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Merge pull request #2302 from akohlmey/consistent-doc-headers 

Consistent subsection headers for commands
This commit is contained in:
Axel Kohlmeyer 2020-08-24 10:52:09 -04:00 committed by GitHub
parent 1879106cc3 b776e1ee3c
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4
doc/src/Build_package.rst
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@ -136,6 +136,7 @@ src directory.
.. _cmake_presets: .. _cmake_presets:
CMake presets for installing many packages CMake presets for installing many packages
""""""""""""""""""""""""""""""""""""""""""
Instead of specifying all the CMake options via the command-line, Instead of specifying all the CMake options via the command-line,
CMake allows initializing its settings cache using script files. CMake allows initializing its settings cache using script files.
@ -168,7 +169,8 @@ one of them as a starting point and customize it to your needs.
in a single cmake run, or change settings incrementally by running in a single cmake run, or change settings incrementally by running
cmake with new flags. cmake with new flags.
**Example:** Example
"""""""
.. code-block:: bash .. code-block:: bash

41
doc/src/Speed_intel.rst
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@ -12,7 +12,8 @@ When offloading to a co-processor from a CPU, the same routine is run
twice, once on the CPU and once with an offload flag. This allows twice, once on the CPU and once with an offload flag. This allows
LAMMPS to run on the CPU cores and co-processor cores simultaneously. LAMMPS to run on the CPU cores and co-processor cores simultaneously.
**Currently Available USER-INTEL Styles:** Currently Available USER-INTEL Styles
"""""""""""""""""""""""""""""""""""""
* Angle Styles: charmm, harmonic * Angle Styles: charmm, harmonic
* Bond Styles: fene, fourier, harmonic * Bond Styles: fene, fourier, harmonic
@ -31,9 +32,10 @@ LAMMPS to run on the CPU cores and co-processor cores simultaneously.
support computing per-atom stress. If any compute or fix in your support computing per-atom stress. If any compute or fix in your
input requires it, LAMMPS will abort with an error message. input requires it, LAMMPS will abort with an error message.
**Speed-ups to expect:** Speed-up to expect
"""""""""""""""""""
The speedups will depend on your simulation, the hardware, which The speedup will depend on your simulation, the hardware, which
styles are used, the number of atoms, and the floating-point styles are used, the number of atoms, and the floating-point
precision mode. Performance improvements are shown compared to precision mode. Performance improvements are shown compared to
LAMMPS *without using other acceleration packages* as these are LAMMPS *without using other acceleration packages* as these are
@ -59,7 +61,8 @@ instructions to reproduce.
---------- ----------
**Accuracy and order of operations:** Accuracy and order of operations
""""""""""""""""""""""""""""""""
In most molecular dynamics software, parallelization parameters In most molecular dynamics software, parallelization parameters
(# of MPI, OpenMP, and vectorization) can change the results due (# of MPI, OpenMP, and vectorization) can change the results due
@ -96,7 +99,8 @@ mode should not be used without appropriate validation.
---------- ----------
**Quick Start for Experienced Users:** Quick Start for Experienced Users
"""""""""""""""""""""""""""""""""
LAMMPS should be built with the USER-INTEL package installed. LAMMPS should be built with the USER-INTEL package installed.
Simulations should be run with 1 MPI task per physical *core*\ , Simulations should be run with 1 MPI task per physical *core*\ ,
@ -136,7 +140,8 @@ For Intel Xeon Phi co-processors (Offload):
---------- ----------
**Required hardware/software:** Required hardware/software
""""""""""""""""""""""""""
When using Intel compilers version 16.0 or later is required. When using Intel compilers version 16.0 or later is required.
@ -159,7 +164,8 @@ For best performance, we recommend that the MCDRAM is configured in
"Cache" mode can also be used, although the performance might be "Cache" mode can also be used, although the performance might be
slightly lower. slightly lower.
**Notes about Simultaneous Multithreading:** Notes about Simultaneous Multithreading
"""""""""""""""""""""""""""""""""""""""
Modern CPUs often support Simultaneous Multithreading (SMT). On Modern CPUs often support Simultaneous Multithreading (SMT). On
Intel processors, this is called Hyper-Threading (HT) technology. Intel processors, this is called Hyper-Threading (HT) technology.
@ -196,7 +202,8 @@ this information can normally be obtained with:
cat /proc/cpuinfo cat /proc/cpuinfo
**Building LAMMPS with the USER-INTEL package:** Building LAMMPS with the USER-INTEL package
"""""""""""""""""""""""""""""""""""""""""""
See the :ref:`Build extras <user-intel>` doc page for See the :ref:`Build extras <user-intel>` doc page for
instructions. Some additional details are covered here. instructions. Some additional details are covered here.
@ -263,7 +270,8 @@ recommended CCFLAG options for best performance are "-O2 -fno-alias
in most of the example Makefiles is to use "-xHost", however this in most of the example Makefiles is to use "-xHost", however this
should not be used when cross-compiling. should not be used when cross-compiling.
**Running LAMMPS with the USER-INTEL package:** Running LAMMPS with the USER-INTEL package
""""""""""""""""""""""""""""""""""""""""""
Running LAMMPS with the USER-INTEL package is similar to normal use Running LAMMPS with the USER-INTEL package is similar to normal use
with the exceptions that one should 1) specify that LAMMPS should use with the exceptions that one should 1) specify that LAMMPS should use
@ -304,7 +312,8 @@ almost all cases.
recommended, especially when running on a machine with Intel recommended, especially when running on a machine with Intel
Hyper-Threading technology disabled. Hyper-Threading technology disabled.
**Run with the USER-INTEL package from the command line:** Run with the USER-INTEL package from the command line
"""""""""""""""""""""""""""""""""""""""""""""""""""""
To enable USER-INTEL optimizations for all available styles used in To enable USER-INTEL optimizations for all available styles used in
the input script, the "-sf intel" :doc:`command-line switch <Run_options>` can be used without any requirement for the input script, the "-sf intel" :doc:`command-line switch <Run_options>` can be used without any requirement for
@ -339,7 +348,8 @@ launching MPI applications):
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision
**Or run with the USER-INTEL package by editing an input script:** Or run with the USER-INTEL package by editing an input script
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
As an alternative to adding command-line arguments, the input script As an alternative to adding command-line arguments, the input script
can be edited to enable the USER-INTEL package. This requires adding can be edited to enable the USER-INTEL package. This requires adding
@ -361,7 +371,8 @@ Alternatively, the :doc:`suffix intel <suffix>` command can be added to
the input script to enable USER-INTEL styles for the commands that the input script to enable USER-INTEL styles for the commands that
follow in the input script. follow in the input script.
**Tuning for Performance:** Tuning for Performance
""""""""""""""""""""""
.. note:: .. note::
@ -431,7 +442,8 @@ series processors will always perform better using MCDRAM. Please
consult your system documentation for the best approach to specify consult your system documentation for the best approach to specify
that MPI runs are performed in MCDRAM. that MPI runs are performed in MCDRAM.
**Tuning for Offload Performance:** Tuning for Offload Performance
""""""""""""""""""""""""""""""
The default settings for offload should give good performance. The default settings for offload should give good performance.
@ -521,7 +533,8 @@ the pair styles in the USER-INTEL package currently support the
:doc:`run_style respa <run_style>` command; only the "pair" option is :doc:`run_style respa <run_style>` command; only the "pair" option is
supported. supported.
**References:** References
""""""""""
* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. * Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). * Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).

