def make_cif(self):
"""
Generates a pymatgen CifFile object using structure info parsed
from SPuDS output.txt.
Returns:
cf: pymatgen CifFile object
"""
# SPuDS ouput structure info
site_list,a_lat,b_lat,c_lat,alp,bet,gam = parse_spuds_out(self)
# Mapped lattice parameters to .cif compatibility
a,b,c,alpha,beta,gamma = map_lattice_menu_1(self,
a_lat,b_lat,c_lat,
alp,bet,gam)
symd = self.symops_dict[self.symops_key] # symops dict data
# Create dict of .cif parameters
data = {}
data['_cell_length_a'] = a
data['_cell_length_b'] = b
data['_cell_length_c'] = c
data['_cell_angle_alpha'] = alpha
data['_cell_angle_beta'] = beta
data['_cell_angle_gamma'] = gamma
data['_space_group_name_H-M_alt'] = symd['name']
data['_symmetry_Int_tables_number'] = symd['number']
data['_symmetry_cell_setting'] = symd['latsym']
data['_space_group_symop_operation_xyz'] = symd['symops']
data['_atom_type_symbol'] = self.ellist
data['_atom_type_oxidation_number'] = self.oxilist
data['_atom_site_label'] = [d[0] for d in site_list]
data['_atom_site_type_symbol'] = [d[1] for d in site_list]
data['_atom_site_symmetry_multiplicity'] = [d[2] for d in site_list]
data['_atom_site_Wycoff_symbol'] = [d[3] for d in site_list]
data['_atom_site_fract_x'] = [d[4] for d in site_list]
data['_atom_site_fract_y'] = [d[5] for d in site_list]
data['_atom_site_fract_z'] = [d[6] for d in site_list]
data['_atom_site_occupancy'] = [d[7] for d in site_list]
# .cif file header
cif_header = 'SPuDS'
# .cif file loops
cif_loops = [['_space_group_symop_operation_xyz'],
['_atom_type_symbol','_atom_type_oxidation_number'],
['_atom_site_label','_atom_site_type_symbol',
'_atom_site_symmetry_multiplicity',
'_atom_site_Wycoff_symbol','_atom_site_fract_x',
'_atom_site_fract_y','_atom_site_fract_z',
'_atom_site_occupancy']]
# Create CifFile object
d = OrderedDict()
d[self.formula] = CifBlock(data,cif_loops,cif_header)
cf = CifFile(d)
return cf
def test_long_loop(self):
data = {'_stuff1': ['A' * 30] * 2,
'_stuff2': ['B' * 30] * 2,
'_stuff3': ['C' * 30] * 2}
loops = [['_stuff1', '_stuff2', '_stuff3']]
cif_str = """data_test
loop_
_stuff1
_stuff2
_stuff3
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"""
self.assertEqual(str(CifBlock(data, loops, 'test')), cif_str)
def test_long_loop(self):
data = {
"_stuff1": ["A" * 30] * 2,
"_stuff2": ["B" * 30] * 2,
"_stuff3": ["C" * 30] * 2,
}
loops = [["_stuff1", "_stuff2", "_stuff3"]]
cif_str = """data_test
loop_
_stuff1
_stuff2
_stuff3
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"""
self.assertEqual(str(CifBlock(data, loops, "test")), cif_str)
def clear_cif_from_crystalmaker(s):
identifier, d = get_pmg_dict(s)
if any('generated by CrystalMaker' in v for v in d.values()):
k = '_atom_site_occupancy'
try:
lenk = len(d[k])
except KeyError:
return s
for i in range(lenk):
d[k][i] = 1.0
loops = [[], []]
for key in d.keys():
if '_symmetry_equiv_pos_as_xyz' in key:
loops[0].append(key)
elif '_atom_' in key:
loops[1].append(key)
s = CifBlock(d, loops, identifier).__str__()
return s
def __init__(self, struct, symprec=None, charges=None):
"""
A wrapper around CifFile to write CIF files from pymatgen structures.
Args:
struct (Structure): structure to write
symprec (float): If not none, finds the symmetry of the structure
and writes the cif with symmetry information. Passes symprec
to the SpacegroupAnalyzer
write_magmoms (bool): If True, will write magCIF file. Incompatible
with symprec
"""
format_str = "{:.8f}"
block = OrderedDict()
loops = []
spacegroup = ("P 1", 1)
if symprec is not None:
sf = SpacegroupAnalyzer(struct, symprec)
spacegroup = (sf.get_space_group_symbol(),
sf.get_space_group_number())
