def main(options):
"""
Main routine to compute inelastic transport characteristics (dI/dV, d2I/dV2, IETS etc)
Parameters
----------
options : an ``options`` instance
"""
CF.CreatePipeOutput(options.DestDir + '/' + options.Logfile)
VC.OptionsCheck(options, 'Inelastica')
CF.PrintMainHeader('Inelastica', options)
options.XV = '%s/%s.XV' % (options.head, options.systemlabel)
options.geom = MG.Geom(options.XV, BufferAtoms=options.buffer)
# Voltage fraction over left-center interface
VfracL = options.VfracL # default is 0.5
print 'Inelastica: Voltage fraction over left-center interface: VfracL =', VfracL
# Set up electrodes and device Greens function
elecL = NEGF.ElectrodeSelfEnergy(options.fnL, options.NA1L, options.NA2L,
options.voltage * VfracL)
elecL.scaling = options.scaleSigL
elecL.semiinf = options.semiinfL
elecR = NEGF.ElectrodeSelfEnergy(options.fnR, options.NA1R, options.NA2R,
options.voltage * (VfracL - 1.))
elecR.scaling = options.scaleSigR
elecR.semiinf = options.semiinfR
# Read phonons
NCfile = NC4.Dataset(options.PhononNetCDF, 'r')
print 'Inelastica: Reading ', options.PhononNetCDF
hw = NCfile.variables['hw'][:]
# Work with GFs etc for positive (V>0: \mu_L>\mu_R) and negative (V<0: \mu_L<\mu_R) bias voltages
GFp = NEGF.GF(options.TSHS,
elecL,
elecR,
Bulk=options.UseBulk,
DeviceAtoms=options.DeviceAtoms,
BufferAtoms=options.buffer)
# Prepare lists for various trace factors
#GF.dGnout = []
#GF.dGnin = []
GFp.P1T = N.zeros(len(hw), N.float) # M.A.M.A (total e-h damping)
GFp.P2T = N.zeros(len(hw), N.float) # M.AL.M.AR (emission)
GFp.ehDampL = N.zeros(len(hw), N.float) # M.AL.M.AL (L e-h damping)
GFp.ehDampR = N.zeros(len(hw), N.float) # M.AR.M.AR (R e-h damping)
GFp.nHT = N.zeros(len(hw), N.float) # non-Hilbert/Isym factor
GFp.HT = N.zeros(len(hw), N.float) # Hilbert/Iasym factor
GFp.dIel = N.zeros(len(hw), N.float)
GFp.dIinel = N.zeros(len(hw), N.float)
GFp.dSel = N.zeros(len(hw), N.float)
GFp.dSinel = N.zeros(len(hw), N.float)
#
GFm = NEGF.GF(options.TSHS,
elecL,
elecR,
Bulk=options.UseBulk,
DeviceAtoms=options.DeviceAtoms,
BufferAtoms=options.buffer)
GFm.P1T = N.zeros(len(hw), N.float) # M.A.M.A (total e-h damping)
GFm.P2T = N.zeros(len(hw), N.float) # M.AL.M.AR (emission)
GFm.ehDampL = N.zeros(len(hw), N.float) # M.AL.M.AL (L e-h damping)
GFm.ehDampR = N.zeros(len(hw), N.float) # M.AR.M.AR (R e-h damping)
GFm.nHT = N.zeros(len(hw), N.float) # non-Hilbert/Isym factor
GFm.HT = N.zeros(len(hw), N.float) # Hilbert/Iasym factor
GFm.dIel = N.zeros(len(hw), N.float)
GFm.dIinel = N.zeros(len(hw), N.float)
GFm.dSel = N.zeros(len(hw), N.float)
GFm.dSinel = N.zeros(len(hw), N.float)
# Calculate transmission at Fermi level
GFp.calcGF(options.energy + options.eta * 1.0j,
options.kpoint[0:2],
ispin=options.iSpin,
etaLead=options.etaLead,
useSigNCfiles=options.signc,
SpectralCutoff=options.SpectralCutoff)
L = options.bufferL
# Pad lasto with zeroes to enable basis generation...
lasto = N.zeros((GFp.HS.nua + L + 1, ), N.int)
lasto[L:] = GFp.HS.lasto
basis = SIO.BuildBasis(options.fn, options.DeviceAtoms[0] + L,
options.DeviceAtoms[1] + L, lasto)
basis.ii -= L
TeF = MM.trace(GFp.TT).real
GFp.TeF = TeF
GFm.TeF = TeF
# Check consistency of PHrun vs TSrun inputs
IntegrityCheck(options, GFp, basis, NCfile)
# Calculate trace factors one mode at a time
print 'Inelastica: LOEscale =', options.LOEscale
if options.LOEscale == 0.0:
