diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index 2acd81a268..dea2354bad 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -48,8 +48,8 @@ Examples fix 1 ellipsoid rigid/meso single fix 1 rods rigid/meso molecule fix 1 spheres rigid/meso single force 1 off off on - fix 1 particles rigid/meso molecule force 1\*5 off off off force 6\*10 off off on - fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque \* off off off + fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on + fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off Description """"""""""" diff --git a/doc/src/group.rst b/doc/src/group.rst index 6371a030ee..3ce885bdc5 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -120,12 +120,12 @@ specified atom types, atom IDs, or molecule IDs into the group. These The first format is a list of values (types or IDs). For example, the second command in the examples above puts all atoms of type 3 or 4 into the group named *water*\ . Each entry in the list can be a -colon-separated sequence A:B or A:B:C, as in two of the examples +colon-separated sequence ``A:B`` or ``A:B:C``, as in two of the examples above. A "sequence" generates a sequence of values (types or IDs), -with an optional increment. The first example with 500:1000 has the +with an optional increment. The first example with ``500:1000`` has the default increment of 1 and would add all atom IDs from 500 to 1000 (inclusive) to the group sub, along with 10,25,50 since they also -appear in the list of values. The second example with 100:10000:10 +appear in the list of values. The second example with ``100:10000:10`` uses an increment of 10 and would thus would add atoms IDs 100,110,120, ... 9990,10000 to the group sub. @@ -269,7 +269,7 @@ group and running further. .. code-block:: LAMMPS variable nsteps equal 5000 - variable rad equal 18-(step/v_nsteps)\*(18-5) + variable rad equal 18-(step/v_nsteps)*(18-5) region ss sphere 20 20 0 v_rad group mobile dynamic all region ss fix 1 mobile nve diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index 295c6a5e40..f116a70922 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -1205,7 +1205,7 @@ coordinates of atoms in the unit cell of the cubic crystal. In the case of, e.g. a conventional fcc unit cell, the "source-value" key in the map associated with this key should be assigned the following value: -.. code-block:: LAMMPS +.. code-block:: text [[0.0, 0.0, 0.0], [0.5, 0.5, 0.0], diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py index ae40b094c2..6e611f9f74 100644 --- a/doc/utils/sphinx-config/LAMMPSLexer.py +++ b/doc/utils/sphinx-config/LAMMPSLexer.py @@ -40,7 +40,7 @@ class LAMMPSLexer(RegexLexer): (r'compute\s+', Keyword, 'compute'), (r'dump\s+', Keyword, 'dump'), (r'region\s+', Keyword, 'region'), - (r'variable\s+', Keyword, 'variable'), + (r'^\s*variable\s+', Keyword, 'variable_cmd'), (r'group\s+', Keyword, 'group'), (r'change_box\s+', Keyword, 'change_box'), (r'uncompute\s+', Keyword, 'uncompute'), @@ -51,6 +51,7 @@ class LAMMPSLexer(RegexLexer): (r'#.*?\n', Comment), ('"', String, 'string'), ('\'', String, 'single_quote_string'), + (r'[0-9]+:[0-9]+(:[0-9]+)?', Number), (r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number), ('\$?\(', Name.Variable, 'expression'), ('\$\{', Name.Variable, 'variable'), @@ -58,6 +59,7 @@ class LAMMPSLexer(RegexLexer): (r'\$[\w_]+', Name.Variable), (r'\s+', Whitespace), (r'[\+\-\*\^\|\/\!%&=<>]', Operator), + (r'[\~\.\w_:,@\-\/\\0-9]+', Text), ], 'keywords' : [ (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword) @@ -99,7 +101,7 @@ class LAMMPSLexer(RegexLexer): (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), default('#pop') ], - 'variable' : [ + 'variable_cmd' : [ (r'[\w_\-\.\[\]]+', Name.Variable.Identifier), default('#pop') ],