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remove trailing whitespace from documentation sources

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Axel Kohlmeyer
2020-03-10 15:51:06 -04:00
parent b9ff623c16
commit e643e88913
293 changed files with 1039 additions and 1039 deletions
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2
doc/src/Build_basics.rst
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@ -142,7 +142,7 @@ please refer to its documentation.
.. _default-none-issues: .. _default-none-issues:
**OpenMP Compiler compatibility info**\ : **OpenMP Compiler compatibility info**\ :
Some compilers do not fully support the 'default(none)' directive Some compilers do not fully support the 'default(none)' directive
and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0 and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0

4
doc/src/Build_extras.rst
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@ -53,7 +53,7 @@ This is the list of packages that may require additional steps.
* :ref:`USER-QUIP <user-quip>` * :ref:`USER-QUIP <user-quip>`
* :ref:`USER-SCAFACOS <user-scafacos>` * :ref:`USER-SCAFACOS <user-scafacos>`
* :ref:`USER-SMD <user-smd>` * :ref:`USER-SMD <user-smd>`
* :ref:`USER-VTK <user-vtk>` * :ref:`USER-VTK <user-vtk>`
---------- ----------
@ -1230,7 +1230,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
.. parsed-literal:: .. parsed-literal::
CCFLAGS: -fopenmp # for GNU and Clang Compilers CCFLAGS: -fopenmp # for GNU and Clang Compilers
CCFLAGS: -qopenmp -restrict # for Intel compilers on Linux CCFLAGS: -qopenmp -restrict # for Intel compilers on Linux
LINKFLAGS: -fopenmp # for GNU and Clang Compilers LINKFLAGS: -fopenmp # for GNU and Clang Compilers
LINKFLAGS: -qopenmp # for Intel compilers on Linux LINKFLAGS: -qopenmp # for Intel compilers on Linux

18
doc/src/Build_link.rst
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@ -101,7 +101,7 @@ change to:
gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/lib/poems \ g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
-L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps -lpoems -lmpi_stubs -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps -lpoems -lmpi_stubs
Note, that you need to link with "g++" instead of "gcc", since LAMMPS Note, that you need to link with "g++" instead of "gcc", since LAMMPS
is C++ code. You can display the currently applied settings for building is C++ code. You can display the currently applied settings for building
@ -115,15 +115,15 @@ Which should output something like:
.. code-block:: bash .. code-block:: bash
# Compiler: # Compiler:
CXX=g++ CXX=g++
# Linker: # Linker:
LD=g++ LD=g++
# Compilation: # Compilation:
CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/lammps/lib/poems -I${HOME}/lammps/src/STUBS CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/lammps/lib/poems -I${HOME}/lammps/src/STUBS
# Linking: # Linking:
LDFLAGS=-g -O LDFLAGS=-g -O
# Libraries: # Libraries:
LDLIBS=-L${HOME}/lammps/lib/poems -L${HOME}/lammps/src/STUBS -lpoems -lmpi_stubs LDLIBS=-L${HOME}/lammps/lib/poems -L${HOME}/lammps/src/STUBS -lpoems -lmpi_stubs
From this you can gather the necessary paths and flags. With From this you can gather the necessary paths and flags. With
@ -165,7 +165,7 @@ traditional make build using "make mode=shlib serial" becomes:
g++ -o caller caller.o -L${HOME}/lammps/src -llammps g++ -o caller caller.o -L${HOME}/lammps/src -llammps
*Locating liblammps.so at runtime*\ : *Locating liblammps.so at runtime*\ :
However, now the `liblammps.so` file is required at runtime and needs However, now the `liblammps.so` file is required at runtime and needs
to be in a folder, where the shared linker program of the operating to be in a folder, where the shared linker program of the operating
system can find it. This would be either a folder like "/usr/local/lib64" system can find it. This would be either a folder like "/usr/local/lib64"
@ -203,7 +203,7 @@ You can verify whether all required shared libraries are found with the
.. code-block:: bash .. code-block:: bash
$ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller $ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
linux-vdso.so.1 (0x00007ffe729e0000) linux-vdso.so.1 (0x00007ffe729e0000)
liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000) liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
@ -217,7 +217,7 @@ If a required library is missing, you would get a 'not found' entry:
.. code-block:: bash .. code-block:: bash
$ ldd caller $ ldd caller
linux-vdso.so.1 (0x00007ffd672fe000) linux-vdso.so.1 (0x00007ffd672fe000)
liblammps.so => not found liblammps.so => not found
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)

2
doc/src/Build_package.rst
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@ -221,7 +221,7 @@ package" will list all the these commands.
directory src and the sub-directories with the package name (e.g. directory src and the sub-directories with the package name (e.g.
src/KSPACE, src/USER-ATC), so that the files are included or excluded src/KSPACE, src/USER-ATC), so that the files are included or excluded
when LAMMPS is built. Only source files in the src folder will be when LAMMPS is built. Only source files in the src folder will be
compiled. compiled.
The following make commands help manage files that exist in both the The following make commands help manage files that exist in both the
src directory and in package sub-directories. You do not normally src directory and in package sub-directories. You do not normally

2
doc/src/Build_settings.rst
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@ -12,7 +12,7 @@ explain how to do this for building both with CMake and make.
* :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command * :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
* :ref:`Memory allocation alignment <align>` * :ref:`Memory allocation alignment <align>`
* :ref:`Workaround for long long integers <longlong>` * :ref:`Workaround for long long integers <longlong>`
* :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library * :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
---------- ----------

2
doc/src/Commands_parse.rst
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@ -116,7 +116,7 @@ LAMMPS:
underscores, or punctuation characters. underscores, or punctuation characters.
.. _five: .. _five:
5. The first word is the command name. All successive words in the line 5. The first word is the command name. All successive words in the line
are arguments. are arguments.

2
doc/src/Commands_structure.rst
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@ -9,7 +9,7 @@ page.
A LAMMPS input script typically has 4 parts: A LAMMPS input script typically has 4 parts:
1. :ref:`Initialization <init>` 1. :ref:`Initialization <init>`
2. :ref:`System definition <system>` 2. :ref:`System definition <system>`
3. :ref:`Simulation settings <settings>` 3. :ref:`Simulation settings <settings>`
4. :ref:`Run a simulation <run>` 4. :ref:`Run a simulation <run>`

4
doc/src/Howto_spc.rst
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@ -20,7 +20,7 @@ atoms and the water molecule to run a rigid SPC model.
| LJ epsilon, sigma of OH, HH = 0.0 | LJ epsilon, sigma of OH, HH = 0.0
| r0 of OH bond = 1.0 | r0 of OH bond = 1.0
| theta of HOH angle = 109.47 | theta of HOH angle = 109.47
| |
Note that as originally proposed, the SPC model was run with a 9 Note that as originally proposed, the SPC model was run with a 9
Angstrom cutoff for both LJ and Coulombic terms. It can also be used Angstrom cutoff for both LJ and Coulombic terms. It can also be used
@ -33,7 +33,7 @@ the partial charge assignments change:
| O charge = -0.8476 | O charge = -0.8476
| H charge = 0.4238 | H charge = 0.4238
| |
See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
the SPC and SPC/E models. the SPC and SPC/E models.

4
doc/src/Howto_tip3p.rst
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@ -30,7 +30,7 @@ set to 0.0, it corresponds to the original 1983 TIP3P model
| r0 of OH bond = 0.9572 | r0 of OH bond = 0.9572
| K of HOH angle = 55 | K of HOH angle = 55
| theta of HOH angle = 104.52 | theta of HOH angle = 104.52
| |
These are the parameters to use for TIP3P with a long-range Coulombic These are the parameters to use for TIP3P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS), see :ref:`(Price) <Price1>` for solver (e.g. Ewald or PPPM in LAMMPS), see :ref:`(Price) <Price1>` for
@ -47,7 +47,7 @@ details:
| r0 of OH bond = 0.9572 | r0 of OH bond = 0.9572
| K of HOH angle = 55 | K of HOH angle = 55
| theta of HOH angle = 104.52 | theta of HOH angle = 104.52
| |
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_. Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.

8
doc/src/Howto_tip4p.rst
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@ -38,7 +38,7 @@ coefficients.
| LJ sigma of O-O = 3.1536 | LJ sigma of O-O = 3.1536
| LJ epsilon, sigma of OH, HH = 0.0 | LJ epsilon, sigma of OH, HH = 0.0
| Coulombic cutoff = 8.5 | Coulombic cutoff = 8.5
| |
For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
http://dx.doi.org/10.1063/1.1931662) these values can be used: http://dx.doi.org/10.1063/1.1931662) these values can be used:
@ -54,7 +54,7 @@ http://dx.doi.org/10.1063/1.1931662) these values can be used:
| LJ sigma of O-O = 3.1668 | LJ sigma of O-O = 3.1668
| LJ epsilon, sigma of OH, HH = 0.0 | LJ epsilon, sigma of OH, HH = 0.0
| Coulombic cutoff = 8.5 | Coulombic cutoff = 8.5
| |
For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
http://dx.doi.org/10.1063/1.2121687), these values can be used: http://dx.doi.org/10.1063/1.2121687), these values can be used:
@ -70,7 +70,7 @@ http://dx.doi.org/10.1063/1.2121687), these values can be used:
| LJ sigma of O-O = 3.1589 | LJ sigma of O-O = 3.1589
| LJ epsilon, sigma of OH, HH = 0.0 | LJ epsilon, sigma of OH, HH = 0.0
| Coulombic cutoff = 8.5 | Coulombic cutoff = 8.5
| |
These are the parameters to use for TIP4P with a long-range Coulombic These are the parameters to use for TIP4P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS): solver (e.g. Ewald or PPPM in LAMMPS):
@ -85,7 +85,7 @@ solver (e.g. Ewald or PPPM in LAMMPS):
| LJ epsilon of O-O = 0.16275 | LJ epsilon of O-O = 0.16275
| LJ sigma of O-O = 3.16435 | LJ sigma of O-O = 3.16435
| LJ epsilon, sigma of OH, HH = 0.0 | LJ epsilon, sigma of OH, HH = 0.0
| |
Note that the when using the TIP4P pair style, the neighbor list Note that the when using the TIP4P pair style, the neighbor list
cutoff for Coulomb interactions is effectively extended by a distance cutoff for Coulomb interactions is effectively extended by a distance

2
doc/src/Howto_triclinic.rst
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@ -78,7 +78,7 @@ The transformation is given by the following equation:
\begin{pmatrix} \begin{pmatrix}
\mathbf{B \times C} \\ \mathbf{B \times C} \\
\mathbf{C \times A} \\ \mathbf{C \times A} \\
\mathbf{A \times B} \mathbf{A \times B}
\end{pmatrix} \cdot \mathbf{X} \end{pmatrix} \cdot \mathbf{X}
where *V* is the volume of the box, **X** is the original vector quantity and where *V* is the volume of the box, **X** is the original vector quantity and

8
doc/src/Install_patch.rst
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@ -32,9 +32,9 @@ up to date.
* Apply the patch by typing the following command from your top-level * Apply the patch by typing the following command from your top-level
LAMMPS directory, where the redirected file is the name of the patch LAMMPS directory, where the redirected file is the name of the patch
file. file.
.. code-block:: bash .. code-block:: bash
$ patch -bp1 < patch.12Dec16 $ patch -bp1 < patch.12Dec16
* A list of updated files print out to the screen. The -b switch * A list of updated files print out to the screen. The -b switch
@ -46,9 +46,9 @@ up to date.
successively, you only need to type this once at the end. The purge successively, you only need to type this once at the end. The purge
command removes deprecated src files if any were removed by the patch command removes deprecated src files if any were removed by the patch
from package sub-directories. from package sub-directories.
.. code-block:: bash .. code-block:: bash
$ make purge $ make purge
$ make package-update $ make package-update

