def find_FancyF(FD_file, woo=None, woh=None):
from Converter import Constants
from McUtils.Zachary import finite_difference
mO = Constants.mass("O", to_AU=True)
mH = Constants.mass("H", to_AU=True)
freqoo = Constants.convert(woo, "wavenumbers", to_AU=True)
muOO = mO / 2
freqoh = Constants.convert(woh, "wavenumbers", to_AU=True)
muOH = ((2 * mO) * mH) / ((2 * mO) + mH)
finite_vals = np.loadtxt(FD_file, skiprows=7)
finite_vals = finite_vals[:, 2:]
finite_vals[:, 0] *= 2
ens = finite_vals[:, 2]
print(
"Energy Difference from Minimum: ",
Constants.convert(finite_vals[:, 2] - min(finite_vals[:, 2]),
"wavenumbers",
to_AU=False))
ohDiffs = np.array([
ens[1] - ens[0], ens[6] - ens[5], ens[11] - ens[10], ens[16] - ens[15],
ens[21] - ens[20]
])
print("OH energy differences: ",
Constants.convert(ohDiffs, "wavenumbers", to_AU=False))
finite_vals[:, :2] = Constants.convert(
finite_vals[:, :2], "angstroms",
to_AU=True) # convert to bohr for math
idx = np.lexsort(
(finite_vals[:, 0], finite_vals[:,
1])) # resort so same oh different oo
finite_vals = finite_vals[idx]
finite_vals = finite_vals.reshape((5, 5, 3))
FR = np.zeros(5)
# compute first derivative wrt oo FR
for j in range(finite_vals.shape[0]):
x = finite_vals[j, :, 0] # roos
y = finite_vals[j, :, 2] # energies
print("OO energy difference: ",
Constants.convert((y[1] - y[0]), "wavenumbers", to_AU=False))
FR[j] = finite_difference(x,
y,
1,
end_point_precision=0,
stencil=5,
only_center=True)[0]
print(f"FR: {FR}")
# compute mixed derivative FrrR
FrrR = finite_difference(finite_vals[:, 1, 1],
FR,
2,
end_point_precision=0,
stencil=5,
only_center=True)[0]
print(f"FrrR: {FrrR}")
Qoo = np.sqrt(1 / muOO / freqoo)
Qoh = np.sqrt(1 / muOH / freqoh)
fancyF = FrrR * Qoh**2 * Qoo
return Constants.convert(fancyF, "wavenumbers", to_AU=False)
def calc_derivs(fd_ohs, fd_oos, FDgrid, FDvalues):
from McUtils.Zachary import finite_difference
derivs = dict()
firstOH = finite_difference(fd_ohs, FDvalues[2, :], 1,
end_point_precision=0, stencil=5, only_center=True)[0]
firstOO = finite_difference(fd_oos, FDvalues[:, 2], 1,
end_point_precision=0, stencil=5, only_center=True)[0]
secondOH = finite_difference(fd_ohs, FDvalues[2, :], 2,
end_point_precision=0, stencil=5, only_center=True)[0]
secondOO = finite_difference(fd_oos, FDvalues[:, 2], 2,
end_point_precision=0, stencil=5, only_center=True)[0]
thirdOH = finite_difference(fd_ohs, FDvalues[2, :], 3,
end_point_precision=0, stencil=5, only_center=True)[0]
thirdOO = finite_difference(fd_oos, FDvalues[:, 2], 3,
end_point_precision=0, stencil=5, only_center=True)[0]
mixedOHOO = finite_difference(FDgrid, FDvalues, (1, 1), stencil=(5, 5),
accuracy=0, end_point_precision=0, only_center=True)[0, 0]
mixedOHOOOO = finite_difference(FDgrid, FDvalues, (1, 2), stencil=(5, 5),
accuracy=0, end_point_precision=0, only_center=True)[0, 0]
mixedOHOHOO = finite_difference(FDgrid, FDvalues, (2, 1), stencil=(5, 5),
accuracy=0, end_point_precision=0, only_center=True)[0, 0]
# convert derivs to XH coordinate
derivs["firstOH"] = firstOH * -1
derivs["firstOO"] = firstOO + (1 / 2) * firstOH
derivs["secondOH"] = secondOH
derivs["secondOO"] = secondOO + (1 / 4) * secondOH + (1 / 2) * mixedOHOO
derivs["thirdOH"] = thirdOH * -1
derivs["thirdOO"] = thirdOO + (1 / 8) * thirdOH + (3 / 4) * mixedOHOHOO + (3 / 2) * mixedOHOOOO
derivs["mixedOHOO"] = secondOH * -1 + mixedOHOO * -1
derivs["mixedOHOOOO"] = mixedOHOHOO * -1 + (-1 / 4) * thirdOH + mixedOHOHOO * -1
