def test_empty(self):
# single line
cb = CifBlock.from_string("data_mwe\nloop_\n_tag\n ''")
self.assertEqual(cb.data['_tag'][0], '')
# multi line
cb = CifBlock.from_string("data_mwe\nloop_\n_tag\n;\n;")
self.assertEqual(cb.data['_tag'][0], '')
cb2 = CifBlock.from_string(str(cb))
self.assertEqual(cb, cb2)
def test_empty(self):
# single line
cb = CifBlock.from_string("data_mwe\nloop_\n_tag\n ''")
self.assertEqual(cb.data['_tag'][0], '')
# multi line
cb = CifBlock.from_string("data_mwe\nloop_\n_tag\n;\n;")
self.assertEqual(cb.data['_tag'][0], '')
cb2 = CifBlock.from_string(str(cb))
self.assertEqual(cb, cb2)
def test_double_quotes_and_underscore_data(self):
cif_str = """data_test
_symmetry_space_group_name_H-M "P -3 m 1"
_thing '_annoying_data'"""
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_symmetry_space_group_name_H-M"], "P -3 m 1")
self.assertEqual(cb["_thing"], "_annoying_data")
self.assertEqual(str(cb), cif_str.replace('"', "'"))
def test_double_quotes_and_underscore_data(self):
cif_str = """data_test
_symmetry_space_group_name_H-M "P -3 m 1"
_thing '_annoying_data'"""
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_symmetry_space_group_name_H-M"], "P -3 m 1")
self.assertEqual(cb["_thing"], "_annoying_data")
self.assertEqual(str(cb), cif_str.replace('"', "'"))
def test_double_quoted_data(self):
cif_str = """data_test
_thing ' '_annoying_data''
_other " "_more_annoying_data""
_more ' "even more" ' """
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_thing"], " '_annoying_data'")
self.assertEqual(cb["_other"], ' "_more_annoying_data"')
self.assertEqual(cb["_more"], ' "even more" ')
def test_double_quoted_data(self):
cif_str = """data_test
_thing ' '_annoying_data''
_other " "_more_annoying_data""
_more ' "even more" ' """
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_thing"], " '_annoying_data'")
self.assertEqual(cb["_other"], ' "_more_annoying_data"')
self.assertEqual(cb["_more"], ' "even more" ')
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_nested_fake_multiline_quotes(self):
cif_str = """data_test
_thing
;
long quotes
;
still in the quote
;
actually going to end now
;"""
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_thing"], " long quotes ; still in the quote"
" ; actually going to end now")
def test_nested_fake_multiline_quotes(self):
cif_str = """data_test
_thing
;
long quotes
;
still in the quote
;
actually going to end now
;"""
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_thing"], " long quotes ; still in the quote"
" ; actually going to end now")
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 test_to_string(self):
with open(self.TEST_FILES_DIR / 'Graphite.cif') as f:
s = f.read()
c = CifBlock.from_string(s)
cif_str_2 = str(CifBlock.from_string(str(c)))
cif_str = """data_53781-ICSD
_database_code_ICSD 53781
_audit_creation_date 2003-04-01
_audit_update_record 2013-02-01
_chemical_name_systematic Carbon
_chemical_formula_structural C
_chemical_formula_sum C1
_chemical_name_structure_type Graphite(2H)
_chemical_name_mineral 'Graphite 2H'
_exptl_crystal_density_diffrn 2.22
_publ_section_title 'Structure of graphite'
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary 'Physical Review (1,1893-132,1963/141,1966-188,1969)'
1917 10 661 696 PHRVAO
loop_
_publ_author_name
'Hull, A.W.'
_cell_length_a 2.47
_cell_length_b 2.47
_cell_length_c 6.8
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 120.
_cell_volume 35.93
_cell_formula_units_Z 4
_symmetry_space_group_name_H-M 'P 63/m m c'
_symmetry_Int_Tables_number 194
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, x-y, -z+1/2'
2 '-x+y, y, -z+1/2'
3 '-y, -x, -z+1/2'
4 '-x+y, -x, -z+1/2'
5 '-y, x-y, -z+1/2'
6 'x, y, -z+1/2'
7 '-x, -x+y, z+1/2'
8 'x-y, -y, z+1/2'
9 'y, x, z+1/2'
10 'x-y, x, z+1/2'
11 'y, -x+y, z+1/2'
12 '-x, -y, z+1/2'
13 '-x, -x+y, -z'
14 'x-y, -y, -z'
15 'y, x, -z'
16 'x-y, x, -z'
17 'y, -x+y, -z'
18 '-x, -y, -z'
19 'x, x-y, z'
20 '-x+y, y, z'
21 '-y, -x, z'
22 '-x+y, -x, z'
23 '-y, x-y, z'
24 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
C0+ 0
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
_atom_site_attached_hydrogens
C1 C0+ 2 b 0 0 0.25 . 1. 0
C2 C0+ 2 c 0.3333 0.6667 0.25 . 1. 0"""
for l1, l2, l3 in zip(
str(c).split("\n"), cif_str.split("\n"),
cif_str_2.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
self.assertEqual(l2.strip(), l3.strip())
def test_to_string(self):
with open(self.TEST_FILES_DIR / 'Graphite.cif') as f:
s = f.read()
c = CifBlock.from_string(s)
cif_str_2 = str(CifBlock.from_string(str(c)))
cif_str = """data_53781-ICSD
_database_code_ICSD 53781
_audit_creation_date 2003-04-01
_audit_update_record 2013-02-01
_chemical_name_systematic Carbon
_chemical_formula_structural C
_chemical_formula_sum C1
_chemical_name_structure_type Graphite(2H)
_chemical_name_mineral 'Graphite 2H'
_exptl_crystal_density_diffrn 2.22
_publ_section_title 'Structure of graphite'
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary 'Physical Review (1,1893-132,1963/141,1966-188,1969)'
1917 10 661 696 PHRVAO
loop_
_publ_author_name
'Hull, A.W.'
