mirror of https://github.com/lammps/lammps.git
Merge pull request #2302 from akohlmey/consistent-doc-headers
Consistent subsection headers for commands
This commit is contained in:
Axel Kohlmeyer
GitHub
commit
7e1a3bd4d5
|
|
@ -136,6 +136,7 @@ src directory.
|
|||
.. _cmake_presets:
|
||||
|
||||
CMake presets for installing many packages
|
||||
""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
Instead of specifying all the CMake options via the command-line,
|
||||
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
|
||||
cmake with new flags.
|
||||
|
||||
**Example:**
|
||||
Example
|
||||
"""""""
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
* 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
|
||||
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
|
||||
precision mode. Performance improvements are shown compared to
|
||||
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
|
||||
(# 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.
|
||||
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.
|
||||
|
||||
|
|
@ -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
|
||||
slightly lower.
|
||||
|
||||
**Notes about Simultaneous Multithreading:**
|
||||
Notes about Simultaneous Multithreading
|
||||
"""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
Modern CPUs often support Simultaneous Multithreading (SMT). On
|
||||
Intel processors, this is called Hyper-Threading (HT) technology.
|
||||
|
|
@ -196,7 +202,8 @@ this information can normally be obtained with:
|
|||
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
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 -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
|
||||
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
|
||||
follow in the input script.
|
||||
|
||||
**Tuning for Performance:**
|
||||
Tuning for Performance
|
||||
""""""""""""""""""""""
|
||||
|
||||
.. note::
|
||||
|
||||
|
|
@ -431,7 +442,8 @@ series processors will always perform better using MCDRAM. Please
|
|||
consult your system documentation for the best approach to specify
|
||||
that MPI runs are performed in MCDRAM.
|
||||
|
||||
**Tuning for Offload Performance:**
|
||||
Tuning for Offload 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
|
||||
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., 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).
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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.
|
||||
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).
|
||||
|
||||
**Building LAMMPS with the USER-OMP package:**
|
||||
Building LAMMPS with the USER-OMP package
|
||||
"""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
See the :ref:`Build extras <user-omp>` doc page for
|
||||
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.
|
||||
|
||||
|
|
@ -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
|
||||
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,
|
||||
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
|
||||
variable.
|
||||
|
||||
**Speed-ups to expect:**
|
||||
Speed-up to expect
|
||||
""""""""""""""""""
|
||||
|
||||
Depending on which styles are accelerated, you should look for a
|
||||
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
|
||||
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
|
||||
package with a single thread/task is faster than running with multiple
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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.
|
||||
|
||||
**Run with the OPT package from the command line:**
|
||||
Run with the OPT package from the command line
|
||||
""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
.. 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
|
||||
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
|
||||
"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
|
||||
|
||||
**Speed-ups to expect:**
|
||||
Speed-up to expect
|
||||
""""""""""""""""""
|
||||
|
||||
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
|
||||
5 to 20% savings.
|
||||
|
||||
**Guidelines for best performance:**
|
||||
Guidelines for best performance
|
||||
"""""""""""""""""""""""""""""""
|
||||
|
||||
Just try out an OPT pair style to see how it performs.
|
||||
|
||||
|
|
|
|||
|
|
@ -92,7 +92,10 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -135,7 +135,10 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -92,4 +92,7 @@ Related commands
|
|||
|
||||
:doc:`angle_style <angle_style>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -60,4 +60,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -68,4 +68,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -62,4 +62,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style cosine/squared <angle_cosine_squared>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -70,7 +70,10 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -61,4 +61,7 @@ Related commands
|
|||
:doc:`angle_coeff <angle_coeff>`,
|
||||
:doc:`angle_style cosine/shift/exp <angle_cosine_shift_exp>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -74,4 +74,7 @@ Related commands
|
|||
:doc:`angle_style cosine/shift <angle_cosine_shift>`,
|
||||
:doc:`dihedral_style cosine/shift/exp <dihedral_cosine_shift_exp>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -62,4 +62,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -62,4 +62,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -113,7 +113,10 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_hybrid <angle_hybrid>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -58,4 +58,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -57,4 +57,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -69,4 +69,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -95,4 +95,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -57,4 +57,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -37,4 +37,7 @@ Related commands
|
|||
|
||||
:doc:`angle_style zero <angle_zero>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -65,4 +65,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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:`pair_style lj/sdk/coul/long <pair_sdk>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
command to :doc:`binary restart files <restart>`, so a angle_style
|
||||
|
|
@ -152,4 +153,7 @@ Related commands
|
|||
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -51,4 +51,7 @@ Related commands
|
|||
|
||||
:doc:`angle_style none <angle_none>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
used with a group-ID that is not "all".