derivs["mixedOHOHOO"] = mixedOHOHOO + (1 / 2) * thirdOH
return derivs
def calc_derivs(fd_ohs, fd_oos, FDgrid, FDvalues):
from McUtils.Zachary import finite_difference
derivs = dict()
derivs["firstOH"] = finite_difference(fd_ohs,
FDvalues[2, :],
1,
end_point_precision=0,
stencil=5,
only_center=True)[0]
derivs["firstOO"] = finite_difference(fd_oos,
FDvalues[:, 2],
1,
end_point_precision=0,
stencil=5,
only_center=True)[0]
derivs["secondOH"] = finite_difference(fd_ohs,
FDvalues[2, :],
2,
end_point_precision=0,
stencil=5,
only_center=True)[0]
derivs["secondOO"] = finite_difference(fd_oos,
FDvalues[:, 2],
2,
end_point_precision=0,
stencil=5,
only_center=True)[0]
derivs["thirdOH"] = finite_difference(fd_ohs,
FDvalues[2, :],
3,
end_point_precision=0,
stencil=5,
only_center=True)[0]
derivs["thirdOO"] = finite_difference(fd_oos,
FDvalues[:, 2],
3,
end_point_precision=0,
stencil=5,
only_center=True)[0]
derivs["mixedOHOO"] = finite_difference(FDgrid,
FDvalues, (1, 1),
stencil=(5, 5),
accuracy=0,
end_point_precision=0,
only_center=True)[0, 0]
derivs["mixedOHOOOO"] = finite_difference(FDgrid,
FDvalues, (1, 2),
stencil=(5, 5),
accuracy=0,
end_point_precision=0,
only_center=True)[0, 0]
derivs["mixedOHOHOO"] = finite_difference(FDgrid,
FDvalues, (2, 1),
stencil=(5, 5),
accuracy=0,
end_point_precision=0,
only_center=True)[0, 0]
return derivs
def run_harOH_DVR(self, plotPhasedWfns=False):
""" Runs a harmonic approximation using DVR to be fast over the OH coordinate at every OO value."""
from McUtils.Zachary import finite_difference
dvr_1D = DVR("ColbertMiller1D")
finite_dict = self.logData.finite_dict(midpoint=True)
roos = np.array(list(finite_dict.keys()))
potential_array = np.zeros((len(finite_dict), self.NumPts, 2))
energies_array = np.zeros((len(finite_dict), self.desiredEnergies))
wavefunctions_array = np.zeros(
(len(finite_dict), self.NumPts, self.desiredEnergies))
for j, n in enumerate(finite_dict):
x = Constants.convert(finite_dict[n][:, 0],
"angstroms",
to_AU=True)
min_idx = np.argmin(finite_dict[n][:, 1])
sx = x - x[min_idx]
y = finite_dict[n][:, 1]
k = finite_difference(sx,
y,
2,
end_point_precision=0,
stencil=5,
only_center=True)[0]
mini = min(sx) - 1.0
maxi = max(sx) + 1.0
res = dvr_1D.run(potential_function="harmonic_oscillator",
k=k,
mass=self.massdict["muOOH"],
divs=self.NumPts,
domain=(mini, maxi),
num_wfns=self.desiredEnergies)
potential = Constants.convert(res.potential_energy.diagonal(),
"wavenumbers",
to_AU=False)
grid = Constants.convert((res.grid + x[min_idx]),
"angstroms",
to_AU=False)
shiftgrid = (n / 2) + grid
potential_array[j, :, 0] = shiftgrid
potential_array[j, :, 1] = potential
ens = Constants.convert((res.wavefunctions.energies + min(y)),
"wavenumbers",
to_AU=False)
energies_array[j, :] = ens
wavefunctions_array[j, :, :] = res.wavefunctions.wavefunctions
epsilon_pots = np.column_stack((roos, energies_array[:, :4]))
npz_filename = os.path.join(
self.DVRdir,
f"{self.method}_HarmOHDVR_energies{self.desiredEnergies}.npz")
# data saved in wavenumbers/angstroms
wavefuns_array = self.wfn_flipper(wavefunctions_array,
plotPhasedWfns=plotPhasedWfns,
pot_array=potential_array)
np.savez(npz_filename,
method="harm",
potential=potential_array,
epsilonPots=epsilon_pots,
wfns_array=wavefuns_array)
return npz_filename
def do_the_freqy_science(finite_dict):
""" For the harmonic approximation..
takes the data from a very fine scan around minimum and uses finite differencing to calculate a force constant
then OH frequency.
