def __init__(self,
volumes,
electronic_energies,
eos='vinet'):
self._volumes = volumes
if np.array(electronic_energies).ndim == 1:
self._electronic_energies = electronic_energies
else:
self._electronic_energies = electronic_energies[0]
self._eos = get_eos(eos)
self._energy = None
self._bulk_modulus = None
self._b_prime = None
try:
(self._energy,
self._bulk_modulus,
self._b_prime,
self._volume) = fit_to_eos(volumes,
self._electronic_energies,
self._eos)
except TypeError:
msg = ["Failed to fit to \"%s\" equation of states." % eos]
if len(volumes) < 4:
msg += ["At least 4 volume points are needed for the fitting."]
msg += ["Careful choice of volume points is recommended."]
raise RuntimeError("\n".join(msg))
def __init__(self, volumes, electronic_energies, eos="vinet"):
self._volumes = volumes
self._electronic_energies = electronic_energies
self._eos = get_eos(eos)
(self._energy, self._bulk_modulus, self._b_prime, self._volume) = fit_to_eos(
volumes, electronic_energies, self._eos
)
def __init__(self, volumes, electronic_energies, eos='vinet'):
self._volumes = volumes
if electronic_energies.ndim == 1:
self._electronic_energies = electronic_energies
else:
self._electronic_energies = electronic_energies[0]
self._eos = get_eos(eos)
(self._energy, self._bulk_modulus, self._b_prime,
self._volume) = fit_to_eos(volumes, self._electronic_energies,
self._eos)
def __init__(
self,
volumes, # Angstrom^3
electronic_energies, # eV
temperatures,
cv, # J/K/mol
entropy, # J/K/mol
fe_phonon, # kJ/mol
eos='vinet',
t_max=None,
energy_plot_factor=None):
self._volumes = np.array(volumes)
self._electronic_energies = np.array(electronic_energies)
self._all_temperatures = np.array(temperatures)
self._cv = np.array(cv)
self._entropy = np.array(entropy)
self._fe_phonon = np.array(fe_phonon) / EvTokJmol
self._eos = get_eos(eos)
self._t_max = t_max
self._energy_plot_factor = energy_plot_factor
self._temperatures = None
self._equiv_volumes = None
self._equiv_energies = None
self._equiv_bulk_modulus = None
self._equiv_parameters = None
self._free_energies = None
self._num_elems = None
self._thermal_expansions = None
self._cp_numerical = None
self._volume_entropy_parameters = None
self._volume_cv_parameters = None
self._volume_entropy = None
self._volume_cv = None
self._cp_polyfit = None
self._dsdv = None
self._gruneisen_parameters = None
self._len = None
def __init__(
self,
volumes, # Angstrom^3
electronic_energies, # eV
temperatures,
cv, # J/K/mol
entropy, # J/K/mol
fe_phonon, # kJ/mol
eos='vinet',
t_max=None):
self._volumes = np.array(volumes)
self._electronic_energies = np.array(electronic_energies)
self._temperatures = np.array(temperatures)
self._cv = np.array(cv)
self._entropy = np.array(entropy)
self._fe_phonon = np.array(fe_phonon) / EvTokJmol
if t_max:
self._max_t_index = self._get_max_t_index(t_max)
else:
self._max_t_index = len(temperatures) - 3
self._eos = get_eos(eos)
self._equiv_volumes = []
self._equiv_energies = []
self._equiv_bulk_modulus = []
self._equiv_parameters = []
self._free_energies = []
self._thermal_expansions = None
self._volume_expansions = None
self._cp_numerical = None
self._volume_entropy_parameters = None
self._volume_cv_parameters = None
self._volume_entropy = None
self._volume_cv = None
self._cp_polyfit = None
self._dsdv = None
self._gruneisen_parameters = None
def __init__(self,
volumes, # Angstrom^3
electronic_energies, # eV
temperatures,
cv, # J/K/mol
entropy, # J/K/mol
fe_phonon, # kJ/mol
eos='vinet',
t_max=None):
self._volumes = np.array(volumes)
self._electronic_energies = np.array(electronic_energies)
self._temperatures = np.array(temperatures)
self._cv = np.array(cv)
self._entropy = np.array(entropy)
self._fe_phonon = np.array(fe_phonon) / EvTokJmol
if t_max:
self._max_t_index = self._get_max_t_index(t_max)
else:
self._max_t_index = len(temperatures) - 3
self._eos = get_eos(eos)
self._equiv_volumes = []
self._equiv_energies = []
self._equiv_bulk_modulus = []
self._equiv_parameters = []
self._free_energies = []
self._thermal_expansions = None
self._volume_expansions = None
self._cp_numerical = None
self._volume_entropy_parameters = None
self._volume_cv_parameters = None
self._volume_entropy = None
self._volume_cv = None
self._cp_polyfit = None
self._dsdv = None
self._gruneisen_parameters = None
def __init__(self,
volumes, # Angstrom^3
electronic_energies, # eV
temperatures,
cv, # J/K/mol
entropy, # J/K/mol
fe_phonon, # kJ/mol
eos='vinet',
t_max=None,
energy_plot_factor=None):
self._volumes = np.array(volumes)
self._electronic_energies = np.array(electronic_energies)
self._all_temperatures = np.array(temperatures)
self._cv = np.array(cv)
self._entropy = np.array(entropy)
self._fe_phonon = np.array(fe_phonon) / EvTokJmol
self._eos = get_eos(eos)
self._t_max = t_max
self._energy_plot_factor = energy_plot_factor
self._temperatures = None
self._equiv_volumes = None
self._equiv_energies = None
self._equiv_bulk_modulus = None
self._equiv_parameters = None
self._free_energies = None
self._num_elems = None
self._thermal_expansions = None
self._cp_numerical = None
self._volume_entropy_parameters = None
self._volume_cv_parameters = None
self._volume_entropy = None
self._volume_cv = None
self._cp_polyfit = None
self._dsdv = None
self._gruneisen_parameters = None
self._len = None
def __init__(self, volumes, electronic_energies, eos='vinet'):
self._volumes = volumes
if np.array(electronic_energies).ndim == 1:
self._electronic_energies = electronic_energies
else:
self._electronic_energies = electronic_energies[0]
self._eos = get_eos(eos)
self._energy = None
self._bulk_modulus = None
self._b_prime = None
try:
(self._energy, self._bulk_modulus, self._b_prime,
self._volume) = fit_to_eos(volumes, self._electronic_energies,
self._eos)
except TypeError:
msg = ["Failed to fit to \"%s\" equation of states." % eos]
if len(volumes) < 4:
msg += ["At least 4 volume points are needed for the fitting."]
