def str_template(name, scale, cell): from pylada.crystal import Structure structure = Structure() structure.name = name structure.scale = scale structure.cell = cell return structure
def test_system():
from pylada.crystal import Structure
from pylada.vasp import Vasp
a = Vasp()
b = Structure()
assert a.system is None
assert a._input['system'].keyword == 'system'
assert a._input['system'].output_map(vasp=a, structure=b) is None
a.system = 'system'
assert a.system == 'system'
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a,
structure=b)['system'] == 'system'
b.name = 'hello'
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(
vasp=a, structure=b)['system'] == 'system: hello'
a.system = None
assert a.system is None
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a,
structure=b)['system'] == 'hello'
a.system = None
assert a.system is None
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a,
structure=b)['system'] == 'hello'
def test_system():
from pylada.crystal import Structure
from pylada.vasp import Vasp
a = Vasp()
b = Structure()
assert a.system is None
assert a._input['system'].keyword == 'system'
assert a._input['system'].output_map(vasp=a, structure=b) is None
a.system = 'system'
assert a.system == 'system'
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'system'
b.name = 'hello'
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'system: hello'
a.system = None
assert a.system is None
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'hello'
a.system = None
assert a.system is None
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'hello'
structure = Structure()
structure.set_cell = (4, 0, 0.5),\
(0, 1, 0),\
(0, 0, 0.5)
structure = fill_structure(structure.cell)
for i, atom in enumerate(structure.atoms):
atom.type = "Si" if i < len(structure.atoms)/2 else "Ge"
result_str = Structure()
result_str.scale = 5.450000e+00
result_str.set_cell = (4.068890e+00, -4.235770e-18, 5.083297e-01),\
(-1.694308e-17, 1.016103e+00, 2.238072e-18),\
(-2.252168e-03, 8.711913e-18, 5.083297e-01)
result_str.weight = 1.000000e+00
result_str.name = ""
result_str.energy = 0.0938967086716
result_str.add_atom = (0.000000e+00, 0.000000e+00, 0.000000e+00), "Si", 0, 0
result_str.add_atom = (2.541649e-01, 2.473273e-01, 2.541649e-01), "Si", 1, 0
result_str.add_atom = (3.567265e+00, 5.062000e-01, -8.956567e-03), "Si", 0, 0
result_str.add_atom = (3.821430e+00, 7.572301e-01, 2.452083e-01), "Si", 1, 0
result_str.add_atom = (3.065136e+00, -1.851371e-03, -1.515736e-02), "Si", 0, 0
result_str.add_atom = (3.319301e+00, 2.491787e-01, 2.390075e-01), "Si", 1, 0
result_str.add_atom = (2.563510e+00, 5.080514e-01, -2.186176e-02), "Si", 0, 0
result_str.add_atom = (2.817675e+00, 7.553787e-01, 2.323031e-01), "Si", 1, 0
result_str.add_atom = (2.055673e+00, -6.642716e-03, -2.235452e-02), "Ge", 0, 0
result_str.add_atom = (2.309838e+00, 2.539701e-01, 2.318104e-01), "Ge", 1, 0
result_str.add_atom = (1.539450e+00, 5.026981e-01, -1.446032e-02), "Ge", 0, 0
result_str.add_atom = (1.793614e+00, 7.607320e-01, 2.397046e-01), "Ge", 1, 0
result_str.add_atom = (1.024061e+00, -5.353269e-03, -7.401445e-03), "Ge", 0, 0
result_str.add_atom = (1.278226e+00, 2.526806e-01, 2.467634e-01), "Ge", 1, 0
def poscar(path="POSCAR", types=None):
""" Tries to read a VASP POSCAR file.
:param path: Path to the POSCAR file. Can also be an object with
file-like behavior.
:type path: str or file object
:param types: Species in the POSCAR.
:type types: None or sequence of str
:return: `pylada.crystal.Structure` instance.
