Merge branch 'master' into fix_numerical_differentiation

doc/utils/check-packages.py

@@ -0,0 +1,97 @@
+#!/usr/bin/env python3
+
+from __future__ import print_function
+from glob import glob
+from argparse import ArgumentParser
+import os, re, sys
+
+parser = ArgumentParser(prog='check-packages.py',
+                        description="Check package table completeness")
+
+parser.add_argument("-v", "--verbose",
+                    action='store_const',
+                    const=True, default=False,
+                    help="Enable verbose output")
+
+parser.add_argument("-d", "--doc",
+                    help="Path to LAMMPS documentation sources")
+parser.add_argument("-s", "--src",
+                    help="Path to LAMMPS sources")
+
+args = parser.parse_args()
+verbose = args.verbose
+src = args.src
+doc = args.doc
+
+if not args.src or not args.doc:
+  parser.print_help()
+  sys.exit(1)
+
+if not os.path.isdir(src):
+    sys.exit("LAMMPS source path %s does not exist" % src)
+
+if not os.path.isdir(doc):
+    sys.exit("LAMMPS documentation source path %s does not exist" % doc)
+
+pkgdirs = glob(os.path.join(src, '[A-Z][A-Z]*'))
+dirs = re.compile(".*/([0-9A-Z-]+)$")
+user = re.compile("USER-.*")
+
+stdpkg = []
+usrpkg = []
+
+# find package names and add to standard and user package lists.
+# anything starting with at least two upper case characters, is a
+# folder, and is not called 'MAKE' is a package 
+
+for d in pkgdirs:
+  pkg = dirs.match(d)[1]
+  if not os.path.isdir(os.path.join(src,pkg)): continue
+  if pkg in ['DEPEND','MAKE','STUBS']: continue
+  if user.match(pkg):
+    usrpkg.append(pkg)
+  else:
+    stdpkg.append(pkg)
+
+print("Found %d standard and %d user packages" % (len(stdpkg),len(usrpkg)))
+
+counter = 0
+fp = open(os.path.join(doc,'Packages_standard.rst'))
+text = fp.read()
+fp.close()
+matches = re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`',text,re.MULTILINE)
+for p in stdpkg:
+  if not p in matches:
+    ++counter
+    print("Standard package %s missing in Packages_standard.rst"
+          % p)
+
+fp = open(os.path.join(doc,'Packages_user.rst'))
+text = fp.read()
+fp.close()
+matches = re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`',text,re.MULTILINE)
+for p in usrpkg:
+  if not p in matches:
+    ++counter
+    print("User package %s missing in Packages_user.rst"
+          % p)
+
+fp = open(os.path.join(doc,'Packages_details.rst'))
+text = fp.read()
+fp.close()
+matches = re.findall(':ref:`([A-Z0-9]+) <PKG-\\1>`',text,re.MULTILINE)
+for p in stdpkg:
+  if not p in matches:
+    ++counter
+    print("Standard package %s missing in Packages_details.rst"
+          % p)
+matches = re.findall(':ref:`(USER-[A-Z0-9]+) <PKG-\\1>`',text,re.MULTILINE)
+for p in usrpkg:
+  if not p in matches:
+    ++counter
+    print("User package %s missing in Packages_details.rst"
+          % p)
+
+if counter:
+    print("Found %d issue(s) with package lists" % counter)
+

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -35,7 +35,7 @@ class LAMMPSLexer(RegexLexer):
             (r'[\w_\.\[\]]+', Name),
             (r'\$[\w_]+', Name.Variable),
             (r'\s+', Whitespace),
-            (r'[\+\-\*\/&=<>]', Operator),
+            (r'[\+\-\*\^\|\/\!%&=<>]', Operator),
         ],
         'variable' : [
             ('[^\}]+', Name.Variable),

doc/utils/sphinx-config/conf.py

@@ -60,7 +60,7 @@ master_doc = 'Manual'
 
 # General information about the project.
 project = 'LAMMPS'
-copyright = '2013 Sandia Corporation'
+copyright = '2003-2020 Sandia Corporation'
 
 def get_lammps_version():
     import os
@@ -128,7 +128,9 @@ html_theme = 'lammps_theme'
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+html_theme_options = {
+   'logo_only' : True
+}
 
 # Add any paths that contain custom themes here, relative to this directory.
 html_theme_path = ['_themes']
@@ -142,7 +144,7 @@ html_title = "LAMMPS documentation"
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+html_logo = 'lammps-logo.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -210,6 +212,9 @@ if 'epub' in sys.argv:
 else:
   html_math_renderer = 'mathjax'
 
+# use relative path for mathjax, so it is looked for in the
+# html tree and the manual becomes readable when offline 
+mathjax_path = 'mathjax/es5/tex-mml-chtml.js'
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {

doc/utils/sphinx-config/false_positives.txt

@@ -173,6 +173,7 @@ backcolor
 Baczewski
 Bagi
 Bagnold
+Bkappa
 Bal
 balancer
 Balankura
@@ -315,6 +316,7 @@ Caswell
 Cates
 cauchy
 cauchystat
+Cavazzoni
 Cavium
 Cawkwell
 cbecker
@@ -612,7 +614,7 @@ dimgray
 dipolar
 dir
 Direc
-dirs
+dirname
 discoverable
 discretization
 discretized
@@ -642,6 +644,7 @@ Donadio
 dotc
 Doty
 doxygen
+downarrow
 Doye
 dpd
 DPD
@@ -1238,6 +1241,7 @@ iostreams
 iparam
 ipi
 ipp
+Ippolito
 IPv
 IPython
 Isele
@@ -1293,6 +1297,7 @@ Janssens
 Jaramillo
 Jarzynski
 jatempl
+javascript
 jcp
 jea
 jec
@@ -1406,6 +1411,7 @@ Kraus
 Kremer
 Kress
 Kronik
+ksh
 kspace
 Kspace
 KSpace
@@ -1540,6 +1546,7 @@ Liu
 Livermore
 lj
 llammps
+LLVM
 lm
 lmp
 lmpptr
@@ -1616,6 +1623,7 @@ manybody
 MANYBODY
 Maras
 Marchetti
+Mariella
 Marrink
 Marroquin
 Marsaglia
@@ -1630,6 +1638,7 @@ Masuhiro
 Matchett
 Materias
 mathbf
+mathjax
 matlab
 matplotlib
 Matsubara
@@ -2611,6 +2620,7 @@ Shenderova
 Shi
 Shiga
 Shinoda
+shlib
 shockvel
 si
 SiC
@@ -2690,6 +2700,7 @@ sqdistharm
 sqrt
 src
 srd
+sright
 Srinivasan
 Srolovitz
 srp
@@ -2962,6 +2973,7 @@ uInfParallel
 uk
 ul
 ulb
+Uleft
 uloop
 ulsph
 uMech
@@ -2994,6 +3006,7 @@ unsplit
 unstrained
 untar
 untilted
+uparrow
 upenn
 upto
 Urbakh
@@ -3117,6 +3130,7 @@ webpage
 Weckner
 WeinanE
 Wennberg
+Westmere
 Westview
 wget
 Whelan

doc/utils/sphinx-config/lammps-logo.png

@@ -0,0 +1 @@
+../../src/JPG/lammps-logo.png