18
doc/src/Speed_omp.rst
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@ -8,18 +8,21 @@ improper), several Kspace styles, and a few fix styles. It uses
the OpenMP interface for multi-threading, but can also be compiled the OpenMP interface for multi-threading, but can also be compiled
without OpenMP support, providing optimized serial styles in that case. without OpenMP support, providing optimized serial styles in that case.
**Required hardware/software:** Required hardware/software
""""""""""""""""""""""""""
To enable multi-threading, your compiler must support the OpenMP interface. To enable multi-threading, your compiler must support the OpenMP interface.
You should have one or more multi-core CPUs, as multiple threads can only be You should have one or more multi-core CPUs, as multiple threads can only be
launched by each MPI task on the local node (using shared memory). launched by each MPI task on the local node (using shared memory).
**Building LAMMPS with the USER-OMP package:** Building LAMMPS with the USER-OMP package
"""""""""""""""""""""""""""""""""""""""""
See the :ref:`Build extras <user-omp>` doc page for See the :ref:`Build extras <user-omp>` doc page for
instructions. instructions.
**Run with the USER-OMP package from the command line:** Run with the USER-OMP package from the command line
"""""""""""""""""""""""""""""""""""""""""""""""""""
These examples assume one or more 16-core nodes. These examples assume one or more 16-core nodes.
@ -52,7 +55,8 @@ details, including the default values used if it is not specified. It
also gives more details on how to set the number of threads via the also gives more details on how to set the number of threads via the
OMP_NUM_THREADS environment variable. OMP_NUM_THREADS environment variable.
**Or run with the USER-OMP package by editing an input script:** Or run with the USER-OMP package by editing an input script
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The discussion above for the mpirun/mpiexec command, MPI tasks/node, The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and threads/MPI task is the same. and threads/MPI task is the same.
@ -70,7 +74,8 @@ per MPI task to use. The command doc page explains other options and
how to set the number of threads via the OMP_NUM_THREADS environment how to set the number of threads via the OMP_NUM_THREADS environment
variable. variable.
**Speed-ups to expect:** Speed-up to expect
""""""""""""""""""
Depending on which styles are accelerated, you should look for a Depending on which styles are accelerated, you should look for a
reduction in the "Pair time", "Bond time", "KSpace time", and "Loop reduction in the "Pair time", "Bond time", "KSpace time", and "Loop
@ -92,7 +97,8 @@ sub-section.
A description of the multi-threading strategy used in the USER-OMP A description of the multi-threading strategy used in the USER-OMP
package and some performance examples are `presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_ package and some performance examples are `presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_
**Guidelines for best performance:** Guidelines for best performance
"""""""""""""""""""""""""""""""
For many problems on current generation CPUs, running the USER-OMP For many problems on current generation CPUs, running the USER-OMP
package with a single thread/task is faster than running with multiple package with a single thread/task is faster than running with multiple

20
doc/src/Speed_opt.rst
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@ -7,15 +7,18 @@ Technologies). It contains a handful of pair styles whose compute()
methods were rewritten in C++ templated form to reduce the overhead methods were rewritten in C++ templated form to reduce the overhead
due to if tests and other conditional code. due to if tests and other conditional code.
**Required hardware/software:** Required hardware/software
""""""""""""""""""""""""""
None. Any hardware. Any compiler.
**Building LAMMPS with the OPT package:** Building LAMMPS with the OPT package
""""""""""""""""""""""""""""""""""""
See the :ref:`Build extras <opt>` doc page for instructions. See the :ref:`Build extras <opt>` doc page for instructions.
**Run with the OPT package from the command line:** Run with the OPT package from the command line
""""""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash .. code-block:: bash
@ -25,7 +28,8 @@ See the :ref:`Build extras <opt>` doc page for instructions.
Use the "-sf opt" :doc:`command-line switch <Run_options>`, which will Use the "-sf opt" :doc:`command-line switch <Run_options>`, which will
automatically append "opt" to styles that support it. automatically append "opt" to styles that support it.
**Or run with the OPT package by editing an input script:** Or run with the OPT package by editing an input script
""""""""""""""""""""""""""""""""""""""""""""""""""""""
Use the :doc:`suffix opt <suffix>` command, or you can explicitly add an Use the :doc:`suffix opt <suffix>` command, or you can explicitly add an
"opt" suffix to individual styles in your input script, e.g. "opt" suffix to individual styles in your input script, e.g.
@ -34,13 +38,15 @@ Use the :doc:`suffix opt <suffix>` command, or you can explicitly add an
pair_style lj/cut/opt 2.5 pair_style lj/cut/opt 2.5
**Speed-ups to expect:** Speed-up to expect
""""""""""""""""""
You should see a reduction in the "Pair time" value printed at the end You should see a reduction in the "Pair time" value printed at the end
of a run. On most machines for reasonable problem sizes, it will be a of a run. On most machines for reasonable problem sizes, it will be a
5 to 20% savings. 5 to 20% savings.
**Guidelines for best performance:** Guidelines for best performance
"""""""""""""""""""""""""""""""
Just try out an OPT pair style to see how it performs. Just try out an OPT pair style to see how it performs.