# LOEscale=0.0 => Original LOE-WBA method, PRB 72, 201101(R) (2005) [cond-mat/0505473].
GFp.calcGF(options.energy + options.eta * 1.0j,
options.kpoint[0:2],
ispin=options.iSpin,
etaLead=options.etaLead,
useSigNCfiles=options.signc,
SpectralCutoff=options.SpectralCutoff)
GFm.calcGF(options.energy + options.eta * 1.0j,
options.kpoint[0:2],
ispin=options.iSpin,
etaLead=options.etaLead,
useSigNCfiles=options.signc,
SpectralCutoff=options.SpectralCutoff)
for ihw in (hw > options.modeCutoff).nonzero()[0]:
calcTraces(options, GFp, GFm, basis, NCfile, ihw)
calcTraces(options, GFm, GFp, basis, NCfile, ihw)
writeFGRrates(options, GFp, hw, NCfile)
else:
# LOEscale=1.0 => Generalized LOE, PRB 89, 081405(R) (2014) [arXiv:1312.7625]
for ihw in (hw > options.modeCutoff).nonzero()[0]:
GFp.calcGF(options.energy + hw[ihw] * options.LOEscale * VfracL +
options.eta * 1.0j,
options.kpoint[0:2],
ispin=options.iSpin,
etaLead=options.etaLead,
useSigNCfiles=options.signc,
SpectralCutoff=options.SpectralCutoff)
GFm.calcGF(options.energy + hw[ihw] * options.LOEscale *
(VfracL - 1.) + options.eta * 1.0j,
options.kpoint[0:2],
ispin=options.iSpin,
etaLead=options.etaLead,
useSigNCfiles=options.signc,
SpectralCutoff=options.SpectralCutoff)
calcTraces(options, GFp, GFm, basis, NCfile, ihw)
if VfracL != 0.5:
GFp.calcGF(options.energy - hw[ihw] * options.LOEscale *
(VfracL - 1.) + options.eta * 1.0j,
options.kpoint[0:2],
ispin=options.iSpin,
etaLead=options.etaLead,
useSigNCfiles=options.signc,
SpectralCutoff=options.SpectralCutoff)
GFm.calcGF(options.energy -
hw[ihw] * options.LOEscale * VfracL +
options.eta * 1.0j,
options.kpoint[0:2],
ispin=options.iSpin,
etaLead=options.etaLead,
useSigNCfiles=options.signc,
SpectralCutoff=options.SpectralCutoff)
calcTraces(options, GFm, GFp, basis, NCfile, ihw)
# Multiply traces with voltage-dependent functions
data = calcIETS(options, GFp, GFm, basis, hw)
NCfile.close()
NEGF.SavedSig.close()
CF.PrintMainFooter('Inelastica')
return data
def readbasis():
global basis
fn = glob.glob('RUN.fdf')
basis = SIO.BuildBasis(fn[0], 1, geom.sym.NN, HS.lasto)
def main(options):
"""
Main routine to compute eigenchannel scattering states
Parameters
----------
options : an ``options`` instance
"""
Log.CreatePipeOutput(options)
VC.OptionsCheck(options)
Log.PrintMainHeader(options)
# Read geometry
XV = '%s/%s.XV' % (options.head, options.systemlabel)
geom = MG.Geom(XV, BufferAtoms=options.buffer)
# Set up device Greens function
elecL = NEGF.ElectrodeSelfEnergy(options.fnL, options.NA1L, options.NA2L,
options.voltage / 2.)
elecL.scaling = options.scaleSigL
elecL.semiinf = options.semiinfL
elecR = NEGF.ElectrodeSelfEnergy(options.fnR, options.NA1R, options.NA2R,
-options.voltage / 2.)
elecR.scaling = options.scaleSigR
elecR.semiinf = options.semiinfR
DevGF = NEGF.GF(options.TSHS,
elecL,
elecR,
Bulk=options.UseBulk,
DeviceAtoms=options.DeviceAtoms,
BufferAtoms=options.buffer)
DevGF.calcGF(options.energy + options.eta * 1.0j,
options.kpoint[0:2],
ispin=options.iSpin,
etaLead=options.etaLead,
useSigNCfiles=options.signc,
SpectralCutoff=options.SpectralCutoff)
NEGF.SavedSig.close() # Make sure saved Sigma is written to file
# Transmission
print('Transmission Ttot(%.4feV) = %.16f' %
(options.energy, N.trace(DevGF.TT).real))
# Build basis
options.nspin = DevGF.HS.nspin
L = options.bufferL
# Pad lasto with zeroes to enable basis generation...
lasto = N.zeros((DevGF.HS.nua + L + 1, ), N.int)
lasto[L:] = DevGF.HS.lasto
basis = SIO.BuildBasis(options.fn, options.DeviceAtoms[0] + L,
options.DeviceAtoms[1] + L, lasto)
basis.ii -= L
# Calculate Eigenchannels
DevGF.calcEigChan(options.numchan)
