def obtain_eigenvectors_from_phonopy(structure, q_vector, NAC=False):
# Checking data
force_atoms_file = structure.get_force_set().item(0)["natom"]
force_atoms_input = np.product(np.diagonal(structure.get_super_cell_phonon())) * structure.get_number_of_atoms()
if force_atoms_file != force_atoms_input:
print("Error: FORCE_SETS file does not match with SUPERCELL MATRIX")
exit()
# Preparing the bulk type object
bulk = PhonopyAtoms(
symbols=structure.get_atomic_types(),
scaled_positions=structure.get_scaled_positions(),
cell=structure.get_cell().T,
)
phonon = Phonopy(
bulk,
structure.get_super_cell_phonon(),
primitive_matrix=structure.get_primitive_matrix(),
is_auto_displacements=False,
)
# Non Analytical Corrections (NAC) from Phonopy [Frequencies only, eigenvectors no affected by this option]
if NAC:
print("Phonopy warning: Using Non Analytical Corrections")
get_is_symmetry = True # from phonopy: settings.get_is_symmetry()
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, get_is_symmetry)
phonon.set_nac_params(nac_params=nac_params)
phonon.set_displacement_dataset(copy.deepcopy(structure.get_force_set()))
phonon.produce_force_constants()
frequencies, eigenvectors = phonon.get_frequencies_with_eigenvectors(q_vector)
# Making sure eigenvectors are orthonormal (can be omitted)
if True:
eigenvectors = eigenvectors_normalization(eigenvectors)
print("Testing eigenvectors orthonormality")
np.set_printoptions(precision=3, suppress=True)
print(np.dot(eigenvectors.T, np.ma.conjugate(eigenvectors)).real)
np.set_printoptions(suppress=False)
# Arranging eigenvectors by atoms and dimensions
number_of_dimensions = structure.get_number_of_dimensions()
number_of_primitive_atoms = structure.get_number_of_primitive_atoms()
arranged_ev = np.array(
[
[
[eigenvectors[j * number_of_dimensions + k, i] for k in range(number_of_dimensions)]
for j in range(number_of_primitive_atoms)
]
for i in range(number_of_primitive_atoms * number_of_dimensions)
]
)
return arranged_ev, frequencies
def ir_intensity_phonopy(
run_dir=".",
vasprun="vasprun.xml",
BornFileName="BORN",
PoscarName="POSCAR",
ForceConstantsName="FORCE_CONSTANTS",
supercell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
nac=True,
symprec=1e-5,
primitive=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
degeneracy_tolerance=1e-5,
vector=[0, 0, 0],
smoothen=False,
):
"""Calculate IR intensity using DFPT and phonopy."""
from phonopy import Phonopy
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import (
parse_BORN,
parse_FORCE_CONSTANTS,
)
import shutil
from phonopy.units import VaspToCm
# from phonopy.phonon.degeneracy import (
# degenerate_sets as get_degenerate_sets,
# )
# adapted from https://github.com/JaGeo/IR
# TODO: Make directory indepndent
cwd = os.getcwd()
print("Directory:", cwd)
os.chdir(run_dir)
if not os.path.exists(vasprun):
shutil.copy2(vasprun, "vasprun.xml")
cmd = str("phonopy --fc vasprun.xml")
os.system(cmd)
born_file = os.path.join(os.getcwd(), BornFileName)
cmd = str("phonopy-vasp-born > ") + str(born_file)
os.system(cmd)
from jarvis.io.vasp.outputs import Vasprun
v = Vasprun(vasprun)
strt = v.all_structures[0]
strt.write_poscar(PoscarName)
unitcell = read_vasp(PoscarName)
phonon = Phonopy(
unitcell,
supercell_matrix=supercell,
primitive_matrix=primitive,
factor=VaspToCm,
symprec=symprec,
)
natoms = phonon.get_primitive().get_number_of_atoms()
force_constants = parse_FORCE_CONSTANTS(filename=ForceConstantsName)
phonon.set_force_constants(force_constants)
masses = phonon.get_primitive().get_masses()
phonon.set_masses(masses)
BORN_file = parse_BORN(phonon.get_primitive(), filename=BornFileName)
BORN_CHARGES = BORN_file["born"]
# print ('born_charges2',BORN_CHARGES)
if nac:
phonon.set_nac_params(BORN_file)
