ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'master' into fire

Browse Source
This commit is contained in:
Steve Plimpton
2020-01-14 08:53:40 -07:00
parent 6297c685e8 87b55a5434
commit 95a3abc74e
416 changed files with 45887 additions and 13900 deletions
Download Patch File Download Diff File Expand all files Collapse all files

244
doc/utils/check-styles.py Executable file
View File

@ -0,0 +1,244 @@
#!/usr/bin/env python3
from __future__ import print_function
from glob import glob
from argparse import ArgumentParser
import os, re, sys
parser = ArgumentParser(prog='check-styles.py',
description="Check style table completeness")
parser.add_argument("-v", "--verbose",
action='store_const',
const=True, default=False,
help="Enable verbose output")
parser.add_argument("-d", "--doc",
help="Path to LAMMPS documentation sources")
parser.add_argument("-s", "--src",
help="Path to LAMMPS sources")
args = parser.parse_args()
verbose = args.verbose
src = args.src
doc = args.doc
if not args.src or not args.doc:
parser.print_help()
sys.exit(1)
if not os.path.isdir(src):
sys.exit("LAMMPS source path %s does not exist" % src)
if not os.path.isdir(doc):
sys.exit("LAMMPS documentation source path %s does not exist" % doc)
headers = glob(os.path.join(src, '*', '*.h'))
headers += glob(os.path.join(src, '*.h'))
angle = {}
atom = {}
body = {}
bond = {}
command = {}
compute = {}
dihedral = {}
dump = {}
fix = {}
improper = {}
integrate = {}
kspace = {}
minimize = {}
pair = {}
reader = {}
region = {}
upper = re.compile("[A-Z]+")
gpu = re.compile("(.+)/gpu$")
intel = re.compile("(.+)/intel$")
kokkos = re.compile("(.+)/kk$")
kokkos_skip = re.compile("(.+)/kk/(host|device)$")
omp = re.compile("(.+)/omp$")
opt = re.compile("(.+)/opt$")
removed = re.compile("(.+)Deprecated$")
def register_style(list,style,info):
if style in list.keys():
list[style]['gpu'] += info['gpu']
list[style]['intel'] += info['intel']
list[style]['kokkos'] += info['kokkos']
list[style]['omp'] += info['omp']
list[style]['opt'] += info['opt']
list[style]['removed'] += info['removed']
else:
list[style] = info
def add_suffix(list,style):
suffix = ""
if list[style]['gpu']:
suffix += 'g'
if list[style]['intel']:
suffix += 'i'
if list[style]['kokkos']:
suffix += 'k'
if list[style]['omp']:
suffix += 'o'
if list[style]['opt']:
suffix += 't'
if suffix:
return style + ' (' + suffix + ')'
else:
return style
def check_style(file,dir,pattern,list,name,suffix=False,skip=()):
f = os.path.join(dir, file)
fp = open(f)
text = fp.read()
fp.close()
matches = re.findall(pattern,text,re.MULTILINE)
counter = 0
for c in list.keys():
# known undocumented aliases we need to skip
if c in skip: continue
s = c
if suffix: s = add_suffix(list,c)
if not s in matches:
if not list[c]['removed']:
print("%s style entry %s" % (name,s),
"is missing or incomplete in %s" % file)
counter += 1
return counter
for h in headers:
if verbose: print("Checking ", h)
fp = open(h)
text = fp.read()
fp.close()
matches = re.findall("(.+)Style\((.+),(.+)\)",text,re.MULTILINE)
for m in matches:
# skip over internal styles w/o explicit documentation
style = m[1]
if upper.match(style):
continue
# detect, process, and flag suffix styles:
info = { 'kokkos': 0, 'gpu': 0, 'intel': 0, \
'omp': 0, 'opt': 0, 'removed': 0 }
suffix = kokkos_skip.match(style)
if suffix:
continue
suffix = gpu.match(style)
if suffix:
style = suffix.groups()[0]
info['gpu'] = 1
suffix = intel.match(style)
if suffix:
style = suffix.groups()[0]
info['intel'] = 1
suffix = kokkos.match(style)
if suffix:
style = suffix.groups()[0]
info['kokkos'] = 1
suffix = omp.match(style)
if suffix:
style = suffix.groups()[0]
info['omp'] = 1
suffix = opt.match(style)
if suffix:
style = suffix.groups()[0]
info['opt'] = 1
deprecated = removed.match(m[2])
if deprecated:
info['removed'] = 1
# register style and suffix flags
if m[0] == 'Angle':
register_style(angle,style,info)
elif m[0] == 'Atom':
register_style(atom,style,info)
elif m[0] == 'Body':
register_style(body,style,info)
elif m[0] == 'Bond':
register_style(bond,style,info)
elif m[0] == 'Command':
register_style(command,style,info)
elif m[0] == 'Compute':
register_style(compute,style,info)
elif m[0] == 'Dihedral':
register_style(dihedral,style,info)
elif m[0] == 'Dump':
register_style(dump,style,info)
elif m[0] == 'Fix':
register_style(fix,style,info)
elif m[0] == 'Improper':
register_style(improper,style,info)
elif m[0] == 'Integrate':
register_style(integrate,style,info)
elif m[0] == 'KSpace':
register_style(kspace,style,info)
elif m[0] == 'Minimize':
register_style(minimize,style,info)
elif m[0] == 'Pair':
register_style(pair,style,info)
elif m[0] == 'Reader':
register_style(reader,style,info)
elif m[0] == 'Region':
register_style(region,style,info)
else:
print("Skipping over: ",m)
print("""Parsed style names w/o suffixes from C++ tree in %s:
Angle styles: %3d Atom styles: %3d
Body styles: %3d Bond styles: %3d
Command styles: %3d Compute styles: %3d
Dihedral styles: %3d Dump styles: %3d
Fix styles: %3d Improper styles: %3d
Integrate styles: %3d Kspace styles: %3d
Minimize styles: %3d Pair styles: %3d
Reader styles: %3d Region styles: %3d""" \
% (src, len(angle), len(atom), len(body), len(bond), \
len(command), len(compute), len(dihedral), len(dump), \
len(fix), len(improper), len(integrate), len(kspace), \
len(minimize), len(pair), len(reader), len(region)))
counter = 0
counter += check_style('Commands_all.rst',doc,":doc:`(.+) <.+>`",
command,'Command',suffix=False)
counter += check_style('Commands_compute.rst',doc,":doc:`(.+) <compute.+>`",
compute,'Compute',suffix=True)
counter += check_style('compute.rst',doc,":doc:`(.+) <compute.+>` -",
compute,'Compute',suffix=False)
counter += check_style('Commands_fix.rst',doc,":doc:`(.+) <fix.+>`",
fix,'Fix',skip=('python'),suffix=True)
counter += check_style('fix.rst',doc,":doc:`(.+) <fix.+>` -",
fix,'Fix',skip=('python'),suffix=False)
counter += check_style('Commands_pair.rst',doc,":doc:`(.+) <pair.+>`",
pair,'Pair',skip=('meam','lj/sf'),suffix=True)
counter += check_style('pair_style.rst',doc,":doc:`(.+) <pair.+>` -",
pair,'Pair',skip=('meam','lj/sf'),suffix=False)
counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <bond.+>`",
bond,'Bond',suffix=True)
counter += check_style('bond_style.rst',doc,":doc:`(.+) <bond.+>` -",
bond,'Bond',suffix=False)
counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <angle.+>`",
angle,'Angle',suffix=True)
counter += check_style('angle_style.rst',doc,":doc:`(.+) <angle.+>` -",
angle,'Angle',suffix=False)
counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <dihedral.+>`",
dihedral,'Dihedral',suffix=True)
counter += check_style('dihedral_style.rst',doc,":doc:`(.+) <dihedral.+>` -",
dihedral,'Dihedral',suffix=False)
counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <improper.+>`",
improper,'Improper',suffix=True)
counter += check_style('improper_style.rst',doc,":doc:`(.+) <improper.+>` -",
improper,'Improper',suffix=False)
counter += check_style('Commands_kspace.rst',doc,":doc:`(.+) <kspace_style>`",
kspace,'KSpace',suffix=True)
if counter:
print("Found %d issue(s) with style lists" % counter)

