def calc_Vcoeffs(self):
from Converter import Constants
from FourierExpansions import calc_cos_coefs, calc_4cos_coefs
print("Using DFT for all potentials...")
dvr_energies = self.DVRresults["energies"] # [degrees vOH=0 ... vOH=6]
dvr_energies[:, 1:] = Constants.convert(dvr_energies[:, 1:],
"wavenumbers",
to_AU=True)
coeff_dict = dict() # build coeff dict
rad = np.radians(dvr_energies[:, 0])
coeff_dict["Vel"] = self.Velcoeffs
if "Vexpansion" in self.PORparams:
if self.PORparams["Vexpansion"] == "fourth":
print("Expaning potential coefficients to four tau")
for i in np.arange(
1,
dvr_energies.shape[1]): # loop through saved energies
energies = np.column_stack((rad, dvr_energies[:, i]))
coeff_dict[f"V{i - 1}"] = calc_4cos_coefs(energies)
elif self.PORparams["Vexpansion"] == "sixth":
print("Expaning potential coefficients to six tau")
for i in np.arange(
1,
dvr_energies.shape[1]): # loop through saved energies
energies = np.column_stack((rad, dvr_energies[:, i]))
coeff_dict[f"V{i - 1}"] = calc_cos_coefs(energies)
else:
raise Exception(
f"Can not expand to {self.PORparams['Vexpansion']}")
return coeff_dict
def calc_scaled_Vcoeffs(energy_dat, Vcoeffs, ens_to_calc, barrier_height, scaling_factor, order):
from FourierExpansions import calc_cos_coefs, calc_4cos_coefs
scaling_factor, scaled_energies = scale_barrier(energy_dat, barrier_height, scaling_factor)
if order == 6:
newVel = calc_cos_coefs(scaled_energies)
elif order == 4:
newVel = calc_4cos_coefs(scaled_energies)
else:
raise Exception(f"{order}th order expansions not currently supported")
scaled_coeffs = dict()
scaled_coeffs["Vel"] = newVel
for i in np.arange(len(Vcoeffs.keys())-1): # loop through saved energies
scaled_coeffs[f"V{i}"] = newVel + Vcoeffs[f"V{i}"]
return scaled_coeffs
def calc_Mixed1_Vcoeffs(self):
from Converter import Constants
from FourierExpansions import calc_4cos_coefs
print("Using CCSD Vel and DFT VOH for potentials...")
dvr_energies = self.DVRresults["energies"] # [degrees vOH=0 ... vOH=6]
dvr_energies[:, 1:] = Constants.convert(dvr_energies[:, 1:],
"wavenumbers",
to_AU=True)
rad = np.radians(dvr_energies[:, 0])
coeff_dict = dict()
coeff_dict["Vel"] = self.Velcoeffs
for i in np.arange(
1, dvr_energies.shape[1]): # loop through saved energies
energies = np.column_stack((rad, dvr_energies[:, i]))
coeff_dict[f"V{i-1}"] = calc_4cos_coefs(energies)
return coeff_dict
def calc_Emil_Vcoeffs(self):
from Converter import Constants
from FourierExpansions import calc_4cos_coefs
print("Using CCSD for all potentials...")
all_data = self.PORparams["EmilEnergies"]
tor_angles = all_data[0, :]
rad = np.radians(tor_angles)
ZPE = all_data[1, :]
ens = all_data[2:, :] + ZPE
ens = Constants.convert(ens, "wavenumbers", to_AU=True)
coeff_dict = dict()
coeff_dict["Vel"] = self.Velcoeffs
for i in np.arange(len(ens)):
dat = np.column_stack((rad, ens[i, :]))
coeff_dict[f"V{i}"] = calc_4cos_coefs(dat)
return coeff_dict
def calculate_VelwZPE(self):
from Converter import Constants
from FourierExpansions import calc_cos_coefs, calc_4cos_coefs, fourier_coeffs, calc_curves
degree_vals = np.linspace(0, 360, len(self.MoleculeInfo.TorFiles))
norm_grad = self.RxnPathResults["norm_grad"]
idx = np.where(norm_grad[:, 1] > 4E-4)
new_degree = degree_vals[idx]
Vel = self.RxnPathResults["electronicE"][:, 1]
Vel_ZPE_dict = dict()
ZPE_dict = dict()
for i, j in enumerate(degree_vals):
freqs = self.RxnPathResults[j]["freqs"] # in hartree
# print(np.column_stack((j, freqs[-1])))
nonzero_freqs = freqs[
7:-1] # throw out translations/rotations and OH frequency
nonzero_freqs_har = Constants.convert(nonzero_freqs,
"wavenumbers",
to_AU=True)
ZPE = np.sum(nonzero_freqs_har) / 2
if j in new_degree:
