Merge branch 'master' into feature-cnt
This commit is contained in:
iafoss
@ -1,31 +1,53 @@
|
||||
from pygments.lexer import RegexLexer, words
|
||||
from pygments.lexer import RegexLexer, words, include, default
|
||||
from pygments.token import *
|
||||
|
||||
LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
|
||||
"balance", "bond_coeff", "bond_style", "bond_write", "boundary", "box",
|
||||
"change_box", "clear", "comm_modify", "comm_style", "compute",
|
||||
"clear", "comm_modify", "comm_style",
|
||||
"compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms",
|
||||
"delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
|
||||
"displace_atoms", "dump", "dump_modify", "dynamical_matrix", "echo", "fix",
|
||||
"fix_modify", "group", "group2ndx", "hyper", "if", "improper_coeff",
|
||||
"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",
|
||||
"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",
|
||||
"partition", "prd", "print", "processors", "python", "quit", "read_data",
|
||||
"read_dump", "read_restart", "region", "replicate", "rerun", "reset_ids",
|
||||
"read_dump", "read_restart", "replicate", "rerun", "reset_ids",
|
||||
"reset_timestep", "restart", "run", "run_style", "server", "set", "shell",
|
||||
"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt",
|
||||
"thermo", "thermo_modify", "thermo_style", "then", "third_order", "timer", "timestep",
|
||||
"uncompute", "undump", "unfix", "units", "variable", "velocity", "write_coeff",
|
||||
"write_data", "write_dump", "write_restart")
|
||||
"units", "velocity", "write_coeff",
|
||||
"write_data", "write_restart")
|
||||
|
||||
#fix ID group-ID style args
|
||||
#compute ID group-ID style args
|
||||
#dump ID group-ID style N file args
|
||||
#region ID style args keyword arg ...
|
||||
#variable name style args ...
|
||||
#group ID style args
|
||||
#uncompute compute-ID
|
||||
#undump dump-ID
|
||||
#unfix fix-ID
|
||||
#write_dump group-ID style file dump-args modify dump_modify-args
|
||||
|
||||
class LAMMPSLexer(RegexLexer):
|
||||
name = 'LAMMPS'
|
||||
tokens = {
|
||||
'root': [
|
||||
(words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword),
|
||||
(r'fix\s+', Keyword, 'fix'),
|
||||
(r'compute\s+', Keyword, 'compute'),
|
||||
(r'dump\s+', Keyword, 'dump'),
|
||||
(r'region\s+', Keyword, 'region'),
|
||||
(r'variable\s+', Keyword, 'variable'),
|
||||
(r'group\s+', Keyword, 'group'),
|
||||
(r'change_box\s+', Keyword, 'change_box'),
|
||||
(r'uncompute\s+', Keyword, 'uncompute'),
|
||||
(r'unfix\s+', Keyword, 'unfix'),
|
||||
(r'undump\s+', Keyword, 'undump'),
|
||||
(r'write_dump\s+', Keyword, 'write_dump'),
|
||||
include('keywords'),
|
||||
(r'#.*?\n', Comment),
|
||||
('"', String, 'string'),
|
||||
('\'', String, 'single_quote_string'),
|
||||
@ -37,6 +59,10 @@ class LAMMPSLexer(RegexLexer):
|
||||
(r'\s+', Whitespace),
|
||||
(r'[\+\-\*\^\|\/\!%&=<>]', Operator),
|
||||
],
|
||||
'keywords' : [
|
||||
(words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword)
|
||||
]
|
||||
,
|
||||
'variable' : [
|
||||
('[^\}]+', Name.Variable),
|
||||
('\}', Name.Variable, '#pop'),
|
||||
@ -53,5 +79,56 @@ class LAMMPSLexer(RegexLexer):
|
||||
('[^\(\)]+', Name.Variable),
|
||||
