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Merge branch 'develop' into distributed-grids

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# Conflicts:
#	doc/src/Developer_utils.rst
#	doc/src/dump.rst
#	doc/src/fix_ave_chunk.rst
#	src/utils.h
This commit is contained in:
Axel Kohlmeyer
2022-09-12 18:31:29 -04:00
parent 0c4583a267 23595aa851
commit e2df4ed2a7
524 changed files with 298740 additions and 6598 deletions
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6
.github/workflows/compile-msvc.yml vendored
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@ -3,9 +3,11 @@ name: "Native Windows Compilation and Unit Tests"
on:
push:
branches: [ develop ]
branches:
- develop
pull_request:
branches: [ $default-branch ]
branches:
- develop
workflow_dispatch:

103
.github/workflows/coverity.yml vendored Normal file
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@ -0,0 +1,103 @@
name: "Run Coverity Scan"
on:
schedule:
- cron: "0 0 * * FRI"
workflow_dispatch:
jobs:
analyze:
name: Analyze
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
container:
image: lammps/buildenv:ubuntu20.04
steps:
- name: Checkout repository
uses: actions/checkout@v3
with:
fetch-depth: 2
- name: Create Build and Download Folder
run: mkdir build download
- name: Cache Coverity
id: cache-coverity
uses: actions/cache@v3
with:
path: ./download/
key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}
- name: Download Coverity if necessary
if: steps.cache-coverity.outputs.cache-hit != 'true'
working-directory: download
run: |
wget -nv https://scan.coverity.com/download/linux64 --post-data "token=${{ secrets.COVERITY_TOKEN }}&project=LAMMPS" -O coverity_tool.tgz
wget -nv https://scan.coverity.com/download/linux64 --post-data "token=${{ secrets.COVERITY_TOKEN }}&project=LAMMPS&md5=1" -O coverity_tool.md5
echo " coverity_tool.tgz" >> coverity_tool.md5
md5sum -c coverity_tool.md5
- name: Setup Coverity
run: |
tar xzf download/coverity_tool.tgz
ln -s cov-analysis-linux64-* coverity
- name: Configure LAMMPS via CMake
shell: bash
working-directory: build
run: |
cmake \
-C ../cmake/presets/clang.cmake \
-C ../cmake/presets/most.cmake \
-C ../cmake/presets/kokkos-openmp.cmake \
-D CMAKE_BUILD_TYPE="RelWithDebug" \
-D CMAKE_TUNE_FLAGS="-Wall -Wextra -Wno-unused-result" \
-D BUILD_MPI=on \
-D BUILD_OMP=on \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_SIZES=SMALLBIG \
-D LAMMPS_EXCEPTIONS=off \
-D PKG_MESSAGE=on \
-D PKG_MPIIO=on \
-D PKG_ATC=on \
-D PKG_AWPMD=on \
-D PKG_BOCS=on \
-D PKG_EFF=on \
-D PKG_H5MD=on \
-D PKG_INTEL=on \
-D PKG_LATBOLTZ=on \
-D PKG_MANIFOLD=on \
-D PKG_MGPT=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_MOLFILE=on \
-D PKG_NETCDF=on \
-D PKG_PTM=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-D PKG_TALLY=on \
../cmake
- name: Run Coverity Scan
shell: bash
working-directory: build
run: |
export PATH=$GITHUB_WORKSPACE/coverity/bin:$PATH
cov-build --dir cov-int cmake --build . --parallel 2
- name: Create tarball with scan results
shell: bash
working-directory: build
run: tar czf lammps.tgz cov-int
- name: Upload scan result to Coverity
shell: bash
run: |
curl --form token=${{ secrets.COVERITY_TOKEN }} \
--form email=${{ secrets.COVERITY_EMAIL }} \
--form file=@build/lammps.tgz \
--form version=${{ github.sha }} \
--form description="LAMMPS automated build" \
https://scan.coverity.com/builds?project=LAMMPS

6
.github/workflows/unittest-macos.yml vendored
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@ -3,9 +3,11 @@ name: "Unittest for MacOS"
on:
push:
branches: [ develop ]
branches:
- develop
pull_request:
branches: [ $default-branch ]
branches:
- develop
workflow_dispatch:

1
cmake/CMakeLists.txt
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@ -376,6 +376,7 @@ pkg_depends(DIELECTRIC EXTRA-PAIR)
pkg_depends(CG-DNA MOLECULE)
pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)

10
cmake/Modules/LAMMPSUtils.cmake
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@ -110,14 +110,16 @@ function(FetchPotentials pkgfolder potfolder)
math(EXPR plusone "${blank}+1")
string(SUBSTRING ${line} 0 ${blank} pot)
string(SUBSTRING ${line} ${plusone} -1 sum)
if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot})
if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
endif()
if(NOT sum STREQUAL oldsum)
message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
string(MD5 TMP_EXT "${CMAKE_BINARY_DIR}")
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}"
EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR})
file(COPY "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}")
file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
endif()
endforeach()
endif()

4
cmake/Modules/Packages/MDI.cmake
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@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.1.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "f9505fccd4c79301a619f6452dad4ad9" CACHE STRING "MD5 checksum for MDI tarball")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.11.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "3791fe5081405c14aac07d4687f1cc58" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
enable_language(C)

13
cmake/presets/clang.cmake
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@ -3,6 +3,13 @@
# prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
if (_tmp_fc STREQUAL "flang")
set(FC_STD_VERSION "-std=f2018")
set(BUILD_MPI OFF)
else()
set(FC_STD_VERSION "-std=f2003")
endif()
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
@ -10,9 +17,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)

1
doc/src/Commands_all.rst
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@ -61,6 +61,7 @@ An alphabetic list of general LAMMPS commands.
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`label <label>`
* :doc:`labelmap <labelmap>`
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`

2
doc/src/Commands_bond.rst
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@ -44,6 +44,7 @@ OPT.
* :doc:`harmonic (iko) <bond_harmonic>`
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
* :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
* :doc:`mesocnt <bond_mesocnt>`
* :doc:`mm3 <bond_mm3>`
* :doc:`morse (o) <bond_morse>`
* :doc:`nonlinear (o) <bond_nonlinear>`
@ -92,6 +93,7 @@ OPT.
* :doc:`fourier/simple (o) <angle_fourier_simple>`
* :doc:`gaussian <angle_gaussian>`
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mesocnt <angle_mesocnt>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`spica (o) <angle_spica>`

1
doc/src/Commands_pair.rst
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@ -201,6 +201,7 @@ OPT.
* :doc:`meam/spline (o) <pair_meam_spline>`
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
* :doc:`mesocnt <pair_mesocnt>`
* :doc:`mesocnt/viscous <pair_mesocnt>`
* :doc:`mesont/tpm <pair_mesont_tpm>`
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`

9
doc/src/Developer_utils.rst
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@ -175,6 +175,12 @@ and parsing files or arguments.
.. doxygenfunction:: is_double
:project: progguide
.. doxygenfunction:: is_id
:project: progguide
.. doxygenfunction:: is_type
:project: progguide
Potential file functions
^^^^^^^^^^^^^^^^^^^^^^^^
@ -208,6 +214,9 @@ Argument processing
.. doxygenfunction:: parse_gridid
:project: progguide
.. doxygenfunction:: expand_type
:project: progguide
Convenience functions
^^^^^^^^^^^^^^^^^^^^^

40
doc/src/Errors_messages.rst
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@ -5453,6 +5453,11 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Mass command must set a type from 1-N where N is the number of atom
types.
*Invalid label2type() function syntax in variable formula*
The first argument must be a label map kind (atom, bond, angle,
dihedral, or improper) and the second argument must be a valid type
label that has been assigned to a numeric type.
*Invalid use of library file() function*
This function is called through the library interface. This
error should not occur. Contact the developers if it does.
@ -5585,9 +5590,18 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*LJ6 off not supported in pair_style buck/long/coul/long*
Self-explanatory.
*Label map is incomplete: all types must be assigned a unique type label*
For a given type-kind (atom types, bond types, etc.) to be written to
the data file, all associated types must be assigned a type label, and
each type label can be assigned to only one numeric type.
*Label wasn't found in input script*
Self-explanatory.
*Labelmap command before simulation box is defined*
The labelmap command cannot be used before a read_data,
read_restart, or create_box command.
*Lattice orient vectors are not orthogonal*
The three specified lattice orientation vectors must be mutually
orthogonal.
@ -5863,6 +5877,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Must not have multiple fixes change box parameter ...*
Self-explanatory.
*Must read Angle Type Labels before Angles*
An Angle Type Labels section of a data file must come before the Angles section.
*Must read Atom Type Labels before Atoms*
An Atom Type Labels section of a data file must come before the Atoms section.
*Must read Atoms before Angles*
The Atoms section of a data file must come before an Angles section.
@ -5893,6 +5913,15 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
The Atoms section of a data file must come before a Velocities
section.
*Must read Bond Type Labels before Bonds*
A Bond Type Labels section of a data file must come before the Bonds section.
*Must read Dihedral Type Labels before Dihedrals*
An Dihedral Type Labels section of a data file must come before the Dihedrals section.
*Must read Improper Type Labels before Impropers*
An Improper Type Labels section of a data file must come before the Impropers section.
*Must re-specify non-restarted pair style (xxx) after read_restart*
For pair styles, that do not store their settings in a restart file,
it must be defined with a new 'pair_style' command after read_restart.
@ -7849,6 +7878,10 @@ keyword to allow for additional bonds to be formed
Number of local atoms times number of columns must fit in a 32-bit
integer for dump.
*Topology type exceeds system topology type*
The number of bond, angle, etc types exceeds the system setting. See
the create_box or read_data command for how to specify these values.
*Tree structure in joint connections*
Fix poems cannot (yet) work with coupled bodies whose joints connect
the bodies in a tree structure.
@ -7873,6 +7906,13 @@ keyword to allow for additional bonds to be formed
*Two groups cannot be the same in fix spring couple*
Self-explanatory.
*The %s type label %s is already in use for type %s*
For a given type-kind (atom types, bond types, etc.), a given type
label can be assigned to only one numeric type.
*Type label string %s for %s type %s is invalid*
See the labelmap command documentation for valid type labels.
*Unable to initialize accelerator for use*
There was a problem initializing an accelerator for the gpu package

1
doc/src/Howto.rst
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@ -34,6 +34,7 @@ Settings howto
:maxdepth: 1
Howto_2d
Howto_type_labels
Howto_triclinic
Howto_thermostat
Howto_barostat

126
doc/src/Howto_type_labels.rst Normal file
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@ -0,0 +1,126 @@
Type labels
===========
.. versionadded:: TBD
Each atom in LAMMPS has an associated numeric atom type. Similarly,
each bond, angle, dihedral, and improper is assigned a bond type,
angle type, and so on. The primary use of these types is to map
potential (force field) parameters to the interactions of the atom,
bond, angle, dihedral, and improper.
By default, type values are entered as integers from 1 to Ntypes
wherever they appear in LAMMPS input or output files. The total number
Ntypes for each interaction is "locked in" when the simulation box
is created.
A recent addition to LAMMPS is the option to use strings - referred
to as type labels - as an alternative. Using type labels instead of
numeric types can be advantageous in various scenarios. For example,
type labels can make inputs more readable and generic (i.e. usable through
the :doc:`include command <include>` for different systems with different
numerical values assigned to types. This generality also applies to
other inputs like data files read by :doc:`read_data <read_data>` or
molecule template files read by the :doc:`molecule <molecule>`
command. See below for a list of other commands that can use
type labels in different ways.
LAMMPS will *internally* continue to use numeric types, which means
that many previous restrictions still apply. For example, the total
number of types is locked in when creating the simulation box, and
potential parameters for each type must be provided even if not used
by any interactions.
A collection of type labels for all type-kinds (atom types, bond types,
etc.) is stored as a "label map" which is simply a list of numeric types
and their associated type labels. Within a type-kind, each type label
must be unique. It can be assigned to only one numeric type. To read
and write type labels to data files for a given type-kind, *all*
associated numeric types need have a type label assigned. Partial
maps can be saved with the :doc:`labelmap write <labelmap>` command
and read back with the :doc:`include <include>` command.
Valid type labels can contain most ASCII characters, but cannot start
with a number, a '#', or a '*'. Also, labels must not contain whitespace
characters. When using the :doc:`labelmap command <labelmap>` in the
LAMMPS input, if certain characters appear in the type label, such as
the single (') or double (") quote or the '#' character, the label
must be put in either double, single, or triple (""") quotes. Triple
quotes allow for the most generic type label strings, but they require
to have a leading and trailing blank space. When defining type labels
the blanks will be ignored. Example:
.. code-block:: LAMMPS
labelmap angle 1 """ C1'-C2"-C3# """
This command will map the string ```C1'-C2"-C3#``` to the angle type 1.
There are two ways to define label maps. One is via the :doc:`labelmap
<labelmap>` command. The other is via the :doc:`read_data <read_data>`
command. A data file can have sections such as *Atom Type Labels*, *Bond
Type Labels*, etc., which assign type labels to numeric types. The
label map can be written out to data files by the :doc:`write_data
<write_data>` command. This map is also written to and read from
restart files, by the :doc:`write_restart <write_restart>` and
:doc:`read_restart <read_restart>` commands.
----------
Use of type labels in LAMMPS input or output
""""""""""""""""""""""""""""""""""""""""""""
Many LAMMPS input script commands that take a numeric type as an
argument can use the associated type label instead. If a type label
is not defined for a particular numeric type, only its numeric type
can be used.
This example assigns labels to the atom types, and then uses the type
labels to redefine the pair coefficients.
.. code-block:: LAMMPS
pair_coeff 1 2 1.0 1.0 # numeric types
labelmap atom 1 C 2 H
pair_coeff C H 1.0 1.0 # type labels
Adding support for type labels to various commands is an ongoing
project. If an input script command (or a section in a file read by a
command) allows substituting a type label for a numeric type argument,
it will be explicitly mentioned in that command's documentation page.
As a temporary measure, input script commands can take advantage of
variables and how they can be expanded during processing of the input.
The variables can use functions that will translate type label strings
to their respective number as defined in the current label map. See the
:doc:`variable <variable>` command for details.
For example, here is how the pair_coeff command could be used with
type labels if it did not yet support them, either with an explicit
variable command or an implicit variable used in the pair_coeff
command.
.. code-block:: LAMMPS
labelmap atom 1 C 2 H
variable atom1 equal label2type(atom,C)
variable atom2 equal label2type(atom,H)
pair_coeff ${atom1} ${atom2} 1.0 1.0
.. code-block:: LAMMPS
labelmap atom 1 C 2 H
pair_coeff $(label2type(atom,C)) $(label2type(atom,H)) 80.0 1.2
----------
Commands that can use label types
"""""""""""""""""""""""""""""""""
Any workflow that involves reading multiple data files, molecule
templates or a combination of the two can be streamlined by using type
labels instead of numeric types, because types are automatically synced
between the files. The creation of simulation-ready reaction templates
for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
type labels, and results in templates that can be used without
modification in multiple simulations or different systems.

49
doc/src/Packages_details.rst
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@ -652,7 +652,7 @@ short-range or long-range interactions.
* :doc:`pair_style lj/cut/dipole/cut <pair_dipole>`
* :doc:`pair_style lj/cut/dipole/long <pair_dipole>`
* :doc:`pair_style lj/long/dipole/long <pair_dipole>`
* :doc: `angle_style dipole <angle_dipole>`
* :doc:`angle_style dipole <angle_dipole>`
* examples/dipole
----------
@ -932,6 +932,10 @@ EXTRA-MOLECULE package
Additional bond, angle, dihedral, and improper styles that are less commonly used.
**Install:**
To use this package, also the :ref:`MOLECULE <PKG-MOLECULE>` package needs to be installed.
**Supporting info:**
* src/EXTRA-MOLECULE: filenames -> commands
@ -1404,7 +1408,7 @@ This package has :ref:`specific installation instructions <machdyn>` on the :doc
* src/MACHDYN: filenames -> commands
* src/MACHDYN/README
* doc/PDF/MACHDYN_LAMMPS_userguide.pdf
* `doc/PDF/MACHDYN_LAMMPS_userguide.pdf <PDF/MACHDYN_LAMMPS_userguide.pdf>`_
* examples/PACKAGES/machdyn
* https://www.lammps.org/movies.html#smd
@ -1556,31 +1560,40 @@ MESONT package
**Contents:**
MESONT is a LAMMPS package for simulation of nanomechanics of
nanotubes (NTs). The model is based on a coarse-grained representation
of NTs as "flexible cylinders" consisting of a variable number of
MESONT is a LAMMPS package for simulation of nanomechanics of nanotubes
(NTs). The model is based on a coarse-grained representation of NTs as
"flexible cylinders" consisting of a variable number of
segments. Internal interactions within a NT and the van der Waals
interaction between the tubes are described by a mesoscopic force field
designed and parameterized based on the results of atomic-level
molecular dynamics simulations. The description of the force field is
provided in the papers listed below. This package contains two
independent implementations of this model: :doc:`pair_style mesocnt
<pair_mesocnt>` is a (minimal) C++ implementation, and :doc:`pair_style
mesont/tpm <pair_mesont_tpm>` is a more general and feature rich
implementation based on a Fortran library in the ``lib/mesont`` folder.
provided in the papers listed below.
This package contains two independent implementations of this model:
:doc:`pair_style mesont/tpm <pair_mesont_tpm>` is the original
implementation of the model based on a Fortran library in the
``lib/mesont`` folder. The second implementation is provided by the
mesocnt styles (:doc:`bond_style mesocnt <bond_mesocnt>`,
:doc:`angle_style mesocnt <angle_mesocnt>` and :doc:`pair_style mesocnt
<pair_mesocnt>`). The mesocnt implementation has the same features as
the original implementation with the addition of friction, but is
directly implemented in C++, interfaces more cleanly with general LAMMPS
functionality, and is typically faster. It also does not require its own
atom style and can be installed without any external libraries.
**Download of potential files:**
The potential files for these pair styles are *very* large and thus
are not included in the regular downloaded packages of LAMMPS or the
git repositories. Instead, they will be automatically downloaded
from a web server when the package is installed for the first time.
The potential files for these pair styles are *very* large and thus are
not included in the regular downloaded packages of LAMMPS or the git
repositories. Instead, they will be automatically downloaded from a web
server when the package is installed for the first time.
**Authors of the *mesont* styles:**
Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia)
Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University
of Alabama), Leonid V. Zhigilei (University of Virginia)
**Author of the *mesocnt* pair style:**
**Author of the *mesocnt* styles:**
Philipp Kloza (U Cambridge)
**Supporting info:**
@ -1590,6 +1603,8 @@ Philipp Kloza (U Cambridge)
* :doc:`atom_style mesont <atom_style>`
* :doc:`pair_style mesont/tpm <pair_mesont_tpm>`
* :doc:`compute mesont <compute_mesont>`
* :doc:`bond_style mesocnt <bond_mesocnt>`
* :doc:`angle_style mesocnt <angle_mesocnt>`
* :doc:`pair_style mesocnt <pair_mesocnt>`
* examples/PACKAGES/mesont
* tools/mesont
@ -2692,7 +2707,7 @@ Dynamics, Ernst Mach Institute, Germany).
* src/SPH: filenames -> commands
* src/SPH/README
* doc/PDF/SPH_LAMMPS_userguide.pdf
* `doc/PDF/SPH_LAMMPS_userguide.pdf <PDF/SPH_LAMMPS_userguide.pdf>`_
* examples/PACKAGES/sph
* https://www.lammps.org/movies.html#sph

2
doc/src/accel_styles.rst
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@ -6,7 +6,7 @@ page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, INTEL, KOKKOS,
OPENMP and OPT packages, respectively. They are only enabled if
OPENMP, and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` page for more info.
You can specify the accelerated styles explicitly in your input script

50
doc/src/angle_coeff.rst
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@ -10,7 +10,7 @@ Syntax
angle_coeff N args
* N = angle type (see asterisk form below)
* N = numeric angle type (see asterisk form below), or type label
* args = coefficients for one or more angle types
Examples
@ -22,6 +22,9 @@ Examples
angle_coeff * 5.0
angle_coeff 2*10 5.0
labelmap angle 1 hydroxyl
angle_coeff hydroxyl 300.0 107.0
Description
"""""""""""
@ -30,18 +33,24 @@ The number and meaning of the coefficients depends on the angle style.
Angle coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple angle types. This takes the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of angle types,
then an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
:math:`N` can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be a
type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command.
Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting
for the same angle type. For example, these commands set the coeffs
for all angle types, then overwrite the coeffs for just angle type 2:
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple angle types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If :math:`N` is the number of angle types,
then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using an :doc:`angle_coeff <angle_coeff>` command can
override a previous setting for the same angle type. For example,
these commands set the coeffs for all angle types, then overwrite the
coeffs for just angle type 2:
.. code-block:: LAMMPS
@ -49,11 +58,11 @@ for all angle types, then overwrite the coeffs for just angle type 2:
angle_coeff 2 50.0 107.0
A line in a data file that specifies angle coefficients uses the exact
same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in an input
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Angle Coeffs" section of a data file, the line that
corresponds to the first example above would be listed as
same format as the arguments of the :doc:`angle_coeff <angle_coeff>`
command in an input script, except that wild-card asterisks should not
be used since coefficients for all :math:`N` types must be listed in the
file. For example, under the "Angle Coeffs" section of a data file, the
line that corresponds to the first example above would be listed as
.. parsed-literal::
@ -61,15 +70,14 @@ corresponds to the first example above would be listed as
The :doc:`angle_style class2 <angle_class2>` is an exception to this
rule, in that an additional argument is used in the input script to
allow specification of the cross-term coefficients. See its
doc page for details.
allow specification of the cross-term coefficients. See its doc page
for details.
----------
The list of all angle styles defined in LAMMPS is given on the
:doc:`angle_style <angle_style>` doc page. They are also listed in more
compact form on the :ref:`Commands angle <angle>` doc
page.
compact form on the :ref:`Commands angle <angle>` doc page.
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated

146
doc/src/angle_mesocnt.rst Normal file
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@ -0,0 +1,146 @@
.. index:: angle_style mesocnt
angle_style mesocnt command
===========================
Syntax
""""""
.. code-block:: LAMMPS
angle_style mesocnt
Examples
""""""""
.. code-block:: LAMMPS
angle_style mesocnt
angle_coeff 1 buckling C 10 10 20.0
angle_coeff 4 harmonic C 8 4 10.0
angle_coeff 2 buckling custom 400.0 50.0 5.0
angle_coeff 1 harmonic custom 300.0
Description
"""""""""""
.. versionadded:: TBD
The *mesocnt* angle style uses the potential
.. math::
E = K_\text{H} \Delta \theta^2, \qquad |\Delta \theta| < \Delta
\theta_\text{B} \\
E = K_\text{H} \Delta \theta_\text{B}^2 +
K_\text{B} (\Delta \theta - \Delta \theta_\text{B}), \qquad |\Delta
\theta| \geq \Delta \theta_\text{B}
where :math:`\Delta \theta = \theta - \pi` is the bending angle of the
nanotube, :math:`K_\text{H}` and :math:`K_\text{B}` are prefactors for
the harmonic and linear regime respectively and :math:`\Delta
\theta_\text{B}` is the buckling angle. Note that the usual 1/2 factor
for the harmonic potential is included in :math:`K_\text{H}`.
The style implements parameterization presets of :math:`K_\text{H}`,
:math:`K_\text{B}` and :math:`\Delta \theta_\text{B}` for mesoscopic
simulations of carbon nanotubes based on the atomistic simulations of
:ref:`(Srivastava) <Srivastava_2>` and buckling considerations of
:ref:`(Zhigilei) <Zhigilei1_1>`.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the examples above, or
in the data file or restart files read by the :doc:`read_data
<read_data>` or :doc:`read_restart <read_restart>` commands:
* mode = *buckling* or *harmonic*
* preset = *C* or *custom*
* additional parameters depending on preset
If mode *harmonic* is chosen, the potential is simply harmonic and
does not switch to the linear term when the buckling angle is
reached. In *buckling* mode, the full piecewise potential is used.
Preset *C* is for carbon nanotubes, and the additional parameters are:
* chiral index :math:`n` (unitless)
* chiral index :math:`m` (unitless)
* :math:`r_0` (distance)
Here, :math:`r_0` is the equilibrium distance of the bonds included in
the angle, see :doc:`bond_style mesocnt <bond_mesocnt>`.
In harmonic mode with preset *custom*, the additional parameter is:
* :math:`K_\text{H}` (energy)
Hence, this setting is simply a wrapper for :doc:`bond_style harmonic
<bond_harmonic>` with an equilibrium angle of 180 degrees.
In harmonic mode with preset *custom*, the additional parameters are:
* :math:`K_\text{H}` (energy)
* :math:`K_\text{B}` (energy)
* :math:`\Delta \theta_\text{B}` (degrees)
:math:`\Delta \theta_\text{B}` is specified in degrees, but LAMMPS
converts it to radians internally; hence :math:`K_\text{H}` is
effectively energy per radian\^2 and :math:`K_\text{B}` is energy per
radian.
----------
In *buckling* mode, this angle style adds the *buckled* property to
all atoms in the simulation, which is an integer flag indicating
whether the bending angle at a given atom has exceeded :math:`\Delta
\theta_\text{B}`. It can be accessed as an atomic variable, e.g. for
custom dump commands, as *i_buckled*.
.. note::
If the initial state of the simulation contains buckled nanotubes
and :doc:`pair_style mesocnt <pair_mesocnt>` is used, the
*i_buckled* atomic variable needs to be initialized before the
pair_style is defined by doing a *run 0* command straight after the
angle_style command. See below for an example.
If CNTs are already buckled at the start of the simulation, this
script will correctly initialize *i_buckled*:
.. code-block:: LAMMPS
angle_style mesocnt
angle_coeff 1 buckling C 10 10 20.0
run 0
pair_style mesocnt 60.0
pair_coeff * * C_10_10.mesocnt 1
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE and MESONT packages. See the :doc:`Build package
<Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none
----------
.. _Srivastava_2:
**(Srivastava)** Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417
(2005).
.. _Zhigilei1_1:
**(Zhigilei)** Volkov and Zhigilei, ACS Nano 4, 6187 (2010).

1
doc/src/angle_style.rst
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@ -90,6 +90,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term
* :doc:`gaussian <angle_gaussian>` - multi-centered Gaussian-based angle potential
* :doc:`harmonic <angle_harmonic>` - harmonic angle
* :doc:`mesocnt <angle_mesocnt>` - piecewise harmonic and linear angle for bending-buckling of nanotubes
* :doc:`mm3 <angle_mm3>` - anharmonic angle
* :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
* :doc:`spica <angle_spica>` - harmonic angle with repulsive SPICA pair style between 1-3 atoms

30
doc/src/bond_coeff.rst
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@ -10,7 +10,7 @@ Syntax
bond_coeff N args
* N = bond type (see asterisk form below)
* N = numeric bond type (see asterisk form below), or type label
* args = coefficients for one or more bond types
Examples
@ -21,7 +21,10 @@ Examples
bond_coeff 5 80.0 1.2
bond_coeff * 30.0 1.5 1.0 1.0
bond_coeff 1*4 30.0 1.5 1.0 1.0
bond_coeff 1 harmonic 200.0 1.0
bond_coeff 1 harmonic 200.0 1.0 (for bond_style hybrid)
labelmap bond 5 carbonyl
bond_coeff carbonyl 80.0 1.2
Description
"""""""""""
@ -31,14 +34,19 @@ The number and meaning of the coefficients depends on the bond style.
Bond coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple bond types. This takes the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of bond types,
then an asterisk with no numeric values means all types from 1 to N. A
:math:`N` can be specified in one of several ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be a
type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple bond types. This takes the form "\*" or "\*n"
or "n\*" or "m\*n". If :math:`N` is the number of bond types, then an
asterisk with no numeric values means all types from 1 to :math:`N`. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
asterisk means all types from n to :math:`N` (inclusive). A middle
asterisk means all types from m to n (inclusive).
Note that using a bond_coeff command can override a previous setting
for the same bond type. For example, these commands set the coeffs
@ -52,8 +60,8 @@ for all bond types, then overwrite the coeffs for just bond type 2:
A line in a data file that specifies bond coefficients uses the exact
same format as the arguments of the bond_coeff command in an input
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Bond Coeffs" section of a data file, the line that
coefficients for all :math:`N` types must be listed in the file. For
example, under the "Bond Coeffs" section of a data file, the line that
corresponds to the first example above would be listed as
.. parsed-literal::

84
doc/src/bond_mesocnt.rst Normal file
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@ -0,0 +1,84 @@
.. index:: bond_style mesocnt
bond_style mesocnt command
===========================
Syntax
""""""
.. code-block:: LAMMPS
bond_style mesocnt
Examples
""""""""
.. code-block:: LAMMPS
bond_style mesocnt
bond_coeff 1 C 10 10 20.0
bond_coeff 4 custom 800.0 10.0
Description
"""""""""""
.. versionadded:: TBD
The *mesocnt* bond style is a wrapper for the :doc:`harmonic
<bond_harmonic>` style, and uses the potential
.. math::
E = K (r - r_0)^2
where :math:`r_0` is the equilibrium bond distance. Note that the
usual 1/2 factor is included in :math:`K`. The style implements
parameterization presets of :math:`K` for mesoscopic simulations of
carbon nanotubes based on the atomistic simulations of
:ref:`(Srivastava) <Srivastava_1>`.
Other presets can be readily implemented in the future.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data
<read_data>` or :doc:`read_restart <read_restart>` commands:
* preset = *C* or *custom*
* additional parameters depending on preset
Preset *C* is for carbon nanotubes, and the additional parameters are:
* chiral index :math:`n` (unitless)
* chiral index :math:`m` (unitless)
* :math:`r_0` (distance)
Preset *custom* is simply a direct wrapper for the :doc:`harmonic
<bond_harmonic>` style, and the additional parameters are:
* :math:`K` (energy/distance\^2)
* :math:`r_0` (distance)
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the MOLECULE
and MESONT packages. See the :doc:`Build package <Build_package>`
page for more info.
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
Default
"""""""
none
----------
.. _Srivastava_1:
**(Srivastava)** Zhigilei, Wei and Srivastava, Phys. Rev. B 71, 165417
(2005).

