Merge branch 'develop' into shake-with-minimize

doc/utils/check-styles.py

@@ -60,7 +60,7 @@ reader = {}
 region = {}
 total = 0
 
-index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$")
+index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style|dump)\s+([a-zA-Z0-9/_]+)$")
 style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)")
 upper = re.compile("[A-Z]+")
 gpu = re.compile("(.+)/gpu$")
@@ -84,7 +84,8 @@ def load_index_entries_in_file(path):
 
 def load_index_entries():
     index = {'compute': set(), 'fix': set(), 'pair_style': set(), 'angle_style': set(),
-             'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(), 'kspace_style': set()}
+             'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(),
+             'kspace_style': set(), 'dump': set()}
     rst_files = glob(os.path.join(doc_dir, '*.rst'))
     for f in rst_files:
         for command_type, style in load_index_entries_in_file(f):
@@ -254,8 +255,9 @@ for command_type, entries in index.items():
 
 print("Total number of style index entries:", total_index)
 
+skip_angle = ('sdk')
 skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
-skip_pair = ('meam/c','lj/sf','reax/c')
+skip_pair = ('meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm')
 skip_compute = ('pressure/cylinder')
 
 counter = 0
@@ -269,13 +271,14 @@ counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",pair
 counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",pair,'Pair',skip=skip_pair,suffix=False)
 counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",bond,'Bond',suffix=True)
 counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",bond,'Bond',suffix=False)
-counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',suffix=True)
-counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',suffix=False)
+counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',skip=skip_angle,suffix=True)
+counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',skip=skip_angle,suffix=False)
 counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",dihedral,'Dihedral',suffix=True)
 counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",dihedral,'Dihedral',suffix=False)
 counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",improper,'Improper',suffix=True)
 counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",improper,'Improper',suffix=False)
 counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",kspace,'KSpace',suffix=True)
+counter += check_style('Commands_dump.rst', doc_dir, ":doc:`(.+) <dump.*>`",dump,'Dump',suffix=True)
 
 if counter:
     print(f"Found {counter} issue(s) with style lists")
@@ -284,12 +287,13 @@ counter = 0
 
 counter += check_style_index("compute", compute, index["compute"], skip=['pressure/cylinder'])
 counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species'])
-counter += check_style_index("angle_style", angle, index["angle_style"])
+counter += check_style_index("angle_style", angle, index["angle_style"], skip=['sdk'])
 counter += check_style_index("bond_style", bond, index["bond_style"])
 counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
 counter += check_style_index("improper_style", improper, index["improper_style"])
 counter += check_style_index("kspace_style", kspace, index["kspace_style"])
-counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf','reax/c'])
+counter += check_style_index("dump", dump, index["dump"])
+counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm'])
 
 if counter:
     print(f"Found {counter} issue(s) with style index")

doc/utils/sphinx-config/_themes/lammps_theme/.gitignore

@@ -0,0 +1 @@
+!*.html

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

@@ -4,17 +4,8 @@
 {% endblock %}
 {% block body %}
   <div id="search-results">
-<script>
-  (function() {
-    var cx = '012685039201307511604:um7if1hinba';
-    var gcse = document.createElement('script');
-    gcse.type = 'text/javascript';
-    gcse.async = true;
-    gcse.src = 'https://cse.google.com/cse.js?cx=' + cx;
-    var s = document.getElementsByTagName('script')[0];
-    s.parentNode.insertBefore(gcse, s);
-  })();
-</script>
-<gcse:searchresults-only></gcse:searchresults-only>
+    <script async src="https://cse.google.com/cse.js?cx=000956471495417073164:5ggs_m6ymw0">
+    </script>
+    <div class="gcse-search"></div>
   </div>
 {% endblock %}

