def main():
if not os.path.isdir('TMXR200X'):
os.makedirs('TMXR200X')
#for database in ['TM1R2006']:
for database in database_files.keys():
fh = open(database_files[database]['module'].lower() + '.py', 'w')
fh.write('# Computer generated code! Hands off!\n')
fh.write('# Generated: ' + str(datetime.date.today()) + '\n')
fh.write('from numpy import array\n')
fh.write('data = ')
data = {} # specification of molecules
info = {} # reference/calculation info
# download structures
file = database_files[database]['pdf']
f = os.path.abspath(download_file(url_root, file, dir='TMXR200X'))
f = pdftotext(f)
geometries = read_geometries(f)
# set number of unpaired electrons and charges
no_unpaired_electrons = []
charges = []
for a in geometries:
magmom = sum(a[1].get_initial_magnetic_moments())
if magmom > 0.0:
no_unpaired_electrons.append((a[0], magmom))
charge = sum(a[1].get_charges())
if abs(charge) > 0.0:
charges.append((a[0], charge))
data = format_data(database, geometries, no_unpaired_electrons,
charges)
# all constituent atoms
atoms = []
for formula, geometry in geometries:
atoms.extend(list(set(geometry.get_chemical_symbols())))
atoms = list(set(atoms))
atoms.sort()
for atom in atoms:
magmom = ground_state_magnetic_moments[atomic_numbers[atom]]
data[atom] = {
'database': database,
'name': atom,
'symbols': atom,
'magmoms': [magmom], # None or list
'charges': None, # None or list
'positions': np.array([[0.0] * 3]),
}
Atom(atom, magmom=magmom)
pprint.pprint(data, stream=fh)
fh.close()
def main():
if not os.path.isdir('TMXR200X'):
os.makedirs('TMXR200X')
#for database in ['TM1R2006']:
for database in database_files.keys():
fh = open(database_files[database]['module'].lower() + '.py', 'w')
fh.write('# Computer generated code! Hands off!\n')
fh.write('# Generated: ' + str(datetime.date.today()) + '\n')
fh.write('from numpy import array\n')
fh.write('data = ')
data = {} # specification of molecules
info = {} # reference/calculation info
# download structures
file = database_files[database]['pdf']
f = os.path.abspath(download_file(url_root, file, dir='TMXR200X'))
f = pdftotext(f)
geometries = read_geometries(f)
# set number of unpaired electrons and charges
no_unpaired_electrons = []
charges = []
for a in geometries:
magmom = sum(a[1].get_initial_magnetic_moments())
if magmom > 0.0:
no_unpaired_electrons.append((a[0], magmom))
charge = sum(a[1].get_charges())
if abs(charge) > 0.0:
charges.append((a[0], charge))
data = format_data(database, geometries, no_unpaired_electrons, charges)
# all constituent atoms
atoms = []
for formula, geometry in geometries:
atoms.extend(list(set(geometry.get_chemical_symbols())))
atoms=list(set(atoms))
atoms.sort()
for atom in atoms:
magmom=ground_state_magnetic_moments[atomic_numbers[atom]]
data[atom] = {
'database': database,
'name': atom,
'symbols': atom,
'magmoms': [magmom], # None or list
'charges': None, # None or list
'positions': np.array([[0.0]*3]),
}
Atom(atom, magmom=magmom)
pprint.pprint(data, stream=fh)
fh.close()