def writeXYZ(self, fn, rep=[1, 1, 1], write_ghosts=False):
"Write .mkl file with unitcell repeated rep times"
geom = copy.deepcopy(self)
for i in range(3):
geom.repeteGeom(self.pbc[i], rep=rep[i])
geom.pbc[i] = [rep[i] * x for x in self.pbc[i]]
SIO.WriteXYZFile(fn, geom.anr, geom.xyz, write_ghosts)
def WriteOutput(self, label, SinglePrec, GammaPoint):
print('\nPhonons.WriteOutput')
### Write MKL- and xyz-files
natoms = self.geom.natoms
hw = self.hw
# Write only real part of eigenvectors
UU = self.UU.reshape(len(hw), 3 * natoms).real
UUdisp = self.UUdisp.reshape(len(hw), 3 * natoms).real
UUcl = self.UUcl.reshape(len(hw), 3 * natoms).real
SIO.WriteMKLFile('%s.mkl' % label, self.geom.anr, self.geom.xyz, hw,
UU, 1, natoms)
SIO.WriteMKLFile('%s.real-displ.mkl' % label, self.geom.anr,
self.geom.xyz, hw, UUdisp, 1, natoms)
SIO.WriteXYZFile('%s.xyz' % label, self.geom.anr, self.geom.xyz)
WriteFreqFile('%s.freq' % label, hw)
WriteVibDOSFile('%s.Gfdos' % label, hw, type='Gaussian')
WriteVibDOSFile('%s.Lfdos' % label, hw, type='Lorentzian')
WriteAXSFFiles('%s.mol.axsf' % label, self.geom.xyz, self.geom.anr, hw,
UU, 1, natoms)
WriteAXSFFiles('%s.mol.real-displ.axsf' % label, self.geom.xyz,
self.geom.anr, hw, UUdisp, 1, natoms)
WriteAXSFFiles('%s.mol.charlength-displ.axsf' % label, self.geom.xyz,
self.geom.anr, hw, UUcl, 1, natoms)
WriteAXSFFilesPer('%s.per.axsf' % label, self.geom.pbc, self.geom.xyz,
self.geom.anr, hw, UU, 1, natoms)
WriteAXSFFilesPer('%s.per.real-displ.axsf' % label, self.geom.pbc,
self.geom.xyz, self.geom.anr, hw, UUdisp, 1, natoms)
WriteAXSFFilesPer('%s.per.charlength-displ.axsf' % label,
self.geom.pbc, self.geom.xyz, self.geom.anr, hw,
UUcl, 1, natoms)
# Netcdf format
ncdffn = '%s.nc' % label
print('Phonons.WriteOutput: Writing ' + ncdffn)
ncdf = NC4.Dataset(ncdffn, 'w')
ncdf.createDimension('one', 1)
ncdf.createDimension('xyz', 3)
ncdf.createDimension('modes', len(hw))
ncdf.createDimension('natoms', self.geom.natoms)
ncdf.createDimension('dyn_atoms', len(self.DynamicAtoms))
ncdf.createVariable('hw', 'd', ('modes', ))
ncdf.variables['hw'][:] = hw
ncdf.variables['hw'].info = 'Phonon frequencies'
ncdf.variables['hw'].unit = 'eV'
ncdf.createVariable('U', 'd', ('modes', 'natoms', 'xyz'))
ncdf.variables['U'][:] = self.UU.real
ncdf.variables['U'].info = 'Real part of the phonon eigenvectors'
ncdf.createVariable('Udisp', 'd', ('modes', 'natoms', 'xyz'))
ncdf.variables['Udisp'][:] = self.UUdisp.real
ncdf.variables[
'Udisp'].info = 'Real part of the phonon displacement vectors'
ncdf.createVariable('Ucl', 'd', ('modes', 'natoms', 'xyz'))
ncdf.variables['Ucl'][:] = self.UUcl.real
ncdf.variables[
'Ucl'].info = 'Real part of displacement vectors scaled for the characteristic length'
ncdf.createVariable('CellVectors', 'd', ('xyz', 'xyz'))
ncdf.variables['CellVectors'][:] = self.geom.pbc
ncdf.variables['CellVectors'].info = 'Unit cell vectors'
ncdf.variables['CellVectors'].unit = 'Ang'
ncdf.createVariable('GeometryXYZ', 'd', ('natoms', 'xyz'))
ncdf.variables['GeometryXYZ'][:] = self.geom.xyz
ncdf.variables[
'GeometryXYZ'].info = 'Atomic coordinates of all atoms in cell'
ncdf.variables['GeometryXYZ'].unit = 'Ang'
ncdf.createVariable('FC', 'd', ('dyn_atoms', 'xyz', 'natoms', 'xyz'))
ncdf.variables['FC'][:] = self.mean
ncdf.variables['FC'].info = 'Force matrix'
ncdf.variables['FC'].unit = 'eV/Ang^2'
