def coordgroups_reduced_rc_to_unitcellsites(coordgroups,
basis,
hall_symbol,
reduce=False):
# Just fake representative assignments for the coordgroups
assignments = range(1, len(coordgroups) + 1)
struct = Structure.create(rc_cell=basis,
assignments=assignments,
rc_reduced_coordgroups=coordgroups,
hall_symbol=hall_symbol)
rescale = 1
atoms = structure_to_ase_atoms(struct)
if reduce:
beforevol = FracScalar.create(atoms.get_volume())
spacegroup, setting = httk.atomistic.data.spacegroups.spacegroup_get_number_and_setting(
hall_symbol)
atoms = primitive_from_conventional_cell(atoms, spacegroup, setting)
aftervol = FracScalar.create(atoms.get_volume())
rescale = (rescale * aftervol / beforevol).simplify()
atomic_symbols = atoms.get_chemical_symbols()
coords = atoms.get_scaled_positions()
cell = atoms.get_cell()
sites = UnitcellSites.create(cell=cell,
occupancies=atomic_symbols,
reduced_coords=coords,
periodicity=atoms.pbc)
cell = Cell(basis=cell)
return sites, cell
def poscar_to_structure(f, included_decimals=''):
cell, scale, volume, coords, coords_reduced, counts, occupations, comment = poscar_to_strs(
f, included_decimals)
frac_cell = FracVector.create(cell, simplify=True)
counts = [int(x) for x in counts]
if coords_reduced:
frac_coords = cartesian_to_reduced(cell, coords)
else:
frac_coords = FracVector.create(coords, simplify=True)
if volume is not None:
volume = FracScalar.create(volume)
if scale is not None:
scale = FracScalar.create(scale)
newoccupations = []
for occupation in occupations:
newoccupations.append(periodictable.atomic_number(occupation))
struct = Structure.create(uc_basis=frac_cell,
uc_volume=volume,
uc_scale=scale,
uc_reduced_coords=frac_coords,
uc_counts=counts,
assignments=newoccupations,
tags={'comment': comment},
periodicity=0)
return struct
def ase_atoms_to_structure(atoms, hall_symbol):
#occupancies = [periodictable.atomic_number(x) for x in atoms.get_chemical_symbols()]
atomic_symbols = atoms.get_chemical_symbols()
#counts = [1]*len(assignments)
coords = atoms.get_scaled_positions()
cell = atoms.get_cell()
if hall_symbol is None:
struct = Structure.create(uc_basis=cell,
uc_occupancies=atomic_symbols,
uc_reduced_occupationscoords=coords,
periodicity=atoms.pbc)
else:
struct = Structure.create(rc_basis=cell,
rc_occupancies=atomic_symbols,
rc_reduced_occupationscoords=coords,
periodicity=atoms.pbc,
hall_symbol=hall_symbol)
return struct
def coordgroups_reduced_rc_to_unitcellsites(coordgroups, basis, hall_symbol):
# Just fake representative assignments for the coordgroups
assignments = range(1, len(coordgroups) + 1)
struct = Structure.create(rc_cell=basis,
assignments=assignments,
rc_reduced_coordgroups=coordgroups,
hall_symbol=hall_symbol)
ioa = IoAdapterString()
struct_to_cif(struct, ioa)
struct = cif_to_structure_reduce(ioa)
return struct.uc_sites, struct.uc_cell
def structure_reduced_uc_to_representative(struct,
backends=['isotropy', 'fake']):
for backend in backends:
if backend == 'isotropy':
try:
from httk.external import isotropy_ext
sys.stderr.write(
"Warning: need to run symmetry finder. This may take a while.\n"
)
struct = isotropy_ext.struct_process_with_isotropy(struct)
return struct
except ImportError:
pass
if backend == 'fake':
try:
from httk.atomistic import Structure
sys.stderr.write(
"Warning: using 'fake' symmetry finder that never finds any symmetry.\n"
)
newstruct = Structure.create(
assignments=struct.assignments,
rc_cell=struct.uc_cell,
rc_reduced_coords=struct.uc_reduced_coords,
rc_counts=struct.uc_counts,
uc_cell=struct.uc_cell,
uc_reduced_coords=struct.uc_reduced_coords,
uc_counts=struct.uc_counts,
spacegroup='P 1',
tags=struct.get_tags(),
refs=struct.get_refs(),
periodicity=struct.uc_sites.pbc)
return newstruct
except ImportError:
raise
pass
raise Exception(
"structure_to_sgstructure: None of the available backends available.")
