def SetupCGrun(templateCGrun,
newCGrun,
NewContactSeparation,
AtomsPerLayer,
IndexShift=0,
ListL=None,
ListR=None,
ZmatRanges=None,
RotationAngle=None,
RotationCenter=None,
RotationAxis=None,
RotationSubset=None,
overwrite=False,
PBStemplate=None,
PBSsubs=None,
submitJob=False):
"""
templateCGrun : Path+foldername to a template CGrun folder which contain
the necessary SIESTA files and a structure which is to
be modified for a new electrode separation
(this function writes a new STRUCT.fdf file)
newCGrun : Path+foldername for the CGrun to be created
NewContactSeparation : The new electrode separation in Ang (defined as the z-distance
over the device between two electrode layers which has not
been relaxed)
AtomsPerLayer : Number of atoms in one electrode layer in a cross-section wrt.
the transport direction
IndexShift : Number of atoms which is periodically translated from left to
right during the formation of the new STRUCT.fdf from the
template *.XV file
ListL/ListR : These atom indices (SIESTA numbering) are forced to be a part of
the electrodes and hence not affected by stretching
RotationAngle/ : Rotate whole CG geometry (or only RotationSubset if specified)
RotationCenter/ an angle RotationAngle (in degrees) around RotationAxis vector through
RotationAxis/ atom index RotationCenter (SIESTA numbering). These manipulations
RotationSubset are implemented BEFORE electrode separation is adjusted.
overwrite : (True/False) Specifies if one is allowed to write in existing
directories
PBStemplate : Path+foldername to a template RUN.pbs file for PBS queueing
PBSsubs : A list of string substitutions to be applied to the template
PBS script in order to generate a new PBS script
(e.g., PBSsubs=[['JOBNAME','newjobname'],...]' will replace
any JOBNAME string with newjobname)
submitJob : (True/False) Submit to batch queue via qsub command?
"""
# Make new directories
head = os.path.split(newCGrun)[0]
if not os.path.isdir(head):
print '\nSetupRuns.SetupCGrun: Creating folder %s' % head
os.mkdir(head)
if not os.path.isdir(newCGrun):
print '\nSetupRuns.SetupCGrun: Creating folder %s' % newCGrun
os.mkdir(newCGrun)
elif not overwrite:
print '\nSetupRuns.SetupCGrun: %s already exists. No further actions taken.'\
%newCGrun
return '' # Quit script
else:
print '\nSetupRuns.SetupCGrun: %s already exists. OVERWRITING FILES!!!'\
%newCGrun
# Copy template files
CopyInputFiles(templateCGrun, newCGrun, ['.fdf', '.vps', '.psf', 'pbs'])
# Read relaxed geometry
XVfiles = glob.glob(templateCGrun + '/*.XV*')
if len(XVfiles) == 1:
geom = MG.Geom(XVfiles[0])
elif len(XVfiles) > 1:
print 'More than one XV file was found in folder %s:' % templateCGrun
for i, xvfile in enumerate(XVfiles):
print ' No. %i :' % i, xvfile
select = raw_input(' ... select file:')
geom = MG.Geom(XVfiles[int(select)])
else:
print 'No XV file was found in folder %s:' % templateCGrun
raw_input(' ... Continue reading geometry from RUN.fdf?')
geom = MG.Geom(templateCGrun + '/RUN.fdf')
# Rotate via indexshift?
if IndexShift > 0:
print 'SetupRuns.SetupCGrun: Applying IndexShift =', IndexShift
for ii in range(IndexShift):
geom.xyz[0][2] += geom.pbc[2][2]
geom.addAtom(geom.xyz[0], geom.snr[0], geom.anr[0])
geom.rmAtom(0)
