAMMPS knows how to parse and
use. Any other sections are skipped:
* Angle Bending Parameters
* Atom Type Definitions
* Atomic Multipole Parameters
* Bond Stretching Parameters
* Charge Penetration Parameters
* Charge Transfer Parameters
* Dipole Polarizability Parameters
* Dispersion Parameters
* Force Field Definition
* Literature References
* Out-of-Plane Bend Parameters
* Pauli Repulsion Parameters
* Pi-Torsion Parameters
* Stretch-Bend Parameters
* Torsion-Torsion Parameters
* Torsional Parameters
* Urey-Bradley Parameters
* Van der Waals Pair Parameters
* Van der Waals Parameters
A Tinker KEY file is composed of lines, each of which has a keyword
followed by zero or more parameters. This is the list of keywords
LAMMPS knows how to parse and use in the same manner Tinker does. Any
other keywords are skipped. The value in parenthesis is the default
value for the keyword if it is not specified, or if the keyfile in the
:doc:`pair_coeff <pair_coeff>` command is specified as NULL:
* a-axis (0.0)
* b-axis (0.0)
* c-axis (0.0)
* ctrn-cutoff (6.0)
* ctrn-taper (0.9 * ctrn-cutoff)
* cutoff
* delta-halgren (0.07)
* dewald (no long-range dispersion unless specified)
* dewald-alpha (0.4)
* dewald-cutoff (7.0)
* dispersion-cutoff (9.0)
* dispersion-taper (9.0 * dispersion-cutoff)
* dpme-grid
* dpme-order (4)
* ewald (no long-range electrostatics unless specified)
* ewald-alpha (0.4)
* ewald-cutoff (7.0)
* gamma-halgren (0.12)
* mpole-cutoff (9.0)
* mpole-taper (0.65 * mpole-cutoff)
* pcg-guess (enabled by default)
* pcg-noguess (disable pcg-guess if specified)
* pcg-noprecond (disable pcg-precond if specified)
* pcg-peek (1.0)
* pcg-precond (enabled by default)
* pewald-alpha (0.4)
* pme-grid
* pme-order (5)
* polar-eps (1.0e-6)
* polar-iter (100)
* polar-predict (no prediction operation unless specified)
* ppme-order (5)
* repulsion-cutoff (6.0)
* repulsion-taper (0.9 * repulsion-cutoff)
* taper
* usolve-cutoff (4.5)
* usolve-diag (2.0)
* vdw-cutoff (9.0)
* vdw-taper (0.9 * vdw-cutoff)
----------
Tinker2lmp.py tool
This conversion tool is found in the tools/tinker directory.
As shown in examples/amoeba/README, these commands produce
the data files found in examples/amoeba, and also illustrate
all the options available to use with the tinker2lmp.py script:
.. code-block:: bash
% python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba # AMOEBA non-periodic system
% python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo # HIPPO non-periodic system
% python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643 # AMOEBA periodic system
% python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643 # HIPPO periodic system
% python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new # system with bitorsions
Switches and their arguments may be specified in any order.
The -xyz switch is required and specifies an input XYZ file as an
argument. The format of this file is an extended XYZ format defined
and used by Tinker for its input. Example \*.xyz files are in the
examples/amoeba directory. The file lists the atoms in the system.
Each atom has the following information: Tinker species name (ignored
by LAMMPS), xyz coordinates, Tinker numeric type, and a list of atom
IDs the atom is bonded to.
Here is more information about the extended XYZ format defined and
used by Tinker, and links to programs that convert standard PDB files
to the extended XYZ format:
* `http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
* `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_
* `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_
The -amoeba or -hippo switch is required. It specifies an input
AMOEBA or HIPPO PRM force field file as an argument. This should be
the same file used by the :doc:`pair_style <pair_style>` command in
the input script.
The -data switch is required. It specifies an output file name for
the LAMMPS data file that will be produced.
For periodic systems, the -pbc switch is required. It specifies the
periodic box size for each dimension (x,y,z). For a Tinker simulation
these are specified in the KEY file.
The -bitorsion switch is only needed if the system contains Tinker
bitorsion interactions. The data for each type of bitorsion
interaction will be written to the specified file, and read by the
:doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>` command. The data
includes 2d arrays of values to which splines are fit, and thus is not
compatible with the LAMMPS data file format.
----------
.. _howto-Ponder:
**(Ponder)** Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
.. _howto-Rackers:
**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021).
.. _howto-Ren:
**(Ren)** Ren and Ponder, J Phys Chem B, 107, 5933 (2003).
.. _howto-Shi:
**(Shi)** Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.

1
doc/src/Manual.rst
View File

@ -110,6 +110,7 @@ Command Reference
angles
dihedrals
impropers
dumps
fix_modify_atc_commands
Bibliography

15
doc/src/Modify_style.rst
View File

@ -100,13 +100,14 @@ Documentation (strict)
Contributions that add new styles or commands or augment existing ones
must include the corresponding new or modified documentation in
`ReStructuredText format <rst>`_ (.rst files in the ``doc/src/`` folder). The
documentation shall be written in American English and the .rst file
must use only ASCII characters so it can be cleanly translated to PDF
files (via `sphinx <sphinx>`_ and PDFLaTeX). Special characters may be included via
embedded math expression typeset in a LaTeX subset.
`ReStructuredText format <rst_>`_ (.rst files in the ``doc/src/``
folder). The documentation shall be written in American English and the
.rst file must use only ASCII characters so it can be cleanly translated
to PDF files (via `sphinx <https://www.sphinx-doc.org>`_ and PDFLaTeX).
Special characters may be included via embedded math expression typeset
in a LaTeX subset.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html
When adding new commands, they need to be integrated into the sphinx
documentation system, and the corresponding command tables and lists
@ -133,7 +134,7 @@ error free completion of the HTML and PDF build will be performed and
also a spell check, a check for correct anchors and labels, and a check
for completeness of references all styles in their corresponding tables
and lists is run. In case the spell check reports false positives they
can be added to the file doc/utils/sphinx-config/false_positives.txt
can be added to the file ``doc/utils/sphinx-config/false_positives.txt``
Contributions that add or modify the library interface or "public" APIs
from the C++ code or the Fortran module must include suitable doxygen

45
doc/src/Packages_details.rst
View File

@ -27,6 +27,7 @@ page gives those details.
:columns: 6
* :ref:`ADIOS <PKG-ADIOS>`
* :ref:`AMOEBA <PKG-AMOEBA>`
* :ref:`ASPHERE <PKG-ASPHERE>`
* :ref:`ATC <PKG-ATC>`
* :ref:`AWPMD <PKG-AWPMD>`
@ -35,7 +36,7 @@ page gives those details.
* :ref:`BPM <PKG-BPM>`
* :ref:`BROWNIAN <PKG-BROWNIAN>`
* :ref:`CG-DNA <PKG-CG-DNA>`
* :ref:`CG-SDK <PKG-CG-SDK>`
* :ref:`CG-SPICA <PKG-CG-SPICA>`
* :ref:`CLASS2 <PKG-CLASS2>`
* :ref:`COLLOID <PKG-COLLOID>`
* :ref:`COLVARS <PKG-COLVARS>`
@ -149,6 +150,24 @@ This package has :ref:`specific installation instructions <adios>` on the :doc:`
----------
.. _PKG-AMOEBA:
AMOEBA package
---------------
**Contents:**
TODO
**Supporting info:**
* src/AMOEBA: filenames -> commands
* :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
* examples/amoeba
* TODO
----------
.. _PKG-ASPHERE:
ASPHERE package
@ -365,28 +384,30 @@ The CG-DNA package requires that also the `MOLECULE <PKG-MOLECULE>`_ and
----------
.. _PKG-CG-SDK:
.. _PKG-CG-SPICA:
CG-SDK package
CG-SPICA package
------------------
**Contents:**
Several pair styles and an angle style which implement the
coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
simulation of ionic liquids, electrolytes, lipids and charged amino
acids.
coarse-grained SPICA (formerly called SDK) model which enables
simulation of biological or soft material systems.
**Author:** Axel Kohlmeyer (Temple U).
**Original Author:** Axel Kohlmeyer (Temple U).
**Maintainers:** Yusuke Miyazaki and Wataru Shinoda (Okayama U).
**Supporting info:**
* src/CG-SDK: filenames -> commands
* src/CG-SDK/README
* :doc:`pair_style lj/sdk/\* <pair_sdk>`
* :doc:`angle_style sdk <angle_sdk>`
* examples/PACKAGES/cgsdk
* src/CG-SPICA: filenames -> commands
* src/CG-SPICA/README
* :doc:`pair_style lj/spica/\* <pair_spica>`
* :doc:`angle_style spica <angle_spica>`
* examples/PACKAGES/cgspica
* https://www.lammps.org/pictures.html#cg
* https://www.spica-ff.org/
----------

13
doc/src/Packages_list.rst
View File

@ -33,6 +33,11 @@ whether an extra library is needed to build and use the package:
- :doc:`dump adios <dump_adios>`
- PACKAGES/adios
- ext
* - :ref:`AMOEBA <PKG-AMOEBA>`
- AMOEBA and HIPPO force fields
- :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
- amoeba
- no
* - :ref:`ASPHERE <PKG-ASPHERE>`
- aspherical particle models
- :doc:`Howto spherical <Howto_spherical>`
@ -73,10 +78,10 @@ whether an extra library is needed to build and use the package:
- src/CG-DNA/README
- PACKAGES/cgdna
- no
* - :ref:`CG-SDK <PKG-CG-SDK>`
- SDK coarse-graining model
- :doc:`pair_style lj/sdk <pair_sdk>`
- PACKAGES/cgsdk
* - :ref:`CG-SPICA <PKG-CG-SPICA>`
- SPICA (SDK) coarse-graining model
- :doc:`pair_style lj/spica <pair_spica>`
- PACKAGES/cgspica
- no
* - :ref:`CLASS2 <PKG-CLASS2>`
- class 2 force fields

138
doc/src/angle_amoeba.rst Normal file
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@ -0,0 +1,138 @@
.. index:: angle_style amoeba
angle_style amoeba command
==========================
Syntax
""""""
.. code-block:: LAMMPS
angle_style amoeba
Examples
""""""""
.. code-block:: LAMMPS
angle_style amoeba
angle_coeff * 75.0 -25.0 1.0 0.3 0.02 0.003
angle_coeff * ba 3.6551 24.895 1.0119 1.5228
angle_coeff * ub -7.6 1.5537
Description
"""""""""""
The *amoeba* angle style uses the potential
.. math::
E & = E_a + E_{ba} + E_{ub} \\
E_a & = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6 \\
E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0) \\
E_{UB} & = K_{ub} (r_{ik} - r_{ub})^2
where :math:`E_a` is the angle term, :math:`E_{ba}` is a bond-angle
term, :math:`E_{UB}` is a Urey-Bradley bond term, :math:`\theta_0` is
the equilibrium angle, :math:`r_1` and :math:`r_2` are the equilibrium
bond lengths, and :math:`r_{ub}` is the equilibrium Urey-Bradley bond
length.
These formulas match how the Tinker MD code performs its angle
calculations for the AMOEBA and HIPPO force fields. See the
:doc:`Howto amoeba <Howto_amoeba>` page for more information about
the implementation of AMOEBA and HIPPO in LAMMPS.
Note that the :math:`E_a` and :math:`E_{ba}` formulas are identical to
those used for the :doc:`angle_style class2/p6 <angle_class2>`
command, however there is no bond-bond cross term formula for
:math:`E_{bb}`. Additionally, there is a :math:`E_{UB}` term for a
Urey-Bradley bond. It is effectively a harmonic bond between the I
and K atoms of angle IJK, even though that bond is not enumerated in
the "Bonds" section of the data file.
There are also two ways that Tinker computes the angle :math:`\theta`
in the :math:`E_a` formula. The first is the standard way of treating
IJK as an "in-plane" angle. The second is an "out-of-plane" method
which Tinker may use if the center atom J in the angle is bonded to
one additional atom in addition to I and K. In this case, all 4 atoms
are used to compute the :math:`E_a` formula, resulting in forces on
all 4 atoms. In the Tinker PRM file, these 2 options are denoted by
*angle* versus *anglep* entries in the "Angle Bending Parameters"
section of the PRM force field file. The *pflag* coefficient
described below selects between the 2 options.
----------
Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ub}`
formulas must be defined for each angle type via the :doc:`angle_coeff
<angle_coeff>` command as in the example above, or in the data file or
restart files read by the :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` commands.
These are the 8 coefficients for the :math:`E_a` formula:
* pflag = 0 or 1
* ubflag = 0 or 1
* :math:`\theta_0` (degrees)
* :math:`K_2` (energy)
* :math:`K_3` (energy)
* :math:`K_4` (energy)
* :math:`K_5` (energy)
* :math:`K_6` (energy)
A pflag value of 0 vs 1 selects between the "in-plane" and
"out-of-plane" options described above. Ubflag is 1 if there is a
Urey-Bradley term associated with this angle type, else it is 0.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence the various :math:`K` values are effectively
energy per radian\^2 or radian\^3 or radian\^4 or radian\^5 or
radian\^6.
For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff
<angle_coeff>` command in the input script lists 5 coefficients, the
first of which is "ba" to indicate they are BondAngle coefficients.
In a data file, these coefficients should be listed under a "BondAngle
Coeffs" heading and you must leave out the "ba", i.e. only list 4
coefficients after the angle type.
* ba
* :math:`N_1` (energy/distance\^2)
* :math:`N_2` (energy/distance\^2)
* :math:`r_1` (distance)
* :math:`r_2` (distance)
The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
since it is the same value from the :math:`E_a` formula.
For the :math:`E_{ub}` formula, each line in a :doc:`angle_coeff
<angle_coeff>` command in the input script lists 3 coefficients, the
first of which is "ub" to indicate they are UreyBradley coefficients.
In a data file, these coefficients should be listed under a
"UreyBradley Coeffs" heading and you must leave out the "ub",
i.e. only list 2 coefficients after the angle type.
* ub
* :math:`K_{ub}` (energy/distance\^2)
* :math:`r_{ub}` (distance)
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the AMOEBA
package. See the :doc:`Build package <Build_package>` doc page for
more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none

2
doc/src/angle_class2.rst
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@ -24,7 +24,7 @@ Examples
.. code-block:: LAMMPS
angle_style class2
angle_coeff * 75.0
angle_coeff * 75.0 25.0 0.3 0.002
angle_coeff 1 bb 10.5872 1.0119 1.5228
angle_coeff * ba 3.6551 24.895 1.0119 1.5228

37
doc/src/angle_sdk.rst → doc/src/angle_spica.rst
View File

@ -1,32 +1,32 @@
.. index:: angle_style sdk
.. index:: angle_style sdk/omp
.. index:: angle_style spica
.. index:: angle_style spica/omp
angle_style sdk command
=======================
angle_style spica command
=========================
Accelerator Variants: *sdk/omp*
Accelerator Variants: *spica/omp*
Syntax
""""""
.. code-block:: LAMMPS
angle_style sdk
angle_style spica
angle_style sdk/omp
angle_style spica/omp
Examples
""""""""
.. code-block:: LAMMPS
angle_style sdk
angle_style spica
angle_coeff 1 300.0 107.0
Description
"""""""""""
The *sdk* angle style is a combination of the harmonic angle potential,
The *spica* angle style is a combination of the harmonic angle potential,
.. math::
@ -34,10 +34,10 @@ The *sdk* angle style is a combination of the harmonic angle potential,
where :math:`\theta_0` is the equilibrium value of the angle and
:math:`K` a prefactor, with the *repulsive* part of the non-bonded
*lj/sdk* pair style between the atoms 1 and 3. This angle potential is
intended for coarse grained MD simulations with the CMM parameterization
using the :doc:`pair_style lj/sdk <pair_sdk>`. Relative to the
pair_style *lj/sdk*, however, the energy is shifted by
*lj/spica* pair style between the atoms 1 and 3. This angle potential is
intended for coarse grained MD simulations with the SPICA (formerly called SDK) parameterization
using the :doc:`pair_style lj/spica <pair_spica>`. Relative to the
pair_style *lj/spica*, however, the energy is shifted by
:math:`\epsilon`, to avoid sudden jumps. Note that the usual 1/2 factor
is included in :math:`K`.
@ -51,9 +51,12 @@ The following coefficients must be defined for each angle type via the
radians internally; hence :math:`K` is effectively energy per
radian\^2.
The required *lj/sdk* parameters are extracted automatically from the
The required *lj/spica* parameters are extracted automatically from the
pair_style.
Style *sdk*, the original implementation of style *spica*, is available
for backward compatibility.
----------
.. include:: accel_styles.rst
@ -64,14 +67,14 @@ Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
CG-SDK package. See the :doc:`Build package <Build_package>` doc
CG-SPICA package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/sdk <pair_sdk>`,
:doc:`pair_style lj/sdk/coul/long <pair_sdk>`
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/spica <pair_spica>`,
:doc:`pair_style lj/spica/coul/long <pair_spica>`
Default
"""""""