def platon_styout_to_structure(ioa, based_on_struct=None):
"""
Example input::
Results for id=[0] dblock_code=[44325-I New: F-43m
=====================================================
Pearson code : cF 8 Sb 4.0 Al 4.0
Cell parameters : 7.7782 7.7782 7.7782 90.000 90.000 90.000
Space group symbol : F -4 3 m Number in IT : 216
Setting x,y,z Origin ( 0.0000 0.0000 0.0000) Gamma = 0.4330
Al1 4(c) 1/4 1/4 1/4 Al 1
Sb1 4(a) 0 0 0 Sb 1
Wyckoff sequence : c a
Volume of Unit Cell : 470.5842
OTHER Standardization with Similar Gamma :
Setting -x,-y,-z Origin ( 0.7500 0.7500 0.7500) Gamma = 0.4330
Sb1 4(c) 1/4 1/4 1/4 Sb 1
Al1 4(a) 0 0 0 Al 1
Wyckoff sequence : c a
Volume of Unit Cell : 470.5842
"""
results = {}
results['cell'] = {}
results['spacegroup'] = {}
results['setting'] = []
results['in_setting'] = False
def cell_params(results, match):
results['cell']['rc_a'] = float(match.group(1))
results['cell']['rc_b'] = float(match.group(2))
results['cell']['rc_c'] = float(match.group(3))
results['cell']['rc_alpha'] = float(match.group(4))
results['cell']['rc_beta'] = float(match.group(5))
results['cell']['rc_gamma'] = float(match.group(6))
def spacegroup(results, match):
results['spacegroup']['symbol'] = match.group(1).strip()
results['spacegroup']['number'] = match.group(2).strip()
#def setting_start(results,match):
# results['setting'].append({'coords':[],'occupancies':[],'wycoff':[]})
# results['in_setting'] = True
def setting_stop(results, match):
results['in_setting'] = False
def read_coords(results, match):
if not results['in_setting']:
results['setting'].append({'coords': [], 'occupancies': [], 'wyckoff': [], 'multiplicities': []})
results['in_setting'] = True
newcoord = FracVector.create([match.group(4), match.group(5), match.group(6)]).limit_denominator(5000000).simplify()
#print("CHECK1",[match.group(4),match.group(5),match.group(6)])
#print("CHECK2:",newcoord)
results['setting'][-1]['coords'].append([match.group(4), match.group(5), match.group(6)])
if based_on_struct is None:
results['setting'][-1]['occupancies'].append(match.group(1))
else:
abstract_symbol = match.group(1).strip()
index = httk.basic.anonymous_symbol_to_int(abstract_symbol)
results['setting'][-1]['occupancies'].append(based_on_struct.assignments[index])
wyckoff_string = match.group(3)
wyckoff_symbol = wyckoff_string[wyckoff_string.index("(") + 1:wyckoff_string.rindex(")")]
multiplicity = int(wyckoff_string[:wyckoff_string.index("(")])
results['setting'][-1]['wyckoff'].append(wyckoff_symbol)
results['setting'][-1]['multiplicities'].append(multiplicity)
results['in_setting'] = True
#def debug(results,match):
# print("DEBUG",match)
out = httk.basic.micro_pyawk(ioa, [
#['^Wyckoff',None,setting_stop],
['^ *$', None, setting_stop],
['^Cell parameters : +([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+) +([0-9.-]+)', None, cell_params],
['^Space group symbol : +(.+) +Number in IT : +([0-9]+)', None, spacegroup],
['^ +([a-zA-Z]+)([0-9]*)#* +([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+)', None, read_coords],
#['^Setting',None,setting_start],
], results=results, debug=False)
#print("HX",out['setting'][0]['wyckoff'])
if based_on_struct is None:
structdata = dict(out['cell'].items() +
[('rc_reduced_occupationscoords', out['setting'][0]['coords']),
('rc_occupancies', out['setting'][0]['occupancies']),
('spacegroup', out['spacegroup']['symbol']),
('wyckoff_symbols', out['setting'][0]['wyckoff'])
])
sgstruct = Structure.create(**structdata)
else:
# Handle both normal structures and scaleless structures
sg = Spacegroup.create(hm_symbol=out['spacegroup']['symbol'], spacegroupnumber=out['spacegroup']['number'])
try:
rc_cell = based_on_struct.rc_cell
structdata = dict(out['cell'].items() +
[('rc_reduced_occupationscoords', out['setting'][0]['coords']),
('rc_occupancies', out['setting'][0]['occupancies']),
('spacegroup', sg),
('rc_cell', rc_cell),
('wyckoff_symbols', out['setting'][0]['wyckoff']),
('multiplicities', out['setting'][0]['multiplicities'])
]
)
sgstruct = based_on_struct.create(**structdata)
sgstruct.add_tags(based_on_struct.get_tags())
sgstruct.add_refs(based_on_struct.get_refs())
except AttributeError:
structdata = dict(out['cell'].items() +
[('rc_reduced_occupationscoords', out['setting'][0]['coords']),
('rc_occupancies', out['setting'][0]['occupancies']),
('spacegroup', sg),
('wyckoff_symbols', out['setting'][0]['wyckoff']),
('multiplicities', out['setting'][0]['multiplicities'])
]
)
sgstruct = based_on_struct.create(**structdata)
sgstruct.add_tags(based_on_struct.get_tags())
sgstruct.add_refs(based_on_struct.get_refs())
sgstruct.add_rc_cells(based_on_struct.get_rc_cells())
return sgstruct
def platon_styout_to_sgstruct(ioa):
"""
Example input::
Results for id=[0] dblock_code=[44325-I New: F-43m
=====================================================
Pearson code : cF 8 Sb 4.0 Al 4.0
Cell parameters : 7.7782 7.7782 7.7782 90.000 90.000 90.000
Space group symbol : F -4 3 m Number in IT : 216
Setting x,y,z Origin ( 0.0000 0.0000 0.0000) Gamma = 0.4330
Al1 4(c) 1/4 1/4 1/4 Al 1
Sb1 4(a) 0 0 0 Sb 1
Wyckoff sequence : c a
Volume of Unit Cell : 470.5842
OTHER Standardization with Similar Gamma :
Setting -x,-y,-z Origin ( 0.7500 0.7500 0.7500) Gamma = 0.4330
Sb1 4(c) 1/4 1/4 1/4 Sb 1
Al1 4(a) 0 0 0 Al 1
Wyckoff sequence : c a
Volume of Unit Cell : 470.5842
"""
results = {}
results['cell'] = {}
results['spacegroup'] = {}
results['setting'] = []
results['in_setting'] = False
def cell_params(results, match):
results['cell']['a'] = float(match.group(1))
results['cell']['b'] = float(match.group(2))
results['cell']['c'] = float(match.group(3))
results['cell']['alpha'] = float(match.group(4))
results['cell']['beta'] = float(match.group(5))
results['cell']['gamma'] = float(match.group(6))
def spacegroup(results, match):
results['spacegroup']['symbol'] = match.group(1)
results['spacegroup']['number'] = int(match.group(2))
#def setting_start(results,match):
# results['setting'].append({'coords':[],'occupancies':[],'wycoff':[]})
# results['in_setting'] = True
def setting_stop(results, match):
results['in_setting'] = False
def read_coords(results, match):
if not results['in_setting']:
results['setting'].append({'coords': [], 'occupancies': [], 'wycoff': []})
results['in_setting'] = True
results['setting'][-1]['coords'].append([match.group(4), match.group(5), match.group(6)])
results['setting'][-1]['occupancies'].append(match.group(1))
results['setting'][-1]['wycoff'].append([match.group(3)])
results['in_setting'] = True
#def debug(results,match):
# print("DEBUG",match)
out = httk.basic.micro_pyawk(ioa, [
#['^Wyckoff',None,setting_stop],
['^ *$', None, setting_stop],
['^Cell parameters : +([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+) +([0-9.-]+)', None, cell_params],
['^Space group symbol : +(.+) +Number in IT : +([0-9]+)', None, spacegroup],
['^ +([a-zA-Z]+)([0-9]*)#* +([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+)', None, read_coords],
#['^Setting',None,setting_start],
], results=results, debug=False)
structdata = dict(out['cell'].items() +
[('coords', out['setting'][0]['coords']),
('occupancies', out['setting'][0]['occupancies']),
('spacegroup', out['spacegroup']['symbol'])
])
sgstruct = Structure.create(**structdata)
return sgstruct
def platon_lis_to_struct_broken(ioa):
"""
Example input format::
============
====================================================== Crystal Data ================================================================
============
Input Cell (Lattice Type: P) - Temp = 0K Reduced Cell (Acta Cryst.(1976),A32,297-298)
--------------------------------------------------------------------------------- ------------------------------------------------
a = 3.47100 Angstrom alpha = 90 Degree a = 3.471 alpha = 90.00 V = 79.6
b = 3.47100 beta = 90 b = 3.471 beta = 90.00
c = 6.60300 gamma = 90 c = 6.603 gamma = 90.00
...