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
none
|
||||
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
|
|
|||
|
|
@ -548,4 +548,7 @@ Related commands
|
|||
|
||||
.. _pizza: https://pizza.sandia.gov
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -65,7 +65,10 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -87,4 +87,7 @@ Related commands
|
|||
|
||||
:doc:`bond_style <bond_style>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -74,7 +74,10 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -72,7 +72,10 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -59,4 +59,7 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -65,4 +65,7 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -65,4 +65,7 @@ Related commands
|
|||
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
|
||||
:doc:`bond_harmonic <bond_harmonic>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -64,4 +64,7 @@ Related commands
|
|||
:doc:`bond_harmonic <bond_harmonic>`,
|
||||
:doc:`bond_style harmonic/shift <bond_harmonic_shift>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -76,4 +76,7 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -55,7 +55,10 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -60,4 +60,7 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -31,8 +31,15 @@ Restrictions
|
|||
""""""""""""
|
||||
none
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
none
|
||||
|
||||
|
||||
:doc:`bond_style zero <bond_zero>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -60,7 +60,10 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -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:`bond_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
|
||||
**Default:**
|
||||
Default
|
||||
"""""""
|
||||
|
||||
|
||||
none
|
||||
|
||||
|
|
|
|||
|
|
@ -108,4 +108,7 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -103,4 +103,7 @@ Related commands
|
|||
|
||||
:doc:`bond_coeff <bond_coeff>`, :doc:`special_bonds <special_bonds>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -70,4 +70,7 @@ Related commands
|
|||
:doc:`bond_style table <bond_table>`,
|
||||
:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -50,4 +50,7 @@ Related commands
|
|||
|
||||
:doc:`bond_style none <bond_none>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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_restart <read_restart>` command.
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
none
|
||||
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
|
|
|||
|
|
@ -37,6 +37,13 @@ Restrictions
|
|||
""""""""""""
|
||||
none
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
**Default:** none
|
||||
none
|
||||
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
which computes this quantity.-
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
|
|||
|
|
@ -173,7 +173,8 @@ example:
|
|||
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
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
This compute calculates a global array with the number of rows =
|
||||
*Nbins*\ , and the number of columns = 1 + 2\*Ntriples, where Ntriples is the
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -119,7 +119,8 @@ Here is an example of how to do this:
|
|||
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]
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -142,4 +143,7 @@ Related commands
|
|||
|
||||
:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -68,7 +68,8 @@ command, for example:
|
|||
compute myChunk all angmom/chunk cc1
|
||||
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
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -44,7 +44,8 @@ which computes this quantity.
|
|||
An example input script that uses this compute is provided
|
||||
in examples/USER/misc/basal.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -69,7 +70,10 @@ Related commands
|
|||
|
||||
:doc:`compute centro/atom <compute_centro_atom>`, :doc:`compute ackland/atom <compute_ackland_atom>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -74,7 +74,8 @@ command.
|
|||
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]
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -97,4 +98,7 @@ Related commands
|
|||
|
||||
:doc:`dump local <dump>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
or more of the hybrid sub-styles.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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.