5
doc/src/angle_charmm.rst
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@ -92,7 +92,10 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none
---------- ----------

5
doc/src/angle_class2.rst
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@ -135,7 +135,10 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none
---------- ----------

5
doc/src/angle_coeff.rst
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@ -92,4 +92,7 @@ Related commands
:doc:`angle_style <angle_style>` :doc:`angle_style <angle_style>`
**Default:** none Default
"""""""
none

5
doc/src/angle_cosine.rst
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@ -60,4 +60,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_cosine_buck6d.rst
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@ -68,4 +68,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_cosine_delta.rst
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@ -62,4 +62,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style cosine/squared <angle_cosine_squared>` :doc:`angle_coeff <angle_coeff>`, :doc:`angle_style cosine/squared <angle_cosine_squared>`
**Default:** none Default
"""""""
none

5
doc/src/angle_cosine_periodic.rst
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@ -70,7 +70,10 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none
---------- ----------

5
doc/src/angle_cosine_shift.rst
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@ -61,4 +61,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_coeff <angle_coeff>`,
:doc:`angle_style cosine/shift/exp <angle_cosine_shift_exp>` :doc:`angle_style cosine/shift/exp <angle_cosine_shift_exp>`
**Default:** none Default
"""""""
none

5
doc/src/angle_cosine_shift_exp.rst
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@ -74,4 +74,7 @@ Related commands
:doc:`angle_style cosine/shift <angle_cosine_shift>`, :doc:`angle_style cosine/shift <angle_cosine_shift>`,
:doc:`dihedral_style cosine/shift/exp <dihedral_cosine_shift_exp>` :doc:`dihedral_style cosine/shift/exp <dihedral_cosine_shift_exp>`
**Default:** none Default
"""""""
none

5
doc/src/angle_cosine_squared.rst
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@ -62,4 +62,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_cross.rst
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@ -62,4 +62,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_dipole.rst
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@ -113,7 +113,10 @@ Related commands
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_hybrid <angle_hybrid>` :doc:`angle_coeff <angle_coeff>`, :doc:`angle_hybrid <angle_hybrid>`
**Default:** none Default
"""""""
none
---------- ----------

5
doc/src/angle_fourier.rst
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@ -58,4 +58,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_fourier_simple.rst
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@ -57,4 +57,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_harmonic.rst
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@ -69,4 +69,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_hybrid.rst
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@ -95,4 +95,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_mm3.rst
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@ -57,4 +57,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_none.rst
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@ -37,4 +37,7 @@ Related commands
:doc:`angle_style zero <angle_zero>` :doc:`angle_style zero <angle_zero>`
**Default:** none Default
"""""""
none

5
doc/src/angle_quartic.rst
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@ -65,4 +65,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_sdk.rst
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@ -73,4 +73,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/sdk <pair_sdk>`, :doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/sdk <pair_sdk>`,
:doc:`pair_style lj/sdk/coul/long <pair_sdk>` :doc:`pair_style lj/sdk/coul/long <pair_sdk>`
**Default:** none Default
"""""""
none

8
doc/src/angle_table.rst
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@ -130,7 +130,8 @@ one that matches the specified keyword.
---------- ----------
**Restart info:** Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This angle style writes the settings for the "angle_style table" This angle style writes the settings for the "angle_style table"
command to :doc:`binary restart files <restart>`, so a angle_style command to :doc:`binary restart files <restart>`, so a angle_style
@ -152,4 +153,7 @@ Related commands
:doc:`angle_coeff <angle_coeff>` :doc:`angle_coeff <angle_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/angle_zero.rst
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@ -51,4 +51,7 @@ Related commands
:doc:`angle_style none <angle_none>` :doc:`angle_style none <angle_none>`
**Default:** none Default
"""""""
none

6
doc/src/atom_modify.rst
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@ -160,7 +160,11 @@ The *first* and *sort* options cannot be used together. Since sorting
is on by default, it will be turned off if the *first* keyword is is on by default, it will be turned off if the *first* keyword is
used with a group-ID that is not "all". used with a group-ID that is not "all".
**Related commands:** none Related commands
""""""""""""""""
none
Default Default
""""""" """""""

5
doc/src/balance.rst
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@ -548,4 +548,7 @@ Related commands
.. _pizza: https://pizza.sandia.gov .. _pizza: https://pizza.sandia.gov
**Default:** none Default
"""""""
none

5
doc/src/bond_class2.rst
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@ -65,7 +65,10 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none Default
"""""""
none
---------- ----------

5
doc/src/bond_coeff.rst
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@ -87,4 +87,7 @@ Related commands
:doc:`bond_style <bond_style>` :doc:`bond_style <bond_style>`
**Default:** none Default
"""""""
none

5
doc/src/bond_fene.rst
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@ -74,7 +74,10 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none Default
"""""""
none
---------- ----------

5
doc/src/bond_fene_expand.rst
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@ -72,7 +72,10 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none Default
"""""""
none
---------- ----------

5
doc/src/bond_gromos.rst
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@ -59,4 +59,7 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none Default
"""""""
none

5
doc/src/bond_harmonic.rst
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@ -65,4 +65,7 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none Default
"""""""
none

5
doc/src/bond_harmonic_shift.rst
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@ -65,4 +65,7 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`, :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
:doc:`bond_harmonic <bond_harmonic>` :doc:`bond_harmonic <bond_harmonic>`
**Default:** none Default
"""""""
none

5
doc/src/bond_harmonic_shift_cut.rst
View File

@ -64,4 +64,7 @@ Related commands
:doc:`bond_harmonic <bond_harmonic>`, :doc:`bond_harmonic <bond_harmonic>`,
:doc:`bond_style harmonic/shift <bond_harmonic_shift>` :doc:`bond_style harmonic/shift <bond_harmonic_shift>`
**Default:** none Default
"""""""
none

5
doc/src/bond_hybrid.rst
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@ -76,4 +76,7 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none Default
"""""""
none

5
doc/src/bond_mm3.rst
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@ -55,7 +55,10 @@ Related commands
:doc:`bond_coeff <bond_coeff>` :doc:`bond_coeff <bond_coeff>`
**Default:** none Default
"""""""
none
---------- ----------

5
doc/src/bond_morse.rst
View File

@ -60,4 +60,7 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none Default
"""""""
none

11
doc/src/bond_none.rst
View File

@ -31,8 +31,15 @@ Restrictions
"""""""""""" """"""""""""
none none
**Related commands:** none Related commands
""""""""""""""""
none
:doc:`bond_style zero <bond_zero>` :doc:`bond_style zero <bond_zero>`
**Default:** none Default
"""""""
none

5
doc/src/bond_nonlinear.rst
View File

@ -60,7 +60,10 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none Default
"""""""
none
---------- ----------

4
doc/src/bond_oxdna.rst
View File

@ -108,7 +108,9 @@ 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
"""""""
none none

5
doc/src/bond_quartic.rst
View File

@ -108,4 +108,7 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none Default
"""""""
none

5
doc/src/bond_special.rst
View File

@ -103,4 +103,7 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`special_bonds <special_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`special_bonds <special_bonds>`
**Default:** none Default
"""""""
none

8
doc/src/bond_table.rst
View File

@ -128,7 +128,8 @@ one that matches the specified keyword.
---------- ----------
**Restart info:** Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This bond style writes the settings for the "bond_style table" This bond style writes the settings for the "bond_style table"
command to :doc:`binary restart files <restart>`, so a bond_style command to :doc:`binary restart files <restart>`, so a bond_style
@ -150,4 +151,7 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>` :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none Default
"""""""
none

