Merge branch 'master' into charge_regulation2

doc/utils/requirements.txt

@@ -1,6 +1,6 @@
 Sphinx
 sphinxcontrib-spelling
-git+https://github.com/akohlmey/sphinx-fortran@parallel-read
+git+git://github.com/akohlmey/sphinx-fortran@parallel-read
 sphinx_tabs
 breathe
 Pygments

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -8,8 +8,8 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
 "delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
 "displace_atoms", "dump_modify", "dynamical_matrix", "echo",
 "fix_modify", "group2ndx", "hyper", "if", "improper_coeff",
-"improper_style", "include", "info", "jump", "kim_init", "kim_interactions",
-"kim_param", "kim_query", "kspace_modify", "kspace_style", "label", "lattice",
+"improper_style", "include", "info", "jump", "kim",
+"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",
@@ -40,7 +40,7 @@ class LAMMPSLexer(RegexLexer):
             (r'compute\s+', Keyword, 'compute'),
             (r'dump\s+', Keyword, 'dump'),
             (r'region\s+', Keyword, 'region'),
-            (r'variable\s+', Keyword, 'variable'),
+            (r'^\s*variable\s+', Keyword, 'variable_cmd'),
             (r'group\s+', Keyword, 'group'),
             (r'change_box\s+', Keyword, 'change_box'),
             (r'uncompute\s+', Keyword, 'uncompute'),
@@ -51,6 +51,7 @@ class LAMMPSLexer(RegexLexer):
             (r'#.*?\n', Comment),
             ('"', String, 'string'),
             ('\'', String, 'single_quote_string'),
+            (r'[0-9]+:[0-9]+(:[0-9]+)?', Number),
             (r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number),
             ('\$?\(', Name.Variable, 'expression'),
             ('\$\{', Name.Variable, 'variable'),
@@ -58,6 +59,7 @@ class LAMMPSLexer(RegexLexer):
             (r'\$[\w_]+', Name.Variable),
             (r'\s+', Whitespace),
             (r'[\+\-\*\^\|\/\!%&=<>]', Operator),
+            (r'[\~\.\w_:,@\-\/\\0-9]+', Text),
         ],
         'keywords' : [
             (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword)
@@ -99,7 +101,7 @@ class LAMMPSLexer(RegexLexer):
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')
         ],
-        'variable' : [
+        'variable_cmd' : [
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')
         ],

doc/utils/sphinx-config/false_positives.txt

@@ -160,6 +160,7 @@ atwt
 augt
 AuO
 automagically
+Auvergne
 Avalos
 avalue
 aveforce
@@ -385,6 +386,7 @@ CGDNA
 cgs
 cgsdk
 CGSDK
+Chaimovich
 Chalopin
 Champaign
 charmm
@@ -1595,6 +1597,7 @@ lammps
 Lammps
 LAMMPS
 lammpsplot
+lammpsplugin
 Lampis
 Lamoureux
 Lanczos
@@ -1752,6 +1755,7 @@ lwsock
 lx
 ly
 Lybrand
+lyon
 Lyulin
 lz
 Maaravi
@@ -1966,6 +1970,7 @@ Monaghan
 Monaghans
 monodisperse
 monodispersity
+monopole
 monovalent
 Montalenti
 Montero
@@ -2111,6 +2116,7 @@ ncol
 ncorr
 ncount
 nd
+ndescriptors
 ndihedrals
 ndihedraltypes
 Ndihedraltype
@@ -2171,6 +2177,7 @@ niu
 Nk
 nktv
 nl
+nlayers
 nlen
 Nlines
 nlo
@@ -2187,6 +2194,7 @@ Nmin
 nmin
 Nmols
 nn
+nnodes
 Nocedal
 nocite
 nocoeff
@@ -2313,6 +2321,7 @@ omegaz
 Omelyan
 omp
 OMP
+oneAPI
 onelevel
 oneway
 onlysalt
@@ -2383,6 +2392,7 @@ parmin
 Parrinello
 Partay
 Particuology
+Pascuet
 pastewka
 Pastewka
 pathangle
@@ -2553,6 +2563,7 @@ ptm
 PTM
 ptol
 ptr
+PTX
 pu
 purdue
 Purohit
@@ -2645,10 +2656,12 @@ Rappe
 Ravelo
 rc
 Rc
+Rci
 Rcm
 rcmax
 Rcmx
 Rcmy
+Rco
 Rcut
 rcutfac
 rdc
@@ -2675,7 +2688,9 @@ Reinders
 reinit
 relaxbox
 relink
+relres
 relTol
+relu
 remappings
 remd
 Ren
@@ -2691,6 +2706,7 @@ representable
 Reproducibility
 reproducibility
 repuls
+reqid
 rescale
 rescaled
 rescales
@@ -2787,6 +2803,8 @@ rozero
 Rperp
 Rr
 rRESPA
+Rsi
+Rso
 Rspace
 rsq
 rst
@@ -2904,6 +2922,7 @@ si
 SiC
 Siepmann
 Sievers
+sigmoid
 Sij
 Sikandar
 Silbert
@@ -3267,6 +3286,7 @@ Tz
 Tzou
 ub
 Uberuaga
+uca
 uChem
 uCond
 uef