Source code for ase.vibrations.infrared

# -*- coding: utf-8 -*-

"""Infrared intensities"""

import os.path as op
from math import sqrt
from sys import stdout

import numpy as np

import ase.units as units
from ase.parallel import parprint, paropen
from ase.vibrations import Vibrations
from ase.utils import basestring, pickleload


[docs]class Infrared(Vibrations): """Class for calculating vibrational modes and infrared intensities using finite difference. The vibrational modes are calculated from a finite difference approximation of the Dynamical matrix and the IR intensities from a finite difference approximation of the gradient of the dipole moment. The method is described in: D. Porezag, M. R. Pederson: "Infrared intensities and Raman-scattering activities within density-functional theory", Phys. Rev. B 54, 7830 (1996) The calculator object (calc) linked to the Atoms object (atoms) must have the attribute: >>> calc.get_dipole_moment(atoms) In addition to the methods included in the ``Vibrations`` class the ``Infrared`` class introduces two new methods; *get_spectrum()* and *write_spectra()*. The *summary()*, *get_energies()*, *get_frequencies()*, *get_spectrum()* and *write_spectra()* methods all take an optional *method* keyword. Use method='Frederiksen' to use the method described in: T. Frederiksen, M. Paulsson, M. Brandbyge, A. P. Jauho: "Inelastic transport theory from first-principles: methodology and applications for nanoscale devices", Phys. Rev. B 75, 205413 (2007) atoms: Atoms object The atoms to work on. indices: list of int List of indices of atoms to vibrate. Default behavior is to vibrate all atoms. name: str Name to use for files. delta: float Magnitude of displacements. nfree: int Number of displacements per degree of freedom, 2 or 4 are supported. Default is 2 which will displace each atom +delta and -delta in each cartesian direction. directions: list of int Cartesian coordinates to calculate the gradient of the dipole moment in. For example directions = 2 only dipole moment in the z-direction will be considered, whereas for directions = [0, 1] only the dipole moment in the xy-plane will be considered. Default behavior is to use the dipole moment in all directions. Example: >>> from ase.io import read >>> from ase.calculators.vasp import Vasp >>> from ase.vibrations import Infrared >>> water = read('water.traj') # read pre-relaxed structure of water >>> calc = Vasp(prec='Accurate', ... ediff=1E-8, ... isym=0, ... idipol=4, # calculate the total dipole moment ... dipol=water.get_center_of_mass(scaled=True), ... ldipol=True) >>> water.set_calculator(calc) >>> ir = Infrared(water) >>> ir.run() >>> ir.summary() ------------------------------------- Mode Frequency Intensity # meV cm^-1 (D/Å)^2 amu^-1 ------------------------------------- 0 16.9i 136.2i 1.6108 1 10.5i 84.9i 2.1682 2 5.1i 41.1i 1.7327 3 0.3i 2.2i 0.0080 4 2.4 19.0 0.1186 5 15.3 123.5 1.4956 6 195.5 1576.7 1.6437 7 458.9 3701.3 0.0284 8 473.0 3814.6 1.1812 ------------------------------------- Zero-point energy: 0.573 eV Static dipole moment: 1.833 D Maximum force on atom in `equilibrium`: 0.0026 eV/Å This interface now also works for calculator 'siesta', (added get_dipole_moment for siesta). Example: >>> #!