frequencies, eigvecs = phonon.get_frequencies_with_eigenvectors(vector)
# frequencies=VaspToTHz*frequencies/VaspToCm
# x, y = ir_intensity(
# phonon_eigenvectors=np.real(eigvecs),
# phonon_eigenvalues=frequencies,
# masses=masses, #np.ones(len(masses)),
# born_charges=born_charges,
# smoothen=smoothen,
# )
NumberOfBands = len(frequencies)
EigFormat = {}
for alpha in range(NumberOfBands):
laufer = 0
for beta in range(natoms):
for xyz in range(0, 3):
EigFormat[beta, alpha, xyz] = eigvecs[laufer][alpha]
laufer = laufer + 1
Intensity = {}
intensities = []
for freq in range(len(frequencies)):
Intensity[freq] = 0
tmp = 0
for alpha in range(3):
asum = 0
for n in range(natoms):
for beta in range(3):
asum = asum + BORN_CHARGES[n, alpha, beta] * np.real(
EigFormat[n, freq, beta]
) / np.sqrt(masses[n])
tmp += asum
Intensity[freq] = Intensity[freq] + np.power(np.absolute(asum), 2)
intensities.append(Intensity[freq])
os.chdir(cwd)
return frequencies, intensities
class AtomicContributionsCalculator:
def __init__(self,
PoscarName='POSCAR',
ForceConstants=False,
ForceFileName='FORCE_SETS',
BornFileName='BORN',
supercell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
nac=False,
symprec=1e-5,
masses=[],
primitive=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
degeneracy_tolerance=1e-4,
factor=VaspToCm,
q=[0, 0, 0]):
"""Class that calculates contributions of each atom to the phonon modes at Gamma
Args:
PoscarName (str): name of the POSCAR that was used for the phonon calculation
BornFileName (str): name of the file with BORN charges (formatted with outcar-born)
ForceConstants (boolean): If True, ForceConstants are read in. If False, forces are read in.
ForceFileName (str): name of the file including force constants or forces
supercell (list of lists): reads in supercell
nac (boolean): If true, NAC is applied. (please be careful if you give a primitive cell. NAC should then be calculated for primitive cell)
symprec (float): contains symprec tag as used in Phonopy
masses (list): Masses in this list are used instead of the ones prepared in Phonopy. Useful for isotopes.
primitive (list of lists): contains rotational matrix to arrive at primitive cell
factor (float): VaspToCm or VaspToTHz or VaspToEv
q (list of int): q point for the plot. So far only Gamma works
"""
self.__unitcell = read_vasp(PoscarName)
self.__supercell = supercell
self.__phonon = Phonopy(self.__unitcell,
supercell_matrix=self.__supercell,
primitive_matrix=primitive,
factor=factor,
symprec=symprec)
self.__natoms = self.__phonon.get_primitive().get_number_of_atoms()
self.__symbols = self.__phonon.get_primitive().get_chemical_symbols()
self.__factor = factor
# If different masses are supplied
if masses:
self.__phonon.set_masses(masses)
self.__masses = self.__phonon.get_primitive().get_masses()
# Forces or Force Constants
if not ForceConstants:
self.__set_ForcesSets(filename=ForceFileName, phonon=self.__phonon)
if ForceConstants:
self.__set_ForceConstants(filename=ForceFileName,
phonon=self.__phonon)
# Apply NAC Correction
if nac:
BORN_file = parse_BORN(self.__phonon.get_primitive(),
filename=BornFileName)
self.__BORN_CHARGES = BORN_file['born']
self.__phonon.set_nac_params(BORN_file)
# frequencies and eigenvectors at Gamma
self._frequencies, self._eigvecs = self.__phonon.get_frequencies_with_eigenvectors(
q)
self.__NumberOfBands = len(self._frequencies)
# Nicer format of the eigenvector file
self.__FormatEigenvectors()
# Get Contributions
self.__set_Contributions()
self.__set_Contributions_withoutmassweight()
# irrepsobject
try:
self.__set_IRLabels(phonon=self.__phonon,
degeneracy_tolerance=degeneracy_tolerance,
factor=factor,
q=q,
symprec=symprec)
except:
print(
"Cannot assign IR labels. Play around with symprec, degeneracy_tolerance. The point group could not be implemented."
