def main(options):
"""
Main routine to compute vibrational modes and frequencies (and optionally
also the corresponding electron-vibration couplings)
Parameters
----------
options : an ``options`` instance
"""
Log.CreatePipeOutput(options)
Log.PrintMainHeader(options)
# Determine SIESTA input fdf files in FCruns
fdf = glob.glob(options.FCwildcard + '/' + options.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)
Log.PrintMainFooter(options)
return DM.h0, DM.s0, DM.hw, DM.heph
else:
DM.WriteOutput(options.DestDir + '/Output', options.SinglePrec,
options.GammaPoint)
Log.PrintMainFooter(options)
return DM.hw
def main(options):
"""
Main routine to compute inelastic transport characteristics (dI/dV, d2I/dV2, IETS etc)
Parameters
----------
options : an ``options`` instance
"""
Log.CreatePipeOutput(options)
VC.OptionsCheck(options)
Log.PrintMainHeader(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()
Log.PrintMainFooter(options)
return data
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
"""
Log.CreatePipeOutput(options)
VC.OptionsCheck(options)
Log.PrintMainHeader(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', 'w')
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', 'w')
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', 'w')
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', 'w')
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', 'w')
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)
Log.PrintMainFooter(options)
def main(options):
dd = len(glob.glob(options.DestDir))
if len(glob.glob('TotalPotential.grid.nc')) == 0 and len(glob.glob('Rho.grid.nc')) == 0:
sys.exit('TotalPotential.nc and Rho.grid.nc not found! Add "SaveTotalPotential true" and "SaveRho true" to RUN.fdf')
if len(glob.glob('TotalPotential.grid.nc')) == 0:
sys.exit('TotalPotential.nc not found! Add "SaveTotalPotential true" to RUN.fdf')
if len(glob.glob('Rho.grid.nc')) == 0:
sys.exit('Rho.grid.nc not found! Add "SaveRho true" to RUN.fdf')
Log.CreatePipeOutput(options)
VC.OptionsCheck(options)
Log.PrintMainHeader(options)
## Step 1: Calculate scattering states from L/R on TranSiesta real space grid.
if glob.glob(options.DestDir+'/kpoints') != []: # Check previous k-points
f, oldk = open(options.DestDir+'/kpoints', 'r'), []
f.readline()
for ii in f.readlines():
oldk += [N.array(ii.split(), N.float)]
oldk = N.array(oldk)
options.kpoints.mesh2file(options.DestDir+'/kpoints')
doK = []
for ikpoint in range(len(options.kpoints.k)):
ikdir = options.DestDir+'/%i'%(ikpoint)
if not os.path.isdir(ikdir):
os.mkdir(ikdir)
doK += [ikpoint]
#Check if some k points are already done
doK = []
nokpts = len(options.kpoints.k)
noFDcalcs = len(glob.glob('./'+options.DestDir+'/*/FDcurr*.nc'))
for ii in range(nokpts):
if len(glob.glob('./'+options.DestDir+'/'+str(ii)+'/FDcurr'+str(ii)+'.nc')) == 1:
pass
else:
doK += [ii]
if noFDcalcs > nokpts-1:
print('\nAll ('+str(nokpts)+') k points are already finished!\n')
elif noFDcalcs > 0 and noFDcalcs < nokpts:
print(str(nokpts-len(doK))+' ('+str(N.round(100.*((1.*nokpts-len(doK))/nokpts), 1))+'%) k points already done. Will proceed with the rest.')
print('You should perhaps remove the loc-basis states in the most recent k folder ')
print('since some of these may not have been calculated before interuption.\n')
else:
if dd == 1:
print('No STM calculations found in existing directory '+str(options.DestDir)+'/. Starting from scratch.')
print('(...by possibly using saved localized-basis states)\n')
else:
print('STM calculation starts.')
args = [(options, ik) for ik in doK]
tmp = MP.runParallel(calcTSWFPar, args, nCPU=options.nCPU)
print('Calculating k-point averaged STM image')
def ShiftOrigin(mat, x, y):
Nx = N.shape(mat)[0]
Ny = N.shape(mat)[1]
NewMat = N.zeros((Nx, Ny))
for ii in range(Nx):
for jj in range(Ny):
NewMat[N.mod(ii+x, Nx), N.mod(jj+y, Ny)] = mat[ii, jj]
return NewMat
file = NC.Dataset('TotalPotential.grid.nc', 'r')
steps = N.array(file.variables['cell'][:], N.float)
theta = N.arccos(N.dot(steps[0], steps[1])/(LA.norm(steps[0])*LA.norm(steps[1])))
currtmp = NC.Dataset('./'+options.DestDir+'/0/FDcurr0.nc', 'r')
dimSTMimage = N.shape(currtmp.variables['Curr'][:, :])
dim1 = dimSTMimage[0]
dim2 = dimSTMimage[1]
STMimage = N.zeros((dim1, dim2))
tmpSTM = N.zeros((dim1*nokpts, dim2))
for ii in range(nokpts):
file = NC.Dataset('./'+options.DestDir+'/'+str(ii)+'/FDcurr'+str(ii)+'.nc', 'r')
ikSTMimage = file.variables['Curr'][:, :]/(nokpts)
STMimage += ShiftOrigin(ikSTMimage, dim1 // 2, dim2 // 2)
tmpSTM[ii*dim1:(ii+1)*dim1, :] = ShiftOrigin(ikSTMimage, dim1 // 2, dim2 // 2)
STMimagekpt = N.zeros((dim1*options.Nk1, dim2*options.Nk2))
for ii in range(options.Nk1):
for jj in range(options.Nk2):
N1 = ii+1
N2 = options.Nk2-jj
kk = (ii+1)*options.Nk2-jj-1
STMimagekpt[(N1-1)*dim1:N1*dim1, (N2-1)*dim2:N2*dim2] = tmpSTM[kk*dim1:(kk+1)*dim1, ::-1]
tmp = open(options.systemlabel+'.XV').readlines()[4+options.DeviceFirst-1:4+options.DeviceLast]
xyz = N.zeros((len(tmp), 4))
for ii in range(len(tmp)):
for jj in range(1, 5):
tmp2 = tmp[ii].split()
xyz[ii, jj-1] = ast.literal_eval(tmp2[jj])
if jj > 1:
xyz[ii, jj-1] = xyz[ii, jj-1]*PC.Bohr2Ang
drAtoms = N.zeros(len(xyz))
for atomIdx in range(len(xyz)-1):
drAtoms[atomIdx] = N.round((xyz[atomIdx+1][3]-xyz[atomIdx][3]), 3)
TipHeight = N.max(drAtoms)
n = writeNC.NCfile('./'+options.DestDir+'/STMimage.nc')
n.write(STMimage, 'STMimage')
n.write(theta, 'theta')
n.write(options.kpoints.k, 'kpoints')
n.write(options.Nk1, 'Nk1')
n.write(options.Nk2, 'Nk2')
n.write(STMimagekpt, 'STMkpoint')
n.write(xyz, 'Geometry')
n.write(TipHeight, 'TipHeight')
n.close()
Log.PrintMainFooter(options)