Updated kim_query documentation to new format

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_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] :pre

[Description:]

"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.

"OpenKIM"_https://openkim.org.  The {kim_query} command must be preceded

by a {kim_init} command. The result of the query is stored in a

"string style variable"_variable.html, the name of which is given as the first

argument of the {kim_query command}.  The second required argument

{query_function} is the name of the query function to be called

(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

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

webpage at "https://query.openkim.org"_https://query.openkim.org/

argument of the {kim_query command}.  (For the case of multiple

return values, the optional {split} keyword can be used after the

variable name to separate the results into multiple variables; see

the "example"_#split_example below.)

The second required argument {query_function} is the name of the

query function to be called (e.g. {get_lattice_constant_cubic}).

All following "arguments"_Commands_parse.html are parameters handed over to

the web query in the format {keyword=value}, where {value} is always

an array of one or more comma-separated items in brackets.

The list of supported keywords and the type and format of their values

depend on the query function used. The current list of query functions

is available on the OpenKIM webpage at

"https://openkim.org/doc/repository/kim-query"_https://openkim.org/doc/repository/kim-query.

NOTE: All query functions require the {model} keyword, which identifies

the IM whose predictions are being queried. This keyword is automatically

generated by {kim_query} based on the IM set in {kim_init} and must not

be specified as an argument to {kim_query}.

NOTE: Each {query_function} is associated with a default method (implemented

as a "KIM Test"_https://openkim.org/getting-started/kim-tests/)

used to compute this property. In cases where there are multiple

methods in OpenKIM for computing a property, a {method} keyword can

be provided to select the method of choice.  See the

"query documentation"_https://openkim.org/doc/repository/kim-query

to see which methods are available for a given {query function}.

{kim_query} Usage Examples and Further Clarifications: :h6

The data obtained by {kim_query} commands can be used as part of the setup

or analysis phases of LAMMPS simulations. Some examples are given below.

kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal

boundary         p p p

kim_query        a0 get_lattice_constant_fcc species=\["Al"\] units=\["angstrom"\]

kim_query        a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\]

lattice          fcc $\{a0\}

... :pre

For example, in the above script, the lattice command would need to be

changed to: "lattice fcc $\{a0\}*$\{_u_distance\}".

:link(split_example)

[Define an equilibrium hcp crystal]

kim_init         EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal

boundary         p p p

kim_query        latconst split get_lattice_constant_hcp species=\["Zr"\] units=\["angstrom"\]

kim_query        latconst split get_lattice_constant_hexagonal crystal=\["hcp"\] species=\["Zr"\] units=\["angstrom"\]

variable         a0 equal latconst_1

variable         c0 equal latconst_2

variable         c_to_a equal $\{c0\}/$\{a0\}

kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal

boundary         p p p

kim_query        a0 get_lattice_constant_fcc species=\["Al"\] units=\["angstrom"\]

kim_query        alpha get_linear_thermal_expansion_fcc species=\["Al"\] units=\{"1/K"\}

kim_query        a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\]

kim_query        alpha get_linear_thermal_expansion_constant_cubic  crystal=\["fcc"\] species=\["Al"\] units=\{"1/K"\} temperature=[293.15] temperature_units=["K"]

variable         DeltaT equal 300

lattice          fcc $\{a0\}*$\{alpha\}*$\{DeltaT\}

... :pre

As in the previous example, the equilibrium lattice constant is obtained

for the Ercolessi and Adams (1994) potential. However, in this case the

crystal is scaled to the appropriate lattice constant at 300 K by using

the linear thermal expansion coefficient predicted by the potential.

crystal is scaled to the appropriate lattice constant at room temperature

(293.15 K) by using the linear thermal expansion constant predicted by the

potential.

NOTE: When passing numerical values as arguments (as in the case

of the temperature in the above example) it is also possible to pass a

tolerance indicating how close to the value is considered a match.

If no tolerance is passed a default value is used. If multiple results

are returned (indicating that the tolerance is too large), {kim_query}

will return an error. See the

"query documentation"_https://openkim.org/doc/repository/kim-query

to see which numerical arguments and tolerances are available for a

given {query function}.

[Compute defect formation energy]

... Build fcc crystal containing some defect and compute the total energy

... which is stored in the variable {Etot}

...

kim_query        Ec get_cohesive_energy_fcc species=\["Al"\] units=\["eV"\]

kim_query        Ec get_cohesive_energy_cubic crystal=\["fcc"\] species=\["Al"\] units=\["eV"\]

variable         Eform equal $\{Etot\} - count(all)*$\{Ec\}

... :pre