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Merge branch 'lammps:develop' into local-composition

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This commit is contained in:
Megan J. McCarthy (Meg)
2023-07-27 03:13:51 -06:00
committed by GitHub
parent 38fd78b867 a4a206e601
commit f533d4ff66
850 changed files with 19766 additions and 13115 deletions
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2
doc/utils/requirements.txt
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@ -2,7 +2,7 @@ Sphinx >= 5.3.0, <7.1.0
sphinxcontrib-spelling
sphinxcontrib-jquery
git+https://github.com/akohlmey/sphinx-fortran@parallel-read
git+https://github.com/executablebooks/sphinx-tabs@v3.4.1
sphinx-tabs>=3.4.1
breathe
Pygments
six

72
doc/utils/sphinx-config/LAMMPSLexer.py
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@ -2,14 +2,15 @@ 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", "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_modify", "dynamical_matrix", "echo", "elif",
"else", "fix_modify", "group2ndx", "hyper", "if",
"atom_style", "angle_write", "balance", "bond_coeff",
"bond_style", "bond_write", "boundary", "clear",
"comm_modify", "comm_style", "compute_modify",
"create_atoms", "create_bonds", "create_box",
"delete_atoms", "delete_bonds", "dielectric",
"dihedral_coeff", "dihedral_style", "dihedral_write",
"dimension", "displace_atoms", "dump_modify",
"dynamical_matrix", "echo", "fitpod",
"fix_modify", "group2ndx", "hyper",
"improper_coeff", "improper_style", "include",
"info", "jump", "kim", "kspace_modify",
"kspace_style", "label", "labelmap", "lattice",
@ -23,7 +24,7 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify",
"read_restart", "replicate", "rerun", "reset_atoms",
"reset_timestep", "restart", "run", "run_style",
"server", "set", "shell", "special_bonds", "suffix",
"tad", "temper", "temper/grem", "temper/npt", "then",
"tad", "temper", "temper/grem", "temper/npt",
"thermo", "thermo_modify", "thermo_style",
"third_order", "timer", "timestep", "units",
"velocity", "write_coeff", "write_data",
@ -45,16 +46,34 @@ class LAMMPSLexer(RegexLexer):
tokens = {
'root': [
(r'fix\s+', Keyword, 'fix'),
(r'fix_modify\s+', Keyword, 'modify_cmd'),
(r'compute\s+', Keyword, 'compute'),
(r'compute_modify\s+', Keyword, 'modify_cmd'),
(r'dump\s+', Keyword, 'dump'),
(r'dump_modify\s+', Keyword, 'modify_cmd'),
(r'region\s+', Keyword, 'region'),
(r'^\s*variable\s+', Keyword, 'variable_cmd'),
(r'variable\s+', Keyword, 'variable_cmd'),
(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'create_box\s+', Keyword, 'create_box'),
(r'delete_bonds\s+', Keyword, 'id_cmd'),
(r'displace_atoms\s+', Keyword, 'id_cmd'),
(r'dynamical_matrix\s+', Keyword, 'id_cmd'),
(r'group2ndx\s+', Keyword, 'ndx_cmd'),
(r'ndx2group\s+', Keyword, 'ndx_cmd'),
(r'jump\s+', Keyword, 'jump_cmd'),
(r'label\s+', Keyword, 'jump_cmd'),
(r'next\s+', Keyword, 'id_cmd'),
(r'kim\s+', Keyword, 'kim_cmd'),
(r'uncompute\s+', Keyword, 'id_cmd'),
(r'unfix\s+', Keyword, 'id_cmd'),
(r'undump\s+', Keyword, 'id_cmd'),
(r'velocity\s+', Keyword, 'id_cmd'),
(r'write_coeff\s+', Keyword, 'ndx_cmd'),
(r'write_data\s+', Keyword, 'ndx_cmd'),
(r'write_dump\s+', Keyword, 'write_dump'),
(r'write_restart\s+', Keyword, 'ndx_cmd'),
include('conditionals'),
include('keywords'),
(r'#.*?\n', Comment),
('"', String, 'string'),
@ -69,8 +88,12 @@ class LAMMPSLexer(RegexLexer):
(r'[\+\-\*\^\|\/\!%&=<>]', Operator),
(r'[\~\.\w_:,@\-\/\\0-9]+', Text),
],
'conditionals' : [
(words(('if','else','elif','then'), suffix=r'\b', prefix=r'\b'), Keyword)
]
,
'keywords' : [
(words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword)
(words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^\s*'), Keyword)
]
,
'variable' : [
@ -90,6 +113,10 @@ class LAMMPSLexer(RegexLexer):
('\(', Name.Variable, 'expression'),
('\)', Name.Variable, '#pop'),
],
'modify_cmd' : [
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
default('#pop')
],
'fix' : [
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
(r'\s+', Whitespace, 'group_id'),
@ -121,16 +148,25 @@ class LAMMPSLexer(RegexLexer):
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
default('#pop')
],
'unfix' : [
'create_box' : [
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
(r'\s+', Whitespace, 'group_id'),
default('#pop')
],
'id_cmd' : [
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
default('#pop')
],
'undump' : [
'ndx_cmd' : [
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
default('#pop')
],
'uncompute' : [
(r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
'jump_cmd' : [
(r'[\w_\-\.\[\]]+', Literal.String.Char),
default('#pop')
],
'kim_cmd' : [
(r'[\w_\-\.\[\]]+', Literal.String.Single),
default('#pop')
],
'write_dump' : [

9
doc/utils/sphinx-config/false_positives.txt
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@ -55,6 +55,7 @@ Ai
Aidan
aij
aimd
aip
airebo
Aj
ajaramil
@ -528,6 +529,7 @@ collisional
Columic
colvars
Colvars
COH
COLVARS
comID
Commun
@ -550,6 +552,7 @@ conformational
Connor
conp
conq
const
ConstMatrix
Contrib
cooperativity
@ -1090,6 +1093,7 @@ Fellinger
femtosecond
femtoseconds
fene
Feng
Fennell
fep
FEP
@ -1555,6 +1559,7 @@ intramolecular
ints
inumeric
inv
invariance
invariants
inversed
invertible
@ -1621,6 +1626,7 @@ Izumi
Izvekov
izz
Izz
Jacobian
Jacobsen
Jadhao
Jadhav
@ -2027,6 +2033,7 @@ Marchetti
Marchi
Mariella
Marinica
Markland
Marrink
Marroquin
Marsaglia
@ -3595,6 +3602,7 @@ THz
Tigran
Tij
Tildesley
Timan
timeI
timespan
timestamp
@ -4092,4 +4100,5 @@ zu
zx
zy
Zybin
Zykova
zz