3
doc/src/angle_style.rst
View File

@ -73,6 +73,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`zero <angle_zero>` - topology but no interactions
* :doc:`hybrid <angle_hybrid>` - define multiple styles of angle interactions
* :doc:`amoeba <angle_amoeba>` - AMOEBA angle
* :doc:`charmm <angle_charmm>` - CHARMM angle
* :doc:`class2 <angle_class2>` - COMPASS (class 2) angle
* :doc:`class2/p6 <angle_class2>` - COMPASS (class 2) angle expanded to 6th order
@ -91,7 +92,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`harmonic <angle_harmonic>` - harmonic angle
* :doc:`mm3 <angle_mm3>` - anharmonic angle
* :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
* :doc:`sdk <angle_sdk>` - harmonic angle with repulsive SDK pair style between 1-3 atoms
* :doc:`spica <angle_spica>` - harmonic angle with repulsive SPICA pair style between 1-3 atoms
* :doc:`table <angle_table>` - tabulated by angle
----------

94
doc/src/atom_style.rst
View File

@ -10,7 +10,7 @@ Syntax
atom_style style args
* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
.. parsed-literal::
@ -78,6 +78,8 @@ coordinates, velocities, atom IDs and types. See the
:doc:`set <set>` commands for info on how to set these various
quantities.
+--------------+-----------------------------------------------------+--------------------------------------+
| *amoeba* | molecular + charge + 1/5 neighbors | AMOEBA/HIPPO polarized force fields |
+--------------+-----------------------------------------------------+--------------------------------------+
| *angle* | bonds and angles | bead-spring polymers with stiffness |
+--------------+-----------------------------------------------------+--------------------------------------+
@ -137,11 +139,13 @@ quantities.
.. note::
It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the :doc:`fix property/atom <fix_property_atom>` command. This command also
allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the :doc:`fix property/atom <fix_property_atom>` page for examples of cases
where this is useful and details on how to initialize, access, and
output the custom values.
atom styles that do not have them via the :doc:`fix property/atom
<fix_property_atom>` command. This command also allows new custom
attributes consisting of extra integer or floating-point values to
be added to atoms. See the :doc:`fix property/atom
<fix_property_atom>` page for examples of cases where this is
useful and details on how to initialize, access, and output the
custom values.
All of the above styles define point particles, except the *sphere*,
*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
@ -154,19 +158,20 @@ per-type basis, using the :doc:`mass <mass>` command, The finite-size
particle styles assign mass to individual particles on a per-particle
basis.
For the *sphere* and *bpm/sphere* styles, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
is a finite-size sphere. If the diameter = 0.0, it is a point
particle. Note that by use of the *disc* keyword with the :doc:`fix
nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
<fix_npt_sphere>` commands for the *sphere* style, spheres can be effectively treated as 2d
discs for a 2d simulation if desired. See also the :doc:`set
density/disc <set>` command. The *sphere* and *bpm/sphere* styles take an optional 0
or 1 argument. A value of 0 means the radius of each sphere is
constant for the duration of the simulation. A value of 1 means the
radii may vary dynamically during the simulation, e.g. due to use of
the :doc:`fix adapt <fix_adapt>` command.
For the *sphere* and *bpm/sphere* styles, the particles are spheres
and each stores a per-particle diameter and mass. If the diameter >
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
is a point particle. Note that by use of the *disc* keyword with the
:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix
npt/sphere <fix_npt_sphere>` commands for the *sphere* style, spheres
can be effectively treated as 2d discs for a 2d simulation if desired.
See also the :doc:`set density/disc <set>` command. The *sphere* and
*bpm/sphere* styles take an optional 0 or 1 argument. A value of 0
means the radius of each sphere is constant for the duration of the
simulation. A value of 1 means the radii may vary dynamically during
the simulation, e.g. due to use of the :doc:`fix adapt <fix_adapt>`
command.
For the *ellipsoid* style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
@ -175,15 +180,16 @@ vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
with its orientation.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element. For physical particles, the per-particle properties are
the same as atom_style full. For interface particles, in addition to
these properties, each particle also has an area, a normal unit vector,
a mean local curvature, the mean and difference of the dielectric constants
of two sides of the interface, and the local dielectric constant at the
boundary element. The distinction between the physical and interface
particles is only meaningful when :doc:`fix polarize <fix_polarize>`
commands are applied to the interface particles.
particle (e.g. an ion), or an interface particle representing a
boundary element. For physical particles, the per-particle properties
are the same as atom_style full. For interface particles, in addition
to these properties, each particle also has an area, a normal unit
vector, a mean local curvature, the mean and difference of the
dielectric constants of two sides of the interface, and the local
dielectric constant at the boundary element. The distinction between
the physical and interface particles is only meaningful when :doc:`fix
polarize <fix_polarize>` commands are applied to the interface
particles.
For the *dipole* style, a point dipole is defined for each point
particle. Note that if you wish the particles to be finite-size
@ -272,16 +278,17 @@ showing the use of the *template* atom style versus *molecular*.
.. note::
When using the *template* style with a :doc:`molecule template <molecule>` that contains multiple molecules, you should
insure the atom types, bond types, angle_types, etc in all the
molecules are consistent. E.g. if one molecule represents H2O and
another CO2, then you probably do not want each molecule file to
define 2 atom types and a single bond type, because they will conflict
with each other when a mixture system of H2O and CO2 molecules is
defined, e.g. by the :doc:`read_data <read_data>` command. Rather the
H2O molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
2 if a single oxygen type is desired), and bond type 2.
When using the *template* style with a :doc:`molecule template
<molecule>` that contains multiple molecules, you should insure the
atom types, bond types, angle_types, etc in all the molecules are
consistent. E.g. if one molecule represents H2O and another CO2,
then you probably do not want each molecule file to define 2 atom
types and a single bond type, because they will conflict with each
other when a mixture system of H2O and CO2 molecules is defined,
e.g. by the :doc:`read_data <read_data>` command. Rather the H2O
molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3
and 2 if a single oxygen type is desired), and bond type 2.
For the *body* style, the particles are arbitrary bodies with internal
attributes defined by the "style" of the bodies, which is specified by
@ -339,6 +346,8 @@ Many of the styles listed above are only enabled if LAMMPS was built
with a specific package, as listed below. See the :doc:`Build package
<Build_package>` page for more info.
The *amoeba* style is part of the AMOEBA package.
The *angle*, *bond*, *full*, *molecular*, and *template* styles are
part of the MOLECULE package.
@ -350,9 +359,11 @@ The *dipole* style is part of the DIPOLE package.
The *peri* style is part of the PERI package for Peridynamics.
The *oxdna* style is part of the CG-DNA package for coarse-grained simulation of DNA and RNA.
The *oxdna* style is part of the CG-DNA package for coarse-grained
simulation of DNA and RNA.
The *electron* style is part of the EFF package for :doc:`electronic force fields <pair_eff>`.
The *electron* style is part of the EFF package for :doc:`electronic
force fields <pair_eff>`.
The *dpd* style is part of the DPD-REACT package for dissipative
particle dynamics (DPD).
@ -363,7 +374,8 @@ dissipative particle dynamics (mDPD), and transport dissipative particle
dynamics (tDPD), respectively.
The *sph* style is part of the SPH package for smoothed particle
hydrodynamics (SPH). See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
hydrodynamics (SPH). See `this PDF guide
<PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
The *mesont* style is part of the MESONT package.

10
doc/src/compute_contact_atom.rst
View File

@ -8,10 +8,11 @@ Syntax
.. parsed-literal::
compute ID group-ID contact/atom
compute ID group-ID contact/atom group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* contact/atom = style name of this compute command
* group2-ID = optional argument to restrict which atoms to consider for contacts (see below)
Examples
""""""""
@ -19,6 +20,7 @@ Examples
.. code-block:: LAMMPS
compute 1 all contact/atom
compute 1 all contact/atom mygroup
Description
"""""""""""
@ -45,6 +47,9 @@ overview of LAMMPS output options.
The per-atom vector values will be a number >= 0.0, as explained
above.
The optional *group2-ID* argument allows to specify from which group atoms
contribute to the coordination number. Default setting is group 'all'.
Restrictions
""""""""""""
@ -63,4 +68,7 @@ Related commands
Default
"""""""
*group2-ID* = all
none

4
doc/src/compute_pair.rst
View File

@ -93,7 +93,9 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>`
:doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>`,
:doc:`fix pair <fix_pair>`
Default
"""""""

86
doc/src/compute_sna_atom.rst
View File

@ -45,7 +45,7 @@ Syntax
* w_1, w_2,... = list of neighbor weights, one for each type
* nx, ny, nz = number of grid points in x, y, and z directions (positive integer)
* zero or more keyword/value pairs may be appended
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner*
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner* or *dgradflag*
.. parsed-literal::
@ -68,9 +68,6 @@ Syntax
*wselfallflag* value = *0* or *1*
*0* = self-contribution only for element of central atom
*1* = self-contribution for all elements
*bikflag* value = *0* or *1* (only implemented for compute snap)
*0* = per-atom bispectrum descriptors are summed over atoms
*1* = per-atom bispectrum descriptors are not summed over atoms
*switchinnerflag* value = *0* or *1*
*0* = do not use inner switching function
*1* = use inner switching function
@ -78,6 +75,12 @@ Syntax
*sinnerlist* = *ntypes* values of *Sinner* (distance units)
*dinner* values = *dinnerlist*
*dinnerlist* = *ntypes* values of *Dinner* (distance units)
*bikflag* value = *0* or *1* (only implemented for compute snap)
*0* = descriptors are summed over atoms of each type
*1* = descriptors are listed separately for each atom
*dgradflag* value = *0* or *1* (only implemented for compute snap)
*0* = descriptor gradients are summed over atoms of each type
*1* = descriptor gradients are listed separately for each atom pair
Examples
""""""""
@ -360,15 +363,6 @@ This option is typically used in conjunction with the *chem* keyword,
and LAMMPS will generate a warning if both *chem* and *bnormflag*
are not both set or not both unset.
The keyword *bikflag* determines whether or not to expand the bispectrum
rows of the global array returned by compute snap. If *bikflag* is set
to *1* then the bispectrum row, which is typically the per-atom bispectrum
descriptors :math:`B_{i,k}` summed over all atoms *i* to produce
:math:`B_k`, becomes bispectrum rows equal to the number of atoms. Thus,
the resulting bispectrum rows are :math:`B_{i,k}` instead of just
:math:`B_k`. In this case, the entries in the final column for these rows
are set to zero.
The keyword *switchinnerflag* with value 1
activates an additional radial switching
function similar to :math:`f_c(r)` above, but acting to switch off
@ -393,6 +387,36 @@ When the central atom and the neighbor atom have different types,
the values of :math:`S_{inner}` and :math:`D_{inner}` are
the arithmetic means of the values for both types.
The keywords *bikflag* and *dgradflag* are only used by compute *snap*.
The keyword *bikflag* determines whether or not to list the descriptors
of each atom separately, or sum them together and list in a single row.
If *bikflag* is set
to *0* then a single bispectrum row is used, which contains the per-atom bispectrum
descriptors :math:`B_{i,k}` summed over all atoms *i* to produce
:math:`B_k`. If *bikflag* is set
to *1* this is replaced by a separate per-atom bispectrum row for each atom.
In this case, the entries in the final column for these rows
are set to zero.
The keyword *dgradflag* determines whether to sum atom gradients or list
them separately. If *dgradflag* is set to 0, the bispectrum
descriptor gradients w.r.t. atom *j* are summed over all atoms *i'*
of type *I* (similar to *snad/atom* above).
If *dgradflag* is set to 1, gradients are listed separately for each pair of atoms.
Each row corresponds
to a single term :math:`\frac{\partial {B_{i,k} }}{\partial {r}^a_j}`
where :math:`{r}^a_j` is the *a-th* position coordinate of the atom with global
index *j*. This also changes
the number of columns to be equal to the number of bispectrum components, with 3
additional columns representing the indices :math:`i`, :math:`j`, and :math:`a`,
as explained more in the Output info section below. The option *dgradflag=1*
requires that *bikflag=1*.
.. note::
Using *dgradflag* = 1 produces a global array with :math:`N + 3N^2 + 1` rows
which becomes expensive for systems with more than 1000 atoms.
.. note::
If you have a bonded system, then the settings of :doc:`special_bonds
@ -503,6 +527,42 @@ components. For the purposes of handling contributions to force, virial,
and quadratic combinations, these :math:`N_{elem}^3` sub-blocks are
treated as a single block of :math:`K N_{elem}^3` columns.
If the *bik* keyword is set to 1, the structure of the snap array is expanded.
The first :math:`N` rows of the snap array
correspond to :math:`B_{i,k}` instead of a single row summed over atoms :math:`i`.
In this case, the entries in the final column for these rows
are set to zero. Also, each row contains only non-zero entries for the
columns corresponding to the type of that atom. This is not true in the case
of *dgradflag* keyword = 1 (see below).
If the *dgradflag* keyword is set to 1, this changes the structure of the
global array completely.
Here the *snad/atom* quantities are replaced with rows corresponding to
descriptor gradient components on single atoms:
.. math::
\frac{\partial {B_{i,k} }}{\partial {r}^a_j}
where :math:`{r}^a_j` is the *a-th* position coordinate of the atom with global
index *j*. The rows are
organized in chunks, where each chunk corresponds to an atom with global index
:math:`j`. The rows in an atom :math:`j` chunk correspond to
atoms with global index :math:`i`. The total number of rows for
these descriptor gradients is therefore :math:`3N^2`.
The number of columns is equal to the number of bispectrum components,
plus 3 additional left-most columns representing the global atom indices
:math:`i`, :math:`j`,
and Cartesian direction :math:`a` (0, 1, 2, for x, y, z).
The first 3 columns of the first :math:`N` rows belong to the reference
potential force components. The remaining K columns contain the
:math:`B_{i,k}` per-atom descriptors corresponding to the non-zero entries
obtained when *bikflag* = 1.
The first column of the last row, after the first
:math:`N + 3N^2` rows, contains the reference potential
energy. The virial components are not used with this option. The total number of
rows is therefore :math:`N + 3N^2 + 1` and the number of columns is :math:`K + 3`.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options. To see how this command

27
doc/src/dump.rst
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@ -1,4 +1,26 @@
.. index:: dump
.. index:: dump atom
.. index:: dump cfg
.. index:: dump custom
.. index:: dump dcd
.. index:: dump local
.. index:: dump xtc
.. index:: dump yaml
.. index:: dump xyz
.. index:: dump atom/gz
.. index:: dump cfg/gz
.. index:: dump custom/gz
.. index:: dump local/gz
.. index:: dump xyz/gz
.. index:: dump atom/mpiio
.. index:: dump cfg/mpiio
.. index:: dump custom/mpiio
.. index:: dump xyz/mpiio
.. index:: dump atom/zstd
.. index:: dump cfg/zstd
.. index:: dump custom/zstd
.. index:: dump xyz/zstd
.. index:: dump local/zstd
dump command
============
@ -783,6 +805,11 @@ To write gzipped dump files, you must either compile LAMMPS with the
-DLAMMPS_GZIP option or use the styles from the COMPRESS package.
See the :doc:`Build settings <Build_settings>` page for details.
While a dump command is active (i.e. has not been stopped by using
the undump command), no commands may be used that will change the
timestep (e.g. :doc:`reset_timestep <reset_timestep>`). LAMMPS
will terminate with an error otherwise.
The *atom/gz*, *cfg/gz*, *custom/gz*, and *xyz/gz* styles are part of
the COMPRESS package. They are only enabled if LAMMPS was built with
that package. See the :doc:`Build package <Build_package>` page for

1
doc/src/dump_image.rst
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@ -1,4 +1,5 @@
.. index:: dump image
.. index:: dump movie
dump image command
==================

