def update_total_energy(line):
if line.startswith("!"):
total_energy = float(line.split()[4])
cuds_entity = sim.get(oclass=QE.TotalEnergy)
if cuds_entity:
cuds_entity[0].value = total_energy
cuds_entity[0].unit = "Ry"
else:
sim.add(QE.TotalEnergy(value=total_energy, unit="Ry"))
def _update_cuds(self, sim):
"""Based off of the structure
Args:
sim (QE.Simulation or list of QE.Simulations): the simulation for which cuds should be updated.
For calculations that require multiple simulations and aggregate the data (such as ev.x), please provide a list of strings.
"""
# Adds the output file that comes standard with most commands to the structure.
sim.add(
QE.Outfile(path=self._file_path_root + self._session._output_file))
def update_volume(line):
if line.startswith(" unit-cell volume"):
volume = float(line.split()[3])
cuds_entity = sim.get(oclass=QE.Cell)[0].get(oclass=QE.Volume)
if cuds_entity:
cuds_entity[0].value = volume
cuds_entity[0].unit = "au^3"
else:
sim.get(oclass=QE.Cell)[0].add(
QE.Volume(value=volume, unit="au^3"))
def update_force(line):
if line.startswith(" atom "):
atom = self.atomlist[int(line.split()[1]) - 1]
force = [float(line.split()[j]) for j in range(6, 9)]
cuds_entity = atom.get(oclass=QE.Force)
if cuds_entity:
cuds_entity[0].vector = force
cuds_entity[0].unit = "N"
else:
atom.add(QE.Force(vector=force, unit="N"))
def update_pressure(line):
if line.startswith(" Computing"):
try:
pressure = float(lines[i + 2].split()[5])
except:
pressure = float(lines[i + 4].split()[5])
cuds_entity = sim.get(oclass=QE.Pressure)
if cuds_entity:
cuds_entity[0].value = pressure
cuds_entity[0].unit = "kbar"
else:
sim.add(QE.Pressure(value=pressure, unit="kbar"))
def _update_cuds(self, sims):
# Updates equilibrium volume and bulk modulus.
with open(self._file_path_root + self._session._output_file,
'r') as file:
lines = file.readlines()
v0 = lines[1].split()[3]
b0 = lines[1].split()[6][1:]
for s in sims:
volume_entity = s.get(oclass=QE.Cell)[0].get(
oclass=QE.EquilibriumVolume)
modulus_entity = s.get(oclass=QE.BulkModulus)
if volume_entity:
volume_entity[0].value = float(v0)
volume_entity[0].unit = "au^3"
else:
s.get(oclass=QE.Cell)[0].add(
QE.EquilibriumVolume(value=v0, unit="au^3"))
if modulus_entity:
modulus_entity[0].value = float(b0)
volume_entity[0].unit = "kbar"
else:
s.add(QE.BulkModulus(value=b0, unit="kbar"))
def _update_cuds(self, sim):
sim.add(
QE.PhOut(path=self._file_path_root + self._session._output_file))
with open(self._file_path_root + self._session._output_file,
'r') as file:
lines = file.readlines()
beginend = []
for i, line in enumerate(lines):
if line.startswith(" ****"):
beginend.append(i)
q_point = self.qpoints[0]
for i in range(beginend[0] + 1, beginend[1]):
freq = float(lines[i].split()[4])
modenum = int(lines[i].split()[2][:-1])
unit = lines[i].split()[5][1:-1]
for mode in q_point.get(oclass=QE.Mode):
if mode.number == modenum:
if mode.get(oclass=QE.Frequency):
mode.get(oclass=QE.Frequency)[0].value = freq
mode.get(oclass=QE.Frequency)[0].unit = unit
else:
mode.add(QE.Frequency(value=freq, unit=unit))
super()._update_cuds(sim)
def update_stress_tensor(i, line):
if line.startswith(" Computing"):
try:
stresslines = [lines[i + j] for j in range(3, 6)]
raw_stress_tensor = [
float(j) for j in "".join(stresslines).split()
]
except:
stresslines = [lines[i + j] for j in range(5, 8)]
raw_stress_tensor = [
float(j) for j in "".join(stresslines).split()
]
stress_tensor_kbar = np.array(raw_stress_tensor).reshape(
(3, 6))[:, 3:6]
cuds_entity = sim.get(oclass=QE.StressTensor)
if cuds_entity:
cuds_entity[0].tensor2 = stress_tensor_kbar
cuds_entity[0].unit = "kbar"
else:
sim.add(
QE.StressTensor(tensor2=stress_tensor_kbar,
unit="kbar"))
import numpy as np
from osp.core.namespaces import QE
from osp.core.utils import pretty_print
from osp.wrappers.quantumespresso.qe_session import qeSession
# Creates simulation
sim = QE.Simulation()
k = QE.K_POINTS(vector6 = (7, 7, 7, 0, 0, 0), unit = "")
# Creates a cell, the element Silicon, a pseudopotential, two atoms and cell parameters
SiCell = QE.Cell()
Si = QE.Element(name = "Si")
SiPseudo = QE.PSEUDOPOTENTIAL(path = "Si.pbe-n-kjpaw_psl.1.0.0.UPF")
Si1 = QE.Atom()
celldm1 = QE.Celldm1(value = 5.43070, unit = "au")
# Adds pseudopotential and atoms to the element
# Describes element's mass
# Adds atoms and cell parameters to the cell
# Positions the atoms
Si.add(SiPseudo, Si1)
Si.add(QE.Mass(value = 28.085, unit = "amu"))
SiParams = QE.CellParams(tensor2 = [[0.5, 0.5, 0.],
[0.5, 0., 0.5],
[0., 0.5, 0.5]], unit = "")
SiCell.add(Si1, SiParams)
Si1.add(QE.Position(vector = (0, 0, 0), unit = ""))
SiCell.add(celldm1)
# Specifies the values of the cell parameters
import numpy as np from osp.core.namespaces import QE from osp.wrappers.quantumespresso.qe_session import qeSession from osp.core.utils import pretty_print sim = QE.Simulation() root = "" session = qeSession(root) quantum_espresso_wrapper = QE.QEWrapper(session = session) quantum_espresso_wrapper.add(sim) cell = QE.Cell() alat = 4. cellParams = cell.add(QE.CellParams(tensor2 = [[1., 0., 0.,], [0., 1., 0.,], [0., 0., 1.,]], unit = "alat")) cell.add(QE.Celldm1(value = alat, unit = "")) O = QE.Element(name = "O") Ba = QE.Element(name = "Ba") Ti = QE.Element(name = "Ti") O.add(QE.Mass(value = 15.999, unit = "amu")) Ba.add(QE.Mass(value = 137.327, unit = "amu")) Ti.add(QE.Mass(value = 47.867, unit = "amu")) O.add(QE.PSEUDOPOTENTIAL(path = "O.pbe-n-kjpaw_psl.1.0.0.UPF")) Ba.add(QE.PSEUDOPOTENTIAL(path = "Ba.pbe-spn-kjpaw_psl.1.0.0.UPF")) Ti.add(QE.PSEUDOPOTENTIAL(path = "Ti.pbe-spn-kjpaw_psl.1.0.0.UPF"))
def _update_cuds(self, sim):
sim.add(
QE.XSF(path=self._file_path_root + self._session._prefix +
".pp.xsf"))
super()._update_cuds(sim)
def _update_cuds(self, sim):
sim.add(
QE.DosDat(path=self._file_path_root + self._session._prefix +
".dos.dat"))
super()._update_cuds(sim)