# Compute bond currents?
if options.kpoint[0] != 0.0 or options.kpoint[1] != 0.0:
print(
'Warning: The current implementation of bond currents is only valid for the Gamma point (should be easy to fix)'
)
BC = False
else:
BC = True
# Eigenchannels from left
ECleft = DevGF.ECleft
for jj in range(options.numchan):
options.iSide, options.iChan = 0, jj + 1
writeWavefunction(options, geom, basis, ECleft[jj])
if BC:
Curr = calcCurrent(options, basis, DevGF.H, ECleft[jj])
writeCurrent(options, geom, Curr)
# Calculate eigenchannels from right
if options.bothsides:
ECright = DevGF.ECright
for jj in range(options.numchan):
options.iSide, options.iChan = 1, jj + 1
writeWavefunction(options, geom, basis, ECright[jj])
if BC:
Curr = calcCurrent(options, basis, DevGF.H, ECright[jj])
writeCurrent(options, geom, Curr)
# Calculate total "bond currents"
if BC:
Curr = -calcCurrent(options, basis, DevGF.H, DevGF.AL)
options.iChan, options.iSide = 0, 0
writeCurrent(options, geom, Curr)
Curr = -calcCurrent(options, basis, DevGF.H, DevGF.AR)
options.iSide = 1
writeCurrent(options, geom, Curr)
# Calculate eigenstates of device Hamiltonian (MPSH)
if options.MolStates > 0.0:
try:
import scipy.linalg as SLA
ev, es = SLA.eigh(DevGF.H, DevGF.S)
print(
'EigenChannels: Eigenvalues (in eV) of computed molecular eigenstates:'
)
print(ev)
# Write eigenvalues to file
fn = options.DestDir + '/' + options.systemlabel + '.EIGVAL'
print('EigenChannels: Writing', fn)
fnfile = open(fn, 'w')
fnfile.write('# Device region = [%i,%i], units in eV\n' %
(options.DeviceFirst, options.DeviceLast))
for i, val in enumerate(ev):
fnfile.write('%i %.8f\n' % (i, val))
fnfile.close()
# Compute selected eigenstates
for ii, val in enumerate(ev):
if N.abs(val) < options.MolStates:
fn = options.DestDir + '/' + options.systemlabel + '.S%.3i.E%.3f' % (
ii, val)
writeWavefunction(options, geom, basis, es[:, ii], fn=fn)
except:
print(
'You need to install scipy to solve the generalized eigenvalue problem'
)
print('for the molecular eigenstates in the nonorthogonal basis')
Log.PrintMainFooter(options)
return DevGF
def main(options):
"""
Main routine to compute elastic transmission probabilities etc.
Parameters
----------
options : an ``options`` instance
"""
CF.CreatePipeOutput(options.DestDir + '/' + options.Logfile)
VC.OptionsCheck(options, 'pyTBT')
CF.PrintMainHeader('pyTBT', options)
# K-points
if options.Gk1 > 1:
Nk1, t1 = options.Gk1, 'GK'
else:
Nk1, t1 = options.Nk1, 'LIN'
if options.Gk2 > 1:
Nk2, t2 = options.Gk2, 'GK'
else:
Nk2, t2 = options.Nk2, 'LIN'
# Generate full k-mesh:
mesh = Kmesh.kmesh(Nk1,
Nk2,
Nk3=1,
meshtype=[t1, t2, 'LIN'],
invsymmetry=not options.skipsymmetry)
mesh.mesh2file(
'%s/%s.%ix%i.mesh' %
(options.DestDir, options.systemlabel, mesh.Nk[0], mesh.Nk[1]))
# Setup self-energies and device GF
elecL = NEGF.ElectrodeSelfEnergy(options.fnL, options.NA1L, options.NA2L,
options.voltage / 2.)
elecL.scaling = options.scaleSigL
elecL.semiinf = options.semiinfL
elecR = NEGF.ElectrodeSelfEnergy(options.fnR, options.NA1R, options.NA2R,
-options.voltage / 2.)
elecR.scaling = options.scaleSigR
elecR.semiinf = options.semiinfR
DevGF = NEGF.GF(options.TSHS,
elecL,
elecR,
Bulk=options.UseBulk,
DeviceAtoms=options.DeviceAtoms,
BufferAtoms=options.buffer)
nspin = DevGF.HS.nspin
# k-sample only self-energies?
if options.singlejunction:
elecL.mesh = mesh
mesh = Kmesh.kmesh(3, 3, 1)
if options.dos:
DOSL = N.zeros((nspin, len(options.Elist), DevGF.nuo), N.float)
DOSR = N.zeros((nspin, len(options.Elist), DevGF.nuo), N.float)
# MPSH projections?
MPSHL = N.zeros((nspin, len(options.Elist), DevGF.nuo), N.float)
MPSHR = N.zeros((nspin, len(options.Elist), DevGF.nuo), N.float)
# evaluate eigenstates at Gamma
import scipy.linalg as SLA
DevGF.setkpoint(N.zeros(2))
ev0, es0 = SLA.eigh(DevGF.H, DevGF.S)
print 'MPSH eigenvalues:', ev0
#print 'MPSH eigenvector normalizations:',N.diag(MM.mm(MM.dagger(es0),DevGF.S,es0)).real # right
# Loop over spin
for iSpin in range(nspin):
# initialize transmission and shot noise arrays
Tkpt = N.zeros((len(options.Elist), mesh.NNk, options.numchan + 1),
N.float)
SNkpt = N.zeros((len(options.Elist), mesh.NNk, options.numchan + 1),
N.float)