1
doc/src/bond_style.rst
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@ -95,6 +95,7 @@ accelerated styles exist.
* :doc:`harmonic <bond_harmonic>` - harmonic bond
* :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond
* :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` - shifted harmonic bond with a cutoff
* :doc:`mesocnt <bond_mesocnt>` - Harmonic bond wrapper with parameterization presets for nanotubes
* :doc:`mm3 <bond_mm3>` - MM3 anharmonic bond
* :doc:`morse <bond_morse>` - Morse bond
* :doc:`nonlinear <bond_nonlinear>` - nonlinear bond

1
doc/src/commands_list.rst
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@ -56,6 +56,7 @@ Commands
kspace_modify
kspace_style
label
labelmap
lattice
log
mass

4
doc/src/compute_property_atom.rst
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@ -198,8 +198,8 @@ Related commands
""""""""""""""""
:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`,
:doc::doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk
:doc:<fix_ave_chunk>`, `fix property/atom <fix_property_atom>`
:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
:doc:`fix property/atom <fix_property_atom>`
Default
"""""""

20
doc/src/compute_stress_atom.rst
View File

@ -222,6 +222,26 @@ result. I.e. the last 2 columns of thermo output will be the same:
<pair_modify>` command, since those are contributions to the global
system pressure.
The compute stress/atom can be used in a number of ways. Here is an
example to compute a 1-d pressure profile in z-direction across the
complete simulation box. You will need to adjust the number of bins and the
selections for time averaging to your specific simulation. This assumes
that the dimensions of the simulation cell does not change.
.. code-block:: LAMMPS
# set number of bins
variable nbins index 20
variable fraction equal 1.0/v_nbins
# define bins as chunks
compute cchunk all chunk/atom bin/1d x lower ${fraction} units reduced
compute stress all stress/atom NULL
# apply conversion to pressure early since we have no variable style for processing chunks
variable press atom -(c_stress[1]+c_stress[2]+c_stress[3])/(3.0*vol*${fraction})
compute binpress all reduce/chunk cchunk sum v_press
fix avg all ave/time 10 40 400 c_binpress mode vector file ave_stress.txt
Output info
"""""""""""

37
doc/src/dihedral_coeff.rst
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@ -10,7 +10,7 @@ Syntax
dihedral_coeff N args
* N = dihedral type (see asterisk form below)
* N = numeric dihedral type (see asterisk form below) or alphanumeric type label
* args = coefficients for one or more dihedral types
Examples
@ -22,26 +22,35 @@ Examples
dihedral_coeff * 80.0 1 3 0.5
dihedral_coeff 2* 80.0 1 3 0.5
labelmap dihedral 1 backbone
dihedral_coeff backbone 80.0 1 3
Description
"""""""""""
Specify the dihedral force field coefficients for one or more dihedral types.
The number and meaning of the coefficients depends on the dihedral style.
Dihedral coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
Specify the dihedral force field coefficients for one or more dihedral
types. The number and meaning of the coefficients depends on the
dihedral style. Dihedral coefficients can also be set in the data file
read by the :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple dihedral types. This takes the
form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is the number of dihedral
types, then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive). A
trailing asterisk means all types from m to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
:math:`N` can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be
an alphanumeric type label, which is a string defined by the
:doc:`labelmap <labelmap>` command or in a corresponding section of a
data file read by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple dihedral types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If :math:`N` is the number of dihedral types,
then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using a dihedral_coeff command can override a previous setting
for the same dihedral type. For example, these commands set the coeffs
for all dihedral types, then overwrite the coeffs for just dihedral type 2:
for all dihedral types, then overwrite the coeffs for just dihedral type
2:
.. code-block:: LAMMPS

111
doc/src/dump.rst
View File

@ -56,24 +56,24 @@ dump command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dump ID group-ID style N file args
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped
* style = *atom* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *grid* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
* N = dump every this many timesteps
* style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *grid* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
* N = dump on timesteps which are multiples of N
* file = name of file to write dump info to
* args = list of arguments for a particular style
.. parsed-literal::
*atom* args = none
*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` page
*atom/gz* args = none
*atom/zstd* args = none
*atom/mpiio* args = none
*atom/adios* args = none, discussed on :doc:`dump atom/adios <dump_adios>` page
*cfg* args = same as *custom* args, see below
*cfg/gz* args = same as *custom* args, see below
*cfg/zstd* args = same as *custom* args, see below
@ -190,14 +190,15 @@ Examples
Description
"""""""""""
Dump a snapshot of atom quantities to one or more files every :math:`N`
timesteps in one of several styles. The *image* and *movie* styles are
the exception: the *image* style renders a JPG, PNG, or PPM image file
of the atom configuration every :math:`N` timesteps while the *movie* style
combines and compresses them into a movie file; both are discussed in
detail on the :doc:`dump image <dump_image>` page. The timesteps on
which dump output is written can also be controlled by a variable.
See the :doc:`dump_modify every <dump_modify>` command.
Dump a snapshot of atom quantities to one or more files once every
:math:`N` timesteps in one of several styles. The *image* and *movie*
styles are the exception: the *image* style renders a JPG, PNG, or PPM
image file of the atom configuration every :math:`N` timesteps while
the *movie* style combines and compresses them into a movie file; both
are discussed in detail on the :doc:`dump image <dump_image>` page.
The timesteps on which dump output is written can also be controlled
by a variable. See the :doc:`dump_modify every <dump_modify>`
command.
Only information for atoms in the specified group is dumped. The
:doc:`dump_modify thresh and region and refresh <dump_modify>` commands
@ -256,7 +257,7 @@ the compression level in both variants.
As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and
*xyz/mpiio* styles are identical in command syntax and in the format
of the dump files they create, to the corresponding styles without
"mpiio," except the single dump file they produce is written in
"mpiio", except the single dump file they produce is written in
parallel via the MPI-IO library. For the remainder of this page,
you should thus consider the *atom* and *atom/mpiio* styles (etc.) to
be inter-changeable. The one exception is how the filename is
@ -301,13 +302,13 @@ where xlo,xhi are the maximum extents of the simulation box in the
:math:`x`-dimension, and similarly for :math:`y` and :math:`z`. The
"xx yy zz" terms are six characters that encode the style of boundary for each
of the six simulation box boundaries (xlo,xhi; ylo,yhi; and zlo,zhi). Each of
the six characters is either p (periodic), f (fixed), s (shrink wrap),
or m (shrink wrapped with a minimum value). See the
the six characters is one of *p* (periodic), *f* (fixed), *s* (shrink wrap),
or *m* (shrink wrapped with a minimum value). See the
:doc:`boundary <boundary>` command for details.
For triclinic simulation boxes (non-orthogonal), an orthogonal
bounding box which encloses the triclinic simulation box is output,
along with the 3 tilt factors (*xy*, *xz*, *yz*) of the triclinic box,
along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic box,
formatted as follows:
.. parsed-literal::
@ -346,8 +347,8 @@ added for each atom via dump_modify.
Style *custom* allows you to specify a list of atom attributes to be
written to the dump file for each atom. Possible attributes are
listed above and will appear in the order specified. You cannot
specify a quantity that is not defined for a particular simulation -
such as *q* for atom style *bond*, since that atom style does not
specify a quantity that is not defined for a particular simulation---such as
*q* for atom style *bond*, since that atom style does not
assign charges. Dumps occur at the very end of a timestep, so atom
attributes will include effects due to fixes that are applied during
the timestep. An explanation of the possible dump custom attributes
@ -447,7 +448,7 @@ Below is an example for a YAML format dump created by the following commands.
dump out all yaml 100 dump.yaml id type x y z vx vy vz ix iy iz
dump_modify out time yes units yes thermo yes format 1 %5d format "% 10.6e"
The tags "time," "units," and "thermo" are optional and enabled by the
The tags "time", "units", and "thermo" are optional and enabled by the
dump_modify command. The list under the "box" tag has three lines for
orthogonal boxes and four lines for triclinic boxes, where the first three are
the box boundaries and the fourth the three tilt factors (:math:`xy`,
@ -499,21 +500,29 @@ popular molecular viewing program.
----------
Dumps are performed on timesteps that are a multiple of :math:`N` (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
Dumps are performed on timesteps that are a multiple of :math:`N`
(including timestep 0) and on the last timestep of a minimization if
the minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of :math:`N`. This behavior can be
changed via the :doc:`dump_modify first <dump_modify>` command, which
can also be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. :math:`N` can be changed between runs by
using the :doc:`dump_modify every <dump_modify>` command (not allowed
for *dcd* style). The :doc:`dump_modify every <dump_modify>` command
also allows a variable to be used to determine the sequence of
timesteps on which dump files are written. In this mode a dump on the
first timestep of a run will also not be written unless the
if the current timestep is not a multiple of :math:`N`. This behavior
can be changed via the :doc:`dump_modify first <dump_modify>` command,
which can also be useful if the dump command is invoked after a
minimization ended on an arbitrary timestep.
The value of :math:`N` can be changed between runs by using the
:doc:`dump_modify every <dump_modify>` command (not allowed for *dcd*
style). The :doc:`dump_modify every <dump_modify>` command also
allows a variable to be used to determine the sequence of timesteps on
which dump files are written. In this mode a dump on the first
timestep of a run will also not be written unless the
:doc:`dump_modify first <dump_modify>` command is used.
If you instead want to dump snapshots based on simulation time (in
time units of the :doc:`units` command), the :doc:`dump_modify
every/time <dump_modify>` command can be used. This can be useful
when the timestep size varies during a simulation run, e.g. by use of
the :doc:`fix dt/reset <fix_dt_reset>` command.
The specified filename determines how the dump file(s) is written.
The default is to write one large text file, which is opened when the
dump command is invoked and closed when an :doc:`undump <undump>`
@ -559,7 +568,7 @@ package installed, viz.,
make mpi # build LAMMPS for your platform
Second, use a dump filename which contains ".mpiio." Note that it
does not have to end in ".mpiio," just contain those characters.
does not have to end in ".mpiio", just contain those characters.
Unlike MPI-IO restart files, which must be both written and read using
MPI-IO, the dump files produced by these MPI-IO styles are identical
in format to the files produced by their non-MPI-IO style
@ -582,19 +591,19 @@ and have the same binary format as if it were written without MPI-IO.
If the filename ends with ".bin" or ".lammpsbin", the dump file (or
files, if "\*" or "%" is also used) is written in binary format. A
binary dump file will be about the same size as a text version, but
will typically write out much faster. Of course, when
post-processing, you will need to convert it back to text format (see
the :ref:`binary2txt tool <binary>`) or write your own code to read
the binary file. The format of the binary file can be understood by
looking at the :file:`tools/binary2txt.cpp` file. This option is only
available for the *atom* and *custom* styles.
binary dump file will be about the same size as a text version, but will
typically write out much faster. Of course, when post-processing, you
will need to convert it back to text format (see the :ref:`binary2txt
tool <binary>`) or write your own code to read the binary file. The
format of the binary file can be understood by looking at the
:file:`tools/binary2txt.cpp` file. This option is only available for
the *atom* and *custom* styles.
If the filename ends with ".gz", the dump file (or files, if "\*" or
"%" is also used) is written in gzipped format. A gzipped dump file
will be about :math:`3\times` smaller than the text version, but will
also take longer to write. This option is not available for the *dcd*
and *xtc* styles.
If the filename ends with ".gz", the dump file (or files, if "\*" or "%"
is also used) is written in gzipped format. A gzipped dump file will be
about :math:`3\times` smaller than the text version, but will also take
longer to write. This option is not available for the *dcd* and *xtc*
styles.
----------
@ -643,12 +652,12 @@ mass. The quantities *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components
of atom velocity and force and atomic charge.
There are several options for outputting atom coordinates. The *x*,
*y*, and *z* attributes write atom coordinates "unscaled," in the
*y*, and *z* attributes write atom coordinates "unscaled", in the
appropriate distance :doc:`units <units>` (:math:`\mathrm{\mathring A}`,
:math:`\sigma`, etc.). Use *xs*, *ys*, *zs* if you want the coordinates
"scaled" to the box size, so that each value is 0.0 to 1.0. If the simulation
:math:`\sigma`, etc.). Use *xs*, *ys*, and *zs* if you want the coordinates
"scaled" to the box size so that each value is 0.0 to 1.0. If the simulation
box is triclinic (tilted), then all atom coords will still be between 0.0 and
1.0. The actual unscaled :math:`(x,y,z)` coordinate is
1.0. The actual unscaled :math:`(x,y,z)` coordinate is
:math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are the non-orthogonal
vectors of the simulation box edges, as discussed on the
:doc:`Howto triclinic <Howto_triclinic>` page.
@ -689,7 +698,7 @@ The *angmomx*, *angmomy*, and *angmomz* attributes are specific to
finite-size aspherical particles that have an angular momentum. Only
the *ellipsoid* atom style defines this quantity.
The *tqx*, *tqy*, *tqz* attributes are for finite-size particles that
The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles that
can sustain a rotational torque due to interactions with other
particles.
@ -728,8 +737,8 @@ If *f_ID* is used as a attribute, then the per-atom vector calculated
by the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the
range from 1 to :math:`M`, which will print the :math:`i`\ th column of the
per-atom array with :math:`M` columns calculated by the fix. See the
discussion above for how :math:`i` can be specified with a wildcard asterisk to
effectively specify multiple values.
discussion above for how :math:`i` can be specified with a wildcard asterisk
to effectively specify multiple values.
The *v_name* attribute allows per-atom vectors calculated by a
:doc:`variable <variable>` to be output. The name in the attribute

13
doc/src/dump_adios.rst
View File

@ -10,10 +10,9 @@ dump custom/adios command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dump ID group-ID atom/adios N file.bp
dump ID group-ID custom/adios N file.bp args
* ID = user-assigned name for the dump
@ -21,7 +20,7 @@ Syntax
* adios = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
* N = dump every this many timesteps
* file.bp = name of file/stream to write to
* args = same options as in :doc:`\ *dump custom*\ <dump>` command
* args = same options as in :doc:`dump custom <dump>` command
Examples
""""""""
@ -35,10 +34,10 @@ Examples
Description
"""""""""""
Dump a snapshot of atom coordinates every N timesteps in the `ADIOS
<adios_>`_ based "BP" file format, or using different I/O solutions in
Dump a snapshot of atom coordinates every :math:`N` timesteps in the `ADIOS
<adios_>`_-based "BP" file format, or using different I/O solutions in
ADIOS, to a stream that can be read on-line by another program.
ADIOS-BP files are binary, portable and self-describing.
ADIOS-BP files are binary, portable, and self-describing.
.. _adios: https://github.com/ornladios/ADIOS2
@ -67,7 +66,7 @@ create a new file at each individual dump.
Restrictions
""""""""""""
The number of atoms per snapshot CAN change with the adios style.
The number of atoms per snapshot **can** change with the adios style.
When using the ADIOS tool 'bpls' to list the content of a .bp file,
bpls will print *__* for the size of the output table indicating that
its size is changing every step.

10
doc/src/dump_cfg_uef.rst
View File

@ -6,7 +6,7 @@ dump cfg/uef command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dump ID group-ID cfg/uef N file mass type xs ys zs args
@ -32,9 +32,8 @@ Description
This command is used to dump atomic coordinates in the
reference frame of the applied flow field when
:doc:`fix nvt/uef <fix_nh_uef>` or
:doc:`fix npt/uef <fix_nh_uef>` or is used. Only the atomic
coordinates and frame-invariant scalar quantities
:doc:`fix nvt/uef <fix_nh_uef>` or :doc:`fix npt/uef <fix_nh_uef>` is used.
Only the atomic coordinates and frame-invariant scalar quantities
will be in the flow frame. If velocities are selected
as output, for example, they will not be in the same
reference frame as the atomic positions.
@ -43,7 +42,8 @@ Restrictions
""""""""""""
This fix is part of the UEF package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
was built with that package. See the :doc:`Build package <Build_package>`
page for more info.
This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>`
or :doc:`fix npt/uef <fix_nh_uef>` is active.

105
doc/src/dump_image.rst
View File

@ -12,7 +12,7 @@ dump movie command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dump ID group-ID style N file color diameter keyword value ...
@ -28,7 +28,7 @@ Syntax
.. parsed-literal::
*atom* = yes/no = do or do not draw atoms
*atom* = *yes* or *no* = do or do not draw atoms
*adiam* size = numeric value for atom diameter (distance units)
*bond* values = color width = color and width of bonds
color = *atom* or *type* or *none*
@ -68,21 +68,20 @@ Syntax
*box* values = yes/no diam = draw outline of simulation box
yes/no = do or do not draw simulation box lines
diam = diameter of box lines as fraction of shortest box length
*axes* values = yes/no length diam = draw xyz axes
yes/no = do or do not draw xyz axes lines next to simulation box
*axes* values = axes length diam = draw xyz axes
axes = *yes* or *no = do or do not draw xyz axes lines next to simulation box
length = length of axes lines as fraction of respective box lengths
diam = diameter of axes lines as fraction of shortest box length
*subbox* values = yes/no diam = draw outline of processor sub-domains
yes/no = do or do not draw sub-domain lines
*subbox* values = lines diam = draw outline of processor sub-domains
lines = *yes* or *no* = do or do not draw sub-domain lines
diam = diameter of sub-domain lines as fraction of shortest box length
*shiny* value = sfactor = shinyness of spheres and cylinders
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
*ssao* value = yes/no seed dfactor = SSAO depth shading
yes/no = turn depth shading on/off
*ssao* value = shading seed dfactor = SSAO depth shading
shading = *yes* or *no* = turn depth shading on/off
seed = random # seed (positive integer)
dfactor = strength of shading from 0.0 to 1.0
.. _dump_modify_image:
dump_modify options for dump image/movie
@ -162,7 +161,7 @@ Examples
Description
"""""""""""
Dump a high-quality rendered image of the atom configuration every N
Dump a high-quality rendered image of the atom configuration every :math:`N`
timesteps and save the images either as a sequence of JPEG or PNG or
PPM files, or as a single movie file. The options for this command as
well as the :doc:`dump_modify <dump_modify>` command control what is
@ -179,7 +178,7 @@ has been run, using the :doc:`rerun <rerun>` command to read snapshots
from an existing dump file, and using these dump commands in the rerun
script to generate the images/movie.
Here are two sample images, rendered as 1024x1024 JPEG files.
Here are two sample images, rendered as :math:`1024\times 1024` JPEG files.
.. |dump1| image:: img/dump1.jpg
:width: 48%
@ -197,8 +196,8 @@ Only atoms in the specified group are rendered in the image. The
alter what atoms are included in the image.
The filename suffix determines whether a JPEG, PNG, or PPM file is
created with the *image* dump style. If the suffix is ".jpg" or
".jpeg", then a `JPEG format <jpeg_format_>`_ file is created, if the
suffix is ".png", then a `PNG format <png_format_>`_ is created, else
".jpeg," then a `JPEG format <jpeg_format_>`_ file is created, if the
suffix is ".png," then a `PNG format <png_format_>`_ is created, else
a `PPM (aka NETPBM) format <ppm_format_>`_ file is created.
The JPEG and PNG files are binary; PPM has a text mode header followed
by binary data. JPEG images have lossy compression, PNG has lossless
@ -232,22 +231,22 @@ details.
----------
Dumps are performed on timesteps that are a multiple of N (including
Dumps are performed on timesteps that are a multiple of :math:`N` (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
if the current timestep is not a multiple of :math:`N`. This behavior can be
changed via the :doc:`dump_modify first <dump_modify>` command, which
can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
ended on an arbitrary timestep. :math:`N` can be changed between runs by
using the :doc:`dump_modify every <dump_modify>` command.
Dump *image* filenames must contain a wildcard character "\*", so that
Dump *image* filenames must contain a wildcard character "\*" so that
one image file per snapshot is written. The "\*" character is replaced
with the timestep value. For example, tmp.dump.\*.jpg becomes
tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
that the :doc:`dump_modify pad <dump_modify>` command can be used to
insure all timestep numbers are the same length (e.g. 00010), which
insure all timestep numbers are the same length (e.g., 00010), which
can make it easier to convert a series of images into a movie in the
correct ordering.
@ -262,7 +261,7 @@ atoms rendered in the image. They can be any atom attribute defined
for the :doc:`dump custom <dump>` command, including *type* and
*element*\ . This includes per-atom quantities calculated by a
:doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`variable <variable>`,
which are prefixed by "c\_", "f\_", or "v\_" respectively. Note that the
which are prefixed by "c\_," "f\_," or "v\_," respectively. Note that the
*diameter* setting can be overridden with a numeric value applied to
all atoms by the optional *adiam* keyword.
@ -277,7 +276,7 @@ to colors is as follows:
* type 5 = aqua
* type 6 = cyan
and repeats itself for types > 6. This mapping can be changed by the
and repeats itself for types :math:`> 6`. This mapping can be changed by the
"dump_modify acolor" command, as described below.
If *type* is specified for the *diameter* setting then the diameter of
@ -298,18 +297,18 @@ and sizes used by the `AtomEye <atomeye_>`_ visualization package.
If other atom attributes are used for the *color* or *diameter*
settings, they are interpreted in the following way.
If "vx", for example, is used as the *color* setting, then the color
If "vx," for example, is used as the *color* setting, then the color
of the atom will depend on the x-component of its velocity. The
association of a per-atom value with a specific color is determined by
a "color map", which can be specified via the dump_modify command, as
a "color map," which can be specified via the dump_modify command, as
described below. The basic idea is that the atom-attribute will be
within a range of values, and every value within the range is mapped
to a specific color. Depending on how the color map is defined, that
mapping can take place via interpolation so that a value of -3.2 is
halfway between "red" and "blue", or discretely so that the value of
halfway between "red" and "blue," or discretely so that the value of
-3.2 is "orange".
If "vx", for example, is used as the *diameter* setting, then the atom
If "vx," for example, is used as the *diameter* setting, then the atom
will be rendered using the x-component of its velocity as the
diameter. If the per-atom value <= 0.0, them the atom will not be
drawn. Note that finite-size spherical particles, as defined by
@ -773,10 +772,11 @@ the number 5.0 would be used. But for a fractional map, the number
The *delta* setting must be specified for all styles, but is only used
for the sequential style; otherwise the value is ignored. It
specifies the bin size to use within the range for assigning
consecutive colors to. For example, if the range is from -10.0 to
10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
the range. The first will be from -10.0 <= color1 < -9.0, then second
from -9.0 <= color2 < -8.0, etc.
consecutive colors to. For example, if the range is from :math:`-10.0` to
:math:`10.0` and a *delta* of :math:`1.0` is used, then 20 colors will be
assigned to the range. The first will be from
:math:`-10.0 \le \text{color1} < -9.0`, then second from
:math:`-9.0 \le color2 < -8.0`, etc.
The *N* setting is how many entries follow. The format of the entries
depends on whether the color map style is continuous, discrete or
@ -793,13 +793,13 @@ as absolute numbers or as fractions (0.0 to 1.0) of the range,
depending on the "a" or "f" in the style setting for the color map.
Here is how the entries are used to determine the color of an
individual atom, given the value X of its atom attribute. X will fall
between 2 of the entry values. The color of the atom is linearly
interpolated (in each of the RGB values) between the 2 colors
associated with those entries. For example, if X = -5.0 and the 2
surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
atom's color will be halfway between "red" and "blue", which happens
to be "purple".
individual atom, given the value :math:`X` of its atom attribute.
:math:`X` will fall between 2 of the entry values. The color of the atom is
linearly interpolated (in each of the RGB values) between the 2 colors
associated with those entries. For example, if :math:`X = -5.0` and the two
surrounding entries are "red" at :math:`-10.0` and "blue" at :math:`0.0`,
then the atom's color will be halfway between "red" and "blue," which happens
to be "purple."
For discrete color maps, each entry has a *lo* and *hi* value and a
*color*\ . The *lo* and *hi* settings are either numbers within the
@ -864,20 +864,20 @@ The *bcolor* keyword can be used with the dump image command, with its
*bond* keyword, when its color setting is *type*, to set the color
that bonds of each type will be drawn in the image.
The specified *type* should be an integer from 1 to Nbondtypes = the
number of bond types. A wildcard asterisk can be used in place of or
The specified *type* should be an integer from 1 to :math:`N`, where :math:`N`
is the number of bond types. A wildcard asterisk can be used in place of or
in conjunction with the *type* argument to specify a range of bond
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
the number of bond types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
is the number of bond types, then an asterisk with no numerical values
means all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n
(inclusive).
The specified *color* can be a single color which is any of the 140
pre-defined colors (see below) or a color name defined by the
dump_modify color option. Or it can be two or more colors separated
by a "/" character, e.g. red/green/blue. In the former case, that
by a "/" character (e.g., red/green/blue). In the former case, that
color is assigned to all the specified bond types. In the latter
case, the list of colors are assigned in a round-robin fashion to each
of the specified bond types.
@ -885,13 +885,13 @@ of the specified bond types.
----------
The *bdiam* keyword can be used with the dump image command, with its
*bond* keyword, when its diam setting is *type*, to set the diameter
*bond* keyword, when its *diam* setting is *type*, to set the diameter
that bonds of each type will be drawn in the image. The specified
*type* should be an integer from 1 to Nbondtypes. As with the
*bcolor* keyword, a wildcard asterisk can be used as part of the
*type* argument to specify a range of bond types. The specified
*diam* is the size in whatever distance :doc:`units <units>` you are
using, e.g. Angstroms.
using (e.g., Angstroms).
----------
@ -922,7 +922,7 @@ dump_modify color option.
----------
The *color* keyword allows definition of a new color name, in addition
to the 140-predefined colors (see below), and associates 3
to the 140-predefined colors (see below), and associates three
red/green/blue RGB values with that color name. The color name can
then be used with any other dump_modify keyword that takes a color
name as a value. The RGB values should each be floating point values
@ -959,15 +959,15 @@ PNG library.
To write *movie* dumps, you must use the -DLAMMPS_FFMPEG switch when
building LAMMPS and have the FFmpeg executable available on the
machine where LAMMPS is being run. Typically it's name is lowercase,
i.e. ffmpeg.
machine where LAMMPS is being run. Typically its name is lowercase
(i.e., "ffmpeg").
See the :doc:`Build settings <Build_settings>` page for details.
Note that since FFmpeg is run as an external program via a pipe,
LAMMPS has limited control over its execution and no knowledge about
errors and warnings printed by it. Those warnings and error messages
will be printed to the screen only. Due to the way image data is
will be printed to the screen only. Due to the way image data are
communicated to FFmpeg, it will often print the message
.. parsed-literal::
@ -976,7 +976,7 @@ communicated to FFmpeg, it will often print the message
which can be safely ignored. Other warnings
and errors have to be addressed according to the FFmpeg documentation.
One known issue is that certain movie file formats (e.g. MPEG level 1
One known issue is that certain movie file formats (e.g., MPEG level 1
and 2 format streams) have video bandwidth limits that can be crossed
when rendering too large of image sizes. Typical warnings look like
this:
@ -987,10 +987,9 @@ this:
[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018
[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018
In this case it is recommended to either reduce the size of the image
or encode in a different format that is also supported by your copy of
FFmpeg, and which does not have this limitation (e.g. .avi, .mkv,
mp4).
In this case it is recommended either to reduce the size of the image
or to encode in a different format that is also supported by your copy of
FFmpeg and which does not have this limitation (e.g., .avi, .mkv, mp4).
Related commands
""""""""""""""""

83
doc/src/dump_modify.rst
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@ -35,10 +35,10 @@ Syntax
*element* args = E1 E2 ... EN, where N = # of atom types
E1,...,EN = element name (e.g., C or Fe or Ga)
*every* arg = N
N = dump every this many timesteps
N = dump on timesteps which are a multiple of N
N can be a variable (see below)
*every/time* arg = Delta
Delta = dump every this interval in simulation time (time units)
Delta = dump once every Delta interval of simulation time (time units)
Delta can be a variable (see below)
*fileper* arg = Np
Np = write one file for every this many processors
@ -176,6 +176,31 @@ extra buffering.
----------
.. versionadded:: 4May2022
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. Using the *scale* or *image* keyword will also
reset all header keywords to their default values.
----------
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
@ -207,13 +232,10 @@ will be accepted.
----------
The *every* keyword can be used with any dump style except the *dcd*
and *xtc* styles. It does two things. It specifies that the interval
between dump snapshots will be set in timesteps, which is the default
if the *every* or *every/time* keywords are not used. See the
*every/time* keyword for how to specify the interval in simulation
time, i.e. in time units of the :doc:`units <units>` command. The
*every* keyword also sets the interval value, which overrides the dump
frequency originally specified by the :doc:`dump <dump>` command.
and *xtc* styles. It specifies that the output of dump snapshots will
now be performed on timesteps which are a multiple of a new :math:`N`
value, This overrides the dump frequency originally specified by the
:doc:`dump <dump>` command.
The *every* keyword can be specified in one of two ways. It can be a
numeric value in which case it must be > 0. Or it can be an
@ -273,6 +295,17 @@ in file tmp.times:
----------
The *every/time* keyword can be used with any dump style except the
*dcd* and *xtc* styles. It changes the frequency of dump snapshots
from being based on the current timestep to being determined by
elapsed simulation time, i.e. in time units of the :doc:`units
<units>` command, and specifies *Delta* for the interval between
snapshots. This can be useful when the timestep size varies during a
simulation run, e.g. by use of the :doc:`fix dt/reset <fix_dt_reset>`
command. The default is to perform output on timesteps which a
multiples of specified timestep value :math:`N`; see the *every*
keyword.
The *every/time* keyword can be used with any dump style except the
*dcd* and *xtc* styles. It does two things. It specifies that the
interval between dump snapshots will be set in simulation time
@ -357,7 +390,7 @@ 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
@ -365,7 +398,7 @@ 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
<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.
@ -380,30 +413,6 @@ performed with dump style *xtc*\ .
----------
.. versionadded:: 4May2022
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*
@ -490,6 +499,8 @@ boundary twice and is really two box lengths to the left of its
current coordinate. Note that for dump style *custom* these various
values can be printed in the dump file by using the appropriate atom
attributes in the dump command itself.
Using this keyword will reset all custom header names set with
*dump_modify colname* to their respective default values.
----------
@ -663,6 +674,8 @@ value of *yes* means atom coords are written in normalized units from
(tilted), then all atom coords will still be between 0.0 and 1.0. A
value of *no* means they are written in absolute distance units
(e.g., :math:`\mathrm{\mathring A}` or :math:`\sigma`).
Using this keyword will reset all custom header names set with
*dump_modify colname* to their respective default values.
----------

13
doc/src/dump_vtk.rst
View File

@ -6,13 +6,13 @@ dump vtk command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dump ID group-ID vtk N file args
* ID = user-assigned name for the dump
* group-ID = ID of the group of atoms to be dumped
* vtk = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
* vtk = style of dump command (other styles such as *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
* N = dump every this many timesteps
* file = name of file to write dump info to
* args = same as arguments for :doc:`dump_style custom <dump>`
@ -28,17 +28,18 @@ Examples
Description
"""""""""""
Dump a snapshot of atom quantities to one or more files every N
Dump a snapshot of atom quantities to one or more files every :math:`N`
timesteps in a format readable by the `VTK visualization toolkit <http://www.vtk.org>`_ or other visualization tools that use it,
e.g. `ParaView <http://www.paraview.org>`_. The timesteps on which dump
such as `ParaView <http://www.paraview.org>`_. The time steps on which dump
output is written can also be controlled by a variable; see the
:doc:`dump_modify every <dump_modify>` command for details.
This dump style is similar to :doc:`dump_style custom <dump>` but uses
the VTK library to write data to VTK simple legacy or XML format
the VTK library to write data to VTK simple legacy or XML format,
depending on the filename extension specified for the dump file. This
can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*,
respectively, for XML format; see the `VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
respectively, for XML format; see the
`VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below), the
:doc:`dump_modify binary <dump_modify>` command allows setting of a

31
doc/src/fix_accelerate_cos.rst
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@ -6,8 +6,7 @@ fix accelerate/cos command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID accelerate value
@ -19,7 +18,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all accelerate/cos 0.02e-5
@ -34,8 +32,8 @@ The acceleration is a periodic function along the z-direction:
a_{x}(z) = A \cos \left(\frac{2 \pi z}{l_{z}}\right)
where :math:`A` is the acceleration amplitude, :math:`l_z` is the z-length
of the simulation box.
where :math:`A` is the acceleration amplitude, :math:`l_z` is the
:math:`z`-length of the simulation box.
At steady state, the acceleration generates a velocity profile:
.. math::
@ -49,17 +47,18 @@ shear viscosity :math:`\eta` by:
V = \frac{A \rho}{\eta}\left(\frac{l_{z}}{2 \pi}\right)^{2}
and it can be obtained from ensemble average of the velocity profile:
.. math::
V = \frac{\sum_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum_i m_{i}}
V = \frac{\sum\limits_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum\limits_i m_{i}},
where :math:`m_i`, :math:`v_{i,x}` and :math:`z_i` are the mass,
x-component velocity and z coordinate of a particle.
where :math:`m_i`, :math:`v_{i,x}`, and :math:`z_i` are the mass,
:math:`x`-component velocity, and :math:`z`-coordinate of a particle,
respectively.
The velocity amplitude :math:`V` can be calculated with :doc:`compute viscosity/cos <compute_viscosity_cos>`,
The velocity amplitude :math:`V` can be calculated with
:doc:`compute viscosity/cos <compute_viscosity_cos>`,
which enables viscosity calculation with periodic perturbation method,
as described by :ref:`Hess<Hess2>`.
Because the applied acceleration drives the system away from equilibration,
@ -79,15 +78,17 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files.
None of the fix_modify options are relevant to this fix.
No global or per-atom quantities are stored by this fix for access by various output commands.
No parameter of this fix can be used with the start/stop keywords of the run command.
No global or per-atom quantities are stored by this fix for access by various
output commands. No parameter of this fix can be used with the start/stop
keywords of the run command.
This fix is not invoked during energy minimization.
Restrictions
""""""""""""
This command is only available when LAMMPS was built with the MISC package.
Since this fix depends on the z-coordinate of atoms, it cannot be used in 2d simulations.
Since this fix depends on the :math:`z`-coordinate of atoms, it cannot be used
in 2d simulations.
Related commands
""""""""""""""""
@ -96,10 +97,10 @@ Related commands
Default
"""""""
none
none
----------
.. _Hess2:
**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
**(Hess)** Hess, B. Journal of Chemical Physics 2002, 116 (1), 209--217.

