def write(struct,
filename=None,
comments=None,
direct=True,
distinct_by_ox=False,
vasp4=False,
**kwargs):
"""
Write a :mod:`~qmpy.Structure` to a file or string.
Arguments:
struct: A `~qmpy.Structure` object.
Keyword Arguments:
filename:
If None, returns a string.
direct:
If True, write POSCAR in fractional coordinates. If False, returns
a POSCAR in cartesian coordinates.
distinct_by_ox:
If True, elements with different specified oxidation states will be
treated as different species. i.e. the elements line of Fe3O4 would
read Fe Fe O (Fe3+, Fe4+, O2-). This can be useful for breaking
symmetry, or for specifying different U-values for different
oxidation state elements.
vasp4:
If True, omits the species line.
Examples::
>>> s = io.read(INSTALL_PATH+'/io/files/POSCAR_BCC')
>>> print io.poscar.write(s)
Cu
1.0
3.000000 0.000000 0.000000
0.000000 3.000000 0.000000
0.000000 0.000000 3.000000
Cu
2
direct
0.0000000000 0.0000000000 0.0000000000
0.5000000000 0.5000000000 0.5000000000
>>> io.poscar.write(s, '/tmp/POSCAR')
"""
comp = struct.comp
struct.atoms = atom_sort(struct.atoms)
cdict = defaultdict(int)
if not distinct_by_ox:
ordered_keys = sorted(comp.keys())
for a in struct:
cdict[a.element_id] += 1
counts = [int(cdict[k]) for k in ordered_keys]
else:
for a in struct.atoms:
if int(a.oxidation_state) != a.oxidation_state:
cdict['%s%+f' % (a.element_id, a.oxidation_state)] += 1
else:
cdict['%s%+d' % (a.element_id, a.oxidation_state)] += 1
ordered_keys = sorted([k for k in cdict.keys()])
counts = [int(cdict[k]) for k in ordered_keys]
if comments is not None:
poscar = '# %s \n1.0\n' % (comments)
else:
poscar = ' '.join(set(a.element_id for a in struct.atoms)) + '\n1.0\n'
cell = '\n'.join(
[' '.join(['%16.12f' % v for v in vec]) for vec in struct.cell])
poscar += cell + '\n'
names = ' '.join(a for a in ordered_keys) + '\n'
ntypes = ' '.join(str(n) for n in counts) + '\n'
if not vasp4:
poscar += names
poscar += ntypes
if direct:
poscar += 'Direct\n'
for x, y, z in struct.coords:
poscar += '%16.12f %16.12f %16.12f\n' % (x, y, z)
else:
poscar += 'Cartesian\n'
for x, y, z in struct.cartesian_coords:
poscar += ' %16.12f %16.12f %16.12f\n' % (x, y, z)
if filename:
open(filename, 'w').write(poscar)
else:
return poscar
def write(struct, filename=None, comments=None, direct=True,
distinct_by_ox=False, vasp4=False, **kwargs):
"""
Write a :mod:`~qmpy.Structure` to a file or string.
Arguments:
struct: A `~qmpy.Structure` object.
Keyword Arguments:
filename:
If None, returns a string.
direct:
If True, write POSCAR in fractional coordinates. If False, returns
a POSCAR in cartesian coordinates.
distinct_by_ox:
If True, elements with different specified oxidation states will be
treated as different species. i.e. the elements line of Fe3O4 would
read Fe Fe O (Fe3+, Fe4+, O2-). This can be useful for breaking
symmetry, or for specifying different U-values for different
oxidation state elements.
vasp4:
If True, omits the species line.
Examples::
>>> s = io.read(INSTALL_PATH+'/io/files/POSCAR_BCC')
>>> print io.poscar.write(s)
Cu
1.0
3.000000 0.000000 0.000000
0.000000 3.000000 0.000000
0.000000 0.000000 3.000000
Cu
2
direct
0.0000000000 0.0000000000 0.0000000000
0.5000000000 0.5000000000 0.5000000000
>>> io.poscar.write(s, '/tmp/POSCAR')
"""
comp = struct.comp
struct.atoms = atom_sort(struct.atoms)
cdict = defaultdict(int)
if not distinct_by_ox:
ordered_keys = sorted(comp.keys())
for a in struct:
cdict[a.element_id] += 1
counts = [ int(cdict[k]) for k in ordered_keys ]
else:
for a in struct.atoms:
if int(a.oxidation_state) != a.oxidation_state:
cdict['%s%+f' % (a.element_id, a.oxidation_state)] += 1
else:
cdict['%s%+d' % (a.element_id, a.oxidation_state)] += 1
ordered_keys = sorted([ k for k in cdict.keys() ])
counts = [ int(cdict[k]) for k in ordered_keys ]
if comments is not None:
poscar = '# %s \n 1.0\n' %(comments)
else:
poscar = ' '.join(set(a.element_id for a in struct.atoms)) + '\n 1.0\n'
cell = '\n'.join([ ' '.join([ '%f' % v for v in vec ]) for vec in
struct.cell ])
poscar += cell +'\n'
names = ' '.join( a for a in ordered_keys ) + '\n'
ntypes = ' '.join( str(n) for n in counts ) + '\n'
if not vasp4:
poscar += names
poscar += ntypes
if direct:
poscar += 'direct\n'
for x,y,z in struct.coords:
poscar += ' %.10f %.10f %.10f\n' % (x,y,z)
else:
poscar += 'cartesian\n'
for x, y, z in struct.cartesian_coords:
poscar += ' %.10f %.10f %.10f\n' % (x,y,z)
if filename:
open(filename, 'w').write(poscar)
else:
return poscar