('\(', Name.Variable, 'expression'),
|
||||
('\)', Name.Variable, '#pop'),
|
||||
],
|
||||
'fix' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
(r'\s+', Whitespace, 'group_id'),
|
||||
default('#pop')
|
||||
],
|
||||
'compute' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
(r'\s+', Whitespace, 'group_id'),
|
||||
default('#pop')
|
||||
],
|
||||
'dump' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
(r'\s+', Whitespace, 'group_id'),
|
||||
default('#pop')
|
||||
],
|
||||
'region' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
default('#pop')
|
||||
],
|
||||
'variable' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
default('#pop')
|
||||
],
|
||||
'group' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
default('#pop')
|
||||
],
|
||||
'change_box' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
default('#pop')
|
||||
],
|
||||
'unfix' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
default('#pop')
|
||||
],
|
||||
'undump' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
default('#pop')
|
||||
],
|
||||
'uncompute' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
default('#pop')
|
||||
],
|
||||
'write_dump' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
default('#pop')
|
||||
],
|
||||
'group_id' : [
|
||||
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
|
||||
default('#pop:2')
|
||||
]
|
||||
}
|
||||
|
||||
@ -1,5 +1,4 @@
|
||||
<div role="navigation" aria-label="breadcrumbs navigation">
|
||||
<div style="text-align: center; margin-bottom: -1.5em; display: block"><b>LAMMPS</b> {{ version }}</div>
|
||||
<ul class="wy-breadcrumbs">
|
||||
<li><a href="{{ pathto(master_doc) }}">Docs</a> »</li>
|
||||
{% for doc in parents %}
|
||||
@ -22,7 +21,7 @@
|
||||
{% endif %}
|
||||
</li>
|
||||
</ul>
|
||||
<hr/>
|
||||
<hr style="margin-top: 6px; margin-bottom: 6px;" width="100%"/>
|
||||
{% if next or prev %}
|
||||
<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
|
||||
{% if next %}
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
</div>
|
||||
{% endif %}
|
||||
|
||||
<hr/>
|
||||
<hr style="margin-top: 6px; margin-bottom: 6px;" width="100%"/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
|
||||
@ -100,6 +100,8 @@
|
||||
{% endif %}
|
||||
</a>
|
||||
|
||||
<div class="lammps_version">Version: <b>{{ version }}</b></div>
|
||||
|
||||
{% include "searchbox.html" %}
|
||||
|
||||
{% endblock %}
|
||||
|
||||
@ -4189,8 +4189,7 @@ div[class^='highlight'] pre {
|
||||
}
|
||||
}
|
||||
.wy-affix {
|
||||
position: fixed;
|
||||
top: 1.618em;
|
||||
position: fixed; top: 0.618em;
|
||||
}
|
||||
|
||||
.wy-menu a:hover {
|
||||
@ -4411,7 +4410,7 @@ div[class^='highlight'] pre {
|
||||
font-weight: bold;
|
||||
display: inline-block;
|
||||
padding: 4px 6px;
|
||||
margin-bottom: 0.809em;
|
||||
/*margin-bottom: 0.809em;*/
|
||||
}
|
||||
.wy-side-nav-search > a:hover, .wy-side-nav-search .wy-dropdown > a:hover {
|
||||
background: rgba(255, 255, 255, 0.1);
|
||||
@ -4540,7 +4539,7 @@ div[class^='highlight'] pre {
|
||||
}
|
||||
|
||||
.wy-nav-content {
|
||||
padding: 1.618em 3.236em;
|
||||
padding: 0.5em 1.0em;
|
||||
height: 100%;
|
||||
margin: auto;
|
||||
}
|
||||
@ -5105,4 +5104,10 @@ span[id*='MathJax-Span'] {
|
||||
padding: 0;