13
doc/src/fix_acks2_reaxff.rst
View File

@ -9,7 +9,7 @@ Accelerator Variants: *acks2/reaxff/kk*
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID acks2/reaxff Nevery cutlo cuthi tolerance params args
@ -37,10 +37,10 @@ Examples
Description
"""""""""""
Perform the atom-condensed Kohn-Sham DFT to second order (ACKS2) charge
Perform the atom-condensed Kohn--Sham DFT to second order (ACKS2) charge
equilibration method as described in :ref:`(Verstraelen) <Verstraelen>`.
ACKS2 impedes unphysical long-range charge transfer sometimes seen with
QEq (e.g. for dissociation of molecules), at increased computational
QEq (e.g., for dissociation of molecules), at increased computational
cost. It is typically used in conjunction with the ReaxFF force field
model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
command, but it can be used with any potential in LAMMPS, so long as it
@ -71,7 +71,8 @@ potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the
bond cutoff distance. Note that these 4 quantities are also in the
ReaxFF potential file, except that eta is defined here as twice the eta
value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
of this fix are hard-coded to be A, eV, and electronic charge.
of this fix are hard-coded to be :math:`\mathrm{\mathring{A}}`, eV, and
electronic charge.
The optional *maxiter* keyword allows changing the max number
of iterations in the linear solver. The default value is 200.
@ -110,7 +111,7 @@ LAMMPS was built with that package. See the :doc:`Build package
This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions less than 10 angstroms.
periodic cell dimensions less than :math:`10~\mathrm{\mathring{A}}`.
This fix may be used in combination with :doc:`fix efield <fix_efield>`
and will apply the external electric field during charge equilibration,
@ -132,7 +133,7 @@ maxiter 200
.. _O'Hearn:
**(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1-C22 (2020).
**(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1--C22 (2020).
.. _Verstraelen:

159
doc/src/fix_adapt.rst
View File

@ -6,7 +6,7 @@ fix adapt command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID adapt N attribute args ... keyword value ...
@ -19,24 +19,24 @@ Syntax
.. parsed-literal::
*pair* args = pstyle pparam I J v_name
pstyle = pair style name, e.g. lj/cut
pstyle = pair style name (e.g., lj/cut)
pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for
v_name = variable with name that calculates value of pparam
*bond* args = bstyle bparam I v_name
bstyle = bond style name, e.g. harmonic
bstyle = bond style name (e.g., harmonic)
bparam = parameter to adapt over time
I = type bond to set parameter for
v_name = variable with name that calculates value of bparam
*angle* args = astyle aparam I v_name
astyle = angle style name, e.g. harmonic
astyle = angle style name (e.g., harmonic)
aparam = parameter to adapt over time
I = type angle to set parameter for
v_name = variable with name that calculates value of aparam
*kspace* arg = v_name
v_name = variable with name that calculates scale factor on K-space terms
v_name = variable with name that calculates scale factor on :math:`k`-space terms
*atom* args = atomparam v_name
atomparam = parameter to adapt over time
atomparam = *charge* or *diameter* or *diameter/disc* = parameter to adapt over time
v_name = variable with name that calculates value of atomparam
* zero or more keyword/value pairs may be appended
@ -44,15 +44,15 @@ Syntax
.. parsed-literal::
*scale* value = *no* or *yes*
*no* = the variable value is the new setting
*yes* = the variable value multiplies the original setting
*reset* value = *no* or *yes*
*no* = values will remain altered at the end of a run
*yes* = reset altered values to their original values at the end of a run
*mass* value = *no* or *yes*
*no* = mass is not altered by changes in diameter
*yes* = mass is altered by changes in diameter
*scale* value = *no* or *yes*
*no* = the variable value is the new setting
*yes* = the variable value multiplies the original setting
*reset* value = *no* or *yes*
*no* = values will remain altered at the end of a run
*yes* = reset altered values to their original values at the end of a run
*mass* value = *no* or *yes*
*no* = mass is not altered by changes in diameter
*yes* = mass is altered by changes in diameter
Examples
""""""""
@ -70,22 +70,22 @@ Examples
Description
"""""""""""
Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs. Pair potential and K-space and atom
attributes which can be varied by this fix are discussed below. Many
other fixes can also be used to time-vary simulation parameters,
e.g. the "fix deform" command will change the simulation box
size/shape and the "fix move" command will change atom positions and
velocities in a prescribed manner. Also note that many commands allow
variables as arguments for specific parameters, if described in that
Change or adapt one or more specific simulation attributes or settings over
time as a simulation runs. Pair potential and :math:`k`-space and atom
attributes which can be varied by this fix are discussed below. Many other
fixes can also be used to time-vary simulation parameters (e.g., the
:doc:`fix deform <fix_deform>` command will change the simulation box
size/shape and the :doc:`fix move <fix_move>` command will change atom
positions and velocities in a prescribed manner). Also note that many commands
allow variables as arguments for specific parameters, if described in that
manner on their doc pages. An equal-style variable can calculate a
time-dependent quantity, so this is another way to vary a simulation
parameter over time.
time-dependent quantity, so this is another way to vary a simulation parameter
over time.
If *N* is specified as 0, the specified attributes are only changed
If :math:`N` is specified as 0, the specified attributes are only changed
once, before the simulation begins. This is all that is needed if the
associated variables are not time-dependent. If *N* > 0, then changes
are made every *N* steps during the simulation, presumably with a
associated variables are not time-dependent. If :math:`N > 0`, then changes
are made every :math:`N` steps during the simulation, presumably with a
variable that is time-dependent.
Depending on the value of the *reset* keyword, attributes changed by
@ -98,9 +98,9 @@ If the *scale* keyword is set to *no*, which is the default, then
the value of the altered parameter will be whatever the variable
generates. If the *scale* keyword is set to *yes*, then the value
of the altered parameter will be the initial value of that parameter
multiplied by whatever the variable generates. I.e. the variable is
multiplied by whatever the variable generates (i.e., the variable is
now a "scale factor" applied in (presumably) a time-varying fashion to
the parameter.
the parameter).
Note that whether scale is *no* or *yes*, internally, the parameters
themselves are actually altered by this fix. Make sure you use the
@ -120,9 +120,9 @@ The *pstyle* argument is the name of the pair style. If
:doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
*pstyle* should be a sub-style name. If there are multiple
sub-styles using the same pair style, then *pstyle* should be specified
as "style:N" where N is which instance of the pair style you wish to
adapt, e.g. the first, second, etc. For example, *pstyle* could be
specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2". The
as "style:N", where :math:`N` is which instance of the pair style you wish to
adapt (e.g., the first or second). For example, *pstyle* could be
specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2." The
*pparam* argument is the name of the parameter to change. This is the
current list of pair styles and parameters that can be varied by this
fix. See the doc pages for individual pair styles and their energy
@ -216,45 +216,46 @@ formulas for the meaning of these parameters:
to this list. All it typically takes is adding an extract() method to
the pair\_\*.cpp file associated with the potential.
Some parameters are global settings for the pair style, e.g. the
viscosity setting "mu" for :doc:`pair_style lubricate <pair_lubricate>`.
Other parameters apply to atom type pairs within the pair style,
e.g. the prefactor "a" for :doc:`pair_style soft <pair_soft>`.
Some parameters are global settings for the pair style (e.g., the
viscosity setting "mu" for :doc:`pair_style lubricate <pair_lubricate>`).
Other parameters apply to atom type pairs within the pair style (e.g., the
prefactor :math:`a` for :doc:`pair_style soft <pair_soft>`).
Note that for many of the potentials, the parameter that can be varied
is effectively a prefactor on the entire energy expression for the
potential, e.g. the lj/cut epsilon. The parameters listed as "scale"
potential (e.g., the lj/cut epsilon). The parameters listed as "scale"
are exactly that, since the energy expression for the
:doc:`coul/cut <pair_coul>` potential (for example) has no labeled
prefactor in its formula. To apply an effective prefactor to some
potentials, multiple parameters need to be altered. For example, the
:doc:`Buckingham potential <pair_buck>` needs both the A and C terms
altered together. To scale the Buckingham potential, you should thus
list the pair style twice, once for A and once for C.
:doc:`Buckingham potential <pair_buck>` needs both the :math:`A` and
:math:`C` terms altered together. To scale the Buckingham potential, you
should thus list the pair style twice, once for :math:`A` and once for
:math:`C`.
If a type pair parameter is specified, the *I* and *J* settings should
be specified to indicate which type pairs to apply it to. If a global
parameter is specified, the *I* and *J* settings still need to be
If a type pair parameter is specified, the :math:`I` and :math:`J` settings
should be specified to indicate which type pairs to apply it to. If a global
parameter is specified, the :math:`I` and :math:`J` settings still need to be
specified, but are ignored.
Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the first example above. I <= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values.
Similar to the :doc:`pair_coeff command <pair_coeff>`, :math:`I` and :math:`J`
can be specified in one of two ways. Explicit numeric values can be used for
each, as in the first example above. :math:`I \le J` is required. LAMMPS sets
the coefficients for the symmetric :math:`J,I` interaction to the same values.
A wild-card asterisk can be used in place of or in conjunction with
the I,J arguments to set the coefficients for multiple pairs of atom
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
the number of atom types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
is the number of atom types, then an asterisk with no numeric values
means all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I <= J are considered; if
asterisks imply type pairs where J < I, they are ignored.
(inclusive). Note that only type pairs with :math:`I \le J` are considered; if
asterisks imply type pairs where :math:`J < I`, they are ignored.
IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
IMPORTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
<pair_hybrid>` is being used, then the *pstyle* will be a sub-style
name. You must specify I,J arguments that correspond to type pair
name. You must specify :math:`I,J` arguments that correspond to type pair
values defined (via the :doc:`pair_coeff <pair_coeff>` command) for
that sub-style.
@ -289,12 +290,11 @@ given bond type is adapted.
A wild-card asterisk can be used in place of or in conjunction with
the bond type argument to set the coefficients for multiple bond
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
the number of bond types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
is the number of bond types, then an asterisk with no numeric values
means all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n (inclusive).
Currently *bond* does not support bond_style hybrid nor bond_style
hybrid/overlay as bond styles. The bond styles that currently work
@ -325,12 +325,11 @@ given angle type is adapted.
A wild-card asterisk can be used in place of or in conjunction with
the angle type argument to set the coefficients for multiple angle
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
the number of angle types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
is the number of angle types, then an asterisk with no numeric values
means all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n (inclusive).
Currently *angle* does not support angle_style hybrid nor angle_style
hybrid/overlay as angle styles. The angle styles that currently work
@ -348,7 +347,7 @@ this fix uses to reset theta0 needs to generate values in radians.
----------
The *kspace* keyword used the specified variable as a scale factor on
the energy, forces, virial calculated by whatever K-Space solver is
the energy, forces, virial calculated by whatever :math:`k`-space solver is
defined by the :doc:`kspace_style <kspace_style>` command. If the
variable has a value of 1.0, then the solver is unaltered.
@ -373,17 +372,17 @@ with equal-style variables. The new value is assigned to the
corresponding attribute for all atoms in the fix group.
If the atom parameter is *diameter* and per-atom density and per-atom
mass are defined for particles (e.g. :doc:`atom_style granular
mass are defined for particles (e.g., :doc:`atom_style granular
<atom_style>`), then the mass of each particle is, by default, also
changed when the diameter changes. The mass is set from the particle
volume for 3d systems (density is assumed to stay constant). For 2d,
the default is for LAMMPS to model particles with a radius attribute
as spheres. However, if the atom parameter is *diameter/disc*, then the
mass is set from the particle area (the density is assumed to be in
mass/distance^2 units). The mass of the particle may also be kept constant
if the *mass* keyword is set to *no*. This can be useful to account for
diameter changes that do not involve mass changes, e.g., thermal expansion.
mass/distance\ :math:`^2` units). The mass of the particle may also be kept
constant if the *mass* keyword is set to *no*. This can be useful to account
for diameter changes that do not involve mass changes (e.g., thermal
expansion).
For example, these commands would shrink the diameter of all granular
particles in the "center" group from 1.0 to 0.1 in a linear fashion
@ -405,11 +404,11 @@ their original values at the end of the last restarted run.
Note that all the parameters changed by this fix are written into a
restart file in their current changed state. A new restarted
simulation does not know their original time=0 values, unless the
simulation does not know the original time=0 values, unless the
input script explicitly resets the parameters (after the restart file
is read), to their original values.
is read) to the original values.
Also note, that the time-dependent variable(s) used in the restart
Also note that the time-dependent variable(s) used in the restart
script should typically be written as a function of time elapsed since
the original simulation began.
@ -430,8 +429,8 @@ the one used in the original script.
In a restarted run, if the *reset* keyword is set to *yes*, and the
run ends in this script (as opposed to just writing more restart
files, parameters will be restored to the values they were at the
beginning of the run command in the restart script. Which as
files), parameters will be restored to the values they were at the
beginning of the run command in the restart script, which as
explained above, may or may not be the original values of the
parameters. Again, an exception is if the *atom* keyword is being
used with *reset yes* (in all the runs). In that case, the original

67
doc/src/fix_adapt_fep.rst
View File

@ -6,7 +6,7 @@ fix adapt/fep command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID adapt/fep N attribute args ... keyword value ...
@ -19,7 +19,7 @@ Syntax
.. parsed-literal::
*pair* args = pstyle pparam I J v_name
pstyle = pair style name, e.g. lj/cut
pstyle = pair style name (e.g., lj/cut)
pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for
v_name = variable with name that calculates value of pparam
@ -66,12 +66,12 @@ Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs.
This is an enhanced version of the :doc:`fix adapt <fix_adapt>` command
with two differences,
with two differences:
* It is possible to modify the charges of chosen atom types only,
instead of scaling all the charges in the system.
* There is a new option *after* for better compatibility with "fix
ave/time".
* There is a new option *after* for better compatibility with
:doc:`fix ave/time <fix_ave_time>`.
This version is suited for free energy calculations using
:doc:`compute ti <compute_ti>` or :doc:`compute fep <compute_fep>`.
@ -92,8 +92,8 @@ If the *scale* keyword is set to *no*, then the value the parameter is
set to will be whatever the variable generates. If the *scale*
keyword is set to *yes*, then the value of the altered parameter will
be the initial value of that parameter multiplied by whatever the
variable generates. I.e. the variable is now a "scale factor" applied
in (presumably) a time-varying fashion to the parameter. Internally,
variable generates (i.e., the variable is now a "scale factor" applied
in (presumably) a time-varying fashion to the parameter). Internally,
the parameters themselves are actually altered; make sure you use the
*reset yes* option if you want the parameters to be restored to their
initial values after the run.
@ -115,7 +115,7 @@ overrides the parameters.
The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
a sub-style name. For example, *pstyle* could be specified as "soft"
or "lubricate". The *pparam* argument is the name of the parameter to
or "lubricate." The *pparam* argument is the name of the parameter to
change. This is the current list of pair styles and parameters that
can be varied by this fix. See the doc pages for individual pair
styles and their energy formulas for the meaning of these parameters:
@ -188,7 +188,7 @@ styles and their energy formulas for the meaning of these parameters:
Note that for many of the potentials, the parameter that can be varied
is effectively a prefactor on the entire energy expression for the
potential, e.g. the lj/cut epsilon. The parameters listed as "scale"
potential (e.g., the lj/cut epsilon). The parameters listed as "scale"
are exactly that, since the energy expression for the
:doc:`coul/cut <pair_coul>` potential (for example) has no labeled
prefactor in its formula. To apply an effective prefactor to some
@ -204,23 +204,23 @@ specified, but are ignored.
Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the first example above. I <= J is required. LAMMPS sets
each, as in the first example above. :math:`I \le J` is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values.
A wild-card asterisk can be used in place of or in conjunction with
the I,J arguments to set the coefficients for multiple pairs of atom
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N` is
the number of atom types, then an asterisk with no numeric values means
all types from 1 to :math:`N`. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from m to :math:`N`
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I <= J are considered; if
asterisks imply type pairs where J < I, they are ignored.
(inclusive). Note that only type pairs with :math:`I \le J` are considered; if
asterisks imply type pairs where :math:`J < I`, they are ignored.
IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is being used, then the *pstyle* will
be a sub-style name. You must specify I,J arguments that correspond
to type pair values defined (via the :doc:`pair_coeff <pair_coeff>`
command) for that sub-style.
IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is
being used, then the *pstyle* will be a sub-style name. You must specify
:math:`I,J` arguments that correspond to type pair values defined (via the
:doc:`pair_coeff <pair_coeff>` command) for that sub-style.
The *v_name* argument for keyword *pair* is the name of an
:doc:`equal-style variable <variable>` which will be evaluated each time
@ -232,8 +232,7 @@ simulation box parameters and timestep and elapsed time. Thus it is
easy to specify parameters that change as a function of time or span
consecutive runs in a continuous fashion. For the latter, see the
*start* and *stop* keywords of the :doc:`run <run>` command and the
*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for
details.
*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for details.
For example, these commands would change the prefactor coefficient of
the :doc:`pair_style soft <pair_soft>` potential from 10.0 to 30.0 in a
@ -247,7 +246,7 @@ linear fashion over the course of a simulation:
----------
The *kspace* keyword used the specified variable as a scale factor on
the energy, forces, virial calculated by whatever K-Space solver is
the energy, forces, virial calculated by whatever :math:`k`-space solver is
defined by the :doc:`kspace_style <kspace_style>` command. If the
variable has a value of 1.0, then the solver is unaltered.
@ -263,8 +262,8 @@ current list of atom parameters that can be varied by this fix:
* charge = charge on particle
* diameter = diameter of particle
The *I* argument indicates which atom types are affected. A wild-card
asterisk can be used in place of or in conjunction with the I argument
The :math:`I` argument indicates which atom types are affected. A wild-card
asterisk can be used in place of or in conjunction with the :math:`I` argument
to set the coefficients for multiple atom types.
The *v_name* argument of the *atom* keyword is the name of an
@ -276,9 +275,9 @@ variables. The new value is assigned to the corresponding attribute
for all atoms in the fix group.
If the atom parameter is *diameter* and per-atom density and per-atom
mass are defined for particles (e.g. :doc:`atom_style granular <atom_style>`), then the mass of each particle is also
changed when the diameter changes (density is assumed to stay
constant).
mass are defined for particles (e.g., :doc:`atom_style granular <atom_style>`),
then the mass of each particle is also changed when the diameter changes
(density is assumed to stay constant).
For example, these commands would shrink the diameter of all granular
particles in the "center" group from 1.0 to 0.1 in a linear fashion
@ -297,11 +296,14 @@ parameters on the outermost rRESPA level.
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
No information about this fix is written to
:doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
@ -310,7 +312,8 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair_style \*/soft <pair_fep_soft>`
:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`,
:doc:`compute ti <compute_ti>`, :doc:`pair_style \*/soft <pair_fep_soft>`
Default
"""""""

62
doc/src/fix_addforce.rst
View File

@ -6,7 +6,7 @@ fix addforce command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID addforce fx fy fz keyword value ...
@ -24,7 +24,7 @@ Syntax
.. parsed-literal::
*every* value = Nevery
Nevery = add force every this many timesteps
Nevery = add force every this many time steps
*region* value = region-ID
region-ID = ID of region atoms must be in to have added force
*energy* value = v_name
@ -42,31 +42,31 @@ Examples
Description
"""""""""""
Add fx,fy,fz to the corresponding component of force for each atom in
the group. This command can be used to give an additional push to
Add :math:`(f_x,f_y,f_z)` to the corresponding component of the force for each
atom in the group. This command can be used to give an additional push to
atoms in a simulation, such as for a simulation of Poiseuille flow in
a channel.
Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style :doc:`variable <variable>`, namely *fx*,
*fy*, *fz*\ . If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value(s) used to determine
the force component.
Any of the three quantities defining the force components, namely :math:`f_x`,
:math:`f_y`, and :math:`f_z`, can be specified as an equal-style or atom-style
:doc:`variable <variable>`. If the value is a variable, it should be specified
as v_name, where name is the variable name. In this case, the variable
will be evaluated each time step, and its value(s) will be used to determine
the force component(s).
Equal-style variables can specify formulas with various mathematical
functions, and include :doc:`thermo_style <thermo_style>` command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent force field.
functions and include :doc:`thermo_style <thermo_style>` command
keywords for the simulation box parameters, time step, and elapsed time.
Thus, it is easy to specify a time-dependent force field.
Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus it is easy to specify a spatially-dependent force
coordinates. Thus, it is easy to specify a spatially-dependent force
field with optional time-dependence as well.
If the *every* keyword is used, the *Nevery* setting determines how
often the forces are applied. The default value is 1, for every
timestep.
time step.
If the *region* keyword is used, the atom must also be in the
specified geometric :doc:`region <region>` in order to have force added
@ -83,10 +83,14 @@ potential energy to formulate a self-consistent minimization problem
(see below).
The *energy* keyword is not allowed if the added force is a constant
vector F = (fx,fy,fz), with all components defined as numeric
vector :math:`\vec F = (f_x,f_y,f_z)`, with all components defined as numeric
constants and not as variables. This is because LAMMPS can compute
the energy for each atom directly as E = -x dot F = -(x\*fx + y\*fy +
z\*fz), so that -Grad(E) = F.
the energy for each atom directly as
.. math::
E = -\vec x \cdot \vec F = -(x f_x + y f_y + z f_z),
so that :math:`-\vec\nabla E = \vec F`.
The *energy* keyword is optional if the added force is defined with
one or more variables, and if you are performing dynamics via the
@ -98,16 +102,16 @@ one or more variables, and you are performing energy minimization via
the "minimize" command. The keyword specifies the name of an
atom-style :doc:`variable <variable>` which is used to compute the
energy of each atom as function of its position. Like variables used
for *fx*, *fy*, *fz*, the energy variable is specified as v_name,
where name is the variable name.
for :math:`f_x`, :math:`f_y`, :math:`f_z`, the energy variable is specified as
v_name, where name is the variable name.
Note that when the *energy* keyword is used during an energy
minimization, you must insure that the formula defined for the
atom-style :doc:`variable <variable>` is consistent with the force
variable formulas, i.e. that -Grad(E) = F. For example, if the force
were a spring-like F = kx, then the energy formula should be E =
-0.5kx\^2. If you don't do this correctly, the minimization will not
converge properly.
variable formulas (i.e., that :math:`-\vec\nabla E = \vec F`).
For example, if the force were a spring-like, :math:`\vec F = -k\vec x`, then
the energy formula should be :math:`E = \frac12 kx^2`. If you do not do this
correctly, the minimization will not converge properly.
----------
@ -128,8 +132,8 @@ the global potential energy of the system as part of
this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this
energy is a fictitious quantity but is needed so that the
:doc:`minimize <minimize>` command can include the forces added by
this fix in a consistent manner. I.e. there is a decrease in
potential energy when atoms move in the direction of the added force.
this fix in a consistent manner (i.e., there is a decrease in
potential energy when atoms move in the direction of the added force).
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
@ -144,12 +148,12 @@ 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.
This fix computes a global scalar and a global 3-vector of forces,
This fix computes a global scalar and a global three-vector of forces,
which can be accessed by various :doc:`output commands
<Howto_output>`. The scalar is the potential energy discussed above.
The vector is the total force on the group of atoms before the forces
on individual atoms are changed by the fix. The scalar and vector
values calculated by this fix are "extensive".
values calculated by this fix are "extensive."
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
@ -157,7 +161,7 @@ the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
use with a minimizer, since the minimizer increments the time step as
the iteration count during the minimization.
.. note::

21
doc/src/fix_addtorque.rst
View File

@ -6,7 +6,7 @@ fix addtorque command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID addtorque Tx Ty Tz
@ -30,13 +30,13 @@ Add a set of forces to each atom in
the group such that:
* the components of the total torque applied on the group (around its
center of mass) are Tx,Ty,Tz
center of mass) are :math:`T_x`, :math:`T_y`, and :math:`T_z`
* the group would move as a rigid body in the absence of other
forces.
This command can be used to drive a group of atoms into rotation.
Any of the 3 quantities defining the torque components can be specified
Any of the three quantities defining the torque components can be specified
as an equal-style :doc:`variable <variable>`, namely *Tx*,
*Ty*, *Tz*\ . If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
@ -53,7 +53,8 @@ time. Thus it is easy to specify a time-dependent torque.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No information about this fix is written to
:doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential "energy" inferred by the added torques
@ -62,8 +63,8 @@ to the global potential energy of the system as part of
this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this
is a fictitious quantity but is needed so that the :doc:`minimize
<minimize>` command can include the forces added by this fix in a
consistent manner. I.e. there is a decrease in potential energy when
atoms move in the direction of the added forces.
consistent manner (i.e., there is a decrease in potential energy when
atoms move in the direction of the added forces).
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>`
@ -74,7 +75,7 @@ accessed by various :doc:`output commands <Howto_output>`. The scalar
is the potential energy discussed above. The vector is the total
torque on the group of atoms before the forces on individual atoms are
changed by the fix. The scalar and vector values calculated by this
fix are "extensive".
fix are "extensive."
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
@ -99,9 +100,9 @@ invoked by the :doc:`minimize <minimize>` command.
Restrictions
""""""""""""
This fix is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>` page for
more info.
Related commands
""""""""""""""""

10
doc/src/fix_amoeba_bitorsion.rst
View File

@ -6,7 +6,7 @@ fix amoeba/bitorsion command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID ameoba/bitorsion filename
@ -55,8 +55,8 @@ should have a line like this in its header section:
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
where :math:`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 :math:`N`
lines:
.. parsed-literal::
@ -68,7 +68,7 @@ lines:
[...]
N 3 314 315 317 318 330
The first column is an index from 1 to N to enumerate the bitorsion
The first column is an index from 1 to :math:`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
@ -124,7 +124,7 @@ 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".
"extensive."
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

38
doc/src/fix_amoeba_pitorsion.rst
View File

@ -6,7 +6,7 @@ fix amoeba/pitorsion command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID ameoba/pitorsion
@ -29,14 +29,16 @@ 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.
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.
to 6-tuples of atoms :math:`IJKLMN` that have a bond between atoms
:math:`K` and :math:`L`, where both :math:`K` and :math:`L` are additionally
bonded to exactly two other atoms. Namely, :math:`K` is also bonded to
:math:`I` and :math:`J`, and :math:`L` is also bonded to :math:`M` and
:math:`N`.
The examples/amoeba directory has a sample input script and data file
for ubiquitin, which illustrates use of the fix amoeba/pitorsion
@ -47,7 +49,7 @@ 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
topology data for bonds, angles, dihedrals, etc. Specifically, it
should have two lines like these in its header section:
.. parsed-literal::
@ -55,9 +57,9 @@ should have two lines like these in its header section:
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:
where :math:`N` is the number of pitorsion 5-body interactions and :math:`M` is
the number of pitorsion types. It should also have two sections in the body
of the data file like these with :math:`M` and :math:`N` lines each:
.. parsed-literal::
@ -77,11 +79,11 @@ of the data file like these with M and N lines each:
[...]
N 3 314 315 317 318 330
For PiTorsion Coeffs, the first column is an index from 1 to M to
For PiTorsion Coeffs, the first column is an index from 1 to :math:`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
For PiTorsions, the first column is an index from 1 to :math:`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
@ -90,8 +92,8 @@ atoms in the two 4-atom dihedrals that overlap to create the pitorsion
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 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
@ -136,7 +138,7 @@ 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".
"extensive."
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
@ -161,8 +163,8 @@ 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.
: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.

17
doc/src/fix_append_atoms.rst
View File

@ -6,7 +6,7 @@ fix append/atoms command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID append/atoms face ... keyword value ...
@ -66,7 +66,7 @@ specific basis atoms as they are created. See the
defined for the unit cell of the lattice. By default, all created
atoms are assigned type = 1 unless this keyword specifies differently.
The *size* keyword defines the size in z of the chunk of material to
The *size* keyword defines the size in :math:`z` of the chunk of material to
be added.
The *random* keyword will give the atoms random displacements around
@ -79,7 +79,8 @@ measured from zhi and is set with the *extent* argument.
The *units* keyword determines the meaning of the distance units used
to define a wall position, but only when a numeric constant is used.
A *box* value selects standard distance units as defined by the
:doc:`units <units>` command, e.g. Angstroms for units = real or metal.
:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}`
for units = real or metal.
A *lattice* value means the distance units are in lattice spacings.
The :doc:`lattice <lattice>` command must have been previously used to
define the lattice spacings.
@ -89,17 +90,21 @@ define the lattice spacings.
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
No information about this fix is written to
:doc:`binary restart files <restart>`. None of the
:doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix style is part of the SHOCK package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
The boundary on which atoms are added with append/atoms must be
shrink/minimum. The opposite boundary may be any boundary type other

20
doc/src/fix_atc.rst
View File

@ -6,7 +6,7 @@ fix atc command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix <fixID> <group> atc <type> <parameter_file>
@ -40,8 +40,8 @@ This fix is the beginning to creating a coupled FE/MD simulation and/or
an on-the-fly estimation of continuum fields. The coupled versions of
this fix do Verlet integration and the post-processing does not. After
instantiating this fix, several other fix_modify commands will be
needed to set up the problem, e.g. define the finite element mesh and
prescribe initial and boundary conditions.
needed to set up the problem (i.e., define the finite element mesh and
prescribe initial and boundary conditions).
.. image:: JPG/atc_nanotube.jpg
:align: center
@ -135,7 +135,7 @@ fix are listed below.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the energy
discussed in the previous paragraph. The scalar value is "extensive".
discussed in the previous paragraph. The scalar value is "extensive."
No parameter of this fix can be used with the
*start/stop* keywords of the :doc:`run <run>` command. This fix is not
@ -147,7 +147,7 @@ Restrictions
Thermal and two_temperature (coupling) types use a Verlet
time-integration algorithm. The hardy type does not contain its own
time-integrator and must be used with a separate fix that does contain
one, e.g. nve, nvt, etc. In addition, currently:
one (e.g., nve, nvt). In addition, currently:
* the coupling is restricted to thermal physics
* the FE computations are done in serial on each processor.
@ -159,8 +159,8 @@ Related commands
After specifying this fix in your input script, several
:doc:`fix_modify AtC <fix_modify>` commands are used to setup the
problem, e.g. define the finite element mesh and prescribe initial and
boundary conditions. Each of these options has its own doc page.
problem (e.g., define the finite element mesh and prescribe initial and
boundary conditions). Each of these options has its own doc page.
*fix_modify* commands for setup:
@ -311,6 +311,6 @@ and Computation (2011), 7:1736.
as a field variable from molecular dynamics simulations." Journal of
Chemical Physics (2013), 139:054115.
Please refer to the standard finite element (FE) texts, e.g. T.J.R
Hughes " The finite element method ", Dover 2003, for the basics of FE
simulation.
Please refer to the standard finite element (FE) texts (e.g., T.J.R.
Hughes, *The Finite Element Method,* Dover 2003) for the basics of FE
simulations.

25
doc/src/fix_atom_swap.rst
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@ -6,7 +6,7 @@ fix atom/swap command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID atom/swap N X seed T keyword values ...
@ -45,10 +45,10 @@ Description
"""""""""""
This fix performs Monte Carlo swaps of atoms of one given atom type
with atoms of the other given atom types. The specified T is used in
with atoms of the other given atom types. The specified :math:`T` is used in
the Metropolis criterion dictating swap probabilities.
Perform X swaps of atoms of one type with atoms of another type
Perform :math:`X` swaps of atoms of one type with atoms of another type
according to a Monte Carlo probability. Swap candidates must be in the
fix group, must be in the region (if specified), and must be of one of
the listed types. Swaps are attempted between candidates that are
@ -57,7 +57,7 @@ atoms. Swaps are not attempted between atoms of the same type since
nothing would happen.
All atoms in the simulation domain can be moved using regular time
integration displacements, e.g. via :doc:`fix nvt <fix_nh>`, resulting
integration displacements (e.g., via :doc:`fix nvt <fix_nh>`), resulting
in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
be needed when running such a hybrid simulation, especially if the
swapped atoms are not well equilibrated.
@ -83,9 +83,8 @@ canonical ensemble, the composition of the system can change. Note
that when using *semi-grand*, atoms in the fix group whose type is not
listed in the *types* keyword are ineligible for attempted
conversion. An attempt is made to switch the selected atom (if
eligible) to one of the other listed types with equal
probability. Acceptance of each attempt depends upon the Metropolis
criterion.
eligible) to one of the other listed types with equal probability.
Acceptance of each attempt depends upon the Metropolis criterion.
The *mu* keyword allows users to specify chemical potentials. This is
required and allowed only when using *semi-grand*\ . All chemical
@ -97,8 +96,8 @@ amount will have no effect on the simulation.
This command may optionally use the *region* keyword to define swap
volume. The specified region must have been previously defined with a
:doc:`region <region>` command. It must be defined with side = *in*\
. Swap attempts occur only between atoms that are both within the
:doc:`region <region>` command. It must be defined with side = *in*\ .
Swap attempts occur only between atoms that are both within the
specified region. Swaps are not otherwise attempted.
You should ensure you do not swap atoms belonging to a molecule, or
@ -123,7 +122,7 @@ Since this fix computes total potential energies before and after
proposed swaps, so even complicated potential energy calculations are
OK, including the following:
* long-range electrostatics (kspace)
* long-range electrostatics (:math:`k`-space)
* many body pair styles
* hybrid pair styles
* eam pair styles
@ -137,7 +136,7 @@ include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
<fix_temp_berendsen>`, :doc:`temp/rescale <fix_temp_rescale>`, and
:doc:`wall fixes <fix_wall>`. For that energy to be included in the
total potential energy of the system (the quantity used when
performing GCMC moves), you MUST enable the :doc:`fix_modify
performing GCMC moves), you **must** enable the :doc:`fix_modify
<fix_modify>` *energy* option for that fix. The doc pages for
individual :doc:`fix <fix>` commands specify if this should be done.
@ -147,7 +146,7 @@ Restart, fix_modify, output, run start/stop, minimize info
This fix writes the state of the fix to :doc:`binary restart files
<restart>`. This includes information about the random number
generator seed, the next timestep for MC exchanges, the number of
exchange attempts and successes etc. See the :doc:`read_restart
exchange attempts and successes, etc. 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.
@ -168,7 +167,7 @@ the following global cumulative quantities:
* 1 = swap attempts
* 2 = swap accepts
The vector values calculated by this fix are "extensive".
The vector values calculated by this fix are "extensive."
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during

128
doc/src/fix_ave_atom.rst
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@ -6,7 +6,7 @@ fix ave/atom command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ...
@ -15,8 +15,8 @@ Syntax
* Nevery = use input values every this many timesteps
* Nrepeat = # of times to use input values for calculating averages
* Nfreq = calculate averages every this many timesteps
one or more input values can be listed
* value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name
* one or more input values can be listed
* value = *x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, c_ID, c_ID[i], f_ID, f_ID[i], v_name
.. parsed-literal::
@ -41,7 +41,9 @@ Description
Use one or more per-atom vectors as inputs every few timesteps, and
average them atom by atom over longer timescales. The resulting
per-atom averages can be used by other :doc:`output commands <Howto_output>` such as the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>` commands.
per-atom averages can be used by other :doc:`output commands <Howto_output>`
such as the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>`
commands.
The group specified with the command means only atoms within the group
have their averages computed. Results are set to 0.0 for atoms not in
@ -53,7 +55,8 @@ component) or can be the result of a :doc:`compute <compute>` or
:doc:`variable <variable>`. In the latter cases, the compute, fix, or
variable must produce a per-atom vector, not a global quantity or
local quantity. If you wish to time-average global quantities from a
compute, fix, or variable, then see the :doc:`fix ave/time <fix_ave_time>` command.
compute, fix, or variable, then see the :doc:`fix ave/time <fix_ave_time>`
command.
Each per-atom value of each input vector is averaged independently.
@ -66,18 +69,18 @@ per-atom vectors.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "n\*" or
"m\*n". If N = the size of the vector (for *mode* = scalar) or the
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
"m\*n." If :math:`N` is the size of the vector (for *mode* = scalar) or the
number of columns in the array (for *mode* = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
with no numeric values means all indices from 1 to :math:`N`. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to N (inclusive). A middle asterisk
asterisk means all indices from m to :math:`N` (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 fix ave/atom commands are
had been listed one by one. For example, these two fix ave/atom commands are
equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
command creates a per-atom array with 6 columns:
command creates a per-atom array with six columns:
.. code-block:: LAMMPS
@ -89,61 +92,66 @@ command creates a per-atom array with 6 columns:
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
timesteps the input values will be used in order to contribute to the
average. The final averaged quantities are generated on timesteps
that are a multiple of *Nfreq*\ . The average is over *Nrepeat*
quantities, computed in the preceding portion of the simulation every
*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and
*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps
contributing to the average value cannot overlap,
i.e. Nrepeat\*Nevery can not exceed Nfreq.
The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and :math:`N_\text{freq}`
arguments specify on what timesteps the input values will be used in order to
contribute to the average. The final averaged quantities are generated on
timesteps that are a multiple of :math:`N_\text{freq}`\ . The average is over
:math:`N_\text{repeat}` quantities, computed in the preceding portion of the
simulation every :math:`N_\text{every}` timesteps. :math:`N_\text{freq}` must
be a multiple of :math:`N_\text{every}` and :math:`N_\text{every}` must be
non-zero even if :math:`N_\text{repeat}` is 1. Also, the timesteps
contributing to the average value cannot overlap; that is,
:math:`N_\text{repeat} N_\text{every}` cannot exceed :math:`N_\text{freq}`.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc.
For example, if :math:`N_\text{every}=2`, :math:`N_\text{repeat}=6`, and
:math:`N_\text{freq}=100`, then values on timesteps 90, 92, 94, 96, 98, and 100
will be used to compute the final average on time step 100. Similarly for
timesteps 190, 192, 194, 196, 198, and 200 on time step 200, etc.
----------
The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
an input value from that compute.
The atom attribute values (*x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, and
*fz*) are self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the
:doc:`compute property/atom <compute_property_atom>` command and then
specifying an input value from that compute.
.. note::
The x,y,z attributes are values that are re-wrapped inside the
periodic box whenever an atom crosses a periodic boundary. Thus if
you time average an atom that spends half its time on either side of
The *x*\ , *y*\ , and *z* attributes are values that are re-wrapped inside
the periodic box whenever an atom crosses a periodic boundary. Thus, if
you time-average an atom that spends half of its time on either side of
the periodic box, you will get a value in the middle of the box. If
this is not what you want, consider averaging unwrapped coordinates,
which can be provided by the :doc:`compute property/atom <compute_property_atom>` command via its xu,yu,zu
attributes.
which can be provided by the
:doc:`compute property/atom <compute_property_atom>`
command via its *xu*, *yu*, and *zu* attributes.
If a value begins with "c\_", a compute ID must follow which has been
If a value begins with "c\_," a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the compute is used. If a
bracketed term containing an index I is appended, the Ith column of
the per-atom array calculated by the compute is used. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.
bracketed term containing an index :math:`I` is appended, the
:math:`I^\text{th}` column of the per-atom array calculated by the compute is
used. Users can also write code for their own compute styles and
:doc:`add them to LAMMPS <Modify>`. See the discussion above for how
:math:`I` can be specified with a wildcard asterisk to effectively specify
multiple values.
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the fix is used. If a
bracketed term containing an index I is appended, the Ith column of
the per-atom array calculated by the fix is used. Note that some
fixes only produce their values on certain timesteps, which must be
compatible with *Nevery*, else an error will result. Users can also
write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`. See the discussion above for how I can be
specified with a wildcard asterisk to effectively specify multiple
values.
If a value begins with "f\_," a fix ID must follow which has been previously
defined in the input script. If no bracketed term is appended, the per-atom
vector calculated by the fix is used. If a bracketed term containing an index
:math:`I` is appended, the :math:`I^\text{th}` column of the per-atom array
calculated by the fix is used. Note that some fixes only produce their values
on certain timesteps, which must be compatible with :math:`N_\text{every}`,
else an error will result. Users can also write code for their own fix styles
and :doc:`add them to LAMMPS <Modify>`. See the discussion above for how
:math:`I` can be specified with a wildcard asterisk to effectively specify
multiple values.
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script as an :doc:`atom-style variable <variable>` Variables of style *atom* can reference
thermodynamic keywords, or invoke other computes, fixes, or variables
If a value begins with "v\_," a variable name must follow which has
been previously defined in the input script as an
:doc:`atom-style variable <variable>`. Variables of style *atom* can reference
thermodynamic keywords or invoke other computes, fixes, or variables
when they are evaluated, so this is a very general means of generating
per-atom quantities to time average.
@ -152,19 +160,22 @@ per-atom quantities to time average.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global scalar or vector quantities are
stored by this fix for access by various :doc:`output commands <Howto_output>`.
No information about this fix is written to
:doc:`binary restart files <restart>`. None of the
:doc:`fix_modify <fix_modify>` options are relevant to this fix.
No global scalar or vector quantities are stored by this fix for access by
various :doc:`output commands <Howto_output>`.
This fix produces a per-atom vector or array which can be accessed by
various :doc:`output commands <Howto_output>`. A vector is produced if
only a single quantity is averaged by this fix. If two or more
quantities are averaged, then an array of values is produced. The
per-atom values can only be accessed on timesteps that are multiples
of *Nfreq* since that is when averaging is performed.
of :math:`N_\text{freq}` since that is when averaging is performed.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
@ -173,7 +184,8 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute <compute>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`compute <compute>`, :doc:`fix ave/histo <fix_ave_histo>`,
:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`variable <variable>`,
Default