32
doc/src/Run_options.rst
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@ -37,7 +37,7 @@ For example, the lmp\_mpi executable might be launched as follows:
.. _echo: .. _echo:
**-echo style** **-echo style**
Set the style of command echoing. The style can be *none* or *screen* Set the style of command echoing. The style can be *none* or *screen*
or *log* or *both*\ . Depending on the style, each command read from or *log* or *both*\ . Depending on the style, each command read from
@ -52,7 +52,7 @@ set by using the :doc:`echo <echo>` command in the input script itself.
.. _help: .. _help:
**-help** **-help**
Print a brief help summary and a list of options compiled into this Print a brief help summary and a list of options compiled into this
executable for each LAMMPS style (atom\_style, fix, compute, executable for each LAMMPS style (atom\_style, fix, compute,
@ -67,7 +67,7 @@ used.
.. _file: .. _file:
**-in file** **-in file**
Specify a file to use as an input script. This is an optional switch Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified, when running LAMMPS in one-partition mode. If it is not specified,
@ -85,7 +85,7 @@ stdin.
.. _run-kokkos: .. _run-kokkos:
**-kokkos on/off keyword/value ...** **-kokkos on/off keyword/value ...**
Explicitly enable or disable KOKKOS support, as provided by the KOKKOS Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
package. Even if LAMMPS is built with this package, as described package. Even if LAMMPS is built with this package, as described
@ -190,7 +190,7 @@ traffic which is slow.
.. _log: .. _log:
**-log file** **-log file**
Specify a log file for LAMMPS to write status information to. In Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the one-partition mode, if the switch is not used, LAMMPS writes to the
@ -211,7 +211,7 @@ Option -plog will override the name of the partition log files file.N.
.. _mpicolor: .. _mpicolor:
**-mpicolor** color **-mpicolor** color
If used, this must be the first command-line argument after the LAMMPS If used, this must be the first command-line argument after the LAMMPS
executable name. It is only used when LAMMPS is launched by an mpirun executable name. It is only used when LAMMPS is launched by an mpirun
@ -238,7 +238,7 @@ links with from the lib/message directory. See the
.. _nocite: .. _nocite:
**-nocite** **-nocite**
Disable writing the log.cite file which is normally written to list Disable writing the log.cite file which is normally written to list
references for specific cite-able features used during a LAMMPS run. references for specific cite-able features used during a LAMMPS run.
@ -251,7 +251,7 @@ details.
.. _package: .. _package:
**-package style args ....** **-package style args ....**
Invoke the :doc:`package <package>` command with style and args. The Invoke the :doc:`package <package>` command with style and args. The
syntax is the same as if the command appeared at the top of the input syntax is the same as if the command appeared at the top of the input
@ -271,7 +271,7 @@ having to edit an input script.
.. _partition: .. _partition:
**-partition 8x2 4 5 ...** **-partition 8x2 4 5 ...**
Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
processors and this switch is not used, LAMMPS runs in one partition, processors and this switch is not used, LAMMPS runs in one partition,
@ -302,7 +302,7 @@ in this context.
.. _plog: .. _plog:
**-plog file** **-plog file**
Specify the base name for the partition log files, so partition N Specify the base name for the partition log files, so partition N
writes log information to file.N. If file is none, then no partition writes log information to file.N. If file is none, then no partition
@ -320,7 +320,7 @@ command-line option.
.. _pscreen: .. _pscreen:
**-pscreen file** **-pscreen file**
Specify the base name for the partition screen file, so partition N Specify the base name for the partition screen file, so partition N
writes screen information to file.N. If file is none, then no writes screen information to file.N. If file is none, then no
@ -338,7 +338,7 @@ specified by the -screen command-line option.
.. _reorder: .. _reorder:
**-reorder** **-reorder**
This option has 2 forms: This option has 2 forms:
@ -476,7 +476,7 @@ optional keyword/value settings.
.. _restart2dump: .. _restart2dump:
**-restart2dump restartfile [remap] group-ID dumpstyle dumpfile arg1 arg2 ...** **-restart2dump restartfile [remap] group-ID dumpstyle dumpfile arg1 arg2 ...**
Convert the restart file into a dump file and immediately exit. This Convert the restart file into a dump file and immediately exit. This
is the same operation as if the following 2-line input script were is the same operation as if the following 2-line input script were
@ -523,7 +523,7 @@ the *nfile* and *fileper* keywords. See the
.. _screen: .. _screen:
**-screen file** **-screen file**
Specify a file for LAMMPS to write its screen information to. In Specify a file for LAMMPS to write its screen information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the one-partition mode, if the switch is not used, LAMMPS writes to the
@ -544,7 +544,7 @@ partition screen files file.N.
.. _suffix: .. _suffix:
**-suffix style args** **-suffix style args**
Use variants of various styles if they exist. The specified style can Use variants of various styles if they exist. The specified style can
be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt*\ , or *hybrid*\ . These be *gpu*\ , *intel*\ , *kk*\ , *omp*\ , *opt*\ , or *hybrid*\ . These
@ -613,7 +613,7 @@ made via the command line.
.. _var: .. _var:
**-var name value1 value2 ...** **-var name value1 value2 ...**
Specify a variable that will be defined for substitution purposes when Specify a variable that will be defined for substitution purposes when
the input script is read. This switch can be used multiple times to the input script is read. This switch can be used multiple times to

4
doc/src/Tools.rst
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@ -624,14 +624,14 @@ replica tool
-------------------------- --------------------------
The tools/replica directory contains the reorder\_remd\_traj python script which The tools/replica directory contains the reorder\_remd\_traj python script which
can be used to reorder the replica trajectories (resulting from the use of the can be used to reorder the replica trajectories (resulting from the use of the
temper command) according to temperature. This will produce discontinuous temper command) according to temperature. This will produce discontinuous
trajectories with all frames at the same temperature in each trajectory. trajectories with all frames at the same temperature in each trajectory.
Additional options can be used to calculate the canonical configurational Additional options can be used to calculate the canonical configurational
log-weight for each frame at each temperature using the pymbar package. See log-weight for each frame at each temperature using the pymbar package. See
the README.md file for further details. Try out the peptide example provided. the README.md file for further details. Try out the peptide example provided.
This tool was written by (and is maintained by) Tanmoy Sanyal, This tool was written by (and is maintained by) Tanmoy Sanyal,
while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)

2
doc/src/angle_sdk.rst
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@ -32,7 +32,7 @@ The *sdk* angle style is a combination of the harmonic angle potential,
.. math:: .. math::
E = K (\theta - \theta_0)^2 E = K (\theta - \theta_0)^2
where :math:`\theta_0` is the equilibrium value of the angle and where :math:`\theta_0` is the equilibrium value of the angle and

4
doc/src/atom_modify.rst
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@ -13,9 +13,9 @@ Syntax
* one or more keyword/value pairs may be appended * one or more keyword/value pairs may be appended
* keyword = *id* or *map* or *first* or *sort* * keyword = *id* or *map* or *first* or *sort*
.. parsed-literal:: .. parsed-literal::
*id* value = *yes* or *no* *id* value = *yes* or *no*
*map* value = *yes* or *array* or *hash* *map* value = *yes* or *array* or *hash*
*first* value = group-ID = group whose atoms will appear first in internal atom lists *first* value = group-ID = group whose atoms will appear first in internal atom lists

4
doc/src/atom_style.rst
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@ -12,9 +12,9 @@ Syntax
atom_style style args atom_style style args
* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *mdpd* or *tdpd* or *electron* or *ellipsoid* or *full* or *line* or *meso* or *molecular* or *peri* or *smd* or *sphere* or *spin* or *tri* or *template* or *hybrid* * style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *mdpd* or *tdpd* or *electron* or *ellipsoid* or *full* or *line* or *meso* or *molecular* or *peri* or *smd* or *sphere* or *spin* or *tri* or *template* or *hybrid*
.. parsed-literal:: .. parsed-literal::
args = none for any style except the following args = none for any style except the following
*body* args = bstyle bstyle-args *body* args = bstyle bstyle-args
bstyle = style of body particles bstyle = style of body particles

10
doc/src/balance.rst
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@ -14,9 +14,9 @@ Syntax
* thresh = imbalance threshold that must be exceeded to perform a re-balance * thresh = imbalance threshold that must be exceeded to perform a re-balance
* one style/arg pair can be used (or multiple for *x*\ ,\ *y*\ ,\ *z*\ ) * one style/arg pair can be used (or multiple for *x*\ ,\ *y*\ ,\ *z*\ )
* style = *x* or *y* or *z* or *shift* or *rcb* * style = *x* or *y* or *z* or *shift* or *rcb*
.. parsed-literal:: .. parsed-literal::
*x* args = *uniform* or Px-1 numbers between 0 and 1 *x* args = *uniform* or Px-1 numbers between 0 and 1
*uniform* = evenly spaced cuts between processors in x dimension *uniform* = evenly spaced cuts between processors in x dimension
numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
@ -37,9 +37,9 @@ Syntax
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *weight* or *out* * keyword = *weight* or *out*
.. parsed-literal:: .. parsed-literal::
*weight* style args = use weighted particle counts for the balancing *weight* style args = use weighted particle counts for the balancing
*style* = *group* or *neigh* or *time* or *var* or *store* *style* = *group* or *neigh* or *time* or *var* or *store*
*group* args = Ngroup group1 weight1 group2 weight2 ... *group* args = Ngroup group1 weight1 group2 weight2 ...
@ -351,7 +351,7 @@ particles in that sub-box.
.. _weighted\_balance: .. _weighted\_balance:
This sub-section describes how to perform weighted load balancing This sub-section describes how to perform weighted load balancing
using the *weight* keyword. using the *weight* keyword.
By default, all particles have a weight of 1.0, which means each By default, all particles have a weight of 1.0, which means each
particle is assumed to require the same amount of computation during a particle is assumed to require the same amount of computation during a

26
doc/src/bond_oxdna.rst
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@ -69,11 +69,11 @@ commands:
coaxial stacking interaction *oxdna/coaxstk* as well as coaxial stacking interaction *oxdna/coaxstk* as well as
hydrogen-bonding interaction *oxdna/hbond* (see also documentation of hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
:doc:`pair_style oxdna/excv <pair_oxdna>`). For the oxDNA2 :doc:`pair_style oxdna/excv <pair_oxdna>`). For the oxDNA2
:ref:`(Snodin) <Snodin0>` bond style the analogous pair styles :ref:`(Snodin) <Snodin0>` bond style the analogous pair styles
*oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
*oxdna2/hbond* and an additional Debye-Hueckel pair style *oxdna2/hbond* and an additional Debye-Hueckel pair style
*oxdna2/dh* have to be defined. The same applies to the oxRNA2 *oxdna2/dh* have to be defined. The same applies to the oxRNA2
:ref:`(Sulc1) <Sulc01>` styles. :ref:`(Sulc1) <Sulc01>` styles.
The coefficients in the above example have to be kept fixed and cannot The coefficients in the above example have to be kept fixed and cannot
be changed without reparameterizing the entire model. be changed without reparameterizing the entire model.
@ -83,17 +83,17 @@ setup tool which creates single straight or helical DNA strands, DNA/RNA
duplexes or arrays of DNA/RNA duplexes can be found in duplexes or arrays of DNA/RNA duplexes can be found in
examples/USER/cgdna/util/. examples/USER/cgdna/util/.
Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
this implementation. The article contains general information this implementation. The article contains general information
on the model, its implementation and performance as well as the structure of on the model, its implementation and performance as well as the structure of
the data and input file. The preprint version of the article can be found the data and input file. The preprint version of the article can be found
`here <PDF/USER-CGDNA.pdf>`_. `here <PDF/USER-CGDNA.pdf>`_.
Please cite also the relevant oxDNA/oxRNA publications. These are Please cite also the relevant oxDNA/oxRNA publications. These are
:ref:`(Ouldridge) <Ouldridge0>` and :ref:`(Ouldridge) <Ouldridge0>` and
:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA, :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA,
:ref:`(Snodin) <Snodin0>` for oxDNA2, :ref:`(Snodin) <Snodin0>` for oxDNA2,
:ref:`(Sulc1) <Sulc01>` for oxRNA2 :ref:`(Sulc1) <Sulc01>` for oxRNA2
and for sequence-specific hydrogen-bonding and stacking interactions and for sequence-specific hydrogen-bonding and stacking interactions
:ref:`(Sulc2) <Sulc02>`. :ref:`(Sulc2) <Sulc02>`.
@ -111,7 +111,7 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`pair_style oxdna/excv <pair_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`, :doc:`pair_style oxdna/excv <pair_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
:doc:`bond_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>` :doc:`bond_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
**Default:** **Default:**