------------------------------------------------------------------------------------------------------------------------------------
Flags Label Fractional Coordinates (x,y,z) Orthogonal Coordinates (XO,YO,ZO) Site SSN*SSOF = S.O.F Move Type
------------------------------------------------------------------------------------------------------------------------------------
- Ag(1) 1/4 1/4 0.61200 0.8677 0.8677 4.0410 4mm 8 1/8 1 - Met
- Zr(2) 1/4 1/4 0.13700 0.8677 0.8677 0.9046 4mm 8 1/8 1 - Met
- Ag(1)a -1/4 -1/4 -0.61200 -0.8677 -0.8677 -4.0410 4mm 8 1/8 1 5.455 Met
- Zr(2)a -1/4 -1/4 -0.13700 -0.8677 -0.8677 -0.9046 4mm 8 1/8 1 5.455 Met
- Ag(1)b -1/4 -1/4 0.38800 -0.8678 -0.8678 2.5620 4mm 8 1/8 1 5.456 Met
- Zr(2)b -1/4 -1/4 0.86300 -0.8678 -0.8678 5.6984 4mm 8 1/8 1 5.456 Met
- Ag(1)c -1/4 3/4 -0.61200 -0.8677 2.6033 -4.0410 4mm 8 1/8 1 5.465 Met
- Zr(2)c -1/4 3/4 -0.13700 -0.8678 2.6033 -0.9046 4mm 8 1/8 1 5.465 Met
- Ag(1)d -1/4 3/4 0.38800 -0.8678 2.6033 2.5620 4mm 8 1/8 1 5.466 Met
- Zr(2)d -1/4 3/4 0.86300 -0.8678 2.6032 5.6984 4mm 8 1/8 1 5.466 Met
- Ag(1)e 3/4 -1/4 -0.61200 2.6033 -0.8677 -4.0410 4mm 8 1/8 1 5.555 Met
- Zr(2)e 3/4 -1/4 -0.13700 2.6033 -0.8677 -0.9046 4mm 8 1/8 1 5.555 Met
- Ag(1)f 3/4 -1/4 0.38800 2.6033 -0.8678 2.5620 4mm 8 1/8 1 5.556 Met
- Zr(2)f 3/4 -1/4 0.86300 2.6032 -0.8678 5.6984 4mm 8 1/8 1 5.556 Met
- Ag(1)g 3/4 3/4 -0.61200 2.6033 2.6033 -4.0410 4mm 8 1/8 1 5.565 Met
- Zr(2)g 3/4 3/4 -0.13700 2.6033 2.6033 -0.9046 4mm 8 1/8 1 5.565 Met
- Ag(1)h 3/4 3/4 0.38800 2.6033 2.6033 2.5620 4mm 8 1/8 1 5.566 Met
- Zr(2)h 3/4 3/4 0.86300 2.6032 2.6032 5.6984 4mm 8 1/8 1 5.566 Met
====================================================================================================================================
"""
ioa = httk.IoAdapterFileReader(ioa)
seen_coords = set()
def read_spacegroup(results, match):
results['spacegroup'] = match.group(1).strip()
def read_a_alpha(results, match):
results['a'] = float(match.group(1).replace('(', '').replace(')', ''))
results['alpha'] = float(match.group(3).replace('(', '').replace(')', ''))
def read_b_beta(results, match):
results['b'] = float(match.group(1).replace('(', '').replace(')', ''))
results['beta'] = float(match.group(3).replace('(', '').replace(')', ''))
def read_c_gamma(results, match):
results['c'] = float(match.group(1).replace('(', '').replace(')', ''))
results['gamma'] = float(match.group(3).replace('(', '').replace(')', ''))
def read_coords(results, match):
sys.stdout.write("\n>>|")
#for i in range(1,14):
# sys.stdout.write(match.group(i)+"|")
species = periodictable.atomic_number(match.group(1))
ratio = FracVector.create(re.sub(r'\([^)]*\)', '', match.group(11)))
a1 = re.sub(r'\([^)]*\)', '', match.group(2))
b1 = re.sub(r'\([^)]*\)', '', match.group(3))
c1 = re.sub(r'\([^)]*\)', '', match.group(4))
a = match.group(2).replace('(', '').replace(')', '')
b = match.group(3).replace('(', '').replace(')', '')
c = match.group(4).replace('(', '').replace(')', '')
coord = FracVector.create([a1, b1, c1]).normalize()
sys.stdout.write(str(species)+" "+str(coord.to_floats()))
limcoord = FracVector.create([a1, b1, c1]).normalize()
coordtuple = ((species, ratio.to_tuple()), limcoord.to_tuple())
if coordtuple in seen_coords:
return
results['occupancies'].append((species, float(ratio)))
results['coords'].append(coord)
seen_coords.add(coordtuple)
def in_table(results, match):
results['in_table'] = True
def end_table(results, match):
results['in_table'] = False
def section(results, match):
results['section'] = match.group(1)
results = {}
results['spacegroup'] = None
results['section'] = None
results['in_table'] = None
results['occupancies'] = []
results['coords'] = []
out = httk.basic.micro_pyawk(ioa, [
['^ *Space Group +(([^ ]+ )+) +', lambda results, match: results['section'] == 'Space Group Symmetry' and results['spacegroup'] is None, read_spacegroup],
['^ *a = +([0-9.()-]+) +(Angstrom)? +alpha = +([0-9.()-]+)', lambda results, match: results['section'] == 'Crystal Data', read_a_alpha],
['^ *b = +([0-9.()-]+) +(Angstrom)? +beta = +([0-9.()-]+)', lambda results, match: results['section'] == 'Crystal Data', read_b_beta],
['^ *c = +([0-9.()-]+) +(Angstrom)? +gamma = +([0-9.()-]+)', lambda results, match: results['section'] == 'Crystal Data', read_c_gamma],
['^ Asymmetric Residue Unit \(= ARU\) Code List *$', lambda results, match: results['in_table'], end_table],
