def test_velocities(self):
si = 14
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
# Silicon structure for testing.
latt = [[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]
struct = Structure(latt, [si, si], coords)
poscar = Poscar(struct)
poscar.set_temperature(900)
v = np.array(poscar.velocities)
for x in np.sum(v, axis=0):
self.assertAlmostEqual(x, 0, 7)
temperature = struct[0].specie.atomic_mass.to("kg") * \
np.sum(v ** 2) / (3 * const.k) * 1e10
self.assertAlmostEqual(temperature, 900, 4,
'Temperature instantiated incorrectly')
poscar.set_temperature(700)
v = np.array(poscar.velocities)
for x in np.sum(v, axis=0):
self.assertAlmostEqual(
x, 0, 7, 'Velocities initialized with a net momentum')
temperature = struct[0].specie.atomic_mass.to("kg") * \
np.sum(v ** 2) / (3 * const.k) * 1e10
self.assertAlmostEqual(temperature, 700, 4,
'Temperature instantiated incorrectly')
def test_velocities(self):
si = 14
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
# Silicon structure for testing.
latt = [[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]
struct = Structure(latt, [si, si], coords)
poscar = Poscar(struct)
poscar.set_temperature(900)
v = np.array(poscar.velocities)
for x in np.sum(v, axis=0):
self.assertAlmostEqual(x, 0, 7)
temperature = struct[0].specie.atomic_mass.to("kg") * \
np.sum(v ** 2) / (3 * const.k) * 1e10
self.assertAlmostEqual(temperature, 900, 4,
'Temperature instantiated incorrectly')
poscar.set_temperature(700)
v = np.array(poscar.velocities)
for x in np.sum(v, axis=0):
self.assertAlmostEqual(
x, 0, 7, 'Velocities initialized with a net momentum')
temperature = struct[0].specie.atomic_mass.to("kg") * \
np.sum(v ** 2) / (3 * const.k) * 1e10
self.assertAlmostEqual(temperature, 700, 4,
'Temperature instantiated incorrectly')
def validate_and_initialize(cls):
"""
Initialize new Poscar instance from given user inputs
"""
# complete the parameters list accepted by the pymatgen Poscar
# object (Checking for correct types is delegated to the pymatgen
# Poscar constructor!)
valid_poscar_kwargs = {
'structure': cls.structure_from_input(),
'comment': None, # do not add any comments
'selective_dynamics': cls.input_constraints,
'true_names': True, # always assume true species names
'velocities': cls.input_velocities,
'predictor_corrector': None, # leave predictor-corrector unset
'predictor_corrector_preamble': None,
'sort_structure': True, # always sort structure
}
# initilize the Poscar instance
poscar_object = Poscar(**valid_poscar_kwargs)
# if temperature is given initialize the atomic velocities accordingly
if cls.input_temperature is not None:
# pymatgen initialization from temperature cannot handle structures
# with only one atom. Check structure length to avoid the AiiDA
# error triggered by the resulting `nan` values
if len(cls.structure_from_input()) <= 1:
raise PoscarWrapperError("Initialization of velocities from "
"temperature only possible for "
"structures containing at least two "
"atoms")
# pymatgen happily accepts any temperature value below 0.0 K and
# initialized to `nan`
if cls.input_temperature < 0.0:
raise PoscarWrapperError("Given temperature must not "
"be smaller than zero (set value: "
"'{}')".format(cls.input_temperature))
poscar_object.set_temperature(cls.input_temperature)
return poscar_object