5
doc/src/bond_write.rst
View File

@ -70,4 +70,7 @@ Related commands
:doc:`bond_style table <bond_table>`, :doc:`bond_style table <bond_table>`,
:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>` :doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
**Default:** none Default
"""""""
none

5
doc/src/bond_zero.rst
View File

@ -50,4 +50,7 @@ Related commands
:doc:`bond_style none <bond_none>` :doc:`bond_style none <bond_none>`
**Default:** none Default
"""""""
none

6
doc/src/box.rst
View File

@ -58,7 +58,11 @@ This command cannot be used after the simulation box is defined by a
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or :doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or
:doc:`read_restart <read_restart>` command. :doc:`read_restart <read_restart>` command.
**Related commands:** none Related commands
""""""""""""""""
none
Default Default
""""""" """""""

11
doc/src/clear.rst
View File

@ -37,6 +37,13 @@ Restrictions
"""""""""""" """"""""""""
none none
**Related commands:** none Related commands
""""""""""""""""
**Default:** none none
Default
"""""""
none

5
doc/src/compute.rst
View File

@ -323,4 +323,7 @@ Related commands
:doc:`uncompute <uncompute>`, :doc:`compute_modify <compute_modify>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/histo <fix_ave_histo>` :doc:`uncompute <uncompute>`, :doc:`compute_modify <compute_modify>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/histo <fix_ave_histo>`
**Default:** none Default
"""""""
none

3
doc/src/compute_ackland_atom.rst
View File

@ -58,7 +58,8 @@ is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of too frequently or to have multiple compute/dump commands, each of
which computes this quantity.- which computes this quantity.-
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector, which can be accessed by This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See any command that uses per-atom values from a compute as input. See

3
doc/src/compute_adf.rst
View File

@ -173,7 +173,8 @@ example:
compute myADF all adf 32 2 2 2 0.5 3.5 0.5 3.5 compute myADF all adf 32 2 2 2 0.5 3.5 0.5 3.5
fix 1 all ave/time 100 1 100 c_myADF[*] file tmp.adf mode vector fix 1 all ave/time 100 1 100 c_myADF[*] file tmp.adf mode vector
**Output info:** Output info
"""""""""""
This compute calculates a global array with the number of rows = This compute calculates a global array with the number of rows =
*Nbins*\ , and the number of columns = 1 + 2\*Ntriples, where Ntriples is the *Nbins*\ , and the number of columns = 1 + 2\*Ntriples, where Ntriples is the

8
doc/src/compute_angle.rst
View File

@ -32,7 +32,8 @@ specified for this command is ignored.
This compute is useful when using :doc:`angle_style hybrid <angle_hybrid>` if you want to know the portion of the total This compute is useful when using :doc:`angle_style hybrid <angle_hybrid>` if you want to know the portion of the total
energy contributed by one or more of the hybrid sub-styles. energy contributed by one or more of the hybrid sub-styles.
**Output info:** Output info
"""""""""""
This compute calculates a global vector of length N where N is the This compute calculates a global vector of length N where N is the
number of sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command, which can be accessed by indices number of sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command, which can be accessed by indices
@ -52,4 +53,7 @@ Related commands
:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>` :doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
**Default:** none Default
"""""""
none

8
doc/src/compute_angle_local.rst
View File

@ -119,7 +119,8 @@ Here is an example of how to do this:
compute 2 all angle/local theta eng compute 2 all angle/local theta eng
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_2[1] c_2[2] dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_2[1] c_2[2]
**Output info:** Output info
"""""""""""
This compute calculates a local vector or local array depending on the This compute calculates a local vector or local array depending on the
number of values. The length of the vector or number of rows in the number of values. The length of the vector or number of rows in the
@ -142,4 +143,7 @@ Related commands
:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>` :doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
**Default:** none Default
"""""""
none

8
doc/src/compute_angmom_chunk.rst
View File

@ -68,7 +68,8 @@ command, for example:
compute myChunk all angmom/chunk cc1 compute myChunk all angmom/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
**Output info:** Output info
"""""""""""
This compute calculates a global array where the number of rows = the This compute calculates a global array where the number of rows = the
number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns = number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns =
@ -89,4 +90,7 @@ Related commands
:doc:`variable angmom() function <variable>` :doc:`variable angmom() function <variable>`
**Default:** none Default
"""""""
none

8
doc/src/compute_basal_atom.rst
View File

@ -44,7 +44,8 @@ which computes this quantity.
An example input script that uses this compute is provided An example input script that uses this compute is provided
in examples/USER/misc/basal. in examples/USER/misc/basal.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom array with 3 columns, which can be This compute calculates a per-atom array with 3 columns, which can be
accessed by indices 1-3 by any command that uses per-atom values from accessed by indices 1-3 by any command that uses per-atom values from
@ -69,7 +70,10 @@ Related commands
:doc:`compute centro/atom <compute_centro_atom>`, :doc:`compute ackland/atom <compute_ackland_atom>` :doc:`compute centro/atom <compute_centro_atom>`, :doc:`compute ackland/atom <compute_ackland_atom>`
**Default:** none Default
"""""""
none
---------- ----------

8
doc/src/compute_body_local.rst
View File

@ -74,7 +74,8 @@ command.
compute 1 all body/local type 1 2 3 compute 1 all body/local type 1 2 3
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4]
**Output info:** Output info
"""""""""""
This compute calculates a local vector or local array depending on the This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the number of keywords. The length of the vector or number of rows in the
@ -97,4 +98,7 @@ Related commands
:doc:`dump local <dump>` :doc:`dump local <dump>`
**Default:** none Default
"""""""
none

8
doc/src/compute_bond.rst
View File

@ -32,7 +32,8 @@ This compute is useful when using :doc:`bond_style hybrid <bond_hybrid>`
if you want to know the portion of the total energy contributed by one if you want to know the portion of the total energy contributed by one
or more of the hybrid sub-styles. or more of the hybrid sub-styles.
**Output info:** Output info
"""""""""""
This compute calculates a global vector of length N where N is the This compute calculates a global vector of length N where N is the
number of sub_styles defined by the :doc:`bond_style hybrid <bond_style>` command, which can be accessed by indices 1-N. number of sub_styles defined by the :doc:`bond_style hybrid <bond_style>` command, which can be accessed by indices 1-N.
@ -52,4 +53,7 @@ Related commands
:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>` :doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
**Default:** none Default
"""""""
none

8
doc/src/compute_bond_local.rst
View File

@ -169,7 +169,8 @@ Here is an example of how to do this:
compute 2 all bond/local dist engpot compute 2 all bond/local dist engpot
dump 1 all local 1000 tmp.dump index c_1[*] c_2[*] dump 1 all local 1000 tmp.dump index c_1[*] c_2[*]
**Output info:** Output info
"""""""""""
This compute calculates a local vector or local array depending on the This compute calculates a local vector or local array depending on the
number of values. The length of the vector or number of rows in the number of values. The length of the vector or number of rows in the
@ -196,4 +197,7 @@ Related commands
:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>` :doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
**Default:** none Default
"""""""
none