#['^ *=+ *$',lambda results,match: results['in_table']==True,end_table],
['^[^ ]* +[^A-Z]*([a-zA-Z]+)[^ ]* +([/0-9.()-]+) +([/0-9.()-]+) +([/0-9.()-]+) +([/0-9.()-]+) +([/0-9.()-]+) +([/0-9.()-]+) +([^ ]*) +([/0-9.()-]+) +([/0-9.()-]+) +([/0-9.()-]+) +([/0-9.()-]+) +([^ \n]+) *$', lambda results, match: results['in_table'], read_coords],
['^ *Flags Label +Fractional Coordinates \(x,y,z\) +Orthogonal Coordinates \(XO,YO,ZO\) +',
lambda results, match: results['in_table'] is None and results['section'] == 'Space Group Symmetry', in_table],
['^ *=+ ([A-Za-z ]+) =+ *$', None, section],
], results=results, debug=False)
# If we only have =1 occupancy everywhere, drop the occupancy ratio
simple_occs = []
for occupancy in out['occupancies']:
if occupancy[1] > (1-1e-6):
occupancies = out['occupancies']
break
simple_occs.append(occupancy[0])
else:
occupancies = simple_occs
#print("OUT",out['occupancies'])
#exit(0)
struct = Structure.create(a=out['a'], b=out['b'], c=out['c'], alpha=out['alpha'], beta=out['beta'],
gamma=out['gamma'], occupancies=occupancies, coords=out['coords'], tags={'platon_sg': out['spacegroup']}).round()
return struct
def platon_styin_to_sgstruct(ioa):
"""
Example input:
F -4 3 M id=[0] dblock_code=[44325-ICSD] formula=
5.5000 5.5000 5.5000 90.0000 90.0000 90.0000
N
Sb1 0.25000 0.25000 0.25000
Al1 0.00000 0.00000 0.00000
END
END
"""
ioa = httk.IoAdapterFileReader(ioa)
# print(ioa.file.read())
# exit()
#
# fi = iter(ioa)
#
# spg_comment = next(fi).strip()
# spgsymbol = spg_comment[:15]
# comment = spg_comment[16:]
# a,b,c,alpha,beta,gamma = [float(x) for x in next(fi).strip().split()]
#
# coords = []
# occupancies = []
# for line in fi:
# strcoord = line.strip().split()
# if strcoord[0] == 'END':
# break
# coord = map(lambda x: float(x.strip()),strcoord[1:4])
# coords.append(coord)
# occupation = strcoord[0]
# occupation = re.sub('[0-9]*#*$', '', occupation)
# occupancies.append(occupation)
def read_spacegroup(results, match):
results['spacegroup'] = match.group(0).strip()
def read_cell(results, match):
results['a'] = float(match.group(1))
results['b'] = float(match.group(2))
results['c'] = float(match.group(3))
results['alpha'] = float(match.group(4))
results['beta'] = float(match.group(5))
results['gamma'] = float(match.group(6))
results['has_cell'] = True
def read_coords(results, match):
results['occupancies'].append(periodictable.atomic_number(match.group(1)))
results['coords'].append([float(match.group(2)), float(match.group(3)), float(match.group(4))])
def read_end(results, match):
results['end'] = True
results = {}
results['spacegroup'] = None
results['has_cell'] = False
results['occupancies'] = []
results['coords'] = []
results['end'] = False
out = httk.basic.micro_pyawk(ioa, [
['^ *([a-zA-Z]+)[^ ]* +([0-9.-]+) +([0-9.-]+) +([0-9.-]+) *$', lambda results, match: results['has_cell'] and not results['end'], read_coords],
['^ *([0-9.-]+) +([0-9.-]+) +([0-9.-]+) +([0-9.-]+) +([0-9.-]+) +([0-9.-]+) *$', lambda results, match: results['spacegroup'] is not None and not results['end'], read_cell],
['^ *([^ ]+ )+ ', lambda results, match: results['spacegroup'] is None and not results['end'], read_spacegroup],
['^ *[Ee][Nn][Dd] *$', lambda results, match: results['has_cell'] and not results['end'], read_end],
], results=results, debug=False)
#spacegroup = "".join(out['spacegroup'].split())
#spacegroup = spacegroup[0]+(spacegroup[1:].lower())
#print("GOT SPACEGROUP",spacegroup)
spacegroup = out['spacegroup']
sgstruct = Structure.create(a=out['a'], b=out['b'], c=out['c'], alpha=out['alpha'], beta=out['beta'],
gamma=out['gamma'], occupancies=out['occupancies'], coords=out['coords'], spacegroup=spacegroup, tags={'platon_sg': spacegroup}).round()
return sgstruct
def platon_lis_to_struct_broken2(ioa):
"""
Example input::
============
====================================================== Crystal Data ================================================================
============
Input Cell (Lattice Type: P) - Temp = 0K Reduced Cell (Acta Cryst.(1976),A32,297-298)
--------------------------------------------------------------------------------- ------------------------------------------------
a = 3.47100 Angstrom alpha = 90 Degree a = 3.471 alpha = 90.00 V = 79.6
b = 3.47100 beta = 90 b = 3.471 beta = 90.00
c = 6.60300 gamma = 90 c = 6.603 gamma = 90.00
...
