def main():
packages = discover()
# Write new/updated rst files if needed
fns_rst = []
for package, modules in sorted(packages.iteritems()):
# write the new file to a StringIO
f = StringIO()
print >> f, '..'
print >> f, ' This file is automatically generated. Do not make '
print >> f, ' changes as these will be overwritten. Rather edit '
print >> f, ' the docstrings in the source code.'
print >> f
underline('``%s`` -- %s' % (package, get_first_docline(package)), '#', f)
print >> f
for module in sorted(modules):
full = package + '.' + module
underline('``%s`` -- %s' % (full, get_first_docline(full)), '=', f)
print >> f, '.. automodule::', full
print >> f, ' :members:'
print >> f
print >> f
# write if the contents have changed
fn_rst = 'rg_%s.rst' % package.replace('.', '_')
fns_rst.append(fn_rst)
write_if_changed(fn_rst, f.getvalue())
# Remove other rst files
for fn_rst in glob('rg_yaff*.rst'):
if fn_rst not in fns_rst:
print 'Removing %s' % fn_rst
os.remove(fn_rst)
def main():
packages = discover()
# Write new/updated rst files if needed
fns_rst = []
for package, modules in sorted(packages.iteritems()):
# write the new file to a StringIO
f1 = StringIO()
write_disclaimer(f1)
underline('``%s`` -- %s' % (package, get_first_docline(package)), '#',
f1)
print >> f1
print >> f1, '.. automodule::', package
print >> f1, ' :members:'
print >> f1
print >> f1, '.. toctree::'
print >> f1, ' :maxdepth: 1'
print >> f1, ' :numbered:'
print >> f1
for module in modules:
f2 = StringIO()
write_disclaimer(f2)
if module.endswith('.h'):
#full = package + '/' + module
fn_h = package.replace('.', '/') + '/' + module
underline('``%s`` -- %s' % (fn_h, get_first_doxygenline(fn_h)),
'#', f2)
print >> f2, '.. doxygenfile::', fn_h
print >> f2, ' :project: horton'
print >> f2
print >> f2
else:
full = package + '.' + module
underline('``%s`` -- %s' % (full, get_first_docline(full)),
'#', f2)
print >> f2, '.. automodule::', full
print >> f2, ' :members:'
print >> f2
print >> f2
# write if the contents have changed
rst_name = 'mod_%s_%s' % (package.replace(
'.', '_'), module.replace('.', '_'))
fn2_rst = 'lib/%s.rst' % rst_name
fns_rst.append(fn2_rst)
write_if_changed(fn2_rst, f2.getvalue())
print >> f1, ' %s' % rst_name
# write if the contents have changed
fn1_rst = 'lib/pck_%s.rst' % package.replace('.', '_')
fns_rst.append(fn1_rst)
write_if_changed(fn1_rst, f1.getvalue())
# Remove other rst files
for fn_rst in glob('lib/*.rst'):
if fn_rst not in fns_rst:
print 'Removing %s' % fn_rst
os.remove(fn_rst)
def main():
packages = discover()
# Write new/updated rst files if needed
fns_rst = []
for package, modules in sorted(packages.iteritems()):
# write the new file to a StringIO
f1 = StringIO()
write_disclaimer(f1)
underline('``%s`` -- %s' % (package, get_first_docline(package)), '#', f1)
print >> f1
print >> f1, '.. automodule::', package
print >> f1, ' :members:'
print >> f1
print >> f1, '.. toctree::'
print >> f1, ' :maxdepth: 1'
print >> f1, ' :numbered:'
print >> f1
for module in modules:
f2 = StringIO()
write_disclaimer(f2)
if module.endswith('.h'):
#full = package + '/' + module
fn_h = package.replace('.', '/') + '/' + module
underline('``%s`` -- %s' % (fn_h, get_first_doxygenline(fn_h)), '#', f2)
print >> f2, '.. doxygenfile::', fn_h
print >> f2, ' :project: horton'
print >> f2
print >> f2
else:
full = package + '.' + module
underline('``%s`` -- %s' % (full, get_first_docline(full)), '#', f2)
print >> f2, '.. automodule::', full
print >> f2, ' :members:'
print >> f2
print >> f2
# write if the contents have changed
rst_name = 'mod_%s_%s' % (package.replace('.', '_'), module.replace('.', '_'))
fn2_rst = 'lib/%s.rst' % rst_name
fns_rst.append(fn2_rst)
write_if_changed(fn2_rst, f2.getvalue())
print >> f1, ' %s' % rst_name
# write if the contents have changed
fn1_rst = 'lib/pck_%s.rst' % package.replace('.', '_')
fns_rst.append(fn1_rst)
write_if_changed(fn1_rst, f1.getvalue())
# Remove other rst files
for fn_rst in glob('lib/*.rst'):
if fn_rst not in fns_rst:
print 'Removing %s' % fn_rst
os.remove(fn_rst)
def main():
packages = discover()
# Write new/updated rst files if needed
fns_rst = []
for package, modules in sorted(packages.iteritems()):
# write the new file to a StringIO
f = StringIO()
print >> f, '..'