"""
import re
from os.path import join, exists, isdir
from copy import deepcopy
from numpy import array, dot, transpose
from numpy.linalg import det
from quantities import angstrom
from . import Structure
from .. import error
# if types is not none, converts to a list of strings.
if types is not None:
if isinstance(types, str):
types = [types] # can't see another way of doing this...
elif not hasattr(types, "__iter__"):
types = [str(types)] # single lone vasp.specie.Specie
else:
types = [str(s) for s in types]
if path is None:
path = "POSCAR"
if not hasattr(path, 'read'):
assert exists(path), IOError("Could not find path %s." % (path))
if isdir(path):
assert exists(join(path, "POSCAR")), IOError("Could not find POSCAR in %s." % (path))
path = join(path, "POSCAR")
result = Structure()
poscar = path if hasattr(path, "read") else open(path, 'r')
try:
# gets name of structure
result.name = poscar.readline().strip()
if len(result.name) > 0 and result.name[0] == "#":
result.name = result.name[1:].strip()
# reads scale
scale = float(poscar.readline().split()[0])
# gets cell vectors.
cell = []
for i in range(3):
line = poscar.readline()
assert len(line.split()) >= 3,\
RuntimeError("Could not read column vector from poscar: %s." % (line))
cell.append([float(f) for f in line.split()[:3]])
result.cell = transpose(array(cell))
vol = det(cell)
if scale < 1.E-8:
scale = abs(scale / vol) ** (1.0 / 3)
print(result)
print(scale)
result.scale = scale * angstrom
# checks for vasp 5 input.
is_vasp_5 = True
line = poscar.readline().split()
for i in line:
if not re.match(r"[A-Z][a-z]?", i):
is_vasp_5 = False
break
if is_vasp_5:
text_types = deepcopy(line)
if types is not None and not set(text_types).issubset(set(types)):
raise error.ValueError("Unknown species in poscar: {0} not in {1}."
.format(text_types, types))
types = text_types
line = poscar.readline().split()
if types is None:
raise RuntimeError("No atomic species given in POSCAR or input.")
# checks/reads for number of each specie
if len(types) < len(line):
raise RuntimeError("Too many atomic species in POSCAR.")
nb_atoms = [int(u) for u in line]
# Check whether selective dynamics, cartesian, or direct.
first_char = poscar.readline().strip().lower()[0]
selective_dynamics = False
if first_char == 's':
selective_dynamics = True
first_char = poscar.readline().strip().lower()[0]
# Checks whether cartesian or direct.
is_direct = first_char not in ['c', 'k']
# reads atoms.
for n, specie in zip(nb_atoms, types):
for i in range(n):
line = poscar.readline().split()
pos = array([float(u) for u in line[:3]], dtype="float64")
if is_direct:
pos = dot(result.cell, pos)
result.add_atom(pos=pos, type=specie)
if selective_dynamics:
for which, freeze in zip(line[3:], ['x', 'y', 'z']):
if which.lower()[0] == 't':
result[-1].freeze = getattr(result[-1], 'freeze', '') + freeze
finally:
poscar.close()
return result
def poscar(path="POSCAR", types=None):
""" Tries to read a VASP POSCAR file.
:param path: Path to the POSCAR file. Can also be an object with
file-like behavior.
:type path: str or file object
:param types: Species in the POSCAR.
:type types: None or sequence of str
:return: `pylada.crystal.Structure` instance.
"""
import re
from os.path import join, exists, isdir
from copy import deepcopy
from numpy import array, dot, transpose
from numpy.linalg import det
from quantities import angstrom
from . import Structure
# if types is not none, converts to a list of strings.
if types is not None:
if isinstance(types, str): types = [types] # can't see another way of doing this...