313
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@ -6,7 +6,7 @@ fix ave/chunk command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID value1 value2 ... keyword args ...
@ -17,7 +17,7 @@ Syntax
* Nfreq = calculate averages every this many timesteps
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
* one or more input values can be listed
* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, mass, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
* value = *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, *density/mass*, *density/number*, *mass*, *temp*, c_ID, c_ID[I], f_ID, f_ID[I], v_name
.. parsed-literal::
@ -145,18 +145,18 @@ Note that for values from a compute or fix that produces a per-atom
array (multiple values per atom), the bracketed index I can be
specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "n\*"
or "m\*n". If N = the size of the vector (for *mode* = scalar) or the
or "m\*n". If :math:`N` = the size of the vector (for *mode* = scalar) or the
number of columns in the array (for *mode* = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
with no numeric values means all indices from 1 to :math:`N`. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to N (inclusive). A middle asterisk
asterisk means all indices from m to :math:`N` (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 fix ave/chunk commands are
had been listed one by one. For example, these two fix ave/chunk commands are
equivalent, since the :doc:`compute property/atom
<compute_property_atom>` command creates, in this case, a per-atom
array with 3 columns:
array with three columns:
.. code-block:: LAMMPS
@ -166,105 +166,109 @@ array with 3 columns:
.. note::
This fix works by creating an array of size *Nchunk* by Nvalues
on each processor. *Nchunk* is the number of chunks which is defined
by the :doc:`compute chunk/atom <compute_chunk_atom>` command.
Nvalues is the number of input values specified. Each processor loops
over its atoms, tallying its values to the appropriate chunk. Then
the entire array is summed across all processors. This means that
using a large number of chunks will incur an overhead in memory and
This fix works by creating an array of size
:math:`N_\text{chunk} \times N_\text{values}` on each processor.
:math:`N_\text{chunk}` is the number of chunks, which is defined by the
:doc:`compute chunk/atom <compute_chunk_atom>` command.
:math:`N_\text{values}` is the number of input values specified.
Each processor loops over its atoms, tallying its values to the appropriate
chunk. Then the entire array is summed across all processors. This means
that using a large number of chunks will incur an overhead in memory and
computational cost (summing across processors), so be careful to
define a reasonable number of chunks.
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
timesteps the input values will be accessed and contribute to the
average. The final averaged quantities are generated on timesteps
that are a multiples of *Nfreq*\ . The average is over *Nrepeat*
quantities, computed in the preceding portion of the simulation every
*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and
*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nrepeat\*Nevery
can not exceed Nfreq.
The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and :math:`N_\text{freq}`
arguments specify on what time steps the input values will be accessed and
contribute to the average. The final averaged quantities are generated on time
steps that are a multiples of :math:`N_\text{freq}`\ . The average is over
:math:`N_\text{repeat}` quantities, computed in the preceding portion of the
simulation every :math:`N_\text{every}` time steps. :math:`N_\text{freq}`
must be a multiple of :math:`N_\text{every}` and :math:`N_\text{every}` must be
non-zero even if :math:`N_\text{repeat} = 1`\ . Also, the time steps
contributing to the average value cannot overlap (i.e.,
:math:`N_\text{repeat}N_\text{every}` cannot exceed :math:`N_\text{freq}`).
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps
100,200,etc.
For example, if :math:`N_\text{every}=2`, :math:`N_\text{repeat}=6`, and
:math:`N_\text{freq}=100`, then values on
time steps 90, 92, 94, 96, 98, 100 will be used to compute the final average
on time step 100. Similarly for time steps 190, 192, 194, 196, 198, 200 on
time step 200, etc. If :math:`N_\text{repeat}=1` and
:math:`N_\text{freq} = 100`, then no time averaging is done; values are simply
generated on time steps 100, 200, etc.
Each input value can also be averaged over the atoms in each chunk.
The way the averaging is done across the *Nrepeat* timesteps to
produce output on the *Nfreq* timesteps, and across multiple *Nfreq*
outputs, is determined by the *norm* and *ave* keyword settings, as
discussed below.
The way the averaging is done across the :math:`N_\text{repeat}` time steps to
produce output on the :math:`N_\text{freq}` time steps, and across multiple
:math:`N_\text{freq}` outputs, is determined by the *norm* and *ave* keyword
settings, as discussed below.
.. note::
To perform per-chunk averaging within a *Nfreq* time window, the
number of chunks *Nchunk* defined by the :doc:`compute chunk/atom
<compute_chunk_atom>` command must remain constant. If the *ave*
keyword is set to *running* or *window* then *Nchunk* must remain
constant for the duration of the simulation. This fix forces the
chunk/atom compute specified by chunkID to hold *Nchunk* constant
for the appropriate time windows, by not allowing it to
re-calculate *Nchunk*, which can also affect how it assigns chunk
IDs to atoms. This is particularly important to understand if the
chunks defined by the :doc:`compute chunk/atom
To perform per-chunk averaging within a :math:`N_\text{freq}` time window,
the number of chunks :math:`N_\text{chunk}` defined by the
:doc:`compute chunk/atom <compute_chunk_atom>` command must remain
constant. If the *ave* keyword is set to *running* or *window* then
:math:`N_\text{chunk}` must remain constant for the duration of the
simulation. This fix forces the chunk/atom compute specified by chunkID to
hold :math:`N_\text{chunk}` constant for the appropriate time windows,
by not allowing it to re-calculate :math:`N_\text{chunk}`, which can also
affect how it assigns chunk IDs to atoms. This is particularly important to
understand if the chunks defined by the :doc:`compute chunk/atom
<compute_chunk_atom>` command are spatial bins. If its *units*
keyword is set to *box* or *lattice*, then the number of bins
*Nchunk* and size of each bin will be fixed over the *Nfreq* time
window, which can affect which atoms are discarded if the
simulation box size changes. If its *units* keyword is set to
*reduced*, then the number of bins *Nchunk* will still be fixed,
but the size of each bin can vary at each timestep if the
simulation box size changes, e.g. for an NPT simulation.
:math:`N_\text{chunk}` and size of each bin will be fixed over the
:math:`N_\text{freq}` time window, which can affect which atoms are
discarded if the simulation box size changes. If its *units* keyword is set
to *reduced*, then the number of bins :math:`N_\text{chunk}` will still be
fixed, but the size of each bin can vary at each time step if the
simulation box size changes (e.g., for an NPT simulation).
----------
The atom attribute values (vx,vy,vz,fx,fy,fz,mass) are
The atom attribute values (*vx*, *vy*, *vz*, *fx*, *fy*, *fz*, *mass*) are
self-explanatory. As noted above, any other atom attributes can be
used as input values to this fix by using the :doc:`compute
property/atom <compute_property_atom>` command and then specifying an
input value from that compute.
The *density/number* value means the number density is computed for
each chunk, i.e. number/volume. The *density/mass* value means the
mass density is computed for each chunk, i.e. total-mass/volume. The
output values are in units of 1/volume or density (mass/volume). See
each chunk (i.e., number/volume). The *density/mass* value means the
mass density is computed for each chunk (i.e., total-mass/volume). The
output values are in units of 1/volume or mass density (mass/volume). See
the :doc:`units <units>` command page for the definition of density
for each choice of units, e.g. gram/cm\^3. If the chunks defined by
for each choice of units (e.g., g/cm\ :math:`^3`). If the chunks defined by
the :doc:`compute chunk/atom <compute_chunk_atom>` command are spatial
bins, the volume is the bin volume. Otherwise it is the volume of the
bins, the volume is the bin volume. Otherwise, it is the volume of the
entire simulation box.
The *temp* value means the temperature is computed for each chunk, by
the formula
The *temp* value means the temperature is computed for each chunk,
by the formula
.. math::
\text{KE} = \frac{\text{DOF}}{2} k_B T,
where KE = total kinetic energy of the chunk of atoms (sum of
:math:`\frac{1}{2} m v^2`), DOF = the total number of degrees of freedom
for all atoms in the chunk, :math:`k_B` = Boltzmann constant, and
:math:`T` = temperature.
where KE is the total kinetic energy of the chunk of atoms (sum of
:math:`\frac{1}{2} m v^2`), DOF is the the total number of degrees of freedom
for all atoms in the chunk, :math:`k_B` is the Boltzmann constant, and
:math:`T` is the absolute temperature.
The DOF is calculated as N\*adof + cdof, where N = number of atoms in
the chunk, adof = degrees of freedom per atom, and cdof = degrees of
freedom per chunk. By default adof = 2 or 3 = dimensionality of
system, as set via the :doc:`dimension <dimension>` command, and cdof =
0.0. This gives the usual formula for temperature.
The DOF is calculated as :math:`N`\ \*adof + cdof, where :math:`N` is the
number of atoms in the chunk, adof is the number of degrees of freedom per
atom, and cdof is the number of degrees of freedom per chunk. By default,
adof = 2 or 3 = dimensionality of system,
as set via the :doc:`dimension <dimension>` command, and cdof = 0.0.
This gives the usual formula for temperature.
Note that currently this temperature only includes translational
degrees of freedom for each atom. No rotational degrees of freedom
are included for finite-size particles. Also no degrees of freedom
are included for finite-size particles. Also, no degrees of freedom
are subtracted for any velocity bias or constraints that are applied,
such as :doc:`compute temp/partial <compute_temp_partial>`, or
:doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`. This is
because those degrees of freedom (e.g. a constrained bond) could apply
such as :doc:`compute temp/partial <compute_temp_partial>`,
:doc:`fix shake <fix_shake>`, or :doc:`fix rigid <fix_rigid>`. This is
because those degrees of freedom (e.g., a constrained bond) could apply
to sets of atoms that are both included and excluded from a specific
chunk, and hence the concept is somewhat ill-defined. In some cases,
you can use the *adof* and *cdof* keywords to adjust the calculated
@ -280,32 +284,32 @@ Note that the per-chunk temperature calculated by this fix and the
different. The compute calculates the temperature for each chunk for
a single snapshot. This fix can do that but can also time average
those values over many snapshots, or it can compute a temperature as
if the atoms in the chunk on different timesteps were collected
if the atoms in the chunk on different time steps were collected
together as one set of atoms to calculate their temperature. The
compute allows the center-of-mass velocity of each chunk to be
subtracted before calculating the temperature; this fix does not.
If a value begins with "c\_", a compute ID must follow which has been
If a value begins with "c\_," a compute ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the compute is used. Users can also write code for
their own compute styles and :doc:`add them to LAMMPS <Modify>`. See
the discussion above for how I can be specified with a wildcard
their own compute styles and :doc:`add them to LAMMPS <Modify>`.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
If a value begins with "f\_", a fix ID must follow which has been
If a value begins with "f\_," a fix ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the fix is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the fix is used. Note that some fixes only produce
their values on certain timesteps, which must be compatible with
*Nevery*, else an error results. Users can also write code for their
own fix styles and :doc:`add them to LAMMPS <Modify>`. See the
their values on certain time steps, which must be compatible with
:math:`N_\text{every}`, else an error results. Users can also write code for
their own fix styles and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
If a value begins with "v\_", a variable name must follow which has
If a value begins with "v\_," a variable name must follow which has
been previously defined in the input script. Variables of style
*atom* can reference thermodynamic keywords and various per-atom
attributes, or invoke other computes, fixes, or variables when they
@ -318,113 +322,113 @@ Additional optional keywords also affect the operation of this fix
and its outputs.
The *norm* keyword affects how averaging is done for the per-chunk
values that are output every *Nfreq* timesteps.
values that are output every :math:`N_\text{freq}` time steps.
It the *norm* setting is *all*, which is the default, a chunk value is
summed over all atoms in all *Nrepeat* samples, as is the count of
It the *norm* setting is *all*, which is the default, a chunk value is summed
over all atoms in all :math:`N_\text{repeat}` samples, as is the count of
atoms in the chunk. The averaged output value for the chunk on the
*Nfreq* timesteps is Total-sum / Total-count. In other words it is an
average over atoms across the entire *Nfreq* timescale. For the
*density/number* and *density/mass* values, the volume (bin volume or
:math:`N_\text{freq}` time steps is Total-sum / Total-count. In other words it
is an average over atoms across the entire :math:`N_\text{freq}` timescale.
For the *density/number* and *density/mass* values, the volume (bin volume or
system volume) used in the final normalization will be the volume at
the final *Nfreq* timestep. For the *temp* values, degrees of freedom
and kinetic energy are summed separately across the entire *Nfreq*
timescale, and the output value is calculated by dividing those two
sums.
the final :math:`N_\text{freq}` time step. For the *temp* values, degrees of
freedom and kinetic energy are summed separately across the entire
:math:`N_\text{freq}` timescale, and the output value is calculated by dividing
those two sums.
If the *norm* setting is *sample*, the chunk value is summed over
atoms for each sample, as is the count, and an "average sample value"
is computed for each sample, i.e. Sample-sum / Sample-count. The
output value for the chunk on the *Nfreq* timesteps is the average of
the *Nrepeat* "average sample values", i.e. the sum of *Nrepeat*
"average sample values" divided by *Nrepeat*\ . In other words it is an
average of an average. For the *density/number* and *density/mass*
values, the volume (bin volume or system volume) used in the
per-sample normalization will be the current volume at each sampling
step.
is computed for each sample (i.e., Sample-sum / Sample-count). The
output value for the chunk on the :math:`N_\text{freq}` time steps is the
average of the :math:`N_\text{repeat}` "average sample values" (i.e., the sum
of :math:`N_\text{repeat}` "average sample values" divided by
:math:`N_\text{repeat}`\ ). In other words, it is an average of an average.
For the *density/number* and *density/mass* values, the volume (bin volume or
system volume) used in the per-sample normalization will be the current volume
at each sampling step.
If the *norm* setting is *none*, a similar computation as for the
*sample* setting is done, except the individual "average sample
values" are "summed sample values". A summed sample value is simply
values" are "summed sample values." A summed sample value is simply
the chunk value summed over atoms in the sample, without dividing by
the number of atoms in the sample. The output value for the chunk on
the *Nfreq* timesteps is the average of the *Nrepeat* "summed sample
values", i.e. the sum of *Nrepeat* "summed sample values" divided by
*Nrepeat*\ . For the *density/number* and *density/mass* values, the
the :math:`N_\text{freq}` timesteps is the average of the
:math:`N_\text{repeat}` "summed sample values" (i.e., the sum of
:math:`N_\text{repeat}` "summed sample values" divided by
:math:`N_\text{repeat}`\ ).
For the *density/number* and *density/mass* values, the
volume (bin volume or system volume) used in the per-sample sum
normalization will be the current volume at each sampling step.
----------
The *ave* keyword determines how the per-chunk values produced every
*Nfreq* steps are averaged with values produced on previous steps that
were multiples of *Nfreq*, before they are accessed by another output
command or written to a file.
:math:`N_\text{freq}` steps are averaged with values produced on previous steps
that were multiples of :math:`N_\text{freq}`, before they are accessed by
another output command or written to a file.
If the *ave* setting is *one*, which is the default, then the chunk
values produced on timesteps that are multiples of *Nfreq* are
independent of each other; they are output as-is without further
averaging.
values produced on timesteps that are multiples of :math:`N_\text{freq}` are
independent of each other; they are output as-is without further averaging.
If the *ave* setting is *running*, then the chunk values produced on
timesteps that are multiples of *Nfreq* are summed and averaged in a
cumulative sense before being output. Each output chunk value is thus
timesteps that are multiples of :math:`N_\text{freq}` are summed and averaged
in a cumulative sense before being output. Each output chunk value is thus
the average of the chunk value produced on that timestep with all
preceding values for the same chunk. This running average begins when
the fix is defined; it can only be restarted by deleting the fix via
the :doc:`unfix <unfix>` command, or re-defining the fix by
re-specifying it.
the :doc:`unfix <unfix>` command, or re-defining the fix by re-specifying it.
If the *ave* setting is *window*, then the chunk values produced on
timesteps that are multiples of *Nfreq* are summed and averaged within
a moving "window" of time, so that the last M values for the same
chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
then the output on step 10000 will be the average of the individual
chunk values on steps 8000,9000,10000. Outputs on early steps will
average over less than M values if they are not available.
timesteps that are multiples of :math:`N_\text{freq}` are summed and averaged
within a moving "window" of time, so that the last :math:`M` values for the
same chunk are used to produce the output. For example, if :math:`M = 3` and
:math:`N_\text{freq} = 1000`, then the output on step 10000 will be the average
of the individual chunk values on time steps 8000, 9000, and 10000. Outputs on
early steps will average over less than :math:`M` values if they are not
available.
----------
The *bias* keyword specifies the ID of a temperature compute that
removes a "bias" velocity from each atom, specified as *bias-ID*\ . It
is only used when the *temp* value is calculated, to compute the
removes a "bias" velocity from each atom, specified as *bias-ID*\ .
It is only used when the *temp* value is calculated, to compute the
thermal temperature of each chunk after the translational kinetic
energy components have been altered in a prescribed way, e.g. to
remove a flow velocity profile. See the doc pages for individual
computes that calculate a temperature to see which ones implement a
bias.
energy components have been altered in a prescribed way (e.g., to
remove a flow velocity profile). See the doc pages for individual
computes that calculate a temperature to see which ones implement a bias.
The *adof* and *cdof* keywords define the values used in the degree of
freedom (DOF) formula described above for temperature calculation
for each chunk. They are only used when the *temp* value is
calculated. They can be used to calculate a more appropriate
temperature for some kinds of chunks. Here are 3 examples:
temperature for some kinds of chunks. Here are three examples:
If spatially binned chunks contain some number of water molecules and
:doc:`fix shake <fix_shake>` is used to make each molecule rigid, then
you could calculate a temperature with 6 degrees of freedom (DOF) (3
translational, 3 rotational) per molecule by setting *adof* to 2.0.
you could calculate a temperature with six degrees of freedom (DOF) (three
translational, three rotational) per molecule by setting *adof* to 2.0.
If :doc:`compute temp/partial <compute_temp_partial>` is used with the
*bias* keyword to only allow the x component of velocity to contribute
*bias* keyword to only allow the :math:`x` component of velocity to contribute
to the temperature, then *adof* = 1.0 would be appropriate.
If each chunk consists of a large molecule, with some number of its
bonds constrained by :doc:`fix shake <fix_shake>` or the entire molecule
by :doc:`fix rigid/small <fix_rigid>`, *adof* = 0.0 and *cdof* could be
set to the remaining degrees of freedom for the entire molecule
(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
(entire chunk in this case), that is, 6 for 3d or 3 for 2d for a rigid
molecule.
----------
The *file* keyword allows a filename to be specified. Every *Nfreq*
timesteps, a section of chunk info will be written to a text file in
the following format. A line with the timestep and number of chunks
is written. Then one line per chunk is written, containing the chunk
ID (1-Nchunk), an optional original ID value, optional coordinate
values for chunks that represent spatial bins, the number of atoms in
the chunk, and one or more calculated values. More explanation of the
The *file* keyword allows a filename to be specified. Every
:math:`N_\text{freq}` timesteps, a section of chunk info will be written to a
text file in the following format. A line with the timestep and number of
chunks is written. Then one line per chunk is written, containing the chunk
ID :math:`(1-N_\text{chunk}),` an optional original ID value, optional
coordinate values for chunks that represent spatial bins, the number of atoms
in the chunk, and one or more calculated values. More explanation of the
optional values is given below. The number of values in each line
corresponds to the number of values specified in the fix ave/chunk
command. The number of atoms and the value(s) are summed or average
@ -437,10 +441,10 @@ output. This option can only be used with the *ave running* setting.
The *format* keyword sets the numeric format of each value when it is
printed to a file via the *file* keyword. Note that all values are
floating point quantities. The default format is %g. You can specify
a higher precision if desired, e.g. %20.16g.
a higher precision if desired (e.g., %20.16g).
The *title1* and *title2* and *title3* keywords allow specification of
the strings that will be printed as the first 3 lines of the output
the strings that will be printed as the first three lines of the output
file, assuming the *file* keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified.
@ -455,34 +459,33 @@ By default, these header lines are as follows:
In the first line, ID and name are replaced with the fix-ID and group
name. The second line describes the two values that are printed at
the first of each section of output. In the third line the values are
replaced with the appropriate value names, e.g. fx or c_myCompute[2].
replaced with the appropriate value names (e.g., *fx* or c_myCompute[2]).
The words in parenthesis only appear with corresponding columns if the
chunk style specified for the :doc:`compute chunk/atom
<compute_chunk_atom>` command supports them. The OrigID column is
only used if the *compress* keyword was set to *yes* for the
:doc:`compute chunk/atom <compute_chunk_atom>` command. This means
that the original chunk IDs (e.g. molecule IDs) will have been
that the original chunk IDs (e.g., molecule IDs) will have been
compressed to remove chunk IDs with no atoms assigned to them. Thus a
compressed chunk ID of 3 may correspond to an original chunk ID or
molecule ID of
415. The OrigID column will list 415 for the third chunk.
molecule ID of 415. The OrigID column will list 415 for the third chunk.
The CoordN columns only appear if a *binning* style was used in the
:doc:`compute chunk/atom <compute_chunk_atom>` command. For *bin/1d*,
*bin/2d*, and *bin/3d* styles the column values are the center point
of the bin in the corresponding dimension. Just Coord1 is used for
*bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*\
. For *bin/sphere*, just Coord1 is used, and it is the radial
*bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*\ .
For *bin/sphere*, just Coord1 is used, and it is the radial
coordinate. For *bin/cylinder*, Coord1 and Coord2 are used. Coord1
is the radial coordinate (away from the cylinder axis), and coord2 is
the coordinate along the cylinder axis.
Note that if the value of the *units* keyword used in the
:doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or
*lattice*, the coordinate values will be in distance :doc:`units
<units>`. If the value of the *units* keyword is *reduced*, the
coordinate values will be in unitless reduced units (0-1). This is
*lattice*, the coordinate values will be in distance :doc:`units <units>`.
If the value of the *units* keyword is *reduced*, the
coordinate values will be in unitless reduced units (0--1). This is
not true for the Coord1 value of style *bin/sphere* or *bin/cylinder*
which both represent radial dimensions. Those values are always in
distance :doc:`units <units>`.
@ -498,20 +501,21 @@ relevant to this fix.
This fix computes a global array of values which can be accessed by
various :doc:`output commands <Howto_output>`. The values can only be
accessed on timesteps that are multiples of *Nfreq* since that is when
averaging is performed. The global array has # of rows = the number
of chunks *Nchunk* as calculated by the specified :doc:`compute
chunk/atom <compute_chunk_atom>` command. The # of columns =
M+1+Nvalues, where M = 1 to 4, depending on whether the optional
accessed on timesteps that are multiples of :math:`N_\text{freq}`, since that
is when averaging is performed. The global array has # of rows = the number
of chunks :math:`N_\text{chunk}`, as calculated by the specified
:doc:`compute chunk/atom <compute_chunk_atom>` command. The # of columns is
:math:`M+1+N_\text{values}`, where :math:`M \in \{1,\dotsc,4\}`,
depending on whether the optional
columns for OrigID and CoordN are used, as explained above. Following
the optional columns, the next column contains the count of atoms in
the chunk, and the remaining columns are the Nvalue quantities. When
the array is accessed with a row I that exceeds the current number of
the array is accessed with a row :math:`I` that exceeds the current number of
chunks, than a 0.0 is returned by the fix instead of an error, since
the number of chunks can vary as a simulation runs depending on how
that value is computed by the compute chunk/atom command.
The array values calculated by this fix are treated as "intensive",
The array values calculated by this fix are treated as "intensive,"
since they are typically already normalized by the count of atoms in
each chunk.
@ -526,7 +530,8 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`,
:doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`
Default

