Merge branch 'develop' into gran-temp

doc/utils/sphinx-config/_static/css/lammps.css

@@ -74,9 +74,16 @@ hr {
 }
 
 .rst-breadcrumbs-buttons {
+    padding-top: 5px;
     margin: 0;
 }
 
+.breadcrumb-item:before {
+   content: "»";
+   color: black;
+   font-size: 16px;
+}
+
 p {
    margin-bottom: 12px;
 }

doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html

@@ -22,9 +22,9 @@
 <div role="navigation" aria-label="{{ _('Page navigation') }}">
   <ul class="wy-breadcrumbs">
     {%- block breadcrumbs %}
-      <li><a href="{{ pathto(master_doc) }}" class="icon icon-home"></a> &raquo;</li>
+      <li><a href="{{ pathto(master_doc) }}" class="icon icon-home"></a></li>
         {%- for doc in parents %}
-          <li class="breadcrumb-item"><a href="{{ doc.link|e }}">{{ doc.title }}</a> &raquo;</li>
+          <li class="breadcrumb-item"><a href="{{ doc.link|e }}">{{ doc.title }}</a></li>
         {%- endfor %}
       <li class="breadcrumb-item active">{{ title }}</li>
     {%- endblock %}
@@ -57,8 +57,7 @@
           {%- elif show_source and has_source and sourcename %}
             <a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> {{ _('View page source') }}</a>
           {%- endif %}
-          <a href="https://www.lammps.org">Website</a>
-          <a href="Commands_all.html">Commands</a>
+          <a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
         {%- endif %}
       </li>
     {%- endblock %}

doc/utils/sphinx-config/conf.py.in

@@ -91,7 +91,7 @@ def get_git_info():
     try:
         gitinfo = subprocess.run(['git','describe'],stdout=subprocess.PIPE,stderr=subprocess.PIPE)
         if gitinfo.returncode == 0:
-            git_n_date = gitinfo.stdout.decode().replace('_',' ')
+            git_n_date = gitinfo.stdout.decode().replace('_',' ').replace('patch ','')
     except:
         pass
     return git_n_date
@@ -344,7 +344,7 @@ latex_documents = [
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+latex_logo = "_static/lammps-logo-large.jpg"
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.

doc/utils/sphinx-config/false_positives.txt

@@ -1,5 +1,6 @@
 aa
 aat
+Abascal
 abc
 abf
 ABI
@@ -97,6 +98,7 @@ amu
 Amzallag
 analytical
 Anders
+Andric
 Andrienko
 Andzelm
 Ang
@@ -242,6 +244,7 @@ bdiam
 bdw
 Beckman
 Becton
+Behler
 Belak
 Bellott
 bem
@@ -361,6 +364,7 @@ Broglie
 brownian
 brownw
 Broyden
+Bruskin
 Brusselle
 Bryantsev
 Btarget
@@ -376,6 +380,7 @@ Buturigakkwaishi
 Buyl
 Bybee
 bz
+Cadarache
 cadetblue
 Cagin
 calc
@@ -433,6 +438,7 @@ cfile
 CFL
 cgdna
 CGDNA
+cgmap
 cgs
 cgsdk
 CGSDK
@@ -873,6 +879,7 @@ ebook
 ebt
 ec
 Ec
+Echeverri
 eco
 ecoul
 ecp
@@ -978,6 +985,7 @@ Eqp
 Eqq
 Eqs
 equi
+equidistance
 equil
 equilibrate
 equilibrated
@@ -1244,6 +1252,7 @@ gfortran
 ghostneigh
 ghostwhite
 Giacomo
+GiB
 gif
 gifsicle
 Gillan
@@ -1436,6 +1445,7 @@ hux
 hwloc
 hx
 hy
+hydronium
 hydrophobicity
 hydrostatic
 hydrostatically
@@ -1785,6 +1795,7 @@ lammps
 Lammps
 LAMMPS
 lammpsbin
+lammpsdata
 lammpsplot
 lammpsplugin
 Lamoureux
@@ -1979,6 +1990,7 @@ magelec
 Maginn
 magneton
 magnetons
+Mahoney
 mainboard
 mainboards
 makefile
@@ -2064,6 +2076,7 @@ mdi
 MDI
 mdpd
 mDPD
+mdtraj
 meam
 MEAM
 meamf
@@ -2236,6 +2249,7 @@ msd
 msi
 MSI
 msm
+msmeam
 msmflag
 msse
 msst
@@ -2456,6 +2470,7 @@ nodeless
 nodeset
 nodesets
 Noehring
+nofix
 Noffset
 noforce
 noguess
@@ -2852,6 +2867,7 @@ ps
 Ps
 pscreen
 pscrozi
+pseudocode
 Pseudocode
 pseudodynamics
 pseudopotential
@@ -3004,12 +3020,14 @@ recursing
 Ree
 refactored
 refactoring
+refactors
 reflectionstyle
 Reinders
 reinit
 reinitflag
 relaxbox
 relink
+relinked
 relres
 relTol
 relu
@@ -3043,6 +3061,7 @@ resquared
 REsquared
 restartfile
 restartinfo
+Restrepo
 rethrowing
 Revenga
 rewrap
@@ -3175,6 +3194,7 @@ Sandia
 sandybrown
 sanitizer
 Sanyal
+Sanz
 Sarath
 sc
 scafacos
@@ -3324,6 +3344,7 @@ snav
 Snodin
 Sodani
 Soderlind
+Solaris
 Solida
 solvated
 solvation
@@ -3424,6 +3445,10 @@ Subclassed
 subcutoff
 subcycle
 subcycling
+subdirectory
+subdirectories
+subdomain
+subdomains
 subhi
 sublo
 Subramaniyan
@@ -3471,6 +3496,7 @@ sz
 Sz
 Tabbernor
 tabinner
+tabstyle
 Tadmor
 Tafipolsky
 tagID
@@ -3700,6 +3726,7 @@ undump
 uniaxial
 uniaxially
 unimodal
+uninstall
 unitarg
 unitless
 Universite
@@ -4026,6 +4053,7 @@ Zi
 ziegenhain
 Ziegenhain
 zincblende
+zj
 Zj
 zlim
 zlo