3
doc/src/compute_centro_atom.rst
View File

@ -101,7 +101,8 @@ is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each with a too frequently or to have multiple compute/dump commands, each with a
*centro/atom* style. *centro/atom* style.
**Output info:** Output info
"""""""""""
By default, this compute calculates the centrosymmetry value for each By default, this compute calculates the centrosymmetry value for each
atom as a per-atom vector, which can be accessed by any command that atom as a per-atom vector, which can be accessed by any command that

3
doc/src/compute_chunk_atom.rst
View File

@ -620,7 +620,8 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.
---------- ----------
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector (the chunk ID), which can This compute calculates a per-atom vector (the chunk ID), which can
be accessed by any command that uses per-atom values from a compute be accessed by any command that uses per-atom values from a compute

8
doc/src/compute_chunk_spread_atom.rst
View File

@ -188,7 +188,8 @@ it is in.
---------- ----------
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector or array, which can be This compute calculates a per-atom vector or array, which can be
accessed by any command that uses per-atom values from a compute as accessed by any command that uses per-atom values from a compute as
@ -212,4 +213,7 @@ Related commands
:doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`compute reduce/chunk <compute_reduce_chunk>` :doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`compute reduce/chunk <compute_reduce_chunk>`
**Default:** none Default
"""""""
none

7
doc/src/compute_cluster_atom.rst
View File

@ -104,7 +104,8 @@ style computes.
because it does not perform a full update of the bond topology data because it does not perform a full update of the bond topology data
structures within LAMMPS. structures within LAMMPS.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector, which can be accessed by This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See any command that uses per-atom values from a compute as input. See
@ -122,7 +123,9 @@ Related commands
:doc:`compute coord/atom <compute_coord_atom>` :doc:`compute coord/atom <compute_coord_atom>`
**Default:** Default
"""""""
The default for fragment/atom is single no. The default for fragment/atom is single no.

8
doc/src/compute_cna_atom.rst
View File

@ -79,7 +79,8 @@ is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each with a too frequently or to have multiple compute/dump commands, each with a
*cna/atom* style. *cna/atom* style.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector, which can be accessed by This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See any command that uses per-atom values from a compute as input. See
@ -98,7 +99,10 @@ Related commands
:doc:`compute centro/atom <compute_centro_atom>` :doc:`compute centro/atom <compute_centro_atom>`
**Default:** none Default
"""""""
none
---------- ----------

8
doc/src/compute_cnp_atom.rst
View File

@ -86,7 +86,8 @@ is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each with a too frequently or to have multiple compute/dump commands, each with a
*cnp/atom* style. *cnp/atom* style.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector, which can be accessed by This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See any command that uses per-atom values from a compute as input. See
@ -118,7 +119,10 @@ Related commands
:doc:`compute cna/atom <compute_cna_atom>` :doc:`compute cna/atom <compute_cna_atom>`
:doc:`compute centro/atom <compute_centro_atom>` :doc:`compute centro/atom <compute_centro_atom>`
**Default:** none Default
"""""""
none
---------- ----------

8
doc/src/compute_com.rst
View File

@ -40,7 +40,8 @@ are the x,y,z coordinates of the center of mass.
how they are set for each atom. You can reset the image flags how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command. (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
**Output info:** Output info
"""""""""""
This compute calculates a global vector of length 3, which can be This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values accessed by indices 1-3 by any command that uses global vector values
@ -59,4 +60,7 @@ Related commands
:doc:`compute com/chunk <compute_com_chunk>` :doc:`compute com/chunk <compute_com_chunk>`
**Default:** none Default
"""""""
none

8
doc/src/compute_com_chunk.rst
View File

@ -66,7 +66,8 @@ command, for example:
compute myChunk all com/chunk cc1 compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
**Output info:** Output info
"""""""""""
This compute calculates a global array where the number of rows = the This compute calculates a global array where the number of rows = the
number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns = number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns =
@ -87,4 +88,7 @@ Related commands
:doc:`compute com <compute_com>` :doc:`compute com <compute_com>`
**Default:** none Default
"""""""
none

8
doc/src/compute_contact_atom.rst
View File

@ -34,7 +34,8 @@ sum of the radii of the two particles.
The value of the contact number will be 0.0 for atoms not in the The value of the contact number will be 0.0 for atoms not in the
specified compute group. specified compute group.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector, whose values can be This compute calculates a per-atom vector, whose values can be
accessed by any command that uses per-atom values from a compute as accessed by any command that uses per-atom values from a compute as
@ -55,4 +56,7 @@ Related commands
:doc:`compute coord/atom <compute_coord_atom>` :doc:`compute coord/atom <compute_coord_atom>`
**Default:** none Default
"""""""
none

3
doc/src/compute_coord_atom.rst
View File

@ -120,7 +120,8 @@ too frequently.
---------- ----------
**Output info:** Output info
"""""""""""
For *cstyle* cutoff, this compute can calculate a per-atom vector or For *cstyle* cutoff, this compute can calculate a per-atom vector or
array. If single *type1* keyword is specified (or if none are array. If single *type1* keyword is specified (or if none are

8
doc/src/compute_damage_atom.rst
View File

@ -40,7 +40,8 @@ This command can be used with all the Peridynamic pair styles.
The damage value will be 0.0 for atoms not in the specified compute The damage value will be 0.0 for atoms not in the specified compute
group. group.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector, which can be accessed by This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See any command that uses per-atom values from a compute as input. See
@ -61,4 +62,7 @@ Related commands
:doc:`compute dilatation/atom <compute_dilatation_atom>`, :doc:`compute dilatation/atom <compute_dilatation_atom>`,
:doc:`compute plasticity/atom <compute_plasticity_atom>` :doc:`compute plasticity/atom <compute_plasticity_atom>`
**Default:** none Default
"""""""
none

8
doc/src/compute_dihedral.rst
View File

@ -31,7 +31,8 @@ group specified for this command is ignored.
This compute is useful when using :doc:`dihedral_style hybrid <dihedral_hybrid>` if you want to know the portion of the This compute is useful when using :doc:`dihedral_style hybrid <dihedral_hybrid>` if you want to know the portion of the
total energy contributed by one or more of the hybrid sub-styles. total energy contributed by one or more of the hybrid sub-styles.
**Output info:** Output info
"""""""""""
This compute calculates a global vector of length N where N is the This compute calculates a global vector of length N where N is the
number of sub_styles defined by the :doc:`dihedral_style hybrid <dihedral_style>` command. which can be accessed by indices number of sub_styles defined by the :doc:`dihedral_style hybrid <dihedral_style>` command. which can be accessed by indices
@ -51,4 +52,7 @@ Related commands
:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>` :doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
**Default:** none Default
"""""""
none

