merged in current master
This commit is contained in:
Steve Plimpton
57
doc/utils/sphinx-config/LAMMPSLexer.py
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57
doc/utils/sphinx-config/LAMMPSLexer.py
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@ -0,0 +1,57 @@
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from pygments.lexer import RegexLexer, words
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from pygments.token import *
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LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
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"balance", "bond_coeff", "bond_style", "bond_write", "boundary", "box",
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"change_box", "clear", "comm_modify", "comm_style", "compute",
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"compute_modify", "create_atoms", "create_bonds", "create_box", "delete_atoms",
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"delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
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"displace_atoms", "dump", "dump_modify", "dynamical_matrix", "echo", "fix",
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"fix_modify", "group", "group2ndx", "hyper", "if", "improper_coeff",
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"improper_style", "include", "info", "jump", "kim_init", "kim_interactions",
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"kim_param", "kim_query", "kspace_modify", "kspace_style", "label", "lattice",
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"log", "mass", "message", "minimize", "min_modify", "min_style", "molecule",
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"ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next",
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"package", "pair_coeff", "pair_modify", "pair_style", "pair_write",
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"partition", "prd", "print", "processors", "python", "quit", "read_data",
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"read_dump", "read_restart", "region", "replicate", "rerun", "reset_ids",
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"reset_timestep", "restart", "run", "run_style", "server", "set", "shell",
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"special_bonds", "suffix", "tad", "temper", "temper/grem", "temper/npt",
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"thermo", "thermo_modify", "thermo_style", "then", "third_order", "timer", "timestep",
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"uncompute", "undump", "unfix", "units", "variable", "velocity", "write_coeff",
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"write_data", "write_dump", "write_restart")
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class LAMMPSLexer(RegexLexer):
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name = 'LAMMPS'
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tokens = {
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'root': [
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(words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword),
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(r'#.*?\n', Comment),
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('"', String, 'string'),
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('\'', String, 'single_quote_string'),
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(r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number),
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('\$?\(', Name.Variable, 'expression'),
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('\$\{', Name.Variable, 'variable'),
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(r'[\w_\.\[\]]+', Name),
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(r'\$[\w_]+', Name.Variable),
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(r'\s+', Whitespace),
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(r'[\+\-\*\/&=<>]', Operator),
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],
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'variable' : [
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('[^\}]+', Name.Variable),
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('\}', Name.Variable, '#pop'),
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],
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'string' : [
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('[^"]+', String),
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('"', String, '#pop'),
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],
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'single_quote_string' : [
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('[^\']+', String),
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('\'', String, '#pop'),
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],
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'expression' : [
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('[^\(\)]+', Name.Variable),
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('\(', Name.Variable, 'expression'),
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('\)', Name.Variable, '#pop'),
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]
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}
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@ -20,6 +20,7 @@ import os
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#sys.path.insert(0, os.path.abspath('.'))
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sys.path.append(os.path.join(os.path.dirname(__file__), '../../src/_ext'))
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# -- General configuration ------------------------------------------------
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@ -31,6 +32,9 @@ import os
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# ones.
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extensions = [
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'sphinx.ext.mathjax',
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'sphinx.ext.imgmath',
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'sphinx.ext.autodoc',
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'table_from_list',
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]
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# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
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# yet we can no longer use Sphinx 15.x, since that breaks with
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@ -201,6 +205,11 @@ htmlhelp_basename = 'LAMMPSdoc'
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html_add_permalinks = ''
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if 'epub' in sys.argv:
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html_math_renderer = 'imgmath'
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else:
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html_math_renderer = 'mathjax'
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# -- Options for LaTeX output ---------------------------------------------
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latex_elements = {
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@ -312,3 +321,11 @@ if spelling_spec:
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spelling_lang='en_US'
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spelling_word_list_filename='false_positives.txt'
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sys.path.append(os.path.join(os.path.dirname(__file__), '.'))
