diff --git a/doc/src/mdi.rst b/doc/src/mdi.rst index 2f7fc65852..cdb5e432cc 100644 --- a/doc/src/mdi.rst +++ b/doc/src/mdi.rst @@ -17,7 +17,7 @@ Syntax *engine* args = zero or more keyword/args pairs keywords = *elements* *elements* args = N_1 N_2 ... N_ntypes - N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types + N_1,N_2,...N_ntypes = chemical symbol for each of ntypes LAMMPS atom types *plugin* args = name keyword value keyword value ... name = name of plugin library (e.g., *lammps* means a liblammps.so library will be loaded) keyword/value pairs in any order, some are required, some are optional @@ -35,7 +35,7 @@ Examples .. code-block:: LAMMPS mdi engine - mdi engine elements 13 29 + mdi engine elements Al Cu mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" & infile in.aimd.engine extra "-log log.aimd.engine.plugin" & command "run 5" @@ -173,13 +173,16 @@ commands, which are described further below. atom type values are consistent in both codes, then the >TYPES command can be used. If not, the optional *elements* keyword can be used to specify what element each LAMMPS atom type corresponds - to. This is specified by the atomic number of the element (e.g., 13 - for Al). An atomic number must be specified for each of the ntypes - LAMMPS atom types. Ntypes is typically specified via the - create_box command or in the data file read by the read_data - command. In this has been done, the MDI driver can send an - >ELEMENTS command to the LAMMPS driver with the atomic number of - each atom. + to. This is specified by the chemical symbol of the element, + e.g. C or Al or Si. A symbol must be specified for each of the + ntypes LAMMPS atom types. Each LAMMPS type must map to a unique + element; two or more types cannot map to the same element. Ntypes + is typically specified via the :doc:`create_box ` + command or in the data file read by the :doc:`read_data + ` command. Once this has been done, the MDI driver can + send an >ELEMENTS command to the LAMMPS driver with the atomic + number of each atom and the LAMMPS engine will be able to map it to + a LAMMPS atom type. The MD and OPTG commands perform an entire MD simulation or energy minimization (to convergence) with no communication from the driver