====================================================================================================================================
10.0 Angstrom Coordination Sphere Around Atom I = Ag(1) [ARU = 1555.01] 1/4 1/4 0.61200 0.8677 0.8677 4.0410
------------------------------------------------------------------------------------------------------------------------------------
Nr d(I,J) To Atom J Symm_Oper. on Atom J ARU(J) Type Phi Mu X Y Z XO YO ZO
------------------------------------------------------------------------------------------------------------------------------------
1 2.9615 -- Zr(4) [ = ] Intra-135.00 34.03 -1/4 -1/4 0.86300 -0.8678 -0.8678 5.6984
2 2.9615 -- Zr(4)n [1+x,1+y,z = 1665.01] Intra 45.00 34.03 3/4 3/4 0.86300 2.6032 2.6032 5.6984
3 2.9615 -- Zr(4)j [x,1+y,z = 1565.01] Intra 135.00 34.03 -1/4 3/4 0.86300 -0.8678 2.6032 5.6984
4 2.9615 -- Zr(4)l [1+x,y,z = 1655.01] Intra -45.00 34.03 3/4 -1/4 0.86300 2.6032 -0.8678 5.6984
5 3.1364 -- Zr(3) [ = ] Intra 0.00 -90.00 1/4 1/4 0.13700 0.8677 0.8677 0.9046
"""
ioa = httk.IoAdapterFileReader(ioa)
seen_coords = set()
def read_spacegroup(results, match):
results['spacegroup'] = match.group(1).strip()
def read_a_alpha(results, match):
results['a'] = float(match.group(1).replace('(', '').replace(')', ''))
results['alpha'] = float(match.group(3).replace('(', '').replace(')', ''))
def read_b_beta(results, match):
results['b'] = float(match.group(1).replace('(', '').replace(')', ''))
results['beta'] = float(match.group(3).replace('(', '').replace(')', ''))
def read_c_gamma(results, match):
results['c'] = float(match.group(1).replace('(', '').replace(')', ''))
results['gamma'] = float(match.group(3).replace('(', '').replace(')', ''))
def read_coords(results, match):
sys.stdout.write("\n>>|")
#for i in range(1,14):
# sys.stdout.write(match.group(i)+"|")
species = periodictable.atomic_number(match.group(1))
ratio = FracVector.create(re.sub(r'\([^)]*\)', '', match.group(11)))
a1 = re.sub(r'\([^)]*\)', '', match.group(2))
b1 = re.sub(r'\([^)]*\)', '', match.group(3))
c1 = re.sub(r'\([^)]*\)', '', match.group(4))
a = match.group(2).replace('(', '').replace(')', '')
b = match.group(3).replace('(', '').replace(')', '')
c = match.group(4).replace('(', '').replace(')', '')
coord = FracVector.create([a1, b1, c1]).normalize()
sys.stdout.write(str(species)+" "+str(coord.to_floats()))
limcoord = FracVector.create([a1, b1, c1]).normalize()
coordtuple = ((species, ratio.to_tuple()), limcoord.to_tuple())
if coordtuple in seen_coords:
return
results['occupancies'].append((species, float(ratio)))
results['coords'].append(coord)
seen_coords.add(coordtuple)
def in_table(results, match):
results['in_table'] = True
def end_table(results, match):
results['in_table'] = False
def section(results, match):
results['section'] = match.group(1)
results = {}
results['spacegroup'] = None
results['section'] = None
results['in_table'] = None
results['occupancies'] = []
results['coords'] = []
out = httk.basic.micro_pyawk(ioa, [
['^ *Space Group +(([^ ]+ )+) +', lambda results, match: results['section'] == 'Space Group Symmetry' and results['spacegroup'] is None, read_spacegroup],
['^ *a = +([0-9.()-]+) +(Angstrom)? +alpha = +([0-9.()-]+)', lambda results, match: results['section'] == 'Crystal Data', read_a_alpha],
['^ *b = +([0-9.()-]+) +(Angstrom)? +beta = +([0-9.()-]+)', lambda results, match: results['section'] == 'Crystal Data', read_b_beta],
['^ *c = +([0-9.()-]+) +(Angstrom)? +gamma = +([0-9.()-]+)', lambda results, match: results['section'] == 'Crystal Data', read_c_gamma],
['^ Asymmetric Residue Unit \(= ARU\) Code List *$', lambda results, match: results['in_table'], end_table],
#['^ *=+ *$',lambda results,match: results['in_table']==True,end_table],
['^[^ ]* +[^ ]* +[^ ]* +[^A-Z]*([a-zA-Z]+)[^ ]* +.* +([/0-9.()-]+) +([/0-9.()-]+) +([/0-9.()-]+) +([/0-9.()-]+) +([/0-9.()-]+) +([/0-9.()-]+) *$', lambda results, match: results['in_table'], read_coords],
['^ *Angstrom Coordination Sphere Around Atom +',
lambda results, match: results['in_table'] is None and results['section'] == 'Space Group Symmetry', in_table],
['^ *=+ ([A-Za-z ]+) =+ *$', None, section],
], results=results, debug=False)
# If we only have =1 occupancy everywhere, drop the occupancy ratio
simple_occs = []
for occupancy in out['occupancies']:
if occupancy[1] > (1-1e-6):
occupancies = out['occupancies']
break
simple_occs.append(occupancy[0])
else:
occupancies = simple_occs
#print("OUT",out['occupancies'])
#exit(0)
struct = Structure.create(a=out['a'], b=out['b'], c=out['c'], alpha=out['alpha'], beta=out['beta'],
gamma=out['gamma'], occupancies=occupancies, coords=out['coords'], tags={'platon_sg': out['spacegroup']}).round()
return struct