83
doc/src/dump_modify.rst
View File

@ -17,7 +17,7 @@ Syntax
* one or more keyword/value pairs may be appended
* these keywords apply to various dump styles
* keyword = *append* or *at* or *balance* or *buffer* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
* keyword = *append* or *at* or *balance* or *buffer* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
.. parsed-literal::
@ -65,6 +65,8 @@ Syntax
*refresh* arg = c_ID = compute ID that supports a refresh operation
*scale* arg = *yes* or *no*
*sfactor* arg = coordinate scaling factor (> 0.0)
*skip* arg = v_name
v_name = variable with name which evaluates to non-zero (skip) or 0
*sort* arg = *off* or *id* or N or -N
off = no sorting of per-atom lines within a snapshot
id = sort per-atom lines by atom ID
@ -176,6 +178,28 @@ extra buffering.
----------
The *colname* keyword can be used to change the default header keyword
for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
and MPIIO variants. The setting for *ID string* replaces the default
text with the provided string. *ID* can be a positive integer when it
represents the column number counting from the left, a negative integer
when it represents the column number from the right (i.e. -1 is the last
column/keyword), or a custom dump keyword (or compute, fix, property, or
variable reference) and then it replaces the string for that specific
keyword. For *atom* dump styles only the keywords "id", "type", "x",
"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
whether scaled or unwrapped coordinates were enabled or disabled, and
it always assumes 8 columns for indexing regardless of whether image
flags are enabled or not. For dump style *cfg* only changes to the
"auxiliary" keywords (6th or later keyword) will become visible.
The *colname* keyword can be used multiple times. If multiple *colname*
settings refer to the same keyword, the last setting has precedence. A
setting of *default* clears all previous settings, reverting all values
to their default names.
----------
The *delay* keyword applies to all dump styles. No snapshots will be
output until the specified *Dstep* timestep or later. Specifying
*Dstep* < 0 is the same as turning off the delay setting. This is a
@ -357,7 +381,7 @@ always occur if the current timestep is a multiple of $N$, the
frequency specified in the :doc:`dump <dump>` command or
:doc:`dump_modify every <dump_modify>` command, including timestep 0.
It will also always occur if the current simulation time is a multiple
of *Delta*, the time interval specified in the doc:`dump_modify
of *Delta*, the time interval specified in the :doc:`dump_modify
every/time <dump_modify>` command.
But if this is not the case, a dump snapshot will only be written if
@ -365,10 +389,10 @@ the setting of this keyword is *yes*\ . If it is *no*, which is the
default, then it will not be written.
Note that if the argument to the :doc:`dump_modify every
<dump_modify>` doc:`dump_modify every/time <dump_modify>` commands is
a variable and not a numeric value, then specifying *first yes* is the
only way to write a dump snapshot on the first timestep after the dump
command is invoked.
<dump_modify>` or doc:`dump_modify every/time <dump_modify>` commands
is a variable and not a numeric value, then specifying *first yes* is
the only way to write a dump snapshot on the first timestep after the
dump command is invoked.
----------
@ -380,28 +404,6 @@ performed with dump style *xtc*\ .
----------
The *colname* keyword can be used to change the default header keyword
for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
and MPIIO variants. The setting for *ID string* replaces the default
text with the provided string. *ID* can be a positive integer when it
represents the column number counting from the left, a negative integer
when it represents the column number from the right (i.e. -1 is the last
column/keyword), or a custom dump keyword (or compute, fix, property, or
variable reference) and then it replaces the string for that specific
keyword. For *atom* dump styles only the keywords "id", "type", "x",
"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
whether scaled or unwrapped coordinates were enabled or disabled, and
it always assumes 8 columns for indexing regardless of whether image
flags are enabled or not. For dump style *cfg* only changes to the
"auxiliary" keywords (6th or later keyword) will become visible.
The *colname* keyword can be used multiple times. If multiple *colname*
settings refer to the same keyword, the last setting has precedence. A
setting of *default* clears all previous settings, reverting all values
to their default names.
----------
The *format* keyword can be used to change the default numeric format output
by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
@ -678,10 +680,28 @@ most effective when the typical magnitude of position data is between
----------
The *skip* keyword can be used with all dump styles. It allows a dump
snapshot to be skipped (not written to the dump file), if a condition
is met. The condition is computed by an :doc:`equal-style variable
<variable>`, which should be specified as v_name, where name is the
variable name. If the variable evaulation returns a non-zero value,
then the dump snapshot is skipped. If it returns zero, the dump
proceeds as usual. Note that :doc:`equal-style variable <variable>`
can contain Boolean operators which effectively evaluate as a true
(non-zero) or false (zero) result.
The *skip* keyword can be useful for debugging purposes, e.g. to dump
only on a particular timestep. Or to limit output to conditions of
interest, e.g. only when the force on some atom exceeds a threshold
value.
----------
The *sort* keyword determines whether lines of per-atom output in a
snapshot are sorted or not. A sort value of *off* means they will
typically be written in indeterminate order, either in serial or
parallel. This is the case even in serial if the :doc:`atom_modify sort <atom_modify>` option is turned on, which it is by default, to
parallel. This is the case even in serial if the :doc:`atom_modify
sort <atom_modify>` option is turned on, which it is by default, to
improve performance. A sort value of *id* means sort the output by
atom ID. A sort value of N or -N means sort the output by the value
in the Nth column of per-atom info in either ascending or descending
@ -727,8 +747,9 @@ are written to the dump file or included in the image. The possible
attributes that can be tested for are the same as those that can be
specified in the :doc:`dump custom <dump>` command, with the exception
of the *element* attribute, since it is not a numeric value. Note
that a different attributes can be used than those output by the :doc:`dump custom <dump>` command. E.g. you can output the coordinates and
stress of atoms whose energy is above some threshold.
that a different attributes can be used than those output by the
:doc:`dump custom <dump>` command. E.g. you can output the
coordinates and stress of atoms whose energy is above some threshold.
If an atom-style variable is used as the attribute, then it can
produce continuous numeric values or effective Boolean 0/1 values

1
doc/src/dump_netcdf.rst
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@ -1,4 +1,5 @@
.. index:: dump netcdf
.. index:: dump netcdf/mpiio
dump netcdf command
===================

8
doc/src/dumps.rst Normal file
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@ -0,0 +1,8 @@
Dump Styles
###############
.. toctree::
:maxdepth: 1
:glob:
dump*

5
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@ -171,6 +171,8 @@ accelerated styles exist.
* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
* :doc:`addforce <fix_addforce>` - add a force to each atom
* :doc:`addtorque <fix_addtorque>` - add a torque to a group of atoms
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>` - torsion/torsion terms in AMOEBA force field
* :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>` - 6-body terms in AMOEBA force field
* :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
* :doc:`atc <fix_atc>` - initiates a coupled MD/FE simulation
* :doc:`atom/swap <fix_atom_swap>` - Monte Carlo atom type swapping
@ -194,7 +196,7 @@ accelerated styles exist.
* :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping
* :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization
* :doc:`charge/regulation <fix_charge_regulation>` - Monte Carlo sampling of charge regulation
* :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field
* :doc:`cmap <fix_cmap>` - CMAP torsion/torsion terms in CHARMM force field
* :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library
* :doc:`controller <fix_controller>` - apply control loop feedback mechanism
* :doc:`damping/cundall <fix_damping_cundall>` - Cundall non-viscous damping for granular simulations
@ -305,6 +307,7 @@ accelerated styles exist.
* :doc:`orient/fcc <fix_orient>` - add grain boundary migration force for FCC
* :doc:`orient/eco <fix_orient_eco>` - add generalized grain boundary migration force
* :doc:`pafi <fix_pafi>` - constrained force averages on hyper-planes to compute free energies (PAFI)
* :doc:`pair <fix_pair>` - access per-atom info from pair styles
* :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
* :doc:`pimd <fix_pimd>` - Feynman path integral molecular dynamics
* :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane

166
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@ -0,0 +1,166 @@
.. index:: fix amoeba/bitorsion
fix amoeba/bitorsion command
============================
Syntax
""""""
.. parsed-literal::
fix ID group-ID ameoba/bitorsion filename
* ID, group-ID are documented in :doc:`fix <fix>` command
* amoeba/bitorsion = style name of this fix command
* filename = force-field file with AMOEBA bitorsion coefficients
Examples
""""""""
.. code-block:: LAMMPS
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
read_data proteinX.data fix bit bitorsions BiTorsions
fix_modify bit energy yes
Description
"""""""""""
This command enables 5-body torsion/torsion interactions to be added
to simulations which use the AMOEBA and HIPPO force fields. It
matches how the Tinker MD code computes its torsion/torsion
interactions for the AMOEBA and HIPPO force fields. See the
:doc:`Howto amoeba <Howto_amoeba>` doc page for more information about
the implementation of AMOEBA and HIPPO in LAMMPS.
Bitorsion interactions add additional potential energy contributions
to pairs of overlapping phi-psi dihedrals of amino-acids, which are
important to properly represent their conformational behavior.
The examples/amoeba directory has a sample input script and data file
for ubiquitin, which illustrates use of the fix amoeba/bitorsion
command.
As in the example above, this fix should be used before reading a data
file that contains a listing of bitorsion interactions. The
*filename* specified should contain the bitorsion parameters for the
AMOEBA or HIPPO force field.
The data file read by the :doc:`read_data <read_data>` command must
contain the topology of all the bitorsion interactions, similar to the
topology data for bonds, angles, dihedrals, etc. Specifically it
should have a line like this in its header section:
.. parsed-literal::
N bitorsions
where N is the number of bitorsion 5-body interactions. It should
also have a section in the body of the data file like this with N
lines:
.. parsed-literal::
BiTorsions
1 1 8 10 12 18 20
2 5 18 20 22 25 27
[...]
N 3 314 315 317 318 330
The first column is an index from 1 to N to enumerate the bitorsion
5-atom tuples; it is ignored by LAMMPS. The second column is the
*type* of the interaction; it is an index into the bitorsion force
field file. The remaining 5 columns are the atom IDs of the atoms in
the two 4-atom dihedrals that overlap to create the bitorsion 5-body
interaction. Note that the *bitorsions* and *BiTorsions* keywords for
the header and body sections match those specified in the
:doc:`read_data <read_data>` command following the data file name.
The data file should be generated by using the
tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS
data file from Tinker input files, including its PRM file which
contains the parameters necessary for computing bitorsion
interactions. The script must be invoked with the optional
"-bitorsion" flag to do this; see the example for the ubiquitin system
in the tools/tinker/README file. The same conversion script also
creates the file of bitorsion coefficient data which is read by this
command.
The potential energy associated with bitorsion interactions can be
output as described below. It can also be included in the total
potential energy of the system, as output by the :doc:`thermo_style
<thermo_style>` command, if the :doc:`fix_modify energy <fix_modify>`
command is used, as in the example above. See the note below about
how to include the bitorsion energy when performing an :doc:`energy
minimization <minimize>`.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the list of bitorsion interactions to :doc:`binary
restart files <restart>`. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy of the bitorsion interactions to
both the global potential energy and peratom potential energies of the
system as part of :doc:`thermodynamic output <thermo_style>` or output
by the :doc:`compute pe/atom <compute_pe_atom>` command. The default
setting for this fix is :doc:`fix_modify energy yes <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the bitorsion interactions to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential
energy discussed above. The scalar value calculated by this fix is
"extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
.. note::
For energy minimization, if you want the potential energy
associated with the bitorsion terms forces to be included in the
total potential energy of the system (the quantity being
minimized), you MUST not disable the :doc:`fix_modify <fix_modify>`
*energy* option for this fix.
Restrictions
""""""""""""
To function as expected this fix command must be issued *before* a
:doc:`read_data <read_data>` command but *after* a :doc:`read_restart
<read_restart>` command.
This fix can only be used if LAMMPS was built with the AMOEBA package.
See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix_modify <fix_modify>`, :doc:`read_data <read_data>`
Default
"""""""
none

178
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@ -0,0 +1,178 @@
.. index:: fix amoeba/pitorsion
fix amoeba/pitorsion command
============================
Syntax
""""""
.. parsed-literal::
fix ID group-ID ameoba/pitorsion
* ID, group-ID are documented in :doc:`fix <fix>` command
* amoeba/pitorsion = style name of this fix command
Examples
""""""""
.. code-block:: LAMMPS
fix pit all amoeba/pitorsion
read_data proteinX.data fix pit "pitorsion types" "PiTorsion Coeffs" &
fix pit pitorsions PiTorsions
fix_modify pit energy yes
Description
"""""""""""
This command enables 6-body pitorsion interactions to be added to
simulations which use the AMOEBA and HIPPO force fields. It matches
how the Tinker MD code computes its pitorsion interactions for the
AMOEBA and HIPPO force fields. See the :doc:`Howto amoeba
<Howto_amoeba>` doc page for more information about the implementation
of AMOEBA and HIPPO in LAMMPS.
Pitorsion interactions add additional potential energy contributions
to 6-tuples of atoms IJKLMN which have a bond between atoms K and L,
where both K and L are additionally bonded to exactly two other atoms.
Namely K is also bonded to I and J. And L is also bonded to M and N.
The examples/amoeba directory has a sample input script and data file
for ubiquitin, which illustrates use of the fix amoeba/pitorsion
command.
As in the example above, this fix should be used before reading a data
file that contains a listing of pitorsion interactions.
The data file read by the :doc:`read_data <read_data>` command must
contain the topology of all the pitorsion interactions, similar to the
topology data for bonds, angles, dihedrals, etc. Specifically it
should have two lines like these in its header section:
.. parsed-literal::
M pitorsion types
N pitorsions
where N is the number of pitorsion 5-body interactions and M is the
number of pitorsion types. It should also have two sections in the body
of the data file like these with M and N lines each:
.. parsed-literal::
PiTorsion Coeffs
1 6.85
2 10.2
[...]
M 6.85
.. parsed-literal::
PiTorsions
1 1 8 10 12 18 20
2 5 18 20 22 25 27
[...]
N 3 314 315 317 318 330
For PiTorsion Coeffs, the first column is an index from 1 to M to
enumerate the pitorsion types. The second column is the single
prefactor coefficient needed for each type.
For PiTorsions, the first column is an index from 1 to N to enumerate
the pitorsion 5-atom tuples; it is ignored by LAMMPS. The second
column is the "type" of the interaction; it is an index into the
PiTorsion Coeffs. The remaining 5 columns are the atom IDs of the
atoms in the two 4-atom dihedrals that overlap to create the pitorsion
5-body interaction.
Note that the *pitorsion types* and *pitorsions* and *PiTorsion
Coeffs* and *PiTorsions* keywords for the header and body sections of
the data file match those specified in the :doc:`read_data
<read_data>` command following the data file name.
The data file should be generated by using the
tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS
data file from Tinker input files, including its PRM file which
contains the parameters necessary for computing pitorsion
interactions.
The potential energy associated with pitorsion interactions can be
output as described below. It can also be included in the total
potential energy of the system, as output by the :doc:`thermo_style
<thermo_style>` command, if the :doc:`fix_modify energy <fix_modify>`
command is used, as in the example above. See the note below about
how to include the pitorsion energy when performing an :doc:`energy
minimization <minimize>`.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the list of pitorsion interactions to :doc:`binary
restart files <restart>`. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy of the pitorsion interactions to
both the global potential energy and peratom potential energies of the
system as part of :doc:`thermodynamic output <thermo_style>` or output
by the :doc:`compute pe/atom <compute_pe_atom>` command. The default
setting for this fix is :doc:`fix_modify energy yes <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the pitorsion interactions to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential
energy discussed above. The scalar value calculated by this fix is
"extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
.. note::
For energy minimization, if you want the potential energy
associated with the pitorsion terms forces to be included in the
total potential energy of the system (the quantity being
minimized), you MUST not disable the :doc:`fix_modify <fix_modify>`
*energy* option for this fix.
Restrictions
""""""""""""
To function as expected this fix command must be issued *before* a
:doc:`read_data <read_data>` command but *after* a :doc:`read_restart
<read_restart>` command.
This fix can only be used if LAMMPS was built with the AMOEBA package.
See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix_modify <fix_modify>`, :doc:`read_data <read_data>`
Default
"""""""
none

66
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@ -26,13 +26,13 @@ Examples
Description
"""""""""""
This command enables CMAP cross-terms to be added to simulations which
use the CHARMM force field. These are relevant for any CHARMM model
of a peptide or protein sequences that is 3 or more amino-acid
residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks) <Brooks2>`
for details, including the analytic energy expressions for CMAP
interactions. The CMAP cross-terms add additional potential energy
contributions to pairs of overlapping phi-psi dihedrals of
This command enables CMAP 5-body interactions to be added to
simulations which use the CHARMM force field. These are relevant for
any CHARMM model of a peptide or protein sequences that is 3 or more
amino-acid residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks)
<Brooks2>` for details, including the analytic energy expressions for
CMAP interactions. The CMAP 5-body terms add additional potential
energy contributions to pairs of overlapping phi-psi dihedrals of
amino-acids, which are important to properly represent their
conformational behavior.
@ -47,15 +47,15 @@ lammps/potentials directory: charmm22.cmap and charmm36.cmap.
The data file read by the "read_data" must contain the topology of all
the CMAP interactions, similar to the topology data for bonds, angles,
dihedrals, etc. Specially it should have a line like this
in its header section:
dihedrals, etc. Specially it should have a line like this in its
header section:
.. parsed-literal::
N crossterms
where N is the number of CMAP cross-terms. It should also have a section
in the body of the data file like this with N lines:
where N is the number of CMAP 5-body interactions. It should also
have a section in the body of the data file like this with N lines:
.. parsed-literal::
@ -66,28 +66,29 @@ in the body of the data file like this with N lines:
[...]
N 3 314 315 317 318 330
The first column is an index from 1 to N to enumerate the CMAP terms;
it is ignored by LAMMPS. The second column is the "type" of the
interaction; it is an index into the CMAP force field file. The
The first column is an index from 1 to N to enumerate the CMAP 5-atom
tuples; it is ignored by LAMMPS. The second column is the "type" of
the interaction; it is an index into the CMAP force field file. The
remaining 5 columns are the atom IDs of the atoms in the two 4-atom
dihedrals that overlap to create the CMAP 5-body interaction. Note
that the "crossterm" and "CMAP" keywords for the header and body
sections match those specified in the read_data command following the
data file name; see the :doc:`read_data <read_data>` page for
more details.
dihedrals that overlap to create the CMAP interaction. Note that the
"crossterm" and "CMAP" keywords for the header and body sections match
those specified in the read_data command following the data file name;
see the :doc:`read_data <read_data>` page for more details.
A data file containing CMAP cross-terms can be generated from a PDB
file using the charmm2lammps.pl script in the tools/ch2lmp directory
of the LAMMPS distribution. The script must be invoked with the
optional "-cmap" flag to do this; see the tools/ch2lmp/README file for
more information.
A data file containing CMAP 5-body interactions can be generated from
a PDB file using the charmm2lammps.pl script in the tools/ch2lmp
directory of the LAMMPS distribution. The script must be invoked with
the optional "-cmap" flag to do this; see the tools/ch2lmp/README file
for more information. The same conversion script also creates the
file of CMAP coefficient data which is read by this command.
The potential energy associated with CMAP interactions can be output
as described below. It can also be included in the total potential
energy of the system, as output by the
:doc:`thermo_style <thermo_style>` command, if the :doc:`fix_modify energy <fix_modify>` command is used, as in the example above. See
the note below about how to include the CMAP energy when performing an
:doc:`energy minimization <minimize>`.
energy of the system, as output by the :doc:`thermo_style
<thermo_style>` command, if the :doc:`fix_modify energy <fix_modify>`
command is used, as in the example above. See the note below about
how to include the CMAP energy when performing an :doc:`energy
minimization <minimize>`.
----------
@ -134,10 +135,11 @@ outermost level.
.. note::
If you want the potential energy associated with the CMAP terms
forces to be included in the total potential energy of the system
(the quantity being minimized), you MUST not disable the
:doc:`fix_modify <fix_modify>` *energy* option for this fix.
For energy minimization, if you want the potential energy
associated with the CMAP terms forces to be included in the total
potential energy of the system (the quantity being minimized), you
MUST not disable the :doc:`fix_modify <fix_modify>` *energy* option
for this fix.
Restrictions
""""""""""""

