Add LAMMPSLexer for LAMMPS code-blocks in docs

doc/src/Commands_input.rst

@@ -17,7 +17,7 @@ one line at a time and each command takes effect when it is read.
 Thus this sequence of commands:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    timestep 0.5
    run      100
@@ -26,7 +26,7 @@ Thus this sequence of commands:
 does something different than this sequence:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    run      100
    timestep 0.5

doc/src/Commands_parse.rst

@@ -22,6 +22,10 @@ comment after a trailing "&" character will prevent the command from
 continuing on the next line.  Also note that for multi-line commands a
 single leading "#" will comment out the entire command.
 
+.. code-block:: LAMMPS
+
+   # this is a comment
+
 (3) The line is searched repeatedly for $ characters, which indicate
 variables that are replaced with a text string.  See an exception in
 (6).
@@ -47,7 +51,7 @@ to use numeric formulas in an input script without having to assign
 them to variable names.  For example, these 3 input script lines:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable X equal (xlo+xhi)/2+sqrt(v_area)
    region 1 block $X 2 INF INF EDGE EDGE
@@ -56,7 +60,7 @@ them to variable names.  For example, these 3 input script lines:
 can be replaced by
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
 
@@ -72,7 +76,7 @@ specified a high-precision "%.20g" is used as the default.
 This can be useful for formatting print output to a desired precision:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
 
@@ -81,7 +85,7 @@ contain nested $ characters for other variables to substitute for.
 Thus you cannot do this:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable        a equal 2
    variable        b2 equal 4
@@ -113,7 +117,7 @@ can be enclosed in triple quotes, in which case "&" characters are not
 needed.  For example:
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    print "Volume = $v"
    print 'Volume = $v'

doc/txt/Commands_input.txt

@@ -1,60 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-LAMMPS input scripts :h3
-
-LAMMPS executes by reading commands from a input script (text file),
-one line at a time.  When the input script ends, LAMMPS exits.  Each
-command causes LAMMPS to take some action.  It may set an internal
-variable, read in a file, or run a simulation.  Most commands have
-default settings, which means you only need to use the command if you
-wish to change the default.
-
-In many cases, the ordering of commands in an input script is not
-important.  However the following rules apply:
-
-(1) LAMMPS does not read your entire input script and then perform a
-simulation with all the settings.  Rather, the input script is read
-one line at a time and each command takes effect when it is read.
-Thus this sequence of commands:
-
-timestep 0.5
-run      100
-run      100 :pre
-
-does something different than this sequence:
-
-run      100
-timestep 0.5
-run      100 :pre
-
-In the first case, the specified timestep (0.5 fs) is used for two
-simulations of 100 timesteps each.  In the 2nd case, the default
-timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
-timestep is used for the 2nd one.
-
-(2) Some commands are only valid when they follow other commands.  For
-example you cannot set the temperature of a group of atoms until atoms
-have been defined and a group command is used to define which atoms
-belong to the group.
-
-(3) Sometimes command B will use values that can be set by command A.
-This means command A must precede command B in the input script if it
-is to have the desired effect.  For example, the
-"read_data"_read_data.html command initializes the system by setting
-up the simulation box and assigning atoms to processors.  If default
-values are not desired, the "processors"_processors.html and
-"boundary"_boundary.html commands need to be used before read_data to
-tell LAMMPS how to map processors to the simulation box.
-
-Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  The "Errors"_Errors.html doc page gives
-more information on what errors mean.  The documentation for each
-command lists restrictions on how the command can be used.
-