)
self.__freqlist = {}
for i in range(0, len(self._frequencies)):
self.__freqlist[i] = i
def show_primitivecell(self):
"""
shows primitive cell used for the plots and evaluations on screen
"""
print(self.__phonon.get_primitive())
def __set_ForcesSets(self, filename, phonon):
"""
sets forces
"""
force_sets = parse_FORCE_SETS(filename=filename)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
def __set_ForceConstants(self, filename, phonon):
"""
sets force constants
"""
force_constants = parse_FORCE_CONSTANTS(filename=filename)
phonon.set_force_constants(force_constants)
def __set_IRLabels(self, phonon, degeneracy_tolerance, factor, q, symprec):
"""
sets list of irreducible labels and list of frequencies without degeneracy
"""
# phonon.set_dynamical_matrix()
self.__Irrep = IrReps(dynamical_matrix=phonon._dynamical_matrix,
q=q,
is_little_cogroup=False,
nac_q_direction=None,
factor=factor,
symprec=symprec,
degeneracy_tolerance=degeneracy_tolerance)
self.__Irrep.run()
self._IRLabels = self.__Irrep._get_ir_labels()
self.__ListOfModesWithDegeneracy = self.__Irrep._get_degenerate_sets()
self.__freqlist = {}
for band in range(len(self.__ListOfModesWithDegeneracy)):
self.__freqlist[band] = self.__ListOfModesWithDegeneracy[band][0]
def __FormatEigenvectors(self):
"""
Formats eigenvectors to a dictionary: the first argument is the number of bands, the second the number of atoms, the third the Cartesian coordinate
"""
self._EigFormat = {}
for alpha in range(self.__NumberOfBands):
laufer = 0
for beta in range(self.__natoms):
for xyz in range(0, 3):
self._EigFormat[beta, alpha,
xyz] = self._eigvecs[laufer][alpha]
laufer = laufer + 1
def _Eigenvector(self, atom, band, xoryorz):
"""
Gives a certain eigenvector corresponding to one specific atom, band and Cartesian coordinate
args:
atom (int) : number of the atoms (same order as in POSCAR)
band (int) : number of the frequency (ordered by energy)
xoryorz (int): Cartesian coordinate of the eigenvector
"""
return np.real(self._EigFormat[atom, band, xoryorz])
def __massEig(self, atom, band, xoryorz):
"""
Gives a certain eigenvector divided by sqrt(mass of the atom) corresponding to one specific atom, band and Cartesian coordinate
args:
atom (int) : number of the atoms (same order as in POSCAR)
band (int) : number of the frequency (ordered by energy)
xoryorz (int): Cartesian coordinate of the eigenvector
"""
return self._Eigenvector(atom, band, xoryorz) / np.sqrt(
self.__masses[atom])
def __set_Contributions(self):
"""
Calculate contribution of each atom to modes"
"""
self._PercentageAtom = {}
for freq in range(len(self._frequencies)):
for atom in range(self.__natoms):
sum = 0
for alpha in range(3):
sum = sum + abs(
self._Eigenvector(atom, freq, alpha) *
self._Eigenvector(atom, freq, alpha))
self._PercentageAtom[freq, atom] = sum
def __get_Contributions(self, band, atom):
"""
Gives contribution of specific atom to modes with certain frequency
args:
band (int): number of the frequency (ordered by energy)
"""
return self._PercentageAtom[band, atom]
def __set_Contributions_withoutmassweight(self):
"""
Calculate contribution of each atom to modes
Here, eigenvectors divided by sqrt(mass of the atom) are used for the calculation
"""
self.__PercentageAtom_massweight = {}
atomssum = {}
saver = {}
for freq in range(len(self._frequencies)):
atomssum[freq] = 0
for atom in range(self.__natoms):
sum = 0
for alpha in range(3):
sum = sum + abs(
self.__massEig(atom, freq, alpha) *
self.__massEig(atom, freq, alpha))
atomssum[freq] = atomssum[freq] + sum
# Hier muss noch was hin, damit rechnung richtig wird
saver[freq, atom] = sum
for freq in range(len(self._frequencies)):
for atom in range(self.__natoms):
self.__PercentageAtom_massweight[
freq, atom] = saver[freq, atom] / atomssum[freq]
def __get_Contributions_withoutmassweight(self, band, atom):
"""
Gives contribution of specific atom to modes with certain frequency