307
doc/src/fix_ave_correlate.rst
View File

@ -6,7 +6,7 @@ fix ave/correlate command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
@ -73,10 +73,12 @@ Description
Use one or more global scalar values as inputs every few timesteps,
calculate time correlations between them at varying time intervals,
and average the correlation data over longer timescales. The
resulting correlation values can be time integrated by
:doc:`variables <variable>` or used by other :doc:`output commands <Howto_output>` such as :doc:`thermo_style custom <thermo_style>`, and can also be written to a file. See the
:doc:`fix ave/correlate/long <fix_ave_correlate_long>` command for an
and average the correlation data over longer timescales. The resulting
correlation values can be time integrated by
:doc:`variables <variable>` or used by other
:doc:`output commands <Howto_output>` such as
:doc:`thermo_style custom <thermo_style>`, and can also be written to a file.
See the :doc:`fix ave/correlate/long <fix_ave_correlate_long>` command for an
alternate method for computing correlation functions efficiently over
very long time windows.
@ -89,9 +91,11 @@ Each listed value can be the result of a :doc:`compute <compute>` or
:doc:`variable <variable>`. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
you wish to spatial- or time-average or histogram per-atom quantities
from a compute, fix, or variable, then see the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`, or
from a compute, fix, or variable, then see the
:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`, or
:doc:`fix ave/histo <fix_ave_histo>` commands. If you wish to convert a
per-atom quantity into a single global value, see the :doc:`compute reduce <compute_reduce>` command.
per-atom quantity into a single global value, see the
:doc:`compute reduce <compute_reduce>` command.
The input values must be all scalars. What kinds of
correlations between input values are calculated is determined by the
@ -110,16 +114,16 @@ be used, since they produce per-atom values.
For input values from a compute or fix or variable , the bracketed
index I can be specified using a wildcard asterisk with the index to
effectively specify multiple values. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If N = the size of the vector, then an
asterisk with no numeric values means all indices from 1 to N. A
"\*n" or "m\*" or "m\*n". If :math:`N` is the size of the vector, then an
asterisk with no numeric values means all indices from 1 to :math:`N`. A
leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to N (inclusive). A middle
asterisk means all indices from m to n (inclusive).
trailing asterisk means all indices from m to :math:`N` (inclusive).
A middle asterisk means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual elements of the
vector had been listed one by one. E.g. these 2 fix ave/correlate
commands are equivalent, since the :doc:`compute pressure
<compute_pressure>` command creates a global vector with 6 values.
vector had been listed one by one. For example, the following two fix
ave/correlate commands are equivalent, since the :doc:`compute pressure
<compute_pressure>` command creates a global vector with six values:
.. code-block:: LAMMPS
@ -139,151 +143,161 @@ commands are equivalent, since the :doc:`compute pressure
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
timesteps the input values will be used to calculate correlation data.
The input values are sampled every *Nevery* timesteps. The
correlation data for the preceding samples is computed on timesteps
that are a multiple of *Nfreq*\ . Consider a set of samples from some
initial time up to an output timestep. The initial time could be the
beginning of the simulation or the last output time; see the *ave*
The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and :math:`N_\text{freq}`
arguments specify on what timesteps the input values will be used to calculate
correlation data. The input values are sampled every :math:`N_\text{every}`
time steps. The correlation data for the preceding samples is computed on
time steps that are a multiple of :math:`N_\text{freq}`\ . Consider a set of
samples from some initial time up to an output timestep. The initial time
could be the beginning of the simulation or the last output time; see the *ave*
keyword for options. For the set of samples, the correlation value
Cij is calculated as:
:math:`C_{ij}` is calculated as:
.. parsed-literal::
.. math::
Cij(delta) = ave(Vi(t)\*Vj(t+delta))
C_{ij}(\Delta t) = \left\langle V_i(t) V_j(t+\Delta t)\right\rangle,
which is the correlation value between input values Vi and Vj,
separated by time delta. Note that the second value Vj in the pair is
always the one sampled at the later time. The ave() represents an
average over every pair of samples in the set that are separated by
time delta. The maximum delta used is of size (\ *Nrepeat*\ -1)\*\ *Nevery*\ .
Thus the correlation between a pair of input values yields *Nrepeat*
correlation datums:
which is the correlation value between input values :math:`V_i` and
:math:`V_j`, separated by time :math:`\Delta t`. Note that the second value
:math:`V_j` in the pair is always the one sampled at the later time. The
average is an average over every pair of samples in the set that are separated
by time :math:`\Delta t`. The maximum :math:`\Delta t` used is of size
:math:`(N_\text{repeat} - 1) N_\text{every}`\ .
Thus the correlation between a pair of input values yields
:math:`N_\text{repeat}` correlation data:
.. parsed-literal::
.. math::
Cij(0), Cij(Nevery), Cij(2\*Nevery), ..., Cij((Nrepeat-1)\*Nevery)
C_{ij}(0), C_{ij}(N_\text{every}), C_{ij}(2N_\text{every}), \dotsc,
C_{ij}\bigl((N_\text{repeat}-1) N_\text{every}\bigr)
For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
timesteps 0,5,10,15,...,100 will be used to compute the final averages
on timestep 100. Six averages will be computed: Cij(0), Cij(5),
Cij(10), Cij(15), Cij(20), and Cij(25). Cij(10) on timestep 100 will
be the average of 19 samples, namely Vi(0)\*Vj(10), Vi(5)\*Vj(15),
Vi(10)\*V j20), Vi(15)\*Vj(25), ..., Vi(85)\*Vj(95), Vi(90)\*Vj(100).
For example, if :math:`N_\text{every}=5`, :math:`N_\text{repeat}=6`, and
:math:`N_\text{freq}=100`, then values on time steps
:math:`0, 5, 10, 15,\dotsc,100` will be used to compute the final averages
on time step 100. Six averages will be computed: :math:`C_{ij}(0)`,
:math:`C_{ij}(5)`, :math:`C_{ij}(10)`, :math:`C_{ij}(15)`, :math:`C_{ij}(20)`,
and :math:`C_{ij}(25)`. :math:`C_{ij}(10)` on time step 100 will
be the average of 19 samples, namely :math:`V_i(0) V_j(10)`,
:math:`V_i(5) V_j(15)`, :math:`V_i(10) V_j(20)`,
:math:`V_i(15) V_j(25), \dotsc,`
:math:`V_i(85) V_j(95)`, and :math:`V_i(90) V_j(100)`.
*Nfreq* must be a multiple of *Nevery*\ ; *Nevery* and *Nrepeat* must be
non-zero. Also, if the *ave* keyword is set to *one* which is the
default, then *Nfreq* >= (\ *Nrepeat*\ -1)\*\ *Nevery* is required.
:math:`N_\text{freq}` must be a multiple of :math:`N_\text{every}`;
:math:`N_\text{every}` and :math:`N_\text{repeat}` must be non-zero.
Also, if the *ave* keyword is set to *one* which is the default, then
:math:`N_\text{freq} \ge (N_\text{repeat} -1) N_\text{every}` is required.
----------
If a value begins with "c\_", a compute ID must follow which has been
If a value begins with "c\_," a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the compute is used. See the discussion above for how I
can be specified with a wildcard asterisk to effectively specify
bracketed term is appended, the :math:`I^\text{th}` element of the global
vector calculated by the compute is used. See the discussion above for how
:math:`I` can be specified with a wildcard asterisk to effectively specify
multiple values.
Note that there is a :doc:`compute reduce <compute_reduce>` command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/correlate. Or it can be a compute
defined not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>`
that can sum per-atom quantities into a global scalar or vector which
can then be accessed by fix ave/correlate. It can also be a compute defined
not in your input script, but by :doc:`thermodynamic output <thermo_style>`
or other fixes such as :doc:`fix nvt <fix_nh>`
or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "f\_", a fix ID must follow which has been
If a value begins with "f\_," a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the fix is used. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.
bracketed term is appended, the :math:`I^\text{th}` element of the global
vector calculated by the fix is used. See the discussion above for how
:math:`I` can be specified with a wildcard asterisk to effectively specify
multiple values.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with *Nevery*, else an error will result.
Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
which must be compatible with :math:`N_\text{every}`, else an error will
result. Users can also write code for their own fix styles and
:doc:`add them to LAMMPS <Modify>`.
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. Only equal-style or
vector-style variables can be referenced; the latter requires a
bracketed term to specify the Ith element of the vector calculated by
the variable. See the :doc:`variable <variable>` command for details.
Note that variables of style *equal* or *vector* define a formula
which can reference individual atom properties or thermodynamic
keywords, or they can invoke other computes, fixes, or variables when
they are evaluated, so this is a very general means of specifying
quantities to time correlate.
If a value begins with "v\_," a variable name must follow which has been
previously defined in the input script. Only equal-style or vector-style
variables can be referenced; the latter requires a bracketed term to specify
the :math:`I^\text{th}` element of the vector calculated by the variable.
See the :doc:`variable <variable>` command for details. Note that variables of
style *equal* or *vector* define a formula which can reference individual atom
properties or thermodynamic keywords, or they can invoke other computes, fixes,
or variables when they are evaluated, so this is a very general means of
specifying quantities to time correlate.
----------
Additional optional keywords also affect the operation of this fix.
The *type* keyword determines which pairs of input values are
correlated with each other. For N input values Vi, for i = 1 to N,
let the number of pairs = Npair. Note that the second value in the
pair Vi(t)\*Vj(t+delta) is always the one sampled at the later time.
correlated with each other. For :math:`N` input values :math:`V_i`,
with :math:`i \in \{1,\dotsc,N\}`, let the number of pairs be
:math:`N_\text{pair}`. Note that the second value in the
pair, :math:`V_i(t) V_j(t+\Delta t)`, is always the one sampled at the later
time.
* If *type* is set to *auto* then each input value is correlated with
itself. I.e. Cii = Vi\*Vi, for i = 1 to N, so Npair = N.
* If *type* is set
to *upper* then each input value is correlated with every succeeding
value. I.e. Cij = Vi\*Vj, for i < j, so Npair = N\*(N-1)/2.
* If *type* is set
to *lower* then each input value is correlated with every preceding
value. I.e. Cij = Vi\*Vj, for i > j, so Npair = N\*(N-1)/2.
itself (i.e., :math:`C_{ii} = V_i^2` for :math:`i \in \{1,\dotsc,N\}`,
so :math:`N_\text{pair} = N`).
* If *type* is set to *upper* then each input value is correlated with every
succeeding value (i.e., :math:`C_{ij} = V_i V_j` for :math:`i < j`, so
:math:`N_\text{pair} = N (N-1)/2`).
* If *type* is set to *lower* then each input value is correlated with every
preceding value (i.e., :math:`C_{ij} = V_i V_j` for :math:`i > j`, so
:math:`N_\text{pair} = N(N-1)/2`).
* If *type* is set to *auto/upper* then each input value is correlated
with itself and every succeeding value. I.e. Cij = Vi\*Vj, for i >= j,
so Npair = N\*(N+1)/2.
with itself and every succeeding value (i.e., :math:`C_{ij} = V_i V_j`
for :math:`i \ge j`, so :math:`N_\text{pair} = N(N+1)/2`).
* If *type* is set to *auto/lower* then each input value is correlated
with itself and every preceding value. I.e. Cij = Vi\*Vj, for i <= j,
so Npair = N\*(N+1)/2.
with itself and every preceding value (i.e., :math:`C_{ij} = V_i V_j`
for :math:`i \le j`, so :math:`N_\text{pair} = N(N+1)/2`).
* If *type* is set to *full* then each input value is correlated with
itself and every other value. I.e. Cij = Vi\*Vj, for i,j = 1,N so
Npair = N\^2.
itself and every other value (i.e., :math:`C_{ij} = V_i V_j` for
:math:`\{i,j\} = \{1,N\}`, so :math:`N_\text{pair} = N^2`).
The *ave* keyword determines what happens to the accumulation of
correlation samples every *Nfreq* timesteps. If the *ave* setting is
*one*, then the accumulation is restarted or zeroed every *Nfreq*
timesteps. Thus the outputs on successive *Nfreq* timesteps are
The *ave* keyword determines what happens to the accumulation of correlation
samples every :math:`N_\text{freq}` timesteps. If the *ave* setting is *one*,
then the accumulation is restarted or zeroed every :math:`N_\text{freq}`
timesteps. Thus the outputs on successive :math:`N_\text{freq}` timesteps are
essentially independent of each other. The exception is that the
Cij(0) = Vi(T)\*Vj(T) value at a timestep T, where T is a multiple of
*Nfreq*, contributes to the correlation output both at time T and at
time T+Nfreq.
:math:`C_{ij}(0) = V_i(t) V_j(t)` value at a time step :math:`t,` where
:math:`t` is a multiple of :math:`N_\text{freq}`, contributes to the
correlation output both at time :math:`t` and at time :math:`t+N_\text{freq}`.
If the *ave* setting is *running*, then the accumulation is never
zeroed. Thus the output of correlation data at any timestep is the
average over samples accumulated every *Nevery* steps since the fix
was defined. it can only be restarted by deleting the fix via the
:doc:`unfix <unfix>` command, or by re-defining the fix by re-specifying
it.
If the *ave* setting is *running*, then the accumulation is never zeroed.
Thus the output of correlation data at any timestep is the average over samples
accumulated every :math:`N_\text{every}` steps since the fix was defined.
It can only be restarted by deleting the fix via the :doc:`unfix <unfix>`
command, or by re-defining the fix by re-specifying it.
The *start* keyword specifies what timestep the accumulation of
The *start* keyword specifies what time step the accumulation of
correlation samples will begin on. The default is step 0. Setting it
to a larger value can avoid adding non-equilibrated data to the
correlation averages.
The *prefactor* keyword specifies a constant which will be used as a
multiplier on the correlation data after it is averaged. It is
effectively a scale factor on Vi\*Vj, which can be used to account for
the size of the time window or other unit conversions.
The *prefactor* keyword specifies a constant which will be used as a multiplier
on the correlation data after it is averaged. It is effectively a scale factor
on :math:`V_i V_j`, which can be used to account for the size of the time
window or other unit conversions.
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, an array of correlation data is written to the file. The
number of rows is *Nrepeat*, as described above. The number of
columns is the Npair+2, also as described above. Thus the file ends
up to be a series of these array sections.
The *file* keyword allows a filename to be specified. Every
:math:`N_\text{freq}` steps, an array of correlation data is written to the
file. The number of rows is :math:`N_\text{repeat}`, as described above.
The number of columns is :math:`N_\text{pair}+2`, also as described above.
Thus the file ends up to be a series of these array sections.
The *overwrite* keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the *ave running* setting.
The *title1* and *title2* and *title3* keywords allow specification of
the strings that will be printed as the first 3 lines of the output
file, assuming the *file* keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified.
The *title1*, *title2*, and *title3* keywords allow specification of
the strings that will be printed as the first three lines of the output file,
assuming the *file* keyword was used. LAMMPS uses default values for each of
these, so they do not need to be specified.
By default, these header lines are as follows:
@ -300,18 +314,19 @@ appropriate fields from the fix ave/correlate command.
----------
Let Sij = a set of time correlation data for input values I and J,
namely the *Nrepeat* values:
Let :math:`S_{ij}` be a set of time correlation data for input values
:math:`I` and :math:`J`, namely the :math:`N_\text{repeat}` values:
.. parsed-literal::
.. math::
Sij = Cij(0), Cij(Nevery), Cij(2\*Nevery), ..., Cij(\*Nrepeat-1)\*Nevery)
S_{ij} = C_{ij}(0), C_{ij}(N_\text{every}), C_{ij}(2N_\text{every}),
\dotsc, C_{ijI}\bigl((N_\text{repeat}-1) N_\text{every}\bigr)
As explained below, these datums are output as one column of a global
As explained below, these data are output as one column of a global
array, which is effectively the correlation matrix.
The *trap* function defined for :doc:`equal-style variables <variable>`
can be used to perform a time integration of this vector of datums,
can be used to perform a time integration of this vector of data,
using a trapezoidal rule. This is useful for calculating various
quantities which can be derived from time correlation data. If a
normalization factor is needed for the time integration, it can be
@ -322,40 +337,43 @@ included in the variable formula or via the *prefactor* keyword.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to
:doc:`binary restart files <restart>`. None of the
:doc:`fix_modify <fix_modify>` options are relevant to this fix.
This fix computes a global array of values which can be accessed by
various :doc:`output commands <Howto_output>`. The values can only be
accessed on timesteps that are multiples of *Nfreq* since that is when
averaging is performed. The global array has # of rows = *Nrepeat*
and # of columns = Npair+2. The first column has the time delta (in
timesteps) between the pairs of input values used to calculate the
correlation, as described above. The second column has the number of
samples contributing to the correlation average, as described above.
The remaining Npair columns are for I,J pairs of the N input values,
as determined by the *type* keyword, as described above.
accessed on timesteps that are multiples of :math:`N_\text{freq}` since that is
when averaging is performed. The global array has # of rows
:math:`N_\text{repeat}` and # of columns :math:`N_\text{pair}+2`. The first
column has the time :math:`\Delta t` (in time steps) between the pairs of input
values used to calculate the correlation, as described above. The second
column has the number of samples contributing to the correlation average, as
described above. The remaining Npair columns are for :math:`I,J` pairs of the
:math:`N` input values, as determined by the *type* keyword, as described
above.
* For *type* = *auto*, the Npair = N columns are ordered: C11, C22, ...,
CNN.
* For *type* = *upper*, the Npair = N\*(N-1)/2 columns are ordered: C12,
C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N.
* For *type* = *lower*, the Npair = N\*(N-1)/2 columns are ordered: C21,
C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1.
* For *type* = *auto/upper*, the Npair = N\*(N+1)/2 columns are ordered:
C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N,
CNN.
* For *type* = *auto/lower*, the Npair = N\*(N+1)/2 columns are ordered:
C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1,
CNN.
* For *type* = *full*, the Npair = N\^2 columns are ordered: C11, C12,
..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
CNN.
* For *type* = *auto*, the :math:`N_\text{pair} = N` columns are ordered:
:math:`C_{11}, C_{22}, \dotsc, C_{NN}`
* For *type* = *upper*, the :math:`N_\text{pair} = N(N-1)/2` columns are
ordered: :math:`C_{12}, C_{13}, \dotsc, C_{1N}, C_{23}, \dotsc, C_{2N},
C_{34}, \dotsc, C_{N-1,N}`
* For *type* = *lower*, the :math:`N_\text{pair} = N(N-1)/2` columns are
ordered: :math:`C_{21}, C_{31}, C_{32}, C_{41}, C_{42}, C_{43I}, \dotsc,
C_{N1}, C_{N2}, \dotsc, C_{N,N-1}`
* For *type* = *auto/upper*, the :math:`N_\text{pair} = N(N+1)/2` columns are
ordered: :math:`C_{11}, C_{12}, C_{13}, \dotsc, C_{1N}, C_{22}, C_{23},
\dotsc, C_{2N}, C_{33}, C_{34}, \dotsc, C_{N-1,N}, C_{NN}`
* For *type* = *auto/lower*, the :math:`N_\text{pair} = N(N+1)/2` columns are
ordered: :math:`C_{11}, C_{21}, C_{22}, C_{31}, C_{32}, C_{33}, C_{41},
\dotsc, C_{44}, C_{N1}, C_{N2}, \dotsc, C_{N,N-1}, C_{NN}`
* For *type* = *full*, the :math:`N_\text{pair} = N^2` columns are ordered:
:math:`C_{11}, C_{12}, \dotsc, C_{1N}, C_{21}, C_{22}, \dotsc, C_{2N},
C_{31}, \dotsc, C_{3N}, \dotsc, C_{N1}, \dotsc, C_{N,N-1}, C_{NN}`
The array values calculated by this fix are treated as intensive. If
The array values calculated by this fix are treated as extensive. If
you need to divide them by the number of atoms, you must do this in a
later processing step, e.g. when using them in a
:doc:`variable <variable>`.
later processing step (e.g., when using them in a :doc:`variable <variable>`).
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
@ -368,7 +386,8 @@ Related commands
""""""""""""""""
:doc:`fix ave/correlate/long <fix_ave_correlate_long>`,
:doc:`compute <compute>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
:doc:`compute <compute>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
:doc:`fix ave/histo <fix_ave_histo>`, :doc:`variable <variable>`
Default

59
doc/src/fix_ave_correlate_long.rst
View File

@ -6,14 +6,14 @@ fix ave/correlate/long command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* ave/correlate/long = style name of this fix command
* Nevery = use input values every this many timesteps
* Nfreq = save state of the time correlation functions every this many timesteps
* Nevery = use input values every this many time steps
* Nfreq = save state of the time correlation functions every this many time steps
* one or more input values can be listed
* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
@ -38,7 +38,7 @@ Syntax
auto/lower = auto + lower
full = correlate each value with every other value, including itself = auto + upper + lower
*start* args = Nstart
Nstart = start accumulating correlations on this timestep
Nstart = start accumulating correlations on this time step
*file* arg = filename
filename = name of file to output correlation data to
*overwrite* arg = none = overwrite output file with only latest output
@ -66,10 +66,11 @@ Examples
Description
"""""""""""
This fix is similar in spirit and syntax to the :doc:`fix ave/correlate <fix_ave_correlate>`.
This fix is similar in spirit and syntax to the
:doc:`fix ave/correlate <fix_ave_correlate>`.
However, this fix allows the efficient calculation of time correlation
functions on-the-fly over extremely long time windows with little
additional CPU overhead, using a multiple-tau method
additional CPU overhead, using a multiple-:math:`\tau` method
:ref:`(Ramirez) <Ramirez>` that decreases the resolution of the stored
correlation function with time. It is not a full drop-in replacement.
@ -78,37 +79,41 @@ specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each listed value can be the result of a compute or fix or the
evaluation of an equal-style variable. See the :doc:`fix ave/correlate <fix_ave_correlate>` page for details.
evaluation of an equal-style variable. See the
:doc:`fix ave/correlate <fix_ave_correlate>` page for details.
The *Nevery* and *Nfreq* arguments specify on what timesteps the input
values will be used to calculate correlation data, and the frequency
with which the time correlation functions will be output to a file.
Note that there is no *Nrepeat* argument, unlike the :doc:`fix ave/correlate <fix_ave_correlate>` command.
The *Nevery* and *Nfreq* arguments specify on what time steps the input
values will be used to calculate correlation data and the frequency
with which the time correlation functions will be output to a file,
respectively.
Note that there is no *Nrepeat* argument, unlike the
:doc:`fix ave/correlate <fix_ave_correlate>` command.
The optional keywords *ncorr*, *nlen*, and *ncount* are unique to this
command and determine the number of correlation points calculated and
the memory and CPU overhead used by this calculation. *Nlen* and
*ncount* determine the amount of averaging done at longer correlation
times. The default values *nlen=16*, *ncount=2* ensure that the
systematic error of the multiple-tau correlator is always below the
times. The default values *nlen* = 16 and *ncount* = 2 ensure that the
systematic error of the multiple-:math:`\tau` correlator is always below the
level of the statistical error of a typical simulation (which depends
on the ensemble size and the simulation length).
The maximum correlation time (in time steps) that can be reached is
given by the formula (nlen-1) \* ncount\^(ncorr-1). Longer correlation
given by the formula :math:`(nlen-1) ncount^{(ncorr-1)}`. Longer correlation
times are discarded and not calculated. With the default values of
the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to
7864320 time steps. If longer correlation times are needed, the value
of ncorr should be increased. Using nlen=16 and ncount=2, with
ncorr=30, the maximum number of steps that can be correlated is
80530636808. If ncorr=40, correlation times in excess of 8e12 time
steps can be calculated.
the parameters (:math:`ncorr=20`, :math:`nlen=16` and :math:`ncount=2`),
this corresponds to 7864320 time steps. If longer correlation times are
needed, the value of ncorr should be increased. Using :math:`nlen=16` and
:math:`ncount=2`, with :math:`ncorr=30`, the maximum number of steps that can
be correlated is 80530636808. If :math:`ncorr=40`, correlation times in excess
of :math:`8\times 10^{12}` time steps can be calculated.
The total memory needed for each correlation pair is roughly
4\*ncorr\*nlen\*8 bytes. With the default values of the parameters, this
corresponds to about 10 KB.
:math:`4 \times ncorr\times nlen \times 8` bytes.
With the default values of the parameters, this corresponds to about 10 KB.
For the meaning of the additional optional keywords, see the :doc:`fix ave/correlate <fix_ave_correlate>` doc page.
For the meaning of the additional optional keywords, see the
:doc:`fix ave/correlate <fix_ave_correlate>` doc page.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -128,7 +133,8 @@ Restrictions
""""""""""""
This compute is part of the EXTRA-FIX package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
@ -140,8 +146,9 @@ Default
none
The option defaults for keywords that are also keywords for the :doc:`fix ave/correlate <fix_ave_correlate>` command are as follows: type =
auto, start = 0, no file output, title 1,2 = strings as described on
The option defaults for keywords that are also keywords for the
:doc:`fix ave/correlate <fix_ave_correlate>` command are as follows:
type = auto, start = 0, no file output, title 1,2 = strings as described on
the :doc:`fix ave/correlate <fix_ave_correlate>` doc page.
The option defaults for keywords unique to this command are as

189
doc/src/fix_ave_histo.rst
View File

@ -10,7 +10,7 @@ fix ave/histo/weight command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID style Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ...
@ -22,7 +22,7 @@ Syntax
* lo,hi = lo/hi bounds within which to histogram
* Nbin = # of histogram bins
* one or more input values can be listed
* value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
* value = *x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, c_ID, c_ID[N], f_ID, f_ID[N], v_name
.. parsed-literal::
@ -126,26 +126,27 @@ length. The first value (a scalar or vector) is what is histogrammed
into bins, in the same manner the fix ave/histo command operates. The
second value (a scalar or vector) is used as a "weight". This means
that instead of each value tallying a "1" to its bin, the
corresponding weight is tallied. E.g. The Nth entry (weight) in the
second vector is tallied to the bin corresponding to the Nth entry in
the first vector.
corresponding weight is tallied. For example, the :math:`N^\text{th}` entry
(weight) in the second vector is tallied to the bin corresponding to the
:math:`N^\text{th}` entry in the first vector.
----------
For input values from a compute or fix or variable, the bracketed
index I can be specified using a wildcard asterisk with the index to
effectively specify multiple values. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* =
scalar) or the number of columns in the array (for *mode* = vector),
then an asterisk with no numeric values means all indices from 1 to N.
"\*n" or "m\*" or "m\*n". If :math:`N` is the size of the vector
(for *mode* = scalar) or the number of columns in the array
(for *mode* = vector), then an asterisk with no numeric values means all
indices from 1 to :math:`N`\ .
A leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to N (inclusive). A middle
trailing asterisk means all indices from m to :math:`N` (inclusive). A middle
asterisk means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual elements of the
vector or columns of the array had been listed one by one. E.g. these
2 fix ave/histo commands are equivalent, since the :doc:`compute
com/chunk <compute_com_chunk>` command creates a global array with 3
vector or columns of the array had been listed one by one. For example, the
following two fix ave/histo commands are equivalent, since the :doc:`compute
com/chunk <compute_com_chunk>` command creates a global array with three
columns:
.. code-block:: LAMMPS
@ -164,31 +165,35 @@ columns:
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
timesteps the input values will be used in order to contribute to the
histogram. The final histogram is generated on timesteps that are
multiple of *Nfreq*\ . It is averaged over *Nrepeat* histograms,
computed in the preceding portion of the simulation every *Nevery*
timesteps. *Nfreq* must be a multiple of *Nevery* and *Nevery* must
be non-zero even if *Nrepeat* is 1. Also, the timesteps
contributing to the histogram value cannot overlap,
i.e. Nrepeat\*Nevery can not exceed Nfreq.
The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and :math:`N_\text{freq}`
arguments specify on what time steps the input values will be used in order to
contribute to the histogram. The final histogram is generated on time steps
that are multiple of :math:`N_\text{freq}`\ . It is averaged over
:math:`N_\text{repeat}` histograms, computed in the preceding portion of the
simulation every :math:`N_\text{every}` time steps.
:math:`N_\text{freq}` must be a multiple of :math:`N_\text{every}` and
:math:`N_\text{every}` must be non-zero even if :math:`N_\text{repeat}` is 1.
Also, the time steps contributing to the histogram value cannot overlap
(i.e., :math:`N_\text{repeat}\times N_\text{every}` cannot exceed
:math:`N_\text{freq}`).
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
on timesteps 90,92,94,96,98,100 will be used to compute the final
histogram on timestep 100. Similarly for timesteps
190,192,194,196,198,200 on timestep 200, etc. If Nrepeat=1 and Nfreq
= 100, then no time averaging of the histogram is done; a histogram is
simply generated on timesteps 100,200,etc.
For example, if :math:`N_\text{every}=2`, :math:`N_\text{repeat}=6`, and
:math:`N_\text{freq}=100`, then input values on time steps 90, 92, 94, 96, 98,
and 100 will be used to compute the final histogram on timestep 100.
Similarly for timesteps 190, 192, 194, 196, 198, and 200 on timestep 200, etc.
If :math:`N_\text{repeat}=1` and :math:`N_\text{freq} = 100`, then no time
averaging of the histogram is done; a histogram is simply generated on
timesteps 100, 200, etc.
----------
The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
an input value from that compute.
The atom attribute values (*x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, and
*fz*) are self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the
:doc:`compute property/atom <compute_property_atom>` command and then
specifying an input value from that compute.
If a value begins with "c\_", a compute ID must follow which has been
If a value begins with "c\_," a compute ID must follow which has been
previously defined in the input script. If *mode* = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
@ -201,35 +206,38 @@ how I can be specified with a wildcard asterisk to effectively specify
multiple values.
Note that there is a :doc:`compute reduce <compute_reduce>` command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/histo. Or it can be a compute defined
not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>`
that can sum per-atom quantities into a global scalar or vector, which
can then be accessed by fix ave/histo. It can also be a compute defined
not in your input script, but by :doc:`thermodynamic output <thermo_style>`
or other fixes such as :doc:`fix nvt <fix_nh>`
or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
write code for their own compute styles and
:doc:`add them to LAMMPS <Modify>`.
If a value begins with "f\_", a fix ID must follow which has been
If a value begins with "f\_," a fix ID must follow which has been
previously defined in the input script. If *mode* = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
global vector calculated by the fix is used. If *mode* = vector, then
if no bracketed term is appended, the global or per-atom or local
vector calculated by the fix is used. If a bracketed term is
appended, the Ith column of the global or per-atom or local array
calculated by the fix is used. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.
appended, the :math:`I^\text{th}` column of the global or per-atom or local
array calculated by the fix is used. See the discussion above for how
:math:`I` can be specified with a wildcard asterisk to effectively specify
multiple values.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with *Nevery*, else an error will result.
Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
which must be compatible with :math:`N_\text{every}`, else an error will
result. Users can also write code for their own fix styles and
:doc:`add them to LAMMPS <Modify>`.
If a value begins with "v\_", a variable name must follow which has
If a value begins with "v\_," a variable name must follow which has
been previously defined in the input script. If *mode* = scalar, then
only equal-style or vector-style variables can be used, which both
produce global values. In this mode, a vector-style variable requires
a bracketed term to specify the Ith element of the vector calculated
by the variable. If *mode* = vector, then only vector-style or
a bracketed term to specify the :math:`I^\text{th}` element of the vector
calculated by the variable. If *mode* = vector, then only vector-style or
atom-style variables can be used, which produce a global or per-atom
vector respectively. The vector-style variable must be used without a
bracketed term. See the :doc:`variable <variable>` command for details.
@ -259,44 +267,44 @@ keyword should be used to specify which output will be used. The
remaining input arguments must still be consistent.
The *beyond* keyword determines how input values that fall outside the
*lo* to *hi* bounds are treated. Values such that *lo* <= value <=
*hi* are assigned to one bin. Values on a bin boundary are assigned
to the lower of the 2 bins. If *beyond* is set to *ignore* then
values < *lo* and values > *hi* are ignored, i.e. they are not binned.
If *beyond* is set to *end* then values < *lo* are counted in the
first bin and values > *hi* are counted in the last bin. If *beyond*
is set to *extend* then two extra bins are created, so that there are
Nbins+2 total bins. Values < *lo* are counted in the first bin and
values > *hi* are counted in the last bin (Nbins+2). Values between
*lo* and *hi* (inclusive) are counted in bins 2 through Nbins+1. The
"coordinate" stored and printed for these two extra bins is *lo* and
*hi*\ .
*lo* to *hi* bounds are treated. Values such that *lo* :math:`\le` value
:math:`\le` *hi* are assigned to one bin. Values on a bin boundary are
assigned to the lower of the two bins. If *beyond* is set to *ignore* then
values :math:`<` *lo* and values :math:`>` *hi* are ignored (i.e., they are not
binned). If *beyond* is set to *end*, then values :math:`<` *lo* are counted in
the first bin and values :math:`>` *hi* are counted in the last bin.
If *beyond* is set to *extend*, then two extra bins are created so that there
are :math:`N_\text{bins}+2` total bins. Values :math:`<` *lo* are counted in
the first bin and values :math:`>` *hi* are counted in the last bin
:math:`(N_\text{bins}+2)`\ . Values between
*lo* and *hi* (inclusive) are counted in bins 2 through
:math:`N_\text{bins}+1`\ . The "coordinate" stored and printed for these two
extra bins is *lo* and *hi*\ .
The *ave* keyword determines how the histogram produced every *Nfreq*
steps are averaged with histograms produced on previous steps that
were multiples of *Nfreq*, before they are accessed by another output
command or written to a file.
The *ave* keyword determines how the histogram produced every
:math:`N_\text{freq}` steps are averaged with histograms produced on previous
steps that were multiples of :math:`N_\text{freq}`, before they are accessed by
another output command or written to a file.
If the *ave* setting is *one*, then the histograms produced on
timesteps that are multiples of *Nfreq* are independent of each other;
they are output as-is without further averaging.
timesteps that are multiples of :math:`N_\text{freq}` are independent of each
other; they are output as-is without further averaging.
If the *ave* setting is *running*, then the histograms produced on
timesteps that are multiples of *Nfreq* are summed and averaged in a
cumulative sense before being output. Each bin value in the histogram
is thus the average of the bin value produced on that timestep with
all preceding values for the same bin. This running average begins
when the fix is defined; it can only be restarted by deleting the fix
via the :doc:`unfix <unfix>` command, or by re-defining the fix by
re-specifying it.
timesteps that are multiples of :math:`N_\text{freq}` are summed and averaged
in a cumulative sense before being output. Each bin value in the histogram
is thus the average of the bin value produced on that timestep with all
preceding values for the same bin. This running average begins when the fix is
defined; it can only be restarted by deleting the fix via the
:doc:`unfix <unfix>` command, or by re-defining the fix by re-specifying it.
If the *ave* setting is *window*, then the histograms produced on
timesteps that are multiples of *Nfreq* are summed within a moving
"window" of time, so that the last M histograms are used to produce
the output. E.g. if M = 3 and Nfreq = 1000, then the output on step
10000 will be the combined histogram of the individual histograms on
steps 8000,9000,10000. Outputs on early steps will be sums over less
than M histograms if they are not available.
timesteps that are multiples of :math:`N_\text{freq}` are summed within a
moving "window" of time, so that the last :math:`M` histograms are used to
produce the output (e.g., if :math:`M = 3` and :math:`N_\text{freq} = 1000`,
then the output on step 10000 will be the combined histogram of the individual
histograms on steps 8000, 9000, and 10000. Outputs on early steps will be sums
over less than :math:`M` histograms if they are not available.
The *start* keyword specifies what timestep histogramming will begin
on. The default is step 0. Often input values can be 0.0 at time 0,
@ -321,8 +329,8 @@ The *overwrite* keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the *ave running* setting.
The *title1* and *title2* and *title3* keywords allow specification of
the strings that will be printed as the first 3 lines of the output
The *title1*, *title2*, and *title3* keywords allow specification of
the strings that will be printed as the first three lines of the output
file, assuming the *file* keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified.
@ -336,7 +344,7 @@ By default, these header lines are as follows:
In the first line, ID is replaced with the fix-ID. The second line
describes the six values that are printed at the first of each section
of output. The third describes the 4 values printed for each bin in
of output. The third describes the four values printed for each bin in
the histogram.
----------
@ -344,13 +352,14 @@ the histogram.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to
:doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
This fix produces a global vector and global array which can be
accessed by various :doc:`output commands <Howto_output>`. The values
can only be accessed on timesteps that are multiples of *Nfreq* since
that is when a histogram is generated. The global vector has 4
can only be accessed on timesteps that are multiples of :math:`N_\text{freq}`
since that is when a histogram is generated. The global vector has four
values:
* 1 = total counts in the histogram
@ -358,19 +367,20 @@ values:
* 3 = min value of all input values, including ones not histogrammed
* 4 = max value of all input values, including ones not histogrammed
The global array has # of rows = Nbins and # of columns = 3. The
The global array has :math:`N_\text{bins}` rows and three columns. The
first column has the bin coordinate, the second column has the count of
values in that histogram bin, and the third column has the bin count
divided by the total count (not including missing counts), so that the
values in the third column sum to 1.0.
The vector and array values calculated by this fix are all treated as
intensive. If this is not the case, e.g. due to histogramming
per-atom input values, then you will need to account for that when
intensive. If this is not the case (e.g., due to histogramming
per-atom input values), then you will need to account for that when
interpreting the values produced by this fix.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command.
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
@ -379,7 +389,8 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`,
:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
Default

130
doc/src/fix_ave_time.rst
View File

@ -6,15 +6,15 @@ fix ave/time command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* ave/time = style name of this fix command
* Nevery = use input values every this many timesteps
* Nevery = use input values every this many time steps
* Nrepeat = # of times to use input values for calculating averages
* Nfreq = calculate averages every this many timesteps
* Nfreq = calculate averages every this many time steps
* one or more input values can be listed
* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
@ -40,7 +40,7 @@ Syntax
running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
*start* args = Nstart
Nstart = start averaging on this timestep
Nstart = start averaging on this time step
*off* arg = M = do not average this value
M = value # from 1 to Nvalues
*file* arg = filename
@ -69,7 +69,7 @@ Examples
Description
"""""""""""
Use one or more global values as inputs every few timesteps, and
Use one or more global values as inputs every few time steps, and
average them over longer timescales. The resulting averages can be
used by other :doc:`output commands <Howto_output>` such as
:doc:`thermo_style custom <thermo_style>`, and can also be written to a
@ -86,9 +86,11 @@ Each listed value can be the result of a :doc:`compute <compute>` or
:doc:`variable <variable>`. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
you wish to spatial- or time-average or histogram per-atom quantities
from a compute, fix, or variable, then see the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`,
from a compute, fix, or variable, then see the
:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`,
or :doc:`fix ave/histo <fix_ave_histo>` commands. If you wish to sum a
per-atom quantity into a single global quantity, see the :doc:`compute reduce <compute_reduce>` command.
per-atom quantity into a single global quantity, see the
:doc:`compute reduce <compute_reduce>` command.
:doc:`Computes <compute>` that produce global quantities are those which
do not have the word *atom* in their style name. Only a few
@ -100,13 +102,13 @@ be used, since they produce per-atom values.
The input values must either be all scalars or all vectors depending
on the setting of the *mode* keyword. In both cases, the averaging is
performed independently on each input value. I.e. each input scalar
performed independently on each input value (i.e., each input scalar
is averaged independently or each element of each input vector is
averaged independently.
averaged independently).
If *mode* = scalar, then the input values must be scalars, or vectors
with a bracketed term appended, indicating the Ith value of the vector
is used.
with a bracketed term appended, indicating the :math:`I^\text{th}` value of the
vector is used.
If *mode* = vector, then the input values must be vectors, or arrays
with a bracketed term appended, indicating the Ith column of the array
@ -118,17 +120,17 @@ the vector or number of rows in the array.
For input values from a compute or fix or variable, the bracketed
index I can be specified using a wildcard asterisk with the index to
effectively specify multiple values. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* =
"\*n" or "m\*" or "m\*n". If :math:`N` is the size of the vector (for *mode* =
scalar) or the number of columns in the array (for *mode* = vector),
then an asterisk with no numeric values means all indices from 1 to N.
A leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to N (inclusive). A middle
asterisk means all indices from m to n (inclusive).
then an asterisk with no numeric values means all indices from 1 to :math:`N`.
A leading asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to :math:`N` (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual elements of the
vector or columns of the array had been listed one by one. E.g. these
2 fix ave/time commands are equivalent, since the :doc:`compute rdf
<compute_rdf>` command creates, in this case, a global array with 3
vector or columns of the array had been listed one by one. For example, the
following two fix ave/time commands are equivalent, since the :doc:`compute rdf
<compute_rdf>` command creates, in this case, a global array with three
columns, each of length 50:
.. code-block:: LAMMPS
@ -147,22 +149,24 @@ columns, each of length 50:
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
timesteps the input values will be used in order to contribute to the
average. The final averaged quantities are generated on timesteps
that are a multiple of *Nfreq*\ . The average is over *Nrepeat*
quantities, computed in the preceding portion of the simulation every
*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and
*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps
The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and :math:`N_\text{freq}`
arguments specify on what time steps the input values will be used in order to
contribute to the average. The final averaged quantities are generated on
time steps that are a multiple of :math:`N_\text{freq}`\ . The average is over
:math:`N_\text{repeat}` quantities, computed in the preceding portion of the
simulation every :math:`N_\text{every}` time steps. :math:`N_\text{freq}` must
be a multiple of :math:`N_\text{every}` and :math:`N_\text{every}` must be
non-zero even if :math:`N_\text{repeat} = 1`. Also, the time steps
contributing to the average value cannot overlap,
i.e. Nrepeat\*Nevery can not exceed Nfreq.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps
100,200,etc.
For example, if :math:`N_\text{every}=2`, :math:`N_\text{repeat}=6`, and
:math:`N_\text{freq}=100`, then values on time steps 90, 92, 94, 96, 98, and
100 will be used to compute the final average on time step 100. Similarly for
time steps 190, 192, 194, 196, 198, and 200 on time step 200, etc.
If :math:`N_\text{repeat}=1` and :math:`N_\text{freq} = 100`, then no time
averaging is done; values are simply generated on time steps
100, 200, etc.
----------
@ -178,8 +182,8 @@ See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
Note that there is a :doc:`compute reduce <compute_reduce>` command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/time. Or it can be a compute defined
that can sum per-atom quantities into a global scalar or vector, which
can then be accessed by fix ave/time. It can also be a compute defined
not in your input script, but by :doc:`thermodynamic output
<thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>` or
:doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
@ -198,7 +202,7 @@ global array calculated by the fix is used. See the discussion above
for how I can be specified with a wildcard asterisk to effectively
specify multiple values.
Note that some fixes only produce their values on certain timesteps,
Note that some fixes only produce their values on certain time steps,
which must be compatible with *Nevery*, else an error will result.
Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
@ -228,32 +232,32 @@ vectors, or columns of global arrays. They can also be global arrays,
which are converted into a series of global vectors (one per column),
as explained above.
The *ave* keyword determines how the values produced every *Nfreq*
steps are averaged with values produced on previous steps that were
multiples of *Nfreq*, before they are accessed by another output
command or written to a file.
The *ave* keyword determines how the values produced every
:math:`N_\text{freq}` steps are averaged with values produced on previous steps
that were multiples of :math:`N_\text{freq}`, before they are accessed by
another output command or written to a file.
If the *ave* setting is *one*, then the values produced on timesteps
that are multiples of *Nfreq* are independent of each other; they are
output as-is without further averaging.
If the *ave* setting is *one*, then the values produced on time steps
that are multiples of :math:`N_\text{freq}` are independent of each other; they
are output as-is without further averaging.
If the *ave* setting is *running*, then the values produced on
timesteps that are multiples of *Nfreq* are summed and averaged in a
cumulative sense before being output. Each output value is thus the
average of the value produced on that timestep with all preceding
time steps that are multiples of :math:`N_\text{freq}` are summed and averaged
in a cumulative sense before being output. Each output value is thus the
average of the value produced on that time step with all preceding
values. This running average begins when the fix is defined; it can
only be restarted by deleting the fix via the :doc:`unfix <unfix>`
command, or by re-defining the fix by re-specifying it.
If the *ave* setting is *window*, then the values produced on
timesteps that are multiples of *Nfreq* are summed and averaged within
time steps that are multiples of *Nfreq* are summed and averaged within
a moving "window" of time, so that the last M values are used to
produce the output. E.g. if M = 3 and Nfreq = 1000, then the output
on step 10000 will be the average of the individual values on steps
8000,9000,10000. Outputs on early steps will average over less than M
values if they are not available.
produce the output. For example, if :math:`M = 3` and
:math:`N_\text{freq} = 1000`, then the output on step 10000 will be the average
of the individual values on steps 8000, 9000, and 10000. Outputs on early
steps will average over less than :math:`M` values if they are not available.
The *start* keyword specifies what timestep averaging will begin on.
The *start* keyword specifies what time step averaging will begin on.
The default is step 0. Often input values can be 0.0 at time 0, so
setting *start* to a larger value can avoid including a 0.0 in a
running or windowed average.
@ -262,9 +266,9 @@ The *off* keyword can be used to flag any of the input values. If a
value is flagged, it will not be time averaged. Instead the most
recent input value will always be stored and output. This is useful
if one of more of the inputs produced by a compute or fix or variable
are effectively constant or are simply current values. E.g. they are
are effectively constant or are simply current values (e.g., they are
being written to a file with other time-averaged values for purposes
of creating well-formatted output.
of creating well-formatted output).
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, one quantity or vector of quantities is written to the file for
@ -288,13 +292,13 @@ effort in Python using the *pyyaml*, *pandas*, and *matplotlib*
packages.
The *overwrite* keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
with the latest output, so that it only contains one time step worth of
output. This option can only be used with the *ave running* setting.
The *format* keyword sets the numeric format of each value when it is
printed to a file via the *file* keyword. Note that all values are
floating point quantities. The default format is %g. You can specify
a higher precision if desired, e.g. %20.16g.
a higher precision if desired (e.g., %20.16g).
The *title1* and *title2* and *title3* keywords allow specification of
the strings that will be printed as the first 2 or 3 lines of the
@ -340,8 +344,8 @@ a YAML format file this name will be in the list of keywords.
This fix produces a global scalar or global vector or global array
which can be accessed by various :doc:`output commands <Howto_output>`.
The values can only be accessed on timesteps that are multiples of
*Nfreq* since that is when averaging is performed.
The values can only be accessed on time steps that are multiples of
:math:`N_\text{freq}` since that is when averaging is performed.
A scalar is produced if only a single input value is averaged and
*mode* = scalar. A vector is produced if multiple input values are
@ -354,17 +358,18 @@ of rows = length of the input vectors and # of columns = number of
inputs.
If the fix produces a scalar or vector, then the scalar and each
element of the vector can be either "intensive" or "extensive",
element of the vector can be either "intensive" or "extensive,"
depending on whether the values contributing to the scalar or vector
element are "intensive" or "extensive". If the fix produces an array,
element are "intensive" or "extensive." If the fix produces an array,
then all elements in the array must be the same, either "intensive" or
"extensive". If a compute or fix provides the value being time
"extensive." If a compute or fix provides the value being time
averaged, then the compute or fix determines whether the value is
intensive or extensive; see the page for that compute or fix for
further info. Values produced by a variable are treated as intensive.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
@ -373,7 +378,8 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`,
:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
:doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
Default