|
||||
}
|
||||
|
||||
.lammps_version {
|
||||
text-align: center;
|
||||
display: block;
|
||||
margin-bottom: 0.809em;
|
||||
}
|
||||
|
||||
/*# sourceMappingURL=theme.css.map */
|
||||
|
||||
@ -334,3 +334,6 @@ from sphinx.highlighting import lexers
|
||||
lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)
|
||||
|
||||
sys.path.append(os.path.join(os.path.dirname(__file__), '../../../python'))
|
||||
|
||||
# avoid syntax highlighting in blocks that don't specify language
|
||||
highlight_language = 'none'
|
||||
|
||||
@ -204,7 +204,6 @@ bcolor
|
||||
bdiam
|
||||
bdw
|
||||
Beckman
|
||||
behaviour
|
||||
Belak
|
||||
Bellott
|
||||
benchmarking
|
||||
@ -262,6 +261,8 @@ Bogaerts
|
||||
Bogusz
|
||||
Bohrs
|
||||
Boltzman
|
||||
BondAngle
|
||||
BondBond
|
||||
bondchk
|
||||
bondmax
|
||||
bondtype
|
||||
@ -394,6 +395,7 @@ cmake
|
||||
CMake
|
||||
cmap
|
||||
Cmax
|
||||
cmd
|
||||
cmdlist
|
||||
Cmin
|
||||
cmm
|
||||
@ -489,6 +491,7 @@ cstring
|
||||
cstyle
|
||||
csvr
|
||||
Ctypes
|
||||
ctypes
|
||||
cuda
|
||||
Cuda
|
||||
CUDA
|
||||
@ -749,6 +752,8 @@ electronegative
|
||||
electronegativity
|
||||
Eleftheriou
|
||||
ElementN
|
||||
elementset
|
||||
elementsets
|
||||
elif
|
||||
Elj
|
||||
Ellad
|
||||
@ -774,6 +779,7 @@ engrot
|
||||
engtrans
|
||||
engvib
|
||||
enobonds
|
||||
EnSight
|
||||
enthalpy
|
||||
enums
|
||||
envoke
|
||||
@ -816,6 +822,8 @@ erotate
|
||||
Ertas
|
||||
ervel
|
||||
Espanol
|
||||
Eshelby
|
||||
eshelby
|
||||
eskm
|
||||
esu
|
||||
esub
|
||||
@ -828,6 +836,8 @@ ethernet
|
||||
etol
|
||||
etot
|
||||
etotal
|
||||
Eulerian
|
||||
eulerian
|
||||
eulerimplicit
|
||||
Europhys
|
||||
ev
|
||||
@ -848,6 +858,8 @@ extrema
|
||||
exy
|
||||
ey
|
||||
ez
|
||||
faceset
|
||||
facesets
|
||||
factorizable
|
||||
factorizations
|
||||
Fahrenberger
|
||||
@ -865,6 +877,7 @@ fdotr
|
||||
fdt
|
||||
Fehlberg
|
||||
Fellinger
|
||||
fe
|
||||
femtosecond
|
||||
femtoseconds
|
||||
fene
|
||||
@ -888,6 +901,7 @@ fhg
|
||||
Fi
|
||||
Fichthorn
|
||||
Fickian
|
||||
fieldname
|
||||
figshare
|
||||
Fij
|
||||
filelink
|
||||
@ -1030,6 +1044,7 @@ Gmask
|
||||
gneb
|
||||
GNEB
|
||||
Goldfarb
|
||||
Gonzalez-Melchor
|
||||
googlemail
|
||||
Gordan
|
||||
GPa
|
||||
@ -1157,6 +1172,8 @@ Hugoniot
|
||||
Hura
|
||||
hux
|
||||
hwloc
|
||||
hx
|
||||
hy
|
||||
hydrophobicity
|
||||
hydrostatic
|
||||
hydrostatically
|
||||
@ -1166,6 +1183,7 @@ hyperdynamics
|
||||
hyperradius
|
||||
hyperspherical
|
||||
hysteretic
|
||||
hz
|
||||
Ibanez
|
||||
ibar
|
||||
ibm
|
||||
@ -1294,6 +1312,7 @@ Izvekov
|
||||
izz
|
||||
Izz
|
||||
Jacobsen
|
||||
Jadhav
|
||||
jagreat
|
||||
Jalalvand
|
||||
james
|
||||
@ -1384,6 +1403,7 @@ Khvostov
|
||||
Ki
|
||||
Kikugawa
|
||||
kim
|
||||
kinetostats
|
||||
kJ
|
||||
kk
|
||||
Klahn
|
||||
@ -1587,6 +1607,7 @@ lucy
|
||||
Luding
|
||||
Lussetti
|
||||
Lustig
|
||||
lval
|
||||
lwsock
|
||||
lx
|
||||
ly
|
||||
@ -1598,7 +1619,7 @@ Mackay
|
||||
Mackrodt
|
||||
Macromolecules
|
||||
macroparticle
|
||||
macOS
|
||||
MacOS
|
||||
Madura
|
||||
Magda
|
||||
Magdeburg
|
||||
@ -1667,6 +1688,7 @@ maxwell
|
||||
Maxwellian
|
||||
maxX
|
||||
Mayergoyz
|
||||
Mayoral
|
||||
mbt
|
||||
Mbytes
|
||||
MBytes
|
||||
@ -1695,6 +1717,7 @@ mediumvioletred
