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Some corrections and additions to kim_commands docs

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This commit is contained in:
Ryan S. Elliott
2019-07-10 22:11:47 -05:00
parent ea68db964a
commit 1a0662c386
1 changed files with 9 additions and 5 deletions
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14
doc/src/kim_commands.txt
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@ -35,7 +35,7 @@ kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657
kim_interactions C H O
kim_init Sim_LAMMPS_IFF_OtherInfo_AuthorList_Year_Species__SM_064312669787_000 real
kim_interactions fixed_types
kim_query a0 get_lattice_constant_fcc species=\["Al"] units=\["angstrom"\] :pre
kim_query a0 get_lattice_constant_fcc species=\["Al"\] units=\["angstrom"\] :pre
[Description:]
@ -105,12 +105,16 @@ The URL for such a page is constructed from the
"extended KIM ID"_https://openkim.org/about-kim-ids/ of the IM:
https://openkim.org/id/extended_KIM_ID
or
https://openkim.org/id/short_KIM_ID
:pre
For example for the Stillinger-Weber potential
listed above the Model Page is located at:
"https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005
or
"https://openkim.org/id/MO_405512056662_005"_https://openkim.org/id/MO_405512056662_005
:pre
See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species.
@ -271,8 +275,8 @@ OpenKIM IM Execution ({kim_interactions}) :h5
The second and final step in using an OpenKIM IM is to execute the
{kim_interactions} command. This command must be preceded by a {kim_init}
command and a "create_box"_create_box.html command,
which defines the number of atom types {N}.
command and a command that creates the simulation box (such as
"create_box"_create_box.html), which defines the number of atom types {N}.
The {kim_interactions} command has one argument {typeargs}. This argument
contains either a list of {N} chemical species, which defines a mapping between
atom types in LAMMPS to the available species in the OpenKIM IM, or the
@ -338,7 +342,7 @@ Note also that parameters like cutoff radii and charge tolerances,
which have an effect on IM predictions, are also included in the
SM definition ensuring reproducibility.
NOTE: When using using {kim_init} and {kim_interactions} to select
NOTE: When using {kim_init} and {kim_interactions} to select
and set up an OpenKIM IM, other LAMMPS commands
for the same functions (such as pair_style, pair_coeff, bond_style,
bond_coeff, fixes related to charge equilibration, etc.) should normally
@ -356,7 +360,7 @@ argument of the {kim_query command}. The second required argument
(e.g. {get_lattice_constant_fcc}).
All following arguments are parameters handed over to the web query
in the format {keyword=value}. The list of supported keywords and
and the type and format of their values depend on the query function
the type and format of their values depend on the query function
used.
NOTE: The current list of supported query functions is available on the OpenKIM