:arg finite_dict:
:returns freqs: frequencies of the shared proton stretch from the force constant of the roh (wavenumbers)"""
from McUtils.Zachary import finite_difference
roos = np.array(list(finite_dict.keys()))
freqs = np.zeros(len(finite_dict))
mO = O * amutokg
mH = H * amutokg
muOH = ((2 * mO) * mH) / ((2 * mO) + mH)
for j, n in enumerate(finite_dict):
x = finite_dict[n][:, 0] * angtom
E = finite_dict[n][:, 1] * hartoj
# plt.plot(x, E, 'ob')
# plt.show()
Ediff = (finite_dict[n][1, 1] - finite_dict[n][2, 1]) * hartowave
# print('E diff: ', E) # check the energy difference between grid points is good (5-10 cm^-1)
k = finite_difference(x,
E,
2,
end_point_precision=0,
stencil=5,
only_center=True)[0]
freqs[j] = (np.sqrt(k / muOH)) / hztowave
fig = plt.figure()
plt.plot(roos, freqs, 'ok')
return fig
def getFC(self):
from McUtils.Zachary import finite_difference
# calculate harmonic force constants
OO_FD = self.finite_vals[10:15, :]
OH_FD = self.finite_vals[2::5, :]
Frr = finite_difference(OO_FD[:, 1] - OO_FD[2, 1],
OO_FD[:, 2],
2,
end_point_precision=0,
stencil=5,
only_center=True)[0]
FRR = finite_difference(OH_FD[:, 0] - OH_FD[2, 0],
OH_FD[:, 2],
2,
end_point_precision=0,
stencil=5,
only_center=True)[0]
return Frr, FRR
def run_harOO_DVR(self, OHDVRres=None, plotPhasedWfns=False):
"""Fits epsilon potentials to a harmonic oscillator and then runs an OO DVR over it"""
from McUtils.Zachary import finite_difference
dvr_1D = DVR("ColbertMiller1D")
OHresults = np.load(OHDVRres)
epsi_pots = OHresults["epsilonPots"]
potential_array = np.zeros((2, self.NumPts, 2))
energies_array = np.zeros((2, self.desiredEnergies))
wavefunctions_array = np.zeros((2, self.NumPts, self.desiredEnergies))
x = Constants.convert(epsi_pots[:, 0], "angstroms", to_AU=True)
for j in np.arange(2):
en = Constants.convert(epsi_pots[:, j + 1],
"wavenumbers",
to_AU=True)
minE_idx = np.argmin(en)
en_s = en[minE_idx - 2:minE_idx + 3]
sx = x - x[minE_idx]
k = finite_difference(sx[minE_idx - 2:minE_idx + 3],
en_s,
2,
end_point_precision=0,
stencil=5,
only_center=True)[0]
mini = min(sx) - 1.0
maxi = max(sx) + 0.5
res = dvr_1D.run(potential_function="harmonic_oscillator",
k=k,
mass=self.massdict["muOO"],
divs=self.NumPts,
domain=(mini, maxi),
num_wfns=self.desiredEnergies)
potential = Constants.convert(res.potential_energy.diagonal() +
en[minE_idx],
"wavenumbers",
to_AU=False)
potential_array[j, :, 0] = Constants.convert(
(res.grid + x[minE_idx]), "angstroms", to_AU=False)
potential_array[j, :, 1] = potential
ens = Constants.convert(res.wavefunctions.energies + en[minE_idx],
"wavenumbers",
to_AU=False)
energies_array[j, :] = ens
wavefunctions_array[j, :, :] = res.wavefunctions.wavefunctions
npz_filename = os.path.join(
self.DVRdir,
f"{self.method}_harmOODVR_w{OHresults['method']}OHDVR_energies{self.desiredEnergies}.npz"
)
# data saved in wavenumbers/angstroms
wavefuns_array = self.wfn_flipper(wavefunctions_array,
plotPhasedWfns=plotPhasedWfns,
pot_array=potential_array)
np.savez(npz_filename,
potential=potential_array,
energy_array=energies_array,
wfns_array=wavefuns_array)
return npz_filename
def getCC(self):
from McUtils.Zachary import finite_difference
FDgrid = np.array(
np.meshgrid(np.unique(self.finite_vals[:, 0]),
np.unique(self.finite_vals[:,
1]))).T # create mesh OO/OH