8
doc/src/compute_dihedral_local.rst
View File

@ -113,7 +113,8 @@ Here is an example of how to do this:
compute 2 all dihedral/local phi compute 2 all dihedral/local phi
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1] dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
**Output info:** Output info
"""""""""""
This compute calculates a local vector or local array depending on the This compute calculates a local vector or local array depending on the
number of values. The length of the vector or number of rows in the number of values. The length of the vector or number of rows in the
@ -135,4 +136,7 @@ Related commands
:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>` :doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
**Default:** none Default
"""""""
none

8
doc/src/compute_dilatation_atom.rst
View File

@ -43,7 +43,8 @@ This command can only be used with a subset of the Peridynamic :doc:`pair styles
The dilatation value will be 0.0 for atoms not in the specified The dilatation value will be 0.0 for atoms not in the specified
compute group. compute group.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector, which can be accessed by This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See any command that uses per-atom values from a compute as input. See
@ -64,4 +65,7 @@ Related commands
:doc:`compute damage/atom <compute_damage_atom>`, :doc:`compute damage/atom <compute_damage_atom>`,
:doc:`compute plasticity/atom <compute_plasticity_atom>` :doc:`compute plasticity/atom <compute_plasticity_atom>`
**Default:** none Default
"""""""
none

8
doc/src/compute_dipole_chunk.rst
View File

@ -71,7 +71,8 @@ command, for example:
compute myChunk all dipole/chunk cc1 compute myChunk all dipole/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
**Output info:** Output info
"""""""""""
This compute calculates a global array where the number of rows = the This compute calculates a global array where the number of rows = the
number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns = number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns =
@ -92,4 +93,7 @@ Related commands
:doc:`compute com/chunk <compute_com_chunk>` :doc:`compute com/chunk <compute_com_chunk>`
**Default:** none Default
"""""""
none

8
doc/src/compute_displace_atom.rst
View File

@ -121,7 +121,8 @@ would be empty.
---------- ----------
**Output info:** Output info
"""""""""""
This compute calculates a per-atom array with 4 columns, which can be This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from accessed by indices 1-4 by any command that uses per-atom values from
@ -143,4 +144,7 @@ Related commands
:doc:`compute msd <compute_msd>`, :doc:`dump custom <dump>`, :doc:`fix store/state <fix_store_state>` :doc:`compute msd <compute_msd>`, :doc:`dump custom <dump>`, :doc:`fix store/state <fix_store_state>`
**Default:** none Default
"""""""
none

8
doc/src/compute_dpd.rst
View File

@ -46,7 +46,8 @@ where :math:`N` is the number of particles in the system
---------- ----------
**Output info:** Output info
"""""""""""
This compute calculates a global vector of length 5 (:math:`U^{cond}`, This compute calculates a global vector of length 5 (:math:`U^{cond}`,
:math:`U^{mech}`, :math:`U^{chem}`, :math:`\theta_{avg}`, :math:`N`), :math:`U^{mech}`, :math:`U^{chem}`, :math:`\theta_{avg}`, :math:`N`),
@ -71,7 +72,10 @@ Related commands
:doc:`compute dpd/atom <compute_dpd_atom>`, :doc:`compute dpd/atom <compute_dpd_atom>`,
:doc:`thermo_style <thermo_style>` :doc:`thermo_style <thermo_style>`
**Default:** none Default
"""""""
none
---------- ----------

8
doc/src/compute_dpd_atom.rst
View File

@ -33,7 +33,8 @@ total chemical energy and
average internal temperature of the entire system or group of dpd average internal temperature of the entire system or group of dpd
particles. particles.
**Output info:** Output info
"""""""""""
This compute calculates a per-particle array with 4 columns (:math:`u^{cond}`, This compute calculates a per-particle array with 4 columns (:math:`u^{cond}`,
:math:`u^{mech}`, :math:`u^{chem}`, :math:`\theta`), which can be accessed :math:`u^{mech}`, :math:`u^{chem}`, :math:`\theta`), which can be accessed
@ -60,7 +61,10 @@ Related commands
:doc:`dump custom <dump>`, :doc:`compute dpd <compute_dpd>` :doc:`dump custom <dump>`, :doc:`compute dpd <compute_dpd>`
**Default:** none Default
"""""""
none
---------- ----------

8
doc/src/compute_edpd_temp_atom.rst
View File

@ -31,7 +31,8 @@ of each eDPD particle based on the local equilibrium hypothesis.
For more details please see :ref:`(Espanol1997) <Espanol1997>` and For more details please see :ref:`(Espanol1997) <Espanol1997>` and
:ref:`(Li2014) <Li2014a>`. :ref:`(Li2014) <Li2014a>`.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector, which can be accessed by This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See the any command that uses per-atom values from a compute as input. See the
@ -51,7 +52,10 @@ Related commands
:doc:`pair_style edpd <pair_mesodpd>` :doc:`pair_style edpd <pair_mesodpd>`
**Default:** none Default
"""""""
none
---------- ----------

3
doc/src/compute_entropy_atom.rst
View File

@ -109,7 +109,8 @@ and for bcc sodium (lattice constant 4.23 Angstroms),
compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 compute 1 all entropy/atom 0.25 7.3 avg yes 5.1
**Output info:** Output info
"""""""""""
By default, this compute calculates the pair entropy value for each By default, this compute calculates the pair entropy value for each
atom as a per-atom vector, which can be accessed by any command that atom as a per-atom vector, which can be accessed by any command that

14
doc/src/compute_erotate_asphere.rst
View File

@ -40,7 +40,8 @@ from its angular momentum if needed.
treated as ellipsoids, not ellipses, meaning their moments of inertia treated as ellipsoids, not ellipses, meaning their moments of inertia
will be the same as in 3d. will be the same as in 3d.
**Output info:** Output info
"""""""""""
This compute calculates a global scalar (the KE). This value can be This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as used by any command that uses a global scalar value from a compute as
@ -67,8 +68,15 @@ the :doc:`atom_style tri <atom_style>` command.
All particles in the group must be finite-size. They cannot be point All particles in the group must be finite-size. They cannot be point
particles. particles.
**Related commands:** none Related commands
""""""""""""""""
none
:doc:`compute erotate/sphere <compute_erotate_sphere>` :doc:`compute erotate/sphere <compute_erotate_sphere>`
**Default:** none Default
"""""""
none