_cell_length_a 2.47
_cell_length_b 2.47
_cell_length_c 6.8
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 120.
_cell_volume 35.93
_cell_formula_units_Z 4
_symmetry_space_group_name_H-M 'P 63/m m c'
_symmetry_Int_Tables_number 194
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, x-y, -z+1/2'
2 '-x+y, y, -z+1/2'
3 '-y, -x, -z+1/2'
4 '-x+y, -x, -z+1/2'
5 '-y, x-y, -z+1/2'
6 'x, y, -z+1/2'
7 '-x, -x+y, z+1/2'
8 'x-y, -y, z+1/2'
9 'y, x, z+1/2'
10 'x-y, x, z+1/2'
11 'y, -x+y, z+1/2'
12 '-x, -y, z+1/2'
13 '-x, -x+y, -z'
14 'x-y, -y, -z'
15 'y, x, -z'
16 'x-y, x, -z'
17 'y, -x+y, -z'
18 '-x, -y, -z'
19 'x, x-y, z'
20 '-x+y, y, z'
21 '-y, -x, z'
22 '-x+y, -x, z'
23 '-y, x-y, z'
24 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
C0+ 0
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
_atom_site_attached_hydrogens
C1 C0+ 2 b 0 0 0.25 . 1. 0
C2 C0+ 2 c 0.3333 0.6667 0.25 . 1. 0"""
for l1, l2, l3 in zip(str(c).split("\n"), cif_str.split("\n"),
cif_str_2.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
self.assertEqual(l2.strip(), l3.strip())
outputFilePath = str(sys.argv[3])
#loading a poscar object we handle .structure.composition, .structure.formula, and .structure.lattice
#validate the POSCAR that is not well-defined and/or ambiguous.
if Poscar.from_file(inputFileFullPath).true_names:
ps = Poscar.from_file(inputFileFullPath).structure
#
#casting poscar structure to dict and cif format files
ps_dict = ps.composition.as_dict()
ps_reduced_dict, ps_reduced_factor = ps.composition.get_reduced_formula_and_factor(
)
ps_cif = ps.to("cif")
#cif_sample[0] = "# generated using pymatgen\ndata_Ga2CoS4\n_symmetry_space_group_name_H-M 'P 1'\n_cell_length_a 5.29198729\n_cell_length_b 5.29198728\n_cell_length_c 6.45268046\n_cell_angle_alpha 114.20867693\n_cell_angle_beta 114.20867699\n_cell_angle_gamma 89.99999995\n_symmetry_Int_Tables_number 1\n_chemical_formula_structural Ga2CoS4\n_chemical_formula_sum 'Ga2 Co1 S4'\n_cell_volume 147.218893696\n_cell_formula_units_Z 1\nloop_\n _symmetry_equiv_pos_site_id\n _symmetry_equiv_pos_as_xyz\n 1 'x, y, z'\nloop_\n _atom_site_type_symbol\n _atom_site_label\n _atom_site_symmetry_multiplicity\n _atom_site_fract_x\n _atom_site_fract_y\n _atom_site_fract_z\n _atom_site_occupancy\n S S1 1 0.874869 0.886340 0.253531 1\n S S2 1 0.632808 0.125131 0.746469 1\n S S3 1 0.113660 0.621337 0.746469 1\n S S4 1 0.378663 0.367192 0.253531 1\n Co Co5 1 0.000000 0.000000 0.000000 1\n Ga Ga6 1 0.500000 0.500000 0.000000 1\n Ga Ga7 1 0.250000 0.750000 0.500000 1\n"
cif_sample_from_the_ps_sample_0_structure = CifBlock.from_string(ps_cif).data
## 20170911 battery properties calculation added by Jclee
IS_BATTERY = False
ps_dict_battery_working_ion = dict()
IF_for_working_ion = 0
for keys in ps_dict.keys():
#if the key is an working ion
if keys == 'Li' or keys == 'Na' or keys == 'K':
IS_BATTERY = True
ps_dict_battery_others = ps_dict.copy()
ps_dict_battery_working_ion = {keys: ps_dict_battery_others.pop(keys)}
IF_for_working_ion = 1
elif keys == 'Mg': # or keys == 'Ca':
IS_BATTERY = True
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)