4
doc/src/bond_quartic.rst
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@ -50,7 +50,7 @@ or :doc:`read_restart <read_restart>` commands:
This potential was constructed to mimic the FENE bond potential for This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with :math:`\sigma = \epsilon = 1.0` coarse-grained polymer chains. When monomers with :math:`\sigma = \epsilon = 1.0`
are used, the following choice of parameters gives a quartic potential that are used, the following choice of parameters gives a quartic potential that
looks nearly like the FENE potential: looks nearly like the FENE potential:
.. math:: .. math::
@ -59,7 +59,7 @@ looks nearly like the FENE potential:
B_2 &= 0.25 \\ B_2 &= 0.25 \\
R_c &= 1.3 \\ R_c &= 1.3 \\
U_0 &= 34.6878 U_0 &= 34.6878
Different parameters can be specified using the :doc:`bond_coeff <bond_coeff>` Different parameters can be specified using the :doc:`bond_coeff <bond_coeff>`
command, but you will need to choose them carefully so they form a suitable command, but you will need to choose them carefully so they form a suitable
bond potential. bond potential.

4
doc/src/boundary.rst
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@ -12,9 +12,9 @@ Syntax
boundary x y z boundary x y z
* x,y,z = *p* or *s* or *f* or *m*\ , one or two letters * x,y,z = *p* or *s* or *f* or *m*\ , one or two letters
.. parsed-literal:: .. parsed-literal::
*p* is periodic *p* is periodic
*f* is non-periodic and fixed *f* is non-periodic and fixed
*s* is non-periodic and shrink-wrapped *s* is non-periodic and shrink-wrapped

4
doc/src/box.rst
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@ -13,9 +13,9 @@ Syntax
* one or more keyword/value pairs may be appended * one or more keyword/value pairs may be appended
* keyword = *tilt* * keyword = *tilt*
.. parsed-literal:: .. parsed-literal::
*tilt* value = *small* or *large* *tilt* value = *small* or *large*

8
doc/src/change_box.rst
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@ -13,9 +13,9 @@ Syntax
* group-ID = ID of group of atoms to (optionally) displace * group-ID = ID of group of atoms to (optionally) displace
* one or more parameter/arg pairs may be appended * one or more parameter/arg pairs may be appended
.. parsed-literal:: .. parsed-literal::
parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *boundary* or *ortho* or *triclinic* or *set* or *remap* parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *boundary* or *ortho* or *triclinic* or *set* or *remap*
*x*\ , *y*\ , *z* args = style value(s) *x*\ , *y*\ , *z* args = style value(s)
style = *final* or *delta* or *scale* or *volume* style = *final* or *delta* or *scale* or *volume*
@ -45,9 +45,9 @@ Syntax
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *units* * keyword = *units*
.. parsed-literal:: .. parsed-literal::
*units* value = *lattice* or *box* *units* value = *lattice* or *box*
lattice = distances are defined in lattice units lattice = distances are defined in lattice units
box = distances are defined in simulation box units box = distances are defined in simulation box units

4
doc/src/comm_modify.rst
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@ -13,9 +13,9 @@ Syntax
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel* * keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel*
.. parsed-literal:: .. parsed-literal::
*mode* value = *single* or *multi* = communicate atoms within a single or multiple distances *mode* value = *single* or *multi* = communicate atoms within a single or multiple distances
*cutoff* value = Rcut (distance units) = communicate atoms from this far away *cutoff* value = Rcut (distance units) = communicate atoms from this far away
*cutoff/multi* type value *cutoff/multi* type value

4
doc/src/compute_ackland_atom.rst
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@ -15,9 +15,9 @@ Syntax
* ackland/atom = style name of this compute command * ackland/atom = style name of this compute command
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *legacy* * keyword = *legacy*
.. parsed-literal:: .. parsed-literal::
*legacy* yes/no = use (\ *yes*\ ) or do not use (\ *no*\ ) legacy ackland algorithm implementation *legacy* yes/no = use (\ *yes*\ ) or do not use (\ *no*\ ) legacy ackland algorithm implementation

4
doc/src/compute_adf.rst
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@ -23,9 +23,9 @@ Syntax
* RkouterN = outer radius of K atom shell for Nth ADF histogram (distance units) * RkouterN = outer radius of K atom shell for Nth ADF histogram (distance units)
* zero or one keyword/value pairs may be appended * zero or one keyword/value pairs may be appended
* keyword = *ordinate* * keyword = *ordinate*
.. parsed-literal:: .. parsed-literal::
*ordinate* value = *degree* or *radian* or *cosine* *ordinate* value = *degree* or *radian* or *cosine*
Choose the ordinate parameter for the histogram Choose the ordinate parameter for the histogram

8
doc/src/compute_angle_local.rst
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@ -15,18 +15,18 @@ Syntax
* angle/local = style name of this compute command * angle/local = style name of this compute command
* one or more values may be appended * one or more values may be appended
* value = *theta* or *eng* or *v\_name* * value = *theta* or *eng* or *v\_name*
.. parsed-literal:: .. parsed-literal::
*theta* = tabulate angles *theta* = tabulate angles
*eng* = tabulate angle energies *eng* = tabulate angle energies
*v_name* = equal-style variable with name (see below) *v_name* = equal-style variable with name (see below)
* zero or more keyword/args pairs may be appended * zero or more keyword/args pairs may be appended
* keyword = *set* * keyword = *set*
.. parsed-literal:: .. parsed-literal::
*set* args = theta name *set* args = theta name
theta = only currently allowed arg theta = only currently allowed arg
name = name of variable to set with theta name = name of variable to set with theta

4
doc/src/compute_body_local.rst
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@ -15,9 +15,9 @@ Syntax
* body/local = style name of this compute command * body/local = style name of this compute command
* one or more keywords may be appended * one or more keywords may be appended
* keyword = *id* or *type* or *integer* * keyword = *id* or *type* or *integer*
.. parsed-literal:: .. parsed-literal::
*id* = atom ID of the body particle *id* = atom ID of the body particle
*type* = atom type of the body particle *type* = atom type of the body particle
*integer* = 1,2,3,etc = index of fields defined by body style *integer* = 1,2,3,etc = index of fields defined by body style

8
doc/src/compute_chunk_atom.rst
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@ -13,9 +13,9 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* chunk/atom = style name of this compute command * chunk/atom = style name of this compute command
.. parsed-literal:: .. parsed-literal::
style = *bin/1d* or *bin/2d* or *bin/3d* or *bin/sphere* or *type* or *molecule* or c_ID, c_ID[I], f_ID, f_ID[I], v_name style = *bin/1d* or *bin/2d* or *bin/3d* or *bin/sphere* or *type* or *molecule* or c_ID, c_ID[I], f_ID, f_ID[I], v_name
*bin/1d* args = dim origin delta *bin/1d* args = dim origin delta
dim = *x* or *y* or *z* dim = *x* or *y* or *z*
@ -51,9 +51,9 @@ Syntax
* zero or more keyword/values pairs may be appended * zero or more keyword/values pairs may be appended
* keyword = *region* or *nchunk* or *static* or *compress* or *bound* or *discard* or *pbc* or *units* * keyword = *region* or *nchunk* or *static* or *compress* or *bound* or *discard* or *pbc* or *units*
.. parsed-literal:: .. parsed-literal::
*region* value = region-ID *region* value = region-ID
region-ID = ID of region atoms must be in to be part of a chunk region-ID = ID of region atoms must be in to be part of a chunk
*nchunk* value = *once* or *every* *nchunk* value = *once* or *every*

4
doc/src/compute_chunk_spread_atom.rst
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@ -16,9 +16,9 @@ Syntax
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command * chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
* one or more inputs can be listed * one or more inputs can be listed
* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N] * input = c\_ID, c\_ID[N], f\_ID, f\_ID[N]
.. parsed-literal:: .. parsed-literal::
c_ID = global vector calculated by a compute with ID c_ID = global vector calculated by a compute with ID
c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below) c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
f_ID = global vector calculated by a fix with ID f_ID = global vector calculated by a fix with ID

4
doc/src/compute_coord_atom.rst
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@ -14,9 +14,9 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* coord/atom = style name of this compute command * coord/atom = style name of this compute command
* cstyle = *cutoff* or *orientorder* * cstyle = *cutoff* or *orientorder*
.. parsed-literal:: .. parsed-literal::
*cutoff* args = cutoff [group group2-ID] typeN *cutoff* args = cutoff [group group2-ID] typeN
cutoff = distance within which to count coordination neighbors (distance units) cutoff = distance within which to count coordination neighbors (distance units)
group *group2-ID* = select group-ID to restrict which atoms to consider for coordination number (optional) group *group2-ID* = select group-ID to restrict which atoms to consider for coordination number (optional)

8
doc/src/compute_dihedral_local.rst
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@ -15,17 +15,17 @@ Syntax
* dihedral/local = style name of this compute command * dihedral/local = style name of this compute command
* one or more values may be appended * one or more values may be appended
* value = *phi* or *v\_name* * value = *phi* or *v\_name*
.. parsed-literal:: .. parsed-literal::
*phi* = tabulate dihedral angles *phi* = tabulate dihedral angles
*v_name* = equal-style variable with name (see below) *v_name* = equal-style variable with name (see below)
* zero or more keyword/args pairs may be appended * zero or more keyword/args pairs may be appended
* keyword = *set* * keyword = *set*
.. parsed-literal:: .. parsed-literal::
*set* args = phi name *set* args = phi name
phi = only currently allowed arg phi = only currently allowed arg
name = name of variable to set with phi name = name of variable to set with phi

4
doc/src/compute_displace_atom.rst
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@ -15,9 +15,9 @@ Syntax
* displace/atom = style name of this compute command * displace/atom = style name of this compute command
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *refresh* * keyword = *refresh*
.. parsed-literal:: .. parsed-literal::
*replace* arg = name of per-atom variable *replace* arg = name of per-atom variable

2
doc/src/compute_dpd.rst
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@ -38,7 +38,7 @@ relations:
.. math:: .. math::
U^{cond} = & \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ U^{cond} = & \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\
U^{mech} = & \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\ U^{mech} = & \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\
U^{chem} = & \displaystyle\sum_{i=1}^{N} u_{i}^{chem} \\ U^{chem} = & \displaystyle\sum_{i=1}^{N} u_{i}^{chem} \\
U = & \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\ U = & \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\

