diff --git a/doc/src/mdi.rst b/doc/src/mdi.rst index d2b8ff185d..2f7fc65852 100644 --- a/doc/src/mdi.rst +++ b/doc/src/mdi.rst @@ -6,7 +6,7 @@ mdi command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS mdi option args @@ -19,7 +19,7 @@ Syntax *elements* args = N_1 N_2 ... N_ntypes N_1,N_2,...N_ntypes = atomic number 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 + 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 keywords = *mdi* or *infile* or *extra* or *command* *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 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 + 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 @@ -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 ` command. If it is only used once in an input script -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 -` command, then it cannot initiate or terminate the connection +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 +` command), then it cannot initiate or terminate the connection multiple times. Instead, the *mdi connect* and *mdi exit* commands 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 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 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 @@ -356,7 +356,7 @@ LAMMPS and MDI units, which the other codes will also perform in their preferred units. 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 """""""""""""""" diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py index 116cdb7388..524d7bf1fa 100644 --- a/doc/utils/sphinx-config/LAMMPSLexer.py +++ b/doc/utils/sphinx-config/LAMMPSLexer.py @@ -9,8 +9,8 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style", "displace_atoms", "dump_modify", "dynamical_matrix", "echo", "elif", "else", "fix_modify", "group2ndx", "hyper", "if", "improper_coeff", "improper_style", "include", "info", "jump", "kim", -"kspace_modify", "kspace_style", "label", "lattice", -"log", "mass", "message", "minimize", "min_modify", "min_style", "molecule", +"kspace_modify", "kspace_style", "label", "labelmap", "lattice", "log", +"mass", "mdi", "message", "minimize", "min_modify", "min_style", "molecule", "ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next", "package", "pair_coeff", "pair_modify", "pair_style", "pair_write", "partition", "prd", "print", "processors", "python", "quit", "read_data",