|
||||
Mees
|
||||
Mehl
|
||||
Mei
|
||||
Melchor
|
||||
Meloni
|
||||
Melrose
|
||||
Mem
|
||||
@ -1709,6 +1732,8 @@ Merz
|
||||
meshless
|
||||
meso
|
||||
mesocnt
|
||||
MESODPD
|
||||
mesodpd
|
||||
MESONT
|
||||
mesont
|
||||
mesoparticle
|
||||
@ -1936,6 +1961,7 @@ Nelement
|
||||
Nelements
|
||||
nemd
|
||||
netcdf
|
||||
netstat
|
||||
Nettleton
|
||||
Neumann
|
||||
Nevent
|
||||
@ -1986,6 +2012,8 @@ Nocedal
|
||||
nocite
|
||||
nocoeff
|
||||
nodeless
|
||||
nodeset
|
||||
nodesets
|
||||
Noehring
|
||||
noforce
|
||||
Noid
|
||||
@ -2055,6 +2083,7 @@ nucleotides
|
||||
num
|
||||
numa
|
||||
numactl
|
||||
numdiff
|
||||
numericalfreedom
|
||||
numerics
|
||||
numpy
|
||||
@ -2163,6 +2192,7 @@ parameterizations
|
||||
parameterize
|
||||
parameterized
|
||||
params
|
||||
ParaView
|
||||
parmin
|
||||
Parrinello
|
||||
Partay
|
||||
@ -2254,6 +2284,7 @@ pN
|
||||
png
|
||||
Podhorszki
|
||||
Poiseuille
|
||||
poisson
|
||||
Polak
|
||||
polarizabilities
|
||||
polarizability
|
||||
@ -2266,6 +2297,7 @@ polyA
|
||||
polybond
|
||||
polydisperse
|
||||
polydispersity
|
||||
polyelectrolyte
|
||||
polyhedra
|
||||
popen
|
||||
Popov
|
||||
@ -2286,8 +2318,6 @@ Prakash
|
||||
pre
|
||||
Pre
|
||||
prec
|
||||
preceed
|
||||
preceeded
|
||||
precession
|
||||
prefactor
|
||||
prefactors
|
||||
@ -2339,6 +2369,7 @@ pymbar
|
||||
pymodule
|
||||
pymol
|
||||
pypar
|
||||
pythonic
|
||||
Pyy
|
||||
pz
|
||||
Pz
|
||||
@ -2561,8 +2592,7 @@ Salles
|
||||
sandia
|
||||
Sandia
|
||||
sandybrown
|
||||
Sanitizer
|
||||
sanitizers
|
||||
sanitizer
|
||||
Sanyal
|
||||
sc
|
||||
scafacos
|
||||
@ -2682,7 +2712,6 @@ smtbq
|
||||
sna
|
||||
snad
|
||||
snapcoeff
|
||||
snaphots
|
||||
snapparam
|
||||
snav
|
||||
Snodin
|
||||
@ -2767,6 +2796,8 @@ Stukowski
|
||||
Su
|
||||
subbox
|
||||
subcutoff
|
||||
subcycle
|
||||
subcycling
|
||||
Subramaniyan
|
||||
subscripted
|
||||
subscripting
|
||||
@ -2781,6 +2812,7 @@ superset
|
||||
supersphere
|
||||
Supinski
|
||||
Surblys
|
||||
surfactant
|
||||
surfactants
|
||||
Suter
|
||||
Sutmann
|
||||
@ -2828,7 +2860,6 @@ tdpd
|
||||
tDPD
|
||||
Tdrude
|
||||
Technol
|
||||
Technolgy
|
||||
Telsa
|
||||
tempCorrCoeff
|
||||
templated
|
||||
@ -2845,6 +2876,7 @@ tfmc
|
||||
tfMC
|
||||
th
|
||||
Thakkar
|
||||
Thaokar
|
||||
thb
|
||||
thei
|
||||
Theodorou
|
||||
@ -3035,11 +3067,13 @@ util
|
||||
utils
|
||||
utsa
|
||||
Uttormark
|
||||
uval
|
||||
uvm
|
||||
uwo
|
||||
Uzdin
|
||||
vacf
|
||||
Vaid
|
||||
Vaiwala
|
||||
valent
|
||||
Valeriu
|
||||
valgrind
|
||||
@ -3068,6 +3102,7 @@ Vectorization
|
||||
vectorized
|
||||
Vegt
|
||||
vel
|
||||
Velázquez
|
||||
Verlag
|
||||
verlet
|
||||
Verlet
|
||||
@ -3152,7 +3187,6 @@ Whelan
|
||||
whitesmoke
|
||||
Wi
|
||||
Wicaksono
|
||||
wih
|
||||
Wijk
|
||||
Wikipedia
|
||||
wildcard
|
||||
@ -3197,6 +3231,7 @@ xmax
|
||||
Xmax
|
||||
xmgrace
|
||||
xMIC
|
||||
xmin
|
||||
xmovie
|
||||
Xmovie
|
||||
xmu
|
||||
@ -3230,6 +3265,8 @@ yhi
|
||||
yi
|
||||
ylat
|
||||
ylo
|
||||
ymax
|
||||
ymin
|
||||
Yoshida
|
||||
ys
|
||||
ysu
|
||||
@ -3264,6 +3301,8 @@ Ziegenhain
|
||||
Zj
|
||||
zlim
|
||||
zlo
|
||||
zmax
|
||||
zmin
|
||||
zmq
|
||||
zN
|
||||
zs
|
||||
|
||||
Reference in New Issue
Block a user