8
doc/src/compute_fep.rst
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@ -16,9 +16,9 @@ Syntax
* temp = external temperature (as specified for constant-temperature run) * temp = external temperature (as specified for constant-temperature run)
* one or more attributes with args may be appended * one or more attributes with args may be appended
* attribute = *pair* or *atom* * attribute = *pair* or *atom*
.. parsed-literal:: .. parsed-literal::
*pair* args = pstyle pparam I J v_delta *pair* args = pstyle pparam I J v_delta
pstyle = pair style name, e.g. lj/cut pstyle = pair style name, e.g. lj/cut
pparam = parameter to perturb pparam = parameter to perturb
@ -31,9 +31,9 @@ Syntax
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *tail* or *volume* * keyword = *tail* or *volume*
.. parsed-literal:: .. parsed-literal::
*tail* value = *no* or *yes* *tail* value = *no* or *yes*
*no* = ignore tail correction to pair energies (usually small in fep) *no* = ignore tail correction to pair energies (usually small in fep)
*yes* = include tail correction to pair energies *yes* = include tail correction to pair energies

8
doc/src/compute_global_atom.rst
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@ -14,9 +14,9 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* global/atom = style name of this compute command * global/atom = style name of this compute command
* index = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name * index = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
.. parsed-literal:: .. parsed-literal::
c_ID = per-atom vector calculated by a compute with ID c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID c_ID[I] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID f_ID = per-atom vector calculated by a fix with ID
@ -25,9 +25,9 @@ Syntax
* one or more inputs can be listed * one or more inputs can be listed
* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name * input = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
.. parsed-literal:: .. parsed-literal::
c_ID = global vector calculated by a compute with ID c_ID = global vector calculated by a compute with ID
c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below) c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
f_ID = global vector calculated by a fix with ID f_ID = global vector calculated by a fix with ID

4
doc/src/compute_group_group.rst
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@ -16,9 +16,9 @@ Syntax
* group2-ID = group ID of second (or same) group * group2-ID = group ID of second (or same) group
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *pair* or *kspace* or *boundary* or *molecule* * keyword = *pair* or *kspace* or *boundary* or *molecule*
.. parsed-literal:: .. parsed-literal::
*pair* value = *yes* or *no* *pair* value = *yes* or *no*
*kspace* value = *yes* or *no* *kspace* value = *yes* or *no*
*boundary* value = *yes* or *no* *boundary* value = *yes* or *no*

4
doc/src/compute_gyration_chunk.rst
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@ -16,9 +16,9 @@ Syntax
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command * chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *tensor* * keyword = *tensor*
.. parsed-literal:: .. parsed-literal::
*tensor* value = none *tensor* value = none

6
doc/src/compute_gyration_shape.rst
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@ -37,11 +37,11 @@ and the relative shape anisotropy, k:
c = & l_z - 0.5(l_y+l_x) \\ c = & l_z - 0.5(l_y+l_x) \\
b = & l_y - l_x \\ b = & l_y - l_x \\
k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2}
where :math:`l_x` <= :math:`l_y` <= :math:`l_z` are the three eigenvalues of the gyration tensor. A general description where :math:`l_x` <= :math:`l_y` <= :math:`l_z` are the three eigenvalues of the gyration tensor. A general description
of these parameters is provided in :ref:`(Mattice) <Mattice1>` while an application to polymer systems of these parameters is provided in :ref:`(Mattice) <Mattice1>` while an application to polymer systems
can be found in :ref:`(Theodorou) <Theodorou1>`. can be found in :ref:`(Theodorou) <Theodorou1>`.
The asphericity is always non-negative and zero only when the three principal The asphericity is always non-negative and zero only when the three principal
moments are equal. This zero condition is met when the distribution of particles moments are equal. This zero condition is met when the distribution of particles

16
doc/src/compute_gyration_shape_chunk.rst
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@ -26,8 +26,8 @@ Examples
Description Description
""""""""""" """""""""""
Define a computation that calculates the eigenvalues of the gyration tensor and Define a computation that calculates the eigenvalues of the gyration tensor and
three shape parameters of multiple chunks of atoms. The computation includes three shape parameters of multiple chunks of atoms. The computation includes
all effects due to atoms passing through periodic boundaries. all effects due to atoms passing through periodic boundaries.
The three computed shape parameters are the asphericity, b, the acylindricity, c, The three computed shape parameters are the asphericity, b, the acylindricity, c,
@ -37,13 +37,13 @@ and the relative shape anisotropy, k:
c = & l_z - 0.5(l_y+l_x) \\ c = & l_z - 0.5(l_y+l_x) \\
b = & l_y - l_x \\ b = & l_y - l_x \\
k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2}
where :math:`l_x` <= :math:`l_y` <= :math`l_z` are the three eigenvalues of the gyration tensor. A general description where :math:`l_x` <= :math:`l_y` <= :math`l_z` are the three eigenvalues of the gyration tensor. A general description
of these parameters is provided in :ref:`(Mattice) <Mattice2>` while an application to polymer systems of these parameters is provided in :ref:`(Mattice) <Mattice2>` while an application to polymer systems
can be found in :ref:`(Theodorou) <Theodorou2>`. The asphericity is always non-negative and zero can be found in :ref:`(Theodorou) <Theodorou2>`. The asphericity is always non-negative and zero
only when the three principal moments are equal. This zero condition is met when the distribution only when the three principal moments are equal. This zero condition is met when the distribution
of particles is spherically symmetric (hence the name asphericity) but also whenever the particle of particles is spherically symmetric (hence the name asphericity) but also whenever the particle
distribution is symmetric with respect to the three coordinate axes, e.g., distribution is symmetric with respect to the three coordinate axes, e.g.,
when the particles are distributed uniformly on a cube, tetrahedron or other Platonic when the particles are distributed uniformly on a cube, tetrahedron or other Platonic
@ -69,7 +69,7 @@ The tensor keyword must be specified in the compute gyration/chunk command.
**Output info:** **Output info:**
This compute calculates a global array with six columns, This compute calculates a global array with six columns,
which can be accessed by indices 1-6. The first three columns are the which can be accessed by indices 1-6. The first three columns are the
eigenvalues of the gyration tensor followed by the asphericity, the acylindricity eigenvalues of the gyration tensor followed by the asphericity, the acylindricity
and the relative shape anisotropy. The computed values can be used by any command and the relative shape anisotropy. The computed values can be used by any command

4
doc/src/compute_hexorder_atom.rst
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@ -14,9 +14,9 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* hexorder/atom = style name of this compute command * hexorder/atom = style name of this compute command
* one or more keyword/value pairs may be appended * one or more keyword/value pairs may be appended
.. parsed-literal:: .. parsed-literal::
keyword = *degree* or *nnn* or *cutoff* keyword = *degree* or *nnn* or *cutoff*
*cutoff* value = distance cutoff *cutoff* value = distance cutoff
*nnn* value = number of nearest neighbors *nnn* value = number of nearest neighbors

4
doc/src/compute_improper_local.rst
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@ -15,9 +15,9 @@ Syntax
* improper/local = style name of this compute command * improper/local = style name of this compute command
* one or more values may be appended * one or more values may be appended
* value = *chi* * value = *chi*
.. parsed-literal:: .. parsed-literal::
*chi* = tabulate improper angles *chi* = tabulate improper angles

4
doc/src/compute_modify.rst
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@ -14,9 +14,9 @@ Syntax
* compute-ID = ID of the compute to modify * compute-ID = ID of the compute to modify
* one or more keyword/value pairs may be listed * one or more keyword/value pairs may be listed
* keyword = *extra/dof* or *extra* or *dynamic/dof* or *dynamic* * keyword = *extra/dof* or *extra* or *dynamic/dof* or *dynamic*
.. parsed-literal:: .. parsed-literal::
*extra/dof* value = N *extra/dof* value = N
N = # of extra degrees of freedom to subtract N = # of extra degrees of freedom to subtract
*extra* syntax is identical to *extra/dof*\ , will be disabled at some point *extra* syntax is identical to *extra/dof*\ , will be disabled at some point

4
doc/src/compute_msd.rst
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@ -15,9 +15,9 @@ Syntax
* msd = style name of this compute command * msd = style name of this compute command
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *com* or *average* * keyword = *com* or *average*
.. parsed-literal:: .. parsed-literal::
*com* value = *yes* or *no* *com* value = *yes* or *no*
*average* value = *yes* or *no* *average* value = *yes* or *no*

4
doc/src/compute_msd_nongauss.rst
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@ -15,9 +15,9 @@ Syntax
* msd/nongauss = style name of this compute command * msd/nongauss = style name of this compute command
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *com* * keyword = *com*
.. parsed-literal:: .. parsed-literal::
*com* value = *yes* or *no* *com* value = *yes* or *no*

4
doc/src/compute_orientorder_atom.rst
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@ -14,9 +14,9 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* orientorder/atom = style name of this compute command * orientorder/atom = style name of this compute command
* one or more keyword/value pairs may be appended * one or more keyword/value pairs may be appended
.. parsed-literal:: .. parsed-literal::
keyword = *cutoff* or *nnn* or *degrees* or *components* keyword = *cutoff* or *nnn* or *degrees* or *components*
*cutoff* value = distance cutoff *cutoff* value = distance cutoff
*nnn* value = number of nearest neighbors *nnn* value = number of nearest neighbors

8
doc/src/compute_pair_local.rst
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@ -15,9 +15,9 @@ Syntax
* pair/local = style name of this compute command * pair/local = style name of this compute command
* one or more values may be appended * one or more values may be appended
* value = *dist* or *eng* or *force* or *fx* or *fy* or *fz* or *pN* * value = *dist* or *eng* or *force* or *fx* or *fy* or *fz* or *pN*
.. parsed-literal:: .. parsed-literal::
*dist* = pairwise distance *dist* = pairwise distance
*eng* = pairwise energy *eng* = pairwise energy
*force* = pairwise force *force* = pairwise force
@ -26,9 +26,9 @@ Syntax
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *cutoff* * keyword = *cutoff*
.. parsed-literal:: .. parsed-literal::
*cutoff* arg = *type* or *radius* *cutoff* arg = *type* or *radius*

2
doc/src/compute_pressure.rst
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@ -66,7 +66,7 @@ second term uses components of the virial tensor:
.. math:: .. math::
P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} + P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} +
\frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V} \frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V}

24
doc/src/compute_property_atom.rst
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@ -14,9 +14,9 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* property/atom = style name of this compute command * property/atom = style name of this compute command
* input = one or more atom attributes * input = one or more atom attributes
.. parsed-literal:: .. parsed-literal::
possible attributes = id, mol, proc, type, mass, possible attributes = id, mol, proc, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz, vx, vy, vz, fx, fy, fz,
@ -36,9 +36,9 @@ Syntax
rho, drho, e, de, cv, rho, drho, e, de, cv,
i_name, d_name i_name, d_name
.. parsed-literal:: .. parsed-literal::
id = atom ID id = atom ID
mol = molecule ID mol = molecule ID
proc = ID of processor that owns atom proc = ID of processor that owns atom
@ -66,25 +66,25 @@ Syntax
corner123x, corner123y, corner123z = corner points of triangle corner123x, corner123y, corner123z = corner points of triangle
nbonds = number of bonds assigned to an atom nbonds = number of bonds assigned to an atom
.. parsed-literal:: .. parsed-literal::
PERI package per-atom properties: PERI package per-atom properties:
vfrac = ??? vfrac = ???
s0 = ??? s0 = ???
.. parsed-literal:: .. parsed-literal::
USER-EFF and USER-AWPMD package per-atom properties: USER-EFF and USER-AWPMD package per-atom properties:
spin = electron spin spin = electron spin
eradius = electron radius eradius = electron radius
ervel = electron radial velocity ervel = electron radial velocity
erforce = electron radial force erforce = electron radial force
.. parsed-literal:: .. parsed-literal::
USER-SPH package per-atom properties: USER-SPH package per-atom properties:
rho = ??? rho = ???
drho = ??? drho = ???
@ -92,9 +92,9 @@ Syntax
de = ??? de = ???
cv = ??? cv = ???
.. parsed-literal:: .. parsed-literal::
:doc:`fix property/atom <fix_property_atom>` per-atom properties: :doc:`fix property/atom <fix_property_atom>` per-atom properties:
i_name = custom integer vector with name i_name = custom integer vector with name
d_name = custom integer vector with name d_name = custom integer vector with name

