sync with GH

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15668 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/src/Section_howto.txt

@@ -2123,7 +2123,7 @@ thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
 run          100000
 variable     v equal (v_v11+v_v22+v_v33)/3.0
 variable     ndens equal count(all)/vol
-print        "average viscosity: $v \[Pa.s/] @ $T K, $\{ndens\} /A^3" :pre
+print        "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre
 
 The fifth method is related to the above Green-Kubo method,
 but uses the Einstein formulation, analogous to the Einstein

doc/src/Section_packages.txt

@@ -845,7 +845,7 @@ PYTHON package :link(PYTHON),h5
 Contents: A "python"_python.html command which allow you to execute
 Python code from a LAMMPS input script.  The code can be in a separate
 file or embedded in the input script itself.  See "Section
-11.2"_Section_python.html#py-2 for an overview of using Python from
+11.2"_Section_python.html#py_2 for an overview of using Python from
 LAMMPS and for other ways to use LAMMPS and Python together.
 
 Building with the PYTHON package assumes you have a Python shared

doc/src/fix_cmap.txt

@@ -56,7 +56,7 @@ CMAP :pre
 
        1       1       8      10      12      18      20
        2       5      18      20      22      25      27
-       ... 
+       \[...\]
        N       3     314     315     317      318    330 :pre
 
 The first column is an index from 1 to N to enumerate the CMAP terms;
@@ -66,7 +66,7 @@ remaining 5 columns are the atom IDs of the atoms in the two 4-atom
 dihedrals that overlap to create the CMAP 5-body interaction.  Note
 that the "crossterm" and "CMAP" keywords for the header and body
 sections match those specified in the read_data command following the
-data file name; see the "read_data"_doc/read_data.html doc page for
+data file name; see the "read_data"_read_data.html doc page for
 more details.
 
 A data file containing CMAP crossterms can be generated from a PDB
@@ -124,9 +124,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
-(Buck) 
-Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
+:link(Buck)
+[(Buck)] Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
 (2006).
 
-(Brooks) 
-Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
+:link(Brooks)
+[(Brooks)] Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).

doc/src/fixes.txt

@@ -24,6 +24,7 @@ Fixes :h1
    fix_bond_create
    fix_bond_swap
    fix_box_relax
+   fix_cmap
    fix_colvars
    fix_controller
    fix_deform

doc/src/lammps.book

@@ -147,6 +147,7 @@ fix_bond_break.html
 fix_bond_create.html
 fix_bond_swap.html
 fix_box_relax.html
+fix_cmap.html
 fix_colvars.html
 fix_controller.html
 fix_deform.html

doc/utils/converters/lammpsdoc/lammps_filters.py

@@ -90,3 +90,24 @@ def promote_doc_keywords(content):
 
 def filter_multiple_horizontal_rules(content):
     return re.sub(r"----------[\s\n]+----------", '', content)
+
+
+def merge_preformatted_sections(content):
+    mergable_section_pattern = re.compile(r"\.\. parsed-literal::\n"
+                                          r"\n"
+                                          r"(?P<listingA>((   [^\n]+\n)|(^\n))+)\n\s*"
+                                          r"^\.\. parsed-literal::\n"
+                                          r"\n"
+                                          r"(?P<listingB>((   [^\n]+\n)|(^\n))+)\n", re.MULTILINE | re.DOTALL)
+
+    m = mergable_section_pattern.search(content)
+
+    while m:
+        content = mergable_section_pattern.sub(r".. parsed-literal::\n"
+                                            r"\n"
+                                            r"\g<listingA>"
+                                            r"\g<listingB>"
+                                            r"\n", content)
+        m = mergable_section_pattern.search(content)
+
+    return content

doc/utils/converters/lammpsdoc/txt2rst.py

@@ -73,10 +73,13 @@ class RSTMarkup(Markup):
     def unescape_rst_chars(self, text):
         text = text.replace('\\*', '*')
         text = text.replace('\\^', '^')
-        text = text.replace('\\_', '_')
+        text = self.unescape_underscore(text)
         text = text.replace('\\|', '|')
         return text
 
+    def unescape_underscore(self, text):
+        return text.replace('\\_', '_')
+
     def inline_math(self, text):
         start_pos = text.find("\\(")
         end_pos = text.find("\\)")
@@ -136,6 +139,7 @@ class RSTFormatting(Formatting):
         return content.strip()
 
     def preformat(self, content):
+        content = self.markup.unescape_underscore(content)
         if self.indent_level > 0:
             return self.list_indent("\n.. parsed-literal::\n\n" + self.indent(content.rstrip()), self.indent_level)
         return "\n.. parsed-literal::\n\n" + self.indent(content.rstrip())
@@ -355,6 +359,7 @@ class Txt2Rst(TxtParser):
         self.document_filters.append(lammps_filters.detect_and_add_command_to_index)
         self.document_filters.append(lammps_filters.filter_multiple_horizontal_rules)
         self.document_filters.append(lammps_filters.promote_doc_keywords)
+        self.document_filters.append(lammps_filters.merge_preformatted_sections)
 
     def is_ignored_textblock_begin(self, line):
         return line.startswith('<!-- HTML_ONLY -->')

doc/utils/converters/tests/test_txt2rst.py

@@ -169,6 +169,13 @@ class TestFormatting(unittest.TestCase):
                          "       Hello\n"
                          "       World\n\n", s)
 
+    def test_preformat_formatting_with_underscore(self):
+        s = self.txt2rst.convert("if MPI.COMM_WORLD.rank == 0:\n"
+                                 "    print(\"Potential energy: \", L.eval(\"pe\")) :pre\n")
+        self.assertEqual("\n.. parsed-literal::\n\n"
+                         "   if MPI.COMM_WORLD.rank == 0:\n"
+                         "       print(\"Potential energy: \", L.eval(\"pe\"))\n\n", s)
+
     def test_header_formatting(self):
         s = self.txt2rst.convert("Level 1 :h1\n"
                                  "Level 2 :h2\n"