Here, eigenvectors divided by sqrt(mass of the atom) are used for the calculation
args:
band (int): number of the frequency (ordered by energy)
"""
return self.__PercentageAtom_massweight[band, atom]
def write_file(self, filename="Contributions.txt"):
"""
Writes contributions of each atom in file
args:
filename (str): filename
"""
file = open(filename, 'w')
file.write('Frequency Contributions \n')
for freq in range(len(self._frequencies)):
file.write('%s ' % (self._frequencies[freq]))
for atom in range(self.__natoms):
file.write('%s ' % (self.__get_Contributions(freq, atom)))
file.write('\n ')
file.close()
def plot(self,
atomgroups,
colorofgroups,
legendforgroups,
freqstart=[],
freqend=[],
freqlist=[],
labelsforfreq=[],
filename="Plot.eps",
transmodes=True,
massincluded=True):
"""
Plots contributions of atoms/several atoms to modes with certain frequencies (freqlist starts at 1 here)
args:
atomgroups (list of list of ints): list that groups atoms, atom numbers start at 1
colorofgroups (list of str): list that matches a color to each group of atoms
legendforgroups (list of str): list that gives a legend for each group of atoms
freqstart (float): min frequency of plot in cm-1
freqend (float): max frequency of plot in cm-1
freqlist (list of int): list of frequencies that will be plotted; if no list is given all frequencies in the range from freqstart to freqend are plotted, list begins at 1
labelsforfreq (list of str): list of labels (str) for each frequency
filename (str): filename for the plot
transmodes (boolean): if transmode is true than translational modes are shown
massincluded (boolean): if false, uses eigenvector divided by sqrt(mass of the atom) for the calculation instead of the eigenvector
"""
p = {}
summe = {}
try:
if labelsforfreq == []:
labelsforfreq = self._IRLabels
except:
print("")
if freqlist == []:
freqlist = self.__freqlist
else:
for freq in range(len(freqlist)):
freqlist[freq] = freqlist[freq] - 1
newfreqlist = []
newlabelsforfreq = []
for freq in range(len(freqlist)):
if not transmodes:
if not freqlist[freq] in [0, 1, 2]:
newfreqlist.append(freqlist[freq])
try:
newlabelsforfreq.append(labelsforfreq[freq])
except:
newlabelsforfreq.append('')
else:
newfreqlist.append(freqlist[freq])
try:
newlabelsforfreq.append(labelsforfreq[freq])
except:
newlabelsforfreq.append('')
self._plot(atomgroups=atomgroups,
colorofgroups=colorofgroups,
legendforgroups=legendforgroups,
freqstart=freqstart,
freqend=freqend,
freqlist=newfreqlist,
labelsforfreq=newlabelsforfreq,
filename=filename,
massincluded=massincluded)
def _plot(self,
atomgroups,
colorofgroups,
legendforgroups,
freqstart=[],
freqend=[],
freqlist=[],
labelsforfreq=[],
filename="Plot.eps",
massincluded=True):
"""
Plots contributions of atoms/several atoms to modes with certain frequencies (freqlist starts at 0 here)
args:
atomgroups (list of list of ints): list that groups atoms, atom numbers start at 1
colorofgroups (list of str): list that matches a color to each group of atoms
legendforgroups (list of str): list that gives a legend for each group of atoms
freqstart (float): min frequency of plot in cm-1
freqend (float): max frequency of plot in cm-1
freqlist (list of int): list of frequencies that will be plotted; this freqlist starts at 0
labelsforfreq (list of str): list of labels (str) for each frequency
filename (str): filename for the plot
massincluded (boolean): if false, uses eigenvector divided by sqrt(mass of the atom) for the calculation instead of the eigenvector
"""
# setting of some parameters in matplotlib: http://matplotlib.org/users/customizing.html
mpl.rcParams["savefig.directory"] = os.chdir(os.getcwd())
mpl.rcParams["savefig.format"] = 'eps'
fig, ax1 = plt.subplots()
p = {}
summe = {}
for group in range(len(atomgroups)):
color1 = colorofgroups[group]
Entry = {}
for freq in range(len(freqlist)):
