def make_command(args):
a = parser.parse_args(args)
if a.pot == "usp":
usp_pot = True
else:
usp_pot = False
for source in a.source:
task = NMRTask(source=source,
num_cores=a.num_cores,
queue=a.queue,
xc_functional=a.xc_functional,
cut_off_energy=a.cut_off_energy,
usp_pot=usp_pot,
pot_type=a.pot_type,
efg_only=a.efg_only)
source_dir, source_name = calc_from_path(source)
target_dir = os.path.join(a.target_dir, source_name)
if not os.path.isdir(target_dir):
os.mkdir(target_dir)
task.make(target_dir)
def make_command(args):
a = parser.parse_args(args)
if a.pot == "usp":
usp_pot = True
else:
usp_pot = False
for source in a.source:
task = NMRTask(source=source,
num_cores=a.num_cores,
queue=a.queue,
xc_functional=a.xc_functional,
cut_off_energy=a.cut_off_energy,
usp_pot=usp_pot,
pot_type=a.pot_type,
efg_only=a.efg_only)
source_dir, source_name = calc_from_path(source)
target_dir = os.path.join(a.target_dir, source_name)
if not os.path.isdir(target_dir):
os.mkdir(target_dir)
task.make(target_dir)
def get_cell(self):
"""
Make sure that self.cell is loaded, possibly by loading from source cell file.
"""
if self.cell is None and self.source is None:
raise Exception("One of cell or source must be provided")
if self.source is None and self.target_name is None:
raise Exception("If no cell is provided, target_name must be specified")
if self.source is not None:
source_dir, self.source_name = calc_from_path(self.source)
if self.cell is None:
self.cell = Cell(os.path.join(source_dir, "{}.cell".format(self.source_name)))
def get_cell(self):
"""
Make sure that self.cell is loaded, possibly by loading from source cell file.
"""
if self.cell is None and self.source is None:
raise Exception("One of cell or source must be provided")
if self.source is None and self.target_name is None:
raise Exception("If no cell is provided, target_name must be specified")
if self.source is not None:
source_dir, source_name = calc_from_path(self.source)
if self.cell is None:
self.cell = Cell(os.path.join(source_dir, "{}.cell".format(source_name)))
def test_success(self):
for input, expected in self.tests_pass:
self.assertEqual(utils.calc_from_path(input), expected)
def test_success(self):
for input, expected in self.tests_pass:
self.assertEqual(utils.calc_from_path(input), expected)
if 'seeds' in structure:
for seed in structure['seeds']:
seed_map[seed] = structure_name
couplings_map = {}
to_mean = {}
for magres_file in magres_files:
print >>sys.stderr, magres_file
try:
atoms = MagresAtoms.load_magres(magres_file)
except:
continue
dir, name = calc_from_path(magres_file)
structure = None
if name in seed_map:
structure = data['structures'][seed_map[name]]
elif name in data['structures']:
structure = data['structures'][name]
if structure is not None:
couplings = structure['couplings']