# Rotation?
if RotationAngle and RotationCenter and RotationAxis:
print 'SetupRuns.SetupCGrun: Rotation applied:'
print ' ... Rotation angle =', RotationAngle, ' deg'
print ' ... Rotation center = atom %i (SIESTA numbering)' % RotationCenter
print ' ... Rotation axis =', RotationAxis
if RotationSubset:
print ' ... RotationSubset =', RotationSubset, ' (SIESTA numbering)'
# Change from SIESTA numbering to Python indices
RotationSubset = [x - 1 for x in RotationSubset]
center = N.array(geom.xyz[RotationCenter - 1])
geom.rotate(RotationAxis,
RotationAngle,
center,
RotateSubset=RotationSubset)
# Adjust electrode separation
if NewContactSeparation:
geom.stretch2NewContactSeparation(NewContactSeparation,
AtomsPerLayer,
ListL=ListL,
ListR=ListR)
if not ZmatRanges:
geom.writeFDF(newCGrun + '/STRUCT.fdf')
else:
geom.writeFDFZmat(newCGrun + '/STRUCT.fdf', ZmatRanges)
geom.writeXYZ(newCGrun + '/STRUCT.xyz')
geom.writeXYZ(newCGrun + '/STRUCT2.xyz', rep=[2, 2, 2])
# PBS files
MakePBS(PBStemplate, newCGrun + '/RUN.pbs', PBSsubs, submitJob, rtype='TS')
def SetupTSrun(CGrun,
templateTSrun,
newTSrun,
AtomsPerLayer,
BlockSize,
LayersLeft,
LayersRight,
DeviceLayerInclLeft=0,
DeviceLayerInclRight=0,
IndexShift=0,
AddLeftList=[],
AddRightList=[],
ListL=None,
ListR=None,
NewContactSeparation=None,
RotationAngle=None,
RotationCenter=None,
RotationAxis=None,
RotationSubset=None,
overwrite=False,
PBStemplate=None,
PBSsubs=None,
submitJob=False):
"""
CGrun : Path+foldername to a relaxed structure CGrun folder on
which to run a TranSIESTA calculation. This folder must
contain an *.XV file
templateTSrun : Path+foldername to an existing TSrun folder which contains
all relevant electrode calculations and *.fdf files
except for STRUCT.fdf
newTSrun : Path+foldername for the TSrun folder to be created
AtomsPerLayer : Number of atoms in the electrodes in a cross section along
the transport direction
BlockSize : Number of atoms in the electrode block from CGrun/*.XV file
LayersLeft/Right : Number of blocks to be pasted to the new enlarged STRUCT.fdf.
DeviceLayerInclLeft : As default TBTRANS takes all relaxed atoms to be the device
If DeviceLayerInclLeft is larger than 0 then TBTRANS
includes the specified number of electode atomic planes into
the device region.
DeviceLayerInclRight : See DeviceLayerInclLeft
IndexShift : Number of atoms which is periodically translated from left to
right contact BEFORE eventual electrode layers are pasted.
AddLeftList : Add list of atoms to the left side
AddRightList : Add list of atoms to the right side
ListL/ListR : These atom indices (SIESTA numbering) are forced to be a part of
the electrodes and hence not affected by stretching
NewContactSeparation : (Optional) value to set a different electrode separation
than in the CG geometry
RotationAngle/ : Rotate whole CG geometry (or only RotationSubset if specified)
RotationCenter/ an angle RotationAngle (in degrees) around RotationAxis vector through
RotationAxis/ atom index RotationCenter (SIESTA numbering). These manipulations
RotationSubset are implemented BEFORE electrode separation is adjusted.
overwrite : (True/False) Specifies if one is allowed to write in existing
directories
PBStemplate : Path+foldername to a template RUN.pbs file for PBS queueing
PBSsubs : A list of string substitutions to be applied to the template
PBS script in order to generate a new PBS script
(e.g., PBSsubs=[['JOBNAME','newjobname'],...]' will replace
any JOBNAME string with newjobname)
submitJob : (True/False) Submit to batch queue via qsub command?