msg += ["Careful choice of volume points is recommended."]
raise RuntimeError("\n".join(msg))
def __init__(self, volumes, energies, eos="vinet"):
"""Init method.
volumes : array_like
Unit cell volumes where energies are obtained.
shape=(volumes, ), dtype='double'.
energies : array_like
Energies obtained at volumes.
shape=(volumes, ), dtype='double'.
eos : str
Identifier of equation of states function.
"""
self._volumes = volumes
if np.array(energies).ndim == 1:
self._energies = energies
else:
self._energies = energies[0]
self._eos = get_eos(eos)
self._energy = None
self._bulk_modulus = None
self._b_prime = None
try:
(
self._energy,
self._bulk_modulus,
self._b_prime,
self._volume,
) = fit_to_eos(volumes, self._energies, self._eos)
except TypeError:
msg = ['Failed to fit to "%s" equation of states.' % eos]
if len(volumes) < 4:
msg += ["At least 4 volume points are needed for the fitting."]
msg += ["Careful choice of volume points is recommended."]
raise RuntimeError("\n".join(msg))
def ev(volume, *p):
return get_eos('murnaghan')(volume, *p)
def ev(volume, *p):
return get_eos('vinet')(volume, *p)
def __init__(
self,
volumes, # angstrom^3
electronic_energies, # eV
temperatures, # K
cv, # J/K/mol
entropy, # J/K/mol
fe_phonon, # kJ/mol
eos="vinet",
t_max=None,
energy_plot_factor=None,
):
"""Init method.
Parameters
----------
volumes: array_like
Unit cell volumes (V) in angstrom^3.
dtype='double'
shape=(volumes,)
electronic_energies: array_like
Electronic energies (U_el) or electronic free energies (F_el) in eV.
It is assumed as formar if ndim==1 and latter if ndim==2.
dtype='double'
shape=(volumes,) or (temperatuers, volumes)
temperatures: array_like
Temperatures ascending order (T) in K.
dtype='double'
shape=(temperatures,)
cv: array_like
Phonon Heat capacity at constant volume in J/K/mol.
dtype='double'
shape=(temperatuers, volumes)
entropy: array_like
Phonon entropy at constant volume (S_ph) in J/K/mol.
dtype='double'
shape=(temperatuers, volumes)
fe_phonon: array_like
Phonon Helmholtz free energy (F_ph) in kJ/mol.
dtype='double'
shape=(temperatuers, volumes)
eos: str
Equation of state used for fitting F vs V.
'vinet', 'murnaghan' or 'birch_murnaghan'.
t_max: float
Maximum temperature to be calculated. This has to be not
greater than the temperature of the third element from the
end of 'temperatre' elements. If max_t=None, the temperature
of the third element from the end is used.
energy_plot_factor: float
This value is multiplied to energy like values only in plotting.
"""
self._volumes = np.array(volumes)
self._electronic_energies = np.array(electronic_energies)
self._all_temperatures = np.array(temperatures)
self._cv = np.array(cv)
self._entropy = np.array(entropy)
self._fe_phonon = np.array(fe_phonon) / EvTokJmol
self._eos = get_eos(eos)
self._t_max = t_max
self._energy_plot_factor = energy_plot_factor
self._temperatures = None
self._equiv_volumes = None
self._equiv_energies = None
self._equiv_bulk_modulus = None
self._equiv_parameters = None
self._free_energies = None
self._num_elems = None
self._thermal_expansions = None
self._cp_numerical = None
self._volume_entropy_parameters = None
self._volume_cv_parameters = None
self._volume_entropy = None
self._volume_cv = None
self._cp_polyfit = None
self._dsdv = None
self._gruneisen_parameters = None
self._len = None