# Go through each coupling in the structure and check if we want it.
for atom in atoms:
if hasattr(atom, 'isc'):
for isc in atom.isc.values():
idx1 = "%s%d" % (isc.atom1.species, isc.atom1.index)
def make_command(args):
a = parser.parse_args(args)
print a.__dict__
sites = []
if a.site is not None:
for site in a.site.split(","):
sites.append(regex_species.findall(site)[0])
else:
sites = [None]
cut_off_energies = map(int, a.cut_off_energy.split(","))
xc_functionals = [s.lower() for s in a.xc_functional.split(",")]
pots = a.pot.split(",")
sources = a.source
param_prod = list(
itertools.product(sources, sites, cut_off_energies, xc_functionals,
pots))
for source, site, cut_off_energy, xc_functional, pot in param_prod:
source_dir, source_name = calc_from_path(source)
# Set up following directory structure:
# [rel/nrel]/[usp/ncp]/[xc_functional]/[structure]/[cutoff]/[site]
dir_path = [a.target_dir]
if len(pots) > 1:
dir_path.append(pot)
if len(xc_functionals) > 1:
dir_path.append(xc_functional)
if len(sources) > 1:
dir_path.append(source_name)
if len(cut_off_energies) > 1:
dir_path.append("%dry" % cut_off_energy)
if len(sites) > 1:
dir_path.append("".join(site))
print dir_path
new_dir = False
for i in range(len(dir_path)):
d = os.path.join(*dir_path[:i + 1])
if not os.path.isdir(d):
os.mkdir(d)
new_dir = True
target_dir = os.path.join(*dir_path)
if site is not None:
jc_s, jc_i = site
jc_i = int(jc_i)
else:
jc_s = None
jc_i = None
if pot == "usp":
usp_pot = True
elif pot == "ncp":
usp_pot = False
try:
task = JcouplingTask(num_cores=a.num_cores,
rel_pot=a.rel,
usp_pot=usp_pot,
xc_functional=xc_functional,
cut_off_energy=cut_off_energy,
queue=a.queue,
jc_s=jc_s,
jc_i=jc_i,
source=source)
task.make(target_dir)
except JcouplingTask.SiteNotPresent, e:
print e
# If we've just made this directory, trash it
if new_dir:
shutil.rmtree(target_dir)
if 'seeds' in structure:
for seed in structure['seeds']:
seed_map[seed] = structure_name
couplings_map = {}
to_mean = {}
for magres_file in magres_files:
print >> sys.stderr, magres_file
try:
atoms = MagresAtoms.load_magres(magres_file)
except:
continue
dir, name = calc_from_path(magres_file)
structure = None
if name in seed_map:
structure = data['structures'][seed_map[name]]
elif name in data['structures']:
structure = data['structures'][name]
if structure is not None:
couplings = structure['couplings']
# Go through each coupling in the structure and check if we want it.
for atom in atoms:
if hasattr(atom, 'isc'):
for isc in atom.isc.values():
idx1 = "%s%d" % (isc.atom1.species, isc.atom1.index)
def make_command(args):
a = parser.parse_args(args)
print a.__dict__
sites = []
if a.site is not None:
for site in a.site.split(","):
sites.append(regex_species.findall(site)[0])
else:
sites = [None]
cut_off_energies = map(int,a.cut_off_energy.split(","))
xc_functionals = [s.lower() for s in a.xc_functional.split(",")]
pots = a.pot.split(",")
sources = a.source
param_prod = list(itertools.product(sources, sites, cut_off_energies, xc_functionals, pots))
for source,site,cut_off_energy,xc_functional,pot in param_prod:
source_dir, source_name = calc_from_path(source)
# Set up following directory structure:
# [rel/nrel]/[usp/ncp]/[xc_functional]/[structure]/[cutoff]/[site]
dir_path = [a.target_dir]
if len(pots) > 1:
dir_path.append(pot)
if len(xc_functionals) > 1:
dir_path.append(xc_functional)
if len(sources) > 1:
dir_path.append(source_name)
if len(cut_off_energies) > 1:
dir_path.append("%dry" % cut_off_energy)
if len(sites) > 1:
dir_path.append("".join(site))
print dir_path
new_dir = False
for i in range(len(dir_path)):
d = os.path.join(*dir_path[:i+1])
if not os.path.isdir(d):
os.mkdir(d)
new_dir = True
target_dir = os.path.join(*dir_path)
if site is not None:
jc_s, jc_i = site
jc_i = int(jc_i)
else:
jc_s = None
jc_i = None
if pot == "usp":
usp_pot = True
elif pot == "ncp":
usp_pot = False
try:
task = JcouplingTask(num_cores=a.num_cores,
rel_pot=a.rel,
usp_pot=usp_pot,
xc_functional=xc_functional,
cut_off_energy=cut_off_energy,
queue=a.queue,
jc_s=jc_s,
jc_i=jc_i,
source=source)
task.make(target_dir)
except JcouplingTask.SiteNotPresent, e:
print e
# If we've just made this directory, trash it
if new_dir:
shutil.rmtree(target_dir)