104
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@ -0,0 +1,104 @@
.. index:: fix pair
fix pair command
=======================
Syntax
""""""
.. parsed-literal::
fix ID group-ID pair N pairstyle name flag ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* pair = style name of this fix command
* N = invoke this fix once every N timesteps
* pairstyle = name of pair style to extract info from (e.g. eam)
* one or more name/flag pairs can be listed
* name = name of quantity the pair style allows extraction of
* flag = 1 if pair style needs to be triggered to produce data for name, 0 if not
Examples
""""""""
.. code-block:: LAMMPS
fix request all pair 100 eam rho 0
fix request all pair 100 amoeba uind 0 uinp 0
Description
"""""""""""
Extract per-atom quantities from a pair style and store them in this
fix so they can be accessed by other LAMMPS commands, e.g. by a
:doc:`dump <dump>` command or by another :doc:`fix <fix>`,
:doc:`compute <compute>`, or :doc:`variable <variable>` command.
These are example use cases:
* extract per-atom density from :doc:`pair_style eam <pair_eam>` to a dump file
* extract induced dipoles from :doc:`pair_style amoeba <pair_amoeba>` to a dump file
* extract accuracy metrics from a machine-learned potential to trigger output when
a condition is met (see the :doc:`dump_modify skip <dump_modify>` command)
The *N* argument determines how often the fix is invoked.
The *pairstyle* argument is the name of the pair style. It can be a
sub-style used in a :doc:`pair_style hybrid <pair_hybrid>` command.
One or more *name/flag* pairs of arguments follow. Each *name* is a
per-atom quantity which the pair style must recognize as an extraction
request. See the doc pages for individual :doc:`pair_styles
<pair_style>` to see what fix pair requests (if any) they support.
The *flag* setting determines whether this fix will also trigger the
pair style to compute the named quantity so it can be extracted. If
the quantity is always computed by the pair style, no trigger is
needed; specify *flag* = 0. If the quantity is not always computed
(e.g. it is expensive to calculate), then specify *flag* = 1. This
will trigger the quantity to be calculated only on timesteps it is
needed. Again, see the doc pages for individual :doc:`pair_styles
<pair_style>` to determine which fix pair requests (if any) need to be
triggered with a *flag* = 1 setting.
The per-atom data extracted from the pair style is stored by this fix
as either a per-atom vector or array. If there is only one *name*
argument specified and the pair style computes a single value for each
atom, then this fix stores it as a per-atom vector. Otherwise a
per-atom array is created, with its data in the order of the *name*
arguments.
For example, :doc:`pair_style amoeba <pair_amoeba>` allows extraction
of two named quantities: "uind" and "uinp", both of which are
3-vectors for each atom, i.e. dipole moments. If this fix specifies
"uind" and "uinp" (in that order), then a 6-column per-atom array will
be created. Columns 1-3 will store the "uind" values; columns 4-6
will store the "uinp" values.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
As explained above, this fix produces a per-atom vector or array which
can be accessed by various :doc:`output commands <Howto_output>`. If
an array is produced, the number of columns is the sum of the number
of per-atom quantities produced by each *name* argument requested from
the pair style.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`compute pair <compute_pair>`
Default
"""""""
none

77
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@ -0,0 +1,77 @@
.. index:: improper_style amoeba
improper_style harmonic command
===============================
Syntax
""""""
.. code-block:: LAMMPS
improper_style amoeba
Examples
""""""""
.. code-block:: LAMMPS
improper_style amoeba
improper_coeff 1 49.6
Description
"""""""""""
The *amoeba* improper style uses the potential
.. math::
E = K (\chi)^2
where :math:`\chi` is the improper angle and :math:`K` is a prefactor.
Note that the usual 1/2 factor is included in :math:`K`.
This formula seems like a simplified version of the formula for the
:doc:`improper_style harmonic <improper_harmonic>` command with
:math:`\chi_0` = 0.0. However the computation of the angle
:math:`\chi` is done differently to match how the Tinker MD code
computes its out-of-plane improper for the AMOEBA and HIPPO force
fields. See the :doc:`Howto amoeba <Howto_amoeba>` doc page for more
information about the implementation of AMOEBA and HIPPO in LAMMPS.
If the 4 atoms in an improper quadruplet (listed in the data file read
by the :doc:`read_data <read_data>` command are ordered I,J,K,L then
atoms I,K,L are considered to lie in a plane and atom J is
out-of-place. The angle :math:`\chi_0` is computed as the Allinger
angle which is defined as the angle between the plane of I,K,L, and
the vector from atom I to atom J.
The following coefficient must be defined for each improper type via
the :doc:`improper_coeff <improper_coeff>` command as in the example
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`K` (energy)
Note that the angle :math:`\chi` is computed in radians; hence
:math:`K` is effectively energy per radian\^2.
----------
Restrictions
""""""""""""
This improper style can only be used if LAMMPS was built with the
AMOEBA package. See the :doc:`Build package <Build_package>` doc page
for more info.
Related commands
""""""""""""""""
:doc:`improper_coeff <improper_coeff>`, `improper_harmonic
:doc:<improper_harmonic>`
Default
"""""""
none

1
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@ -77,6 +77,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`zero <improper_zero>` - topology but no interactions
* :doc:`hybrid <improper_hybrid>` - define multiple styles of improper interactions
* :doc:`amoeba <improper_amoeba>` - AMOEBA out-of-plane improper
* :doc:`class2 <improper_class2>` - COMPASS (class 2) improper
* :doc:`cossq <improper_cossq>` - improper with a cosine squared term
* :doc:`cvff <improper_cvff>` - CVFF improper

17
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@ -29,15 +29,16 @@ Examples
Description
"""""""""""
The *kim command* includes a set of sub-commands that allow LAMMPS users to use
interatomic models (IM) (potentials and force fields) and their predictions for
various physical properties archived in the
`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
repository.
The *kim command* includes a set of sub-commands that allow LAMMPS
users to use interatomic models (IM) (potentials and force fields) and
their predictions for various physical properties archived in the
`Open Knowledgebase of Interatomic Models (OpenKIM)
<https://openkim.org>`_ repository.
Using OpenKIM provides LAMMPS users with immediate access to a large number of
verified IMs and their predictions. OpenKIM IMs have multiple benefits including
`reliability, reproducibility and convenience <https://openkim.org/doc/overview/kim-features/>`_.
Using OpenKIM provides LAMMPS users with immediate access to a large
number of verified IMs and their predictions. OpenKIM IMs have
multiple benefits including `reliability, reproducibility and
convenience <https://openkim.org/doc/overview/kim-features/>`_.
.. _IM_types:

50
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@ -49,29 +49,27 @@ sometimes be faster. Either style should give the same answers.
The *multi* style is a modified binning algorithm that is useful for
systems with a wide range of cutoff distances, e.g. due to different
size particles. For granular pair styles, cutoffs are set to the
sum of the maximum atomic radii for each atom type.
For the *bin* style, the bin size is set to 1/2 of
the largest cutoff distance between any pair of atom types and a
single set of bins is defined to search over for all atom types. This
can be inefficient if one pair of types has a very long cutoff, but
other type pairs have a much shorter cutoff. The *multi* style uses
different sized bins for collections of different sized particles, where
"size" may mean the physical size of the particle or its cutoff
distance for interacting with other particles. Different
size particles. For granular pair styles, cutoffs are set to the sum of
the maximum atomic radii for each atom type. For the *bin* style, the
bin size is set to 1/2 of the largest cutoff distance between any pair
of atom types and a single set of bins is defined to search over for all
atom types. This can be inefficient if one pair of types has a very
long cutoff, but other type pairs have a much shorter cutoff. The
*multi* style uses different sized bins for collections of different
sized particles, where "size" may mean the physical size of the particle
or its cutoff distance for interacting with other particles. Different
sets of bins are then used to construct the neighbor lists as as further
described by Shire, Hanley, and Stratford :ref:`(Shire) <bytype-Shire>`.
This imposes some extra setup overhead, but the searches themselves
may be much faster. By default, each atom type defines a separate
collection of particles. For systems where two or more atom types
have the same size (either physical size or cutoff distance), the
definition of collections can be customized, which can result in less
overhead and faster performance. See the :doc:`neigh_modify <neigh_modify>`
command for how to define custom collections. Whether the collection
definition is customized or not, also see the
:doc:`comm_modify mode multi <comm_modify>` command for communication
options that further improve performance in a manner consistent with
neighbor style multi.
This imposes some extra setup overhead, but the searches themselves may
be much faster. By default, each atom type defines a separate collection
of particles. For systems where two or more atom types have the same
size (either physical size or cutoff distance), the definition of
collections can be customized, which can result in less overhead and
faster performance. See the :doc:`neigh_modify <neigh_modify>` command
for how to define custom collections. Whether the collection definition
is customized or not, also see the :doc:`comm_modify mode multi
<comm_modify>` command for communication options that further improve
performance in a manner consistent with neighbor style multi.
An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest
cutoff distance and multiple sets of bins are defined to search over for
@ -80,6 +78,16 @@ algorithm in LAMMPS but was found to be significantly slower than the new
approach. For now we are keeping the old option in case there are use cases
where multi/old outperforms the new multi style.
.. note::
If there are multiple sub-styles in a :doc:`hybrid/overlay pair style
<pair_hybrid>` that cover the same atom types, but have significantly
different cutoffs, the *multi* style does not apply. Instead, the
:doc:`pair_modify neigh/trim <pair_modify>` setting applies (which is
*yes* by default). Please check the neighbor list summary printed at
the beginning of a calculation to verify that the desired set of
neighbor list builds is performed.
The :doc:`neigh_modify <neigh_modify>` command has additional options
that control how often neighbor lists are built and which pairs are

265
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@ -0,0 +1,265 @@
.. index:: pair_style amoeba
.. index:: pair_style hippo
pair_style amoeba command
=========================
pair_style hippo command
========================
Syntax
""""""
.. code-block:: LAMMPS
pair_style style
* style = *amoeba* or *hippo*
Examples
""""""""
.. code-block:: LAMMPS
pair_style amoeba
pair_coeff * * protein.prm.amoeba protein.key.amoeba
.. code-block:: LAMMPS
pair_style hippo
pair_coeff * * water.prm.hippo water.key.hippo
Additional info
"""""""""""""""
* :doc:`Howto amoeba <Howto_amoeba>`
* examples/amoeba
* tools/amoeba
* potentials/\*.amoeba
* potentials/\*.hippo
Description
"""""""""""
The *amoeba* style computes the AMOEBA polarizable field formulated
by Jay Ponder's group at the U Washington at St Louis :ref:`(Ren)
<amoeba-Ren>`, :ref:`(Shi) <amoeba-Shi>`. The *hippo* style computes
the HIPPO polarizable force field, an extension to AMOEBA, formulated
by Josh Rackers and collaborators in the Ponder group :ref:`(Rackers)
<amoeba-Rackers>`.
These force fields can be used when polarization effects are desired
in simulations of water, organic molecules, and biomolecules including
proteins, provided that parameterizations (Tinker PRM force field
files) are available for the systems you are interested in. Files in
the LAMMPS potentials directory with a "amoeba" or "hippo" suffix can
be used. The Tinker distribution and website have additional force
field files as well.
As discussed on the :doc:`Howto amoeba <Howto_amoeba>` doc page, the
intermolecular (non-bonded) portion of the AMOEBA force field contains
these terms:
.. math::
U_{amoeba} = U_{multipole} + U_{polar} + U_{hal}
while the HIPPO force field contains these terms:
.. math::
U_{hippo} = U_{multipole} + U_{polar} + U_{qxfer} + U_{repulsion} + U_{dispersion}
Conceptually, these terms compute the following interactions:
* :math:`U_{hal}` = buffered 14-7 van der Waals with offsets applied to hydrogen atoms
* :math:`U_{repulsion}` = Pauli repulsion due to rearrangement of electron density
* :math:`U_{dispersion}` = dispersion between correlated, instantaneous induced dipole moments
* :math:`U_{multipole}` = electrostatics between permanent point charges, dipoles, and quadrupoles
* :math:`U_{polar}` = electronic polarization between induced point dipoles
* :math:`U_{qxfer}` = charge transfer effects
Note that the AMOEBA versus HIPPO force fields typically compute the
same term differently using their own formulas. The references on
this doc page give full details for both force fields.
The formulas for the AMOEBA energy terms are:
.. math::
U_{hal} = \epsilon_{ij} \left( \frac{1.07}{\rho_{ij} + 0.07} \right)^7 \left( \frac{1.12}{\rho_{ij}^7 + 0.12} - 2 \right)
U_{multipole} = \vec{M_i}\bold{T_{ij}}\vec{M_j}
\vec{M} = \left( q, \vec{\mu_{perm}}, \bold{\Theta} \right)
U_{polar} = \frac{1}{2}\vec{\mu_i}^{ind} \vec{E_i}^{perm}
The formulas for the HIPPO energy terms are:
.. math::
U_{multipole} = Z_i \frac{1}{r_{ij}} Z_j + Z_i T_{ij}^{damp} \vec{M_j} + Z_j T_{ji}^{damp} \vec{M_i} + \vec{M_i} T_{ij}^{damp} \vec{M_j}
\vec{M} = \left( Q, \vec{\mu_{perm}}, \bold{\Theta} \right)
U_{polar} = \frac{1}{2}\vec{\mu_i}^{ind} \vec{E_i}^{perm}
U_{qxfer} = \epsilon_i e^{-\eta_j r_{ij}} + \epsilon_j e^{-\eta_i r_{ij}}
U_{repulsion} = \frac{K_i K_j}{r_{ij}} S^2
S^2 = \left( \int{\phi_i \phi_j} dv \right)^2 = \vec{M_i}\bold{T_{ij}^{repulsion}}\vec{M_j}
U_{dispersion} = -\frac{C_6^iC_6^j}{r_{ij}^6} \left( f_{damp}^{dispersion} \right)_{ij}^2
.. note::
The AMOEBA and HIPPO force fields compute long-range charge, dipole,
and quadrupole interactions as well as long-range dispersion
effects. However, unlike other models with long-range interactions
in LAMMPS, this does not require use of a KSpace style via the
:doc:`kspace_style <kspace_style>` command. That is because for
AMOEBA and HIPPO the long-range computations are intertwined with
the pairwise computations. So these pair style include both short-
and long-range computations. This means the energy and virial
computed by the pair style as well as the "Pair" timing reported by
LAMMPS will include the long-range calculations.
The implementation of the AMOEBA and HIPPO force fields in LAMMPS was
done using F90 code provided by the Ponder group from their `Tinker MD
code <https://dasher.wustl.edu/tinker/>`_.
The current implementation (July 2022) of AMOEBA in LAMMPS matches the
version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren)
<amoeba-Ren>`, and :ref:`(Shi) <amoeba-Shi>`. Likewise the current
implementation of HIPPO in LAMMPS matches the version discussed in
:ref:`(Rackers) <amoeba-Rackers>`.
----------
Only a single pair_coeff command is used with either the *amoeba* and
*hippo* styles which specifies two Tinker files, a PRM and KEY file.
.. code-block:: LAMMPS
pair_coeff * * ../potentials/protein.prm.amoeba ../potentials/protein.key.amoeba
pair_coeff * * ../potentials/water.prm.hippo ../potentials/water.key.hippo
Examples of the PRM files are in the potentials directory with an
\*.amoeba or \*.hippo suffix. The examples/amoeba directory has
examples of both PRM and KEY files.
A Tinker PRM file is composed of sections, each of which has multiple
lines. A Tinker KEY file is composed of lines, each of which has a
keyword followed by zero or more parameters.
The list of PRM sections and KEY keywords which LAMMPS recognizes are
listed on the :doc:`Howto amoeba <Howto_amoeba>` doc page. If not
recognized, the section or keyword is skipped.
Note that if the KEY file is specified as NULL, then no file is
required; default values for various AMOEBA/HIPPO settings are used.
The :doc:`Howto amoeba <Howto_amoeba>` doc page also gives the default
settings.
----------
The *amoeba* and *hippo* pair styles support extraction of two
per-atom quantities by the :doc:`fix pair <fix_pair>` command. This
allows the quantities to be output to files by the :doc:`dump <dump>`
or otherwise processed by other LAMMPS commamds.
The names of the two quantites are "uind" and "uinp" for the induced
dipole moments for each atom. Neither quantity needs to be triggered
by the :doc:`fix pair <fix_pair>` command in order for these pair
styles to calculate it.
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
These pair styles do not support the :doc:`pair_modify <pair_modify>`
mix, shift, table, and tail options.
These pair styles do not write their information to :doc:`binary
restart files <restart>`, since it is stored in potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.
These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*\ , *middle*\ , *outer* keywords.
----------
Restrictions
""""""""""""
These pair styles are part of the AMOEBA package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build
package <Build_package>` doc page for more info.
The AMOEBA and HIPPO potential (PRM) and KEY files provided with
LAMMPS in the potentials and examples/amoeba directories are Tinker
files parameterized for Tinker units. Their numeric parameters are
converted by LAMMPS to its real units :doc:`units <units>`. Thus you
can only use these pair styles with real units.
These potentials do not yet calculate per-atom energy or virial
contributions.
As explained on the :doc:`AMOEBA and HIPPO howto <Howto_amoeba>` page,
use of these pair styles to run a simulation with the AMOEBA or HIPPO
force fields requires several things.
The first is a data file generated by the tools/tinker/tinker2lmp.py
conversion script which uses Tinker file force field file input to
create a data file compatible with LAMMPS.
The second is use of these commands:
* :doc:`atom_style amoeba <atom_style>`
* :doc:`fix property/atom <fix_property_atom>`
* :doc:`special_bonds one/five <special_bonds>`
And third, depending on the model being simulated, these
commands for intramolecular interactions may also be required:
* :doc:`bond_style class2 <bond_class2>`
* :doc:`angle_style amoeba <angle_amoeba>`
* :doc:`dihedral_style fourier <dihedral_fourier>`
* :doc:`improper_style amoeba <improper_amoeba>`
* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
----------
Related commands
""""""""""""""""
:doc:`atom_style amoeba <atom_style>`,
:doc:`bond_style class2 <bond_class2>`,
:doc:`angle_style amoeba <angle_amoeba>`,
:doc:`dihedral_style fourier <dihedral_fourier>`,
:doc:`improper_style amoeba <improper_amoeba>`,
:doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`,
:doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`,
:doc:`special_bonds one/five <special_bonds>`,
:doc:`fix property/atom <fix_property_atom>`
Default
"""""""
none
----------
.. _amoeba-Ponder:
**(Ponder)** Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
.. _amoeba-Rackers:
**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021).
.. _amoeba-Ren:
**(Ren)** Ren and Ponder, J Phys Chem B, 107, 5933 (2003).
.. _amoeba-Shi:
**(Shi)** Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.