doc/utils/sphinx-config/false_positives.txt

@@ -269,6 +269,7 @@ binutils
 biomolecular
 biomolecule
 Biomolecules
+biomolecules
 Biophys
 Biosym
 biquadratic
@@ -278,6 +279,7 @@ Bispectrum
 bitbucket
 bitmapped
 bitmask
+bitorsion
 bitrate
 bitrates
 Bitzek
@@ -289,6 +291,7 @@ blocksize
 blueviolet
 bn
 bni
+bnumeric
 bo
 Bochkarev
 Bochum
@@ -373,6 +376,7 @@ Caltech
 Camilloni
 Camiloni
 Campana
+Cangi
 Cao
 Capolungo
 Caro
@@ -420,6 +424,8 @@ CGDNA
 cgs
 cgsdk
 CGSDK
+cgspica
+CGSPICA
 Chaimovich
 Chalopin
 Champaign
@@ -442,6 +448,7 @@ chiralIDs
 ChiralIDs
 chirality
 Cho
+Chodera
 ChooseOffset
 chris
 Christoph
@@ -576,6 +583,7 @@ cstring
 cstyle
 csvr
 ctrl
+ctrn
 ctypes
 Ctypes
 cuda
@@ -696,6 +704,7 @@ devel
 Devemy
 deviatoric
 Devine
+dewald
 df
 dfftw
 DFT
@@ -773,6 +782,7 @@ DPD
 dpdTheta
 dphi
 DPhil
+dpme
 dr
 dR
 dragforce
@@ -1276,6 +1286,7 @@ gzipped
 Haak
 Hafskjold
 halfstepback
+halgren
 Halperin
 Halver
 Hamaker
@@ -1283,6 +1294,7 @@ Hamel
 Hammerschmidt
 Hanley
 haptic
+Haque
 Hara
 Harpertown
 Harting
@@ -1334,6 +1346,7 @@ hiID
 Hijazi
 Hilger
 Hinestrosa
+hipCUB
 hipFFT
 histo
 histogrammed
@@ -1471,6 +1484,7 @@ intra
 intralayer
 intramolecular
 ints
+inumeric
 inv
 invariants
 inversed
@@ -1627,6 +1641,7 @@ Kemper
 kepler
 keV
 Keyes
+keyfile
 Khersonskii
 Khrapak
 Khvostov
@@ -1688,6 +1703,7 @@ kTln
 ktypeN
 Kub
 Kubo
+Kuksenok
 Kumagai
 Kumar
 Kurebayashi
@@ -1702,6 +1718,7 @@ Ladd
 lagrangian
 lambdai
 LambdaLanczos
+Lambrecht
 lamda
 lammps
 Lammps
@@ -2076,6 +2093,7 @@ Mishin
 Mishra
 mistyped
 mistyrose
+Miyazaki
 Mj
 mK
 mkdir
@@ -2087,6 +2105,7 @@ mlparks
 Mniszewski
 mnt
 mobi
+Mobley
 modc
 Modell
 modelled
@@ -2137,6 +2156,7 @@ mpiexec
 mpiio
 mpirun
 mplayer
+mpole
 mps
 mradius
 Mrovec
@@ -2171,6 +2191,7 @@ multicore
 multielectron
 multinode
 multiphysics
+Multipole
 multiscale
 multisectioning
 multithreading
@@ -2358,6 +2379,7 @@ nodesets
 Noehring
 Noffset
 noforce
+noguess
 Noid
 nolib
 nonequilibrium
@@ -2366,6 +2388,7 @@ nonGaussian
 nonlocal
 Nonlocal
 Noordhoek
+noprecond
 nopreliminary
 Nord
 norder
@@ -2471,6 +2494,7 @@ ohenrich
 ok
 Okabe
 Okamoto
+Okazaki
 O'Keefe
 OKeefe
 oldlace
@@ -2542,6 +2566,7 @@ palegreen
 paleturquoise
 palevioletred
 Panagiotopoulos
+Pande
 Pandit
 Papaconstantopoulos
 papayawhip
@@ -2576,6 +2601,7 @@ Pavia
 Paxton
 pbc
 pc
+pcg
 pchain
 Pchain
 pcmoves
@@ -2609,7 +2635,9 @@ Persp
 peru
 Peskin
 Pettifor
+pewald
 pfactor
+pflag
 pgi
 ph
 Philipp
@@ -2642,6 +2670,7 @@ pIp
 Pisarev
 Pishevar
 Pitera
+pitorsion
 pj
 pjintve
 pKa
@@ -2657,6 +2686,7 @@ plt
 plumedfile
 pmb
 pmcmoves
+pme
 Pmolrotate
 Pmoltrans
 pN
@@ -2680,8 +2710,11 @@ polydispersity
 polyelectrolyte
 polyhedra
 Polym
+polymorph
 polymorphism
+Ponder
 popen
+Popoola
 Popov
 popstore
 Poresag
@@ -2698,6 +2731,7 @@ potin
 Pourtois
 powderblue
 PowerShell
+ppme
 ppn
 pppm
 Prakash
@@ -2707,6 +2741,7 @@ pre
 Pre
 prec
 precession
+precond
 prefactor
 prefactors
 prepend
@@ -2728,6 +2763,7 @@ pscrozi
 pseudodynamics
 pseudopotential
 pSp
+pSPICA
 Pstart
 Pstop
 pstyle
@@ -2801,6 +2837,8 @@ Qsb
 qtb
 quadratically
 quadrupolar
+quadrupole
+quadrupoles
 Quant
 quartic
 quat
@@ -2817,6 +2855,7 @@ qw
 qx
 qy
 qz
+Rackers
 radialscreened
 radialscreenedspin
 radialspin
@@ -2825,6 +2864,7 @@ radians
 Rafferty
 rahman
 Rahman
+Rajamanickam
 Ralf
 Raman
 ramped
@@ -3055,6 +3095,7 @@ Schimansky
 Schiotz
 Schlitter
 Schmid
+Schnieders
 Schoen
 Schotte
 Schratt
@@ -3085,6 +3126,7 @@ semiaxes
 semimetals
 Semin
 Sensable
+Seo
 Sep
 seqdep
 Serpico
@@ -3189,12 +3231,15 @@ Souza
 sp
 spacings
 Spearot
+specieslist
 specular
 spellcheck
 Spellmeyer
 Speybroeck
 sph
 SPH
+spica
+SPICA
 Spickermann
 splined
 spparks
@@ -3423,6 +3468,7 @@ tmin
 Tmin
 tmp
 tN
+tnumeric
 Tobias
 Toennies
 Tohoku
@@ -3511,6 +3557,9 @@ Tz
 Tzou
 ub
 Uberuaga
+ubflag
+Ubflag
+ubiquitin
 uca
 uChem
 uCond
@@ -3564,12 +3613,14 @@ upenn
 upto
 Urbakh
 Urbana
+UreyBradley
 Usabiaga
 usec
 uSemiParallel
 userguide
 username
 usleep
+usolve
 usr
 util
 utils
@@ -3603,6 +3654,7 @@ Vcm
 vdfmax
 vdim
 vdisplace
+vdw
 vdW
 vdwl
 vec
@@ -3677,19 +3729,26 @@ vx
 Vx
 vxcm
 vxmu
+vxx
+vxy
+vxz
 vy
 Vy
 vycm
+vyy
+vyz
 vz
 Vz
 vzcm
 vzi
+vzz
 Waals
 Wadley
 wallstyle
 walltime
 Waltham
 Waroquier
+Wataru
 wavepacket
 wB
 Wbody
@@ -3750,6 +3809,7 @@ Xeon
 xflag
 xhi
 xHost
+Xia
 Xiaohu
 Xiaowang
 Xie