def generate(data):
"""
Sets up the database generator depending on the use input
provided by the plugin manager.
"""
import lauescript.database as db
from lauescript.types.data import GENERATOR
if config.arg('clean'):
clean = True
else:
clean = False
temperatures = []
# ===========================================================================
# for arg in mo['options']:
# try:
# temperatures.append(float(arg))
# except:
# pass
#===========================================================================
if not clean:
db.generate_database(data,
config.get_frequency_cutoff(),
clean=False,
temperatures=temperatures,
path=config.config.DatabasePath,
root=config.get_config_value('Database', 'modelcompountrootdirectory'),
newh=config.get_config_value('APD', 'newH'))
return
if config.arg('save'):
save = True
else:
save = False
data = GENERATOR(temperatures, save)
db.generate_database(data, config.get_frequency_cutoff(),
root=config.get_config_value('Database', 'modelcompountrootdirectory'),
frequency_scale=config.get_config_valueFloat('Database', 'frequency_scale'),
newh=config.get_config_value('APD', 'newH'))
def FlexLoad(data, loader, dabapath, config, filename='./', noTransfer=False, planarityThreshold=.1):
"""
A more flexible variation of the 'Load' function.
The actual 'loading' is handled by the 'Loader'
class which relies on InputOutputProviders to
access files independent of their specific file
format.
FlexLoad itself is only integrating the molecule
returned by the 'Loader' in the APD-Toolkit's
data structure and subsequently populating the
data structure with the necessary model molecules.
"""
printer = config.get_active_printer()
loader.auto_setup(filename)
data.register_molecule(loader.load('exp'), 'exp')
data['exp'].give_cell(loader.get_cell())
T = config.arg('temp')
if not T:
T = loader.get_temperature()
if not T:
printer.highlight('Warning: No temperature specified. Falling back to default.')
T = 100
T = int(T)
data.give_temperature(T)
dabapa = dabapath + '/APD_DABA_{:.1f}_.txt'.format(data.temperature)
printer('Crystal temperature: {:.1f} K'.format(data.temperature))
try:
dabapointer = open(dabapa)
except IOError:
printer('inout.py: Error: File {} not found.'.format(dabapa))
printer('Calling database generator to generate appropriate database file.\n\n')
import lauescript.database as db
frequency_cutoff = config.get_frequency_cutoff()
db.generate_database(data, frequency_cutoff, clean=False, temperatures=[data.temperature], path=dabapath,
newh=config.get_config_valueBool('APD', 'newH'))
dabapointer = open(dabapa)
database = dabapointer.readlines()
printer()
if noTransfer:
read_database(data, database, invlist=[], readAll=True)
return
correctionsPointer = open(dabapath + '/empirical_corrections.txt')
for invdict, orientations, compounds in invstring.get_invariom_names(names=[i.name for i in data['exp'].atoms],
cart=[i.cart for i in data['exp'].atoms],
dictionary=True,
orientations=True,
compounds=open(dabapath + '/APD_MAP.txt'),
corrections=correctionsPointer,
dynamic=True,
output=printer,
verbose=False,
newH=config.get_config_valueBool('APD', 'newH'),
planarityThreshold=planarityThreshold):
invlist = [item for _, item in compounds.items()]
read_database(data, database, invlist)
kill = False
misses = []
for atom in data['exp'].atoms:
invname = invdict[atom.name]
orientation = orientations[atom.name]
atom.add_invariom(invname, orientation)
if invname in compounds.keys() and not atom.model_compound:
modelname = compounds[invname]
atom.model_compound = data[modelname]
atom.set_active_invariom(invname)
elif invname not in compounds.keys() and not atom.model_compound:
misses.append((atom, invname))
kill = True
printer('Trying dynamic invariom name for atom {}. {} not available'.format(atom.name, invname))
printer()
if kill:
for atom in misses:
atom = atom[0]
neighbours = cg.get_framework_neighbours(atom, useH=False)
if len(neighbours) > 1:
for atom2 in neighbours:
if not atom2.get_active_invariom():
message = 'Error: The following invarioms are missing in the database:\n'
message += '\n'.join(['{:<6} <-> {:>}'.format(miss[0].name, miss[1]) for miss in misses])
message += '\n\n!!!Terminating program due to fatal error: MISSING INVARIOMS!!!'
core.apd_exit(message=message)
atom.tolerate()
printer('WARNING: Tolerating missing invariom for {}.'.format(atom.name))
else:
message = 'Error: The following invarioms are missing in the database:\n'
message += '\n'.join(['{:<6} <-> {:>}'.format(miss[0].name, miss[1]) for miss in misses])
message += '\n\n!!!Terminating program due to fatal error: MISSING INVARIOMS!!!'
core.apd_exit(message=message)
return
message = 'Error: The following invarioms are missing in the database:\n'
message += '\n'.join(['{:<6} <-> {:>}'.format(miss[0].name, miss[1]) for miss in misses])
message += '\n\n!!!Terminating program due to fatal error: MISSING INVARIOMS!!!'
core.apd_exit(message=message)