26
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@ -444,6 +444,19 @@ identical to the FS EAM files (see above).
----------
The *eam*, *eam/alloy*, *eam/fs*, and *eam/he* pair styles support
extraction of two per-atom quantities by the :doc:`fix pair
<fix_pair>` command. This allows the quantities to be output to files
by the :doc:`dump <dump>` or otherwise processed by other LAMMPS
commamds.
The names of the two quantites are "rho" and "fp" for the density and
derivative of the embedding energy for each atom. Neither quantity
needs to be triggered by the :doc:`fix pair <fix_pair>` command in
order for these pair styles to calculate it.
----------
.. include:: accel_styles.rst
----------
@ -459,21 +472,26 @@ a pair_coeff command with I != J arguments for the eam styles.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
The eam pair styles do not write their information to :doc:`binary restart files <restart>`, since it is stored in tabulated potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.
The eam pair styles do not write their information to :doc:`binary
restart files <restart>`, since it is stored in tabulated potential
files. Thus, you need to re-specify the pair_style and pair_coeff
commands in an input script that reads a restart file.
The eam pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*, *middle*, *outer* keywords.
----------
Restrictions
""""""""""""
All of these styles are part of the MANYBODY package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
enabled if LAMMPS was built with that package. See the :doc:`Build
package <Build_package>` page for more info.
Related commands
""""""""""""""""

32
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View File

@ -13,7 +13,7 @@ Syntax
* one or more keyword/value pairs may be listed
* keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner*
or *tabinner/disp* or *tail* or *compute* or *nofdotr* or *special* or
*compute/tally*
*compute/tally* or *neigh/trim*
.. parsed-literal::
@ -37,6 +37,7 @@ Syntax
which = *lj/coul* or *lj* or *coul*
w1,w2,w3 = 1-2, 1-3, 1-4 weights from 0.0 to 1.0 inclusive
*compute/tally* value = *yes* or *no*
*neigh/trim* value = *yes* or *no*
Examples
""""""""
@ -283,6 +284,31 @@ the *pair* keyword. Use *no* to disable, or *yes* to enable.
The "pair_modify pair compute/tally" command must be issued
**before** the corresponding compute style is defined.
The *neigh/trim* keyword controls whether an explicit cutoff is set for
each neighbor list request issued by individual pair sub-styles when
using :doc:`pair hybrid/overlay <pair_hybrid>`. When this keyword is
set to *no*, then the cutoff of each pair sub-style neighbor list will
be set equal to the largest cutoff, even if a shorter cutoff is
specified for a particular sub-style. If possible the neighbor list
will be copied directly from another list. When this keyword is set to
*yes* then the cutoff of the neighbor list will be explicitly set to the
value requested by the pair sub-style, and if possible the list will be
created by trimming neighbors from another list with a longer cutoff,
otherwise a new neighbor list will be created with the specified cutoff.
The *yes* option can be faster when there are multiple pair styles with
different cutoffs since the number of pair-wise distance checks between
neighbors is reduced (but the time required to build the neighbor lists
is increased). The *no* option could be faster when two or more neighbor
lists have similar (but not exactly the same) cutoffs.
.. note::
The "pair_modify neigh/trim" command *only* applies when there are
multiple pair sub-styles for the same atoms with different cutoffs,
i.e. when using pair style hybrid/overlay. If you have different
cutoffs for different pairs for atoms type, the :doc:`neighbor style
multi <neighbor>` should be used to create optimized neighbor lists.
----------
Restrictions
@ -298,13 +324,13 @@ Related commands
:doc:`pair_style <pair_style>`, :doc:`pair_style hybrid <pair_hybrid>`,
:doc:`pair_coeff <pair_coeff>`, :doc:`thermo_style <thermo_style>`,
:doc:`compute \*/tally <compute_tally>`
:doc:`compute \*/tally <compute_tally>`, :doc:`neighbor multi <neighbor>`
Default
"""""""
The option defaults are mix = geometric, shift = no, table = 12,
tabinner = sqrt(2.0), tail = no, and compute = yes.
tabinner = sqrt(2.0), tail = no, compute = yes, and neigh/trim yes.
Note that some pair styles perform mixing, but only a certain style of
mixing. See the doc pages for individual pair styles for details.

100
doc/src/pair_sdk.rst → doc/src/pair_spica.rst
View File

@ -1,27 +1,27 @@
.. index:: pair_style lj/sdk
.. index:: pair_style lj/sdk/gpu
.. index:: pair_style lj/sdk/kk
.. index:: pair_style lj/sdk/omp
.. index:: pair_style lj/sdk/coul/long
.. index:: pair_style lj/sdk/coul/long/gpu
.. index:: pair_style lj/sdk/coul/long/omp
.. index:: pair_style lj/sdk/coul/msm
.. index:: pair_style lj/sdk/coul/msm/omp
.. index:: pair_style lj/spica
.. index:: pair_style lj/spica/gpu
.. index:: pair_style lj/spica/kk
.. index:: pair_style lj/spica/omp
.. index:: pair_style lj/spica/coul/long
.. index:: pair_style lj/spica/coul/long/gpu
.. index:: pair_style lj/spica/coul/long/omp
.. index:: pair_style lj/spica/coul/msm
.. index:: pair_style lj/spica/coul/msm/omp
pair_style lj/sdk command
=========================
pair_style lj/spica command
===========================
Accelerator Variants: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp*
Accelerator Variants: *lj/spica/gpu*, *lj/spica/kk*, *lj/spica/omp*
pair_style lj/sdk/coul/long command
===================================
pair_style lj/spica/coul/long command
=====================================
Accelerator Variants: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp*
Accelerator Variants: *lj/spica/coul/long/gpu*, *lj/spica/coul/long/omp*
pair_style lj/sdk/coul/msm command
==================================
pair_style lj/spica/coul/msm command
====================================
Accelerator Variants: *lj/sdk/coul/msm/omp*
Accelerator Variants: *lj/spica/coul/msm/omp*
Syntax
""""""
@ -30,14 +30,14 @@ Syntax
pair_style style args
* style = *lj/sdk* or *lj/sdk/coul/long*
* style = *lj/spica* or *lj/spica/coul/long*
* args = list of arguments for a particular style
.. parsed-literal::
*lj/sdk* args = cutoff
*lj/spica* args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
*lj/sdk/coul/long* args = cutoff (cutoff2)
*lj/spica/coul/long* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -46,21 +46,21 @@ Examples
.. code-block:: LAMMPS
pair_style lj/sdk 2.5
pair_style lj/spica 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8
pair_style lj/sdk/coul/long 10.0
pair_style lj/sdk/coul/long 10.0 12.0
pair_style lj/spica/coul/long 10.0
pair_style lj/spica/coul/long 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
pair_style lj/sdk/coul/msm 10.0
pair_style lj/sdk/coul/msm 10.0 12.0
pair_style lj/spica/coul/msm 10.0
pair_style lj/spica/coul/msm 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
Description
"""""""""""
The *lj/sdk* styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
The *lj/spica* styles compute a 9/6, 12/4, 12/5, or 12/6 Lennard-Jones potential,
given by
.. math::
@ -71,14 +71,20 @@ given by
E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^4 \right]
\qquad r < r_c \\
E = & \frac{12}{7}\left(\frac{12}{5}\right)^{\left(\frac{5}{7}\right)} \epsilon
\left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^5 \right]
\qquad r < r_c \\
E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
as required for the SDK Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) <Shinoda3>` and :ref:`(DeVane) <DeVane>`. Rc is the cutoff.
as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) <Shinoda3>`, :ref:`(DeVane) <DeVane>`, :ref:`(Seo) <Seo>`, and :ref:`(Miyazaki) <Miyazaki>`.
Rc is the cutoff.
Summary information on these force fields can be found at https://www.spica-ff.org
Style *lj/sdk/coul/long* computes the adds Coulombic interactions
Style *lj/spica/coul/long* computes the adds Coulombic interactions
with an additional damping factor applied so it can be used in
conjunction with the :doc:`kspace_style <kspace_style>` command and
its *ewald* or *pppm* or *pppm/cg* option. The Coulombic cutoff
@ -92,7 +98,7 @@ above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands, or by mixing as described below:
* cg_type (lj9_6, lj12_4, or lj12_6)
* cg_type (lj9_6, lj12_4, lj12_5, or lj12_6)
* epsilon (energy units)
* sigma (distance units)
* cutoff1 (distance units)
@ -108,11 +114,15 @@ and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
For *lj/sdk/coul/long* and *lj/sdk/coul/msm* only the LJ cutoff can be
For *lj/spica/coul/long* and *lj/spica/coul/msm* only the LJ cutoff can be
specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
The original implementation of the above styles are
style *lj/sdk*, *lj/sdk/coul/long*, and *lj/sdk/coul/msm*,
and available for backward compatibility.
----------
.. include:: accel_styles.rst
@ -123,24 +133,24 @@ Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/sdk pair styles *cannot* be mixed,
and cutoff distance for all of the lj/spica pair styles *cannot* be mixed,
since different pairs may have different exponents. So all parameters
for all pairs have to be specified explicitly through the "pair_coeff"
command. Defining then in a data file is also not supported, due to
limitations of that file format.
All of the lj/sdk pair styles support the
All of the lj/spica pair styles support the
:doc:`pair_modify <pair_modify>` shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The *lj/sdk/coul/long* pair styles support the
The *lj/spica/coul/long* pair styles support the
:doc:`pair_modify <pair_modify>` table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
All of the lj/sdk pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
All of the lj/spica pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The lj/sdk and lj/cut/coul/long pair styles do not support
The lj/spica and lj/cut/coul/long pair styles do not support
the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa <run_style>` command.
----------
@ -148,8 +158,8 @@ the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style re
Restrictions
""""""""""""
All of the lj/sdk pair styles are part of the CG-SDK package. The
*lj/sdk/coul/long* style also requires the KSPACE package to be built
All of the lj/spica pair styles are part of the CG-SPICA package. The
*lj/spica/coul/long* style also requires the KSPACE package to be built
(which is enabled by default). They are only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
@ -157,7 +167,7 @@ doc page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style sdk <angle_sdk>`
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style spica <angle_spica>`
Default
"""""""
@ -168,8 +178,16 @@ none
.. _Shinoda3:
**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27-36 (2007).
.. _DeVane:
**(DeVane)** Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
.. _Seo:
**(Seo)** Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019).
.. _Miyazaki:
**(Miyazaki)** Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020).

30
doc/src/pair_srp.rst
View File

@ -1,18 +1,23 @@
.. index:: pair_style srp
.. index:: pair_style srp/react
pair_style srp command
======================
pair_style srp/react command
============================
Syntax
""""""
.. code-block:: LAMMPS
pair_style srp cutoff btype dist keyword value ...
pair_style srp/react cutoff btype dist react-id keyword value ...
* cutoff = global cutoff for SRP interactions (distance units)
* btype = bond type to apply SRP interactions to (can be wildcard, see below)
* distance = *min* or *mid*
* react-id = id of either fix bond/break or fix bond/create
* zero or more keyword/value pairs may be appended
* keyword = *exclude*
@ -36,13 +41,19 @@ Examples
pair_coeff 1 2 none
pair_coeff 2 2 srp 40.0
fix create all bond/create 100 1 2 1.0 1 prob 0.2 19852
pair_style hybrid dpd 1.0 1.0 12345 srp/react 0.8 * min create exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp/react 40.0
pair_style hybrid srp 0.8 2 mid
pair_coeff 1 1 none
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
Description
"""""""""""
Style *srp* computes a soft segmental repulsive potential (SRP) that
acts between pairs of bonds. This potential is useful for preventing
@ -121,6 +132,18 @@ at the cutoff distance :math:`r_c`.
----------
Pair style *srp/react* interfaces the pair style *srp* with the
bond breaking and formation mechanisms provided by fix *bond/break*
and fix *bond/create*, respectively. When using this pair style, whenever a
bond breaking (or formation) reaction occurs, the corresponding fictitious
particle is deleted (or inserted) during the same simulation time step as
the reaction. This is useful in the simulation of reactive systems involving
large polymeric molecules :ref:`(Palkar) <Palkar>` where the segmental repulsive
potential is necessary to minimize topological violations, and also needs to be
turned on and off according to the progress of the reaction.
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -178,3 +201,8 @@ The default keyword value is exclude = yes.
**(Sirk)** Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
Chem Phys, 136 (13) 134903, 2012.
.. _Palkar:
**(Palkar)** Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022

9
doc/src/pair_style.rst
View File

@ -116,6 +116,7 @@ accelerated styles exist.
* :doc:`agni <pair_agni>` - AGNI machine-learning potential
* :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
* :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
* :doc:`amoeba <pair_amoeba>` -
* :doc:`atm <pair_atm>` - Axilrod-Teller-Muto potential
* :doc:`awpmd/cut <pair_awpmd>` - Antisymmetrized Wave Packet MD potential for atoms and electrons
* :doc:`beck <pair_beck>` - Beck potential
@ -202,6 +203,7 @@ accelerated styles exist.
* :doc:`hbond/dreiding/lj <pair_hbond_dreiding>` - DREIDING hydrogen bonding LJ potential
* :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse potential
* :doc:`hdnnp <pair_hdnnp>` - High-dimensional neural network potential
* :doc:`hippo <pair_amoeba>` -
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` - registry-dependent interlayer potential (ILP)
* :doc:`ilp/tmd <pair_ilp_tmd>` - interlayer potential (ILP) potential for transition metal dichalcogenides (TMD)
* :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
@ -258,9 +260,9 @@ accelerated styles exist.
* :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulomb for TIP4P water
* :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function
* :doc:`lj/relres <pair_lj_relres>` - LJ using multiscale Relative Resolution (RelRes) methodology :ref:`(Chaimovich) <Chaimovich2>`.
* :doc:`lj/sdk <pair_sdk>` - LJ for SDK coarse-graining
* :doc:`lj/sdk/coul/long <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb
* :doc:`lj/sdk/coul/msm <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb via MSM
* :doc:`lj/spica <pair_spica>` - LJ for SPICA coarse-graining
* :doc:`lj/spica/coul/long <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb
* :doc:`lj/spica/coul/msm <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb via MSM
* :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces
* :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential
* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
@ -348,6 +350,7 @@ accelerated styles exist.
* :doc:`spin/magelec <pair_spin_magelec>` -
* :doc:`spin/neel <pair_spin_neel>` -
* :doc:`srp <pair_srp>` -
* :doc:`srp/react <pair_srp>` -
* :doc:`sw <pair_sw>` - Stillinger-Weber 3-body potential
* :doc:`sw/angle/table <pair_sw_angle_table>` - Stillinger-Weber potential with tabulated angular term
* :doc:`sw/mod <pair_sw>` - modified Stillinger-Weber 3-body potential