elif not hasattr(types, "__iter__"): types = [str(types)] # single lone vasp.specie.Specie
else: types = [str(s) for s in types]
if path is None: path = "POSCAR"
if not hasattr(path, 'read'):
assert exists(path), IOError("Could not find path %s." % (path))
if isdir(path):
assert exists(join(path, "POSCAR")), IOError("Could not find POSCAR in %s." % (path))
path = join(path, "POSCAR")
result = Structure()
poscar = path if hasattr(path, "read") else open(path, 'r')
try:
# gets name of structure
result.name = poscar.readline().strip()
if len(result.name) > 0:
if result.name[0] == "#": result.name = result.name[1:].strip()
# reads scale
scale = float(poscar.readline().split()[0])
# gets cell vectors.
cell = []
for i in range(3):
line = poscar.readline()
assert len(line.split()) >= 3,\
RuntimeError("Could not read column vector from poscar: %s." % (line))
cell.append( [float(f) for f in line.split()[:3]] )
result.cell = transpose(array(cell))
vol = det(cell)
if scale < 1.E-8 : scale = abs(scale/vol) **(1.0/3)
result.scale = scale * angstrom
# checks for vasp 5 input.
is_vasp_5 = True
line = poscar.readline().split()
for i in line:
if not re.match(r"[A-Z][a-z]?", i):
is_vasp_5 = False
break
if is_vasp_5:
text_types = deepcopy(line)
if types is not None and not set(text_types).issubset(set(types)):
raise RuntimeError( "Unknown species in poscar: {0} not in {1}."\
.format(text_types, types) )
types = text_types
line = poscar.readline().split()
assert types is not None, RuntimeError("No atomic species given in POSCAR or input.")
# checks/reads for number of each specie
assert len(types) >= len(line), RuntimeError("Too many atomic species in POSCAR.")
nb_atoms = [int(u) for u in line]
# Check whether selective dynamics, cartesian, or direct.
first_char = poscar.readline().strip().lower()[0]
selective_dynamics = False
if first_char == 's':
selective_dynamics = True
first_char = poscar.readline().strip().lower()[0]
# Checks whether cartesian or direct.
is_direct = first_char not in ['c', 'k']
# reads atoms.
for n, specie in zip(nb_atoms, types):
for i in range(n):
line = poscar.readline().split()
pos = array([float(u) for u in line[:3]], dtype="float64")
if is_direct: pos = dot(result.cell, pos)
result.add_atom(pos=pos, type=specie)
if selective_dynamics:
for which, freeze in zip(line[3:], ['x', 'y', 'z']):
if which.lower()[0] == 't':
result[-1].freeze = getattr(result[-1], 'freeze', '') + freeze
finally: poscar.close()
return result
# Structure definition.
from pylada.crystal import Structure
from pylada.crystal.defects import third_order_charge_correction
from quantities import eV
structure = Structure()
structure.name = 'Ga2CdO4: b5'
structure.scale = 1.0
structure.energy = -75.497933000000003
structure.weight = 1.0
structure.set_cell = (-0.0001445, 4.3538020, 4.3537935),\
(4.3538700, -0.0001445, 4.3538615),\
(4.3538020, 4.3537935, -0.0001445)
structure.add_atoms = [(7.61911540668, 7.61923876219, 7.61912846850), 'Cd'],\
[(1.08833559332, 1.08834823781, 1.08832253150), 'Cd'],\
[(4.35372550000, 4.35379350000, 4.35372550000), 'Ga'],\
[(4.35379775000, 2.17685850000, 2.17682450000), 'Ga'],\
[(2.17682450000, 4.35386575000, 2.17682875000), 'Ga'],\
[(2.17682875000, 2.17686275000, 4.35379775000), 'Ga'],\
[(2.32881212361, 2.32884849688, 2.32881647755), 'O'],\
[(2.32887187256, 4.20174404476, 4.20169148188), 'O'],\
[(4.20168277385, 2.32891695560, 4.20168347161), 'O'],\
[(4.20168782554, 4.20174474241, 2.32887622633), 'O'],\
[(6.37863887654, 6.37873414925, 6.37863016865), 'O'],\
[(6.37857477364, 4.50584295539, 4.50575516433), 'O'],\
[(4.50576822615, 6.37867004441, 4.50576752839), 'O'],\
[(4.50576317445, 4.50584225759, 6.37857477367), 'O']
# this is converged to less than 1meV
third = third_order_charge_correction(structure, epsilon=10.0, n=20)
assert abs(third - 0.11708438633232088*eV) < 1e-12