|
||||
|
|
@ -52,4 +53,7 @@ Related commands
|
|||
|
||||
:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -169,7 +169,8 @@ Here is an example of how to do this:
|
|||
compute 2 all bond/local dist engpot
|
||||
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
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
*centro/atom* style.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
By default, this compute calculates the centrosymmetry value for each
|
||||
atom as a per-atom vector, which can be accessed by any command that
|
||||
|
|
|
|||
|
|
@ -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
|
||||
be accessed by any command that uses per-atom values from a compute
|
||||
|
|
|
|||
|
|
@ -188,7 +188,8 @@ it is in.
|
|||
|
||||
----------
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -104,7 +104,8 @@ style computes.
|
|||
because it does not perform a full update of the bond topology data
|
||||
structures within LAMMPS.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -122,7 +123,9 @@ Related commands
|
|||
|
||||
:doc:`compute coord/atom <compute_coord_atom>`
|
||||
|
||||
**Default:**
|
||||
Default
|
||||
"""""""
|
||||
|
||||
|
||||
The default for fragment/atom is single no.
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
*cna/atom* style.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -98,7 +99,10 @@ Related commands
|
|||
|
||||
:doc:`compute centro/atom <compute_centro_atom>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
*cnp/atom* style.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -118,7 +119,10 @@ Related commands
|
|||
:doc:`compute cna/atom <compute_cna_atom>`
|
||||
:doc:`compute centro/atom <compute_centro_atom>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
(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
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -66,7 +66,8 @@ command, for example:
|
|||
compute myChunk all com/chunk cc1
|
||||
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
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
specified compute group.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
This compute calculates a per-atom vector, whose values can be
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -120,7 +120,8 @@ too frequently.
|
|||
|
||||
----------
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
For *cstyle* cutoff, this compute can calculate a per-atom vector or
|
||||
array. If single *type1* keyword is specified (or if none are
|
||||
|
|
|
|||
|
|
@ -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
|
||||
group.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -61,4 +62,7 @@ Related commands
|
|||
:doc:`compute dilatation/atom <compute_dilatation_atom>`,
|
||||
:doc:`compute plasticity/atom <compute_plasticity_atom>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -113,7 +113,8 @@ Here is an example of how to do this:
|
|||
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]
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -135,4 +136,7 @@ Related commands
|
|||
|
||||
:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
compute group.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -64,4 +65,7 @@ Related commands
|
|||
:doc:`compute damage/atom <compute_damage_atom>`,
|
||||
:doc:`compute plasticity/atom <compute_plasticity_atom>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -71,7 +71,8 @@ command, for example:
|
|||
compute myChunk all dipole/chunk cc1
|
||||
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
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -121,7 +121,8 @@ would be empty.
|
|||
|
||||
----------
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -143,4 +144,7 @@ Related commands
|
|||
|
||||
:doc:`compute msd <compute_msd>`, :doc:`dump custom <dump>`, :doc:`fix store/state <fix_store_state>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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}`,
|
||||
: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:`thermo_style <thermo_style>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -33,7 +33,8 @@ total chemical energy and
|
|||
average internal temperature of the entire system or group of dpd
|
||||
particles.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -60,7 +61,10 @@ Related commands
|
|||
|
||||
:doc:`dump custom <dump>`, :doc:`compute dpd <compute_dpd>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -31,7 +31,8 @@ of each eDPD particle based on the local equilibrium hypothesis.
|
|||
For more details please see :ref:`(Espanol1997) <Espanol1997>` and
|
||||
:ref:`(Li2014) <Li2014a>`.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -51,7 +52,10 @@ Related commands
|
|||
|
||||
:doc:`pair_style edpd <pair_mesodpd>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
|
|||
|
|
@ -40,7 +40,8 @@ from its angular momentum if needed.
|
|||
treated as ellipsoids, not ellipses, meaning their moments of inertia
|
||||
will be the same as in 3d.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -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
|
||||
particles.