ncdf.createVariable('AtomNumbers', 'i', ('natoms', ))
ncdf.variables['AtomNumbers'][:] = self.geom.anr
ncdf.variables[
'AtomNumbers'].info = 'Element number for each atom (anr)'
ncdf.createVariable('SpeciesNumbers', 'i', ('natoms', ))
ncdf.variables['SpeciesNumbers'][:] = self.geom.snr
ncdf.variables['SpeciesNumbers'].info = 'Siesta species number (snr)'
ncdf.createVariable('Masses', 'd', ('dyn_atoms', ))
ncdf.variables['Masses'][:] = self.Masses
ncdf.variables['Masses'].info = 'Atomic masses of each dynamic atom'
ncdf.variables['Masses'].unit = 'Atomic units'
ncdf.createVariable('DynamicAtoms', 'i', ('dyn_atoms', ))
ncdf.variables['DynamicAtoms'][:] = self.DynamicAtoms
ncdf.variables[
'DynamicAtoms'].info = 'Dynamic atoms (SIESTA numbering)'
try:
self.h0
ncdf.createDimension('dev_atoms', len(self.DeviceAtoms))
ncdf.createDimension('nspin', len(self.h0))
ncdf.createDimension('norb', len(self.h0[0]))
ncdf.createVariable('DeviceAtoms', 'i', ('dev_atoms', ))
ncdf.variables['DeviceAtoms'][:] = self.DeviceAtoms
ncdf.variables[
'DeviceAtoms'].info = 'Device atoms (SIESTA numbering)'
ncdf.createVariable('kpoint', 'd', ('xyz', ))
ncdf.variables['kpoint'][:] = self.kpoint
ncdf.variables[
'kpoint'].info = 'Vector in orthogonal space (not in reciprocal space)'
ncdf.createVariable('H0', 'd', ('nspin', 'norb', 'norb'))
ncdf.variables['H0'][:] = self.h0.real
ncdf.variables['H0'].info = 'Real part of electronic Hamiltonian'
ncdf.variables['H0'].unit = 'eV'
ncdf.createVariable('S0', 'd', ('nspin', 'norb', 'norb'))
ncdf.variables['S0'][:] = self.s0.real
ncdf.variables['S0'].info = 'Electronic overlap matrix'
if not GammaPoint:
ncdf.createVariable('H0.imag', 'd', ('nspin', 'norb', 'norb'))
ncdf.variables['H0.imag'][:] = self.h0.imag
ncdf.variables[
'H0.imag'].info = 'Imaginary part of Hamiltonian'
ncdf.createVariable('S0.imag', 'd', ('nspin', 'norb', 'norb'))
ncdf.variables['S0.imag'][:] = self.s0.imag
ncdf.variables['S0.imag'].info = 'Imaginary part of overlap'
print('Phonons.WriteOutput: Wrote H and S to ' + ncdffn)
except:
print('Hamiltonian etc not computed')
# Precision for He_ph (and gradients)
if SinglePrec:
atype = 'f'
else:
atype = 'd'
try:
self.heph
ncdf.createVariable('He_ph', atype,
('modes', 'nspin', 'norb', 'norb'))
ncdf.variables['He_ph'][:] = self.heph.real
ncdf.variables['He_ph'].info = 'Real part of EPH couplings'
ncdf.variables['He_ph'].unit = 'eV'
if not GammaPoint:
ncdf.createVariable('ImHe_ph', atype,
('modes', 'nspin', 'norb', 'norb'))
ncdf.variables['ImHe_ph'][:] = self.heph.imag
ncdf.variables[
'ImHe_ph'].info = 'Imaginary part of EPH couplings'
print('Phonons.WriteOutput: Wrote He_ph to ' + ncdffn)
except:
print('EPH couplings etc not computed')
try:
self.gradients
ncdf.createVariable('grad.re', atype,
('modes', 'nspin', 'norb', 'norb'))
ncdf.variables['grad.re'][:] = self.gradients.real
ncdf.variables['grad.re'].info = 'Real part of gradients'
ncdf.variables['grad.re'].unit = 'eV/Ang'
if not GammaPoint:
ncdf.createVariable('grad.im', atype,
('modes', 'nspin', 'norb', 'norb'))
ncdf.variables['grad.im'][:] = self.gradients.imag
ncdf.variables['grad.im'].info = 'Imaginary part of gradients'
print('Phonons.WriteOutput: Wrote gradients to ' + ncdffn)
except:
print('Phonons.WriteOutpot: Gradients not computed')
ncdf.close()
print('Phonons.WriteOutput: Finished ' + ncdffn)