print >> f, ' This file is automatically generated. Do not make '
print >> f, ' changes as these will be overwritten. Rather edit '
print >> f, ' the documentation in the source code.'
print >> f
underline('``%s`` -- %s' % (package, get_first_docline(package)), '#',
f)
print >> f
for module in modules:
if module.endswith('.h'):
#full = package + '/' + module
fn_h = package.replace('.', '/') + '/' + module
underline('``%s``' % fn_h, '=', f)
print >> f, '.. doxygenfile::', fn_h
print >> f, ' :project: horton'
print >> f
print >> f
else:
full = package + '.' + module
underline('``%s`` -- %s' % (full, get_first_docline(full)),
'=', f)
print >> f, '.. automodule::', full
print >> f, ' :members:'
print >> f
print >> f
# write if the contents have changed
fn_rst = 'lib/%s.rst' % package.replace('.', '_')
fns_rst.append(fn_rst)
write_if_changed(fn_rst, f.getvalue())
# Remove other rst files
for fn_rst in glob('lib/*.rst'):
if fn_rst not in fns_rst:
print 'Removing %s' % fn_rst
os.remove(fn_rst)
def main():
packages = discover()
# Write new/updated rst files if needed
fns_rst = []
for package, modules in sorted(packages.iteritems()):
print package, modules
# write the new file to a StringIO
f = StringIO()
print >> f, '..'
print >> f, ' This file is automatically generated. Do not make '
print >> f, ' changes as these will be overwritten. Rather edit '
print >> f, ' the docstrings in the source code.'
print >> f
underline('``%s`` -- %s' % (package, get_first_docline(package)), '#',
f)
print >> f
for module in sorted(modules):
full = package + '.' + module
print >> f, '.. _seclab_rg_%s_%s:'
print >> f
underline('``%s`` -- %s' % (full, get_first_docline(full)), '=', f)
print >> f, '.. automodule::', full
print >> f, ' :members:'
print >> f
print >> f
# write if the contents have changed
fn_rst = 'rg_%s.rst' % package.replace('.', '_')
fns_rst.append(fn_rst)
write_if_changed(fn_rst, f.getvalue())
fns_rst.append('rg_qff.rst')
fns_rst.append('rg_qffinputei.rst')
# Remove other rst files
for fn_rst in glob('rg_*.rst'):
if fn_rst not in fns_rst:
print 'Removing %s' % fn_rst
os.remove(fn_rst)
def main():
packages = discover()
# Write new/updated rst files if needed
fns_rst = []
for package, modules in sorted(packages.items()):
# write the new file to a StringIO
f = StringIO()
f.write(u'..\n')
f.write(u' This file is automatically generated. Do not make\n')
f.write(u' changes as these will be overwritten. Rather edit\n')
f.write(u' the docstrings in the source code.\n')
f.write(u'\n')
underline('``%s`` -- %s' % (package, get_first_docline(package)), '#',
f)
f.write(u'\n')
for module in sorted(modules):