# This is an example program using the High-Throughput toolkit (httk)
# This program saves a structure object
import httk
from httk.core import *
from httk.atomistic import Structure
basis = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]
coordgroups = [[[0.5, 0.5, 0.5]], [[0.0, 0.0, 0.0]],
[[0.5, 0.0, 0.0], [0.0, 0.5, 0.0], [0.0, 0.0, 0.5]]]
assignments = ['Pb', 'Ti', 'O']
struct = Structure.create(uc_basis=basis,
uc_reduced_coordgroups=coordgroups,
assignments=assignments,
uc_volume=62.79)
# One alternative
struct.io.save("PbTiO3.vasp")
print("PbTiO3.vasp saved (POSCAR format)")
# Another alternative
httk.save(struct, "PbTiO3_alt.vasp")
print("PbTiO3_alt.vasp saved (POSCAR format)")
basis = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]
coordgroups = [[[0.5, 0.5, 0.5]], [[0.0, 0.0, 0.0]], [[0.5, 0.0, 0.0]]]
assignments = ['Pb', 'Ti', 'O']
def structure_to_ase_atoms(struct):
ensure_ase_is_imported()
struct = Structure.use(struct)
if struct.has_uc_repr:
symbollist, scaled_positions = httk.iface.ase_if.uc_structure_to_symbols_and_scaled_positions(
struct)
scaled_positions = scaled_positions.to_floats()
cell = struct.uc_basis.to_floats()
symbols = []
for s in symbollist:
if is_sequence(s):
if len(s) == 1:
symbols += [s[0]]
else:
symbols += [str(s)]
else:
symbols += [s]
atoms = Atoms(symbols=symbols,
cell=cell,
scaled_positions=scaled_positions,
pbc=True)
elif struct.has_rc_repr:
symbollist, scaled_positions = httk.iface.ase_if.rc_structure_to_symbols_and_scaled_positions(
struct)
symbols = []
for s in symbollist:
if is_sequence(s):
if len(s) == 1:
symbols += [s[0]]
else:
symbols += [str(s)]
else:
symbols += [s]
hall = struct.rc_sites.hall_symbol
symops = get_symops_strs(hall)
rot, trans = ase.spacegroup.spacegroup.parse_sitesym(symops)
spgnbr, setting = spacegroup_get_number_and_setting(hall)
spg = ase.spacegroup.spacegroup.spacegroup_from_data(
no=spgnbr,
symbol=hall,
centrosymmetric=None,
scaled_primitive_cell=None,
reciprocal_cell=None,
subtrans=None,
sitesym=None,
rotations=rot,
translations=trans,
datafile=None)
atoms = crystal(symbols,
scaled_positions,
spg,
cellpar=[
float(struct.rc_a),
float(struct.rc_b),
float(struct.rc_c),
float(struct.rc_alpha),
float(struct.rc_beta),
float(struct.rc_gamma)
])
else:
raise Exception(
"ase_glue.structure_to_ase_atoms: structure has neither primcell, nor representative, representation."
)
return atoms
def spglib_out_to_struct(out):
cell = FracVector.from_floats(out[0].tolist())
coords = FracVector.from_floats(out[1].tolist())
occupations = out[2]
print("OCCUPATIONS:", occupations)
return Structure.create(cell=cell, coords=coords, occupations=occupations)
def readstruct(ioa, struct, importers=None):
fileadapter = ioadapters.IoAdapterFileReader(ioa)
if fileadapter.ext == 'structure':
struct.parse(fileadapter)
if importers is None:
try_importers = ['ase', 'openbabel']
else:
try_importers = importers
for importer in try_importers:
if importer == 'ase':
try:
import ase.io
atoms = ase.io.read(fileadapter.filename_open_workaround())
species = atoms.get_atomic_numbers()
coords = atoms.get_positions()
basis = atoms.get_cell()
return Structure(basis=basis, coords=coords, species=species)
except Exception as e:
if importers is not None:
reraise_from(
Exception,
"Error while trying ase importer: " + str(info[1]), e)
elif importer == 'openbabel':
try:
import openbabel
file = fileadapter.file
filename = fileadapter.filename
# Use babel to read data from file
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats(
obConversion.FormatFromExt(fileadapter.filename),
obConversion.FindFormat("pdb"))
obmol = openbabel.OBMol()
obConversion.ReadString(obmol, file.read())
unitcell = openbabel.toUnitCell(
obmol.GetData(openbabel.UnitCell))
unitcell.FillUnitCell(obmol)
basisvecs = unitcell.GetCellVectors()
basis = array([[
basisvecs[0].GetX(), basisvecs[0].GetY(),
basisvecs[0].GetZ()
],
[
basisvecs[1].GetX(), basisvecs[1].GetY(),
basisvecs[1].GetZ()
],
[
basisvecs[2].GetX(), basisvecs[2].GetY(),
basisvecs[2].GetZ()
]])
coords = []
species = []
for obatom in openbabel.OBMolAtomIter(obmol):
cart = openbabel.vector3(obatom.GetX(), obatom.GetY(),
obatom.GetZ())
coords.append([cart.GetX(), cart.GetY(), cart.GetZ()])
species.append(obatom.GetAtomicNum())
return Structure(basis=basis, coords=coords, species=species)
except:
if importers is not None:
info = sys.exc_info()
reraise_from(
Exception, "Error while trying openbabel importer: " +
str(info[1]), info)
raise Exception("Could not figure out a way to read structure")
return None
def cifdata_to_struct(cifdata, debug=False):
if len(cifdata) > 1:
raise Exception("httk.atomistic.atomisticio.structure_cif_io: cifdata to struct with more than one image in cifdata.")
