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update the kim commands doc

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This commit is contained in:
Yaser Afshar
2021-02-22 17:10:01 -06:00
parent d6380f2fd3
commit 120cdcd7f6
1 changed files with 18 additions and 11 deletions
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doc/src/kim_commands.rst
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@ -123,6 +123,8 @@ Syntax
kim init model user_units unitarg
kim interactions typeargs
.. _typeargs_options:
* model = name of the KIM interatomic model (the KIM ID for models archived in
OpenKIM)
* user_units = the LAMMPS :doc:`units <units>` style assumed in the LAMMPS
@ -192,7 +194,10 @@ the required units of the IM or the IM must be able to adjust its units to
match. (The latter is only possible with some KIM PMs; SMs can never adjust
their units.) If a match is possible, the LAMMPS :doc:`units <units>` command is
called to set the units to *user_units*\ . If the match fails, the simulation
is terminated with an error.
is terminated with an error. The *kim init* command also sets the
default value for the :doc:`skin <neighbor>` (extra distance beyond force
cutoff) as 2.0 Angstroms and sets the default value for the
:doc:`timestep <timestep>` size as 1.0 femtosecond.
Here is an example of a LAMMPS script to compute the cohesive energy of a
face-centered cubic (fcc) lattice for the MEAM potential by Pascuet and
@ -392,13 +397,16 @@ the *kim interactions* command executes the following LAMMPS input commands:
.. note::
Changing a periodic boundary to a non-periodic one, or in general using the
:doc:`change_box <change_box>` command after the interactions are set via
*kim interactions* or *pair_coeff* commands might affect some of the
settings. For example, SM models containing Coulombic terms in the
interactions require different settings if a periodic boundary changes to a
non-periodic one. In these cases, *kim interactions* must be called again
after the *change_box* command to provide the correct settings.
*kim interactions* must be called each time after the
:doc:`change_box <change_box>` command to provide the correct settings (it
should be called with the same :ref:`typeargs <typeargs_options>` as the
first call.) The reason is that changing a periodic boundary to a
non-periodic one, or in general, using the *change_box* command after the
interactions are set via *kim interactions* or *pair_coeff* commands might
affect some of the settings. For example, SM models containing Coulombic
terms in the interactions require different settings if a periodic boundary
changes to a non-periodic one. In other cases, the second call to
*kim interactions* does not affect any other settings.
.. _query:
@ -675,6 +683,8 @@ Syntax
kim param get param_name index_range variable formatarg
kim param set param_name index_range values
.. _formatarg_options:
* param_name = name of a KIM portable model parameter (which is published by the
PM and available for access). The specific string used to identify a parameter
is defined by the PM. For example, for the
@ -686,9 +696,6 @@ Syntax
* variable(s) = single name or list of names of (string style) LAMMPS
variable(s) where a query result or parameter get result is stored. Variables
that do not exist will be created by the command
.. _formatarg_options:
* formatarg = *list, split, or explicit* (optional):
.. parsed-literal::