def process_vasprun(cls, dir_name, taskname, filename, parse_dos):
"""
Process a vasprun.xml file.
"""
vasprun_file = os.path.join(dir_name, filename)
r = Vasprun(vasprun_file)
d = r.to_dict
d["dir_name"] = os.path.abspath(dir_name)
d["completed_at"] = \
str(datetime.datetime.fromtimestamp(os.path.getmtime(
vasprun_file)))
d["cif"] = str(CifWriter(r.final_structure))
d["density"] = r.final_structure.density
if parse_dos:
try:
d["dos"] = r.complete_dos.to_dict
except Exception:
logger.warn(
"No valid dos data exist in {}.\n Skipping dos".format(
dir_name))
if taskname == "relax1" or taskname == "relax2":
d["task"] = {"type": "aflow", "name": taskname}
else:
d["task"] = {"type": "standard", "name": "standard"}
return d
def write_structure(structure, filename):
"""
Write a structure to a file based on file extension. For example, anything
ending in a "cif" is assumed to be a Crystallographic Information Format
file. Supported formats include CIF, POSCAR, CSSR and pymatgen's JSON
serialized structures.
Args:
structure (Structure/IStructure): Structure to write
filename (str): A filename to write to.
"""
fname = os.path.basename(filename)
if fnmatch(fname, "*.cif*"):
writer = CifWriter(structure)
elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"):
writer = Poscar(structure)
elif fnmatch(fname.lower(), "*.cssr*"):
writer = Cssr(structure)
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename, "w") as f:
json.dump(structure, f, cls=PMGJSONEncoder)
return
else:
raise ValueError("Unrecognized file extension!")
writer.write_file(filename)
def test_CifWriter(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
writer = CifWriter(poscar.structure, find_spacegroup=True)
ans = """#generated using pymatgen
data_FePO4
_symmetry_space_group_name_H-M Pnma
_cell_length_a 10.41176687
_cell_length_b 6.06717188
_cell_length_c 4.75948954
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 62
_chemical_formula_structural FePO4
_chemical_formula_sum 'Fe4 P4 O16'
_cell_volume 300.65685512
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_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
Fe Fe1 1 0.218728 0.750000 0.474867 1
Fe Fe2 1 0.281272 0.250000 0.974867 1
Fe Fe3 1 0.718728 0.750000 0.025133 1
Fe Fe4 1 0.781272 0.250000 0.525133 1
P P5 1 0.094613 0.250000 0.418243 1
P P6 1 0.405387 0.750000 0.918243 1
P P7 1 0.594613 0.250000 0.081757 1
P P8 1 0.905387 0.750000 0.581757 1
O O9 1 0.043372 0.750000 0.707138 1
O O10 1 0.096642 0.250000 0.741320 1
O O11 1 0.165710 0.046072 0.285384 1
O O12 1 0.165710 0.453928 0.285384 1
O O13 1 0.334290 0.546072 0.785384 1
O O14 1 0.334290 0.953928 0.785384 1
O O15 1 0.403358 0.750000 0.241320 1
O O16 1 0.456628 0.250000 0.207138 1
O O17 1 0.543372 0.750000 0.792862 1
O O18 1 0.596642 0.250000 0.758680 1
O O19 1 0.665710 0.046072 0.214616 1
O O20 1 0.665710 0.453928 0.214616 1
O O21 1 0.834290 0.546072 0.714616 1
O O22 1 0.834290 0.953928 0.714616 1
O O23 1 0.903358 0.750000 0.258680 1
O O24 1 0.956628 0.250000 0.292862 1
"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
def convert_fmt(args):
iformat = args.input_format[0]
oformat = args.output_format[0]
filename = args.input_filename[0]
out_filename = args.output_filename[0]
try:
if iformat == "smart":
structure = read_structure(filename)
if iformat == "POSCAR":
p = Poscar.from_file(filename)
structure = p.structure
elif iformat == "CIF":
r = CifParser(filename)
structure = r.get_structures()[0]
elif iformat == "CSSR":
structure = Cssr.from_file(filename).structure
if oformat == "smart":
write_structure(structure, out_filename)
elif oformat == "POSCAR":
p = Poscar(structure)
p.write_file(out_filename)
elif oformat == "CIF":
w = CifWriter(structure)
w.write_file(out_filename)
elif oformat == "CSSR":
c = Cssr(structure)
c.write_file(out_filename)
elif oformat == "VASP":
input_set = MPVaspInputSet()
ts = TransformedStructure(structure, [],
history=[{
"source":
"file",
"datetime":
str(datetime.datetime.now()),
"original_file":
open(filename).read()
}])
ts.write_vasp_input(input_set, output_dir=out_filename)
elif oformat == "MITVASP":
input_set = MITVaspInputSet()
ts = TransformedStructure(structure, [],
history=[{
"source":
"file",
"datetime":
str(datetime.datetime.now()),
"original_file":
open(filename).read()
}])
ts.write_vasp_input(input_set, output_dir=out_filename)
except Exception as ex:
print "Error converting file. Are they in the right format?"
print str(ex)
def test_specie_cifwriter(self):
si4 = Specie("Si", 4)
si3 = Specie("Si", 3)
n = Specie("N", -3)
coords = list()
coords.append(np.array([0, 0, 0]))
coords.append(np.array([0.75, 0.5, 0.75]))
coords.append(np.array([0.5, 0.5, 0.5]))
lattice = Lattice(np.array([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]))
struct = Structure(lattice, [si4, {si3:0.5, n:0.5}, n], coords)
writer = CifWriter(struct)
ans = """#generated using pymatgen
data_Si1.5N1.5
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 3.84019793
_cell_length_b 3.84019899
_cell_length_c 3.84019793
_cell_angle_alpha 119.99999086
_cell_angle_beta 90.00000000
_cell_angle_gamma 60.00000914
_symmetry_Int_Tables_number 1
_chemical_formula_structural Si1.5N1.5
_chemical_formula_sum 'Si1.5 N1.5'
_cell_volume 40.0447946443
_cell_formula_units_Z 0
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Si3+ 3.0
Si4+ 4.0
N3- -3.0
loop_
_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
Si4+ Si1 1 0.000000 0.000000 0.000000 1
Si3+ Si2 1 0.750000 0.500000 0.750000 0.5
N3- N3 1 0.750000 0.500000 0.750000 0.5
N3- N4 1 0.500000 0.500000 0.500000 1
"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
def batch_write_vasp_input(structures,
vasp_input_set,
output_dir,
make_dir_if_not_present=True,
subfolder=None,
sanitize=False,
include_cif=False):
"""
Batch write vasp input for a sequence of structures to
output_dir, following the format output_dir/{group}/{formula}_{number}.
Args:
structures:
Sequence of Structures.
vasp_input_set:
pymatgen.io.vaspio_set.VaspInputSet like object that creates
vasp input files from structures
output_dir:
Directory to output files
make_dir_if_not_present:
Create the directory if not present. Defaults to True.
subfolder:
function to create subdirectory name from structure.
Defaults to simply "formula_count".
sanitize:
Boolean indicating whether to sanitize the structure before
writing the VASP input files. Sanitized output are generally easier
for viewing and certain forms of analysis. Defaults to False.
include_cif:
Boolean indication whether to output a CIF as well. CIF files are
generally better supported in visualization programs.
"""
for i, s in enumerate(structures):
formula = re.sub("\s+", "", s.formula)
if subfolder is not None:
subdir = subfolder(s)
dirname = os.path.join(output_dir, subdir)
else:
dirname = os.path.join(output_dir, '{}_{}'.format(formula, i))
if sanitize:
s = s.copy(sanitize=True)
vasp_input_set.write_input(
s, dirname, make_dir_if_not_present=make_dir_if_not_present)
if include_cif:
from pymatgen.io.cifio import CifWriter
writer = CifWriter(s)
writer.write_file(
os.path.join(dirname, "{}_{}.cif".format(formula, i)))
def test_symmetrized(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
writer = CifWriter(poscar.structure, find_spacegroup=True,
symprec=0.1)
ans = """#generated using pymatgen
data_FePO4
_symmetry_space_group_name_H-M Pnma
_cell_length_a 10.41176687
_cell_length_b 6.06717188
_cell_length_c 4.75948954
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 62
_chemical_formula_structural FePO4
_chemical_formula_sum 'Fe4 P4 O16'
_cell_volume 300.65685512
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
2 '-x, -y, -z'
3 '-x+1/2, -y, z+1/2'
4 'x+1/2, y, -z+1/2'
5 'x+1/2, -y+1/2, -z+1/2'
6 '-x+1/2, y+1/2, z+1/2'
7 '-x, y+1/2, -z'
8 'x, -y+1/2, z'
loop_
_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
Fe Fe1 4 0.218728 0.750000 0.474867 1
P P2 4 0.094613 0.250000 0.418243 1
O O3 4 0.043372 0.750000 0.707138 1
O O4 4 0.096642 0.250000 0.741320 1
O O5 8 0.165710 0.046072 0.285384 1"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
def batch_write_vasp_input(transformed_structures,
vasp_input_set,
output_dir,
create_directory=True,
subfolder=None,
include_cif=False):
"""
Batch write vasp input for a sequence of transformed structures to
output_dir, following the format output_dir/{group}/{formula}_{number}.
Args:
transformed_structures:
Sequence of TransformedStructures.
vasp_input_set:
pymatgen.io.vaspio_set.VaspInputSet like object that creates
vasp input files from structures
output_dir:
Directory to output files
create_directory:
Create the directory if not present. Defaults to True.
subfolder:
function to create subdirectory name from transformed_structure.
eg. lambda x: x.other_parameters["tags"][0] to use the first tag.
include_cif:
Boolean indication whether to output a CIF as well. CIF files are
generally better supported in visualization programs.
"""
for i, s in enumerate(transformed_structures):
formula = re.sub("\s+", "", s.final_structure.formula)
if subfolder is not None:
subdir = subfolder(s)
dirname = os.path.join(output_dir, subdir,
"{}_{}".format(formula, i))
else:
dirname = os.path.join(output_dir, "{}_{}".format(formula, i))
s.write_vasp_input(vasp_input_set,
dirname,
create_directory=create_directory)
if include_cif:
from pymatgen.io.cifio import CifWriter
writer = CifWriter(s.final_structure)
writer.write_file(os.path.join(dirname, "{}.cif".format(formula)))
def move_atom(input_cif, output_cif, atom_idx, displacement_vec):
"""
Reads input cif (as file name), moves atom by displacement vector (in
angstroms), and writes to output_cif (as file name).
Currently, doesn't take into account the symmetry operations. This is
theoretically possible with PyMatGen, although I found it to be buggy so
decided it might not be worth it.
Useful things to look up for implementing this:
pymatgen.symmetry.analyzer.SpacegroupAnalyzer.get_symmetrized_structure
and its resulting method
find_equivalent_sites()
"""
parser = CifParser(input_cif)
struct = parser.get_structures()[0]
lat_const = np.array(struct.lattice.abc)
frac_pos = struct[atom_idx].frac_coords
new_pos = frac_pos + displacement_vec / lat_const
struct[atom_idx] = struct[atom_idx].species_and_occu.elements[0], new_pos
writer = CifWriter(struct)
writer.write_file(output_cif)
def test_specie_cifwriter(self):
si4 = Specie("Si", 4)
si3 = Specie("Si", 3)
n = Specie("N", -3)
coords = list()
coords.append(np.array([0, 0, 0]))
coords.append(np.array([0.75, 0.5, 0.75]))
coords.append(np.array([0.5, 0.5, 0.5]))
lattice = Lattice(
np.array([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]))
struct = Structure(lattice, [si4, {si3: 0.5, n: 0.5}, n], coords)
writer = CifWriter(struct)
ans = """#\#CIF1.1
##########################################################################
# Crystallographic Information Format file
# Produced by PyCifRW module
#
# This is a CIF file. CIF has been adopted by the International
# Union of Crystallography as the standard for data archiving and
# transmission.
#
# For information on this file format, follow the CIF links at
# http://www.iucr.org
##########################################################################
data_Si1.5N1.5
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 3.8401979337
_cell_length_b 3.84019899434
_cell_length_c 3.84019793372
_cell_angle_alpha 119.999990864
_cell_angle_beta 90.0
_cell_angle_gamma 60.0000091373
_chemical_name_systematic 'Generated by pymatgen'
_symmetry_Int_Tables_number 1
_chemical_formula_structural Si1.5N1.5
_chemical_formula_sum 'Si1.5 N1.5'
_cell_volume 40.0447946443
_cell_formula_units_Z 0
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Si4+ 4.0
N3- -3.0
Si3+ 3.0
loop_
_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_attached_hydrogens
_atom_site_B_iso_or_equiv
_atom_site_occupancy
Si4+ Si1 1 0.000000 0.000000 0.000000 0 . 1
N3- N2 1 0.750000 0.500000 0.750000 0 . 0.5
Si3+ Si3 1 0.750000 0.500000 0.750000 0 . 0.5
N3- N4 1 0.500000 0.500000 0.500000 0 . 1
"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
def test_CifWriter(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
writer = CifWriter(poscar.structure, find_spacegroup=True)
print str(writer)
ans = """#\#CIF1.1
##########################################################################
# Crystallographic Information Format file
# Produced by PyCifRW module
#
# This is a CIF file. CIF has been adopted by the International
# Union of Crystallography as the standard for data archiving and
# transmission.
#
# For information on this file format, follow the CIF links at
# http://www.iucr.org
##########################################################################
data_FePO4
_symmetry_space_group_name_H-M Pnma
_cell_length_a 10.4117668699
_cell_length_b 6.06717187997
_cell_length_c 4.75948953998
_cell_angle_alpha 90.0
_cell_angle_beta 90.0
_cell_angle_gamma 90.0
_chemical_name_systematic 'Generated by pymatgen'
_symmetry_Int_Tables_number 62
_chemical_formula_structural FePO4
_chemical_formula_sum 'Fe4 P4 O16'
_cell_volume 300.65685512
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_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_attached_hydrogens
_atom_site_B_iso_or_equiv
_atom_site_occupancy
Fe Fe1 1 0.218728 0.750000 0.474867 0 . 1
Fe Fe2 1 0.281272 0.250000 0.974867 0 . 1
Fe Fe3 1 0.718728 0.750000 0.025133 0 . 1
Fe Fe4 1 0.781272 0.250000 0.525133 0 . 1
P P5 1 0.094613 0.250000 0.418243 0 . 1
P P6 1 0.405387 0.750000 0.918243 0 . 1
P P7 1 0.594613 0.250000 0.081757 0 . 1
P P8 1 0.905387 0.750000 0.581757 0 . 1
O O9 1 0.043372 0.750000 0.707138 0 . 1
O O10 1 0.096642 0.250000 0.741320 0 . 1
O O11 1 0.165710 0.046072 0.285384 0 . 1
O O12 1 0.165710 0.453928 0.285384 0 . 1
O O13 1 0.334290 0.546072 0.785384 0 . 1
O O14 1 0.334290 0.953928 0.785384 0 . 1
O O15 1 0.403358 0.750000 0.241320 0 . 1
O O16 1 0.456628 0.250000 0.207138 0 . 1
O O17 1 0.543372 0.750000 0.792862 0 . 1
O O18 1 0.596642 0.250000 0.758680 0 . 1
O O19 1 0.665710 0.046072 0.214616 0 . 1
O O20 1 0.665710 0.453928 0.214616 0 . 1
O O21 1 0.834290 0.546072 0.714616 0 . 1
O O22 1 0.834290 0.953928 0.714616 0 . 1
O O23 1 0.903358 0.750000 0.258680 0 . 1
O O24 1 0.956628 0.250000 0.292862 0 . 1
"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