# prepare output files
outFile = options.DestDir + '/%s.%ix%i' % (options.systemlabel,
mesh.Nk[0], mesh.Nk[1])
if nspin < 2: thisspinlabel = outFile
else: thisspinlabel = outFile + ['.UP', '.DOWN'][iSpin]
fo = open(thisspinlabel + '.AVTRANS', 'write')
fo.write('# Nk1(%s)=%i Nk2(%s)=%i eta=%.2e etaLead=%.2e\n' %
(mesh.type[0], mesh.Nk[0], mesh.type[1], mesh.Nk[1],
options.eta, options.etaLead))
fo.write('# E Ttot(E) Ti(E)(i=1-%i) RelErrorTtot(E)\n' %
options.numchan)
foSN = open(thisspinlabel + '.AVNOISE', 'write')
foSN.write('# Nk1(%s)=%i Nk2(%s)=%i eta=%.2e etaLead=%.2e\n' %
(mesh.type[0], mesh.Nk[0], mesh.type[1], mesh.Nk[1],
options.eta, options.etaLead))
foSN.write('# E SNtot(E) SNi(E)(i=1-%i)\n' % options.numchan)
foFF = open(thisspinlabel + '.FANO', 'write')
foFF.write('# Nk1(%s)=%i Nk2(%s)=%i eta=%.2e etaLead=%.2e\n' %
(mesh.type[0], mesh.Nk[0], mesh.type[1], mesh.Nk[1],
options.eta, options.etaLead))
foFF.write('# E Fano factor \n')
# Loop over energy
for ie, ee in enumerate(options.Elist):
Tavg = N.zeros((options.numchan + 1, len(mesh.w)), N.float)
SNavg = N.zeros((options.numchan + 1, len(mesh.w)), N.float)
AavL = N.zeros((DevGF.nuo, DevGF.nuo), N.complex)
AavR = N.zeros((DevGF.nuo, DevGF.nuo), N.complex)
# Loops over k-points
for ik in range(mesh.NNk):
DevGF.calcGF(ee + options.eta * 1.0j,
mesh.k[ik, :2],
ispin=iSpin,
etaLead=options.etaLead,
useSigNCfiles=options.signc,
SpectralCutoff=options.SpectralCutoff)
# Transmission and shot noise
T, SN = DevGF.calcTEIG(options.numchan)
for iw in range(len(mesh.w)):
Tavg[:, iw] += T * mesh.w[iw, ik]
SNavg[:, iw] += SN * mesh.w[iw, ik]
Tkpt[ie, ik] = T
SNkpt[ie, ik] = SN
# DOS calculation:
if options.dos:
if options.SpectralCutoff > 0.0:
AavL += mesh.w[0, ik] * MM.mm(DevGF.AL.L, DevGF.AL.R,
DevGF.S)
AavR += mesh.w[0, ik] * MM.mm(DevGF.AR.L, DevGF.AR.R,
DevGF.S)
else:
AavL += mesh.w[0, ik] * MM.mm(DevGF.AL, DevGF.S)
AavR += mesh.w[0, ik] * MM.mm(DevGF.AR, DevGF.S)
# Print calculated quantities
err = (N.abs(Tavg[0, 0] - Tavg[0, 1]) +
N.abs(Tavg[0, 0] - Tavg[0, 2])) / 2
relerr = err / Tavg[0, 0]
print 'ispin= %i, e= %.4f, Tavg= %.8f, RelErr= %.1e' % (
iSpin, ee, Tavg[0, 0], relerr)
transline = '\n%.10f ' % ee
noiseline = '\n%.10f ' % ee
for ichan in range(options.numchan + 1):
if ichan == 0:
transline += '%.8e ' % Tavg[ichan, 0]
noiseline += '%.8e ' % SNavg[ichan, 0]
else:
transline += '%.4e ' % Tavg[ichan, 0]
noiseline += '%.4e ' % SNavg[ichan, 0]
transline += '%.2e ' % relerr
fo.write(transline)
foSN.write(noiseline)
foFF.write('\n%.10f %.8e' % (ee, SNavg[0, 0] / Tavg[0, 0]))
# Partial density of states:
if options.dos:
DOSL[iSpin, ie, :] += N.diag(AavL).real / (2 * N.pi)
DOSR[iSpin, ie, :] += N.diag(AavR).real / (2 * N.pi)
MPSHL[iSpin, ie, :] += N.diag(MM.mm(MM.dagger(es0), AavL,
es0)).real / (2 * N.pi)
MPSHR[iSpin, ie, :] += N.diag(MM.mm(MM.dagger(es0), AavR,
es0)).real / (2 * N.pi)
print 'ispin= %i, e= %.4f, DOSL= %.4f, DOSR= %.4f' % (
iSpin, ee, N.sum(DOSL[iSpin,
ie, :]), N.sum(DOSR[iSpin, ie, :]))
fo.write('\n')
fo.close()
foSN.write('\n')
foSN.close()
foFF.write('\n')
foFF.close()
# Write k-point-resolved transmission
fo = open(thisspinlabel + '.TRANS', 'write')
for ik in range(mesh.NNk):
w = mesh.w[:, ik]
fo.write('\n\n# k = %f, %f w = %f %f %f %f' %
(mesh.k[ik, 0], mesh.k[ik, 1], w[0], w[1], w[2], w[3]))
for ie, ee in enumerate(options.Elist):
transline = '\n%.10f ' % ee
for ichan in range(options.numchan + 1):
if ichan == 0:
transline += '%.8e ' % Tkpt[ie, ik, ichan]
else:
transline += '%.4e ' % Tkpt[ie, ik, ichan]
fo.write(transline)
fo.write('\n')
fo.close()
# Write k-point-resolved shot noise
fo = open(thisspinlabel + '.NOISE', 'write')
for ik in range(mesh.NNk):
w = mesh.w[:, ik]
fo.write('\n\n# k = %f, %f w = %f %f %f %f' %
(mesh.k[ik, 0], mesh.k[ik, 1], w[0], w[1], w[2], w[3]))
for ie, ee in enumerate(options.Elist):
noiseline = '\n%.10f ' % ee
for ichan in range(options.numchan + 1):
if ichan == 0:
noiseline += '%.8e ' % SNkpt[ie, ik, ichan]
else:
noiseline += '%.4e ' % SNkpt[ie, ik, ichan]
fo.write(noiseline)
fo.write('\n')
fo.close()
# End loop over spin
NEGF.SavedSig.close() # Make sure saved Sigma is written to file
if options.dos:
# Read basis
L = options.bufferL
# Pad lasto with zeroes to enable basis generation...
lasto = N.zeros((DevGF.HS.nua + L + 1, ), N.int)
lasto[L:] = DevGF.HS.lasto
basis = SIO.BuildBasis(options.fn, 1 + L, DevGF.HS.nua + L, lasto)
basis.ii -= L
WritePDOS(outFile + '.PDOS.gz', options, DevGF, DOSL + DOSR, basis)
WritePDOS(outFile + '.PDOSL.gz', options, DevGF, DOSL, basis)
WritePDOS(outFile + '.PDOSR.gz', options, DevGF, DOSR, basis)
WriteMPSH(outFile + '.MPSH.gz', options, DevGF, MPSHL + MPSHR, ev0)
WriteMPSH(outFile + '.MPSHL.gz', options, DevGF, MPSHL, ev0)
WriteMPSH(outFile + '.MPSHR.gz', options, DevGF, MPSHR, ev0)
CF.PrintMainFooter('pyTBT')
def main(options):
Log.CreatePipeOutput(options)
#VC.OptionsCheck(options)
Log.PrintMainHeader(options)
try:
fdf = glob.glob(options.onlyTSdir + '/RUN.fdf')
TSrun = True
except:
fdf = glob.glob(options.FCwildcard +
'/RUN.fdf') # This should be made an input flag
TSrun = False
SCDM = Supercell_DynamicalMatrix(fdf, TSrun)
# Write high-symmetry path
WritePath(options.DestDir + '/symmetry-path', SCDM.Sym.path, options.steps)
# Write mesh
k1, k2, k3 = ast.literal_eval(options.mesh)
rvec = 2 * N.pi * N.array([SCDM.Sym.b1, SCDM.Sym.b2, SCDM.Sym.b3])
import Inelastica.physics.mesh as Kmesh
# Full mesh
kmesh = Kmesh.kmesh(2**k1,
2**k2,
2**k3,
meshtype=['LIN', 'LIN', 'LIN'],
invsymmetry=False)
WriteKpoints(options.DestDir + '/mesh_%ix%ix%i' % tuple(kmesh.Nk),
N.dot(kmesh.k, rvec))
# Mesh reduced by inversion symmetry
kmesh = Kmesh.kmesh(2**k1,
2**k2,
2**k3,
meshtype=['LIN', 'LIN', 'LIN'],
invsymmetry=True)
WriteKpoints(options.DestDir + '/mesh_%ix%ix%i_invsym' % tuple(kmesh.Nk),
N.dot(kmesh.k, rvec))
# Evaluate electron k-points
if options.kfile:
# Prepare Hamiltonian etc in Gamma for whole supercell
natoms = SIO.GetFDFlineWithDefault(fdf[0], 'NumberOfAtoms', int, -1,
'Error')
SCDM.PrepareGradients(options.onlySdir,
N.array([0., 0., 0.]),
1,
natoms,
AbsEref=False,
atype=N.complex,
TSrun=TSrun)
SCDM.nao = SCDM.h0.shape[-1]
SCDM.FirstOrb = SCDM.OrbIndx[0][0] # First atom = 1
SCDM.LastOrb = SCDM.OrbIndx[SCDM.Sym.basis.NN -
1][1] # Last atom = Sym.NN
SCDM.rednao = SCDM.LastOrb + 1 - SCDM.FirstOrb
# Read kpoints
kpts, dk, klabels, kticks = ReadKpoints(options.kfile)
if klabels:
# Only write ascii if labels exist
WriteKpoints(options.DestDir + '/kpoints', kpts, klabels)
# Prepare netcdf
ncfn = options.DestDir + '/Electrons.nc'
ncf = NC4.Dataset(ncfn, 'w')
# Grid
ncf.createDimension('gridpts', len(kpts))
ncf.createDimension('vector', 3)
grid = ncf.createVariable('grid', 'd', ('gridpts', 'vector'))
grid[:] = kpts
grid.units = '1/Angstrom'
# Geometry
ncf.createDimension('atoms', SCDM.Sym.basis.NN)
xyz = ncf.createVariable('xyz', 'd', ('atoms', 'vector'))
xyz[:] = SCDM.Sym.basis.xyz
xyz.units = 'Angstrom'
pbc = ncf.createVariable('pbc', 'd', ('vector', 'vector'))
pbc.units = 'Angstrom'
pbc[:] = [SCDM.Sym.a1, SCDM.Sym.a2, SCDM.Sym.a3]
rvec1 = ncf.createVariable('rvec', 'd', ('vector', 'vector'))
rvec1.units = '1/Angstrom (incl. factor 2pi)'
rvec1[:] = rvec
ncf.sync()
# Loop over kpoints
for i, k in enumerate(kpts):
if i < 100: # Print only for the first 100 points
ev, evec = SCDM.ComputeElectronStates(k,
verbose=True,
TSrun=TSrun)
else:
ev, evec = SCDM.ComputeElectronStates(k,
verbose=False,
TSrun=TSrun)
# otherwise something simple
if i % 100 == 0:
print('%i out of %i k-points computed' % (i, len(kpts)))
if i == 0:
ncf.createDimension('nspin', SCDM.nspin)
ncf.createDimension('orbs', SCDM.rednao)
if options.nbands and options.nbands < SCDM.rednao:
nbands = options.nbands
else:
nbands = SCDM.rednao
ncf.createDimension('bands', nbands)
evals = ncf.createVariable('eigenvalues', 'd',
('gridpts', 'nspin', 'bands'))
evals.units = 'eV'
evecsRe = ncf.createVariable(
'eigenvectors.re', 'd',