FDvalues = np.reshape(self.finite_vals[:, 2], (5, 5))
FancyF3 = finite_difference(FDgrid,
FDvalues, (1, 2),
stencil=(5, 5),
accuracy=0,
end_point_precision=0,
only_center=True)[0, 0]
return (1 / 2) * FancyF3
def find_FancyF(self):
import os
from Converter import Constants
from McUtils.Zachary import finite_difference
mO = Constants.mass("O", to_AU=True)
mH = Constants.mass("H", to_AU=True)
freqoo = Constants.convert(self.omegaOO, "wavenumbers", to_AU=True)
muOO = mO / 2
freqoh = Constants.convert(self.omegaOH, "wavenumbers", to_AU=True)
muOH = ((2 * mO) * mH) / ((2 * mO) + mH)
fs_dir = os.path.join(self.molecule.mol_dir, "Finite Scan Data",
"twoD")
if self.molecule.MoleculeName == "H9O4pls":
finite_vals = np.loadtxt(f"{fs_dir}/2D_finiteSPEtet_01_008.dat",
skiprows=7)
elif self.molecule.MoleculeName == "H7O3pls":
finite_vals = np.loadtxt(f"{fs_dir}/2D_finiteSPEtri_01_008.dat",
skiprows=7)
else:
raise Exception("Can't compute FancyF of that molecule")
finite_vals = finite_vals[:, 2:]
finite_vals[:, 0] *= 2 # multiply OO/2 by 2 for OO values
finite_vals[:, :2] = Constants.convert(
finite_vals[:, :2], "angstroms",
to_AU=True) # convert OO/OH to bohr
finite_vals[:, 2] -= min(
finite_vals[:, 2]) # shift minimum to 0 so that energies match
FDgrid = np.array(
np.meshgrid(np.unique(finite_vals[:, 0]),
np.unique(finite_vals[:, 1]))).T # create mesh OO/OH
FDvalues = np.reshape(finite_vals[:, 2], (5, 5))
FrrR = finite_difference(FDgrid,
FDvalues, (1, 2),
stencil=(5, 5),
accuracy=0,
end_point_precision=0,
only_center=True)[0, 0]
Qoo = np.sqrt(1 / muOO / freqoo)
Qoh = np.sqrt(1 / muOH / freqoh)
fancyF = FrrR * Qoh**2 * Qoo
return Constants.convert(fancyF, "wavenumbers", to_AU=False)
def deriv_dipoles(interp_dipoles, roh_eq=1.0125, plot=False):
""" Calculates the first derivatives of the interpolated dipole surfaces to be used in linear transition
moment approximation
:param interp_dipoles: big ol' array (col0:roo(ang), col1:roh(ang), col2:x-component,
col3:y-component, col4:z-component, 3rd dimension: all different roos)
:type interp_dipoles: np.ndarray
:param roh_eq: equilibrium bond distance of the roh.
:type roh_eq: float (4 decimal places)
:param plot: If true, plots the dipole surface and its derivative (default=False)
:type plot: bool
:return: dipole derivatives (same shape as input)
:rtype: np.ndarray
"""
from McUtils.Zachary import finite_difference
import matplotlib.pyplot as plt
rohs = interp_dipoles[0, :, 1]
dip_vecs = interp_dipoles[:, :, 2:]
eq_roh_idx = np.abs(rohs - roh_eq).argmin()
g = rohs[eq_roh_idx - 2:eq_roh_idx + 3]
new_dip_derivs = np.zeros((len(dip_vecs), 4))
for j in np.arange(3):
for k, dip_vec in enumerate(dip_vecs):
y = dip_vec[eq_roh_idx - 2:eq_roh_idx + 3, j]
new_dip_derivs[k, 0] = interp_dipoles[k, 0, 0]
new_dip_derivs[k, j + 1] = finite_difference(g,
y,
2,
end_point_precision=0,
stencil=5,
only_center=True)[0]
if plot:
plt.plot(g, y, 'o')
plt.plot(g, new_dip_derivs[k, :, j + 2])
plt.xlabel('OH bond Distance ($\mathrm{\AA}$)')
plt.ylabel('Dipole UNITS')
plt.show()
plt.close()
return new_dip_derivs
def do_the_freqy_science(file):
""" to continue with the harmonic approximation..
takes the data from a very fine scan around minimum and uses finite differencing to calculate a force constant
then HO frequency.
:arg file: a PES file, (five) points very close to minimum.