element = cifdata[0][1]
if debug:
import pprint
pp = pprint.PrettyPrinter()
debugout = dict(element)
if 'symmetry_equiv_pos_as_xyz' in debugout:
del debugout['symmetry_equiv_pos_as_xyz']
if 'space_group_symop_operation_xyz' in debugout:
del debugout['space_group_symop_operation_xyz']
if 'space_group_symop_id' in debugout:
del debugout['space_group_symop_id']
pp.pprint(debugout)
rc_lengths = FracVector.create([element['cell_length_a'], element['cell_length_b'], element['cell_length_c']])
rc_cosangles = FracVector.create_cos([element['cell_angle_alpha'], element['cell_angle_beta'], element['cell_angle_gamma']],degrees=True)
hall_symbol = None
hm_symbol = None
spacegroupnumber = None
setting = None
symops = None
if 'symmetry_space_group_name_hall' in element:
hall_symbol = element['symmetry_space_group_name_hall']
if 'space_group_symop_operation_xyz' in element:
symops = element['space_group_symop_operation_xyz']
elif 'symmetry_equiv_pos_as_xyz' in element:
symops = element['symmetry_equiv_pos_as_xyz']
if 'symmetry_space_group_name_h-m' in element:
hm_symbol = element['symmetry_space_group_name_h-m']
if 'symmetry_Int_Tables_number' in element:
spacegroupnumber = int(element['symmetry_Int_Tables_number'])
# cif verb symmetry_cell_setting really is not defined as it would seems logical. Due to ensuing confusion, we better simply ignore it
#if 'symmetry_cell_setting' in element:
# setting = element['symmetry_cell_setting']
if hall_symbol is None and symops is None and hm_symbol is None and spacegroupnumber is None:
raise Exception("No symmetry information given in cif file, impossible to interpret coordinate data!")
spacegroup = Spacegroup.create(hall_symbol=hall_symbol, hm_symbol=hm_symbol, spacegroupnumber=spacegroupnumber, setting=setting, symops=symops)
rc_occupancies = []
rc_reduced_occupationscoords = []
wyckoff_symbols = None
multiplicities = None
if 'atom_site_wyckoff_symbol' in element:
wyckoff_symbols = element['atom_site_wyckoff_symbol']
elif 'atom_site_wyckoff_label' in element:
wyckoff_symbols = element['atom_site_wyckoff_label']
if 'atom_site_symmetry_multiplicity' in element:
multiplicities = [int(x) for x in element['atom_site_symmetry_multiplicity']]
for atom in range(len(element['atom_site_label'])):
if 'atom_site_occupancy' in element:
ratio = element['atom_site_occupancy'][atom]
else:
ratio = 1
symbol = str(re.match('[A-Z][a-z]?',element['atom_site_label'][atom]).group(0))
occup = {'atom': periodictable.atomic_number(symbol), 'ratio': FracVector.create(ratio), }
coord = [element['atom_site_fract_x'][atom], element['atom_site_fract_y'][atom], element['atom_site_fract_z'][atom]]
rc_occupancies += [occup]
rc_reduced_occupationscoords += [coord]
#print("X",rc_lengths,rc_angles,rc_reduced_occupationscoords,rc_occupancies,spacegroup,setting,wyckoff_symbols,multiplicities)
tags = {}
if 'chemical_name_common' in element:
if is_sequence(element['chemical_name_common']):
tags['name'] = element['chemical_name_common'][0]
tags['names'] = ",".join(element['chemical_name_common'])
else:
tags['name'] = element['chemical_name_common']
elif 'chemical_name_systematic' in element:
if is_sequence(element['chemical_name_systematic']):
tags['name'] = element['chemical_name_systematic'][0]
tags['names'] = ",".join(element['chemical_name_systematic'])
else:
tags['name'] = element['chemical_name_systematic']
authorlist = None
if 'publ_author_name' in element:
authorlist = []
authors = element['publ_author_name']
if not basic.is_sequence(authors):
authors = [authors]
for author in authors:
authorparts = author.partition(",")
lastname = authorparts[0].strip()
givennames = authorparts[2].strip()
authorlist += [Author.create(lastname, givennames)]
# I didn't find this in the spec, on the other hand, the publ_ space is "not specified", so, this seems
# as a logical extension of the author list in case of a cif file that has been published in a book.
# I see no harm in including it, at least.
editorlist = None
if 'publ_editor_name' in element:
editorlist = []
editors = element['publ_editor_name']
if not basic.is_sequence(editors):
editors = [editors]
for editor in editors:
editorparts = editor.partition(",")
lastname = editorparts[0].strip()
givennames = editorparts[2].strip()
editorlist += [Author.create(lastname, givennames)]
refs = None
if 'journal_name_full' in element or 'journal_name_abbrev' in element:
journal = None
journal_page_first = None
journal_page_last = None
journal_volume = None
journal_title = None
journal_book_title = None
journal_year = None
journal_issue = None
journal_publisher = None
journal_publisher_city = None
if 'journal_name_abbrev' in element:
journal = element['journal_name_abbrev']
if 'journal_name_full' in element:
journal = element['journal_name_full']
if 'journal_page_first' in element:
journal_page_first = element['journal_page_first']
if 'journal_page_last' in element:
journal_page_last = element['journal_page_last']
if 'journal_volume' in element:
journal_volume = element['journal_volume']
if 'journal_issue' in element:
journal_issue = element['journal_issue']
if 'journal_title' in element:
journal_title = element['journal_title']
if 'journal_book_title' in element:
journal_book_title = element['journal_book_title']
if 'journal_year' in element:
journal_year = element['journal_year']
if 'journal_publisher' in element:
journal_publisher = element['journal_publisher']
if 'journal_publisher_city' in element:
journal_publisher_city = element['journal_publisher_city']
if 'journal_book_publisher' in element:
journal_publisher = element['journal_book_publisher']
if 'journal_book_publisher_city' in element:
journal_publisher_city = element['journal_book_publisher_city']
refs = [Reference.create(authors=authorlist, editors=editorlist, journal=journal, journal_issue=journal_issue, journal_volume=journal_volume,
page_first=journal_page_first, page_last=journal_page_last, title=journal_title, year=journal_year, book_publisher=journal_publisher,
book_publisher_city=journal_publisher_city, book_title=journal_book_title)]