('gridpts', 'nspin', 'orbs', 'bands'))
evecsIm = ncf.createVariable(
'eigenvectors.im', 'd',
('gridpts', 'nspin', 'orbs', 'bands'))
# Check eigenvectors
print('SupercellPhonons: Checking eigenvectors at', k)
for j in range(SCDM.nspin):
ev2 = N.diagonal(
MM.mm(MM.dagger(evec[j]), SCDM.h0_k[j], evec[j]))
print(' ... spin %i: Allclose=' % j,
N.allclose(ev[j], ev2, atol=1e-5, rtol=1e-3))
ncf.sync()
# Write to NetCDF
evals[i, :] = ev[:, :nbands]
evecsRe[i, :] = evec[:, :, :nbands].real
evecsIm[i, :] = evec[:, :, :nbands].imag
ncf.sync()
# Include basis orbitals in netcdf file
if SCDM.Sym.basis.NN == len(SCDM.OrbIndx):
lasto = N.zeros(SCDM.Sym.basis.NN + 1, N.float)
lasto[:SCDM.Sym.basis.NN] = SCDM.OrbIndx[:SCDM.Sym.basis.NN, 0]
lasto[SCDM.Sym.basis.NN] = SCDM.OrbIndx[SCDM.Sym.basis.NN - 1,
1] + 1
else:
lasto = SCDM.OrbIndx[:SCDM.Sym.basis.NN + 1, 0]
orbbasis = SIO.BuildBasis(fdf[0], 1, SCDM.Sym.basis.NN, lasto)
# Note that the above basis is for the geometry with an atom FC-moved in z.
#print dir(orbbasis)
#print orbbasis.xyz # Hence, this is not the correct geometry of the basis atoms!
center = ncf.createVariable('orbcenter', 'i', ('orbs', ))
center[:] = N.array(orbbasis.ii - 1, dtype='int32')
center.description = 'Atom index (counting from 0) of the orbital center'
nn = ncf.createVariable('N', 'i', ('orbs', ))
nn[:] = N.array(orbbasis.N, dtype='int32')
ll = ncf.createVariable('L', 'i', ('orbs', ))
ll[:] = N.array(orbbasis.L, dtype='int32')
mm = ncf.createVariable('M', 'i', ('orbs', ))
mm[:] = N.array(orbbasis.M, dtype='int32')
# Cutoff radius and delta
Rc = ncf.createVariable('Rc', 'd', ('orbs', ))
Rc[:] = orbbasis.coff
Rc.units = 'Angstrom'
delta = ncf.createVariable('delta', 'd', ('orbs', ))
delta[:] = orbbasis.delta
delta.units = 'Angstrom'
# Radial components of the orbitals
ntb = len(orbbasis.orb[0])
ncf.createDimension('ntb', ntb)
rii = ncf.createVariable('rii', 'd', ('orbs', 'ntb'))
rii[:] = N.outer(orbbasis.delta, N.arange(ntb))
rii.units = 'Angstrom'
radialfct = ncf.createVariable('radialfct', 'd', ('orbs', 'ntb'))
radialfct[:] = orbbasis.orb
# Sort eigenvalues to connect crossing bands?
if options.sorting:
for i in range(SCDM.nspin):
evals[:, i, :] = SortBands(evals[:, i, :])
# Produce nice plots if labels exist
if klabels:
if SCDM.nspin == 1:
PlotElectronBands(options.DestDir + '/Electrons.agr', dk,
evals[:, 0, :], kticks)
elif SCDM.nspin == 2:
PlotElectronBands(options.DestDir + '/Electrons.UP.agr', dk,
evals[:, 0, :], kticks)
PlotElectronBands(options.DestDir + '/Electrons.DOWN.agr', dk,
evals[:, 1, :], kticks)
ncf.close()
if TSrun: # only electronic calculation
# Ugly hack to get my old code to work again. -Magnus
if options.FermiSurface == True:
from . import BandStruct as BS
options.fdfFile = 'RUN.fdf'
options.eMin, options.eMax = -10, 10
options.NNk = 101
BS.general = options
BS.main()
return SCDM.Sym.path
# Compute phonon eigenvalues
if options.qfile:
SCDM.SymmetrizeFC(options.radius)
SCDM.SetMasses()
qpts, dq, qlabels, qticks = ReadKpoints(options.qfile)
if qlabels:
# Only write ascii if labels exist
WriteKpoints(options.DestDir + '/qpoints', qpts, qlabels)
# Prepare netcdf
ncfn = options.DestDir + '/Phonons.nc'
ncf = NC4.Dataset(ncfn, 'w')
# Grid
ncf.createDimension('gridpts', len(qpts))
ncf.createDimension('vector', 3)
grid = ncf.createVariable('grid', 'd', ('gridpts', 'vector'))
grid[:] = qpts
grid.units = '1/Angstrom'
# Geometry
ncf.createDimension('atoms', SCDM.Sym.basis.NN)
xyz = ncf.createVariable('xyz', 'd', ('atoms', 'vector'))
xyz[:] = SCDM.Sym.basis.xyz
xyz.units = 'Angstrom'
pbc = ncf.createVariable('pbc', 'd', ('vector', 'vector'))
pbc.units = 'Angstrom'
pbc[:] = [SCDM.Sym.a1, SCDM.Sym.a2, SCDM.Sym.a3]
rvec1 = ncf.createVariable('rvec', 'd', ('vector', 'vector'))
