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another doc page change

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Steve Plimpton
2023-02-24 16:27:15 -07:00
parent fae0442130
commit 7d3b9e4dda
1 changed files with 12 additions and 9 deletions
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doc/src/mdi.rst
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@ -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 <create_box>`
command or in the data file read by the :doc:`read_data
<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