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_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 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_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
