Merge branch 'master' into bond/react-new-examples-and-package

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
 disarmmd
 discoverable
 discretization
@@ -643,6 +645,7 @@ Donadio
 dotc
 Doty
 doxygen
+downarrow
 Doye
 dpd
 DPD
@@ -1239,6 +1242,7 @@ iostreams
 iparam
 ipi
 ipp
+Ippolito
 IPv
 IPython
 Isele
@@ -1294,6 +1298,7 @@ Janssens
 Jaramillo
 Jarzynski
 jatempl
+javascript
 jcp
 jea
 jec
@@ -1407,6 +1412,7 @@ Kraus
 Kremer
 Kress
 Kronik
+ksh
 kspace
 Kspace
 KSpace
@@ -1541,6 +1547,7 @@ Liu
 Livermore
 lj
 llammps
+LLVM
 lm
 lmp
 lmpptr
@@ -1617,6 +1624,7 @@ manybody
 MANYBODY
 Maras
 Marchetti
+Mariella
 Marrink
 Marroquin
 Marsaglia
@@ -1631,6 +1639,7 @@ Masuhiro
 Matchett
 Materias
 mathbf
+mathjax
 matlab
 matplotlib
 Matsubara
@@ -2009,6 +2018,7 @@ Nrecompute
 Nrepeat
 nreset
 Nrho
+Nroff
 nrun
 Ns
 Nsample
@@ -2611,6 +2621,7 @@ Shenderova
 Shi
 Shiga
 Shinoda
+shlib
 shockvel
 si
 SiC
@@ -2690,6 +2701,7 @@ sqdistharm
 sqrt
 src
 srd
+sright
 Srinivasan
 Srolovitz
 srp
@@ -2962,6 +2974,7 @@ uInfParallel
 uk
 ul
 ulb
+Uleft
 uloop
 ulsph
 uMech
@@ -2994,6 +3007,7 @@ unsplit
 unstrained
 untar
 untilted
+uparrow
 upenn
 upto
 Urbakh
@@ -3117,6 +3131,7 @@ webpage
 Weckner
 WeinanE
 Wennberg
+Westmere
 Westview
 wget
 Whelan

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

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