4
doc/src/compute_property_chunk.rst
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@ -14,9 +14,9 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* property/chunk = style name of this compute command * property/chunk = style name of this compute command
* input = one or more attributes * input = one or more attributes
.. parsed-literal:: .. parsed-literal::
attributes = count, id, coord1, coord2, coord3 attributes = count, id, coord1, coord2, coord3
count = # of atoms in chunk count = # of atoms in chunk
id = original chunk IDs before compression by :doc:`compute chunk/atom <compute_chunk_atom>` id = original chunk IDs before compression by :doc:`compute chunk/atom <compute_chunk_atom>`

12
doc/src/compute_property_local.rst
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@ -14,9 +14,9 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* property/local = style name of this compute command * property/local = style name of this compute command
* one or more attributes may be appended * one or more attributes may be appended
.. parsed-literal:: .. parsed-literal::
possible attributes = natom1 natom2 ntype1 ntype2 possible attributes = natom1 natom2 ntype1 ntype2
patom1 patom2 ptype1 ptype2 patom1 patom2 ptype1 ptype2
batom1 batom2 btype batom1 batom2 btype
@ -24,9 +24,9 @@ Syntax
datom1 datom2 datom3 datom4 dtype datom1 datom2 datom3 datom4 dtype
iatom1 iatom2 iatom3 iatom4 itype iatom1 iatom2 iatom3 iatom4 itype
.. parsed-literal:: .. parsed-literal::
natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff) natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff) ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff) patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
@ -42,9 +42,9 @@ Syntax
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *cutoff* * keyword = *cutoff*
.. parsed-literal:: .. parsed-literal::
*cutoff* arg = *type* or *radius* *cutoff* arg = *type* or *radius*

4
doc/src/compute_rdf.rst
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@ -18,9 +18,9 @@ Syntax
* jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) * jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below)
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *cutoff* * keyword = *cutoff*
.. parsed-literal:: .. parsed-literal::
*cutoff* value = Rcut *cutoff* value = Rcut
Rcut = cutoff distance for RDF computation (distance units) Rcut = cutoff distance for RDF computation (distance units)

12
doc/src/compute_reduce.rst
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@ -16,9 +16,9 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* style = *reduce* or *reduce/region* * style = *reduce* or *reduce/region*
.. parsed-literal:: .. parsed-literal::
*reduce* arg = none *reduce* arg = none
*reduce/region* arg = region-ID *reduce/region* arg = region-ID
region-ID = ID of region to use for choosing atoms region-ID = ID of region to use for choosing atoms
@ -26,9 +26,9 @@ Syntax
* mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq* * mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq*
* one or more inputs can be listed * one or more inputs can be listed
* input = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name * input = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
.. parsed-literal:: .. parsed-literal::
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
c_ID = per-atom or local vector calculated by a compute with ID c_ID = per-atom or local vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below) c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
@ -38,9 +38,9 @@ Syntax
* zero or more keyword/args pairs may be appended * zero or more keyword/args pairs may be appended
* keyword = *replace* * keyword = *replace*
.. parsed-literal:: .. parsed-literal::
*replace* args = vec1 vec2 *replace* args = vec1 vec2
vec1 = reduced value from this input vector will be replaced vec1 = reduced value from this input vector will be replaced
vec2 = replace it with vec1[N] where N is index of max/min value from vec2 vec2 = replace it with vec1[N] where N is index of max/min value from vec2

4
doc/src/compute_reduce_chunk.rst
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@ -17,9 +17,9 @@ Syntax
* mode = *sum* or *min* or *max* * mode = *sum* or *min* or *max*
* one or more inputs can be listed * one or more inputs can be listed
* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_ID * input = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_ID
.. parsed-literal:: .. parsed-literal::
c_ID = per-atom vector calculated by a compute with ID c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom vector calculated by a fix with ID f_ID = per-atom vector calculated by a fix with ID

4
doc/src/compute_rigid_local.rst
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@ -15,9 +15,9 @@ Syntax
* rigid/local = style name of this compute command * rigid/local = style name of this compute command
* rigidID = ID of fix rigid/small command or one of its variants * rigidID = ID of fix rigid/small command or one of its variants
* input = one or more rigid body attributes * input = one or more rigid body attributes
.. parsed-literal:: .. parsed-literal::
possible attributes = id, mol, mass, possible attributes = id, mol, mass,
x, y, z, xu, yu, zu, ix, iy, iz x, y, z, xu, yu, zu, ix, iy, iz
vx, vy, vz, fx, fy, fz, vx, vy, vz, fx, fy, fz,

4
doc/src/compute_saed.rst
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@ -17,9 +17,9 @@ Syntax
* type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) * type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *Kmax* or *Zone* or *dR\_Ewald* or *c* or *manual* or *echo* * keyword = *Kmax* or *Zone* or *dR\_Ewald* or *c* or *manual* or *echo*
.. parsed-literal:: .. parsed-literal::
*Kmax* value = Maximum distance explored from reciprocal space origin *Kmax* value = Maximum distance explored from reciprocal space origin
(inverse length units) (inverse length units)
*Zone* values = z1 z2 z3 *Zone* values = z1 z2 z3

4
doc/src/compute_slice.rst
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@ -17,9 +17,9 @@ Syntax
* Nstop = stopping index within input vector(s) * Nstop = stopping index within input vector(s)
* Nskip = extract every Nskip elements from input vector(s) * Nskip = extract every Nskip elements from input vector(s)
* input = c\_ID, c\_ID[N], f\_ID, f\_ID[N] * input = c\_ID, c\_ID[N], f\_ID, f\_ID[N]
.. parsed-literal:: .. parsed-literal::
c_ID = global vector calculated by a compute with ID c_ID = global vector calculated by a compute with ID
c_ID[I] = Ith column of global array calculated by a compute with ID c_ID[I] = Ith column of global array calculated by a compute with ID
f_ID = global vector calculated by a fix with ID f_ID = global vector calculated by a fix with ID

18
doc/src/compute_sna_atom.rst
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@ -20,7 +20,7 @@ Syntax
compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
@ -32,9 +32,9 @@ Syntax
* w\_1, w\_2,... = list of neighbor weights, one for each type * w\_1, w\_2,... = list of neighbor weights, one for each type
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* * keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag*
.. parsed-literal:: .. parsed-literal::
*rmin0* value = parameter in distance to angle conversion (distance units) *rmin0* value = parameter in distance to angle conversion (distance units)
*switchflag* value = *0* or *1* *switchflag* value = *0* or *1*
*0* = do not use switching function *0* = do not use switching function
@ -63,7 +63,7 @@ Description
Define a computation that calculates a set of quantities related to the Define a computation that calculates a set of quantities related to the
bispectrum components of the atoms in a group. These computes are bispectrum components of the atoms in a group. These computes are
used primarily for calculating the dependence of energy, force, and used primarily for calculating the dependence of energy, force, and
stress components on the linear coefficients in the stress components on the linear coefficients in the
:doc:`snap pair\_style <pair_snap>`, which is useful when training a :doc:`snap pair\_style <pair_snap>`, which is useful when training a
SNAP potential to match target data. SNAP potential to match target data.
@ -103,7 +103,7 @@ coefficient as
.. math:: .. math::
u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)} u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)}
The *w\_i'* neighbor weights are dimensionless numbers that are chosen The *w\_i'* neighbor weights are dimensionless numbers that are chosen
@ -126,7 +126,7 @@ real-valued and invariant under rotation :ref:`(Bartok) <Bartok20101>`.
.. math:: .. math::
B_{j_1,j_2,j} = B_{j_1,j_2,j} =
\sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^j_{m,m'})^* \sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^j_{m,m'})^*
H {\scriptscriptstyle \begin{array}{l} {j} {m} {m'} \\ H {\scriptscriptstyle \begin{array}{l} {j} {m} {m'} \\
{j_1} {m_1} {m'_1} \\ {j_1} {m_1} {m'_1} \\
@ -175,7 +175,7 @@ section below on output for a detailed explanation.
Compute *snap* calculates a global array contains information related Compute *snap* calculates a global array contains information related
to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ , to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ ,
and *snav/atom*\ . The first row of the array contains the summation of and *snav/atom*\ . The first row of the array contains the summation of
*sna/atom* over all atoms, but broken out by type. The last six rows *sna/atom* over all atoms, but broken out by type. The last six rows
of the array contain the summation of *snav/atom* over all atoms, broken of the array contain the summation of *snav/atom* over all atoms, broken
out by type. In between these are 3\*\ *N* rows containing the same values out by type. In between these are 3\*\ *N* rows containing the same values
@ -288,12 +288,12 @@ block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
notation. Each of these sub-blocks contains one column for each notation. Each of these sub-blocks contains one column for each
bispectrum component, the same as for compute *sna/atom* bispectrum component, the same as for compute *sna/atom*
Compute *snap* evaluates a global array. Compute *snap* evaluates a global array.
The columns are arranged into The columns are arranged into
*ntypes* blocks, listed in order of atom type *I*\ . Each block *ntypes* blocks, listed in order of atom type *I*\ . Each block
contains one column for each bispectrum component, the same as for compute contains one column for each bispectrum component, the same as for compute
*sna/atom*\ . A final column contains the corresponding energy, force component *sna/atom*\ . A final column contains the corresponding energy, force component
on an atom, or virial stress component. The rows of the array appear on an atom, or virial stress component. The rows of the array appear
in the following order: in the following order:
* 1 row: *sna/atom* quantities summed for all atoms of type *I* * 1 row: *sna/atom* quantities summed for all atoms of type *I*

4
doc/src/compute_temp_asphere.rst
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@ -15,9 +15,9 @@ Syntax
* temp/asphere = style name of this compute command * temp/asphere = style name of this compute command
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *bias* or *dof* * keyword = *bias* or *dof*
.. parsed-literal:: .. parsed-literal::
*bias* value = bias-ID *bias* value = bias-ID
bias-ID = ID of a temperature compute that removes a velocity bias bias-ID = ID of a temperature compute that removes a velocity bias
*dof* value = *all* or *rotate* *dof* value = *all* or *rotate*

4
doc/src/compute_temp_body.rst
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@ -15,9 +15,9 @@ Syntax
* temp/body = style name of this compute command * temp/body = style name of this compute command
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *bias* or *dof* * keyword = *bias* or *dof*
.. parsed-literal:: .. parsed-literal::
*bias* value = bias-ID *bias* value = bias-ID
bias-ID = ID of a temperature compute that removes a velocity bias bias-ID = ID of a temperature compute that removes a velocity bias
*dof* value = *all* or *rotate* *dof* value = *all* or *rotate*

