from magres.atoms import MagresAtoms
from magres.utils import load_all_magres, get_numeric, parse_atom_list
parser = argparse.ArgumentParser(description='Extract magnetic shielding parameters from a set of calculations.')
parser.add_argument('-N', '--numbers', action="store_const", help="Parse numbers from path and print. This is useful for e.g. convergence calculations.", default=False, const=True)
parser.add_argument('source_dir', help='Directory to look for calculations below.')
parser.add_argument('--iso', action='append')
parser.add_argument('atoms', nargs='?', type=str, default=None, help='Which atoms to print shieldings of. Specify with atom list notation, e.g. "H1" or "H1,H2,H3" or "H,C" or "H1-3".')
a = parser.parse_args(sys.argv[1:])
atoms_filter_str = a.atoms
if atoms_filter_str:
atoms_filter = parse_atom_list(atoms_filter_str)
else:
atoms_filter = lambda x: True
tensors = ['ms']
lines = []
print "# Number\tAtom\tIso\tAniso\tAsym\tPath"
if os.path.isfile(a.source_dir):
magres_atoms = [MagresAtoms.load_magres(a.source_dir)]
else:
magres_atoms = load_all_magres(a.source_dir)
isos = {}
parser.add_argument('source_dir', help='Directory to look for calculations in')
parser.add_argument('atoms1', nargs='?', type=str, default=None,
help='Only print couplings from these atoms. Specify with atom list notation, e.g. "H1", "H1,H2,'
'H3", "H,C", or "H1-3".')
parser.add_argument('atoms2', nargs='?', type=str, default=None,
help='Only print couplings to these atoms. Specify with atom list notation, e.g. "H1", "H1,H2,'
'H3", "H,C", or "H1-3".')
a = parser.parse_args(sys.argv[1:])
atoms1 = a.atoms1
atoms2 = a.atoms2
if atoms1:
atoms1_filter = parse_atom_list(atoms1)
else:
atoms1_filter = lambda x: True
if atoms2:
atoms2_filter = parse_atom_list(atoms2)
else:
atoms2_filter = lambda x: True
all_Js = {}
tensors = ['isc', 'isc_fc', 'isc_spin', 'isc_orbital_p', 'isc_orbital_d']
if a.J_tensor:
print("# Showing in Hz (J)")
property = "J_iso"
parser.add_argument(
'atoms',
nargs='?',
type=str,
default=None,
help=
'Which atoms to print shieldings of. Specify with atom list notation, e.g. "H1" or "H1,H2,'
'H3" or "H,C" or "H1-3".')
a = parser.parse_args(sys.argv[1:])
atoms_filter_str = a.atoms
if atoms_filter_str:
atoms_filter = parse_atom_list(atoms_filter_str)
else:
atoms_filter = lambda x: True
tensors = [
'efg',
] # 'efg_local', 'efg_nonlocal']
lines = []
if a.numbers:
print("# Number\tAtom\tCq\tEta\tPath")
else:
print("# Atom\tCq\tEta\tPath")
if os.path.isfile(a.source):
parser.add_argument(
'atoms2',
nargs='?',
type=str,
default=None,
help=
'Only print couplings to these atoms. Specify with atom list notation, e.g. "H1", "H1,H2,'
'H3", "H,C", or "H1-3".')
a = parser.parse_args(sys.argv[1:])
atoms1 = a.atoms1
atoms2 = a.atoms2
if atoms1:
atoms1_filter = parse_atom_list(atoms1)
else:
atoms1_filter = lambda x: True
if atoms2:
atoms2_filter = parse_atom_list(atoms2)
else:
atoms2_filter = lambda x: True
all_Js = {}
tensors = ['isc', 'isc_fc', 'isc_spin', 'isc_orbital_p', 'isc_orbital_d']
if a.J_tensor:
print("# Showing in Hz (J)")
property = "J_iso"