35
doc/src/read_dump.rst
View File

@ -24,12 +24,13 @@ Syntax
*fx*,\ *fy*,\ *fz* = force components
* zero or more keyword/value pairs may be appended
* keyword = *nfile* or *box* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*
* keyword = *nfile* or *box* or *timestep* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*
.. parsed-literal::
*nfile* value = Nfiles = how many parallel dump files exist
*box* value = *yes* or *no* = replace simulation box with dump box
*timestep* value = *yes* or *no* = reset simulation timestep with dump timestep
*replace* value = *yes* or *no* = overwrite atoms with dump atoms
*purge* value = *yes* or *no* = delete all atoms before adding dump atoms
*trim* value = *yes* or *no* = trim atoms not in dump snapshot
@ -60,6 +61,7 @@ Examples
read_dump dump.dcd 0 x y z box yes format molfile dcd
read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
read_dump dump.file 5000 x y vx vy trim yes
read_dump dump.file 5000 x y vx vy add yes box no timestep no
read_dump ../run7/dump.file.gz 10000 x y z box yes
read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
read_dump dump.dcd 0 x y z format molfile dcd
@ -71,9 +73,9 @@ Description
"""""""""""
Read atom information from a dump file to overwrite the current atom
coordinates, and optionally the atom velocities and image flags and
the simulation box dimensions. This is useful for restarting a run
from a particular snapshot in a dump file. See the
coordinates, and optionally the atom velocities and image flags, the
simulation timestep, and the simulation box dimensions. This is useful
for restarting a run from a particular snapshot in a dump file. See the
:doc:`read_restart <read_restart>` and :doc:`read_data <read_data>`
commands for alternative methods to do this. Also see the
:doc:`rerun <rerun>` command for a means of reading multiple snapshots
@ -89,9 +91,9 @@ Also note that reading per-atom information from a dump snapshot is
limited to the atom coordinates, velocities and image flags, as
explained below. Other atom properties, which may be necessary to run
a valid simulation, such as atom charge, or bond topology information
for a molecular system, are not read from (or even contained in) dump
files. Thus this auxiliary information should be defined in the usual
way, e.g. in a data file read in by a :doc:`read_data <read_data>`
for a molecular system, are not read from (or may not even be contained
in) dump files. Thus this auxiliary information should be defined in
the usual way, e.g. in a data file read in by a :doc:`read_data <read_data>`
command, before using the read_dump command, or by the :doc:`set <set>`
command, after the dump snapshot is read.
@ -165,11 +167,10 @@ variable *ntimestep*:
uint64_t ntimestep 5*scalar
(0) 0 50 100 150 200
Note that the *xyz*
and *molfile* formats do not store the timestep. For these formats,
timesteps are numbered logically, in a sequential manner, starting
from 0. Thus to access the 10th snapshot in an *xyz* or *mofile*
formatted dump file, use *Nstep* = 9.
Note that the *xyz* and *molfile* formats do not store the timestep.
For these formats, timesteps are numbered logically, in a sequential
manner, starting from 0. Thus to access the 10th snapshot in an *xyz*
or *mofile* formatted dump file, use *Nstep* = 9.
The dimensions of the simulation box for the selected snapshot are
also read; see the *box* keyword discussion below. For the *native*
@ -266,8 +267,10 @@ for how this is done, determined by the specified fields and optional
keywords.
The timestep of the snapshot becomes the current timestep for the
simulation. See the :doc:`reset_timestep <reset_timestep>` command if
you wish to change this after the dump snapshot is read.
simulation unless the *timestep* keyword is specified with a *no* value
(default setting is *yes*). See the :doc:`reset_timestep <reset_timestep>`
command if you wish to change this to a different value after the dump
snapshot is read.
If the *box* keyword is specified with a *yes* value, then the current
simulation box dimensions are replaced by the dump snapshot box
@ -391,7 +394,7 @@ Related commands
Default
"""""""
The option defaults are box = yes, replace = yes, purge = no, trim =
no, add = no, scaled = no, wrapped = yes, and format = native.
The option defaults are box = yes, timestep = yes, replace = yes, purge = no,
trim = no, add = no, scaled = no, wrapped = yes, and format = native.
.. _vmd: http://www.ks.uiuc.edu/Research/vmd

104
doc/src/special_bonds.rst
View File

@ -11,7 +11,7 @@ Syntax
special_bonds keyword values ...
* one or more keyword/value pairs may be appended
* keyword = *amber* or *charmm* or *dreiding* or *fene* or *lj/coul* or *lj* or *coul* or *angle* or *dihedral*
* keyword = *amber* or *charmm* or *dreiding* or *fene* or *lj/coul* or *lj* or *coul* or *angle* or *dihedral* or *one/five*
.. parsed-literal::
@ -27,6 +27,7 @@ Syntax
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
*angle* value = *yes* or *no*
*dihedral* value = *yes* or *no*
*one/five* value = *yes* or *no*
Examples
""""""""
@ -45,10 +46,10 @@ Description
Set weighting coefficients for pairwise energy and force contributions
between pairs of atoms that are also permanently bonded to each other,
either directly or via one or two intermediate bonds. These weighting
factors are used by nearly all :doc:`pair styles <pair_style>` in LAMMPS
that compute simple pairwise interactions. Permanent bonds between
atoms are specified by defining the bond topology in the data file
read by the :doc:`read_data <read_data>` command. Typically a
factors are used by nearly all :doc:`pair styles <pair_style>` in
LAMMPS that compute simple pairwise interactions. Permanent bonds
between atoms are specified by defining the bond topology in the data
file read by the :doc:`read_data <read_data>` command. Typically a
:doc:`bond_style <bond_style>` command is also used to define a bond
potential. The rationale for using these weighting factors is that
the interaction between a pair of bonded atoms is all (or mostly)
@ -58,31 +59,34 @@ atoms should be excluded (or reduced by a weighting factor).
.. note::
These weighting factors are NOT used by :doc:`pair styles <pair_style>` that compute many-body interactions, since the
"bonds" that result from such interactions are not permanent, but are
created and broken dynamically as atom conformations change. Examples
of pair styles in this category are EAM, MEAM, Stillinger-Weber,
Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no
sense to define permanent bonds between atoms that interact via these
potentials, though such bonds may exist elsewhere in your system,
e.g. when using the :doc:`pair_style hybrid <pair_hybrid>` command.
Thus LAMMPS ignores special_bonds settings when many-body potentials
are calculated. Please note, that the existence of explicit bonds
for atoms that are described by a many-body potential will alter the
neighbor list and thus can render the computation of those interactions
invalid, since those pairs are not only used to determine direct
pairwise interactions but also neighbors of neighbors and more.
The recommended course of action is to remove such bonds, or - if
that is not possible - use a special bonds setting of 1.0 1.0 1.0.
These weighting factors are NOT used by :doc:`pair styles
<pair_style>` that compute many-body interactions, since the
"bonds" that result from such interactions are not permanent, but
are created and broken dynamically as atom conformations change.
Examples of pair styles in this category are EAM, MEAM,
Stillinger-Weber, Tersoff, COMB, AIREBO, and ReaxFF. In fact, it
generally makes no sense to define permanent bonds between atoms
that interact via these potentials, though such bonds may exist
elsewhere in your system, e.g. when using the :doc:`pair_style
hybrid <pair_hybrid>` command. Thus LAMMPS ignores special_bonds
settings when many-body potentials are calculated. Please note,
that the existence of explicit bonds for atoms that are described
by a many-body potential will alter the neighbor list and thus can
render the computation of those interactions invalid, since those
pairs are not only used to determine direct pairwise interactions
but also neighbors of neighbors and more. The recommended course
of action is to remove such bonds, or - if that is not possible -
use a special bonds setting of 1.0 1.0 1.0.
.. note::
Unlike some commands in LAMMPS, you cannot use this command
multiple times in an incremental fashion: e.g. to first set the LJ
settings and then the Coulombic ones. Each time you use this command
it sets all the coefficients to default values and only overrides the
one you specify, so you should set all the options you need each time
you use it. See more details at the bottom of this page.
settings and then the Coulombic ones. Each time you use this
command it sets all the coefficients to default values and only
overrides the one you specify, so you should set all the options
you need each time you use it. See more details at the bottom of
this page.
The Coulomb factors are applied to any Coulomb (charge interaction)
term that the potential calculates. The LJ factors are applied to the
@ -94,14 +98,14 @@ exclude it completely.
The first of the 3 coefficients (LJ or Coulombic) is the weighting
factor on 1-2 atom pairs, which are pairs of atoms directly bonded to
each other. The second coefficient is the weighting factor on 1-3 atom
pairs which are those separated by 2 bonds (e.g. the two H atoms in a
water molecule). The third coefficient is the weighting factor on 1-4
atom pairs which are those separated by 3 bonds (e.g. the first and fourth
atoms in a dihedral interaction). Thus if the 1-2 coefficient is set
to 0.0, then the pairwise interaction is effectively turned off for
all pairs of atoms bonded to each other. If it is set to 1.0, then
that interaction will be at full strength.
each other. The second coefficient is the weighting factor on 1-3
atom pairs which are those separated by 2 bonds (e.g. the two H atoms
in a water molecule). The third coefficient is the weighting factor
on 1-4 atom pairs which are those separated by 3 bonds (e.g. the first
and fourth atoms in a dihedral interaction). Thus if the 1-2
coefficient is set to 0.0, then the pairwise interaction is
effectively turned off for all pairs of atoms bonded to each other.
If it is set to 1.0, then that interaction will be at full strength.
.. note::
@ -184,21 +188,27 @@ interaction between atoms 2 and 5 will be unaffected (full weighting
of 1.0). If the *dihedral* keyword is specified as *no* which is the
default, then the 2,5 interaction will also be weighted by 0.5.
The *one/five* keyword enable calculation and storage of a list of 1-5
neighbors in the molecular topology for each atom. It is required by
some pair styles, such as :doc:`pair_style amoeba <pair_style>` and
:doc:`pair_style hippo <pair_style>`.
----------
.. note::
LAMMPS stores and maintains a data structure with a list of the
first, second, and third neighbors of each atom (within the bond topology of
the system). If new bonds are created (or molecules added containing
atoms with more special neighbors), the size of this list needs to
grow. Note that adding a single bond always adds a new first neighbor
but may also induce \*many\* new second and third neighbors, depending on the
molecular topology of your system. Using the *extra/special/per/atom*
keyword to either :doc:`read_data <read_data>` or :doc:`create_box <create_box>`
reserves empty space in the list for this N additional first, second, or third
neighbors to be added. If you do not do this, you may get an error
when bonds (or molecules) are added.
first, second, and third neighbors of each atom (within the bond
topology of the system). If new bonds are created (or molecules
added containing atoms with more special neighbors), the size of
this list needs to grow. Note that adding a single bond always
adds a new first neighbor but may also induce \*many\* new second
and third neighbors, depending on the molecular topology of your
system. Using the *extra/special/per/atom* keyword to either
:doc:`read_data <read_data>` or :doc:`create_box <create_box>`
reserves empty space in the list for this N additional first,
second, or third neighbors to be added. If you do not do this, you
may get an error when bonds (or molecules) are added.
----------
@ -226,16 +236,16 @@ In the first case you end up with (after the second command):
LJ: 0.0 0.0 0.0
Coul: 0.0 0.0 1.0
while only in the second case, you get the desired settings of:
while only in the second case do you get the desired settings of:
.. parsed-literal::
LJ: 0.0 1.0 1.0
Coul: 0.0 0.0 1.0
This happens because the LJ (and Coul) settings are reset to
their default values before modifying them, each time the
*special_bonds* command is issued.
This happens because the LJ (and Coul) settings are reset to their
default values before modifying them, each time the *special_bonds*
command is issued.
Restrictions
""""""""""""

28
doc/src/variable.rst
View File

@ -685,7 +685,9 @@ of a run, according to this formula:
The run begins on startstep and ends on stopstep. Startstep and
stopstep can span multiple runs, using the *start* and *stop* keywords
of the :doc:`run <run>` command. See the :doc:`run <run>` command for
details of how to do this.
details of how to do this. If called in between runs or during a
:doc:`run 0 <run>` command, the ramp(x,y) function will return the
value of x.
The stagger(x,y) function uses the current timestep to generate a new
timestep. X,y > 0 and x > y are required. The generated timesteps
@ -781,10 +783,14 @@ according to this formula:
where dt = the timestep size.
The run begins on startstep. Startstep can span multiple runs, using
the *start* keyword of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this. Note that the
:doc:`thermo_style <thermo_style>` keyword elaplong =
timestep-startstep.
the *start* keyword of the :doc:`run <run>` command. See the :doc:`run
<run>` command for details of how to do this. Note that the
:doc:`thermo_style <thermo_style>` keyword elaplong = timestep-startstep.
If used between runs this function will return
the value according to the end of the last run or the value of x if
used before *any* runs. This function assumes the length of the time
step does not change and thus may not be used in combination with
:doc:`fix dt/reset <fix_dt_reset>`.
The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments:
x = value0, y = amplitude, z = period. They use the elapsed time to
@ -799,10 +805,14 @@ run, according to one of these formulas, where omega = 2 PI / period:
where dt = the timestep size.
The run begins on startstep. Startstep can span multiple runs, using
the *start* keyword of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this. Note that the
:doc:`thermo_style <thermo_style>` keyword elaplong =
timestep-startstep.
the *start* keyword of the :doc:`run <run>` command. See the :doc:`run
<run>` command for details of how to do this. Note that the
:doc:`thermo_style <thermo_style>` keyword elaplong = timestep-startstep.
If used between runs these functions will return
the value according to the end of the last run or the value of x if
used before *any* runs. These functions assume the length of the time
step does not change and thus may not be used in combination with
:doc:`fix dt/reset <fix_dt_reset>`.
----------

18
doc/utils/check-styles.py
View File

@ -60,7 +60,7 @@ reader = {}
region = {}
total = 0
index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$")
index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style|dump)\s+([a-zA-Z0-9/_]+)$")
style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)")
upper = re.compile("[A-Z]+")
gpu = re.compile("(.+)/gpu$")
@ -84,7 +84,8 @@ def load_index_entries_in_file(path):
def load_index_entries():
index = {'compute': set(), 'fix': set(), 'pair_style': set(), 'angle_style': set(),
'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(), 'kspace_style': set()}
'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(),
'kspace_style': set(), 'dump': set()}
rst_files = glob(os.path.join(doc_dir, '*.rst'))
for f in rst_files:
for command_type, style in load_index_entries_in_file(f):
@ -254,8 +255,9 @@ for command_type, entries in index.items():
print("Total number of style index entries:", total_index)
skip_angle = ('sdk')
skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
skip_pair = ('meam/c','lj/sf','reax/c')
skip_pair = ('meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm')
skip_compute = ('pressure/cylinder')
counter = 0
@ -269,13 +271,14 @@ counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",pair
counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",pair,'Pair',skip=skip_pair,suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",bond,'Bond',suffix=True)
counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",bond,'Bond',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',suffix=True)
counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',skip=skip_angle,suffix=True)
counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',skip=skip_angle,suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",dihedral,'Dihedral',suffix=True)
counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",dihedral,'Dihedral',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",improper,'Improper',suffix=True)
counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",improper,'Improper',suffix=False)
counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",kspace,'KSpace',suffix=True)
counter += check_style('Commands_dump.rst', doc_dir, ":doc:`(.+) <dump.*>`",dump,'Dump',suffix=True)
if counter:
print(f"Found {counter} issue(s) with style lists")
@ -284,12 +287,13 @@ counter = 0
counter += check_style_index("compute", compute, index["compute"], skip=['pressure/cylinder'])
counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species'])
counter += check_style_index("angle_style", angle, index["angle_style"])
counter += check_style_index("angle_style", angle, index["angle_style"], skip=['sdk'])
counter += check_style_index("bond_style", bond, index["bond_style"])
counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
counter += check_style_index("improper_style", improper, index["improper_style"])
counter += check_style_index("kspace_style", kspace, index["kspace_style"])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf','reax/c'])
counter += check_style_index("dump", dump, index["dump"])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm'])
if counter:
print(f"Found {counter} issue(s) with style index")

46
doc/utils/sphinx-config/false_positives.txt
View File

@ -269,6 +269,7 @@ binutils
biomolecular
biomolecule
Biomolecules
biomolecules
Biophys
Biosym
biquadratic
@ -278,6 +279,7 @@ Bispectrum
bitbucket
bitmapped
bitmask
bitorsion
bitrate
bitrates
Bitzek
@ -421,6 +423,8 @@ CGDNA
cgs
cgsdk
CGSDK
cgspica
CGSPICA
Chaimovich
Chalopin
Champaign
@ -443,6 +447,7 @@ chiralIDs
ChiralIDs
chirality
Cho
Chodera
ChooseOffset
chris
Christoph
@ -577,6 +582,7 @@ cstring
cstyle
csvr
ctrl
ctrn
ctypes
Ctypes
cuda
@ -697,6 +703,7 @@ devel
Devemy
deviatoric
Devine
dewald
df
dfftw
DFT
@ -774,6 +781,7 @@ DPD
dpdTheta
dphi
DPhil
dpme
dr
dR
dragforce
@ -1277,6 +1285,7 @@ gzipped
Haak
Hafskjold
halfstepback
halgren
Halperin
Halver
Hamaker
@ -1284,6 +1293,7 @@ Hamel
Hammerschmidt
Hanley
haptic
Haque
Hara
Harpertown
Harting
@ -1627,6 +1637,7 @@ Kemper
kepler
keV
Keyes
keyfile
Khersonskii
Khrapak
Khvostov
@ -1688,6 +1699,7 @@ kTln
ktypeN
Kub
Kubo
Kuksenok
Kumagai
Kumar
Kurebayashi
@ -1702,6 +1714,7 @@ Ladd
lagrangian
lambdai
LambdaLanczos
Lambrecht
lamda
lammps
Lammps
@ -2076,6 +2089,7 @@ Mishin
Mishra
mistyped
mistyrose
Miyazaki
Mj
mK
mkdir
@ -2087,6 +2101,7 @@ mlparks
Mniszewski
mnt
mobi
Mobley
modc
Modell
modelled
@ -2137,6 +2152,7 @@ mpiexec
mpiio
mpirun
mplayer
mpole
mps
mradius
Mrovec
@ -2171,6 +2187,7 @@ multicore
multielectron
multinode
multiphysics
Multipole
multiscale
multisectioning
multithreading
@ -2358,6 +2375,7 @@ nodesets
Noehring
Noffset
noforce
noguess
Noid
nolib
nonequilibrium
@ -2366,6 +2384,7 @@ nonGaussian
nonlocal
Nonlocal
Noordhoek
noprecond
nopreliminary
Nord
norder
@ -2471,6 +2490,7 @@ ohenrich
ok
Okabe
Okamoto
Okazaki
O'Keefe
OKeefe
oldlace
@ -2542,6 +2562,7 @@ palegreen
paleturquoise
palevioletred
Panagiotopoulos
Pande
Pandit
Papaconstantopoulos
papayawhip
@ -2576,6 +2597,7 @@ Pavia
Paxton
pbc
pc
pcg
pchain
Pchain
pcmoves
@ -2609,7 +2631,9 @@ Persp
peru
Peskin
Pettifor
pewald
pfactor
pflag
pgi
ph
Philipp
@ -2642,6 +2666,7 @@ pIp
Pisarev
Pishevar
Pitera
pitorsion
pj
pjintve
pKa
@ -2657,6 +2682,7 @@ plt
plumedfile
pmb
pmcmoves
pme
Pmolrotate
Pmoltrans
pN
@ -2681,6 +2707,7 @@ polyelectrolyte
polyhedra
Polym
polymorphism
Ponder
popen
Popoola
Popov
@ -2699,6 +2726,7 @@ potin
Pourtois
powderblue
PowerShell
ppme
ppn
pppm
Prakash
@ -2708,6 +2736,7 @@ pre
Pre
prec
precession
precond
prefactor
prefactors
prepend
@ -2729,6 +2758,7 @@ pscrozi
pseudodynamics
pseudopotential
pSp
pSPICA
Pstart
Pstop
pstyle
@ -2802,6 +2832,8 @@ Qsb
qtb
quadratically
quadrupolar
quadrupole
quadrupoles
Quant
quartic
quat
@ -2818,6 +2850,7 @@ qw
qx
qy
qz
Rackers
radialscreened
radialscreenedspin
radialspin
@ -3057,6 +3090,7 @@ Schimansky
Schiotz
Schlitter
Schmid
Schnieders
Schoen
Schotte
Schratt
@ -3087,6 +3121,7 @@ semiaxes
semimetals
Semin
Sensable
Seo
Sep
seqdep
Serpico
@ -3191,12 +3226,15 @@ Souza
sp
spacings
Spearot
specieslist
specular
spellcheck
Spellmeyer
Speybroeck
sph
SPH
spica
SPICA
Spickermann
splined
spparks
@ -3513,6 +3551,9 @@ Tz
Tzou
ub
Uberuaga
ubflag
Ubflag
ubiquitin
uca
uChem
uCond
@ -3566,12 +3607,14 @@ upenn
upto
Urbakh
Urbana
UreyBradley
Usabiaga
usec
uSemiParallel
userguide
username
usleep
usolve
usr
util
utils
@ -3605,6 +3648,7 @@ Vcm
vdfmax
vdim
vdisplace
vdw
vdW
vdwl
vec
@ -3698,6 +3742,7 @@ wallstyle
walltime
Waltham
Waroquier
Wataru
wavepacket
wB
Wbody
@ -3758,6 +3803,7 @@ Xeon
xflag
xhi
xHost
Xia
Xiaohu
Xiaowang
Xie

11
examples/PACKAGES/cgsdk/README → examples/PACKAGES/cgspica/README
View File

@ -1,7 +1,8 @@
LAMMPS CG-SDK example problems
LAMMPS CG-SPICA example problems
Each of these sub-directories contains a sample problem for the SDK
coarse grained MD potentials that you can run with LAMMPS.
Each of these sub-directories contains a sample problem for
the SPICA (formerly called SDK) coarse grained MD potentials
that you can run with LAMMPS.
These are the two sample systems
@ -9,11 +10,11 @@ peg-verlet: coarse grained PEG surfactant/water mixture lamella
verlet version
this example uses the plain LJ term only, no charges.
two variants are provided regular harmonic angles and
the SDK variant that includes 1-3 LJ repulsion.
the SPICA variant that includes 1-3 LJ repulsion.
sds-monolayer: coarse grained SDS surfactant monolayers at water/vapor
interface.
this example uses the SDK LJ term with coulomb and shows
this example uses the SPICA LJ term with coulomb and shows
how to use the combined coulomb style vs. hybrid/overlay
with possible optimizations due to the small number of
charged particles in this system

0
examples/PACKAGES/cgsdk/peg-verlet/data.pegc12e8.gz → examples/PACKAGES/cgspica/peg-verlet/data.pegc12e8.gz
View File

2
examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8 → examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8
View File

@ -9,7 +9,7 @@ atom_style angle
processors * * 1
# read topology and force field
pair_style lj/sdk 15.0
pair_style lj/sdk 15.0 # compatible with "lj/spica"
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0

4
examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8-angle → examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8-angle
View File

@ -9,9 +9,9 @@ atom_style angle
processors * * 1
# read topology and force field
pair_style lj/sdk 15.0
pair_style lj/sdk 15.0 # compatible with "lj/spica"
bond_style harmonic
angle_style sdk
angle_style sdk # compatible with "spica"
special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1
View File

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4
View File

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8.g++.1
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0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8.g++.4
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0
examples/PACKAGES/cgsdk/sds-monolayer/data.sds.gz → examples/PACKAGES/cgspica/sds-monolayer/data.sds.gz
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4
examples/PACKAGES/cgsdk/sds-monolayer/in.sds-hybrid → examples/PACKAGES/cgspica/sds-monolayer/in.sds-hybrid
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@ -5,9 +5,9 @@ dimension 3
atom_style full
processors * * 1
pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5
pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5 # "lj/sdk" is compatible with "lj/spica"
bond_style harmonic
angle_style sdk
angle_style sdk # compatible with "spica"
special_bonds lj/coul 0.0 0.0 1.0
read_data data.sds.gz

4
examples/PACKAGES/cgsdk/sds-monolayer/in.sds-regular → examples/PACKAGES/cgspica/sds-monolayer/in.sds-regular
View File

@ -5,9 +5,9 @@ dimension 3
atom_style full
processors * * 1
pair_style lj/sdk/coul/long 15.0
pair_style lj/sdk/coul/long 15.0 # compatible with "lj/spica/coul/long"
bond_style harmonic
angle_style sdk
angle_style sdk # compatible with "spica"
special_bonds lj/coul 0.0 0.0 1.0
read_data data.sds.gz

0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-hybrid.g++.1
View File

0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-hybrid.g++.4
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0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-regular.g++.1
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0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-regular.g++.4
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16
examples/PACKAGES/srp_react/README Normal file
View File

@ -0,0 +1,16 @@
This directory contains an input script for performing
simulations with the srp/react pair style. The pair style
srp/react interfaces fix bond/break and fix bond/create commands
with the segmental repulsive potential. This is useful in simulating
reactions with soft potentials such as DPD where minimizing
topological violations is important.
The input script in.srp_react is an example of a simulation of
a degrading nanogel particle. An initial equilibrated structure
of a nanogel particle (prior to degradation) is read from the
restart file. The degradation reaction is simulated via
the fix bond/break command. The simulation will generate the
file bonds_broken.txt containing the number of bonds
broken and fraction of bonds intact over the simulation time.
For more details see the LAMMPS online documentation and the
paper: Palkar, V., & Kuksenok, O. (2022). JPC B, 126, 336.

22959
examples/PACKAGES/srp_react/gel_equil.dat Normal file
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95
examples/PACKAGES/srp_react/in.srp_react Normal file
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@ -0,0 +1,95 @@
## srp_react example script
## Author: Vaibhav Palkar
##
## Simulates controlled degradation of a nanogel particle
## in a simulation box and prints statistics regarding
## the fraction of bonds broken over time.
variable rseeddpd equal 26817
variable rseedvel equal 5991
variable breakstep equal 10
variable probbreak equal 0.0009
variable rseedbreak equal 6777
# simulation time
#***********************************************
variable mainsteps equal 10000
# simulation setup
#***********************************************
units lj
atom_style molecular
boundary p p p
bond_style harmonic
#lattice fcc 3.0
comm_modify cutoff 4.0 vel yes
# initial nanogel
#***********************************************
read_data gel_equil.dat
# define groups, create solvent atoms
#**************************************************
group Npoly type 1 2 3 4
group water type 5
group N_all type 1 2 3 4 5
# density check
#***********************************************
variable N_atoms equal count(all)
variable tdens equal count(all)/vol
print "The system density is now ${tdens}"
# bond break settings
# #***********************************************
fix break N_all bond/break ${breakstep} 2 0 prob ${probbreak} ${rseedbreak}
# interaction parameter setting
#***********************************************
mass * 1.0
bond_coeff * 500.0 0.70
special_bonds lj 1 1 1
newton on
pair_style hybrid dpd 1.0 1.0 ${rseeddpd} srp/react 0.8 * mid break
#***********************************************
pair_coeff *5 *5 dpd 78.000 4.5 1.0
pair_coeff *4 5 dpd 79.500 4.5 1.0
pair_coeff *5 6 none
pair_coeff 6 6 srp/react 80.00 0.800
# initial velocity
#***********************************************
velocity all create 1.0 ${rseedvel} dist gaussian mom yes
# integrator control
#***********************************************
neighbor 0.3 bin
neigh_modify every 1 delay 5 check no
timestep 0.02
# Access variables of fix bond/break
#**********************************************
variable Nbreak equal f_break[2] # Number of bonds broken
variable TIME equal time
# ensemble setting
#***********************************************
fix 1 all nve
# print bonds breaking stats
# ***********************************************
variable TotBreak equal 100 # total breakable bonds in current system
fix print_bonds_broken all print 100 "${TIME} ${Nbreak} $((v_TotBreak-v_Nbreak)/v_TotBreak)" file bonds_broken.txt screen no title "time bonds_broken fraction_bonds_intact"
# thermo output
#***********************************************
thermo 100
thermo_style custom step temp pe ke etotal epair
thermo_modify flush yes norm no
reset_timestep 0
#dump 1 Npoly custom 5000 traj.lammpstrj id type x y z
#*********************************************
run ${mainsteps}
#***********************************************

1
examples/README
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@ -59,6 +59,7 @@ sub-directories:
accelerate: use of all the various accelerator packages
airebo: polyethylene with AIREBO potential
amoeba: small water and bio models with AMOEBA and HIPPO potentials
atm: Axilrod-Teller-Muto potential
balance: dynamic load balancing, 2d system
body: body particles, 2d system

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Data files in this directory were created using the
tools/tinker/tinker2lmp.py script as follows:
** water_dimer:
% python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba
% python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo
** water_hexamer:
% python tinker2lmp.py -xyz water_hexamer.xyz -amoeba amoeba_water.prm -data data.water_hexamer.amoeba
% python tinker2lmp.py -xyz water_hexamer.xyz -hippo hippo_water.prm -data data.water_hexamer.hippo
** water_box:
% python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643
% python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643
** ubiquitin:
% python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data

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!! DATE: 2022-07-05 UNITS: real
parameters ./amoeba.prm
verbose
neighbor-list
tau-temperature 1.0
tau-pressure 2.0
a-axis 54.99
b-axis 41.91
c-axis 41.91
vdw-cutoff 12.0
ewald
ewald-alpha 0.4
pewald-alpha 0.5
ewald-cutoff 7.0
#pme-grid 60 45 45
pme-grid 60 48 48
pme-order 5
polar-eps 0.00001

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!! DATE: 2022-07-05 UNITS: real
parameters ./amoeba.prm
digits 8
cutoff 10
taper 8
polar-eps 1e-5
usolve-diag 1.0

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!! DATE: 2022-07-05 UNITS: real
##############################
## ##
## Force Field Definition ##
## ##
##############################
forcefield AMOEBA-WATER-2003
bond-cubic -2.55
bond-quartic 3.793125
angle-cubic -0.014
angle-quartic 0.000056
angle-pentic -0.0000007
angle-sextic 0.000000022
opbendtype ALLINGER
opbend-cubic -0.014
opbend-quartic 0.000056
opbend-pentic -0.0000007
opbend-sextic 0.000000022
torsionunit 0.5
vdwtype BUFFERED-14-7
radiusrule CUBIC-MEAN
radiustype R-MIN
radiussize DIAMETER
epsilonrule HHG
dielectric 1.0
polarization MUTUAL
vdw-12-scale 0.0
vdw-13-scale 0.0
vdw-14-scale 1.0
vdw-15-scale 1.0
mpole-12-scale 0.0
mpole-13-scale 0.0
mpole-14-scale 0.4
#mpole-15-scale 0.8
polar-12-scale 0.0
polar-13-scale 0.0
polar-14-scale 1.0
polar-15-scale 1.0
polar-12-intra 0.0
polar-13-intra 0.0
polar-14-intra 0.5
polar-15-intra 1.0
direct-11-scale 0.0
direct-12-scale 1.0
direct-13-scale 1.0
direct-14-scale 1.0
mutual-11-scale 1.0
mutual-12-scale 1.0
mutual-13-scale 1.0
mutual-14-scale 1.0
#############################
## ##
## Literature References ##
## ##
#############################
P. Ren and J. W. Ponder, "A Polarizable Atomic Multipole Water Model
for Molecular Mechanics Simulation", J. Phys. Chem. B, 107, 5933-5947
(2003)
Y. Kong, "Multipole Electrostatic Methods for Protein Modeling with
Reaction Field Treatment", Ph.D. thesis, DBBS Program in Molecular
Biophysics, Washington University, St. Louis, August, 1997 [available
online from http://dasher.wustl.edu/ponder/]
alternative valence parameters to match symmetric and antisymmetric
stretch frequencies by David Semrouni, Ecole Polytechnique, Paris
#############################
## ##
## Atom Type Definitions ##
## ##
#############################
atom 1 1 O "AMOEBA Water O" 8 15.995 2
atom 2 2 H "AMOEBA Water H" 1 1.008 1
################################
## ##
## Van der Waals Parameters ##
## ##
################################
vdw 1 3.4050 0.1100
vdw 2 2.6550 0.0135 0.910
##################################
## ##
## Bond Stretching Parameters ##
## ##
##################################
#bond 1 2 529.60 0.9572 !! original AMOEBA water
bond 1 2 556.85 0.9572
################################
## ##
## Angle Bending Parameters ##
## ##
################################
#angle 2 1 2 34.05 108.50 !! original AMOEBA water
angle 2 1 2 48.70 108.50
###############################
## ##
## Urey-Bradley Parameters ##
## ##
###############################
#ureybrad 2 1 2 38.25 1.5537 !! original AMOEBA water
ureybrad 2 1 2 -7.60 1.5537
###################################
## ##
## Atomic Multipole Parameters ##
## ##
###################################
multipole 1 -2 -2 -0.51966
0.00000 0.00000 0.14279
0.37928
0.00000 -0.41809
0.00000 0.00000 0.03881
multipole 2 1 2 0.25983
-0.03859 0.00000 -0.05818
-0.03673
0.00000 -0.10739
-0.00203 0.00000 0.14412
########################################
## ##
## Dipole Polarizability Parameters ##
## ##
########################################
polarize 1 0.837 0.390 2
polarize 2 0.496 0.390 1

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!! DATE: 2022-07-05 UNITS: real
parameters ./amoeba.prm
digits 10
openmp-threads 1
ewald
ewald-alpha 0.4
pewald-alpha 0.5
pme-grid 24 24 24
neighbor-list
a-axis 18.643
cutoff 7
taper 6
polar-eps 1e-5
usolve-diag 1.0

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1988
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LAMMPS data file created from Tinker water_dimer.xyz and amoeba_water.prm files
6 atoms
4 bonds
2 angles
2 atom types
1 bond types
1 angle types
-1.463996 0.933234 xlo xhi
-0.756549 0.75612 ylo yhi
-0.009705 2.935934 zlo zhi
Masses
1 15.995
2 1.008
Atoms
1 1 1 0 -0.024616 -0.001154 -0.003748
2 1 2 0 -0.244211 -0.000666 0.933978
3 1 2 0 0.932234 -0.000406 -0.008705
4 2 1 0 -0.892721 0.000120 2.773674
5 2 2 0 -1.462996 0.755120 2.933870
6 2 2 0 -1.461809 -0.755549 2.934934
Bonds
1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
Angles
1 1 2 1 3
2 1 5 4 6
Bond Coeffs
1 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs
1 0 1 108.5 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
BondAngle Coeffs
1 0.0 0.0 0.0 0.0
UreyBradley Coeffs
1 -7.6 1.5537
Tinker Types
1 1
2 2
3 2
4 1
5 2
6 2

