def run(self, verbose=False):
if verbose:
print ("#%11s" + "%14s"*4) % ("T", "E_0", "B_0", "B'_0", "V_0")
for i in range(self._max_t_index + 2):
t = self._temperatures[i]
fe = []
for j, e in enumerate(self._electronic_energies):
fe.append(e + self._fe_phonon[i][j])
self._free_energies.append(fe)
ee, eb, ebp, ev = fit_to_eos(self._volumes, fe, self._eos)
ep = [ee, eb, ebp, ev]
self._equiv_volumes.append(ev)
self._equiv_energies.append(ee)
self._equiv_bulk_modulus.append(eb * EVAngstromToGPa)
self._equiv_parameters.append(ep)
if verbose:
print "%14.6f"*5 % (t,
ep[0],
ep[1] * EVAngstromToGPa,
ep[2],
ep[3])
self._set_volume_expansion()
self._set_thermal_expansion() # len = len(t) - 1
self._set_heat_capacity_P_numerical() # len = len(t) - 2
self._set_heat_capacity_P_polyfit()
self._set_gruneisen_parameter() # To be run after thermal expansion.
def run(self, verbose=False):
if verbose:
print(("#%11s" + "%14s" * 4) % ("T", "E_0", "B_0", "B'_0", "V_0"))
max_t_index = self._get_max_t_index(self._all_temperatures)
for i in range(max_t_index + 2):
t = self._all_temperatures[i]
fe = []
for j, e in enumerate(self._electronic_energies):
fe.append(e + self._fe_phonon[i][j])
self._free_energies.append(fe)
ee, eb, ebp, ev = fit_to_eos(self._volumes, fe, self._eos)
if ee is None:
continue
else:
ep = [ee, eb, ebp, ev]
self._temperatures.append(t)
self._equiv_volumes.append(ev)
self._equiv_energies.append(ee)
self._equiv_bulk_modulus.append(eb * EVAngstromToGPa)
self._equiv_parameters.append(ep)
if verbose:
print(("%14.6f" * 5) %
(t, ep[0], ep[1] * EVAngstromToGPa, ep[2], ep[3]))
self._max_t_index = self._get_max_t_index(self._temperatures)
self._set_volume_expansion()
self._set_thermal_expansion() # len = len(t) - 1
self._set_heat_capacity_P_numerical() # len = len(t) - 2
self._set_heat_capacity_P_polyfit()
self._set_gruneisen_parameter() # To be run after thermal expansion.
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 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
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, 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 run(self, verbose=False):
"""Fit parameters to EOS at temperatures
Even if fitting failed, simply omit the volume point. In this case,
the failed temperature point doesn't exist in the returned arrays.
"""
if verbose:
print(("#%11s" + "%14s" * 4) % ("T", "E_0", "B_0", "B'_0", "V_0"))
# Plus one temperature point is necessary for computing e.g. beta.
num_elems = self._get_num_elems(self._all_temperatures) + 1
if num_elems > len(self._all_temperatures):
num_elems -= 1
temperatures = []
parameters = []
free_energies = []
for i in range(num_elems): # loop over temperaturs
if self._electronic_energies.ndim == 1:
el_energy = self._electronic_energies
else:
el_energy = self._electronic_energies[i]
fe = [
ph_e + el_e
for ph_e, el_e in zip(self._fe_phonon[i], el_energy)
]
try:
ep = fit_to_eos(self._volumes, fe, self._eos)
except TypeError:
print("Fitting failure at T=%.1f" % self._all_temperatures[i])
if ep is None:
# Simply omit volume point where the fitting failed.
continue
else:
[ee, eb, ebp, ev] = ep
t = self._all_temperatures[i]
temperatures.append(t)
parameters.append(ep)
free_energies.append(fe)
if verbose:
print(("%14.6f" * 5) %
(t, ep[0], ep[1] * EVAngstromToGPa, ep[2], ep[3]))
self._free_energies = np.array(free_energies)
self._temperatures = np.array(temperatures)
self._equiv_parameters = np.array(parameters)
self._equiv_volumes = np.array(self._equiv_parameters[:, 3])
self._equiv_energies = np.array(self._equiv_parameters[:, 0])
self._equiv_bulk_modulus = np.array(self._equiv_parameters[:, 1] *
EVAngstromToGPa)
self._num_elems = len(self._temperatures)
# For computing following values at temperatures, finite difference
# method is used. Therefore number of temperature points are needed
# larger than self._num_elems that nearly equals to the temparature
# point we expect.
self._set_thermal_expansion()
self._set_heat_capacity_P_numerical()
self._set_heat_capacity_P_polyfit()
self._set_gruneisen_parameter() # To be run after thermal expansion.
self._len = len(self._thermal_expansions)
assert (self._len + 1 == self._num_elems)
def run(self, verbose=False):
"""Fit parameters to EOS at temperatures
Even if fitting failed, simply omit the volume point. In this case,
the failed temperature point doesn't exist in the returned arrays.
"""
if verbose:
print(("#%11s" + "%14s" * 4) % ("T", "E_0", "B_0", "B'_0", "V_0"))
# Plus one temperature point is necessary for computing e.g. beta.
num_elems = self._get_num_elems(self._all_temperatures) + 1
if num_elems > len(self._all_temperatures):
num_elems -= 1
temperatures = []
parameters = []
free_energies = []
for i in range(num_elems): # loop over temperaturs
if self._electronic_energies.ndim == 1:
el_energy = self._electronic_energies
else:
el_energy = self._electronic_energies[i]
fe = [ph_e + el_e
for ph_e, el_e in zip(self._fe_phonon[i], el_energy)]
try:
ep = fit_to_eos(self._volumes, fe, self._eos)
except TypeError:
print("Fitting failure at T=%.1f" % self._all_temperatures[i])
if ep is None:
# Simply omit volume point where the fitting failed.
continue
else:
[ee, eb, ebp, ev] = ep
t = self._all_temperatures[i]
temperatures.append(t)
parameters.append(ep)
free_energies.append(fe)
if verbose:
print(("%14.6f" * 5) %
(t, ep[0], ep[1] * EVAngstromToGPa, ep[2], ep[3]))
self._free_energies = np.array(free_energies)
self._temperatures = np.array(temperatures)
self._equiv_parameters = np.array(parameters)
self._equiv_volumes = np.array(self._equiv_parameters[:, 3])
self._equiv_energies = np.array(self._equiv_parameters[:, 0])
self._equiv_bulk_modulus = np.array(
self._equiv_parameters[:, 1] * EVAngstromToGPa)
self._num_elems = len(self._temperatures)
# For computing following values at temperatures, finite difference
# method is used. Therefore number of temperature points are needed
# larger than self._num_elems that nearly equals to the temparature
# point we expect.
self._set_thermal_expansion()
self._set_heat_capacity_P_numerical()
self._set_heat_capacity_P_polyfit()
self._set_gruneisen_parameter() # To be run after thermal expansion.
self._len = len(self._thermal_expansions)
assert(self._len + 1 == self._num_elems)