:returns freq: frequency of the shared proton stretch from the force constant of the roh (wavenumbers)"""
pts = np.loadtxt(file)
angtom = 1E-10
hartoj = 4.35974E-18
amutokg = 1.66054E-27
hztowave = 2.99792E10 * (2 * np.pi)
x = pts[:, 0] * angtom
y = pts[:, 1] * hartoj
E = (pts[1, 1] - pts[2, 1]) * 219474.6
# print('E diff: ', E) # check the energy difference between grid points is good (5-10 cm^-1)
k = finite_difference(x, y, 2, end_point_precision=0, accuracy=0)[2]
H = 1.007825
O = 15.994915
mO = O * amutokg
mH = H * amutokg
muOH = ((2 * mO) * mH) / ((2 * mO) + mH)
freq = (np.sqrt(k / muOH)) / hztowave
return freq
def run_harmonic_dvr(finitedat_dict,
desired_energies=None,
num_pts=None,
mass='H',
plots=False,
save=False):
""" Runs the DVR over the OH coordinate at every OO value.
:param desired_energies: number of energies/wavefunctions to save to results objects
:type desired_energies: int
:param num_pts: number of points to cut DVR grid into
:type num_pts: int
:param plots: If True, plots and saves the potential energy of the cut with the wavefunctions overlaid
at their appropriate energies. (default=False)
:type plots: bool
:param save: If True, saves the results as .npy files (default=False)
:type save: bool
:return: energies_array (col0-?: energies, rows: oo values),
wavefunctions_array (col0-?: wavefunction values, 3rd dimension: oo values)
:rtype: 2 np.ndarrays
"""
from McUtils.Zachary import finite_difference
dvr_1D = DVR("ColbertMiller1D")
roos = np.array(list(finitedat_dict.keys()))
energies_array = np.zeros((len(finitedat_dict), desired_energies))
wavefunctions_array = np.zeros(
(len(finitedat_dict), num_pts, desired_energies))
mO = O / amutome
if mass == 'H':
mH = H / amutome
muOH = ((2 * mO) * mH) / ((2 * mO) + mH)
mu = muOH
if mass == 'D':
mD = D / amutome
muOD = ((2 * mO) * mD) / ((2 * mO) + mD)
mu = muOD
for j, n in enumerate(finitedat_dict):
x = finitedat_dict[n][:, 0] * angtobohr
sx = x - np.amin(x)
y = finitedat_dict[n][:, 1]
k = finite_difference(sx,
y,
2,
end_point_precision=0,
stencil=5,
only_center=True)[0]
mini = min(sx) - 1.0
maxi = max(sx) + 1.0
res = dvr_1D.run(potential_function="harmonic_oscillator",
k=k,
mass=mu,
divs=num_pts,
domain=(mini, maxi),
num_wfns=desired_energies)
potential = res.potential_energy.diagonal() * hartowave
ens = (res.wavefunctions.energies + min(y)) * hartowave
energies_array[j, :] = ens
wavefunctions_array[j, :, :] = res.wavefunctions.wavefunctions
if plots:
ang_grid = (res.grid + np.amin(x)) / angtobohr
plt.rcParams.update({'font.size': 22})
plt.plot(ang_grid, potential, '-k', linewidth=6.0)
# plt.ylim(0, 25000)
# colors = ["purple", "violet", "orchid", "plum", "hotpink"]
# for i, wf in enumerate(res.wavefunctions):
# wfn = wf.data # * 5000
# wfn += ens[i]
# plt.plot(ang_grid, wfn, colors[i])
ng = np.linspace(-0.55, -0.1, 10)
g = [ens[0]] * 10
plt.plot(ng, g, "royalblue", linewidth=6.0)
e = [ens[1]] * 10
plt.plot(ng, e, 'crimson', linewidth=6.0)
plt.ylim(0, 8000)
plt.xlim(-0.7, 0.2)
plt.show()
# plt.title("%s" % n)
# plt.savefig(os.path.join(
# os.path.dirname(os.path.dirname(__file__)), 'figures', 'cut DVR', 'no linesTGMho_rigid_Roo_%.3f.png' % n))
plt.close()
oh_pots = np.column_stack((roos, energies_array[:, :3]))
if save:
VAA_dir = os.path.join(os.path.dirname(os.path.dirname(__file__)),
"VAA")
np.save(
os.path.join(VAA_dir, 'anharmonic data', 'rigid_DVR_OHpots.npy'),
oh_pots)
np.save(
os.path.join(VAA_dir, 'anharmonic data', 'rigid_DVR_energies.npy'),
energies_array)
np.save(
os.path.join(VAA_dir, 'anharmonic data', 'DVR wfns',
'rigid_DVR_wavefunctions.npy'), wavefunctions_array)
return oh_pots, wavefunctions_array