8
doc/src/compute_erotate_rigid.rst
View File

@ -38,7 +38,8 @@ compute command is ignored. The rotational energy of all the rigid
bodies defined by the fix rigid command in included in the bodies defined by the fix rigid command in included in the
calculation. calculation.
**Output info:** Output info
"""""""""""
This compute calculates a global scalar (the summed rotational energy This compute calculates a global scalar (the summed rotational energy
of all the rigid bodies). This value can be used by any command that of all the rigid bodies). This value can be used by any command that
@ -59,4 +60,7 @@ Related commands
:doc:`compute ke/rigid <compute_ke_rigid>` :doc:`compute ke/rigid <compute_ke_rigid>`
**Default:** none Default
"""""""
none

8
doc/src/compute_erotate_sphere.rst
View File

@ -35,7 +35,8 @@ of inertia for a sphere and w is the particle's angular velocity.
spheres, not disks, meaning their moment of inertia will be the same spheres, not disks, meaning their moment of inertia will be the same
as in 3d. as in 3d.
**Output info:** Output info
"""""""""""
This compute calculates a global scalar (the KE). This value can be This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as used by any command that uses a global scalar value from a compute as
@ -60,4 +61,7 @@ Related commands
:doc:`compute erotate/asphere <compute_erotate_asphere>` :doc:`compute erotate/asphere <compute_erotate_asphere>`
**Default:** none Default
"""""""
none

8
doc/src/compute_erotate_sphere_atom.rst
View File

@ -39,7 +39,8 @@ The value of the rotational kinetic energy will be 0.0 for atoms not
in the specified compute group or for point particles with a radius = in the specified compute group or for point particles with a radius =
0.0. 0.0.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector, which can be accessed by This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See any command that uses per-atom values from a compute as input. See
@ -57,4 +58,7 @@ Related commands
:doc:`dump custom <dump>` :doc:`dump custom <dump>`
**Default:** none Default
"""""""
none

8
doc/src/compute_event_displace.rst
View File

@ -43,7 +43,8 @@ further than the threshold distance.
then this compute will not be able to distinguish that motion from then this compute will not be able to distinguish that motion from
local atom displacements and may generate "false positives." local atom displacements and may generate "false positives."
**Output info:** Output info
"""""""""""
This compute calculates a global scalar (the flag). This value can be This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as used by any command that uses a global scalar value from a compute as
@ -65,4 +66,7 @@ Related commands
:doc:`prd <prd>`, :doc:`tad <tad>` :doc:`prd <prd>`, :doc:`tad <tad>`
**Default:** none Default
"""""""
none

3
doc/src/compute_fep.rst
View File

@ -279,7 +279,8 @@ trajectories during which the volume fluctuates or changes :ref:`(Allen and Tild
---------- ----------
**Output info:** Output info
"""""""""""
This compute calculates a global vector of length 3 which contains the This compute calculates a global vector of length 3 which contains the
energy difference ( :math:`U_1-U_0` ) as c_ID[1], the energy difference ( :math:`U_1-U_0` ) as c_ID[1], the

8
doc/src/compute_global_atom.rst
View File

@ -205,7 +205,8 @@ assignment of global values to atoms.
---------- ----------
**Output info:** Output info
"""""""""""
If a single input is specified this compute produces a per-atom If a single input is specified this compute produces a per-atom
vector. If multiple inputs are specified, this compute produces a vector. If multiple inputs are specified, this compute produces a
@ -228,4 +229,7 @@ Related commands
:doc:`compute <compute>`, :doc:`fix <fix>`, :doc:`variable <variable>`, :doc:`compute <compute>`, :doc:`fix <fix>`, :doc:`variable <variable>`,
:doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`compute reduce <compute_reduce>` :doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`compute reduce <compute_reduce>`
**Default:** none Default
"""""""
none

9
doc/src/compute_group_group.rst
View File

@ -128,7 +128,8 @@ group-group calculations are performed.
---------- ----------
**Output info:** Output info
"""""""""""
This compute calculates a global scalar (the energy) and a global This compute calculates a global scalar (the energy) and a global
vector of length 3 (force), which can be accessed by indices 1-3. vector of length 3 (force), which can be accessed by indices 1-3.
@ -154,7 +155,11 @@ system and not valid if particles have been moved since.
Not all :doc:`Kspace styles <kspace_style>` support the calculation of Not all :doc:`Kspace styles <kspace_style>` support the calculation of
group/group interactions. The regular *ewald* and *pppm* styles do. group/group interactions. The regular *ewald* and *pppm* styles do.
**Related commands:** none Related commands
""""""""""""""""
none
Default Default
""""""" """""""

8
doc/src/compute_gyration.rst
View File

@ -56,7 +56,8 @@ and taking a sqrt() would be invalid.
reset the image flags (e.g. to 0) before invoking this compute by reset the image flags (e.g. to 0) before invoking this compute by
using the :doc:`set image <set>` command. using the :doc:`set image <set>` command.
**Output info:** Output info
"""""""""""
This compute calculates a global scalar (:math:`R_g`) and a global vector of This compute calculates a global scalar (:math:`R_g`) and a global vector of
length 6 (:math:`{R_g}^2` tensor), which can be accessed by indices 1-6. These length 6 (:math:`{R_g}^2` tensor), which can be accessed by indices 1-6. These
@ -78,4 +79,7 @@ Related commands
:doc:`compute gyration/chunk <compute_gyration_chunk>`, :doc:`compute gyration/chunk <compute_gyration_chunk>`,
:doc:`compute gyration/shape <compute_gyration_shape>` :doc:`compute gyration/shape <compute_gyration_shape>`
**Default:** none Default
"""""""
none

14
doc/src/compute_gyration_chunk.rst
View File

@ -92,7 +92,8 @@ command, for example:
compute myChunk all gyration/chunk cc1 compute myChunk all gyration/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
**Output info:** Output info
"""""""""""
This compute calculates a global vector if the *tensor* keyword is not This compute calculates a global vector if the *tensor* keyword is not
specified and a global array if it is. The length of the vector or specified and a global array if it is. The length of the vector or
@ -112,8 +113,15 @@ Restrictions
"""""""""""" """"""""""""
none none
**Related commands:** none Related commands
""""""""""""""""
none
:doc:`compute gyration <compute_gyration>` :doc:`compute gyration <compute_gyration>`
**Default:** none Default
"""""""
none

8
doc/src/compute_gyration_shape.rst
View File

@ -63,7 +63,8 @@ is bounded between zero (if all points are spherically symmetric) and one
atom. You can reset the image flags (e.g. to 0) before invoking this atom. You can reset the image flags (e.g. to 0) before invoking this
compute by using the :doc:`set image <set>` command. compute by using the :doc:`set image <set>` command.
**Output info:** Output info
"""""""""""
This compute calculates a global vector of This compute calculates a global vector of
length 6, which can be accessed by indices 1-6. The first three values are the length 6, which can be accessed by indices 1-6. The first three values are the
@ -87,7 +88,10 @@ Related commands
:doc:`compute gyration <compute_gyration>` :doc:`compute gyration <compute_gyration>`
**Default:** none Default
"""""""
none
---------- ----------

