diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 73345b7e88..4c0d6ae768 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -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 ` 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 ` to change - the default :doc:`package kokkos ` 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 + ` to change the default :doc:`package kokkos ` + 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 ` 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 ` to change the default - :doc:`package kokkos ` 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 ` + to change the default :doc:`package kokkos ` 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 diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index 4ec872cb89..56b5c2a162 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -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 ` command; see -its page for a listing and an explanation of each attribute. +is the same as for the :doc:`dump_style custom ` command; see its +documentation page for a listing and an explanation of each attribute. .. note:: diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index d886fa7dab..07490ecf64 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -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 API -:ref:`(Elliott) `, 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 `_ 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 API :ref:`(Elliott) `, 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 `_ 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 `_ 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 +`_ 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 ` for details. Furthermore, when using *kim* command to run KIM SMs, any packages required by diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index f6ea0973e1..eb0f8797fc 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -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 ` 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 ` and :doc:`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 ` 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 +` and :doc:`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 ` are used, they are invoked on timesteps that are a function of their