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Added preliminary doc for kim_interactions fixed_types

This commit is contained in:
Ellad Tadmor 2019-07-09 09:43:34 -04:00
parent 39c8a7de6e
commit 30086950b8
1 changed files with 15 additions and 3 deletions
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18
doc/src/kim_commands.txt
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@ -19,7 +19,7 @@ kim_query variable formatarg query_function queryargs :pre
model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM)
user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script
unitarg = {unit_conversion_mode} (optional)
typeargs = atom type to species mapping (one entry per atom type)
typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping
variable = name of a (string style) variable where the result of the query is stored
formatarg = {split} (optional)
query_function = name of the OpenKIM web API query function to be used
@ -33,6 +33,8 @@ kim_interactions Si
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode
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
@ -272,8 +274,13 @@ The second and final step in using an OpenKIM IM is to execute the
command and a "create_box"_create_box.html command,
which defines the number of atom types {N}.
The {kim_interactions} command has one argument {typeargs}. This argument
contains a list of {N} chemical species, which defines a mapping between
atom types in LAMMPS to the available species in the OpenKIM IM.
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
keyword {fixed_types} for models that have a preset fixed mapping (i.e.
the mapping between LAMMPS atom types and chemical species is defined by
the model and cannot be changed). In the latter case, the user must consult
the model documentation to see how many atom types there are and how they
map to the chemcial species.
For example, consider an OpenKIM IM that supports Si and C species.
If the LAMMPS simulation has four atom types, where the first three are Si,
@ -282,6 +289,11 @@ and the fourth is C, the following {kim_interactions} command would be used:
kim_interactions Si Si Si C
:pre
Alternatively, for a model with a fixed mapping the command would be:
kim_interactions fixed_types
:pre
The {kim_interactions} command performs all the necessary steps to set up
the OpenKIM IM selected in the {kim_init} command. The specific actions depend
on whether the IM is a KIM PM or a KIM SM. For a KIM PM,