# Needs the refined struture when using symprec. This converts
# primitive to conventional structures, the standard for CIF.
struct = sf.get_refined_structure()
latt = struct.lattice
comp = struct.composition
no_oxi_comp = comp.element_composition
block["_symmetry_space_group_name_H-M"] = spacegroup[0]
for cell_attr in ['a', 'b', 'c']:
block["_cell_length_" + cell_attr] = format_str.format(
getattr(latt, cell_attr))
for cell_attr in ['alpha', 'beta', 'gamma']:
block["_cell_angle_" + cell_attr] = format_str.format(
getattr(latt, cell_attr))
block["_symmetry_Int_Tables_number"] = spacegroup[1]
block["_chemical_formula_structural"] = no_oxi_comp.reduced_formula
block["_chemical_formula_sum"] = no_oxi_comp.formula
block["_cell_volume"] = "%.8f" % latt.volume
reduced_comp, fu = no_oxi_comp.get_reduced_composition_and_factor()
block["_cell_formula_units_Z"] = str(int(fu))
if symprec is None:
block["_symmetry_equiv_pos_site_id"] = ["1"]
block["_symmetry_equiv_pos_as_xyz"] = ["x, y, z"]
else:
sf = SpacegroupAnalyzer(struct, symprec)
symmops = []
for op in sf.get_symmetry_operations():
v = op.translation_vector
symmops.append(
SymmOp.from_rotation_and_translation(
op.rotation_matrix, v))
ops = [op.as_xyz_string() for op in symmops]
block["_symmetry_equiv_pos_site_id"] = \
["%d" % i for i in range(1, len(ops) + 1)]
block["_symmetry_equiv_pos_as_xyz"] = ops
loops.append(
["_symmetry_equiv_pos_site_id", "_symmetry_equiv_pos_as_xyz"])
try:
symbol_to_oxinum = OrderedDict([(el.__str__(), float(el.oxi_state))
for el in sorted(comp.elements)])
block["_atom_type_symbol"] = symbol_to_oxinum.keys()
block["_atom_type_oxidation_number"] = symbol_to_oxinum.values()
loops.append(["_atom_type_symbol", "_atom_type_oxidation_number"])
except (TypeError, AttributeError):
symbol_to_oxinum = OrderedDict([(el.symbol, 0)
for el in sorted(comp.elements)])
atom_site_type_symbol = []
atom_site_symmetry_multiplicity = []
atom_site_fract_x = []
atom_site_fract_y = []
atom_site_fract_z = []
atom_site_label = []
atom_site_occupancy = []
atom_site_charge_label = []
count = 1
if symprec is None:
for site in struct:
for sp, occu in sorted(site.species_and_occu.items()):
atom_site_type_symbol.append(sp.__str__())
atom_site_symmetry_multiplicity.append("1")
atom_site_fract_x.append("{0:f}".format(site.a))
atom_site_fract_y.append("{0:f}".format(site.b))
atom_site_fract_z.append("{0:f}".format(site.c))
atom_site_label.append("{}{}".format(sp.symbol, count))
atom_site_occupancy.append(occu.__str__())
count += 1
else:
# The following just presents a deterministic ordering.
unique_sites = [
(sorted(sites,
key=lambda s: tuple([abs(x)
for x in s.frac_coords]))[0],
len(sites))
for sites in sf.get_symmetrized_structure().equivalent_sites
]
for site, mult in sorted(unique_sites,
key=lambda t:
(t[0].species_and_occu.average_electroneg,
-t[1], t[0].a, t[0].b, t[0].c)):
for sp, occu in site.species_and_occu.items():
atom_site_type_symbol.append(sp.__str__())
atom_site_symmetry_multiplicity.append("%d" % mult)
atom_site_fract_x.append("{0:f}".format(site.a))
atom_site_fract_y.append("{0:f}".format(site.b))
atom_site_fract_z.append("{0:f}".format(site.c))
atom_site_label.append("{}{}".format(sp.symbol, count))
atom_site_occupancy.append(occu.__str__())
count += 1
block["_atom_site_type_symbol"] = atom_site_type_symbol
block["_atom_site_label"] = atom_site_label
block["_atom_site_symmetry_multiplicity"] = \
atom_site_symmetry_multiplicity
block["_atom_site_fract_x"] = atom_site_fract_x
block["_atom_site_fract_y"] = atom_site_fract_y
block["_atom_site_fract_z"] = atom_site_fract_z
block["_atom_site_occupancy"] = atom_site_occupancy
block["_atom_site_charge"] = charges
loops.append([
"_atom_site_type_symbol",
"_atom_site_label",
"_atom_site_symmetry_multiplicity",
"_atom_site_fract_x",
"_atom_site_fract_y",
"_atom_site_fract_z",
"_atom_site_occupancy",
"_atom_site_charge",
])
d = OrderedDict()
d[comp.reduced_formula] = CifBlock(block, loops, comp.reduced_formula)
self._cf = CifFile(d)