# This is based on some assumptions... IF a journal_* type tree exists, then we assume this is a 'published' cif, and
# in that case the only reference we want to keep is the one to the published work. Citations in the citation_* tree is going to be
# all the citations from that paper, which we do not want, *unless* they mark citation_coordinate_linkage. However,
# if no journal_* tree exists, then this is a 'generic' structure cif, where the citations should point to all publications of
# this structure; and we don't want to assume 'citation_coordinate_linkage'
add_all_citations = False
if refs is None or len(refs) == 0:
add_all_citations = True
if 'citation_journal_full' in element or 'citation_journal_abbrev' in element or 'citation_book_title' in element:
if refs is None:
refs = []
if 'citation_journal_full' in element:
N = len(element['citation_journal_full'])
elif 'citation_journal_abbrev' in element:
N = len(element['citation_journal_abbrev'])
elif 'citation_book_title' in element:
N = len(element['citation_book_title'])
for i in range(N):
if not add_all_citations and ('citation_coordinate_linkage' not in element or (element['citation_coordinate_linkage'][i].lower() != 'yes' and element['citation_coordinate_linkage'][i].lower() != 'y')):
continue
journal = None
journal_page_first = None
journal_page_last = None
journal_volume = None
journal_title = None
journal_book_title = None
journal_issue = None
journal_publisher = None
journal_publisher_city = None
if 'citation_journal_full' in element:
journal = element['citation_journal_full'][i]
if 'citation_journal_abbrev' in element:
journal = element['citation_journal_abbrev'][i]
if 'citation_page_first' in element:
journal_page_first = element['citation_page_first'][i]
if 'citation_page_last' in element:
journal_page_last = element['citation_page_last'][i]
if 'citation_journal_volume' in element:
journal_volume = element['citation_journal_volume'][i]
if 'citation_journal_issue' in element:
journal_issue = element['citation_journal_issue'][i]
if 'citation_title' in element:
journal_title = element['citation_title'][i]
if 'citation_book_title' in element:
journal_book_title = element['citation_book_title'][i]
if 'journal_year' in element:
journal_year = element['journal_year'][i]
if 'citation_book_publisher' in element:
journal_publisher = element['citation_book_publisher'][i]
if 'citation_book_publisher_city' in element:
journal_publisher_city = element['citation_book_publisher_city'][i]
refs += [Reference.create(authors=authorlist, editors=editorlist, journal=journal, journal_issue=journal_issue, journal_volume=journal_volume,
page_first=journal_page_first, page_last=journal_page_last, title=journal_title, year=journal_year, book_publisher=journal_publisher,
book_publisher_city=journal_publisher_city, book_title=journal_book_title)]
struct = Structure.create(rc_lengths=rc_lengths,
rc_cosangles=rc_cosangles,
rc_reduced_occupationscoords=rc_reduced_occupationscoords,
rc_occupancies=rc_occupancies,
spacegroup=spacegroup, setting=setting,
periodicity=0,
wyckoff_symbols=wyckoff_symbols, multiplicities=multiplicities, tags=tags, refs=refs)
return struct
def cif_reader_that_can_only_read_isotropy_cif(ioa):
def cell_length(results, match):
results['length_'+match.group(1)] = FracVector.create(match.group(2))
def cell_angle(results, match):
results['angle_'+match.group(1)] = FracVector.create(match.group(2))
def print_hm_and_hall(results):
grpnbr = results['grpnbr']
setting = results['setting']
hmsymb = results['hmfull']
hallsymb = spacegroups.spacegroup_get_hall(str(grpnbr)+":"+setting)
results['hall_symbol'] = hallsymb
def hm_symbol_origin(results, match):
results['out'] = True
results['hmfull'] = match.group(1)
results['hm'] = match.group(2)
if match.group(3) == 'hexagonal axes':
results['setting'] = '1'
else:
results['setting'] = str(match.group(3))
if 'hm' in results and 'grpnbr' in results:
print_hm_and_hall(results)
def hm_symbol_no_origin(results, match):
results['out'] = True
results['hmfull'] = match.group(1)
results['hm'] = match.group(1)
results['setting'] = "1"
if 'hm' in results and 'grpnbr' in results:
print_hm_and_hall(results)
def groupnbr(results, match):
results['grpnbr'] = match.group(1)
if 'hm' in results and 'grpnbr' in results:
print_hm_and_hall(results)
def coords(results, match):
newcoord = httk.FracVector.create([match.group(5), match.group(6), match.group(7)])
occup = {'atom': periodictable.atomic_number(match.group(2)), 'ratio': FracVector.create(match.group(8)), }
if match.group(4) == 'alpha':
wyckoff = '&'
else:
wyckoff = match.group(4)
multiplicities = int(match.group(3))
if newcoord in results['seen_coords']:
idx = results['seen_coords'][newcoord]
results['occups'][idx].append(occup)
else:
results['seen_coords'][newcoord] = results['idx']
results['coords'].append(newcoord)
results['occups'].append([occup])
results['wyckoff'].append(wyckoff)
results['multiplicities'].append(multiplicities)
results['idx'] += 1
results = {'idx': 0, 'occups': [], 'wyckoff': [], 'multiplicities': [], 'coords': [], 'seen_coords': {}}
httk.basic.micro_pyawk(ioa, [
['^_cell_length_([^ ]*) (.*) *$', None, cell_length],
['^_cell_angle_([^ ]*) (.*) *$', None, cell_angle],
['^_symmetry_Int_Tables_number +(.*)$', None, groupnbr],
['^_symmetry_space_group_name_H-M +"(([^()]+) \(origin choice ([0-9]+)\))" *$', None, hm_symbol_origin],
['^_symmetry_space_group_name_H-M +"(([^()]+) \((hexagonal axes)\))" *$', None, hm_symbol_origin],
['^_symmetry_space_group_name_H-M +"([^()]+)" *$', None, hm_symbol_no_origin],
['^ *([^ ]+) +([^ ]+) +([^ ]+) +([^ ]+) +([0-9.-]+) +([0-9.-]+) +([0-9.-]+) +([0-9.-]+) *$', None, coords],
], debug=False, results=results)
struct = Structure.create(rc_a=results['length_a'], rc_b=results['length_b'], rc_c=results['length_c'],
rc_alpha=results['angle_alpha'], rc_beta=results['angle_beta'], rc_gamma=results['angle_gamma'],
rc_reduced_occupationscoords=results['coords'], rc_occupancies=results['occups'],
spacegroup=results['hall_symbol'], wyckoff_symbols=results['wyckoff'], multiplicities=results['multiplicities'])
return struct