2
doc/utils/converters/lammpsdoc/rst_anchor_check.py
View File

@ -42,7 +42,7 @@ def main():
else:
anchors[label] = [(filename, line_number+1)]
print("found %d anchor labels" % len(anchors))
print("Found %d anchor labels" % len(anchors))
count = 0

8
doc/utils/sphinx-config/conf.py
View File

@ -20,6 +20,7 @@ import os
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#sys.path.insert(0, os.path.abspath('.'))
sys.path.append(os.path.join(os.path.dirname(__file__), '../../src/_ext'))
# -- General configuration ------------------------------------------------
@ -30,7 +31,10 @@ import os
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.mathjax', 'sphinx.ext.imgmath'
'sphinx.ext.mathjax',
'sphinx.ext.imgmath',
'sphinx.ext.autodoc',
'table_from_list',
]
# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
# yet we can no longer use Sphinx 15.x, since that breaks with
@ -323,3 +327,5 @@ import LAMMPSLexer
from sphinx.highlighting import lexers
lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)
sys.path.append(os.path.join(os.path.dirname(__file__), '../../../python'))

10
doc/utils/sphinx-config/false_positives.txt
View File

@ -214,6 +214,7 @@ Berne
Bertotti
Bessarab
Beutler
Bext
bgq
Bh
Biersack
@ -1048,6 +1049,7 @@ Gunsteren
Gunzenmuller
Guo
gw
gyromagnetic
gz
gzipped
Haak
@ -1068,6 +1070,7 @@ Haswell
Haugk
Hayoun
Hayre
hbar
hbcut
hbn
hbnewflag
@ -1146,6 +1149,7 @@ ico
icosahedral
idealgas
IDR
idx
ielement
ieni
ifdefs
@ -1412,6 +1416,7 @@ Lammps
LAMMPS
lammpsplot
Lamoureux
Lande
Landron
langevin
Langevin
@ -1784,6 +1789,7 @@ mtk
Mtotal
muB
Muccioli
mui
Mukherjee
Mulders
multi
@ -2084,7 +2090,9 @@ Ouyang
overlayed
Ovito
oxdna
oxrna
oxDNA
oxRNA
padua
Padua
palegoldenrod
@ -2481,6 +2489,8 @@ Runge
runtime
Rutuparna
rx
ry
rz
Ryckaert
Rycroft
Rydbergs