/usr/bin/env python3 >>> from ase.io import read >>> from ase.calculators.siesta import Siesta >>> from ase.vibrations import Infrared >>> bud = read('bud1.xyz') >>> calc = Siesta(label='bud', ... meshcutoff=250 * Ry, ... basis='DZP', ... kpts=[1, 1, 1]) >>> calc.set_fdf('DM.MixingWeight', 0.08) >>> calc.set_fdf('DM.NumberPulay', 3) >>> calc.set_fdf('DM.NumberKick', 20) >>> calc.set_fdf('DM.KickMixingWeight', 0.15) >>> calc.set_fdf('SolutionMethod', 'Diagon') >>> calc.set_fdf('MaxSCFIterations', 500) >>> calc.set_fdf('PAO.BasisType', 'split') >>> #50 meV = 0.003674931 * Ry >>> calc.set_fdf('PAO.EnergyShift', 0.003674931 * Ry ) >>> calc.set_fdf('LatticeConstant', 1.000000 * Ang) >>> calc.set_fdf('WriteCoorXmol', 'T') >>> bud.set_calculator(calc) >>> ir = Infrared(bud) >>> ir.run() >>> ir.summary() """ def __init__(self, atoms, indices=None, name='ir', delta=0.01, nfree=2, directions=None): Vibrations.__init__(self, atoms, indices=indices, name=name, delta=delta, nfree=nfree) if atoms.constraints: print('WARNING! \n Your Atoms object is constrained. ' 'Some forces may be unintended set to zero. \n') if directions is None: self.directions = np.asarray([0, 1, 2]) else: self.directions = np.asarray(directions) self.ir = True self.ram = False def read(self, method='standard', direction='central'): self.method = method.lower() self.direction = direction.lower() assert self.method in ['standard', 'frederiksen'] def load(fname, combined_data=None): if combined_data is not None: try: return combined_data[op.basename(fname)] except KeyError: return combined_data[fname] # Old version return pickleload(open(fname, 'rb')) if direction != 'central': raise NotImplementedError( 'Only central difference is implemented at the moment.') if op.isfile(self.name + '.all.pckl'): # Open the combined pickle-file combined_data = load(self.name + '.all.pckl') else: combined_data = None # Get "static" dipole moment and forces name = '%s.eq.pckl' % self.name [forces_zero, dipole_zero] = load(name, combined_data) self.dipole_zero = (sum(dipole_zero**2)**0.5) / units.Debye self.force_zero = max([sum((forces_zero[j])**2)**0.5 for j in self.indices]) ndof = 3 * len(self.indices) H = np.empty((ndof, ndof)) dpdx = np.empty((ndof, 3)) r = 0 for a in self.indices: for i in 'xyz': name = '%s.%d%s' % (self.name, a, i) [fminus, dminus] = load(name + '-.pckl', combined_data) [fplus, dplus] = load(name + '+.pckl', combined_data) if self.nfree == 4: [fminusminus, dminusminus] = load( name + '--.pckl', combined_data) [fplusplus, dplusplus] = load( name + '++.pckl', combined_data) if self.method == 'frederiksen': fminus[a] += -fminus.sum(0) fplus[a] += -fplus.sum(0) if self.nfree == 4: fminusminus[a] += -fminus.sum(0) fplusplus[a] += -fplus.sum(0) if self.nfree == 2: H[r] = (fminus - fplus)[self.indices].ravel() / 2.0 dpdx[r] = (dminus - dplus) if self.nfree == 4: H[r] = (-fminusminus + 8 * fminus - 8 * fplus + fplusplus)[self.indices].ravel() / 12.0 dpdx[r] = (-dplusplus + 8 * dplus - 8 * dminus + dminusminus) / 6.0 H[r] /= 2 * self.delta dpdx[r] /= 2 * self.delta for n in range(3): if n not in self.directions: dpdx[r][n] = 0 dpdx[r][n] = 0 r += 1 # Calculate eigenfrequencies and eigenvectors m = self.atoms.get_masses() H += H.copy().T self.H = H m = self.atoms.get_masses() self.im = np.repeat(m[self.indices]**-0.5, 3) omega2, modes = np.linalg.eigh(self.im[:, None] * H * self.im) self.modes = modes.T.copy() # Calculate intensities dpdq = np.array([dpdx[j] / sqrt(m[self.indices[j // 3]] * units._amu / units._me) for j in range(ndof)]) dpdQ = np.dot(dpdq.T, modes) dpdQ = dpdQ.T intensities = np.array([sum(dpdQ[j]**2) for j in range(ndof)]) # Conversion factor: s = units._hbar * 1e10 / sqrt(units._e * units._amu) self.hnu = s * omega2.astype(complex)**0.5 # Conversion factor from atomic units to (D/Angstrom)^2/amu. conv = (1.0 / units.Debye)**2 * units._amu / units._me self.intensities = intensities * conv def intensity_prefactor(self, intensity_unit): if intensity_unit == '(D/A)2/amu': return 1.0, '(D/Å)^2 amu^-1' elif intensity_unit == 'km/mol': # conversion factor from Porezag PRB 54 (1996) 7830 return 42.255, 'km/mol' else: raise RuntimeError('Intensity unit >' + intensity_unit + '< unknown.')