f.write(u'\n')
f.write(u'\n')
full = package + '.' + module
underline(u'``%s`` -- %s' % (full, get_first_docline(full)), '=',
f)
f.write(u'.. automodule:: ' + full + '\n')
f.write(u' :members:\n')
# write if the contents have changed
fn_rst = 'rg_%s.rst' % package.replace('.', '_')
fns_rst.append(fn_rst)
write_if_changed(fn_rst, f.getvalue())
# Remove other rst files
for fn_rst in glob('rg_yaff*.rst'):
if fn_rst not in fns_rst:
print('Removing %s' % fn_rst)
os.remove(fn_rst)
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>
#
# --
from cStringIO import StringIO
from horton.log import Biblio
from horton.context import context
from common import write_if_changed
biblio = Biblio(context.get_fn('references.bib'))
def key(item):
return int(item[1].tags['year']), item[0]
f = StringIO()
print >> f, 'Literature'
print >> f, '##########'
items = biblio._records.items()
items.sort(key=key)
for key, reference in items:
print >> f
print >> f, '.. [%s] %s' % (key, reference.format_rst())
s = f.getvalue()
write_if_changed('tech_ref_literature.rst', s)
from cStringIO import StringIO
import os
from horton.periodic import periodic
from horton.log import log
from horton.gbasis.gobasis import go_basis_families_list
from common import write_rst_table, write_if_changed
log.set_level(log.silent)
table = [['Basis set name', 'Supported elements']]
for family in go_basis_families_list:
family.load()
numbers = sorted(family.basis_atom_map.keys())
s = []
for i in xrange(len(numbers)):
if (i > 0 and i < len(numbers)-1) and numbers[i-1] == numbers[i]-1 \
and numbers[i+1] == numbers[i]+1:
if s[-1] != '-':
s.append('-')
else:
s.append(periodic[numbers[i]].symbol)
range_str = ' '.join(s).replace(' - ', '--').replace(' ', ', ')
table.append([family.name, range_str])
f = StringIO()
write_rst_table(f, table, nhead=1)
write_if_changed('basis.rst.inc', f.getvalue())
npoint = None
elements.add((int(words[0]), int(words[1])))
grids = sorted(grids)
alts = ['coarse', 'medium', 'fine', 'veryfine', 'ultrafine', 'insane']
elements = sorted(elements)
f = StringIO()
def print_markers():
print >> f, '======= === ====', ' '.join(['========='] * len(grids))
print_markers()
print >> f, 'Element Z Zeff', ' '.join([grid.ljust(9) for grid in grids])
print >> f, '\ \ \ ', ' '.join([alt.ljust(9) for alt in alts])
print_markers()
for z, zeff in elements:
print >> f, '%7s %3i %4i' % (periodic[z].symbol, z, zeff),
for grid in grids:
npoint = npoints.get((z, zeff, grid))
if npoint is None:
print >> f, '-- ',
else:
print >> f, '%9i' % npoint,
print >> f
print_markers()
write_if_changed('grids.rst.inc', f.getvalue())
def main():
"""Main program."""