Entry[freq] = 0
for number in atomgroups[group]:
# set the first atom to 0
atom = int(number) - 1
for freq in range(len(freqlist)):
if massincluded:
Entry[freq] = Entry[freq] + self.__get_Contributions(
freqlist[freq], atom)
else:
Entry[freq] = Entry[
freq] + self.__get_Contributions_withoutmassweight(
freqlist[freq], atom)
if group == 0:
summe[freq] = 0
# plot bar chart
p[group] = ax1.barh(np.arange(len(freqlist)),
list(Entry.values()),
left=list(summe.values()),
color=color1,
edgecolor="black",
height=1,
label=legendforgroups[group])
# needed for "left" in the bar chart plot
for freq in range(len(freqlist)):
if group == 0:
summe[freq] = Entry[freq]
else:
summe[freq] = summe[freq] + Entry[freq]
labeling = {}
for freq in range(len(freqlist)):
labeling[freq] = round(self._frequencies[freqlist[freq]], 1)
# details for the plot
plt.rc("font", size=8)
ax1.set_yticklabels(list(labeling.values()))
ax1.set_yticks(np.arange(0.0, len(self._frequencies) + 0.0))
ax2 = ax1.twinx()
ax2.set_yticklabels(labelsforfreq)
ax2.set_yticks(np.arange(0.0, len(self._frequencies) + 0.0))
# start and end of the yrange
start, end = self.__get_freqbordersforplot(freqstart, freqend,
freqlist)
ax1.set_ylim(start - 0.5, end - 0.5)
ax2.set_ylim(start - 0.5, end - 0.5)
ax1.set_xlim(0.0, 1.0)
ax1.set_xlabel('Contribution of Atoms to Modes')
if self.__factor == VaspToCm:
ax1.set_ylabel('Wavenumber (cm$^{-1}$)')
elif self.__factor == VaspToTHz:
ax1.set_ylabel('Frequency (THz)')
elif self.__factor == VaspToEv:
ax1.set_ylabel('Frequency (eV)')
else:
ax1.set_ylabel('Frequency')
ax1.legend(bbox_to_anchor=(0, 1.02, 1, 0.2),
loc="lower left",
mode="expand",
borderaxespad=0,
ncol=len(atomgroups))
plt.savefig(filename, bbox_inches="tight")
plt.show()
def __get_freqbordersforplot(self, freqstart, freqend, freqlist):
if freqstart == []:
start = 0.0
else:
for freq in range(len(freqlist)):
if self._frequencies[freqlist[freq]] > freqstart:
start = freq
break
else:
start = len(freqlist)
if freqend == []:
end = len(freqlist)
else:
for freq in range(len(freqlist) - 1, 0, -1):
if self._frequencies[freqlist[freq]] < freqend:
end = freq + 1
break
else:
end = len(freqlist)
return start, end
def plot_irred(self,
atomgroups,
colorofgroups,
legendforgroups,
transmodes=False,
irreps=[],
filename="Plot.eps",
freqstart=[],
freqend=[],
massincluded=True):
"""
Plots contributions of atoms/several atoms to modes with certain irreducible representations (selected by Mulliken symbol)
args:
atomgroups (list of list of ints): list that groups atoms, atom numbers start at 1
colorofgroups (list of str): list that matches a color to each group of atoms
legendforgroups (list of str): list that gives a legend for each group of atoms
transmodes (boolean): translational modes are included if true
irreps (list of str): list that includes the irreducible modes that are plotted
filename (str): filename for the plot
massincluded (boolean): if false, uses eigenvector divided by sqrt(mass of the atom) for the calculation instead of the eigenvector
"""
freqlist = []
labelsforfreq = []
for band in range(len(self.__freqlist)):
if self._IRLabels[band] in irreps:
if not transmodes:
if not self.__freqlist[band] in [0, 1, 2]:
freqlist.append(self.__freqlist[band])
labelsforfreq.append(self._IRLabels[band])
else:
freqlist.append(self.__freqlist[band])
labelsforfreq.append(self._IRLabels[band])
self._plot(atomgroups=atomgroups,
colorofgroups=colorofgroups,
legendforgroups=legendforgroups,
filename=filename,
freqlist=freqlist,
labelsforfreq=labelsforfreq,
freqstart=freqstart,
freqend=freqend,
massincluded=massincluded)
# labels = ['$\Gamma$', 'X', 'U|K', '$\Gamma$', 'L']
# DOS grid
# from kpoints_gen import get_grid_num
# k_grids = get_grid_num(phonon.get_primitive().cell, precision=pdos_precision)
phonon.run_mesh(
pdos_mesh,
# is_mesh_symmetry=False,
with_eigenvectors=True,
is_gamma_center=True,
)