doc/txt/Commands_parse.txt

@@ -1,136 +0,0 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Parsing rules for input scripts :h3
-
-Each non-blank line in the input script is treated as a command.
-LAMMPS commands are case sensitive.  Command names are lower-case, as
-are specified command arguments.  Upper case letters may be used in
-file names or user-chosen ID strings.
-
-Here are 6 rules for how each line in the input script is parsed by
-LAMMPS:
-
-(1) If the last printable character on the line is a "&" character,
-the command is assumed to continue on the next line.  The next line is
-concatenated to the previous line by removing the "&" character and
-line break.  This allows long commands to be continued across two or
-more lines.  See the discussion of triple quotes in (6) for how to
-continue a command across multiple line without using "&" characters.
-
-(2) All characters from the first "#" character onward are treated as
-comment and discarded.  See an exception in (6).  Note that a
-comment after a trailing "&" character will prevent the command from
-continuing on the next line.  Also note that for multi-line commands a
-single leading "#" will comment out the entire command.
-
-(3) The line is searched repeatedly for $ characters, which indicate
-variables that are replaced with a text string.  See an exception in
-(6).
-
-If the $ is followed by curly brackets, then the variable name is the
-text inside the curly brackets.  If no curly brackets follow the $,
-then the variable name is the single character immediately following
-the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
-"x".
-
-How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable.html doc page for details.
-It can be a variable that stores multiple text strings, and return one
-of them.  The returned text string can be multiple "words" (space
-separated) which will then be interpreted as multiple arguments in the
-input command.  The variable can also store a numeric formula which
-will be evaluated and its numeric result returned as a string.
-
-As a special case, if the $ is followed by parenthesis, then the text
-inside the parenthesis is treated as an "immediate" variable and
-evaluated as an "equal-style variable"_variable.html.  This is a way
-to use numeric formulas in an input script without having to assign
-them to variable names.  For example, these 3 input script lines:
-
-variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete :pre
-
-can be replaced by
-
-region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
-
-so that you do not have to define (or discard) a temporary variable X.
-
-Additionally, the "immediate" variable expression may be followed by a
-colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
-The format string must be appropriate for a double-precision
-floating-point value.  The format string is used to output the result
-of the variable expression evaluation.  If a format string is not
-specified a high-precision "%.20g" is used as the default.
-
-This can be useful for formatting print output to a desired precision:
-
-print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
-
-Note that neither the curly-bracket or immediate form of variables can
-contain nested $ characters for other variables to substitute for.
-Thus you cannot do this:
-
-variable        a equal 2
-variable        b2 equal 4
-print           "B2 = $\{b$a\}" :pre
-
-Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v_x-1.0), since the latter is valid syntax for an
-"equal-style variable"_variable.html.
-
-See the "variable"_variable.html command for more details of how
-strings are assigned to variables and evaluated, and how they can be
-used in input script commands.
-
-(4) The line is broken into "words" separated by white-space (tabs,
-spaces).  Note that words can thus contain letters, digits,
-underscores, or punctuation characters.
-
-(5) The first word is the command name.  All successive words in the
-line are arguments.
-
-(6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in either single or double or triple quotes.  A
-long single argument enclosed in single or double quotes can span
-multiple lines if the "&" character is used, as described above.  When
-the lines are concatenated together (and the "&" characters and line
-breaks removed), the text will become a single line.  If you want
-multiple lines of an argument to retain their line breaks, the text
-can be enclosed in triple quotes, in which case "&" characters are not
-needed.  For example:
-
-print "Volume = $v"
-print 'Volume = $v'
-if "$\{steps\} > 1000" then quit
-variable a string "red green blue &
-                   purple orange cyan"
-print """
-System volume = $v
-System temperature = $t
-""" :pre
-
-In each case, the single, double, or triple quotes are removed when
-the single argument they enclose is stored internally.
-
-See the "dump modify format"_dump_modify.html, "print"_print.html,
-"if"_if.html, and "python"_python.html commands for examples.
-
-A "#" or "$" character that is between quotes will not be treated as a
-comment indicator in (2) or substituted for as a variable in (3).
-
-NOTE: If the argument is itself a command that requires a quoted
-argument (e.g. using a "print"_print.html command as part of an
-"if"_if.html or "run every"_run.html command), then single, double, or
-triple quotes can be nested in the usual manner.  See the doc pages
-for those commands for examples.  Only one of level of nesting is
-allowed, but that should be sufficient for most use cases.
-

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -0,0 +1,57 @@
+from pygments.lexer import RegexLexer, words
+from pygments.token import *
+
+LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
+"balance", "bond_coeff", "bond_style", "bond_write", "boundary", "box",
+"change_box", "clear", "comm_modify", "comm_style", "compute",
+"compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms",
+"delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
+"displace_atoms", "dump", "dump_modify", "dynamical_matrix", "echo", "fix",
+"fix_modify", "group", "group2ndx", "hyper", "if", "improper_coeff",
+"improper_style", "include", "info", "jump", "kim_init", "kim_interactions",
+"kim_param", "kim_query", "kspace_modify", "kspace_style", "label", "lattice",
+"log", "mass", "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",
+"read_dump", "read_restart", "region", "replicate", "rerun", "reset_ids",
+"reset_timestep", "restart", "run", "run_style", "server", "set", "shell",
+"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt",
+"thermo", "thermo_modify", "thermo_style", "then", "third_order", "timer", "timestep",
+"uncompute", "undump", "unfix", "units", "variable", "velocity", "write_coeff",
+"write_data", "write_dump", "write_restart")
+
+class LAMMPSLexer(RegexLexer):
+    name = 'LAMMPS'
+    tokens = {
+        'root': [
+            (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword),
+            (r'#.*?\n', Comment),
+            ('"', String, 'string'),
+            ('\'', String, 'single_quote_string'),
+            (r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number),
+            ('\$?\(', Name.Variable, 'expression'),
+            ('\$\{', Name.Variable, 'variable'),
+            (r'[\w_\.\[\]]+', Name),
+            (r'\$[\w_]+', Name.Variable),
+            (r'\s+', Whitespace),
+            (r'[\+\-\*\/&=<>]', Operator),
+        ],
+        'variable' : [
+            ('[^\}]+', Name.Variable),
+            ('\}', Name.Variable, '#pop'),
+        ],
+        'string' : [
+            ('[^"]+', String),
+            ('"', String, '#pop'),
+        ],
+        'single_quote_string' : [
+            ('[^\']+', String),
+            ('\'', String, '#pop'),
+        ],
+        'expression' : [
+            ('[^\(\)]+', Name.Variable),
+            ('\(', Name.Variable, 'expression'),
+            ('\)', Name.Variable, '#pop'),
+        ]
+    }

doc/utils/sphinx-config/conf.py

@@ -317,3 +317,9 @@ if spelling_spec:
 
     spelling_lang='en_US'
     spelling_word_list_filename='false_positives.txt'
+
+sys.path.append(os.path.join(os.path.dirname(__file__), '.'))
+import LAMMPSLexer
+from sphinx.highlighting import lexers
+
+lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)