# Load dependency information -> libxc version
with open('../dependencies.json') as f:
dependencies = json.load(f)
# Order does not matter here. Just make it easy to look things up
dependencies = dict((d['name'], d) for d in dependencies)
libxc_version = dependencies['libxc']['version_ci']
# find the qaworkdir
qaworkdir = os.getenv('QAWORKDIR')
if qaworkdir is None:
qaworkdir = '../qaworkdir'
# find all the functional keys by processing funcs_key.c
keys = []
with open('%s/cached/libxc-%s/funcs_key.c' %
(qaworkdir, libxc_version)) as f:
for line in f:
if line.startswith('{'):
words = line.strip()[1:-3].split(',')
key = words[0][1:-1]
if len(key) > 0:
keys.append(key)
# sort the functions
splitkeys = []
for key in keys:
words = key.split('_')
if words[0] == 'hyb':
prefix = '_'.join(words[:2])
mid = words[2]
suffix = '_'.join(words[3:])
else:
prefix = words[0]
mid = words[1]
suffix = '_'.join(words[2:])
splitkeys.append((prefix, mid, suffix))
splitkeys.sort(cmp=cmp_splitkey)
keys = []
for splitkey in splitkeys:
splitkey = [part for part in splitkey if len(part) > 0]
keys.append('_'.join(splitkey))
# make a rst table of all functionals
s = StringIO()
print >> s, '.. _ref_functionals:'
print >> s
print >> s, 'LibXC Functionals'
print >> s, '#################'
print >> s
print >> s, 'The following functionals are available in HORTON through `LibXC'
print >> s, '<http://www.tddft.org/programs/octopus/wiki/index.php/Libxc>`_ %s.' % \
libxc_version
print >> s, '[marques2012]_'
print >> s
for key in keys:
try:
w = ULibXCWrapper(key)
print >> s, '**%s**' % key
print >> s, ' | %s' % w.name
for line in w.refs.split('\n'):
line = line.strip()
if len(line) > 0:
print >> s, ' | *%s*' % line
print >> s
except ValueError:
# A bug in libxc ...
print 'FAILED to load functional', key
write_if_changed('tech_ref_functionals.rst', s.getvalue())
words = line.strip()[1:-3].split(',')
key = words[0][1:-1]
if len(key) > 0 and 'mgga' not in key:
keys.append(key)
# make a rst table of all functionals
from horton import LibXCWrapper
from cStringIO import StringIO
from common import write_if_changed
s = StringIO()
print >> s, '.. _ref_functionals:'
print >> s
print >> s, 'LibXC Functionals'
print >> s, '#################'
print >> s
print >> s, 'The following functionals are available in Horton through `LibXC <http://www.tddft.org/programs/octopus/wiki/index.php/Libxc>`_ %s. [marques2012]_' % libxc_version
print >> s, '(The MGGA functionals are not supported yet in Horton.)'
print >> s
for key in keys:
print >> s, '**%s**' % key
w = LibXCWrapper(key)
print >> s, ' | %s' % w.name
for line in w.refs.split('\n'):
print >> s, ' | *%s*' % line
print >> s
write_if_changed('ref_functionals.rst', s.getvalue())
from glob import glob
from cStringIO import StringIO
import json, os
from common import write_rst_table, write_if_changed
cases = []
for fn_py in sorted(glob('../data/examples/hf_dft/*.py')):
with open(fn_py) as f:
s = ''
for line in f:
if line.startswith('#JSON'):
s += line[5:]
if len(s) == 0:
raise RuntimeError(
'Could not find JSON line in HF/DFT example script.')
meta = json.loads(s)
case = [
meta['difficulty'],
os.path.basename(fn_py), meta['lot'], meta['scf'], meta['description']
]
cases.append(case)
cases.sort()
table = [['File name', 'LOT', 'SCF', 'Description']
] + [case[1:] for case in cases]
f = StringIO()
write_rst_table(f, table)
write_if_changed('hf_dft_examples.rst.inc', f.getvalue())
npoint = int(line.split()[-1])
words = line.split()
if line[0] != '#' and len(words) == 2:
assert isinstance(npoint, int)
npoints[int(words[0]), int(words[1]), grid] = npoint
npoint = None
elements.add((int(words[0]), int(words[1])))
grids = sorted(grids)
alts = ['coarse', 'medium', 'fine', 'veryfine', 'ultrafine', 'insane']
elements = sorted(elements)
table = [
['Element', 'Z', 'Zeff'] + grids,
[' ', ' ', ' '] + alts,
]
for z, zeff in elements:
row = [periodic[z].symbol, str(z), str(zeff)]
for grid in grids:
npoint = npoints.get((z, zeff, grid))
if npoint is None:
row.append('--')
else:
row.append(str(npoint))
table.append(row)
f = StringIO()
write_rst_table(f, table, nhead=2)
write_if_changed('grids.rst.inc', f.getvalue())
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>
#
# --
from cStringIO import StringIO
from horton.log import Biblio
from horton.context import context
from common import write_if_changed
biblio = Biblio(context.get_fn('references.bib'))
def key(item):
return int(item[1].tags['year']), item[0]
f = StringIO()
print >> f, 'Literature'
print >> f, '##########'
items = biblio._records.items()
items.sort(key=key)
for key, reference in items:
print >> f
print >> f, '.. [%s] %s' % (key, reference.format_rst())
s = f.getvalue()
write_if_changed('tech_ref_literature.rst', s)
def main():
"""Main program."""