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import LAMMPSLexer
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from sphinx.highlighting import lexers
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lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)
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sys.path.append(os.path.join(os.path.dirname(__file__), '../../../python'))
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@ -71,6 +71,7 @@ AlO
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Alonso
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amap
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Amatrix
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AMD
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amino
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Amirjalayer
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Amit
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@ -108,6 +109,7 @@ Archlinux
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arcsin
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arg
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args
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arrhenius
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Arun
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arXiv
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asin
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@ -162,6 +164,7 @@ azimuthal
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Azuri
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ba
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Babadi
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Babaei
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backcolor
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Baczewski
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Bagi
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@ -210,6 +213,7 @@ Berne
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Bertotti
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Bessarab
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Beutler
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Bext
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bgq
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Bh
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Biersack
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@ -275,10 +279,12 @@ Broadwell
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Broglie
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brownian
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brownw
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Broyden
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Bryantsev
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Btarget
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btype
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buckPlusAttr
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builtin
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Bulatov
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Bureekaew
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burlywood
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@ -305,6 +311,7 @@ Cavium
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Cawkwell
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cbecker
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ccache
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ccachepiecewise
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ccmake
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ccNspecies
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CCu
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@ -408,6 +415,8 @@ computable
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compute
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concat
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cond
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conda
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Conda
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Condens
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conf
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config
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@ -516,6 +525,7 @@ Dasgupta
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dashpot
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dat
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datafile
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datatype
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datums
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Davidchack
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Daw
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@ -622,6 +632,7 @@ Doye
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dpd
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DPD
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dpdTheta
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dphi
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DPhil
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dr
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dR
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@ -705,6 +716,7 @@ Eike
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eim
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eimp
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Eindhoven
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Eisenforschung
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Ejtehadi
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El
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elaplong
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@ -778,6 +790,7 @@ erotate
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Ertas
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ervel
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Espanol
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eskm
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esu
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esub
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esw
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@ -922,6 +935,7 @@ funcs
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functionalities
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functionals
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funroll
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fuer
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fx
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fy
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fz
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@ -986,6 +1000,7 @@ gmask
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Gmask
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gneb
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GNEB
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Goldfarb
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googlemail
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Gordan
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GPa
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@ -1028,6 +1043,7 @@ Gunsteren
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Gunzenmuller
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Guo
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gw
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gyromagnetic
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gz
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gzipped
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Haak
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@ -1047,6 +1063,7 @@ Haswell
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Haugk
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Hayoun
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Hayre
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hbar
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hbcut
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hbn
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hbnewflag
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@ -1166,6 +1183,7 @@ initio
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initializations
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InP
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inregion
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Institut
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integrators
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Integrators
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intel
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@ -1242,6 +1260,7 @@ Jacobsen
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jagreat
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Jalalvand
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james
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Janssen
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Janssens
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Jaramillo
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Jarzynski
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@ -1325,6 +1344,7 @@ Khersonskii
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Khrapak
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Khvostov
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Ki
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Kikugawa
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kim
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kJ
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kk
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@ -1386,6 +1406,7 @@ Lammps
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LAMMPS
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lammpsplot
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Lamoureux
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Lande
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Landron
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langevin
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Langevin
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@ -1403,6 +1424,7 @@ Laupretre
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lavenderblush
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lawngreen
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lB
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lbfgs
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lbl
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LBtype
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lcbop
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@ -1503,6 +1525,7 @@ logfreq
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logicals
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Lomdahl
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Lond
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lookup
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lookups
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Lookups
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LoopVar
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@ -1532,6 +1555,7 @@ Mackay
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Mackrodt
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Macromolecules
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macroparticle
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macOS
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Madura
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Magda
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Magdeburg
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@ -1576,6 +1600,8 @@ Materias
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mathbf
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matlab
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matplotlib
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Matsubara
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Mattice
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Mattox
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Mattson
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maxangle
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@ -1753,6 +1779,7 @@ mtk
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Mtotal
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muB
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Muccioli
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mui
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Mukherjee
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Mulders
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multi
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@ -1998,6 +2025,7 @@ Nz
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ocl
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octahedral
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octants
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Ohara
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ohenrich
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ok
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Okabe
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@ -2028,6 +2056,7 @@ openmp
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openmpi
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opls
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Oppelstrup
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optimizations
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orangered
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organometallic
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orientational
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@ -2039,6 +2068,7 @@ Orsi
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ortho
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orthonormal
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orthorhombic
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oso
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ot
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Otype
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Ouldridge
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@ -2049,7 +2079,9 @@ Ouyang
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overlayed
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Ovito
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oxdna
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oxrna
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oxDNA
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oxRNA
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padua
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Padua
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palegoldenrod
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@ -2123,6 +2155,7 @@ ph
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Phillpot
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phiphi
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phonon
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phonons
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phophorous
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phosphide
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Phs
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@ -2136,6 +2169,7 @@ picograms
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picosecond
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picoseconds
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pid
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piecewise
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Pieniazek
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Pieter
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pimd
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@ -2269,6 +2303,7 @@ qoffload
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qopenmp
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qoverride
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qtb
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quadratically
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quadrupolar
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Quant
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quartic
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@ -2418,6 +2453,7 @@ Rodrigues
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Rohart
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Ronchetti
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Rosati
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Rosenberger
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Rossky
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rosybrown
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rotationally
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@ -2478,10 +2514,12 @@ Schulten
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Schunk
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Schuring
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Schwen
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screenshots
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Scripta
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sdk
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sdpd
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SDPD
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se
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seagreen
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Secor
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sectoring
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@ -2508,6 +2546,7 @@ setvel
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sfftw
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Sg
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Shan
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Shanno
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shapex
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shapey
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shapez
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@ -2575,6 +2614,7 @@ Snodin
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Sodani
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Soderlind
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solvated
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solvation
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Sorensen
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soundspeed
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Souza
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@ -2659,6 +2699,7 @@ Sunderland
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superset
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supersphere
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Supinski
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Surblys
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surfactants
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Suter
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Sutmann
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@ -2935,6 +2976,7 @@ vectorial
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vectorization
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Vectorization
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vectorized
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Vegt
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vel
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Verlag
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verlet
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@ -3134,3 +3176,4 @@ zx
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zy
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Zybin
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zz
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Zm
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