######### eigenvectors #########
# freq, eigvec = phonon.get_frequencies_with_eigenvectors([0.00000333,0.00000333,0.])
# freq, eigvec = phonon.get_frequencies_with_eigenvectors([0.,0.000001,0.])
freq, eigvec = phonon.get_frequencies_with_eigenvectors(G)
eigvec = eigvec.T
np.savez('freqNeigvec', freq=freq, eigvec=eigvec)
########## Plot ################
from subprocess import call
#### Band plot
if run_mode == 'phonon':
#
N_q = 100
bands = ssp.make_band(path, N_q)
phonon.run_band_structure(
bands,
with_eigenvectors=True,
)
class IR:
def __init__(self, PoscarName='POSCAR', BornFileName='BORN', ForceConstants=False, ForceFileName='FORCE_SETS',
supercell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]]
, nac=False, symprec=1e-5, masses=[], primitive=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
degeneracy_tolerance=1e-5):
"""
Class for calculating the IR spectra in the dipole approximation according to:
P. Giannozzi and S. Baroni, J. Chem. Phys. 100, 8537 (1994).
and
D. Karhanek, T. Bucko, J. Hafner, J. Phys.: Condens. Matter 22 265006 (2010).
This class was also carefully compared to the results of the script by D. Karhanek available at http://homepage.univie.ac.at/david.karhanek/downloads.html
args:
PoscarNamse (str): name of the POSCAR that was used for the phonon calculation
BornFileName (str): name of the file with BORN charges (formatted with outcar-born)
ForceConstants (boolean): If True, ForceConstants are read in. If False, forces are read in.
ForceFileName (str): name of the file including force constants or forces
supercell (list of lists): reads in supercell
nac (boolean): If true, NAC is applied.
symprec (float): contains symprec tag as used in Phonopy
masses (list): Masses in this list are used instead of the ones prepared in Phonopy. Useful for isotopes.
primitive (list of lists): contains rotational matrix to arrive at primitive cell
degeneracy_tolerance (float): tolerance for degenerate modes
"""
self.__unitcell = read_vasp(PoscarName)
self.__supercell = supercell
self.__phonon = Phonopy(self.__unitcell, supercell_matrix=self.__supercell, primitive_matrix=primitive,
factor=VaspToCm, symprec=symprec)
self.__natoms = self.__phonon.get_primitive().get_number_of_atoms()
self._degeneracy_tolerance = degeneracy_tolerance
# If different masses are supplied
if not ForceConstants:
self.__force_sets = parse_FORCE_SETS(filename=ForceFileName)
self.__phonon.set_displacement_dataset(self.__force_sets)
self.__phonon.produce_force_constants()
if ForceConstants:
force_constants = parse_FORCE_CONSTANTS(filename=ForceFileName)
self.__phonon.set_force_constants(force_constants)
if masses:
self.__phonon._build_supercell()
self.__phonon._build_primitive_cell()
# if ForceConstants:
# force_constants = parse_FORCE_CONSTANTS(filename=ForceFileName)
# self.__phonon.set_force_constants(force_constants)
self.__phonon.set_masses(masses)
self.__masses = self.__phonon.get_primitive().get_masses()
# Forces or Force Constants
# Read in BORN file
BORN_file = parse_BORN(self.__phonon.get_primitive(), filename=BornFileName)
self.__BORN_CHARGES = BORN_file['born']
# Apply NAC Correction
if nac:
self.__phonon.set_nac_params(BORN_file)
self._frequencies, self._eigvecs = self.__phonon.get_frequencies_with_eigenvectors([0, 0, 0])
self.__NumberOfBands = len(self._frequencies)
# Nicer format of the eigenvector file
self.__FormatEigenvectors()