rvec1.units = '1/Angstrom (incl. factor 2pi)'
rvec1[:] = rvec
ncf.sync()
# Loop over q
for i, q in enumerate(qpts):
if i < 100: # Print only for the first 100 points
hw, U = SCDM.ComputePhononModes_q(q, verbose=True)
else:
hw, U = SCDM.ComputePhononModes_q(q, verbose=False)
# otherwise something simple
if i % 100 == 0:
print('%i out of %i q-points computed' % (i, len(qpts)))
if i == 0:
ncf.createDimension('bands', len(hw))
ncf.createDimension('displ', len(hw))
evals = ncf.createVariable('eigenvalues', 'd',
('gridpts', 'bands'))
evals.units = 'eV'
evecsRe = ncf.createVariable('eigenvectors.re', 'd',
('gridpts', 'bands', 'displ'))
evecsIm = ncf.createVariable('eigenvectors.im', 'd',
('gridpts', 'bands', 'displ'))
# Check eigenvectors
print('SupercellPhonons.Checking eigenvectors at', q)
tmp = MM.mm(N.conjugate(U), SCDM.FCtilde, N.transpose(U))
const = PC.hbar2SI * (1e20 / (PC.eV2Joule * PC.amu2kg))**0.5
hw2 = const * N.diagonal(tmp)**0.5 # Units in eV
print(' ... Allclose=',
N.allclose(hw, N.absolute(hw2), atol=1e-5, rtol=1e-3))
ncf.sync()
# Write only AXSF files for the first q-point
PH.WriteAXSFFiles(options.DestDir + '/q%i_re.axsf' % i,
SCDM.Sym.basis.xyz, SCDM.Sym.basis.anr, hw,
U.real, 1, SCDM.Sym.basis.NN)
PH.WriteAXSFFiles(options.DestDir + '/q%i_im.axsf' % i,
SCDM.Sym.basis.xyz, SCDM.Sym.basis.anr, hw,
U.imag, 1, SCDM.Sym.basis.NN)
PH.WriteFreqFile(options.DestDir + '/q%i.freq' % i, hw)
evals[i] = hw
evecsRe[i] = U.real
evecsIm[i] = U.imag
ncf.sync()
# Sort eigenvalues to connect crossing bands?
if options.sorting:
evals = SortBands(evals)
# Produce nice plots if labels exist
if qlabels:
PlotPhononBands(options.DestDir + '/Phonons.agr', dq,
N.array(evals[:]), qticks)
ncf.close()
# Compute e-ph couplings
if options.kfile and options.qfile:
SCDM.ReadGradients()
ncf = NC4.Dataset(options.DestDir + '/EPH.nc', 'w')
ncf.createDimension('kpts', len(kpts))
ncf.createDimension('qpts', len(qpts))
ncf.createDimension('modes', len(hw))
ncf.createDimension('nspin', SCDM.nspin)
ncf.createDimension('bands', SCDM.rednao)
ncf.createDimension('vector', 3)
kgrid = ncf.createVariable('kpts', 'd', ('kpts', 'vector'))
kgrid[:] = kpts
qgrid = ncf.createVariable('qpts', 'd', ('qpts', 'vector'))
qgrid[:] = qpts
evalfkq = ncf.createVariable('evalfkq', 'd',
('kpts', 'qpts', 'nspin', 'bands'))
# First (second) band index n (n') is the initial (final) state, i.e.,
# Mkq(k,q,mode,spin,n,n') := < n',k+q | dV_q(mode) | n,k >
MkqAbs = ncf.createVariable(
'Mkqabs', 'd',
('kpts', 'qpts', 'modes', 'nspin', 'bands', 'bands'))
GkqAbs = ncf.createVariable(
'Gkqabs', 'd',
('kpts', 'qpts', 'modes', 'nspin', 'bands', 'bands'))
ncf.sync()
# Loop over k-points
for i, k in enumerate(kpts):
kpts[i] = k
# Compute initial electronic states
evi, eveci = SCDM.ComputeElectronStates(k, verbose=True)
# Loop over q-points
for j, q in enumerate(qpts):
# Compute phonon modes
hw, U = SCDM.ComputePhononModes_q(q, verbose=True)
# Compute final electronic states
evf, evecf = SCDM.ComputeElectronStates(k + q, verbose=True)
evalfkq[i, j, :] = evf
# Compute electron-phonon couplings
m, g = SCDM.ComputeEPHcouplings_kq(
k, q) # (modes,nspin,bands,bands)
# Data to file
# M (modes,spin,i,l) = m(modes,k,j) init(i,j) final(k,l)
# 0 1 2 0,1 0 1
# ^-------^
# ^----------------------^
for ispin in range(SCDM.nspin):
evecfd = MM.dagger(evecf[ispin]) # (bands,bands)
M = N.tensordot(N.tensordot(m[:, ispin],
eveci[ispin],
axes=[2, 0]),
evecfd,
axes=[1, 1])
G = N.tensordot(N.tensordot(g[:, ispin],
eveci[ispin],
axes=[2, 0]),
evecfd,
axes=[1, 1])
MkqAbs[i, j, :, ispin] = N.absolute(M)
GkqAbs[i, j, :, ispin] = N.absolute(G)
ncf.sync()
ncf.close()
return SCDM.Sym.path
def calcTSWF(options, ikpoint):
kpoint = options.kpoints.k[ikpoint]
def calcandwrite(A, txt, kpoint, ikpoint):