18
doc/src/fix_aveforce.rst
View File

@ -6,7 +6,7 @@ fix aveforce command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID aveforce fx fy fz keyword value ...
@ -48,13 +48,13 @@ component. The actual force on each atom is then set to the average
value plus the component specified in this command. This means each
atom in the group receives the same force.
Any of the fx,fy,fz values can be specified as NULL which means the
force in that dimension is not changed. Note that this is not the
Any of the *fx*, *fy*, or *fz* values can be specified as :code:`NULL`, which
means the force in that dimension is not changed. Note that this is not the
same as specifying a 0.0 value, since that sets all forces to the same
average value without adding in any additional force.
Any of the 3 quantities defining the force components can be specified
as an equal-style :doc:`variable <variable>`, namely *fx*, *fy*, *fz*\ .
Any of the three quantities defining the force components, namely *fx*, *fy*,
and *fz*, can be specified as an equal-style :doc:`variable <variable>`\ .
If the value is a variable, it should be specified as v_name, where
name is the variable name. In this case, the variable will be
evaluated each timestep, and its value used to determine the average
@ -78,17 +78,17 @@ to it.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No information about this fix is written to
:doc:`binary restart files <restart>`.
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.
This fix computes a global 3-vector of forces, which can be accessed
This fix computes a global three-vector of forces, which can be accessed
by various :doc:`output commands <Howto_output>`. This is the total
force on the group of atoms before the forces on individual atoms are
changed by the fix. The vector values calculated by this fix are
"extensive".
changed by the fix. The vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

119
doc/src/fix_balance.rst
View File

@ -6,7 +6,7 @@ fix balance command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID balance Nfreq thresh style args keyword args ...
@ -19,7 +19,7 @@ Syntax
.. parsed-literal::
shift args = dimstr Niter stopthresh
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
dimstr = sequence of letters containing *x* or *y* or *z*, each not more than once
Niter = # of times to iterate within each dimension of dimstr sequence
stopthresh = stop balancing when this imbalance threshold is reached
*rcb* args = none
@ -72,10 +72,10 @@ perform "static" balancing, before or between runs, see the
Load-balancing is typically most useful if the particles in the
simulation box have a spatially-varying density distribution or
where the computational cost varies significantly between different
atoms. E.g. a model of a vapor/liquid interface, or a solid with
atoms (e.g., a model of a vapor/liquid interface, or a solid with
an irregular-shaped geometry containing void regions, or
:doc:`hybrid pair style simulations <pair_hybrid>` which combine
pair styles with different computational cost. In these cases, the
:doc:`hybrid pair style simulations <pair_hybrid>` that combine
pair styles with different computational cost). In these cases, the
LAMMPS default of dividing the simulation box volume into a
regular-spaced grid of 3d bricks, with one equal-volume sub-domain
per processor, may assign numbers of particles per processor in a
@ -92,28 +92,30 @@ processor.
.. note::
The weighting options listed above are documented with the
:doc:`balance <balance>` command in :ref:`this section of the balance command <weighted_balance>` doc page. That section
:doc:`balance <balance>` command in :ref:`this section of the balance
command <weighted_balance>` doc page. That section
describes the various weighting options and gives a few examples of
how they can be used. The weighting options are the same for both the
fix balance and :doc:`balance <balance>` commands.
Note that the :doc:`processors <processors>` command allows some control
over how the box volume is split across processors. Specifically, for
a Px by Py by Pz grid of processors, it allows choice of Px, Py, and
Pz, subject to the constraint that Px \* Py \* Pz = P, the total number
of processors. This is sufficient to achieve good load-balance for
a :math:`P_x \times P_y \times P_z` grid of processors, it allows choices of
:math:`P_x`, :math:`P_y`, and :math:`P_z` subject to the constraint that
:math:`P_x P_y P_z = P`, the total number of processors.
This is sufficient to achieve good load-balance for
some problems on some processor counts. However, all the processor
sub-domains will still have the same shape and same volume.
sub-domains will still have the same shape and the same volume.
On a particular timestep, a load-balancing operation is only performed
On a particular time step, a load-balancing operation is only performed
if the current "imbalance factor" in particles owned by each processor
exceeds the specified *thresh* parameter. The imbalance factor is
defined as the maximum number of particles (or weight) owned by any
processor, divided by the average number of particles (or weight) per
processor. Thus an imbalance factor of 1.0 is perfect balance.
processor. Thus, an imbalance factor of 1.0 is perfect balance.
As an example, for 10000 particles running on 10 processors, if the
most heavily loaded processor has 1200 particles, then the factor is
most heavily loaded processor has 1200 particles, then the imbalance factor is
1.2, meaning there is a 20% imbalance. Note that re-balances can be
forced even if the current balance is perfect (1.0) be specifying a
*thresh* < 1.0.
@ -125,28 +127,29 @@ forced even if the current balance is perfect (1.0) be specifying a
may not be achieved. For example, "grid" methods (defined below) that
create a logical 3d grid cannot achieve perfect balance for many
irregular distributions of particles. Likewise, if a portion of the
system is a perfect lattice, e.g. the initial system is generated by
the :doc:`create_atoms <create_atoms>` command, then "grid" methods may
be unable to achieve exact balance. This is because entire lattice
planes will be owned or not owned by a single processor.
system is a perfect, non-rotated lattice (e.g., the initial system is
generated by the :doc:`create_atoms <create_atoms>` command with no
rotations), then "grid" methods may be unable to achieve exact balance.
This is because entire lattice planes will be owned or not owned by a single
processor.
.. note::
The imbalance factor is also an estimate of the maximum speed-up
you can hope to achieve by running a perfectly balanced simulation
versus an imbalanced one. In the example above, the 10000 particle
versus an imbalanced one. In the example above, the 10000-particle
simulation could run up to 20% faster if it were perfectly balanced,
versus when imbalanced. However, computational cost is not strictly
proportional to particle count, and changing the relative size and
shape of processor sub-domains may lead to additional computational
and communication overheads, e.g. in the PPPM solver used via the
:doc:`kspace_style <kspace_style>` command. Thus you should benchmark
and communication overheads (e.g., in the PPPM solver used via the
:doc:`kspace_style <kspace_style>` command). Thus, you should benchmark
the run times of a simulation before and after balancing.
----------
The method used to perform a load balance is specified by one of the
listed styles, which are described in detail below. There are 2 kinds
listed styles, which are described in detail below. There are two kinds
of styles.
The *shift* style is a "grid" method which produces a logical 3d grid
@ -198,11 +201,12 @@ The *group-ID* is ignored. However the impact of balancing on
different groups of atoms can be affected by using the *group* weight
style as described below.
The *Nfreq* setting determines how often a re-balance is performed. If
*Nfreq* > 0, then re-balancing will occur every *Nfreq* steps. Each
time a re-balance occurs, a reneighboring is triggered, so *Nfreq*
should not be too small. If *Nfreq* = 0, then re-balancing will be
done every time reneighboring normally occurs, as determined by the
The :math:`N_\text{freq}` setting determines how often a re-balance is
performed. If :math:`N_\text{freq} > 0`, then re-balancing will occur every
:math:`N_\text{freq}` steps. Each time a re-balance occurs, a reneighboring is
triggered, so :math:`N_\text{freq}` should not be too small. If
:math:`N_\text{freq} = 0`, then re-balancing will be done every time
reneighboring normally occurs, as determined by the
the :doc:`neighbor <neighbor>` and :doc:`neigh_modify <neigh_modify>`
command settings.
@ -216,7 +220,7 @@ above. It changes the positions of cutting planes between processors
in an iterative fashion, seeking to reduce the imbalance factor.
The *dimstr* argument is a string of characters, each of which must be
an "x" or "y" or "z". Each character can appear zero or one time,
*x* or *y* or *z*. Each character can appear zero or one time,
since there is no advantage to balancing on a dimension more than
once. You should normally only list dimensions where you expect there
to be a density variation in the particles.
@ -224,8 +228,8 @@ to be a density variation in the particles.
Balancing proceeds by adjusting the cutting planes in each of the
dimensions listed in *dimstr*, one dimension at a time. For a single
dimension, the balancing operation (described below) is iterated on up
to *Niter* times. After each dimension finishes, the imbalance factor
is re-computed, and the balancing operation halts if the *stopthresh*
to :math:`N_\text{iter}` times. After each dimension finishes, the imbalance
factor is re-computed, and the balancing operation halts if the *stopthresh*
criterion is met.
A re-balance operation in a single dimension is performed using a
@ -265,15 +269,15 @@ the normal reneighboring procedure.
by the extent of a processor's sub-domain in one dimension. The size
of this bracketing region shrinks based on the local density, as
described above, which should typically be 1/2 or more every
iteration. Thus if *Niter* is specified as 10, the cutting plane will
typically be positioned to better than 1 part in 1000 accuracy
(relative to the perfect target position). For *Niter* = 20, it will
be accurate to better than 1 part in a million. Thus there is no need
to set *Niter* to a large value. This is especially true if you are
re-balancing often enough that each time you expect only an incremental
adjustment in the cutting planes is necessary. LAMMPS will check if
the threshold accuracy is reached (in a dimension) is less iterations
than *Niter* and exit early.
iteration. Thus if :math:`N_\text{iter}` is specified as 10, the cutting
plane will typically be positioned to better than 1 part in 1000 accuracy
(relative to the perfect target position). For :math:`N_\text{iter} = 20`,
it will be accurate to better than 1 part in a million. Thus there is no
need to set :math:`N_\text{iter}` to a large value. This is especially true
if you are re-balancing often enough that each time you expect only an
incremental adjustment in the cutting planes is necessary. LAMMPS will
check if the threshold accuracy is reached (in a dimension) is less
iterations than :math:`N_\text{iter}` and exit early.
----------
@ -281,12 +285,12 @@ The *rcb* style invokes a "tiled" method for balancing, as described
above. It performs a recursive coordinate bisectioning (RCB) of the
simulation domain. The basic idea is as follows.
The simulation domain is cut into 2 boxes by an axis-aligned cut in
The simulation domain is cut into two boxes by an axis-aligned cut in
the longest dimension, leaving one new box on either side of the cut.
All the processors are also partitioned into 2 groups, half assigned
All the processors are also partitioned into two groups, half assigned
to the box on the lower side of the cut, and half to the box on the
upper side. (If the processor count is odd, one side gets an extra
processor.) The cut is positioned so that the number of atoms in the
upper side. If the processor count is odd, one side gets an extra
processor. The cut is positioned so that the number of atoms in the
lower box is exactly the number that the processors assigned to that
box should own for load balance to be perfect. This also makes load
balance for the upper box perfect. The positioning is done
@ -309,7 +313,7 @@ results of each re-balancing operation. The file contains the bounds
of the sub-domain for each processor after the balancing operation
completes. The format of the file is compatible with the
`Pizza.py <pizza_>`_ *mdump* tool which has support for manipulating and
visualizing mesh files. An example is shown here for a balancing by 4
visualizing mesh files. An example is shown here for a balancing by four
processors for a 2d problem:
.. parsed-literal::
@ -349,27 +353,28 @@ processors for a 2d problem:
3 1 9 10 11 12
4 1 13 14 15 16
The coordinates of all the vertices are listed in the NODES section, 5
per processor. Note that the 4 sub-domains share vertices, so there
The coordinates of all the vertices are listed in the NODES section, five
per processor. Note that the four sub-domains share vertices, so there
will be duplicate nodes in the list.
The "SQUARES" section lists the node IDs of the 4 vertices in a
The "SQUARES" section lists the node IDs of the four vertices in a
rectangle for each processor (1 to 4).
For a 3d problem, the syntax is similar with 8 vertices listed for
each processor, instead of 4, and "SQUARES" replaced by "CUBES".
For a 3d problem, the syntax is similar but with eight vertices listed for
each processor instead of four, and "SQUARES" replaced by "CUBES."
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to
:doc:`binary restart files <restart>`. None of the
:doc:`fix_modify <fix_modify>` options are relevant to this fix.
This fix computes a global scalar which is the imbalance factor
after the most recent re-balance and a global vector of length 3 with
additional information about the most recent re-balancing. The 3
additional information about the most recent re-balancing. The three
values in the vector are as follows:
* 1 = max # of particles per processor
@ -380,22 +385,24 @@ As explained above, the imbalance factor is the ratio of the maximum
number of particles (or total weight) on any processor to the average
number of particles (or total weight) per processor.
These quantities can be accessed by various :doc:`output commands <Howto_output>`. The scalar and vector values calculated
by this fix are "intensive".
These quantities can be accessed by various
:doc:`output commands <Howto_output>`. The scalar and vector values calculated
by this fix are "intensive."
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
----------
Restrictions
""""""""""""
For 2d simulations, the *z* style cannot be used. Nor can a "z"
For 2d simulations, the *z* style cannot be used, nor can *z*
appear in *dimstr* for the *shift* style.
Balancing through recursive bisectioning (\ *rcb* style) requires
:doc:`comm_style tiled <comm_style>`
:doc:`comm_style tiled <comm_style>`\ .
Related commands
""""""""""""""""

15
doc/src/fix_mdi_qm.rst
View File

@ -125,13 +125,14 @@ LAMMPS atom type corresponds to. This is specified by the atomic
number of the element, e.g. 13 for Al. An atomic number must be
specified for each of the ntypes LAMMPS atom types. Ntypes is
typically specified via the create_box command or in the data file
read by the read_data command. If this keyword is not specified, then
this fix will send the LAMMPS atom type for each atom to the MDI
engine. If both the LAMMPS driver and the MDI engine are initialized
so that atom type values are consistent in both codes, then the
*elements* keyword is not needed. Otherwise the keyword can be used
to insure the two codes are consistent in their definition of atomic
species.
read by the read_data command.
If this keyword is specified, then this fix will send the MDI
">ELEMENTS" command to the engine, to insure the two codes are
consistent in their definition of atomic species. If this keyword is
not specified, then this fix will send the MDI >TYPES command to the
engine. This is fine if both the LAMMPS driver and the MDI engine are
initialized so that the atom type values are consistent in both codes.
----------

2
doc/src/fix_orient_eco.rst
View File

@ -98,7 +98,7 @@ to track the grain boundary motion throughout the simulation.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc: `binary restart
No information about this fix is written to :doc:`binary restart
files <restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by

41
doc/src/improper_coeff.rst
View File

@ -10,7 +10,7 @@ Syntax
improper_coeff N args
* N = improper type (see asterisk form below)
* N = numeric improper type (see asterisk form below), or type label
* args = coefficients for one or more improper types
Examples
@ -22,27 +22,34 @@ Examples
improper_coeff * 80.2 -1 2
improper_coeff *4 80.2 -1 2
labelmap improper 1 benzene
improper_coeff benzene 300.0 0.0
Description
"""""""""""
Specify the improper force field coefficients for one or more improper
types. The number and meaning of the coefficients depends on the
improper style. Improper coefficients can also be set in the data
file read by the :doc:`read_data <read_data>` command or in a restart
file.
improper style. Improper coefficients can also be set in the data file
read by the :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple improper types. This takes
the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of improper
types, then an asterisk with no numeric values means all types from 1
to N. A leading asterisk means all types from 1 to n (inclusive). A
trailing asterisk means all types from n to N (inclusive). A middle
asterisk means all types from m to n (inclusive).
:math:`N` can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or :math:`N` can be a
type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple improper types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If :math:`N` = the number of improper types,
then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using an improper_coeff command can override a previous
setting for the same improper type. For example, these commands set
the coeffs for all improper types, then overwrite the coeffs for just
setting for the same improper type. For example, these commands set the
coeffs for all improper types, then overwrite the coeffs for just
improper type 2:
.. code-block:: LAMMPS
@ -53,9 +60,9 @@ improper type 2:
A line in a data file that specifies improper coefficients uses the
exact same format as the arguments of the improper_coeff command in an
input script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Improper Coeffs" section of a data file, the line that
corresponds to the first example above would be listed as
coefficients for all :math:`N` types must be listed in the file. For
example, under the "Improper Coeffs" section of a data file, the line
that corresponds to the first example above would be listed as
.. parsed-literal::

100
doc/src/labelmap.rst Normal file
View File

@ -0,0 +1,100 @@
.. index:: labelmap
labelmap command
==================
Syntax
""""""
.. code-block:: LAMMPS
labelmap option args
* *option* = *atom* or *bond* or *angle* or *dihedral* or *improper* or *clear* or *write*
.. parsed-literal::
*clear* = no args
*write* arg = filename
*atom* or *bond* or *angle* or *dihedral* or *improper*
args = list of one or more numeric-type/type-label pairs
Examples
""""""""
.. code-block:: LAMMPS
labelmap atom 3 carbon 4 'c3"' 5 "c1'" 6 "c#"
labelmap bond 1 carbonyl 2 nitrile 3 """ c1'-c2" """
labelmap atom $(label2type(atom,carbon)) C # change type label from 'carbon' to 'C'
labelmap clear
labelmap write mymap.include
Description
"""""""""""
.. versionadded:: TBD
Define alphanumeric type labels to associate with one or more numeric
atom, bond, angle, dihedral or improper types. A collection of type
labels for all atom types, bond types, etc. is stored as a label map.
The label map can also be defined by the :doc:`read_data <read_data>`
command when it reads these sections in a data file: Atom Type Labels,
Bond Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for a general discussion of how type
labels can be used.
Valid type labels can contain any alphanumeric character, but must not
start with a number, a '#', or a '*' character. They can contain other
standard ASCII characters such as angular or square brackets '<' and '>'
or '[' and ']', parenthesis '(' and ')', dash '-', underscore '_', plus
'+' and equals '=' signs and more. They must not contain blanks or any
other whitespace. Note that type labels must be put in single or double
quotation marks if they contain the '#' character or if they contain a
double (") or single quotation mark ('). If the label contains both
a single and a double quotation mark, then triple quotation (""") must
be used. When enclosing a type label with quotation marks, the
LAMMPS input parser may require adding leading or trailing blanks
around the type label so it can identify the enclosing quotation
marks. Those blanks will be removed when defining the label.
A *labelmap* command can only modify the label map for one type-kind
(atom types, bond types, etc). Any number of numeric-type/type-label
pairs may follow. If a type label already exists for the same numeric
type, it will be overwritten. Type labels must be unique; assigning the
same type label to multiple numeric types within the same type-kind is
not allowed. When reading and writing data files, it is required that
there is a label defined for *every* numeric type within a given
type-kind in order to write out the type label section for that
type-kind.
The *clear* option resets the labelmap and thus discards all previous
settings.
The *write* option takes a filename as argument and writes the current
label mappings to a file as labelmap commands, so the file can be copied
into a new LAMMPS input file or read in using the :doc:`include
<include>` command.
----------
Restrictions
""""""""""""
This command must come after the simulation box is defined by a
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
:doc:`create_box <create_box>` command.
Labelmaps are currently not supported when using the KOKKOS package.
Related commands
""""""""""""""""
:doc:`read_data <read_data>`, :doc:`write_data <write_data>`,
:doc:`molecule <molecule>`, :doc:`fix bond/react <fix_bond_react>`
Default
"""""""
none

21
doc/src/mass.rst
View File

@ -10,7 +10,7 @@ Syntax
mass I value
* I = atom type (see asterisk form below)
* I = atom type (see asterisk form below), or type label
* value = mass
Examples
@ -22,6 +22,9 @@ Examples
mass * 62.5
mass 2* 62.5
labelmap atom 1 C
mass C 12.01
Description
"""""""""""
@ -30,12 +33,16 @@ values can also be set in the :doc:`read_data <read_data>` data file
using the "Masses" keyword. See the :doc:`units <units>` command for
what mass units to use.
The I index can be specified in one of two ways. An explicit numeric
value can be used, as in the first example above. Or a wild-card
asterisk can be used to set the mass for multiple atom types. This
takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of
atom types, then an asterisk with no numeric values means all types
from 1 to N. A leading asterisk means all types from 1 to n
The I index can be specified in one of several ways. An explicit
numeric value can be used, as in the first example above. Or I can be
a type label, which is an alphanumeric string defined by the
:doc:`labelmap <labelmap>` command or in a section of a data file read
by the :doc:`read_data <read_data>` command, and which converts
internally to a numeric type. Or a wild-card asterisk can be used to
set the mass for multiple atom types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n", where m and n are numbers. If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).

22
doc/src/mdi.rst
View File

@ -14,7 +14,7 @@ Syntax
.. parsed-literal::
*engine* args = zero or more keyword arg pairs
*engine* args = zero or more keyword/args pairs
keywords = *elements*
*elements* args = N_1 N_2 ... N_ntypes
N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
@ -24,7 +24,7 @@ Syntax
keywords = *mdi* or *infile* or *extra* or *command*
*mdi* value = args passed to MDI for driver to operate with plugins (required)
*infile* value = filename the engine will read at start-up (optional)
*extra* value = aditional command-line args to pass to engine library when loaded
*extra* value = aditional command-line args to pass to engine library when loaded (optional)
*command* value = a LAMMPS input script command to execute (required)
*connect* args = none
*exit* args = none
@ -289,11 +289,11 @@ are required. The -name setting can be anything you choose. MDI
drivers and engines can query their names to verify they are values
they expect.
The *infile* keyword is also required. It is the name of an input
script which the engine will open and process. MDI will pass it as a
The *infile* keyword is optional. It sets the name of an input script
which the engine will open and process. MDI will pass it as a
command-line argument to the library when it is launched. The file
typically contains settings that an MD or QM code will use for its
subsequent calculations.
calculations.
The *extra* keyword is optional. It contains additional command-line
arguments which MDI will pass to the library when it is launched.
@ -309,12 +309,12 @@ could specify a filename with multiple LAMMPS commands.
.. note::
When the single *command* is complete, LAMMPS will send an MDI
EXIT command to the plugin engine and the plugin will be removed.
The "mdi plugin" command will then exit and the next command
(if any) in the LAMMPS input script will be processed. A subsequent
"mdi plugin" command could then load the same library plugin or
a different one if desired.
When the *command* is complete, LAMMPS will send an MDI EXIT
command to the plugin engine and the plugin will be removed. The
"mdi plugin" command will then exit and the next command (if any)
in the LAMMPS input script will be processed. A subsequent "mdi
plugin" command could then load the same or a different MDI
plugin if desired.
----------

100
doc/src/molecule.rst
View File

@ -70,8 +70,9 @@ and underscores.
A single template can contain multiple molecules, listed one per file.
Some of the commands listed above currently use only the first
molecule in the template, and will issue a warning if the template
contains multiple molecules. The :doc:`atom_style template <atom_style>` command allows multiple-molecule templates
to define a system with more than one templated molecule.
contains multiple molecules. The :doc:`atom_style template
<atom_style>` command allows multiple-molecule templates to define a
system with more than one templated molecule.
Each filename can be followed by optional keywords which are applied
only to the molecule in the file as used in this template. This is to
@ -88,6 +89,12 @@ molecule file. E.g. if *toff* = 2, and the file uses atom types
individual values will be ignored if the molecule template does not
use that attribute (e.g. no bonds).
.. note::
Offsets are **ignored** on lines using type labels, as the type
labels will determine the actual types directly depending on the
current :doc:`labelmap <labelmap>` settings.
The *scale* keyword scales the size of the molecule. This can be
useful for modeling polydisperse granular rigid bodies. The scale
factor is applied to each of these properties in the molecule file, if
@ -118,14 +125,18 @@ The format of an individual molecule file is similar but
(not identical) to the data file read by the :doc:`read_data <read_data>`
commands, and is as follows.
A molecule file has a header and a body. The header appears first.
The first line of the header is always skipped; it typically contains
a description of the file. Then lines are read one at a time. Lines
can have a trailing comment starting with '#' that is ignored. If the
line is blank (only white-space after comment is deleted), it is
A molecule file has a header and a body. The header appears first. The
first line of the header and thus of the molecule file is *always* skipped;
it typically contains a description of the file or a comment from the software
that created the file.
Then lines are read one line at a time. Lines can have a trailing
comment starting with '#' that is ignored. There *must* be at least one
blank between any valid content and the comment. If the line is blank
(i.e. contains only white-space after comments are deleted), it is
skipped. If the line contains a header keyword, the corresponding
value(s) is read from the line. If it does not contain a header
keyword, the line begins the body of the file.
value(s) is/are read from the line. A line that is *not* blank and does
*not* contains a header keyword begins the body of the file.
The body of the file contains zero or more sections. The first line
of a section has only a keyword. The next line is skipped. The
@ -173,31 +184,43 @@ These are the allowed section keywords for the body of the file.
* *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
atom/bond/angle/etc type can be specified either as a number (numeric
type) or as an alphanumeric type label. The latter is only allowed if
type labels have been defined, either by the :doc:`labelmap
<labelmap>` command or in data files read by the :doc:`read_data
<read_data>` command which have sections for Atom Type Labels, Bond
Type Labels, Angle Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
When using type labels, any values specified as *offset* are ignored.
If a Bonds section is specified then the Special Bond Counts and
Special Bonds sections can also be used, if desired, to explicitly
list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
details below). This is optional since if these sections are not
included, LAMMPS will auto-generate this information. Note that
LAMMPS uses this info to properly exclude or weight bonded pairwise
interactions between bonded atoms. See the
:doc:`special_bonds <special_bonds>` command for more details. One
reason to list the special bond info explicitly is for the
:doc:`thermalized Drude oscillator model <Howto_drude>` which treats the
bonds between nuclear cores and Drude electrons in a different manner.
interactions between bonded atoms. See the :doc:`special_bonds
<special_bonds>` command for more details. One reason to list the
special bond info explicitly is for the :doc:`thermalized Drude
oscillator model <Howto_drude>` which treats the bonds between nuclear
cores and Drude electrons in a different manner.
.. note::
Whether a section is required depends on how the molecule
template is used by other LAMMPS commands. For example, to add a
molecule via the :doc:`fix deposit <fix_deposit>` command, the Coords
and Types sections are required. To add a rigid body via the :doc:`fix pour <fix_pour>` command, the Bonds (Angles, etc) sections are not
Whether a section is required depends on how the molecule template
is used by other LAMMPS commands. For example, to add a molecule
via the :doc:`fix deposit <fix_deposit>` command, the Coords and
Types sections are required. To add a rigid body via the :doc:`fix
pour <fix_pour>` command, the Bonds (Angles, etc) sections are not
required, since the molecule will be treated as a rigid body. Some
sections are optional. For example, the :doc:`fix pour <fix_pour>`
command can be used to add "molecules" which are clusters of
finite-size granular particles. If the Diameters section is not
specified, each particle in the molecule will have a default diameter
of 1.0. See the doc pages for LAMMPS commands that use molecule
templates for more details.
specified, each particle in the molecule will have a default
diameter of 1.0. See the doc pages for LAMMPS commands that use
molecule templates for more details.
Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
@ -222,7 +245,7 @@ order.
* one line per atom
* line syntax: ID type
* type = atom type of atom
* type = atom type of atom (1-Natomtype, or type label)
----------
@ -289,7 +312,7 @@ included, the default mass for each atom is derived from its volume
* one line per bond
* line syntax: ID type atom1 atom2
* type = bond type (1-Nbondtype)
* type = bond type (1-Nbondtype, or type label)
* atom1,atom2 = IDs of atoms in bond
The IDs for the two atoms in each bond should be values
@ -301,7 +324,7 @@ from 1 to Natoms, where Natoms = # of atoms in the molecule.
* one line per angle
* line syntax: ID type atom1 atom2 atom3
* type = angle type (1-Nangletype)
* type = angle type (1-Nangletype, or type label)
* atom1,atom2,atom3 = IDs of atoms in angle
The IDs for the three atoms in each angle should be values from 1 to
@ -315,7 +338,7 @@ which the angle is computed) is the atom2 in the list.
* one line per dihedral
* line syntax: ID type atom1 atom2 atom3 atom4
* type = dihedral type (1-Ndihedraltype)
* type = dihedral type (1-Ndihedraltype, or type label)
* atom1,atom2,atom3,atom4 = IDs of atoms in dihedral
The IDs for the four atoms in each dihedral should be values from 1 to
@ -328,7 +351,7 @@ ordered linearly within the dihedral.
* one line per improper
* line syntax: ID type atom1 atom2 atom3 atom4
* type = improper type (1-Nimpropertype)
* type = improper type (1-Nimpropertype, or type label)
* atom1,atom2,atom3,atom4 = IDs of atoms in improper
The IDs for the four atoms in each improper should be values from 1 to
@ -447,11 +470,15 @@ This section is only needed when molecules created using the template
will be constrained by SHAKE via the "fix shake" command. The other
two Shake sections must also appear in the file.
The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
in the SHAKE cluster that this atom belongs to. The number of values
that must appear is determined by the shake flag for the atom (see the
Shake Flags section above). All atoms in a particular cluster should
list their a,b,c values identically.
The a,b,c values are bond types for all bonds in the SHAKE cluster that
this atom belongs to. Bond types may be either numbers (from 1 to Nbondtypes)
or bond type labels as defined by the :doc:`labelmap <labelmap>` command
or a "Bond Type Labels" section of a data file.
The number of values that must appear is determined by the shake flag
for the atom (see the Shake Flags section above). All atoms in a
particular cluster should list their a,b,c values identically.
If flag = 0, no a,b,c values are listed on the line, just the
(ignored) ID.
@ -459,8 +486,9 @@ If flag = 0, no a,b,c values are listed on the line, just the
If flag = 1, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the second non-central atom (value c in the Shake Atoms section), and c =
the angle type (1 to Nangletypes) of the angle between the 3 atoms.
the second non-central atom (value c in the Shake Atoms section), and c
= the angle type (1 to Nangletypes, or angle type label) of the angle
between the 3 atoms.
If flag = 2, only a is listed, where a = bondtype of the bond between
the 2 atoms in the cluster.
@ -473,9 +501,9 @@ and the second non-central atom (value c in the Shake Atoms section).
If flag = 4, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and
the second non-central atom (value c in the Shake Atoms section), and c =
bondtype of the bond between the central atom and the third non-central
atom (value d in the Shake Atoms section).
the second non-central atom (value c in the Shake Atoms section), and c
= bondtype of the bond between the central atom and the third
non-central atom (value d in the Shake Atoms section).
See the :doc:`fix shake <fix_shake>` page for a further description
of SHAKE clusters.