8
doc/src/compute_temp_chunk.rst
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@ -16,18 +16,18 @@ Syntax
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command * chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
* zero or more values can be listed as value1,value2,etc * zero or more values can be listed as value1,value2,etc
* value = *temp* or *kecom* or *internal* * value = *temp* or *kecom* or *internal*
.. parsed-literal:: .. parsed-literal::
temp = temperature of each chunk temp = temperature of each chunk
kecom = kinetic energy of each chunk based on velocity of center of mass kecom = kinetic energy of each chunk based on velocity of center of mass
internal = internal kinetic energy of each chunk internal = internal kinetic energy of each chunk
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *com* or *bias* or *adof* or *cdof* * keyword = *com* or *bias* or *adof* or *cdof*
.. parsed-literal:: .. parsed-literal::
*com* value = *yes* or *no* *com* value = *yes* or *no*
yes = subtract center-of-mass velocity from each chunk before calculating temperature yes = subtract center-of-mass velocity from each chunk before calculating temperature
no = do not subtract center-of-mass velocity no = do not subtract center-of-mass velocity

8
doc/src/compute_temp_profile.rst
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@ -15,9 +15,9 @@ Syntax
* temp/profile = style name of this compute command * temp/profile = style name of this compute command
* xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension * xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
* binstyle = *x* or *y* or *z* or *xy* or *yz* or *xz* or *xyz* * binstyle = *x* or *y* or *z* or *xy* or *yz* or *xz* or *xyz*
.. parsed-literal:: .. parsed-literal::
*x* arg = Nx *x* arg = Nx
*y* arg = Ny *y* arg = Ny
*z* arg = Nz *z* arg = Nz
@ -29,9 +29,9 @@ Syntax
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *out* * keyword = *out*
.. parsed-literal:: .. parsed-literal::
*out* value = *tensor* or *bin* *out* value = *tensor* or *bin*

4
doc/src/compute_temp_sphere.rst
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@ -15,9 +15,9 @@ Syntax
* temp/sphere = style name of this compute command * temp/sphere = style name of this compute command
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *bias* or *dof* * keyword = *bias* or *dof*
.. parsed-literal:: .. parsed-literal::
*bias* value = bias-ID *bias* value = bias-ID
bias-ID = ID of a temperature compute that removes a velocity bias bias-ID = ID of a temperature compute that removes a velocity bias
*dof* value = *all* or *rotate* *dof* value = *all* or *rotate*

4
doc/src/compute_ti.rst
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@ -15,9 +15,9 @@ Syntax
* ti = style name of this compute command * ti = style name of this compute command
* one or more attribute/arg pairs may be appended * one or more attribute/arg pairs may be appended
* keyword = pair style (lj/cut, gauss, born, etc) or *tail* or *kspace* * keyword = pair style (lj/cut, gauss, born, etc) or *tail* or *kspace*
.. parsed-literal:: .. parsed-literal::
pair style args = atype v_name1 v_name2 pair style args = atype v_name1 v_name2
atype = atom type (see asterisk form below) atype = atom type (see asterisk form below)
v_name1 = variable with name1 that is energy scale factor and function of lambda v_name1 = variable with name1 that is energy scale factor and function of lambda

4
doc/src/compute_voronoi_atom.rst
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@ -16,9 +16,9 @@ Syntax
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *only\_group* or *surface* or *radius* or *edge\_histo* or *edge\_threshold* * keyword = *only\_group* or *surface* or *radius* or *edge\_histo* or *edge\_threshold*
or *face\_threshold* or *neighbors* or *peratom* or *face\_threshold* or *neighbors* or *peratom*
.. parsed-literal:: .. parsed-literal::
*only_group* = no arg *only_group* = no arg
*occupation* = no arg *occupation* = no arg
*surface* arg = sgroup-ID *surface* arg = sgroup-ID

6
doc/src/compute_xrd.rst
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@ -17,9 +17,9 @@ Syntax
* type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) * type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *2Theta* or *c* or *LP* or *manual* or *echo* * keyword = *2Theta* or *c* or *LP* or *manual* or *echo*
.. parsed-literal:: .. parsed-literal::
*2Theta* values = Min2Theta Max2Theta *2Theta* values = Min2Theta Max2Theta
Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
(radians or degrees) (radians or degrees)
@ -111,7 +111,7 @@ The analytic approximation is computed using the formula
.. math:: .. math::
f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{4} f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{4}
a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )+c a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )+c
Coefficients parameterized by :ref:`(Peng) <Peng>` are assigned for each Coefficients parameterized by :ref:`(Peng) <Peng>` are assigned for each

8
doc/src/create_atoms.rst
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@ -13,9 +13,9 @@ Syntax
* type = atom type (1-Ntypes) of atoms to create (offset for molecule creation) * type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
* style = *box* or *region* or *single* or *random* * style = *box* or *region* or *single* or *random*
.. parsed-literal:: .. parsed-literal::
*box* args = none *box* args = none
*region* args = region-ID *region* args = region-ID
region-ID = particles will only be created if contained in the region region-ID = particles will only be created if contained in the region
@ -28,9 +28,9 @@ Syntax
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *units* * keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *units*
.. code-block:: LAMMPS .. code-block:: LAMMPS
*mol* value = template-ID seed *mol* value = template-ID seed
template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
seed = random # seed (positive integer) seed = random # seed (positive integer)

4
doc/src/create_box.rst
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@ -15,9 +15,9 @@ Syntax
* region-ID = ID of region to use as simulation domain * region-ID = ID of region to use as simulation domain
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* * keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom*
.. parsed-literal:: .. parsed-literal::
*bond/types* value = # of bond types *bond/types* value = # of bond types
*angle/types* value = # of angle types *angle/types* value = # of angle types
*dihedral/types* value = # of dihedral types *dihedral/types* value = # of dihedral types

8
doc/src/delete_atoms.rst
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@ -12,9 +12,9 @@ Syntax
delete_atoms style args keyword value ... delete_atoms style args keyword value ...
* style = *group* or *region* or *overlap* or *porosity* * style = *group* or *region* or *overlap* or *porosity*
.. parsed-literal:: .. parsed-literal::
*group* args = group-ID *group* args = group-ID
*region* args = region-ID *region* args = region-ID
*overlap* args = cutoff group1-ID group2-ID *overlap* args = cutoff group1-ID group2-ID
@ -28,9 +28,9 @@ Syntax
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *compress* or *bond* or *mol* * keyword = *compress* or *bond* or *mol*
.. parsed-literal:: .. parsed-literal::
*compress* value = *no* or *yes* *compress* value = *no* or *yes*
*bond* value = *no* or *yes* *bond* value = *no* or *yes*
*mol* value = *no* or *yes* *mol* value = *no* or *yes*

4
doc/src/delete_bonds.rst
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@ -13,9 +13,9 @@ Syntax
* group-ID = group ID * group-ID = group ID
* style = *multi* or *atom* or *bond* or *angle* or *dihedral* or *improper* or *stats* * style = *multi* or *atom* or *bond* or *angle* or *dihedral* or *improper* or *stats*
.. parsed-literal:: .. parsed-literal::
*multi* arg = none *multi* arg = none
*atom* arg = an atom type or range of types (see below) *atom* arg = an atom type or range of types (see below)
*bond* arg = a bond type or range of types (see below) *bond* arg = a bond type or range of types (see below)

2
doc/src/dihedral_helix.rst
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@ -30,7 +30,7 @@ The *helix* dihedral style uses the potential
.. math:: .. math::
E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] +
C [1 + \cos(\theta + \frac{\pi}{4})] C [1 + \cos(\theta + \frac{\pi}{4})]

2
doc/src/dihedral_quadratic.rst
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@ -30,7 +30,7 @@ The *quadratic* dihedral style uses the potential:
.. math:: .. math::
E = K (\phi - \phi_0)^2 E = K (\phi - \phi_0)^2
This dihedral potential can be used to keep a dihedral in a predefined This dihedral potential can be used to keep a dihedral in a predefined

8
doc/src/displace_atoms.rst
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@ -13,9 +13,9 @@ Syntax
* group-ID = ID of group of atoms to displace * group-ID = ID of group of atoms to displace
* style = *move* or *ramp* or *random* or *rotate* * style = *move* or *ramp* or *random* or *rotate*
.. parsed-literal:: .. parsed-literal::
*move* args = delx dely delz *move* args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units) delx,dely,delz = distance to displace in each dimension (distance units)
any of delx,dely,delz can be a variable (see below) any of delx,dely,delz can be a variable (see below)
@ -33,9 +33,9 @@ Syntax
theta = angle of rotation (degrees) theta = angle of rotation (degrees)
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
.. parsed-literal:: .. parsed-literal::
keyword = *units* keyword = *units*
value = *box* or *lattice* value = *box* or *lattice*

18
doc/src/dump.rst
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@ -42,9 +42,9 @@ Syntax
* N = dump every this many timesteps * N = dump every this many timesteps
* file = name of file to write dump info to * file = name of file to write dump info to
* args = list of arguments for a particular style * args = list of arguments for a particular style
.. parsed-literal:: .. parsed-literal::
*atom* args = none *atom* args = none
*atom/gz* args = none *atom/gz* args = none
*atom/mpiio* args = none *atom/mpiio* args = none
@ -69,9 +69,9 @@ Syntax
*xyz/mpiio* args = none *xyz/mpiio* args = none
* *custom* or *custom/gz* or *custom/mpiio* or *netcdf* or *netcdf/mpiio* args = list of atom attributes * *custom* or *custom/gz* or *custom/mpiio* or *netcdf* or *netcdf/mpiio* args = list of atom attributes
.. parsed-literal:: .. parsed-literal::
possible attributes = id, mol, proc, procp1, type, element, mass, possible attributes = id, mol, proc, procp1, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu, x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz, xsu, ysu, zsu, ix, iy, iz,
@ -81,9 +81,9 @@ Syntax
angmomx, angmomy, angmomz, tqx, tqy, tqz, angmomx, angmomy, angmomz, tqx, tqy, tqz,
c_ID, c_ID[N], f_ID, f_ID[N], v_name c_ID, c_ID[N], f_ID, f_ID[N], v_name
.. parsed-literal:: .. parsed-literal::
id = atom ID id = atom ID
mol = molecule ID mol = molecule ID
proc = ID of processor that owns atom proc = ID of processor that owns atom
@ -114,9 +114,9 @@ Syntax
i_name = per-atom integer vector with name, managed by fix property/atom i_name = per-atom integer vector with name, managed by fix property/atom
* *local* args = list of local attributes * *local* args = list of local attributes
.. parsed-literal:: .. parsed-literal::
possible attributes = index, c_ID, c_ID[I], f_ID, f_ID[I] possible attributes = index, c_ID, c_ID[I], f_ID, f_ID[I]
index = enumeration of local values index = enumeration of local values
c_ID = local vector calculated by a compute with ID c_ID = local vector calculated by a compute with ID
@ -716,7 +716,7 @@ LAMMPS was built with that package. See the :doc:`Build package <Build_package>
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`dump atom/adios <dump_adios>`, :doc:`dump custom/adios <dump_adios>`, :doc:`dump atom/adios <dump_adios>`, :doc:`dump custom/adios <dump_adios>`,
:doc:`dump h5md <dump_h5md>`, :doc:`dump image <dump_image>`, :doc:`dump h5md <dump_h5md>`, :doc:`dump image <dump_image>`,
:doc:`dump molfile <dump_molfile>`, :doc:`dump_modify <dump_modify>`, :doc:`dump molfile <dump_molfile>`, :doc:`dump_modify <dump_modify>`,
:doc:`undump <undump>` :doc:`undump <undump>`