if isinstance(A, MM.SpectralMatrix):
A=A.full()
A=A*PC.Rydberg2eV # Change to 1/Ryd
ev, U = LA.eigh(A)
Utilde = N.empty(U.shape, U.dtype)
for jj, val in enumerate(ev): # Problems with negative numbers
if val<0: val=0
Utilde[:, jj]=N.sqrt(val/(2*N.pi))*U[:, jj]
indx2 = N.where(abs(abs(ev)>1e-4))[0] # Pick non-zero states
ev=ev[indx2]
Utilde=Utilde[:, indx2]
indx=ev.real.argsort()[::-1]
fn=options.DestDir+'/%i/'%(ikpoint)+options.systemlabel+'.%s'%(txt)
path = './'+options.DestDir+'/'
#FermiEnergy = SIO.HS(options.systemlabel+'.TSHS').ef
def noWfs(side):
tmp = len(glob.glob(path+str(ikpoint)+'/'+options.systemlabel+'.A'+side+'*'))
return tmp
if noWfs('L')==0 or noWfs('R')==0 and len(glob.glob(path+str(ikpoint)+'/FD*'))==0:
print('Calculating localized-basis states from spectral function %s ...'%(txt))
tlb = time.clock()
calcWF2(options, geom, options.DeviceAtoms, basis, Utilde[:, indx], [N1, N2, N3, minN3, maxN3], Fold=True, k=kpoint, fn=fn)
times = N.round(time.clock()-tlb, 2); timem = N.round(times/60, 2)
print('Finished in '+str(times)+' s = '+str(timem)+' min')
if noWfs('L')>0 and noWfs('R')>0 and len(glob.glob(path+str(ikpoint)+'/FD*'))==0 and str('%s'%(txt))==str('AR'):
print('\nLocalized-basis states are calculated in k point '+str(ikpoint)+'/.')
print('------------------------------------------------------')
print('Finite-difference calculation of vacuum states starts!')
timeFD = time.clock()
STMFD.main(options, kpoint, ikpoint)
print('FD calculation in k-point folder '+str(ikpoint)+'/ done in '+str(N.round((time.clock()-timeFD)/60, 2))+' min.')
print('------------------------------------------------------')
if options.savelocwfs == False:
os.system('rm -f '+path+str(ikpoint)+'/'+options.systemlabel+'*')
#Read geometry
XV = '%s/%s.XV'%(options.head, options.systemlabel)
geom = MG.Geom(XV, BufferAtoms=options.buffer)
#Set up device Greens function
elecL = NEGF.ElectrodeSelfEnergy(options.fnL, options.NA1L, options.NA2L, options.voltage/2.)
elecL.scaling = options.scaleSigL
elecL.semiinf = options.semiinfL
elecR = NEGF.ElectrodeSelfEnergy(options.fnR, options.NA1R, options.NA2R, -options.voltage/2.)
elecR.scaling = options.scaleSigR
elecR.semiinf = options.semiinfR
DevGF = NEGF.GF(options.TSHS, elecL, elecR, Bulk=options.UseBulk,
DeviceAtoms=options.DeviceAtoms,
BufferAtoms=options.buffer)
DevGF.calcGF(options.energy+options.eta*1.0j, kpoint[0:2], ispin=options.iSpin,
etaLead=options.etaLead, useSigNCfiles=options.signc, SpectralCutoff=options.SpectralCutoff)
NEGF.SavedSig.close() #Make sure saved Sigma is written to file
#Transmission
print('Transmission Ttot(%.4feV) = %.16f'%(options.energy, N.trace(DevGF.TT).real))
#Build basis
options.nspin = DevGF.HS.nspin
L = options.bufferL
#Pad lasto with zeroes to enable basis generation...
lasto = N.zeros((DevGF.HS.nua+L+1,), N.int)
lasto[L:] = DevGF.HS.lasto
basis = SIO.BuildBasis(options.fn,
options.DeviceAtoms[0]+L,
options.DeviceAtoms[1]+L, lasto)
basis.ii -= L
file = NC.Dataset('TotalPotential.grid.nc', 'r')
N1, N2, N3 = len(file.dimensions['n1']), len(file.dimensions['n2']), len(file.dimensions['n3'])
cell = file.variables['cell'][:]
file.close()
#Find device region in a3 axis
U = LA.inv(N.array([cell[0]/N1, cell[1]/N2, cell[2]/N3]).transpose())
gridindx = N.dot(geom.xyz[options.DeviceAtoms[0]-1:options.DeviceAtoms[1]]/PC.Bohr2Ang, U)
minN3, maxN3 = N.floor(N.min(gridindx[:, 2])).astype(N.int), N.ceil(N.max(gridindx[:, 2])).astype(N.int)
if not N.allclose(geom.pbc, cell*PC.Bohr2Ang):
print('Error: TotalPotential.grid.nc has different cell compared to geometry')
sys.exit(1)
print('\nk-point folder '+str(ikpoint)+'/')
print('Checking/calculating localized-basis states ...')
calcandwrite(DevGF.AL, 'AL', kpoint, ikpoint)
calcandwrite(DevGF.AR, 'AR', kpoint, ikpoint)