def main(options):
CF.CreatePipeOutput(options.DestDir+'/'+options.Logfile)
CF.PrintMainHeader('Phonons',vinfo,options)
# Determine SIESTA input fdf files in FCruns
fdf = glob.glob(options.FCwildcard+'/RUN.fdf')
print 'Phonons.Analyze: This run uses'
FCfirst,FClast = min(options.DynamicAtoms),max(options.DynamicAtoms)
print ' ... FCfirst = %4i, FClast = %4i, Dynamic atoms = %4i'\
%(FCfirst,FClast,len(options.DynamicAtoms))
print ' ... DeviceFirst = %4i, DeviceLast = %4i, Device atoms = %4i'\
%(options.DeviceFirst,options.DeviceLast,options.DeviceLast-options.DeviceFirst+1)
print ' ... PBC First = %4i, PBC Last = %4i, Device atoms = %4i'\
%(options.PBCFirst,options.PBCLast,options.PBCLast-options.PBCFirst+1)
print '\nSetting array type to %s\n'%options.atype
# Build Dynamical Matrix
DM = DynamicalMatrix(fdf,options.DynamicAtoms)
DM.SetMasses(options.Isotopes)
# Compute modes
DM.ComputePhononModes(DM.mean)
# Compute e-ph coupling
if options.CalcCoupl:
DM.PrepareGradients(options.onlySdir,options.kpoint,options.DeviceFirst,options.DeviceLast,options.AbsEref,options.atype)
DM.ComputeEPHcouplings(options.PBCFirst,options.PBCLast,options.EPHAtoms,options.Restart,options.CheckPointNetCDF,
WriteGradients=options.WriteGradients)
# Write data to files
DM.WriteOutput(options.DestDir+'/Output',options.SinglePrec,options.GammaPoint)
CF.PrintMainFooter('Phonons')
return DM.h0,DM.s0,DM.hw,DM.heph
else:
DM.WriteOutput(options.DestDir+'/Output',options.SinglePrec,options.GammaPoint)
CF.PrintMainFooter('Phonons')
return DM.hw
def main(options):
CF.CreatePipeOutput(options.DestDir + '/' + options.Logfile)
VC.OptionsCheck(options, 'EigenChannels')
CF.PrintMainHeader('EigenChannels', vinfo, 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, EigT = DevGF.ECleft, DevGF.EigTleft
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, EigT = DevGF.ECright, DevGF.EigTright
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
file = open(fn, 'w')
file.write('# Device region = [%i,%i], units in eV\n' %
(options.DeviceFirst, options.DeviceLast))
for i in range(len(ev)):
file.write('%i %.8f\n' % (i, ev[i]))
file.close()
# Compute selected eigenstates
for ii in range(len(ev)):
if N.abs(ev[ii]) < options.MolStates:
fn = options.DestDir + '/' + options.systemlabel + '.S%.3i.E%.3f' % (
ii, ev[ii])
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'
CF.PrintMainFooter('EigenChannels')
def main(options):
CF.CreatePipeOutput(options.DestDir+'/'+options.Logfile)
VC.OptionsCheck(options,'Inelastica')
CF.PrintMainHeader('Inelastica',vinfo,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