# Get dipole approximation of the intensitiess
self.__set_intensities()
def __FormatEigenvectors(self):
"""
Formats eigenvectors to a dictionary: the first argument is the number of bands, the second the number of atoms, the third the Cartesian coordinate
"""
self._EigFormat = {}
for alpha in range(self.__NumberOfBands):
laufer = 0
for beta in range(self.__natoms):
for xyz in range(0, 3):
self._EigFormat[beta, alpha, xyz] = self._eigvecs[laufer][alpha]
laufer = laufer + 1
def _Eigenvector(self, atom, band, xoryorz):
"""
Gives a certain eigenvector corresponding to one specific atom, band and Cartesian coordinate
args:
atom (int) : number of the atoms (same order as in POSCAR)
band (int) : number of the frequency (ordered by energy)
xoryorz (int): Cartesian coordinate of the eigenvector
"""
return np.real(self._EigFormat[atom, band, xoryorz])
def __massEig(self, atom, band, xoryorz):
"""
Gives a certain eigenvector divided by sqrt(mass of the atom) corresponding to one specific atom, band and Cartesian coordinate
args:
atom (int) : number of the atoms (same order as in POSCAR)
band (int) : number of the frequency (ordered by energy)
xoryorz (int): Cartesian coordinate of the eigenvector
"""
return self._Eigenvector(atom, band, xoryorz) / np.sqrt(self.__masses[atom])
def __set_intensities(self):
"""
Calculates the oscillator strenghts according to "P. Giannozzi and S. Baroni, J. Chem. Phys. 100, 8537 (1994)."
"""
Intensity = {}
for freq in range(len(self._frequencies)):
Intensity[freq] = 0
for alpha in range(3):
sum = 0
for l in range(self.__natoms):
for beta in range(3):
sum = sum + self.__BORN_CHARGES[l, alpha, beta] * self.__massEig(l, freq, beta)
Intensity[freq] = Intensity[freq] + np.power(np.absolute(sum), 2)
# get degenerate modes
freqlist_deg = get_degenerate_sets(self._frequencies, cutoff=self._degeneracy_tolerance)
ReformatIntensity = []
for i in Intensity:
ReformatIntensity.append(Intensity[i])
# if degenerate modes exist:
if (len(freqlist_deg) < len(self._frequencies)):
Intensity_deg = {}
for sets in range(len(freqlist_deg)):
Intensity_deg[sets] = 0
for band in range(len(freqlist_deg[sets])):
Intensity_deg[sets] = Intensity_deg[sets] + ReformatIntensity[freqlist_deg[sets][band]]
ReformatIntensity = []
for i in range(len(Intensity_deg)):
ReformatIntensity.append(Intensity_deg[i])
Freq = []
for band in range(len(freqlist_deg)):
Freq.append(self._frequencies[freqlist_deg[band][0]])
self.__frequencies_deg = np.array(Freq)
else:
self.__frequencies_deg = self._frequencies
self.__Intensity = np.array(ReformatIntensity)
def get_intensities(self):
"""
returns calculated oscillator strengths as a numpy array
"""
return self.__Intensity
def get_frequencies(self):
"""
returns frequencies as a numpy array
"""
return self.__frequencies_deg
def get_spectrum(self):
"""
returns spectrum as a dict of numpy arrays
"""
"""
Degeneracy should be treated for the Oscillator strengths
"""
spectrum = {'Frequencies': self.get_frequencies(), 'Intensities': self.get_intensities()}
return spectrum
# only gaussian broadening so far
def get_gaussiansmearedspectrum(self, sigma):
"""
returns a spectrum with gaussian-smeared intensities
args:
sigma (float): smearing
"""
#unsmearedspectrum = self.get_spectrum()
frequencies = self.get_frequencies()
Intensity = self.get_intensities()