[docs] def summary(self, method='standard', direction='central', intensity_unit='(D/A)2/amu', log=stdout): hnu = self.get_energies(method, direction) s = 0.01 * units._e / units._c / units._hplanck iu, iu_string = self.intensity_prefactor(intensity_unit) if intensity_unit == '(D/A)2/amu': iu_format = '%9.4f' elif intensity_unit == 'km/mol': iu_string = ' ' + iu_string iu_format = ' %7.1f' if isinstance(log, basestring): log = paropen(log, 'a') parprint('-------------------------------------', file=log) parprint(' Mode Frequency Intensity', file=log) parprint(' # meV cm^-1 ' + iu_string, file=log) parprint('-------------------------------------', file=log) for n, e in enumerate(hnu): if e.imag != 0: c = 'i' e = e.imag else: c = ' ' e = e.real parprint(('%3d %6.1f%s %7.1f%s ' + iu_format) % (n, 1000 * e, c, s * e, c, iu * self.intensities[n]), file=log) parprint('-------------------------------------', file=log) parprint('Zero-point energy: %.3f eV' % self.get_zero_point_energy(), file=log) parprint('Static dipole moment: %.3f D' % self.dipole_zero, file=log) parprint('Maximum force on atom in `equilibrium`: %.4f eV/Å' % self.force_zero, file=log) parprint(file=log)
[docs] def get_spectrum(self, start=800, end=4000, npts=None, width=4, type='Gaussian', method='standard', direction='central', intensity_unit='(D/A)2/amu', normalize=False): """Get infrared spectrum. The method returns wavenumbers in cm^-1 with corresponding absolute infrared intensity. Start and end point, and width of the Gaussian/Lorentzian should be given in cm^-1. normalize=True ensures the integral over the peaks to give the intensity. """ frequencies = self.get_frequencies(method, direction).real intensities = self.intensities return self.fold(frequencies, intensities, start, end, npts, width, type, normalize)
[docs] def write_spectra(self, out='ir-spectra.dat', start=800, end=4000, npts=None, width=10, type='Gaussian', method='standard', direction='central', intensity_unit='(D/A)2/amu', normalize=False): """Write out infrared spectrum to file. First column is the wavenumber in cm^-1, the second column the absolute infrared intensities, and the third column the absorbance scaled so that data runs from 1 to 0. Start and end point, and width of the Gaussian/Lorentzian should be given in cm^-1.""" energies, spectrum = self.get_spectrum(start, end, npts, width, type, method, direction, normalize) # Write out spectrum in file. First column is absolute intensities. # Second column is absorbance scaled so that data runs from 1 to 0 spectrum2 = 1. - spectrum / spectrum.max() outdata = np.empty([len(energies), 3]) outdata.T[0] = energies outdata.T[1] = spectrum outdata.T[2] = spectrum2 fd = open(out, 'w') fd.write('# %s folded, width=%g cm^-1\n' % (type.title(), width)) iu, iu_string = self.intensity_prefactor(intensity_unit) if normalize: iu_string = 'cm ' + iu_string fd.write('# [cm^-1] %14s\n' % ('[' + iu_string + ']')) for row in outdata: fd.write('%.3f %15.5e %15.5e \n' % (row[0], iu * row[1], row[2])) fd.close()
# np.savetxt(out, outdata, fmt='%.3f %15.5e %15.5e') InfraRed = Infrared # old name