# Load dependency information -> libxc version
with open('../dependencies.json') as f:
dependencies = json.load(f)
# Order does not matter here. Just make it easy to look things up
dependencies = dict((d['name'], d) for d in dependencies)
libxc_version = dependencies['libxc']['version_ci']
# find the qaworkdir
qaworkdir = os.getenv('QAWORKDIR')
if qaworkdir is None:
qaworkdir = '../qaworkdir'
# find all the functional keys by processing funcs_key.c
keys = []
with open('%s/cached/libxc-%s/funcs_key.c' % (qaworkdir, libxc_version)) as f:
for line in f:
if line.startswith('{'):
words = line.strip()[1:-3].split(',')
key = words[0][1:-1]
if len(key) > 0:
keys.append(key)
# sort the functions
splitkeys = []
for key in keys:
words = key.split('_')
if words[0] == 'hyb':
prefix = '_'.join(words[:2])
mid = words[2]
suffix = '_'.join(words[3:])
else:
prefix = words[0]
mid = words[1]
suffix = '_'.join(words[2:])
splitkeys.append((prefix, mid, suffix))
splitkeys.sort(cmp=cmp_splitkey)
keys = []
for splitkey in splitkeys:
splitkey = [part for part in splitkey if len(part) > 0]
keys.append('_'.join(splitkey))
# make a rst table of all functionals
s = StringIO()
print >> s, '.. _ref_functionals:'
print >> s
print >> s, 'LibXC Functionals'
print >> s, '#################'
print >> s
print >> s, 'The following functionals are available in HORTON through `LibXC'
print >> s, '<http://www.tddft.org/programs/octopus/wiki/index.php/Libxc>`_ %s.' % \
libxc_version
print >> s, '[marques2012]_'
print >> s
for key in keys:
try:
w = ULibXCWrapper(key)
print >> s, '**{}**: {}'.format(key, w.name)
print >> s
for ref, doi, _biblio in w.refs:
print >> s, ' | {}'.format(ref),
if len(doi) > 0:
print >> s, ' https://doi.org/{}'.format(doi)
else:
print >> s
print >> s
except ValueError:
# A bug in libxc ...
print 'FAILED to load functional', key
write_if_changed('tech_ref_functionals.rst', s.getvalue())
# along with this program; if not, see <http://www.gnu.org/licenses/>
#
# --
'''Update the table with HF/DFT examples based on files in data/examples/hf_dft.'''
from glob import glob
from cStringIO import StringIO
import json, os
from common import write_rst_table, write_if_changed
cases = []
for fn_py in sorted(glob('../data/examples/hf_dft/*.py')):
with open(fn_py) as f:
s = ''
for line in f:
if line.startswith('#JSON'):
s += line[5:]
if len(s) == 0:
raise RuntimeError('Could not find JSON line in HF/DFT example script.')
meta = json.loads(s)
case = [meta['difficulty'], os.path.basename(fn_py), meta['lot'],
meta['scf'], meta['description']]
cases.append(case)
cases.sort()
table = [['File name', 'LOT', 'SCF', 'Description']] + [case[1:] for case in cases]
f = StringIO()
write_rst_table(f, table)
write_if_changed('hf_dft_examples.rst.inc', f.getvalue())