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Doc edits for mdi.rst

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This commit is contained in:
Karl Hammond
2022-10-04 18:49:35 -05:00
parent dd072f7e08
commit 3c11fa39b6
2 changed files with 11 additions and 11 deletions
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18
doc/src/mdi.rst
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@ -6,7 +6,7 @@ mdi command
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
mdi option args mdi option args
@ -19,7 +19,7 @@ Syntax
*elements* args = N_1 N_2 ... N_ntypes *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 = atomic number for each of ntypes LAMMPS atom types
*plugin* args = name keyword value keyword value ... *plugin* args = name keyword value keyword value ...
name = name of plugin library, e.g. lammps means a liblammps.so library will be loaded 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 keyword/value pairs in any order, some are required, some are optional
keywords = *mdi* or *infile* or *extra* or *command* keywords = *mdi* or *infile* or *extra* or *command*
*mdi* value = args passed to MDI for driver to operate with plugins (required) *mdi* value = args passed to MDI for driver to operate with plugins (required)
@ -173,8 +173,8 @@ commands, which are described further below.
atom type values are consistent in both codes, then the >TYPES atom type values are consistent in both codes, then the >TYPES
command can be used. If not, the optional *elements* keyword can command can be used. If not, the optional *elements* keyword can
be used to specify what element each LAMMPS atom type corresponds 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 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 for Al). An atomic number must be specified for each of the ntypes
LAMMPS atom types. Ntypes is typically specified via the LAMMPS atom types. Ntypes is typically specified via the
create_box command or in the data file read by the read_data 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 command. In this has been done, the MDI driver can send an
@ -325,15 +325,15 @@ able to initiate and terminate the connection to the engine code.
The only current MDI driver command in LAMMPS is the :doc:`fix mdi/qm The only current MDI driver command in LAMMPS is the :doc:`fix mdi/qm
<fix_mdi_qm>` command. If it is only used once in an input script <fix_mdi_qm>` command. If it is only used once in an input script
then it can initiate and terminate the connection. But if it is being then it can initiate and terminate the connection, but if it is being
issued multiple times, e.g. in a loop that issues a :doc:`clear issued multiple times (e.g., in a loop that issues a :doc:`clear
<clear>` command, then it cannot initiate or terminate the connection <clear>` command), then it cannot initiate or terminate the connection
multiple times. Instead, the *mdi connect* and *mdi exit* commands multiple times. Instead, the *mdi connect* and *mdi exit* commands
should be used outside the loop to initiate or terminate the connection. should be used outside the loop to initiate or terminate the connection.
See the examples/mdi/in.series.driver script for an example of how See the examples/mdi/in.series.driver script for an example of how
this is done. The LOOP in that script is reading a series of data this is done. The LOOP in that script is reading a series of data
file configurations and passing them to an MDI engine (e.g. quantum file configurations and passing them to an MDI engine (e.g., quantum
code) for energy and force evaluation. A *clear* command inside the code) for energy and force evaluation. A *clear* command inside the
loop wipes out the current system so a new one can be defined. This loop wipes out the current system so a new one can be defined. This
operation also destroys all fixes. So the :doc:`fix mdi/qm operation also destroys all fixes. So the :doc:`fix mdi/qm
@ -356,7 +356,7 @@ LAMMPS and MDI units, which the other codes will also perform in their
preferred units. preferred units.
LAMMPS can also be used as an MDI engine in other unit choices it LAMMPS can also be used as an MDI engine in other unit choices it
supports, e.g. *lj*, but then no unit conversion is performed. supports (e.g., *lj*), but then no unit conversion is performed.
Related commands Related commands
"""""""""""""""" """"""""""""""""

4
doc/utils/sphinx-config/LAMMPSLexer.py
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@ -9,8 +9,8 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
"displace_atoms", "dump_modify", "dynamical_matrix", "echo", "elif", "else", "displace_atoms", "dump_modify", "dynamical_matrix", "echo", "elif", "else",
"fix_modify", "group2ndx", "hyper", "if", "improper_coeff", "fix_modify", "group2ndx", "hyper", "if", "improper_coeff",
"improper_style", "include", "info", "jump", "kim", "improper_style", "include", "info", "jump", "kim",
"kspace_modify", "kspace_style", "label", "lattice", "kspace_modify", "kspace_style", "label", "labelmap", "lattice", "log",
"log", "mass", "message", "minimize", "min_modify", "min_style", "molecule", "mass", "mdi", "message", "minimize", "min_modify", "min_style", "molecule",
"ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next", "ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next",
"package", "pair_coeff", "pair_modify", "pair_style", "pair_write", "package", "pair_coeff", "pair_modify", "pair_style", "pair_write",
"partition", "prd", "print", "processors", "python", "quit", "read_data", "partition", "prd", "print", "processors", "python", "quit", "read_data",