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
none
|
||||
|
||||
|
||||
:doc:`compute erotate/sphere <compute_erotate_sphere>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
calculation.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
This compute calculates a global scalar (the summed rotational energy
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
as in 3d.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -60,4 +61,7 @@ Related commands
|
|||
|
||||
:doc:`compute erotate/asphere <compute_erotate_asphere>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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 =
|
||||
0.0.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -57,4 +58,7 @@ Related commands
|
|||
|
||||
:doc:`dump custom <dump>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -43,7 +43,8 @@ further than the threshold distance.
|
|||
then this compute will not be able to distinguish that motion from
|
||||
local atom displacements and may generate "false positives."
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -65,4 +66,7 @@ Related commands
|
|||
|
||||
:doc:`prd <prd>`, :doc:`tad <tad>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
energy difference ( :math:`U_1-U_0` ) as c_ID[1], the
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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 chunk/atom <compute_chunk_atom>`, :doc:`compute reduce <compute_reduce>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -128,7 +128,8 @@ group-group calculations are performed.
|
|||
|
||||
----------
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
This compute calculates a global scalar (the energy) and a global
|
||||
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
|
||||
group/group interactions. The regular *ewald* and *pppm* styles do.
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
none
|
||||
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
|
|
|||
|
|
@ -56,7 +56,8 @@ and taking a sqrt() would be invalid.
|
|||
reset the image flags (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 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
|
||||
|
|
@ -78,4 +79,7 @@ Related commands
|
|||
:doc:`compute gyration/chunk <compute_gyration_chunk>`,
|
||||
:doc:`compute gyration/shape <compute_gyration_shape>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -92,7 +92,8 @@ command, for example:
|
|||
compute myChunk all gyration/chunk cc1
|
||||
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
|
||||
specified and a global array if it is. The length of the vector or
|
||||
|
|
@ -112,8 +113,15 @@ Restrictions
|
|||
""""""""""""
|
||||
none
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
none
|
||||
|
||||
|
||||
:doc:`compute gyration <compute_gyration>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -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
|
||||
compute by using the :doc:`set image <set>` command.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
This compute calculates a global vector of
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
compute by using the :doc:`set image <set>` command.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
This compute calculates a global array with six columns,
|
||||
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/shape <compute_gyration_shape>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -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.
|
||||
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:`variable <variable>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -97,7 +97,8 @@ too frequently.
|
|||
:doc:`special_bonds <special_bonds>` command that includes all pairs in
|
||||
the neighbor list.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
properties fluctuate less than the corresponding conventional properties.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
This compute calculates a global vector that includes the n properties
|
||||
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
|
||||
this compute.
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -60,7 +60,8 @@ Here is an example of how to do this:
|
|||
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]
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -82,4 +83,7 @@ Related commands
|
|||
|
||||
:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -67,7 +67,8 @@ command, for example:
|
|||
compute myChunk all inertia/chunk cc1
|
||||
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
|
||||
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>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -43,7 +43,8 @@ that calculate temperature can subtract out different non-thermal
|
|||
components of velocity and/or include different degrees of freedom
|
||||
(translational, rotational, etc).
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -62,4 +63,7 @@ Related commands
|
|||
|
||||
:doc:`compute erotate/sphere <compute_erotate_sphere>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -32,7 +32,8 @@ the velocity of each atom.
|
|||
The value of the kinetic energy will be 0.0 for atoms not in the
|
||||
specified compute group.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -50,4 +51,7 @@ Related commands
|
|||
|
||||
:doc:`dump custom <dump>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
|
|
@ -60,7 +60,8 @@ of freedom in eFF.
|
|||
The value of the kinetic energy will be 0.0 for atoms (nuclei or
|
||||
electrons) not in the specified compute group.
|
||||
|
||||
**Output info:**
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
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
|
||||
|
|
@ -80,4 +81,7 @@ Related commands
|
|||
|
||||
:doc:`dump custom <dump>`
|
||||
|
||||
**Default:** none
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue