def strout2poscar(src='str.out'):
"""
str.outをposcarの記述に変換し, Poscar objをreturn
"""
with open(src, 'r') as rfile:
lines = rfile.readlines()
latt_tmp = [[float(x) for x in y.split()] for y in lines[0:3]]
trans = [[float(x) for x in y.split()] for y in lines[3:6]]
sites_tmp = [[float(x) for x in y.split()[0:3]] for y in lines[6:]]
elements = [x.split()[3].split('+')[0].split('-')[0] for x in lines[6:]]
num_atoms = [elements.count(e)
for e in sorted(set(elements), key=elements.index)]
latt = np.dot(np.array(trans), np.array(latt_tmp))
sites = np.dot(np.array(sites_tmp), np.array(latt_tmp))
posc_str = "posc_orig\n"
posc_str += "1.00\n"
posc_str += "\n".join([" ".join([str(f) for f in l]) for l in latt])
posc_str += "\n"
posc_str += " ".join(sorted(set(elements), key=elements.index)) + "\n"
posc_str += " ".join([str(d) for d in num_atoms]) + "\n"
posc_str += "Cartesian\n"
posc_str += "\n".join([" ".join([str(f) for f in s]) for s in sites])
return Poscar.from_string(posc_str)
def test_init(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
comp = poscar.struct.composition
self.assertEqual(comp, Composition.from_formula("Fe4P4O16"))
#Vasp 4 type with symbols at the end.
poscar_string = """Test1
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
direct
0.000000 0.000000 0.000000 Si
0.750000 0.500000 0.750000 F"""
poscar = Poscar.from_string(poscar_string)
self.assertEqual(poscar.struct.composition, Composition.from_formula("SiF"))
#Vasp 4 tyle file with default names, i.e. no element symbol found.
poscar_string = """Test2
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
direct
0.000000 0.000000 0.000000
0.750000 0.500000 0.750000"""
poscar = Poscar.from_string(poscar_string)
self.assertEqual(poscar.struct.composition, Composition.from_formula("HHe"))
#Vasp 4 tyle file with default names, i.e. no element symbol found.
poscar_string = """Test3
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
Selective dynamics
direct
0.000000 0.000000 0.000000 T T T Si
0.750000 0.500000 0.750000 F F F O"""
poscar = Poscar.from_string(poscar_string)
self.assertEqual(poscar.selective_dynamics, [[True, True, True], [False, False, False]])
def from_poscar_string(poscar_string, transformations=[]):
"""
Generates TransformedStructure from a poscar string.
Args:
poscar_string:
Input POSCAR string.
"""
p = Poscar.from_string(poscar_string)
if not p.true_names:
raise ValueError("Transformation can be craeted only from POSCAR strings with proper VASP5 element symbols.")
raw_string = re.sub("'", "\"", poscar_string)
s = p.struct
source_info = {'source': "uploaded POSCAR", 'datetime':str(datetime.datetime.now()), 'original_file':raw_string}
return TransformedStructure(s, transformations, [source_info])
def get_minkowski_red(structure):
"""
get a minkowski reduced structure
"""
from pymatgen.io.vaspio import Poscar
output = run_aconvasp_command(['aconvasp', '--kpath'], structure)
started = False
poscar_string = ""
for line in output[0].split("\n"):
if started or line.find("KPOINTS TO RUN") != -1:
poscar_string = poscar_string + line + "\n"
if line.find("STRUCTURE TO RUN") != -1:
started = True
if line.find("KPOINTS TO RUN") != -1:
started = False
return Poscar.from_string(poscar_string).struct