8
doc/src/compute_gyration_shape_chunk.rst
View File

@ -64,7 +64,8 @@ The tensor keyword must be specified in the compute gyration/chunk command.
atom. You can reset the image flags (e.g. to 0) before invoking this atom. You can reset the image flags (e.g. to 0) before invoking this
compute by using the :doc:`set image <set>` command. compute by using the :doc:`set image <set>` 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
@ -89,7 +90,10 @@ Related commands
:doc:`compute gyration/chunk <compute_gyration_chunk>` :doc:`compute gyration/chunk <compute_gyration_chunk>`
:doc:`compute gyration/shape <compute_gyration_shape>` :doc:`compute gyration/shape <compute_gyration_shape>`
**Default:** none Default
"""""""
none
---------- ----------

8
doc/src/compute_heat_flux.rst
View File

@ -119,7 +119,8 @@ result should be: average conductivity ~0.29 in W/mK.
---------- ----------
**Output info:** Output info
"""""""""""
This compute calculates a global vector of length 6. This compute calculates a global vector of length 6.
The first 3 components are the :math:`x`, :math:`y`, :math:`z` The first 3 components are the :math:`x`, :math:`y`, :math:`z`
@ -157,7 +158,10 @@ Related commands
:doc:`fix ave/correlate <fix_ave_correlate>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
:doc:`variable <variable>` :doc:`variable <variable>`
**Default:** none Default
"""""""
none
---------- ----------

3
doc/src/compute_hexorder_atom.rst
View File

@ -97,7 +97,8 @@ too frequently.
:doc:`special_bonds <special_bonds>` command that includes all pairs in :doc:`special_bonds <special_bonds>` command that includes all pairs in
the neighbor list. the neighbor list.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom array with 2 columns, giving the This compute calculates a per-atom array with 2 columns, giving the
real and imaginary parts :math:`q_n`, a complex number restricted to the real and imaginary parts :math:`q_n`, a complex number restricted to the

8
doc/src/compute_hma.rst
View File

@ -155,7 +155,8 @@ An example input script that uses this compute is included in
examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA
properties fluctuate less than the corresponding conventional properties. properties fluctuate less than the corresponding conventional properties.
**Output info:** Output info
"""""""""""
This compute calculates a global vector that includes the n properties This compute calculates a global vector that includes the n properties
requested as arguments to the command (the potential energy, pressure and/or heat requested as arguments to the command (the potential energy, pressure and/or heat
@ -182,7 +183,10 @@ Related commands
formulation of the hessian provided by Pair's single_hessian, which is used by formulation of the hessian provided by Pair's single_hessian, which is used by
this compute. this compute.
**Default:** none Default
"""""""
none
---------- ----------

8
doc/src/compute_improper.rst
View File

@ -31,7 +31,8 @@ group specified for this command is ignored.
This compute is useful when using :doc:`improper_style hybrid <improper_hybrid>` if you want to know the portion of the This compute is useful when using :doc:`improper_style hybrid <improper_hybrid>` if you want to know the portion of the
total energy contributed by one or more of the hybrid sub-styles. total energy contributed by one or more of the hybrid sub-styles.
**Output info:** Output info
"""""""""""
This compute calculates a global vector of length N where N is the This compute calculates a global vector of length N where N is the
number of sub_styles defined by the :doc:`improper_style hybrid <improper_style>` command. which can be accessed by indices number of sub_styles defined by the :doc:`improper_style hybrid <improper_style>` command. which can be accessed by indices
@ -51,4 +52,7 @@ Related commands
:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>` :doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
**Default:** none Default
"""""""
none

8
doc/src/compute_improper_local.rst
View File

@ -60,7 +60,8 @@ Here is an example of how to do this:
compute 2 all improper/local chi compute 2 all improper/local chi
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1] dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
**Output info:** Output info
"""""""""""
This compute calculates a local vector or local array depending on the This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the number of keywords. The length of the vector or number of rows in the
@ -82,4 +83,7 @@ Related commands
:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>` :doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
**Default:** none Default
"""""""
none

8
doc/src/compute_inertia_chunk.rst
View File

@ -67,7 +67,8 @@ command, for example:
compute myChunk all inertia/chunk cc1 compute myChunk all inertia/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
**Output info:** Output info
"""""""""""
This compute calculates a global array where the number of rows = the This compute calculates a global array where the number of rows = the
number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns = number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns =
@ -88,4 +89,7 @@ Related commands
:doc:`variable inertia() function <variable>` :doc:`variable inertia() function <variable>`
**Default:** none Default
"""""""
none

8
doc/src/compute_ke.rst
View File

@ -43,7 +43,8 @@ that calculate temperature can subtract out different non-thermal
components of velocity and/or include different degrees of freedom components of velocity and/or include different degrees of freedom
(translational, rotational, etc). (translational, rotational, etc).
**Output info:** Output info
"""""""""""
This compute calculates a global scalar (the summed KE). This value This compute calculates a global scalar (the summed KE). This value
can be used by any command that uses a global scalar value from a can be used by any command that uses a global scalar value from a
@ -62,4 +63,7 @@ Related commands
:doc:`compute erotate/sphere <compute_erotate_sphere>` :doc:`compute erotate/sphere <compute_erotate_sphere>`
**Default:** none Default
"""""""
none

8
doc/src/compute_ke_atom.rst
View File

@ -32,7 +32,8 @@ the velocity of each atom.
The value of the kinetic energy will be 0.0 for atoms not in the The value of the kinetic energy will be 0.0 for atoms not in the
specified compute group. specified compute group.
**Output info:** Output info
"""""""""""
This compute calculates a per-atom vector, which can be accessed by This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See any command that uses per-atom values from a compute as input. See
@ -50,4 +51,7 @@ Related commands
:doc:`dump custom <dump>` :doc:`dump custom <dump>`
**Default:** none Default
"""""""
none

8
doc/src/compute_ke_atom_eff.rst
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@ -60,7 +60,8 @@ of freedom in eFF.
The value of the kinetic energy will be 0.0 for atoms (nuclei or The value of the kinetic energy will be 0.0 for atoms (nuclei or
electrons) not in the specified compute group. electrons) not in the specified compute group.
**Output info:** Output info
"""""""""""
This compute calculates a scalar quantity for each atom, which can be This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See the accessed by any command that uses per-atom computes as input. See the
@ -80,4 +81,7 @@ Related commands
:doc:`dump custom <dump>` :doc:`dump custom <dump>`
**Default:** none Default
"""""""
none

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