49
doc/src/pair_coeff.rst
View File

@ -10,7 +10,7 @@ Syntax
pair_coeff I J args
* I,J = atom types (see asterisk form below)
* I,J = numeric atom types (see asterisk form below), or type labels
* args = coefficients for one or more pairs of atom types
Examples
@ -26,6 +26,10 @@ Examples
pair_coeff * 3 morse.table ENTRY1
pair_coeff 1 2 lj/cut 1.0 1.0 2.5 # (for pair_style hybrid)
labelmap atom 1 C
labelmap atom 2 H
pair_coeff C H 1.0 1.0 2.5
Description
"""""""""""
@ -34,20 +38,27 @@ atom types. The number and meaning of the coefficients depends on the
pair style. Pair coefficients can also be set in the data file read
by the :doc:`read_data <read_data>` command or in a restart file.
I and J can be specified in one of two ways. Explicit numeric values
can be used for each, as in the first example above. I <= J is
required. LAMMPS sets the coefficients for the symmetric J,I
interaction to the same values.
I and J can be specified in one of several ways. Explicit numeric
values can be used for each, as in the first example above. Or, one
or both of the types in the I,J pair can be a type label, which is an
alphanumeric string defined by the :doc:`labelmap <labelmap>` command
or in a section of a data file read by the :doc:`read_data
<read_data>` command, and which converts internally to a numeric type.
Internally, LAMMPS will set coefficients for the symmetric J,I
interaction to the same values as the I,J interaction.
A wildcard asterisk can be used in place of or in conjunction with the
I,J arguments to set the coefficients for multiple pairs of atom
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
number of atom types, then an asterisk with no numeric values means all
types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I <= J are considered; if
asterisks imply type pairs where J < I, they are ignored.
For numeric values only, a wildcard asterisk can be used in place of or
in conjunction with the I,J arguments to set the coefficients for
multiple pairs of atom types. This takes the form "\*" or "\*n" or
"n\*" or "m\*n". If :math:`N` is the number of atom types, then an
asterisk with no numeric values means all types from 1 to :math:`N`. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to :math:`N` (inclusive). A middle
asterisk means all types from m to n (inclusive). For the asterisk
syntax, only type pairs with I <= J are considered; if asterisks imply
type pairs where J < I, they are ignored. Again internally, LAMMPS will
set the coefficients for the symmetric J,I interactions to the same
values as the I <= J interactions.
Note that a pair_coeff command can override a previous setting for the
same I,J pair. For example, these commands set the coeffs for all I,J
@ -63,11 +74,11 @@ same format as the arguments of the pair_coeff command in an input
script, with the exception of the I,J type arguments. In each line of
the "Pair Coeffs" section of a data file, only a single type I is
specified, which sets the coefficients for type I interacting with
type I. This is because the section has exactly N lines, where N =
the number of atom types. For this reason, the wild-card asterisk
should also not be used as part of the I argument. Thus in a data
file, the line corresponding to the first example above would be listed
as
type I. This is because the section has exactly :math:`N` lines, where
:math:`N` is the number of atom types. For this reason, the wild-card
asterisk should also not be used as part of the I argument. Thus in a
data file, the line corresponding to the first example above would be
listed as
.. parsed-literal::

2
doc/src/pair_dipole.rst
View File

@ -249,7 +249,7 @@ Style *lj/long/dipole/long* has the same functionality as style
*lj/cut/dipole/long*, except it also has an option to compute 12/6
Lennard-Jones interactions for use with a long-range dispersion kspace
style. This is done by setting its *flag_lj* argument to *long*. For
long-range LJ interactions, the doc:`kspace_style ewald/disp
long-range LJ interactions, the :doc:`kspace_style ewald/disp
<kspace_style>` command must be used.
----------

5
doc/src/pair_harmonic_cut.rst
View File

@ -33,7 +33,8 @@ Style *harmonic/cut* computes pairwise repulsive-only harmonic interactions with
E = k (r_c - r)^2 \qquad r < r_c
:math:`r_c` is the cutoff.
where :math:`r_c` is the cutoff. Note that the usual 1/2 factor is
included in :math:`k`.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -41,7 +42,7 @@ above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`k` (energy units)
* :math:`k` (energy/distance^2 units)
* :math:`r_c` (distance units)
----------

242
doc/src/pair_mesocnt.rst
View File

@ -1,68 +1,153 @@
.. index:: pair_style mesocnt
.. index:: pair_style mesocnt/viscous
pair_style mesocnt command
==========================
pair_style mesocnt/viscous command
==================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style mesocnt
pair_style style neigh_cutoff mode neigh_mode
* style = *mesocnt* or *mesocnt/viscous*
* neigh_cutoff = neighbor list cutoff (distance units)
* mode = *chain* or *segment* (optional)
* neigh_mode = *id* or *topology* (optional)
Examples
""""""""
.. code-block:: LAMMPS
pair_style mesocnt
pair_coeff * * 10_10.cnt
pair_style mesocnt 30.0
pair_coeff * * C_10_10.mesocnt 2
pair_style mesocnt/viscous 60.0 chain topology
pair_coeff * * C_10_10.mesocnt 0.001 20.0 0.2 2 4
Description
"""""""""""
Style *mesocnt* implements a mesoscopic potential
for the interaction of carbon nanotubes (CNTs). In this potential,
CNTs are modelled as chains of cylindrical segments in which
each infinitesimal surface element interacts with all other
CNT surface elements with the Lennard-Jones (LJ) term adopted from
the :doc:`airebo <pair_airebo>` style. The interaction energy
is then computed by integrating over the surfaces of all interacting
CNTs.
Style *mesocnt* implements a mesoscopic potential for the interaction
of carbon nanotubes (CNTs), or other quasi-1D objects such as other
kinds of nanotubes or nanowires. In this potential, CNTs are modelled
as chains of cylindrical segments in which each infinitesimal surface
element interacts with all other CNT surface elements with the
Lennard-Jones (LJ) term adopted from the :doc:`airebo <pair_airebo>`
style. The interaction energy is then computed by integrating over the
surfaces of all interacting CNTs.
The potential is based on interactions between one cylindrical
segment and infinitely or semi-infinitely long CNTs as described
in :ref:`(Volkov1) <Volkov1>`. Chains of segments are
converted to these (semi-)infinite CNTs bases on an approximate
chain approach outlined in :ref:`(Volkov2) <Volkov2>`.
This allows to simplify the computation of the interactions
significantly and reduces the computational times to the
same order of magnitude as for regular bead spring models
where beads interact with the standard :doc:`pair_lj/cut <pair_lj>`
potential.
In LAMMPS, cylindrical segments are represented by bonds. Each segment
is defined by its two end points ("nodes") which correspond to atoms
in LAMMPS. For the exact functional form of the potential and
implementation details, the reader is referred to the original papers
:ref:`(Volkov1) <Volkov1>` and :ref:`(Volkov2) <Volkov2>`.
In LAMMPS, cylindrical segments are represented by bonds. Each
segment is defined by its two end points ("nodes") which correspond
to atoms in LAMMPS. For the exact functional form of the potential
and implementation details, the reader is referred to the
original papers :ref:`(Volkov1) <Volkov1>` and
:ref:`(Volkov2) <Volkov2>`.
.. versionchanged:: TBD
The potential requires tabulated data provided in a single ASCII
text file specified in the :doc:`pair_coeff <pair_coeff>` command.
The first line of the file provides a time stamp and
general information. The second line lists four integers giving
the number of data points provided in the subsequent four
data tables. The third line lists four floating point numbers:
the CNT radius R, the LJ parameter sigma and two numerical
parameters delta1 and delta2. These four parameters are given
in Angstroms. This is followed by four data tables each separated
by a single empty line. The first two tables have two columns
and list the parameters uInfParallel and Gamma respectively.
The last two tables have three columns giving data on a quadratic
array and list the parameters Phi and uSemiParallel respectively.
uInfParallel and uSemiParallel are given in eV/Angstrom, Phi is
given in eV and Gamma is unitless.
The potential supports two modes, *segment* and *chain*. By default,
*chain* mode is enabled. In *segment* mode, interactions are
pair-wise between all neighboring segments based on a segment-segment
approach (keyword *segment* in pair_style command). In *chain* mode,
interactions are calculated between each segment and infinitely or
semi-infinitely long CNTs as described in :ref:`(Volkov1) <Volkov1>`.
Chains of segments are converted to these (semi-)infinite CNTs bases
on an approximate chain approach outlined in :ref:`(Volkov2)
<Volkov2>`. Hence, interactions are calculated on a segment-chain
basis (keyword *chain* in the pair_style command). Using *chain* mode
allows to simplify the computation of the interactions significantly
and reduces the computational times to the same order of magnitude as
for regular bead spring models where beads interact with the standard
:doc:`pair_lj/cut <pair_lj>` potential. However, this method is only
valid when the curvature of the CNTs in the system is small. When
CNTs are buckled (see :doc:`angle_mesocnt <angle_mesocnt>`), local
curvature can be very high and the pair_style automatically switches
to *segment* mode for interactions involving buckled CNTs.
The potential further implements two different neighbor list
construction modes. Mode *id* uses atom and mol IDs to construct
neighbor lists while *topology* modes uses only the bond topology of
the system. While *id* mode requires bonded atoms to have consecutive
LAMMPS atom IDs and atoms in different CNTs to have different LAMMPS
molecule IDs, *topology* mode has no such requirement. Using *id* mode
is faster and is enabled by default.
.. note::
Neighbor *id* mode requires all CNTs in the system to have distinct
LAMMPS molecule IDs and bonded atoms to have consecutive LAMMPS atom
IDs. If this is not possible (e.g. in simulations of CNT rings),
*topology* mode needs to be enabled in the pair_style command.
.. versionadded:: TBD
In addition to the LJ interactions described above, style
*mesocnt/viscous* explicitly models friction between neighboring
segments. Friction forces are a function of the relative velocity
between a segment and its neighboring approximate chain (even in
*segment* mode) and only act along the axes of the interacting segment
and chain. In this potential, friction forces acting per unit length
of a nanotube segment are modelled as a shifted logistic function:
.. math::
F^{\text{FRICTION}}(v) / L = \frac{F^{\text{max}}}{1 +
\exp(-k(v-v_0))} - \frac{F^{\text{max}}}{1 + \exp(k v_0)}
----------
In the pair_style command, the modes described above can be toggled
using the *segment* or *chain* keywords. The neighbor list cutoff
defines the cutoff within which atoms are included in the neighbor
list for constructing neighboring CNT chains. This is different from
the potential cutoff, which is directly calculated from parameters
specified in the potential file. We recommend using a neighbor list
cutoff of at least 3 times the maximum segment length used in the
simulation to ensure proper neighbor chain construction.
.. note::
CNT ends are treated differently by all *mesocnt* styles. Atoms on
CNT ends need to be assigned different LAMMPS atom types than atoms
not on CNT ends.
Style *mesocnt* requires tabulated data provided in a single ASCII
text file, as well as a list of integers corresponding to all LAMMPS
atom types representing CNT ends:
* filename
* :math:`N` CNT end atom types
For example, if your LAMMPS simulation of (10, 10) nanotubes has 4
atom types where atom types 1 and 3 are assigned to 'inner' nodes and
atom types 2 and 4 are assigned to CNT end nodes, the pair_coeff
command would be:
.. code-block:: LAMMPS
pair_coeff * * C_10_10.mesocnt 2 4
Likewise, style *mesocnt/viscous* also requires the same information
as style *mesocnt*, with the addition of 3 parameters for the viscous
friction forces as listed above:
* filename
* :math:`F^{\text{max}}`
* :math:`k`
* :math:`v_0`
* :math:`N` CNT end atom types
Using the same example system as with style *mesocnt* with the
addition of friction, the pair_coeff command is:
.. code-block:: LAMMPS
pair_coeff * * C_10_10.mesocnt 0.03 20.0 0.20 2 4
Potential files for CNTs can be readily generated using the freely
available code provided on
@ -71,45 +156,51 @@ available code provided on
https://github.com/phankl/cntpot
Using the same approach, it should also be possible to
generate potential files for other 1D systems such as
boron nitride nanotubes.
Using the same approach, it should also be possible to generate
potential files for other 1D systems mentioned above.
.. note::
Because of their size, *mesocnt* style potential files
are not bundled with LAMMPS. When compiling LAMMPS from
source code, the file ``C_10_10.mesocnt`` should be downloaded
transparently from `https://download.lammps.org/potentials/C_10_10.mesocnt <https://download.lammps.org/potentials/C_10_10.mesocnt>`_
This file has as number of data points per table 1001.
This is sufficient for NVT simulations. For proper energy
conservation, we recommend using a potential file where
the resolution for Phi is at least 2001 data points.
Because of their size, *mesocnt* style potential files are not
bundled with LAMMPS. When compiling LAMMPS from source code, the
file ``C_10_10.mesocnt`` should be downloaded separately from
`https://download.lammps.org/potentials/C_10_10.mesocnt
<https://download.lammps.org/potentials/C_10_10.mesocnt>`_
.. note::
The first line of the potential file provides a time stamp and
general information. The second line lists four integers giving the
number of data points provided in the subsequent four data
tables. The third line lists four floating point numbers: the CNT
radius R, the LJ parameter sigma and two numerical parameters
delta1 and delta2. These four parameters are given in
Angstroms. This is followed by four data tables each separated by a
single empty line. The first two tables have two columns and list
the parameters uInfParallel and Gamma respectively. The last two
tables have three columns giving data on a quadratic array and list
the parameters Phi and uSemiParallel respectively. uInfParallel
and uSemiParallel are given in eV/Angstrom, Phi is given in eV and
Gamma is unitless.
The *mesocnt* style requires CNTs to be represented
as a chain of atoms connected by bonds. Atoms need
to be numbered consecutively within one chain.
Atoms belonging to different CNTs need to be assigned
different molecule IDs.
If a simulation produces many warnings about segment-chain
interactions falling outside the interpolation range, we recommend
generating a potential file with lower values of delta1 and delta2.
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair style does not support mixing.
These pair styles does not support mixing.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
These pair styles does not support the :doc:`pair_modify
<pair_modify>` shift, table, and tail options.
The *mesocnt* pair style 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.
These 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.
This pair style can only be used via the *pair* keyword of the
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.
@ -118,12 +209,21 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
This style is part of the MESONT package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
These styles are part of the MESONT package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This pair potential requires the :doc:`newton <newton>` setting to be
These pair styles require the :doc:`newton <newton>` setting to be
"on" for pair interactions.
These pair styles require all 3 :doc:`special_bonds lj
<special_bonds>` settings to be non-zero for proper neighbor list
construction.
Pair style *mesocnt/viscous* requires you to use the :doc:`comm_modify
vel yes <comm_modify>` command so that velocities are stored by ghost
atoms.
Related commands
""""""""""""""""
@ -132,7 +232,7 @@ Related commands
Default
"""""""
none
mode = chain, neigh_mode = id
----------

7
doc/src/pair_style.rst
View File

@ -81,12 +81,12 @@ only the global settings in that command are reset. Any previous
doc:`pair_coeff <pair_coeff>` and :doc:`pair_modify <pair_modify>`
command settings are preserved. The only exception is that if the
global cutoff in the pair_style command is changed, it will override
the corresponding cutoff in any of the previous doc:`pair_modify
the corresponding cutoff in any of the previous :doc:`pair_modify
<pair_coeff>` commands.
Two pair styles which do not follow this rule are the pair_style
*table* and *hybrid* commands. A new pair_style command for these
styles will wipe out all previously specified doc:`pair_coeff
styles will wipe out all previously specified :doc:`pair_coeff
<pair_coeff>` and :doc:`pair_modify <pair_modify>` settings, including
for the sub-styles of the *hybrid* command.
@ -278,7 +278,8 @@ accelerated styles exist.
* :doc:`meam <pair_meam>` - modified embedded atom method (MEAM) in C
* :doc:`meam/spline <pair_meam_spline>` - splined version of MEAM
* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
* :doc:`mesocnt <pair_mesocnt>` - mesoscale model for (carbon) nanotubes
* :doc:`mesocnt <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes
* :doc:`mesocnt/viscous <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes with friction
* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
* :doc:`mesont/tpm <pair_mesont_tpm>` - nanotubes mesoscopic force field
* :doc:`mie/cut <pair_mie>` - Mie potential

225
doc/src/read_data.rst
View File

@ -164,6 +164,12 @@ other types already exist. All five offset values must be specified,
but individual values will be ignored if the data file does not use
that attribute (e.g. no bonds).
.. note::
Offsets are **ignored** on lines using type labels, as the type
labels will determine the actual types directly depending on the
current :doc:`labelmap <labelmap>` settings.
The *shift* keyword can be used to specify an (Sx, Sy, Sz)
displacement applied to the coordinates of each atom. Sz must be 0.0
for a 2d simulation. This is a mechanism for adding structured
@ -227,22 +233,27 @@ The file will be read line by line, but there is a limit of 254
characters per line and characters beyond that limit will be ignored.
A data file has a header and a body. The header appears first. The
first line of the header is always skipped; it typically contains a
description of the file. Then lines are read one at a time. Lines
can have a trailing comment starting with '#' that is ignored. If the
line is blank (only white-space after comment is deleted), it is
skipped. If the line contains a header keyword, the corresponding
value(s) is read from the line. If it does not contain a header
keyword, the line begins the body of the file.
first line of the header and thus of the data file is *always* skipped;
it typically contains a description of the file or a comment from the
software that created the file.
The body of the file contains zero or more sections. The first line
of a section has only a keyword. This line can have a trailing
comment starting with '#' that is either ignored or can be used to
check for a style match, as described below. The next line is
skipped. The remaining lines of the section contain values. The
number of lines depends on the section keyword as described below.
Zero or more blank lines can be used between sections. Sections can
appear in any order, with a few exceptions as noted below.
Then lines are read one line at a time. Lines can have a trailing
comment starting with '#' that is ignored. There *must* be at least one
blank between any valid content and the comment. If a line is blank
(i.e. contains only white-space after comments are deleted), it is
skipped. If the line contains a header keyword, the corresponding
value(s) is/are read from the line. A line that is *not* blank and does
*not* contain a header keyword begins the body of the file.
The body of the file contains zero or more sections. The first line of
a section has only a keyword. This line can have a trailing comment
starting with '#' that is either ignored or can be used to check for a
style match, as described below. There must be a blank between the
keyword and any comment. The *next* line is *always* skipped. The
remaining lines of the section contain values. The number of lines
depends on the section keyword as described below. Zero or more blank
lines can be used *between* sections. Sections can appear in any order,
with a few exceptions as noted below.
The keyword *fix* can be used one or more times. Each usage specifies
a fix that will be used to process a specific portion of the data
@ -477,6 +488,7 @@ These are the section keywords for the body of the file.
* *Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies* = atom-property sections
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
* *Atom Type Labels, Bond Type Labels, Angle Type Labels, Dihedral Type Labels, Improper Type Labels* = type label maps
* *Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs* = force field sections
* *BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs* = class 2 force field sections
@ -503,7 +515,8 @@ section is described including the number of lines it must contain and
rules (if any) for where it can appear in the data file.
Any individual line in the various sections can have a trailing
comment starting with "#" for annotation purposes. E.g. in the
comment starting with "#" for annotation purposes. There must be at least
one blank between valid content and the comment. E.g. in the
Atoms section:
.. parsed-literal::
@ -536,6 +549,26 @@ input script.
----------
*Angle Type Labels* section:
* one line per angle type
* line syntax: ID label
.. parsed-literal::
ID = angle type (1-N)
label = alphanumeric type label
Define alphanumeric type labels for each numeric angle type. These
can be used in the Angles section in place of a numeric type, but only
if the this section appears before the Angles section.
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
allowed syntax of type labels and a general discussion of how type
labels can be used.
----------
*AngleAngle Coeffs* section:
* one line per improper type
@ -568,7 +601,7 @@ input script.
.. parsed-literal::
ID = number of angle (1-Nangles)
type = angle type (1-Nangletype)
type = angle type (1-Nangletype, or type label)
atom1,atom2,atom3 = IDs of 1st,2nd,3rd atom in angle
example:
@ -580,8 +613,15 @@ example:
The 3 atoms are ordered linearly within the angle. Thus the central
atom (around which the angle is computed) is the atom2 in the list.
E.g. H,O,H for a water molecule. The *Angles* section must appear
after the *Atoms* section. All values in this section must be
integers (1, not 1.0).
after the *Atoms* section.
All values in this section must be integers (1, not 1.0). However,
the type can be a numeric value or an alphanumeric label. The latter
is only allowed if the type label has been defined by the
:doc:`labelmap <labelmap>` command or an Angle Type Labels section
earlier in the data file. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
----------
@ -597,6 +637,26 @@ integers (1, not 1.0).
----------
*Atom Type Labels* section:
* one line per atom type
* line syntax: ID label
.. parsed-literal::
ID = numeric atom type (1-N)
label = alphanumeric type label
Define alphanumeric type labels for each numeric atom type. These
can be used in the Atoms section in place of a numeric type, but only
if the Atom Type Labels section appears before the Atoms section.
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
allowed syntax of type labels and a general discussion of how type
labels can be used.
----------
*Atoms* section:
* one line per atom
@ -670,7 +730,7 @@ of analysis.
The per-atom values have these meanings and units, listed alphabetically:
* atom-ID = integer ID of atom
* atom-type = type of atom (1-Ntype)
* atom-type = type of atom (1-Ntype, or type label)
* bodyflag = 1 for body particles, 0 for point particles
* bond_nt = bond NT factor for MESONT particles (?? units)
* buckling = buckling factor for MESONT particles (?? units)
@ -722,6 +782,13 @@ not used (e.g. an atomic system with no bonds), and you don't care if
unique atom IDs appear in dump files, then the atom-IDs can all be set
to 0.
The atom-type can be a numeric value or an alphanumeric label. The
latter is only allowed if the type label has been defined by the
:doc:`labelmap <labelmap>` command or an Atom Type Labels section
earlier in the data file. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
The molecule ID is a second identifier attached to an atom. Normally, it
is a number from 1 to N, identifying which molecule the atom belongs
to. It can be 0 if it is a non-bonded atom or if you don't care to
@ -932,6 +999,26 @@ script.
----------
*Bond Type Labels* section:
* one line per bond type
* line syntax: ID label
.. parsed-literal::
ID = bond type (1-N)
label = alphanumeric type label
Define alphanumeric type labels for each numeric bond type. These can
be used in the Bonds section in place of a numeric type, but only if
the this section appears before the Angles section.
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
allowed syntax of type labels and a general discussion of how type
labels can be used.
----------
*BondAngle Coeffs* section:
* one line per angle type
@ -976,7 +1063,7 @@ script.
.. parsed-literal::
ID = bond number (1-Nbonds)
type = bond type (1-Nbondtype)
type = bond type (1-Nbondtype, or type label)
atom1,atom2 = IDs of 1st,2nd atom in bond
* example:
@ -985,8 +1072,15 @@ script.
12 3 17 29
The *Bonds* section must appear after the *Atoms* section. All values
in this section must be integers (1, not 1.0).
The *Bonds* section must appear after the *Atoms* section.
All values in this section must be integers (1, not 1.0). However,
the type can be a numeric value or an alphanumeric label. The latter
is only allowed if the type label has been defined by the
:doc:`labelmap <labelmap>` command or a Bond Type Labels section
earlier in the data file. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
----------
@ -1014,6 +1108,26 @@ Coefficients can also be set via the
----------
*Dihedral Type Labels* section:
* one line per dihedral type
* line syntax: ID label
.. parsed-literal::
ID = dihedral type (1-N)
label = alphanumeric type label
Define alphanumeric type labels for each numeric dihedral type. These
can be used in the Dihedrals section in place of a numeric type, but
only if the this section appears before the Dihedrals section.
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
allowed syntax of type labels and a general discussion of how type
labels can be used.
----------
*Dihedrals* section:
* one line per dihedral
@ -1022,7 +1136,7 @@ Coefficients can also be set via the
.. parsed-literal::
ID = number of dihedral (1-Ndihedrals)
type = dihedral type (1-Ndihedraltype)
type = dihedral type (1-Ndihedraltype, or type label)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in dihedral
* example:
@ -1032,8 +1146,15 @@ Coefficients can also be set via the
12 4 17 29 30 21
The 4 atoms are ordered linearly within the dihedral. The *Dihedrals*
section must appear after the *Atoms* section. All values in this
section must be integers (1, not 1.0).
section must appear after the *Atoms* section.
All values in this section must be integers (1, not 1.0). However,
the type can be a numeric value or an alphanumeric label. The latter
is only allowed if the type label has been defined by the
:doc:`labelmap <labelmap>` command or a Dihedral Type Labels section
earlier in the data file. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
----------
@ -1115,6 +1236,26 @@ Coefficients can also be set via the
----------
*Improper Type Labels* section:
* one line per improper type
* line syntax: ID label
.. parsed-literal::
ID = improper type (1-N)
label = alphanumeric type label
Define alphanumeric type labels for each numeric improper type. These
can be used in the Impropers section in place of a numeric type, but
only if the this section appears before the Impropers section.
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
allowed syntax of type labels and a general discussion of how type
labels can be used.
----------
*Impropers* section:
* one line per improper
@ -1123,7 +1264,7 @@ Coefficients can also be set via the
.. parsed-literal::
ID = number of improper (1-Nimpropers)
type = improper type (1-Nimpropertype)
type = improper type (1-Nimpropertype, or type label)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in improper
* example:
@ -1133,11 +1274,19 @@ Coefficients can also be set via the
12 3 17 29 13 100
The ordering of the 4 atoms determines the definition of the improper
angle used in the formula for each :doc:`improper style <improper_style>`. See the doc pages for individual styles
for details.
angle used in the formula for each :doc:`improper style
<improper_style>`. See the doc pages for individual styles for
details.
The *Impropers* section must appear after the *Atoms* section. All
values in this section must be integers (1, not 1.0).
The *Impropers* section must appear after the *Atoms* section.
All values in this section must be integers (1, not 1.0). However,
the type can be a numeric value or an alphanumeric label. The latter
is only allowed if the type label has been defined by the
:doc:`labelmap <labelmap>` command or a Improper Type Labels section
earlier in the data file. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
----------
@ -1181,7 +1330,7 @@ The *Lines* section must appear after the *Atoms* section.
.. parsed-literal::
ID = atom type (1-N)
ID = atom type (1-N or atom type label)
mass = mass value
* example:
@ -1195,6 +1344,13 @@ This defines the mass of each atom type. This can also be set via the
used for atom styles that define a mass for individual atoms -
e.g. :doc:`atom_style sphere <atom_style>`.
Using type labels instead of atom type numbers is only allowed if the
type label has been defined by the :doc:`labelmap <labelmap>` command or
a Atom Type Labels section earlier in the data file. See the
:doc:`Howto type labels <Howto_type_labels>` doc page for the allowed
syntax of type labels and a general discussion of how type labels can be
used.
----------
*MiddleBondTorsion Coeffs* section:
@ -1363,11 +1519,14 @@ To read gzipped data files, you must compile LAMMPS with the
-DLAMMPS_GZIP option. See the :doc:`Build settings <Build_settings>`
doc page for details.
Labelmaps are currently not supported when using the KOKKOS package.
Related commands
""""""""""""""""
:doc:`read_dump <read_dump>`, :doc:`read_restart <read_restart>`,
:doc:`create_atoms <create_atoms>`, :doc:`write_data <write_data>`
:doc:`create_atoms <create_atoms>`, :doc:`write_data <write_data>`,
:doc:`labelmap <labelmap>`
Default
"""""""

17
doc/src/restart.rst
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@ -12,7 +12,7 @@ Syntax
restart N root keyword value ...
restart N file1 file2 keyword value ...
* N = write a restart file every this many timesteps
* N = write a restart file on timesteps which are multipls of N
* N can be a variable (see below)
* root = filename to which timestep # is appended
* file1,file2 = two full filenames, toggle between them when writing file
@ -42,13 +42,14 @@ Description
"""""""""""
Write out a binary restart file with the current state of the
simulation every so many timesteps, in either or both of two modes, as
a run proceeds. A value of 0 means do not write out any restart
files. The two modes are as follows. If one filename is specified, a
series of filenames will be created which include the timestep in the
filename. If two filenames are specified, only 2 restart files will
be created, with those names. LAMMPS will toggle between the 2 names
as it writes successive restart files.
simulation on timesteps which are a multiple of N. A value of N = 0
means do not write out any restart files, which is the default.
Restart files are written in one (or both) of two modes as a run
proceeds. If one filename is specified, a series of filenames will be
created which include the timestep in the filename. If two filenames
are specified, only 2 restart files will be created, with those names.
LAMMPS will toggle between the 2 names as it writes successive restart
files.
Note that you can specify the restart command twice, once with a
single filename and once with two filenames. This would allow you,

10
doc/src/variable.rst
View File

@ -66,7 +66,7 @@ Syntax
bound(group,dir,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), torque(group,dim,region),
inertia(group,dimdim,region), omega(group,dim,region)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label)
feature functions = is_active(category,feature), is_available(category,feature), is_defined(category,id)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
@ -505,7 +505,7 @@ references, and references to other variables.
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) |
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x) |
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), label2type(kind,label) |
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom values | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] |
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@ -962,6 +962,12 @@ types, bond types and so on. For the full list of available keywords
*name* and their meaning, see the documentation for extract_setting()
via the link in this paragraph.
The label2type() function converts type labels into numeric types, using label
maps created by the :doc:`labelmap <labelmap>` or :doc:`read_data <read_data>`
commands. The first argument is the label map kind (atom, bond, angle,
dihedral, or improper) and the second argument is the label. The function
returns the corresponding numeric type.
----------
Feature Functions

47
doc/src/write_data.rst
View File

@ -12,12 +12,14 @@ Syntax
* file = name of data file to write out
* zero or more keyword/value pairs may be appended
* keyword = *pair* or *nocoeff*
* keyword = *pair* or *nocoeff* or *nofix* or *nolabelmap*
.. parsed-literal::
*nocoeff* = do not write out force field info
*nofix* = do not write out extra sections read by fixes
*nolabelmap* = do not write out type labels
*types* value = *numeric* or *labels*
*pair* value = *ii* or *ij*
*ii* = write one line of pair coefficient info per atom type
*ij* = write one line of pair coefficient info per IJ atom type pair
@ -94,16 +96,39 @@ data file is read.
----------
The *nocoeff* keyword requests that no force field parameters should
be written to the data file. This can be very helpful, if one wants
to make significant changes to the force field or if the parameters
are read in separately anyway, e.g. from an include file.
Use of the *nocoeff* keyword means no force field parameters are
written to the data file. This can be helpful, for example, if you
want to make significant changes to the force field or if the force
field parameters are read in separately, e.g. from an include file.
The *nofix* keyword requests that no extra sections read by fixes
should be written to the data file (see the *fix* option of the
:doc:`read_data <read_data>` command for details). For example, this
option excludes sections for user-created per-atom properties
from :doc:`fix property/atom <fix_property_atom>`.
Use of the *nofix* keyword means no extra sections read by fixes are
written to the data file (see the *fix* option of the :doc:`read_data
<read_data>` command for details). For example, this option excludes
sections for user-created per-atom properties from :doc:`fix
property/atom <fix_property_atom>`.
The *nolabelmap* and *types* keywords refer to type labels that may be
defined for numeric atom types, bond types, angle types, etc. The
label map can be defined in two ways, either by the :doc:`labelmap
<labelmap>` command or in data files read by the :doc:`read_data
<read_data>` command which have sections for Atom Type Labels, Bond
Type Labels, Angle Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
Use of the *nolabelmap* keyword means that even if type labels exist
for a given type-kind (Atoms, Bonds, Angles, etc.), type labels are
not written to the data file. By default, they are written if they
exist. A type label must be defined for every numeric type (within a
given type-kind) to be written to the data file.
The *types* keyword determines how atom types, bond types, angle
types, etc are written into these data file sections: Atoms, Bonds,
Angles, etc. The default is the *numeric* setting, even if type label
maps exist. If the *labels* setting is used, type labels will be
written to the data file, if the corresponding label map exists. Note
that when using *types labels*, the *nolabelmap* keyword cannot be
used.
The *pair* keyword lets you specify in what format the pair
coefficient information is written into the data file. If the value
@ -144,4 +169,4 @@ Related commands
Default
"""""""
The option defaults are pair = ii.
The option defaults are pair = ii and types_style = numeric.