if self.PORparams["twoD"]: # "twoD" in self.PORparams and
Vel_ZPE_dict[j] = Vel[i]
else:
Vel_ZPE_dict[j] = Vel[i] + ZPE
ZPE_dict[j] = ZPE
else:
pass
if "EmilData" in self.PORparams or "MixedData1" in self.PORparams:
# put together ZPE
print("CCSD Vel")
ZPE = np.array([(d, v) for d, v in ZPE_dict.items()])
sort_idxZ = np.argsort(ZPE[:, 0])
ZPE = ZPE[sort_idxZ]
ZPE[:, 0] = np.radians(ZPE[:, 0])
fit_ZPE = calc_4cos_coefs(ZPE)
# zpe_y = calc_curves(np.radians(np.arange(0, 360, 1)), fit_ZPE, function="4cos")
emil_angles = self.RxnPathResults["EmilelectronicE"][:, 0]
emil_ZPE = calc_curves(np.radians(emil_angles),
fit_ZPE,
function="4cos")
Vel_ZPE = np.column_stack(
(np.radians(emil_angles),
emil_ZPE + self.RxnPathResults["EmilelectronicE"][:, 1]))
VelwZPE_coeffs1 = calc_4cos_coefs(Vel_ZPE)
new_x = np.radians(np.arange(0, 360, 1))
y = calc_curves(new_x, VelwZPE_coeffs1, function="4cos")
y -= min(y) # shift curve so minima are at 0 instead of negative
VelwZPE_coeffs = calc_4cos_coefs(np.column_stack((new_x, y)))
npy_name = f"{self.MoleculeInfo.MoleculeName}_Emil_Velcoeffs_4order.npy"
csv_name = f"{self.MoleculeInfo.MoleculeName}_Emil_Velcoeffs_4order.csv"
else:
print("DFT Vel")
Vel_ZPE = np.array([(d, v) for d, v in Vel_ZPE_dict.items()])
sort_idx = np.argsort(Vel_ZPE[:, 0])
Vel_ZPE = Vel_ZPE[sort_idx]
Vel_ZPE[:, 0] = np.radians(Vel_ZPE[:, 0])
new_x = np.radians(np.arange(0, 360, 1))
if "MixedData2" in self.PORparams or self.PORparams[
"Vexpansion"] is "fourth":
VelwZPE_coeffs1 = calc_4cos_coefs(Vel_ZPE)
y = calc_curves(new_x, VelwZPE_coeffs1, function="4cos")
y -= min(
y) # shift curve so minima are at 0 instead of negative
VelwZPE_coeffs = calc_4cos_coefs(np.column_stack((new_x, y)))
npy_name = f"{self.MoleculeInfo.MoleculeName}_Velcoeffs_4order.npy"
csv_name = f"{self.MoleculeInfo.MoleculeName}_Velcoeffs_4order.csv"
elif self.PORparams["None"] and self.PORparams["twoD"]:
VelwZPE_coeffs1 = fourier_coeffs(Vel_ZPE)
y = calc_curves(new_x, VelwZPE_coeffs1, function="fourier")
y -= min(
y) # shift curve so minima are at 0 instead of negative
VelwZPE_coeffs = fourier_coeffs(np.column_stack((new_x, y)))
npy_name = f"{self.MoleculeInfo.MoleculeName}_Velcoeffs_6cos6sin_2D.npy"
csv_name = f"{self.MoleculeInfo.MoleculeName}_Velcoeffs_6cos6sin_2D.csv"
elif self.PORparams["None"] and self.PORparams["twoD"] is False:
VelwZPE_coeffs1 = fourier_coeffs(Vel_ZPE)
y = calc_curves(new_x, VelwZPE_coeffs1, function="fourier")
y -= min(
y) # shift curve so minima are at 0 instead of negative
VelwZPE_coeffs = fourier_coeffs(np.column_stack((new_x, y)))
npy_name = f"{self.MoleculeInfo.MoleculeName}_Velcoeffs_6cos6sin.npy"
csv_name = f"{self.MoleculeInfo.MoleculeName}_Velcoeffs_6cos6sin.csv"
elif self.PORparams["twoD"]:
VelwZPE_coeffs1 = calc_cos_coefs(Vel_ZPE)
y = calc_curves(new_x, VelwZPE_coeffs1)
y -= min(
y) # shift curve so minima are at 0 instead of negative
VelwZPE_coeffs = calc_cos_coefs(np.column_stack((new_x, y)))
npy_name = f"{self.MoleculeInfo.MoleculeName}_Velcoeffs_6order_2D.npy"
csv_name = f"{self.MoleculeInfo.MoleculeName}_Velcoeffs_6order_2D.csv"
else:
VelwZPE_coeffs1 = calc_cos_coefs(Vel_ZPE)
y = calc_curves(new_x, VelwZPE_coeffs1)
y -= min(
y) # shift curve so minima are at 0 instead of negative
VelwZPE_coeffs = calc_cos_coefs(np.column_stack((new_x, y)))
npy_name = f"{self.MoleculeInfo.MoleculeName}_Velcoeffs_6order.npy"
csv_name = f"{self.MoleculeInfo.MoleculeName}_Velcoeffs_6order.csv"
# save results
np.save(os.path.join(self.MoleculeInfo.MoleculeDir, npy_name),
VelwZPE_coeffs)
np.savetxt(os.path.join(self.MoleculeInfo.MoleculeDir, csv_name),
VelwZPE_coeffs)
return os.path.join(self.MoleculeInfo.MoleculeDir, npy_name)