4
doc/src/dump_adios.rst
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@ -1,5 +1,5 @@
.. index:: dump atom/adios .. index:: dump atom/adios
.. index:: dump custom/adios .. index:: dump custom/adios
dump atom/adios command dump atom/adios command
========================= =========================

4
doc/src/dump_cfg_uef.rst
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@ -15,9 +15,9 @@ Syntax
* group-ID = ID of the group of atoms to be dumped * group-ID = ID of the group of atoms to be dumped
* N = dump every this many timesteps * N = dump every this many timesteps
* file = name of file to write dump info to * file = name of file to write dump info to
.. parsed-literal:: .. parsed-literal::
args = same as args for :doc:`dump custom <dump>` args = same as args for :doc:`dump custom <dump>`

20
doc/src/dump_image.rst
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@ -23,9 +23,9 @@ Syntax
* diameter = atom attribute that determines size of each atom * diameter = atom attribute that determines size of each atom
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *atom* or *adiam* or *bond* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *persp* or *box* or *axes* or *subbox* or *shiny* or *ssao* * keyword = *atom* or *adiam* or *bond* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *persp* or *box* or *axes* or *subbox* or *shiny* or *ssao*
.. parsed-literal:: .. parsed-literal::
*atom* = yes/no = do or do not draw atoms *atom* = yes/no = do or do not draw atoms
*adiam* size = numeric value for atom diameter (distance units) *adiam* size = numeric value for atom diameter (distance units)
*bond* values = color width = color and width of bonds *bond* values = color width = color and width of bonds
@ -568,9 +568,9 @@ To manually convert JPEG, PNG or PPM files into an animated GIF or
MPEG or other movie file you can use: MPEG or other movie file you can use:
* a) Use the ImageMagick convert program. * a) Use the ImageMagick convert program.
.. code-block:: bash .. code-block:: bash
% convert *.jpg foo.gif % convert *.jpg foo.gif
% convert -loop 1 *.ppm foo.mpg % convert -loop 1 *.ppm foo.mpg
@ -596,9 +596,9 @@ MPEG or other movie file you can use:
FFmpeg is a command line tool that is available on many platforms and FFmpeg is a command line tool that is available on many platforms and
allows extremely flexible encoding and decoding of movies. allows extremely flexible encoding and decoding of movies.
.. code-block:: bash .. code-block:: bash
cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
@ -619,18 +619,18 @@ Play the movie:
* b) Use the freely available mplayer or ffplay tool to view a * b) Use the freely available mplayer or ffplay tool to view a
movie. Both are available for multiple OSes and support a large movie. Both are available for multiple OSes and support a large
variety of file formats and decoders. variety of file formats and decoders.
.. code-block:: bash .. code-block:: bash
% mplayer foo.mpg % mplayer foo.mpg
% ffplay bar.avi % ffplay bar.avi
* c) Use the `Pizza.py <http://www.sandia.gov/~sjplimp/pizza.html>`_ * c) Use the `Pizza.py <http://www.sandia.gov/~sjplimp/pizza.html>`_
`animate tool <http://www.sandia.gov/~sjplimp/pizza/doc/animate.html>`_, `animate tool <http://www.sandia.gov/~sjplimp/pizza/doc/animate.html>`_,
which works directly on a series of image files. which works directly on a series of image files.
.. code-block:: python .. code-block:: python
a = animate("foo*.jpg") a = animate("foo*.jpg")
* d) QuickTime and other Windows- or MacOS-based media players can * d) QuickTime and other Windows- or MacOS-based media players can

8
doc/src/dump_modify.rst
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@ -15,9 +15,9 @@ Syntax
* one or more keyword/value pairs may be appended * one or more keyword/value pairs may be appended
* these keywords apply to various dump styles * these keywords apply to various dump styles
* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap* * keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
.. parsed-literal:: .. parsed-literal::
*append* arg = *yes* or *no* *append* arg = *yes* or *no*
*at* arg = N *at* arg = N
N = index of frame written upon first dump N = index of frame written upon first dump
@ -68,9 +68,9 @@ Syntax
* these keywords apply only to the *image* and *movie* :doc:`styles <dump_image>` * these keywords apply only to the *image* and *movie* :doc:`styles <dump_image>`
* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* * keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
.. parsed-literal:: .. parsed-literal::
*acolor* args = type color *acolor* args = type color
type = atom type or range of types (see below) type = atom type or range of types (see below)
color = name of color or color1/color2/... color = name of color or color1/color2/...

6
doc/src/dynamical_matrix.rst
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@ -15,9 +15,9 @@ Syntax
* style = *regular* or *eskm* * style = *regular* or *eskm*
* gamma = finite different displacement length (distance units) * gamma = finite different displacement length (distance units)
* one or more keyword/arg pairs may be appended * one or more keyword/arg pairs may be appended
.. parsed-literal:: .. parsed-literal::
keyword = *file* or *binary* keyword = *file* or *binary*
*file* name = name of output file for the dynamical matrix *file* name = name of output file for the dynamical matrix
*binary* arg = *yes* or *no* or *gzip* *binary* arg = *yes* or *no* or *gzip*
@ -51,7 +51,7 @@ matrix defined by
\Phi_{ij}^{\alpha\beta} = \frac{\partial^2 U}{\partial x_{i,\alpha} \partial x_{j,\beta}} \Phi_{ij}^{\alpha\beta} = \frac{\partial^2 U}{\partial x_{i,\alpha} \partial x_{j,\beta}}
The output for the dynamical matrix is printed three elements at a time. The output for the dynamical matrix is printed three elements at a time.
The three elements are the three :math:`\beta` elements for a respective The three elements are the three :math:`\beta` elements for a respective
i/:math:`\alpha`/j combination. Each line is printed in order of j i/:math:`\alpha`/j combination. Each line is printed in order of j

8
doc/src/fix_adapt.rst
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@ -16,9 +16,9 @@ Syntax
* N = adapt simulation settings every this many timesteps * N = adapt simulation settings every this many timesteps
* one or more attribute/arg pairs may be appended * one or more attribute/arg pairs may be appended
* attribute = *pair* or *kspace* or *atom* * attribute = *pair* or *kspace* or *atom*
.. parsed-literal:: .. parsed-literal::
*pair* args = pstyle pparam I J v_name *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 pparam = parameter to adapt over time
@ -37,9 +37,9 @@ Syntax
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *scale* or *reset* * keyword = *scale* or *reset*
.. parsed-literal:: .. parsed-literal::
*scale* value = *no* or *yes* *scale* value = *no* or *yes*
*no* = the variable value is the new setting *no* = the variable value is the new setting
*yes* = the variable value multiplies the original setting *yes* = the variable value multiplies the original setting

8
doc/src/fix_adapt_fep.rst
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@ -16,9 +16,9 @@ Syntax
* N = adapt simulation settings every this many timesteps * N = adapt simulation settings every this many timesteps
* one or more attribute/arg pairs may be appended * one or more attribute/arg pairs may be appended
* attribute = *pair* or *kspace* or *atom* * attribute = *pair* or *kspace* or *atom*
.. parsed-literal:: .. parsed-literal::
*pair* args = pstyle pparam I J v_name *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 pparam = parameter to adapt over time
@ -33,9 +33,9 @@ Syntax
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *scale* or *reset* or *after* * keyword = *scale* or *reset* or *after*
.. parsed-literal:: .. parsed-literal::
*scale* value = *no* or *yes* *scale* value = *no* or *yes*
*no* = the variable value is the new setting *no* = the variable value is the new setting
*yes* = the variable value multiplies the original setting *yes* = the variable value multiplies the original setting

8
doc/src/fix_addforce.rst
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@ -14,16 +14,16 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* addforce = style name of this fix command * addforce = style name of this fix command
* fx,fy,fz = force component values (force units) * fx,fy,fz = force component values (force units)
.. parsed-literal:: .. parsed-literal::
any of fx,fy,fz can be a variable (see below) any of fx,fy,fz can be a variable (see below)
* zero or more keyword/value pairs may be appended to args * zero or more keyword/value pairs may be appended to args
* keyword = *every* or *region* or *energy* * keyword = *every* or *region* or *energy*
.. parsed-literal:: .. parsed-literal::
*every* value = Nevery *every* value = Nevery
Nevery = add force every this many timesteps Nevery = add force every this many timesteps
*region* value = region-ID *region* value = region-ID

4
doc/src/fix_append_atoms.rst
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@ -16,9 +16,9 @@ Syntax
* face = *zhi* * face = *zhi*
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *basis* or *size* or *freq* or *temp* or *random* or *units* * keyword = *basis* or *size* or *freq* or *temp* or *random* or *units*
.. parsed-literal:: .. parsed-literal::
*basis* values = M itype *basis* values = M itype
M = which basis atom M = which basis atom
itype = atom type (1-N) to assign to this basis atom itype = atom type (1-N) to assign to this basis atom

4
doc/src/fix_atom_swap.rst
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@ -19,9 +19,9 @@ Syntax
* T = scaling temperature of the MC swaps (temperature units) * T = scaling temperature of the MC swaps (temperature units)
* one or more keyword/value pairs may be appended to args * one or more keyword/value pairs may be appended to args
* keyword = *types* or *mu* or *ke* or *semi-grand* or *region* * keyword = *types* or *mu* or *ke* or *semi-grand* or *region*
.. parsed-literal:: .. parsed-literal::
*types* values = two or more atom types *types* values = two or more atom types
*mu* values = chemical potential of swap types (energy units) *mu* values = chemical potential of swap types (energy units)
*ke* value = *no* or *yes* *ke* value = *no* or *yes*

4
doc/src/fix_ave_atom.rst
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@ -18,9 +18,9 @@ Syntax
* Nfreq = calculate averages every this many timesteps * Nfreq = calculate averages every this many timesteps
one or more input values can be listed 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 * value = x, y, z, vx, vy, vz, fx, fy, fz, c\_ID, c\_ID[i], f\_ID, f\_ID[i], v\_name
.. parsed-literal:: .. parsed-literal::
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
c_ID = per-atom vector calculated by a compute with ID c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)

8
doc/src/fix_ave_chunk.rst
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@ -19,9 +19,9 @@ Syntax
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command * chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
* one or more input values can be listed * one or more input values can be listed
* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c\_ID, c\_ID[I], f\_ID, f\_ID[I], v\_name * value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c\_ID, c\_ID[I], f\_ID, f\_ID[I], v\_name
.. parsed-literal:: .. parsed-literal::
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
density/number, density/mass = number or mass density density/number, density/mass = number or mass density
temp = temperature temp = temperature
@ -33,9 +33,9 @@ Syntax
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *title1* or *title2* or *title3* * keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *title1* or *title2* or *title3*
.. parsed-literal:: .. parsed-literal::
*norm* arg = *all* or *sample* or *none* = how output on *Nfreq* steps is normalized *norm* arg = *all* or *sample* or *none* = how output on *Nfreq* steps is normalized
all = output is sum of atoms across all *Nrepeat* samples, divided by atom count all = output is sum of atoms across all *Nrepeat* samples, divided by atom count
sample = output is sum of *Nrepeat* sample averages, divided by *Nrepeat* sample = output is sum of *Nrepeat* sample averages, divided by *Nrepeat*

