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small documentation improvements

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This commit is contained in:
Axel Kohlmeyer
2022-12-16 22:09:30 -05:00
parent 9d4af4098c
commit 17d69b7dbd
4 changed files with 44 additions and 43 deletions
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40
doc/src/Speed_kokkos.rst
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@ -212,14 +212,15 @@ threads/task as Nt. The product of these two values should be N, i.e.
.. note::
The default for the :doc:`package kokkos <package>` command when
running on KNL is to use "half" neighbor lists and set the Newton flag
to "on" for both pairwise and bonded interactions. This will typically
be best for many-body potentials. For simpler pairwise potentials, it
may be faster to use a "full" neighbor list with Newton flag to "off".
Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to change
the default :doc:`package kokkos <package>` options. See its page for
details and default settings. Experimenting with its options can provide
a speed-up for specific calculations. For example:
running on KNL is to use "half" neighbor lists and set the Newton
flag to "on" for both pairwise and bonded interactions. This will
typically be best for many-body potentials. For simpler pairwise
potentials, it may be faster to use a "full" neighbor list with
Newton flag to "off". Use the "-pk kokkos" :doc:`command-line switch
<Run_options>` to change the default :doc:`package kokkos <package>`
options. See its documentation page for details and default
settings. Experimenting with its options can provide a speed-up for
specific calculations. For example:
.. code-block:: bash
@ -271,17 +272,18 @@ one or more nodes, each with two GPUs:
.. note::
The default for the :doc:`package kokkos <package>` command when
running on GPUs is to use "full" neighbor lists and set the Newton flag
to "off" for both pairwise and bonded interactions, along with threaded
communication. When running on Maxwell or Kepler GPUs, this will
typically be best. For Pascal GPUs and beyond, using "half" neighbor lists and
setting the Newton flag to "on" may be faster. For many pair styles,
setting the neighbor binsize equal to twice the CPU default value will
give speedup, which is the default when running on GPUs. Use the "-pk
kokkos" :doc:`command-line switch <Run_options>` to change the default
:doc:`package kokkos <package>` options. See its page for details and
default settings. Experimenting with its options can provide a speed-up
for specific calculations. For example:
running on GPUs is to use "full" neighbor lists and set the Newton
flag to "off" for both pairwise and bonded interactions, along with
threaded communication. When running on Maxwell or Kepler GPUs, this
will typically be best. For Pascal GPUs and beyond, using "half"
neighbor lists and setting the Newton flag to "on" may be faster. For
many pair styles, setting the neighbor binsize equal to twice the CPU
default value will give speedup, which is the default when running on
GPUs. Use the "-pk kokkos" :doc:`command-line switch <Run_options>`
to change the default :doc:`package kokkos <package>` options. See
its documentation page for details and default
settings. Experimenting with its options can provide a speed-up for
specific calculations. For example:
.. code-block:: bash

4
doc/src/dump_vtk.rst
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@ -90,8 +90,8 @@ hexahedrons in either legacy .vtk or .vtu XML format.
Style *vtk* allows you to specify a list of atom attributes to be
written to the dump file for each atom. The list of possible attributes
is the same as for the :doc:`dump_style custom <dump>` command; see
its page for a listing and an explanation of each attribute.
is the same as for the :doc:`dump_style custom <dump>` command; see its
documentation page for a listing and an explanation of each attribute.
.. note::

30
doc/src/kim_commands.rst
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@ -1333,13 +1333,13 @@ For example,
Citation of OpenKIM IMs
"""""""""""""""""""""""
When publishing results obtained using OpenKIM IMs researchers are requested
to cite the OpenKIM project :ref:`(Tadmor) <kim-mainpaper>`, KIM API
:ref:`(Elliott) <kim-api>`, and the specific IM codes used in the simulations,
in addition to the relevant scientific references for the IM. The citation
format for an IM is displayed on its page on
`OpenKIM <https://openkim.org>`_ along with the corresponding BibTex file, and
is automatically added to the LAMMPS citation reminder.
When publishing results obtained using OpenKIM IMs researchers are
requested to cite the OpenKIM project :ref:`(Tadmor) <kim-mainpaper>`,
KIM API :ref:`(Elliott) <kim-api>`, and the specific IM codes used in
the simulations, in addition to the relevant scientific references for
the IM. The citation format for an IM is displayed on its page on
`OpenKIM <https://openkim.org>`_ along with the corresponding BibTex
file, and is automatically added to the LAMMPS citation reminder.
Citing the IM software (KIM infrastructure and specific PM or SM codes) used in
the simulation gives credit to the researchers who developed them and enables
@ -1348,15 +1348,15 @@ open source efforts like OpenKIM to function.
Restrictions
""""""""""""
The *kim* command is part of the KIM package. It is only enabled if LAMMPS is
built with that package. A requirement for the KIM package, is the KIM API
library that must be downloaded from the
`OpenKIM website <https://openkim.org/kim-api/>`_ and installed before LAMMPS is
The *kim* command is part of the KIM package. It is only enabled if
LAMMPS is built with that package. A requirement for the KIM package,
is the KIM API library that must be downloaded from the `OpenKIM website
<https://openkim.org/kim-api/>`_ and installed before LAMMPS is
compiled. When installing LAMMPS from binary, the kim-api package is a
dependency that is automatically downloaded and installed. The *kim query*
command requires the *libcurl* library to be installed. The *kim property*
command requires *Python* 3.6 or later and the *kim-property* python package to
be installed. See the KIM section of the
dependency that is automatically downloaded and installed. The *kim
query* command requires the *libcurl* library to be installed. The *kim
property* command requires *Python* 3.6 or later and the *kim-property*
python package to be installed. See the KIM section of the
:doc:`Packages details <Packages_details>` for details.
Furthermore, when using *kim* command to run KIM SMs, any packages required by

13
doc/src/rerun.rst
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@ -192,13 +192,12 @@ calculated which saves time. The :doc:`comm_modify cutoff
acquired from far enough away for operations like bond and angle
evaluations, if no pair style is being used.
Every time a snapshot is read, the timestep for the simulation is
reset, as if the :doc:`reset_timestep <reset_timestep>` command were
used. This command has some restrictions as to what fixes can be
defined. See its page for details. For example, the :doc:`fix
deposit <fix_deposit>` and :doc:`fix dt/reset <fix_dt_reset>` fixes
are in this category. They also make no sense to use with a rerun
command.
Every time a snapshot is read, the timestep for the simulation is reset,
as if the :doc:`reset_timestep <reset_timestep>` command were used.
This command has some restrictions as to what fixes can be defined. See
its documentation page for details. For example, the :doc:`fix deposit
<fix_deposit>` and :doc:`fix dt/reset <fix_dt_reset>` fixes are in this
category. They also make no sense to use with a rerun command.
If time-averaging fixes like :doc:`fix ave/time <fix_ave_time>` are
used, they are invoked on timesteps that are a function of their