6
doc/utils/sphinx-config/LAMMPSLexer.py
View File

@ -6,7 +6,7 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
"clear", "comm_modify", "comm_style",
"compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms",
"delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
"displace_atoms", "dump_modify", "dynamical_matrix", "echo",
"displace_atoms", "dump_modify", "dynamical_matrix", "echo", "elif", "else",
"fix_modify", "group2ndx", "hyper", "if", "improper_coeff",
"improper_style", "include", "info", "jump", "kim",
"kspace_modify", "kspace_style", "label", "lattice",
@ -16,8 +16,8 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
"partition", "prd", "print", "processors", "python", "quit", "read_data",
"read_dump", "read_restart", "replicate", "rerun", "reset_ids",
"reset_timestep", "restart", "run", "run_style", "server", "set", "shell",
"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt",
"thermo", "thermo_modify", "thermo_style", "then", "third_order", "timer", "timestep",
"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt", "then",
"thermo", "thermo_modify", "thermo_style", "third_order", "timer", "timestep",
"units", "velocity", "write_coeff",
"write_data", "write_restart")

11
doc/utils/sphinx-config/false_positives.txt
View File

@ -61,6 +61,7 @@ ajs
akohlmey
Aktulga
al
alabel
alain
Alain
Alamos
@ -287,6 +288,7 @@ bitrates
Bitzek
Bjerrum
Bkappa
blabel
Blaise
blanchedalmond
blocksize
@ -750,6 +752,7 @@ dissipative
Dissipative
distharm
dl
dlabel
dlambda
DLAMMPS
dll
@ -1427,6 +1430,7 @@ ijk
ijkl
ik
Ikeshoji
ilabel
Ilie
ilmenau
Ilmenau
@ -1716,6 +1720,8 @@ Kusters
Kutta
Kuznetsov
kx
labelmap
Labelmap
Lachet
Lackmann
Ladd
@ -1939,6 +1945,8 @@ Manolopoulos
manpages
manybody
MANYBODY
mapID
mapIDs
Maras
Marchetti
Marchi
@ -2252,6 +2260,7 @@ nanoparticles
nanotube
Nanotube
nanotubes
nanowires
Narulkar
nasa
nasr
@ -2259,6 +2268,7 @@ natively
Natoli
natoms
Natoms
Natomtype
Nattempt
navajowhite
Navier
@ -3555,6 +3565,7 @@ typeargs
typedefs
typeI
typeJ
typelabel
typeN
typesafe
Tz

2
examples/PACKAGES/dielectric/data.confined
View File

@ -13,7 +13,7 @@ Masses
2 1
3 1
Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature
Atoms # dielectric : id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature
1 0 1 0 0 0 9.99798 0 0 1 0.866 8 6 6 0
2 0 1 0 0.500101 0.866201 9.99798 0 0 1 0.866 8 6 6 0

1521
examples/PACKAGES/mesont/cnt.data
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237628
examples/PACKAGES/mesont/data.film_mesocnt Normal file
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38
examples/PACKAGES/mesont/in.cnt
View File

@ -1,38 +0,0 @@
#Initialisation
units nano
dimension 3
boundary p p p
atom_style full
comm_modify cutoff 11.0
neighbor 7.80 bin
newton on
#Read data
read_data cnt.data
replicate 1 2 2
#Force field
bond_style harmonic
bond_coeff 1 268896.77 2.0
angle_style harmonic
angle_coeff 1 46562.17 180.0
pair_style mesocnt
pair_coeff * * C_10_10.mesocnt
#Output
thermo 1000
dump xyz all xyz 1000 cnt.xyz
#Simulation setup
timestep 1.0e-05
#Nose-Hoover thermostat
fix nvt all nvt temp 300 300 0.001
run 10000

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# initialisation
units metal
dimension 3
boundary p p s
atom_style full
special_bonds lj 1 1 1
neigh_modify every 5 delay 0 check yes
newton on
read_data data.film_mesocnt
# force field
bond_style mesocnt
bond_coeff 1 C 10 10 10
angle_style mesocnt
angle_coeff 1 buckling C 10 10 10
pair_style mesocnt 40 chain
pair_coeff * * C_10_10.mesocnt 1
# output
compute epair all pe pair
compute ebond all pe bond
compute eangle all pe angle
compute epair_atom all pe/atom pair
compute ebond_atom all pe/atom bond
compute eangle_atom all pe/atom angle
fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
thermo_style custom step temp etotal ke pe c_ebond c_eangle c_epair
thermo 10
#dump custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
# simulation setup
velocity all create 600.0 2022 loop geom
timestep 0.01
fix nvt all nvt temp 300.0 300.0 1
run 100

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LAMMPS (3 Aug 2022)
# initialisation
units metal
dimension 3
boundary p p s
atom_style full
special_bonds lj 1 1 1
neigh_modify every 5 delay 0 check yes
newton on
read_data data.film_mesocnt
Reading data file ...
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
1 by 1 by 1 MPI processor grid
reading atoms ...
79596 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
79200 bonds
reading angles ...
78804 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 1 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.012 seconds
read_data CPU = 0.160 seconds
# force field
bond_style mesocnt
bond_coeff 1 C 10 10 10
angle_style mesocnt
angle_coeff 1 buckling C 10 10 10
pair_style mesocnt 40 chain
pair_coeff * * C_10_10.mesocnt 1
Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
# output
compute epair all pe pair
compute ebond all pe bond
compute eangle all pe angle
compute epair_atom all pe/atom pair
compute ebond_atom all pe/atom bond
compute eangle_atom all pe/atom angle
fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
thermo_style custom step temp etotal ke pe c_ebond c_eangle c_epair
thermo 10
#dump custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
# simulation setup
velocity all create 600.0 2022 loop geom
timestep 0.01
fix nvt all nvt temp 300.0 300.0 1
run 100
Neighbor list info ...
update: every = 5 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 42
ghost atom cutoff = 42
binsize = 21, bins = 239 239 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesocnt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 49.89 | 49.89 | 49.89 Mbytes
Step Temp TotEng KinEng PotEng c_ebond c_eangle c_epair
0 600 1355.8735 6173.0767 -4817.2032 28.668731 21.29199 -4867.1639
10 389.92732 1373.1839 4011.7521 -2638.5683 848.77485 1387.6166 -4874.9597
20 311.7468 1388.0161 3207.3949 -1819.3788 1211.534 1868.6817 -4899.5945
30 291.75586 1385.2114 3001.7189 -1616.5075 1184.1423 2133.2088 -4933.8586
40 320.42607 1364.2644 3296.6912 -1932.4267 951.62534 2088.33 -4972.382
50 341.37701 1346.0547 3512.2441 -2166.1894 956.59158 1891.9196 -5014.7005
60 333.15461 1337.5518 3427.6483 -2090.0965 1137.7331 1825.9946 -5053.8242
70 324.47061 1328.7153 3338.3033 -2009.588 1133.3639 1953.8288 -5096.7807
80 324.39487 1315.4948 3337.5241 -2022.0293 979.16213 2141.4697 -5142.6611
90 323.39973 1302.3471 3327.2856 -2024.9385 972.70286 2185.7686 -5183.41
100 322.73067 1289.0538 3320.402 -2031.3482 1100.1024 2088.3804 -5219.831
Loop time of 4.1637 on 1 procs for 100 steps with 79596 atoms
Performance: 20.751 ns/day, 1.157 hours/ns, 24.017 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.705 | 3.705 | 3.705 | 0.0 | 88.98
Bond | 0.29317 | 0.29317 | 0.29317 | 0.0 | 7.04
Neigh | 0.078491 | 0.078491 | 0.078491 | 0.0 | 1.89
Comm | 0.0019462 | 0.0019462 | 0.0019462 | 0.0 | 0.05
Output | 0.00099817 | 0.00099817 | 0.00099817 | 0.0 | 0.02
Modify | 0.079874 | 0.079874 | 0.079874 | 0.0 | 1.92
Other | | 0.004224 | | | 0.10
Nlocal: 79596 ave 79596 max 79596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2567 ave 2567 max 2567 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.1337e+06 ave 1.1337e+06 max 1.1337e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1133696
Ave neighs/atom = 14.243128
Ave special neighs/atom = 5.9402985
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (3 Aug 2022)
# initialisation
units metal
dimension 3
boundary p p s
atom_style full
special_bonds lj 1 1 1
neigh_modify every 5 delay 0 check yes
newton on
read_data data.film_mesocnt
Reading data file ...
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
2 by 2 by 1 MPI processor grid
reading atoms ...
79596 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
79200 bonds
reading angles ...
78804 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 1 1 1
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.005 seconds
read_data CPU = 0.156 seconds
# force field
bond_style mesocnt
bond_coeff 1 C 10 10 10
angle_style mesocnt
angle_coeff 1 buckling C 10 10 10
pair_style mesocnt 40 chain
pair_coeff * * C_10_10.mesocnt 1
Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12
# output
compute epair all pe pair
compute ebond all pe bond
compute eangle all pe angle
compute epair_atom all pe/atom pair
compute ebond_atom all pe/atom bond
compute eangle_atom all pe/atom angle
fix angle_mesocnt_buckled all property/atom i_buckled ghost yes
thermo_style custom step temp etotal ke pe c_ebond c_eangle c_epair
thermo 10
#dump custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled
# simulation setup
velocity all create 600.0 2022 loop geom
timestep 0.01
fix nvt all nvt temp 300.0 300.0 1
run 100
Neighbor list info ...
update: every = 5 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 42
ghost atom cutoff = 42
binsize = 21, bins = 239 239 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesocnt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.47 | 16.58 | 16.89 Mbytes
Step Temp TotEng KinEng PotEng c_ebond c_eangle c_epair
0 600 1355.8735 6173.0767 -4817.2032 28.668731 21.29199 -4867.1639
10 389.92732 1373.1839 4011.7521 -2638.5683 848.77485 1387.6166 -4874.9597
20 311.7468 1388.0161 3207.3949 -1819.3788 1211.534 1868.6817 -4899.5945
30 291.75586 1385.2114 3001.7189 -1616.5075 1184.1423 2133.2088 -4933.8586
40 320.42607 1364.2644 3296.6912 -1932.4267 951.62534 2088.33 -4972.382
50 341.37701 1346.0547 3512.2441 -2166.1894 956.59158 1891.9196 -5014.7005
60 333.15461 1337.5518 3427.6483 -2090.0965 1137.7331 1825.9946 -5053.8242
70 324.47061 1328.7153 3338.3033 -2009.588 1133.3639 1953.8288 -5096.7807
80 324.39487 1315.4948 3337.5241 -2022.0293 979.16213 2141.4697 -5142.6611
90 323.39973 1302.3471 3327.2856 -2024.9385 972.70286 2185.7686 -5183.41
100 322.73067 1289.0538 3320.402 -2031.3482 1100.1024 2088.3804 -5219.831
Loop time of 1.25052 on 4 procs for 100 steps with 79596 atoms
Performance: 69.091 ns/day, 0.347 hours/ns, 79.967 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.87036 | 0.97558 | 1.1135 | 9.0 | 78.01
Bond | 0.071751 | 0.076357 | 0.084244 | 1.7 | 6.11
Neigh | 0.023232 | 0.023239 | 0.023244 | 0.0 | 1.86
Comm | 0.0046002 | 0.15227 | 0.26319 | 24.1 | 12.18
Output | 0.00032696 | 0.00037811 | 0.00045537 | 0.0 | 0.03
Modify | 0.019263 | 0.020646 | 0.023155 | 1.1 | 1.65
Other | | 0.00204 | | | 0.16
Nlocal: 19899 ave 21951 max 18670 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 1323.5 ave 1412 max 1255 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 283424 ave 325466 max 258171 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1133696
Ave neighs/atom = 14.243128
Ave special neighs/atom = 5.9402985
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (09 Jan 2020)
#Initialisation
units nano
dimension 3
boundary p p p
atom_style full
comm_modify cutoff 11.0
neighbor 7.80 bin
newton on
#Read data
read_data cnt.data
orthogonal box = (0 0 0) to (600 600 60)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
498 bonds
reading angles ...
496 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000180006 secs
read_data CPU = 0.00125766 secs
replicate 1 2 2
orthogonal box = (0 0 0) to (600 1200 120)
1 by 1 by 1 MPI processor grid
2000 atoms
1992 bonds
1984 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.00054121 secs
replicate CPU = 0.000902414 secs
#Force field
bond_style harmonic
bond_coeff 1 268896.77 2.0
angle_style harmonic
angle_coeff 1 46562.17 180.0
pair_style mesocnt
pair_coeff * * 10_10.cnt
Reading potential file 10_10.cnt with DATE: 2020-01-13
#Output
thermo 1000
dump xyz all xyz 1000 cnt.xyz
#Simulation setup
timestep 1.0e-05
#Nose-Hoover thermostat
fix nvt all nvt temp 300 300 0.001
run 10000
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.177
ghost atom cutoff = 11
binsize = 5.0885, bins = 118 236 24
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesocnt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.21 | 11.21 | 11.21 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304
1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182
2000 300.43933 -28320.212 11980.296 -3902.0877 -0.0045324757
3000 300.4263 -36049.855 11338.405 -12274.161 -0.0018833539
4000 299.13368 -43471.21 11926.882 -19160.553 -0.00043030866
5000 293.77858 -50083.893 12334.927 -25586.884 -0.0015653738
6000 296.4851 -56330.135 12325.63 -31730.376 -0.0012795986
7000 298.20879 -62120.359 12582.297 -37192.574 -0.0013845796
8000 299.45547 -67881.692 13058.926 -42425.669 -0.00021100885
9000 301.82622 -73333.698 13598.257 -47240.197 -0.0006009197
10000 307.16873 -78292.306 13818.929 -51756.96 -0.0005609903
Loop time of 4.0316 on 1 procs for 10000 steps with 2000 atoms
Performance: 2143.072 ns/day, 0.011 hours/ns, 2480.408 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5955 | 2.5955 | 2.5955 | 0.0 | 64.38
Bond | 1.1516 | 1.1516 | 1.1516 | 0.0 | 28.57
Neigh | 0.001163 | 0.001163 | 0.001163 | 0.0 | 0.03
Comm | 0.0019577 | 0.0019577 | 0.0019577 | 0.0 | 0.05
Output | 0.020854 | 0.020854 | 0.020854 | 0.0 | 0.52
Modify | 0.21637 | 0.21637 | 0.21637 | 0.0 | 5.37
Other | | 0.04409 | | | 1.09
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13320 ave 13320 max 13320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13320
Ave neighs/atom = 6.66
Ave special neighs/atom = 5.952
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (09 Jan 2020)
#Initialisation
units nano
dimension 3
boundary p p p
atom_style full
comm_modify cutoff 11.0
neighbor 7.80 bin
newton on
#Read data
read_data cnt.data
orthogonal box = (0 0 0) to (600 600 60)
2 by 2 by 1 MPI processor grid
reading atoms ...
500 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
498 bonds
reading angles ...
496 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.000354767 secs
read_data CPU = 0.00286365 secs
replicate 1 2 2
orthogonal box = (0 0 0) to (600 1200 120)
1 by 4 by 1 MPI processor grid
2000 atoms
1992 bonds
1984 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
special bonds CPU = 0.00019598 secs
replicate CPU = 0.00055337 secs
#Force field
bond_style harmonic
bond_coeff 1 268896.77 2.0
angle_style harmonic
angle_coeff 1 46562.17 180.0
pair_style mesocnt
pair_coeff * * 10_10.cnt
Reading potential file 10_10.cnt with DATE: 2020-01-13
#Output
thermo 1000
dump xyz all xyz 1000 cnt.xyz
#Simulation setup
timestep 1.0e-05
#Nose-Hoover thermostat
fix nvt all nvt temp 300 300 0.001
run 10000
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.177
ghost atom cutoff = 11
binsize = 5.0885, bins = 118 236 24
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mesocnt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.725 | 2.725 | 2.725 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304
1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182
2000 300.43861 -28320.205 11980.287 -3902.1202 -0.0045324738
3000 300.41076 -36049.308 11339.149 -12273.513 -0.0018848513
4000 299.13326 -43471.424 11927.668 -19159.998 -0.00042845101
5000 293.78857 -50083.216 12333.969 -25586.752 -0.0015664633
6000 296.45482 -56329.621 12326.419 -31730.328 -0.0012773686
7000 298.19097 -62119.086 12581.4 -37192.937 -0.0013862831
8000 299.46424 -67880.989 13057.62 -42425.908 -0.00020874264
9000 301.80677 -73332.208 13597.237 -47240.532 -0.00060074773
10000 307.17104 -78292.912 13818.889 -51757.51 -0.00056148282
Loop time of 1.23665 on 4 procs for 10000 steps with 2000 atoms
Performance: 6986.607 ns/day, 0.003 hours/ns, 8086.351 timesteps/s
96.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.66321 | 0.68439 | 0.71413 | 2.5 | 55.34
Bond | 0.28561 | 0.29434 | 0.30976 | 1.7 | 23.80
Neigh | 0.00043321 | 0.00043637 | 0.00043917 | 0.0 | 0.04
Comm | 0.026656 | 0.05346 | 0.097228 | 12.7 | 4.32
Output | 0.0070224 | 0.0073031 | 0.0081415 | 0.6 | 0.59
Modify | 0.12769 | 0.15394 | 0.18743 | 6.5 | 12.45
Other | | 0.04279 | | | 3.46
Nlocal: 500 ave 504 max 496 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 22 ave 24 max 20 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3330 ave 3368 max 3292 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 13320
Ave neighs/atom = 6.66
Ave special neighs/atom = 5.952
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS Description
6 atoms
2 atom types
0.0000000000000000 10.800000000000001 xlo xhi
0.0000000000000000 5.4000000000000004 ylo yhi
0.0000000000000000 5.4000000000000004 zlo zhi
3.3065463576978537E-016 3.3065463576978537E-016 3.3065463576978537E-016 xy xz yz
Masses
1 238.05078125000000
2 15.994915008544922
Atoms
1 1 1 0.0 2.70000 8.10000 0.00000
2 1 2 0.0 1.35000 9.45000 1.35000
3 1 2 0.0 4.05000 9.45000 1.35000
4 1 1 0.0 2.70000 10.80000 2.70000
5 1 2 0.0 1.35000 12.15000 4.05000
6 1 2 0.0 4.05000 12.15000 4.05000

27
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LAMMPS Description
9 atoms
2 atom types
0.0000000000000000 16.199999999999999 xlo xhi
0.0000000000000000 5.4000000000000004 ylo yhi
0.0000000000000000 5.4000000000000004 zlo zhi
3.3065463576978537E-016 3.3065463576978537E-016 3.3065463576978537E-016 xy xz yz
Masses
1 238.05078125000000
2 15.994915008544922
Atoms
1 1 1 0.0 2.70000 8.10000 0.00000
2 1 2 0.0 1.35000 9.45000 1.35000
3 1 2 0.0 4.05000 9.45000 1.35000
4 1 1 0.0 2.70000 10.80000 2.70000
5 1 2 0.0 1.35000 12.15000 4.05000
6 1 2 0.0 4.05000 12.15000 4.05000
7 1 1 0.0 2.70000 13.50000 5.40000
8 1 2 0.0 1.35000 14.85000 6.75000
9 1 2 0.0 4.05000 14.85000 6.75000

30
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LAMMPS Description
12 atoms
2 atom types
0.0000000000000000 10.800000000000001 xlo xhi
0.0000000000000000 10.800000000000001 ylo yhi
0.0000000000000000 5.4000000000000004 zlo zhi
6.6130927153957075E-016 3.3065463576978537E-016 3.3065463576978537E-016 xy xz yz
Masses
1 238.05078125000000
2 15.994915008544922
Atoms
1 1 1 0.0 2.70000 8.10000 0.00000
2 1 2 0.0 1.35000 9.45000 1.35000
3 1 2 0.0 4.05000 9.45000 1.35000
4 1 1 0.0 5.40000 8.10000 2.70000
5 1 2 0.0 4.05000 9.45000 4.05000
6 1 2 0.0 6.75000 9.45000 4.05000
7 1 1 0.0 2.70000 10.80000 2.70000
8 1 2 0.0 1.35000 12.15000 4.05000
9 1 2 0.0 4.05000 12.15000 4.05000
10 1 1 0.0 5.40000 10.80000 5.40000
11 1 2 0.0 4.05000 12.15000 6.75000
12 1 2 0.0 6.75000 12.15000 6.75000

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LATTE is a semi-empirical tight-binding quantum code, developed
primarily at Los Alamos National Labs.
See these links:
https://www.osti.gov/biblio/1526907-los-alamos-transferable-tight-binding-energetics-latte-version
https://github.com/lanl/LATTE
LAMMPS has 2 ways of working with LATTE:
(1) Via its LATTE package and the fix latte command
must run LAMMPS on a single processor, it calls LATTE as a library
(2) Via its MDI package and the code-coupling MDI library
(a) can run LAMMPS and LATTE as stand-alone codes
LAMMPS can be run on any number of procs
LATTE must run on a single proc, but can use OpenMP
(b) can run LAMMPS with LATTE as a plug-in library
must run LAMMPS on a single processor
Examples for use case (1) are in the examples/latte dir. Use case (2)
is illustrated in this dir.
NOTE: If you compare MDI runs in this dir to similar fix latte runs in
examples/latte, the answers for energy and virial will be differnt.
This is b/c the version of LATTE used by the fix latte command within
the LATTE package is older than the version of LATTE used here.
------------------
Building 3 codes needed to run these examples
(1) Download and build MDI
% git clone git@github.com:MolSSI-MDI/MDI_Library.git mdi
% cd mdi
% mkdir build; cd build
% cmake .. # includes support for all langauges (incl Fortran, Python)
% make
(2) Download and build LATTE with MDI support
% git clone git@github.com:lanl/LATTE.git latte
% cd latte
% git checkout skimLATTE-progress # goto branch with MDI support
% cp makefiles/makefile.CHOICES.mdi makefile.CHOICES # so can now edit
% edit makefile.CHOICES settings to have these settings:
MAKELIB = OFF, SHARED = ON, MDI = ON
MDI_PATH must point to CMake build of MDI in (1),
e.g. /home/sjplimp/mdi/build/MDI_Library
comment out 2 LIB lines with CUDA-CUDART_LIBRARY
% make clean
% make # creates liblatte.so and LATTE_DOUBLE with support for MDI
(3) Build LAMMPS with its MDI package
also with the MOLECULE package for these example scripts
Build with traditional make
% cd lammps/lib/mdi
% python Install.py -m mpi # downloads and builds MDI
% cd ../../src
% make yes-mdi yes-molecule
$ make mpi # creates lmp_mpi
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
% make # creates lmp
Build with CMake
% cd lammps
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
% make # creates lmp
(4) Copy LAMMPS and LATTE executables into this dir
Copy the LAMMPS executable (lmp_mpi or lmp) into this dir as lmp_mpi.
Copy the LATTE executable LATTE_DOUBLE into this dir.
The run commands below assume you have done this.
(5) Insure LD_LIBRARY_PATH includes the dir where MDI was built in (1)
with its libmdi.so file, e.g. mdi/build/MDI_Library. This is needed
so when LATTE_DOUBLE runs as an executable it will able to find
libmdi.so.
------------------
Notes on LATTE usage
You must run this version of LATTE on a single MPI processor.
However, you can use OpenMP with LATTE. To do this you need to build
LATTE with OpenMP support by editing the makefile.CHOICES file to
include -fopenmp with FFLAGS and LINKFLAGS. Also -lapack and -lblas
need to be added to LIB, and those libraries must be available on your
system. For best performance you should also build LATTE with its
PROGRESS and BML libraries. Building those libs is more complex,
see details here:
https://github.com/lanl/LATTE_SUPER/tree/allMachines/Laptop
At run time, you need to also first set an environment variable for
the number of OpenMP threads to use, e.g.
% export OMP_NUM_THREADS=12
By default LATTE reads the latte.in file for its parameters. That
file specifies other files LATTE will read. With MDI, the driver code
(e.g. LAMMPS) can use the >FNAME command to specify an alternate
filename to use instead of latte.in.
By default LATTE writes out a log.latte file with info about its
calculations. An "OUTFILE= logfile" setting in latte.in can rename
this file.
---------
Run example #1: AIMD
* Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.aimd -log log.aimd.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.aimd -log log.aimd.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run in plugin mode: 1 proc
lmp_mpi -mdi \
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
-in in.aimd.plugin -log log.aimd.lammps.plugin
NOTE: The -plugin_path needs to point to where LATTE was built in step
(2).
---------
Run example #2: sequence of configurations
* Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.series -log log.series.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.series -log log.series.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run in plugin mode: 1 proc
lmp_mpi -mdi \
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
-in in.series.plugin -log log.series.lammps.plugin
NOTE: The -plugin_path needs to point to where LATTE was built in step
(2).

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ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.7 2.7 0 -0.601491 0.335597 -0.87242 -2.27066e-14 -1.33391e-14 2.31141e-14
2 2 1.35 4.05 1.35 8.2897 4.55901 5.97376 2.35473 2.21578e-14 7.40069e-15
3 2 4.05 4.05 1.35 1.7742 6.51885 0.385522 -2.35473 2.97071e-15 -2.01341e-14
4 1 2.7 1.65327e-16 2.7 -0.325605 -1.03244 0.724324 -2.90278e-14 6.77422e-15 2.86766e-15
5 2 1.35 1.35 4.05 2.42711 -1.49109 -2.41596 2.35473 5.79901e-15 -1.19594e-14
6 2 4.05 1.35 4.05 1.30688 0.784281 -1.73922 -2.35473 -1.38761e-14 1.09382e-14
ITEM: TIMESTEP
1
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69985 2.70008 -0.000218105 -0.601467 0.335616 -0.872428 0.00470101 0.00380515 -0.00141625
2 2 1.35212 4.05114 1.35149 8.64389 4.55886 5.97363 2.34251 -0.00209926 -0.00172976
3 2 4.0504 4.05163 1.3501 1.41949 6.51866 0.385561 -2.34936 -0.00247497 0.00051716
4 1 2.69992 -0.00025811 2.70018 -0.325581 -1.03243 0.724334 0.00481137 0.00249244 0.00195665
5 2 1.35065 1.34963 4.0494 2.78199 -1.49112 -2.4159 2.3517 -0.00043711 0.000874754
6 2 4.05028 1.3502 4.04957 0.951796 0.784184 -1.73923 -2.35436 -0.00128625 -0.00020256
ITEM: TIMESTEP
2
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.6997 2.70017 -0.000436214 -0.601396 0.335673 -0.872449 0.00939888 0.00756163 -0.00288164
2 2 1.35432 4.05228 1.35299 8.99615 4.55837 5.97323 2.32921 -0.00431846 -0.00355855
3 2 4.05071 4.05326 1.35019 1.06567 6.5181 0.385678 -2.34304 -0.00494314 0.00103532
4 1 2.69984 -0.000516214 2.70036 -0.325507 -1.03239 0.724364 0.00976944 0.00512657 0.00403686
5 2 1.35139 1.34925 4.04879 3.13634 -1.49122 -2.4157 2.34776 -0.000851489 0.00177498
6 2 4.05048 1.35039 4.04913 0.596838 0.783892 -1.73928 -2.3531 -0.00257512 -0.000406965
ITEM: TIMESTEP
3
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69955 2.70025 -0.00065433 -0.601277 0.335769 -0.872486 0.0141006 0.0112702 -0.00439552
2 2 1.35661 4.05342 1.35448 9.34633 4.55754 5.97255 2.31482 -0.00666433 -0.00549143
3 2 4.05093 4.05489 1.35029 0.712875 6.51717 0.385873 -2.33577 -0.00740896 0.00154764
4 1 2.69976 -0.000774304 2.70054 -0.325382 -1.03232 0.724417 0.0148831 0.00790884 0.00624833
5 2 1.35222 1.34888 4.04819 3.49003 -1.49137 -2.41536 2.3429 -0.0012407 0.00270313
6 2 4.05058 1.35059 4.0487 0.242138 0.783407 -1.73935 -2.35094 -0.00386511 -0.000612161
ITEM: TIMESTEP
4
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.6994 2.70034 -0.000872457 -0.60111 0.335902 -0.872539 0.0188131 0.0149318 -0.00595718
2 2 1.359 4.05456 1.35597 9.69425 4.55635 5.97156 2.29933 -0.00914346 -0.00753331
3 2 4.05107 4.05652 1.35039 0.361248 6.51586 0.386144 -2.32753 -0.00987687 0.00204727
4 1 2.69967 -0.00103238 2.70072 -0.325204 -1.03223 0.724492 0.020161 0.0108455 0.00859866
5 2 1.35314 1.34851 4.04758 3.84292 -1.49159 -2.41488 2.33711 -0.00160232 0.00366164
6 2 4.0506 1.35078 4.04826 -0.112168 0.782727 -1.73946 -2.34789 -0.00515472 -0.000817084
ITEM: TIMESTEP
5
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69925 2.70042 -0.0010906 -0.600896 0.336071 -0.872607 0.0235434 0.0185473 -0.00756588
2 2 1.36146 4.0557 1.35747 10.0397 4.55478 5.97026 2.2827 -0.0117623 -0.00968894
3 2 4.05111 4.05815 1.35048 0.0109366 6.51419 0.386489 -2.31832 -0.0123511 0.00252727
4 1 2.69959 -0.00129042 2.70091 -0.324972 -1.0321 0.724592 0.0256115 0.0139425 0.0110953
5 2 1.35414 1.34814 4.04698 4.19487 -1.49186 -2.41425 2.33039 -0.00193394 0.0046529
6 2 4.05052 1.35098 4.04783 -0.465946 0.781852 -1.7396 -2.34393 -0.00644244 -0.00102066
ITEM: TIMESTEP
6
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.6991 2.7005 -0.00130876 -0.600633 0.336277 -0.872692 0.0282985 0.0221175 -0.00922083
2 2 1.36401 4.05684 1.35896 10.3827 4.55279 5.96863 2.26494 -0.0145272 -0.0119629
3 2 4.05107 4.05978 1.35058 -0.337913 6.51214 0.386904 -2.30814 -0.0148362 0.00298071
4 1 2.69951 -0.00154843 2.70109 -0.324684 -1.03194 0.724717 0.0312427 0.0172058 0.0137455
5 2 1.35523 1.34776 4.04638 4.54573 -1.49217 -2.41347 2.32273 -0.00223319 0.00567932
6 2 4.05036 1.35117 4.04739 -0.819058 0.780784 -1.73977 -2.33906 -0.00772673 -0.00122181
ITEM: TIMESTEP
7
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69895 2.70059 -0.00152695 -0.600322 0.336519 -0.872794 0.0330853 0.0256435 -0.0109212
2 2 1.36665 4.05797 1.36045 10.7228 4.55038 5.96665 2.24601 -0.0174443 -0.0143597
3 2 4.05094 4.0614 1.35068 -0.685154 6.50971 0.387385 -2.29698 -0.0173365 0.00340068
4 1 2.69943 -0.00180639 2.70127 -0.324338 -1.03175 0.724871 0.0370626 0.020641 0.0165564
5 2 1.35641 1.34739 4.04577 4.89536 -1.49253 -2.41254 2.31411 -0.0024977 0.00674323
6 2 4.05012 1.35137 4.04696 -1.17137 0.779522 -1.73997 -2.33329 -0.00900604 -0.00141944
ITEM: TIMESTEP
8
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.6988 2.70067 -0.00174516 -0.599962 0.336797 -0.872914 0.0379108 0.0291262 -0.0126661
2 2 1.36938 4.05911 1.36194 11.06 4.54752 5.96429 2.2259 -0.0205196 -0.0168834
3 2 4.05073 4.06303 1.35077 -1.03064 6.50691 0.387927 -2.28482 -0.0198564 0.00378025
4 1 2.69935 -0.0020643 2.70145 -0.323932 -1.03153 0.725054 0.0430788 0.0242538 0.0195348
5 2 1.35768 1.34702 4.04517 5.24362 -1.49292 -2.41144 2.30452 -0.0027252 0.00784692
6 2 4.04978 1.35156 4.04652 -1.52274 0.778068 -1.7402 -2.32659 -0.0102788 -0.00161245
ITEM: TIMESTEP
9
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69865 2.70076 -0.0019634 -0.599553 0.337109 -0.873051 0.0427817 0.0325667 -0.0144547
2 2 1.37218 4.06025 1.36343 11.3941 4.54418 5.96155 2.20459 -0.023759 -0.019538
3 2 4.05043 4.06466 1.35087 -1.37421 6.50372 0.388522 -2.27166 -0.0224003 0.00411244
4 1 2.69927 -0.00232215 2.70163 -0.323464 -1.03126 0.725268 0.0492987 0.0280495 0.0226874
5 2 1.35904 1.34664 4.04457 5.59036 -1.49335 -2.41017 2.29396 -0.00291347 0.00899259
6 2 4.04935 1.35176 4.04609 -1.87303 0.776422 -1.74045 -2.31898 -0.0115434 -0.00179972
ITEM: TIMESTEP
10
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
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2 2 1.37507 4.06138 1.36492 11.7248 4.54034 5.95839 2.18206 -0.0271682 -0.0223275
3 2 4.05004 4.06628 1.35097 -1.71572 6.50015 0.389163 -2.25748 -0.0249726 0.0043903
4 1 2.69919 -0.00257993 2.70181 -0.322932 -1.03096 0.725515 0.0557294 0.0320331 0.0260207
5 2 1.36048 1.34627 4.04397 5.93543 -1.4938 -2.40872 2.2824 -0.00306026 0.0101825
6 2 4.04884 1.35195 4.04565 -2.2221 0.774587 -1.74074 -2.31042 -0.0127983 -0.00198013
ITEM: TIMESTEP
11
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69835 2.70092 -0.00240001 -0.598586 0.337838 -0.873382 0.0526872 0.0393256 -0.0181586
2 2 1.37805 4.06252 1.36641 12.0521 4.53597 5.9548 2.15829 -0.0307526 -0.0252554
3 2 4.04957 4.06791 1.35106 -2.05501 6.49619 0.389841 -2.24228 -0.0275775 0.00460683
4 1 2.69911 -0.00283763 2.70199 -0.322334 -1.03061 0.725796 0.0623777 0.0362096 0.0295409
5 2 1.362 1.3459 4.04336 6.27868 -1.49427 -2.40709 2.26985 -0.00316333 0.0114188
6 2 4.04824 1.35215 4.04522 -2.56981 0.772563 -1.74105 -2.30093 -0.0140417 -0.00215255
ITEM: TIMESTEP
12
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.6982 2.70101 -0.00261837 -0.598027 0.338253 -0.873575 0.0577351 0.0426463 -0.0200718
2 2 1.3811 4.06365 1.3679 12.3757 4.53105 5.95076 2.13326 -0.0345179 -0.0283253
3 2 4.04901 4.06953 1.35116 -2.39194 6.49183 0.390547 -2.22604 -0.0302194 0.00475506
4 1 2.69903 -0.00309524 2.70217 -0.321667 -1.03022 0.726114 0.06925 0.0405836 0.0332542
5 2 1.36362 1.34552 4.04276 6.61997 -1.49475 -2.40527 2.25627 -0.00322051 0.0127037
6 2 4.04756 1.35234 4.04478 -2.91602 0.770353 -1.74139 -2.29048 -0.0152721 -0.00231583
ITEM: TIMESTEP
13
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69805 2.70109 -0.00283679 -0.597416 0.338702 -0.873788 0.0628554 0.0459295 -0.0220243
2 2 1.38423 4.06478 1.36939 12.6954 4.52555 5.94625 2.10694 -0.0384688 -0.0315401
3 2 4.04837 4.07115 1.35126 -2.72634 6.48707 0.39127 -2.20874 -0.0329024 0.00482793
4 1 2.69895 -0.00335274 2.70236 -0.320929 -1.02979 0.726471 0.0763523 0.0451591 0.0371659
5 2 1.36531 1.34515 4.04216 6.95912 -1.49523 -2.40326 2.24165 -0.00322965 0.0140393
6 2 4.04678 1.35253 4.04434 -3.26057 0.767958 -1.74175 -2.27906 -0.0164877 -0.0024688
ITEM: TIMESTEP
14
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.6979 2.70118 -0.00305527 -0.596753 0.339184 -0.874022 0.0680546 0.0491768 -0.0240145
2 2 1.38745 4.06591 1.37087 13.0111 4.51944 5.94124 2.07932 -0.0426096 -0.0349018
3 2 4.04765 4.07277 1.35136 -3.05804 6.4819 0.391997 -2.19038 -0.035631 0.00481829
4 1 2.69887 -0.00361013 2.70254 -0.320118 -1.0293 0.726868 0.0836894 0.0499393 0.0412807
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6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901

21
examples/QM/LATTE/dump.8Sep22.series.plugin.4uo2 Normal file
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@ -0,0 +1,21 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
12
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 6.6130927153957075e-16
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 8.1 0 -0.433947 2.16479 1.55466
2 2 1.35 9.45 1.35 1.64718 -0.119006 0.375837
3 2 4.05 9.45 1.35 0.999862 -1.02573 0.037629
4 1 5.4 8.1 2.7 0.433947 2.16479 1.55466
5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
10 1 5.4 0 0 0.211437 1.63064 -0.0728897
11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959

15
examples/QM/LATTE/electrons.dat Normal file
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@ -0,0 +1,15 @@
Noelem= 2
Element basis Numel Es Ep Ed Ef Mass HubbardU Wss Wpp Wdd Wff
U sdf 6.0 -4.08 0.0 0.816 -0.586 238.05078 9.0 0.0 0.0 0.0 0.0
O sp 6.0 -23.77 -8.85 0.0 0.0 15.994915 12.2 0.0 0.0 0.0 0.0
W spd 6.0 -4.52 0.53 -2.91 0.0 183.84 7.048 0.0 0.0 0.0 0.0
Mo sd 6.0 -3.29 0.0 -1.98 0.0 95.95 6.48 0.0 0.0 0.0 0.0
S sp 6.0 -14.00 -3.97 0.0 0.0 32.06 8.28 0.0 -0.4278 0.0 0.0
N sp 5.000000 -18.543798 -7.862407 0.000000 0.000000 14.006700 17.053958 0.000000 -0.6934 0.000000 0.000000
H s 1.000000 -6.237968 0.000000 0.000000 0.000000 1.007900 13.684855 -2.23400 0.000000 0.000000 0.000000
C sp 4.000000 -13.736556 -4.748938 0.000000 0.000000 12.010000 10.522540 0.000000 -0.618100 0.000000 0.000000
O sp 6.000000 -23.833752 -9.645001 0.000000 0.000000 15.999400 14.443874 0.000000 -0.757650 0.000000 0.000000

26
examples/QM/LATTE/in.aimd Normal file
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# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.mpi &
id type x y z vx vy vz fx fy fz
run 20

27
examples/QM/LATTE/in.aimd.plugin Normal file
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@ -0,0 +1,27 @@
# AIMD test of two UO2 molecules with LATTE in MDI plugin mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.plugin &
id type x y z vx vy vz fx fy fz
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
command "run 20"

37
examples/QM/LATTE/in.series Normal file
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@ -0,0 +1,37 @@
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI stand-alone mode
variable files index 2uo2 3uo2 4uo2
mdi connect
label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
write_dump all custom dump.series.mpi.${files} &
id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP
mdi exit

32
examples/QM/LATTE/in.series.plugin Normal file
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@ -0,0 +1,32 @@
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI plugin mode
variable files index 2uo2 3uo2 4uo2
label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
command "run 0"
write_dump all custom dump.series.plugin.${files} &
id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP

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