def read_cart_forces(self, unit="eV ang^-1"):
"""
Read and return a |numpy-array| with the cartesian forces in unit ``unit``.
Shape (num_steps, natom, 3)
"""
return units.ArrayWithUnit(self.read_value("fcart"),
"Ha bohr^-1").to(unit)
def fit(self, volumes, energies, vol_unit="ang^3", ene_unit="eV"):
"""
Fit energies [eV] as function of volumes [Angstrom**3].
Returns `EosFit` instance that gives access to the optimal volume,
the minumum energy, and the bulk modulus.
Notice that the units for the bulk modulus is eV/Angstrom^3.
"""
# Convert volumes to Ang**3 and energies to eV (if needed).
volumes = units.ArrayWithUnit(volumes, vol_unit).to("ang^3")
energies = units.EnergyArray(energies, ene_unit).to("eV")
return EOS_Fit(volumes, energies, self._func, self._eos_name)
def get_fstats_dict(self, step):
"""
Return |AttrDict| with stats on the forces at the given ``step``.
"""
# [time, natom, 3]
var = self.reader.read_variable("fcart")
forces = units.ArrayWithUnit(var[step], "Ha bohr^-1").to("eV ang^-1")
fmods = np.array([np.linalg.norm(force) for force in forces])
return AttrDict(
fmin=fmods.min(),
fmax=fmods.max(),
fmean=fmods.mean(),
fstd=fmods.std(),
drift=np.linalg.norm(forces.sum(axis=0)),
)
def fit(self, volumes, energies, vol_unit="ang^3", energy_unit="eV"):
"""
Fit energies (in eV) as function of volumes (in Angstrom**3).
Args:
volumes (list/np.array)
energies (list/np.array)
vol_unit (str): volume units
energy_unit (str): energy units
Returns:
EOSFit: EOSFit object that gives access to the optimal volume,
the minumum energy, and the bulk modulus.
Note: the units for the bulk modulus is eV/Angstrom^3.
"""
# Convert volumes to Ang**3 and energies to eV (if needed).
volumes = units.ArrayWithUnit(volumes, vol_unit).to("ang^3")
energies = units.EnergyArray(energies, energy_unit).to("eV")
return EOSFit(volumes, energies, self._func, self._eos_name)