diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 16d8ea785d..437b768df6 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -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,