8
doc/src/fix_ave_correlate.rst
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@ -18,9 +18,9 @@ Syntax
* Nfreq = calculate time window averages every this many timesteps * Nfreq = calculate time window averages every this many timesteps
* one or more input values can be listed * one or more input values can be listed
* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name * value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
.. parsed-literal:: .. parsed-literal::
c_ID = global scalar calculated by a compute with ID c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
f_ID = global scalar calculated by a fix with ID f_ID = global scalar calculated by a fix with ID
@ -30,9 +30,9 @@ Syntax
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *type* or *ave* or *start* or *prefactor* or *file* or *overwrite* or *title1* or *title2* or *title3* * keyword = *type* or *ave* or *start* or *prefactor* or *file* or *overwrite* or *title1* or *title2* or *title3*
.. parsed-literal:: .. parsed-literal::
*type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full* *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full*
auto = correlate each value with itself auto = correlate each value with itself
upper = correlate each value with each succeeding value upper = correlate each value with each succeeding value

8
doc/src/fix_ave_correlate_long.rst
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@ -17,9 +17,9 @@ Syntax
* Nfreq = save state of the time correlation functions every this many timesteps * Nfreq = save state of the time correlation functions every this many timesteps
* one or more input values can be listed * one or more input values can be listed
* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name * value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
.. parsed-literal:: .. parsed-literal::
c_ID = global scalar calculated by a compute with ID c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID c_ID[I] = Ith component of global vector calculated by a compute with ID
f_ID = global scalar calculated by a fix with ID f_ID = global scalar calculated by a fix with ID
@ -28,9 +28,9 @@ Syntax
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *p* or *m* * keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *p* or *m*
.. parsed-literal:: .. parsed-literal::
*type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full* *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full*
auto = correlate each value with itself auto = correlate each value with itself
upper = correlate each value with each succeeding value upper = correlate each value with each succeeding value

8
doc/src/fix_ave_histo.rst
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@ -23,9 +23,9 @@ Syntax
* Nbin = # of histogram bins * Nbin = # of histogram bins
* one or more input values can be listed * 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:: .. parsed-literal::
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
c_ID = scalar or vector calculated by a compute with ID c_ID = scalar or vector calculated by a compute with ID
c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below) c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
@ -36,9 +36,9 @@ Syntax
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *mode* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3* * keyword = *mode* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
.. parsed-literal:: .. parsed-literal::
*mode* arg = *scalar* or *vector* *mode* arg = *scalar* or *vector*
scalar = all input values are scalars scalar = all input values are scalars
vector = all input values are vectors vector = all input values are vectors

8
doc/src/fix_ave_time.rst
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@ -18,9 +18,9 @@ Syntax
* Nfreq = calculate averages every this many timesteps * Nfreq = calculate averages every this many timesteps
* one or more input values can be listed * one or more input values can be listed
* value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name * value = c\_ID, c\_ID[N], f\_ID, f\_ID[N], v\_name
.. parsed-literal:: .. parsed-literal::
c_ID = global scalar or vector calculated by a compute with ID c_ID = global scalar or vector calculated by a compute with ID
c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below) c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
f_ID = global scalar or vector calculated by a fix with ID f_ID = global scalar or vector calculated by a fix with ID
@ -30,9 +30,9 @@ Syntax
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *title1* or *title2* or *title3* * keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *title1* or *title2* or *title3*
.. parsed-literal:: .. parsed-literal::
*mode* arg = *scalar* or *vector* *mode* arg = *scalar* or *vector*
scalar = all input values are global scalars scalar = all input values are global scalars
vector = all input values are global vectors or global arrays vector = all input values are global vectors or global arrays

8
doc/src/fix_aveforce.rst
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@ -14,16 +14,16 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* aveforce = style name of this fix command * aveforce = style name of this fix command
* fx,fy,fz = force component values (force units) * fx,fy,fz = force component values (force units)
.. parsed-literal:: .. parsed-literal::
any of fx,fy,fz can be a variable (see below) any of fx,fy,fz can be a variable (see below)
* zero or more keyword/value pairs may be appended to args * zero or more keyword/value pairs may be appended to args
* keyword = *region* * keyword = *region*
.. parsed-literal:: .. parsed-literal::
*region* value = region-ID *region* value = region-ID
region-ID = ID of region atoms must be in to have added force region-ID = ID of region atoms must be in to have added force

8
doc/src/fix_balance.rst
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@ -16,9 +16,9 @@ Syntax
* Nfreq = perform dynamic load balancing every this many steps * Nfreq = perform dynamic load balancing every this many steps
* thresh = imbalance threshold that must be exceeded to perform a re-balance * thresh = imbalance threshold that must be exceeded to perform a re-balance
* style = *shift* or *rcb* * style = *shift* or *rcb*
.. parsed-literal:: .. parsed-literal::
shift args = dimstr Niter stopthresh 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 Niter = # of times to iterate within each dimension of dimstr sequence
@ -27,9 +27,9 @@ Syntax
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *weight* or *out* * keyword = *weight* or *out*
.. parsed-literal:: .. parsed-literal::
*weight* style args = use weighted particle counts for the balancing *weight* style args = use weighted particle counts for the balancing
*style* = *group* or *neigh* or *time* or *var* or *store* *style* = *group* or *neigh* or *time* or *var* or *store*
*group* args = Ngroup group1 weight1 group2 weight2 ... *group* args = Ngroup group1 weight1 group2 weight2 ...

4
doc/src/fix_bond_break.rst
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@ -18,9 +18,9 @@ Syntax
* Rmax = bond longer than Rmax can break (distance units) * Rmax = bond longer than Rmax can break (distance units)
* zero or more keyword/value pairs may be appended to args * zero or more keyword/value pairs may be appended to args
* keyword = *prob* * keyword = *prob*
.. parsed-literal:: .. parsed-literal::
*prob* values = fraction seed *prob* values = fraction seed
fraction = break a bond with this probability if otherwise eligible fraction = break a bond with this probability if otherwise eligible
seed = random number seed (positive integer) seed = random number seed (positive integer)

4
doc/src/fix_bond_create.rst
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@ -19,9 +19,9 @@ Syntax
* bondtype = type of created bonds * bondtype = type of created bonds
* zero or more keyword/value pairs may be appended to args * zero or more keyword/value pairs may be appended to args
* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* * keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype*
.. parsed-literal:: .. parsed-literal::
*iparam* values = maxbond, newtype *iparam* values = maxbond, newtype
maxbond = max # of bonds of bondtype the itype atom can have maxbond = max # of bonds of bondtype the itype atom can have
newtype = change the itype atom to this type when maxbonds exist newtype = change the itype atom to this type when maxbonds exist

4
doc/src/fix_box_relax.rst
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@ -13,9 +13,9 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* box/relax = style name of this fix command * box/relax = style name of this fix command
.. parsed-literal:: .. parsed-literal::
one or more keyword value pairs may be appended one or more keyword value pairs may be appended
keyword = *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *nreset* or *vmax* or *dilate* or *scaleyz* or *scalexz* or *scalexy* or *fixedpoint* keyword = *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *nreset* or *vmax* or *dilate* or *scaleyz* or *scalexz* or *scalexy* or *fixedpoint*
*iso* or *aniso* or *tri* value = Ptarget = desired pressure (pressure units) *iso* or *aniso* or *tri* value = Ptarget = desired pressure (pressure units)

4
doc/src/fix_colvars.rst
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@ -15,9 +15,9 @@ Syntax
* colvars = style name of this fix command * colvars = style name of this fix command
* configfile = the configuration file for the colvars module * configfile = the configuration file for the colvars module
* keyword = *input* or *output* or *seed* or *tstat* * keyword = *input* or *output* or *seed* or *tstat*
.. parsed-literal:: .. parsed-literal::
*input* arg = colvars.state file name or prefix or NULL (default: NULL) *input* arg = colvars.state file name or prefix or NULL (default: NULL)
*output* arg = output filename prefix (default: out) *output* arg = output filename prefix (default: out)
*seed* arg = seed for random number generator (default: 1966) *seed* arg = seed for random number generator (default: 1966)

6
doc/src/fix_controller.rst
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@ -19,9 +19,9 @@ Syntax
* Ki = integral gain in PID equation (unitless) * Ki = integral gain in PID equation (unitless)
* Kd = derivative gain in PID equation (unitless) * Kd = derivative gain in PID equation (unitless)
* pvar = process variable of form c\_ID, c\_ID[I], f\_ID, f\_ID[I], or v\_name * pvar = process variable of form c\_ID, c\_ID[I], f\_ID, f\_ID[I], or v\_name
.. parsed-literal:: .. parsed-literal::
c_ID = global scalar calculated by a compute with ID c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID c_ID[I] = Ith component of global vector calculated by a compute with ID
f_ID = global scalar calculated by a fix with ID f_ID = global scalar calculated by a fix with ID
@ -100,7 +100,7 @@ the following dynamic equation:
.. math:: .. math::
\frac{dc}{dt} = \hat{E} -\alpha (K_p e + K_i \int_0^t e \, dt + K_d \frac{de}{dt} ) \frac{dc}{dt} = \hat{E} -\alpha (K_p e + K_i \int_0^t e \, dt + K_d \frac{de}{dt} )
where *c* is the continuous time analog of the control variable, where *c* is the continuous time analog of the control variable,
*e* =\ *pvar*\ -\ *setpoint* is the error in the process variable, and *e* =\ *pvar*\ -\ *setpoint* is the error in the process variable, and
:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are constants :math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are constants

8
doc/src/fix_deform.rst
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@ -18,9 +18,9 @@ Syntax
* deform = style name of this fix command * deform = style name of this fix command
* N = perform box deformation every this many timesteps * N = perform box deformation every this many timesteps
* one or more parameter/arg pairs may be appended * one or more parameter/arg pairs may be appended
.. parsed-literal:: .. parsed-literal::
parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* parameter = *x* or *y* or *z* or *xy* or *xz* or *yz*
*x*\ , *y*\ , *z* args = style value(s) *x*\ , *y*\ , *z* args = style value(s)
style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable*
@ -66,9 +66,9 @@ Syntax
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *remap* or *flip* or *units* * keyword = *remap* or *flip* or *units*
.. parsed-literal:: .. parsed-literal::
*remap* value = *x* or *v* or *none* *remap* value = *x* or *v* or *none*
x = remap coords of atoms in group into deforming box x = remap coords of atoms in group into deforming box
v = remap velocities of all atoms when they cross periodic boundaries v = remap velocities of all atoms when they cross periodic boundaries

4
doc/src/fix_deposit.rst
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@ -19,9 +19,9 @@ Syntax
* seed = random # seed (positive integer) * seed = random # seed (positive integer)
* one or more keyword/value pairs may be appended to args * one or more keyword/value pairs may be appended to args
* keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *mol* or *rigid* or *shake* or *units* * keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *mol* or *rigid* or *shake* or *units*
.. parsed-literal:: .. parsed-literal::
*region* value = region-ID *region* value = region-ID
region-ID = ID of region to use as insertion volume region-ID = ID of region to use as insertion volume
*id* value = *max* or *next* *id* value = *max* or *next*

4
doc/src/fix_dpd_source.rst
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@ -19,9 +19,9 @@ Syntax
* edpd/source or tdpd/source = style name of this fix command * edpd/source or tdpd/source = style name of this fix command
* index (only specified for tdpd/source) = index of chemical species (1 to Nspecies) * index (only specified for tdpd/source) = index of chemical species (1 to Nspecies)
* keyword = *sphere* or *cuboid* * keyword = *sphere* or *cuboid*
.. parsed-literal:: .. parsed-literal::
*sphere* values = cx,cy,cz,radius,source *sphere* values = cx,cy,cz,radius,source
cx,cy,cz = x,y,z center of spherical domain (distance units) cx,cy,cz = x,y,z center of spherical domain (distance units)
radius = radius of a spherical domain (distance units) radius = radius of a spherical domain (distance units)

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