rangex = np.linspace(0, np.nanmax(frequencies) + 50, num=int(np.nanmax(frequencies) + 50) * 100)
y = np.zeros(int(np.nanmax(frequencies) + 50) * 100)
for i in range(len(frequencies)):
y = y + self.__gaussiansmearing(rangex, frequencies[i], Intensity[i], sigma)
smearedspectrum = {'Frequencies': rangex, 'Intensities': y}
return smearedspectrum
def __gaussiansmearing(self, rangex, frequency, Intensity, sigma):
"""
applies gaussian smearing to a range of x values, a certain frequency, a given intensity
args:
rangex (ndarray): Which values are in your spectrum
frequency (float): frequency corresponding to the intensity that will be smeared
Intensity (float): Intensity that will be smeared
sigma (float): value for the smearing
"""
y = np.zeros(rangex.size)
y = Intensity * np.exp(-np.power((rangex - frequency), 2) / (2 * np.power(sigma, 2))) * np.power(
np.sqrt(2 * np.pi) * sigma, -1)
return y
def write_spectrum(self, filename, type='yaml'):
"""
writes oscillator strenghts to file
args:
filename(str): Filename
type(str): either txt or yaml
"""
#TODO: csv
spectrum = self.get_spectrum()
if type == 'txt':
self.__write_file(filename, spectrum)
elif type == 'yaml':
self.__write_file_yaml(filename, spectrum)
def write_gaussiansmearedspectrum(self, filename, sigma, type='txt'):
"""
writes smeared oscillator strenghts to file
args:
filename(str): Filename
sigma(float): smearing of the spectrum
type(str): either txt or yaml
"""
#TODO csv
spectrum = self.get_gaussiansmearedspectrum(sigma)
if type == 'txt':
self.__write_file(filename, spectrum)
elif type == 'yaml':
self.__write_file_yaml(filename, spectrum)
def __write_file(self, filename, spectrum):
"""
writes dict for any spectrum into txt file
args:
filename(str): Filename
spectrum (dict): Includes nparray for 'Frequencies'
and 'Intensities'
"""
Freq = np.array(spectrum['Frequencies'].tolist())
Intens = np.array(spectrum['Intensities'].tolist())
file = open(filename, 'w')
file.write('Frequency (cm-1) Oscillator Strengths \n')
for i in range(len(Freq)):
file.write('%s %s \n' % (Freq[i], Intens[i]))
file.close()
def __write_file_yaml(self, filename, spectrum):
"""
writes dict for any spectrum into yaml file
args:
filename(str): Filename
spectrum (dict): Includes nparray for 'Frequencies'
and 'Intensities'
"""
Freq = np.array(spectrum['Frequencies'].tolist())
Intens = np.array(spectrum['Intensities'].tolist())
file = open(filename, 'w')
file.write('Frequency: \n')
for i in range(len(Freq)):
file.write('- %s \n' % (Freq[i]))
file.write('Oscillator Strengths: \n')
for i in range(len(Intens)):
file.write('- %s \n' % (Intens[i]))
file.close()
def plot_spectrum(self, filename):
"""
Plots frequencies in cm-1 and oscillator strengths
args:
filename(str): name of the file
"""
spectrum = self.get_spectrum()
plt.stem(spectrum['Frequencies'].tolist(), spectrum['Intensities'].tolist(), markerfmt=' ')
plt.xlabel('Wave number (cm$^{-1}$)')
plt.ylabel('Oscillator Strengths')
plt.savefig(filename)
plt.show()
def plot_gaussiansmearedspectrum(self, filename, sigma):
"""
Plots frequencies in cm-1 and smeared oscillator strengths
args:
filename(str): name of the file
sigma(float): smearing
"""
spectrum = self.get_gaussiansmearedspectrum(sigma)
plt.plot(spectrum['Frequencies'].tolist(), spectrum['Intensities'].tolist())
plt.xlabel('Wave number (cm$^{-1}$)')
plt.ylabel('Oscillator Strengths')
plt.savefig(filename)
plt.show()