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LAMMPS data file created from Tinker water_dimer.xyz and hippo_water.prm files
6 atoms
4 bonds
2 angles
2 atom types
1 bond types
1 angle types
-1.463996 0.933234 xlo xhi
-0.756549 0.75612 ylo yhi
-0.009705 2.935934 zlo zhi
Masses
1 15.999
2 1.008
Atoms
1 1 1 0 -0.024616 -0.001154 -0.003748
2 1 2 0 -0.244211 -0.000666 0.933978
3 1 2 0 0.932234 -0.000406 -0.008705
4 2 1 0 -0.892721 0.000120 2.773674
5 2 2 0 -1.462996 0.755120 2.933870
6 2 2 0 -1.461809 -0.755549 2.934934
Bonds
1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
Angles
1 1 2 1 3
2 1 5 4 6
Bond Coeffs
1 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs
1 0 0 107.7 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
BondAngle Coeffs
1 0.0 0.0 0.0 0.0
UreyBradley Coeffs
1 0.0 0.0
Tinker Types
1 1
2 2
3 2
4 1
5 2
6 2

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LAMMPS data file created from Tinker water_hexamer.xyz and amoeba_water.prm files
18 atoms
12 bonds
6 angles
2 atom types
1 bond types
1 angle types
-2.517835 2.675716 xlo xhi
-1.523041 2.01883 ylo yhi
-1.734766 2.220847 zlo zhi
Masses
1 15.995
2 1.008
Atoms
1 1 1 0 -1.502169 -0.191359 1.434927
2 1 2 0 -0.601054 -0.596972 1.553718
3 1 2 0 -2.006698 -0.422327 2.219847
4 2 1 0 -1.744575 -0.382348 -1.309144
5 2 2 0 -1.888941 -0.479653 -0.347624
6 2 2 0 -2.516835 -0.766765 -1.733766
7 3 1 0 -0.560409 2.017830 -0.121984
8 3 2 0 -0.947720 1.533567 0.625228
9 3 2 0 -0.989831 1.592736 -0.877419
10 4 1 0 0.964803 -1.165765 1.439987
11 4 2 0 0.979557 -1.522041 0.527833
12 4 2 0 1.542224 -0.393692 1.344373
13 5 1 0 0.974705 -1.401503 -1.335970
14 5 2 0 0.065161 -1.118951 -1.522886
15 5 2 0 1.470709 -0.570933 -1.277710
16 6 1 0 2.002280 1.057824 -0.124502
17 6 2 0 1.141637 1.532266 -0.140121
18 6 2 0 2.674716 1.735342 -0.237995
Bonds
1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
5 1 7 8
6 1 7 9
7 1 10 11
8 1 10 12
9 1 13 14
10 1 13 15
11 1 16 17
12 1 16 18
Angles
1 1 2 1 3
2 1 5 4 6
3 1 8 7 9
4 1 11 10 12
5 1 14 13 15
6 1 17 16 18
Bond Coeffs
1 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs
1 0 1 108.5 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
BondAngle Coeffs
1 0.0 0.0 0.0 0.0
UreyBradley Coeffs
1 -7.6 1.5537
Tinker Types
1 1
2 2
3 2
4 1
5 2
6 2
7 1
8 2
9 2
10 1
11 2
12 2
13 1
14 2
15 2
16 1
17 2
18 2

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LAMMPS data file created from Tinker water_hexamer.xyz and hippo_water.prm files
18 atoms
12 bonds
6 angles
2 atom types
1 bond types
1 angle types
-2.517835 2.675716 xlo xhi
-1.523041 2.01883 ylo yhi
-1.734766 2.220847 zlo zhi
Masses
1 15.999
2 1.008
Atoms
1 1 1 0 -1.502169 -0.191359 1.434927
2 1 2 0 -0.601054 -0.596972 1.553718
3 1 2 0 -2.006698 -0.422327 2.219847
4 2 1 0 -1.744575 -0.382348 -1.309144
5 2 2 0 -1.888941 -0.479653 -0.347624
6 2 2 0 -2.516835 -0.766765 -1.733766
7 3 1 0 -0.560409 2.017830 -0.121984
8 3 2 0 -0.947720 1.533567 0.625228
9 3 2 0 -0.989831 1.592736 -0.877419
10 4 1 0 0.964803 -1.165765 1.439987
11 4 2 0 0.979557 -1.522041 0.527833
12 4 2 0 1.542224 -0.393692 1.344373
13 5 1 0 0.974705 -1.401503 -1.335970
14 5 2 0 0.065161 -1.118951 -1.522886
15 5 2 0 1.470709 -0.570933 -1.277710
16 6 1 0 2.002280 1.057824 -0.124502
17 6 2 0 1.141637 1.532266 -0.140121
18 6 2 0 2.674716 1.735342 -0.237995
Bonds
1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
5 1 7 8
6 1 7 9
7 1 10 11
8 1 10 12
9 1 13 14
10 1 13 15
11 1 16 17
12 1 16 18
Angles
1 1 2 1 3
2 1 5 4 6
3 1 8 7 9
4 1 11 10 12
5 1 14 13 15
6 1 17 16 18
Bond Coeffs
1 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs
1 0 0 107.7 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
BondAngle Coeffs
1 0.0 0.0 0.0 0.0
UreyBradley Coeffs
1 0.0 0.0
Tinker Types
1 1
2 2
3 2
4 1
5 2
6 2
7 1
8 2
9 2
10 1
11 2
12 2
13 1
14 2
15 2
16 1
17 2
18 2

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!! DATE: 2022-07-05 UNITS: real
parameters ./hippo.prm
digits 8
cutoff 10
taper 8
polar-eps 1e-5
usolve-diag 1.0

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!! DATE: 2022-07-05 UNITS: real
##############################
## ##
## Force Field Definition ##
## ##
##############################
forcefield HIPPO-WATER-2019
bond-cubic -2.55
bond-quartic 3.793125
angle-cubic -0.014
angle-quartic 0.000056
angle-pentic -0.0000007
angle-sextic 0.000000022
opbendtype ALLINGER
opbend-cubic -0.014
opbend-quartic 0.000056
opbend-pentic -0.0000007
opbend-sextic 0.000000022
torsionunit 0.5
dielectric 1.0
polarization MUTUAL
rep-12-scale 0.0
rep-13-scale 0.0
rep-14-scale 1.0
rep-15-scale 1.0
disp-12-scale 0.0
disp-13-scale 0.0
disp-14-scale 0.4
#disp-15-scale 0.8
mpole-12-scale 0.0
mpole-13-scale 0.0
mpole-14-scale 0.4
#mpole-15-scale 0.8
polar-12-scale 0.0
polar-13-scale 0.0
polar-14-scale 1.0
polar-15-scale 1.0
polar-12-intra 0.0
polar-13-intra 0.0
polar-14-intra 0.5
polar-15-intra 1.0
direct-11-scale 0.0
direct-12-scale 1.0
direct-13-scale 1.0
direct-14-scale 1.0
mutual-11-scale 1.0
mutual-12-scale 1.0
mutual-13-scale 1.0
mutual-14-scale 1.0
induce-12-scale 0.2
induce-13-scale 1.0
induce-14-scale 1.0
induce-15-scale 1.0
#############################
## ##
## Literature References ##
## ##
#############################
This is a preliminary parameter set for water based on the HIPPO
(Hydrogen-like Intermolecular Polarizable Potential) force field.
It uses terms describing charge penetration, damped dispersion, and
anisotropic repulsion as per the papers below. The parameters are as
of 13 May 2019 and are from Roseane dos Reis Silva and Josh Rackers
in the Ponder lab at Washington University. These parameter values
are under development and are subject to change.
J. A. Rackers, Q. Wang, C. Liu, J.-P. Piquemal, P. Ren and J. W. Ponder,
An Optimized Charge Penetration Model for Use with the AMOEBA Force Field,
Physical Chemistry Chemical Physics, 19, 276-291 (2017)
J. A. Rackers, C. Liu, P. Ren and J. W. Ponder, A Physically Grounded
Damped Dispersion Model with Particle Mesh Ewald Summation, Journal
of Chemical Physics, 149, 084115 (2018)
J. A. Rackers and J. W. Ponder, Classical Pauli Repulsion: An Anisotropic,
Atomic Multipole Model, Journal of Chemical Physics, 150, 084104 (2019)
#############################
## ##
## Atom Type Definitions ##
## ##
#############################
atom 1 1 O "HIPPO Water O" 8 15.999 2
atom 2 2 H "HIPPO Water H" 1 1.008 1
##################################
## ##
## Bond Stretching Parameters ##
## ##
##################################
bond 1 2 556.85 0.9572 !! all
################################
## ##
## Angle Bending Parameters ##
## ##
################################
#angle 2 1 2 48.70 108.50 !! orig
#angle 2 1 2 48.70 107.70 !! 13
#angle 2 1 2 48.70 107.70 !! 12
#angle 2 1 2 48.70 107.70 !! 16t-i2
#angle 2 1 2 48.70 107.70 !! 16t-i6
#angle 2 1 2 48.70 107.70 !! 17t-i3
angle 2 1 2 48.70 107.70 !! 17t-i6
##################################
## ##
## Pauli Repulsion Parameters ##
## ##
##################################
#repulsion 1 2.8478 4.6069 3.3353 !! orig
#repulsion 2 2.0560 4.8356 0.7423 !! orig
#repulsion 1 2.7716 4.4097 3.3789 !! 13
#repulsion 2 2.0410 4.8567 0.6592 !! 13
#repulsion 1 2.7875 4.4310 3.3914 !! 12
#repulsion 2 2.0510 4.8314 0.6557 !! 12
#repulsion 1 2.8604 4.5590 3.3554 !! t16-i2
#repulsion 2 2.0508 4.8497 0.7264 !! t16-i2
#repulsion 1 2.8618 4.4770 3.3790 !! t16-i6
#repulsion 2 2.0658 4.9052 0.6831 !! t16-i6
#repulsion 1 2.8644 4.4964 3.3594 !! t17-i3
#repulsion 2 2.0605 4.8965 0.6958 !! t17-i3
repulsion 1 2.8758 4.4394 3.3883 !! t17-i6
repulsion 2 2.0610 4.9367 0.6505 !! t17-i6
#############################
## ##
## Dispersion Parameters ##
## ##
#############################
#dispersion 1 16.4682 4.4288 !! orig
#dispersion 2 2.9470 4.9751 !! orig
#dispersion 1 17.0790 4.3977 !! 13
#dispersion 2 4.2262 4.9255 !! 13
#dispersion 1 17.0607 4.3872 !! 12
#dispersion 2 4.2382 4.9542 !! 12
#dispersion 1 16.6803 4.4470 !! t16-i2
#dispersion 2 3.4415 4.9267 !! t16-i2
#dispersion 1 16.7807 4.4427 !! t16-i6
#dispersion 2 3.8508 4.9261 !! t16-i6
#dispersion 1 16.6579 4.2763 !! t17-i3
#dispersion 2 3.2999 4.9597 !! t17-i3
dispersion 1 16.7190 4.3418 !! t17-i6
dispersion 2 3.4239 4.9577 !! t17-i6
###################################
## ##
## Atomic Multipole Parameters ##
## ##
###################################
!! orig
#multipole 1 -2 -2 -0.38280
0.00000 0.00000 0.05477
0.69866
0.00000 -0.60471
0.00000 0.00000 -0.09395
#multipole 2 1 2 0.19140
0.00000 0.00000 -0.20097
0.03881
0.00000 0.02214
0.00000 0.00000 -0.06095
!! 13
#multipole 1 -2 -2 -0.38296
0.00000 0.00000 0.05086
0.70053
0.00000 -0.61138
0.00000 0.00000 -0.08915
#multipole 2 1 2 0.19148
0.00000 0.00000 -0.20142
0.06672
0.00000 0.04168
0.01245 0.00000 -0.10840
!! 12
#multipole 1 -2 -2 -0.38468
0.00000 0.00000 0.05069
0.70076
0.00000 -0.61593
0.00000 0.00000 -0.08483
#multipole 2 1 2 0.19234
0.00000 0.00000 -0.20236
0.06136
0.00000 0.04166
0.00591 0.00000 -0.10302
!! t16-i2
#multipole 1 -2 -2 -0.38236
0.00000 0.00000 0.05488
0.69693
0.00000 -0.60514
0.00000 0.00000 -0.09179
#multipole 2 1 2 0.19118
0.00000 0.00000 -0.20081
0.04614
0.00000 0.02258
0.00000 0.00000 -0.07172
!! t16-i6
#multipole 1 -2 -2 -0.37854
0.00000 0.00000 0.05439
0.68442
0.00000 -0.61857
0.00000 0.00000 -0.06585
#multipole 2 1 2 0.18927
0.00000 0.00000 -0.19918
0.05839
0.00000 0.03699
0.00683 0.00000 -0.09538
!! t17-i3
#multipole 1 -2 -2 -0.37944
0.00000 0.00000 0.05496
0.69091
0.00000 -0.60566
0.00000 0.00000 -0.08525
#multipole 2 1 2 0.18972
0.00000 0.00000 -0.20057
0.05030
0.00000 0.03290
0.00187 0.00000 -0.08320
!! t17-i6
multipole 1 -2 -2 -0.37724
0.00000 0.00000 0.05410
0.68565
0.00000 -0.60559
0.00000 0.00000 -0.08006
multipole 2 1 2 0.18862
0.00000 0.00000 -0.19902
0.06206
0.00000 0.04341
0.00709 0.00000 -0.10547
#####################################
## ##
## Charge Penetration Parameters ##
## ##
#####################################
#chgpen 1 6.0000 4.4288 !! orig
#chgpen 2 1.0000 4.9751 !! orig
#chgpen 1 6.0000 4.3977 !! 13
#chgpen 2 1.0000 4.9255 !! 13
#chgpen 1 6.0000 4.3872 !! 12
#chgpen 2 1.0000 4.9542 !! 12
#chgpen 1 6.0000 4.4470 !! t16-i2
#chgpen 2 1.0000 4.9767 !! t16-i2
#chgpen 1 6.0000 4.4427 !! t16-i6
#chgpen 2 1.0000 4.9261 !! t16-i6
#chgpen 1 6.0000 4.3763 !! t17-i3
#chgpen 2 1.0000 4.9597 !! t17-i3
chgpen 1 6.0000 4.3418 !! t17-i6
chgpen 2 1.0000 4.9577 !! t17-i6
########################################
## ##
## Dipole Polarizability Parameters ##
## ##
########################################
#polarize 1 0.7482 2 !! orig
#polarize 2 0.3703 1 !! orig
#polarize 1 0.7448 2 !! 13
#polarize 2 0.3897 1 !! 13
#polarize 1 0.7442 2 !! 12
#polarize 2 0.3874 1 !! 12
#polarize 1 0.7499 2 !! t16-i2
#polarize 2 0.3706 1 !! t16-i2
#polarize 1 0.7403 2 !! t16-i6
#polarize 2 0.3774 1 !! t16-i6
#polarize 1 0.7416 2 !! t17-i3
#polarize 2 0.3670 1 !! t17-i3
polarize 1 0.7332 2 !! t17-i6
polarize 2 0.3691 1 !! t17-i6
##################################
## ##
## Charge Transfer Parameters ##
## ##
##################################
#chgtrn 1 3.5788 0.0000 !! orig
#chgtrn 2 0.0000 3.3292 !1 orig
#chgtrn 1 3.5856 0.0000 !! 13
#chgtrn 2 0.0000 3.3482 !! 13
#chgtrn 1 3.5867 0.0000 !! t16-i2
#chgtrn 2 0.0000 3.3105 !! t16-i2
#chgtrn 1 3.5812 0.0000 !! t16-i6
#chgtrn 2 0.0000 3.2909 !! t16-i6
#chgtrn 1 3.5762 0.0000 !! t17-i3
#chgtrn 2 0.0000 3.2881 !! t17-i3
chgtrn 1 3.5551 0.0000 !! t17-i6
chgtrn 2 0.0000 3.2812 !! t17-i6

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examples/amoeba/hippo_water_box.key Normal file
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!! DATE: 2022-07-05 UNITS: real
parameters ./hippo.prm
digits 8
verbose
ewald
ewald-alpha 0.4
pewald-alpha 0.5
dewald
dewald-alpha 0.45
dpme-grid 16 16 16
neighbor-list
a-axis 18.643
cutoff 7
taper 6
polar-eps 1e-5
usolve-diag 1.0

52
examples/amoeba/in.ubiquitin Normal file
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# solvated ubiquitin molecule with AMOEBA force field
units real
boundary p p p
atom_modify sort 0 0.0
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style fourier
improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
# read data file
read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pit "pitorsion types" "PiTorsion Coeffs" &
fix pit pitorsions PiTorsions &
fix bit bitorsions BiTorsions
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 1
run 10

43
examples/amoeba/in.water_box.amoeba Normal file
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# replicate water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100

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