"""
# Make new directory
if not os.path.isdir(newTSrun):
print '\nSetupRuns.SetupTSrun: Creating folder %s' % newTSrun
os.mkdir(newTSrun)
elif not overwrite:
print '\nSetupRuns.SetupTSrun: %s already exists. No further actions taken.'\
%newTSrun
return '' # Quit script
else:
print '\nSetupRuns.SetupTSrun: %s already exists. OVERWRITING FILES!!!'\
%newTSrun
# Copy all sub-directories
for elm in glob.glob(templateTSrun + '/*'):
tail = os.path.split(elm)[1]
if os.path.isdir(elm):
CopyTree(elm, newTSrun + '/' + tail, overwrite=overwrite)
# Copy template files
CopyInputFiles(templateTSrun, newTSrun, ['.fdf', '.vps', '.psf', '.pbs'])
# Read relaxed geometry
XVfiles = glob.glob(CGrun + '/*.XV*')
if len(XVfiles) == 1:
geom = MG.Geom(XVfiles[0])
elif len(XVfiles) > 1:
print 'More than one XV file was found in folder %s:' % CGrun
for i, xvfile in enumerate(XVfiles):
print ' No. %i :' % i, xvfile
select = raw_input(' ... select file:')
geom = MG.Geom(XVfiles[int(select)])
else:
print 'No XV file was found in folder %s:' % CGrun
raw_input(' ... Continue reading geometry from RUN.fdf?')
geom = MG.Geom(CGrun + '/RUN.fdf')
# Rotate via indexshift?
if IndexShift > 0:
print 'SetupRuns.SetupTSrun: Applying IndexShift =', IndexShift
for ii in range(IndexShift):
geom.xyz[0][2] += geom.pbc[2][2]
geom.addAtom(geom.xyz[0], geom.snr[0], geom.anr[0])
geom.rmAtom(0)
# Overwrite STRUCT files
if RotationAngle and RotationCenter and RotationAxis:
print 'SetupRuns.SetupTSrun: Rotation applied:'
print ' ... Rotation angle =', RotationAngle, ' deg'
print ' ... Rotation center = atom %i (SIESTA numbering)' % RotationCenter
print ' ... Rotation axis =', RotationAxis
if RotationSubset:
print ' ... RotationSubset =', RotationSubset, ' (SIESTA numbering)'
# Change from SIESTA numbering to Python indices
RotationSubset = [x - 1 for x in RotationSubset]
center = N.array(geom.xyz[RotationCenter - 1])
geom.rotate(RotationAxis,
RotationAngle,
center,
RotateSubset=RotationSubset)
# Paste electrode layers via BlockSize specifications
geom.PasteElectrodeLayers(BlockSize, AtomsPerLayer, LayersLeft,
LayersRight)
# Change contact separation?
if NewContactSeparation:
geom.stretch2NewContactSeparation(NewContactSeparation,
AtomsPerLayer,
ListL=ListL,
ListR=ListR)
# Add electrode atoms to the left
if len(AddLeftList) > 0:
dz = AddLeftList[AtomsPerLayer, 2] - AddLeftList[0, 2]
tmp = N.array(geom.xyz)
minz = min(tmp[:, 2])
maxz = max(AddLeftList[:, 2])
for ii in reversed(range(len(AddLeftList))):
tmp = list(AddLeftList[ii, :] +
(-maxz + minz - dz) * N.array([0.0, 0.0, 1.0], N.float))
geom.prependAtom(tmp, geom.snr[0], geom.anr[0])
geom.pbc[2][2] += len(AddLeftList) / AtomsPerLayer * dz
# Add electrode atoms to the right
if len(AddRightList) > 0:
dz = AddRightList[AtomsPerLayer, 2] - AddRightList[0, 2]
tmp = N.array(geom.xyz)
maxz = tmp[0, 2] - dz + geom.pbc[2][2]
minz = min(AddRightList[:, 2])
for ii in range(len(AddRightList)):
geom.addAtom(
list(AddRightList[ii, :] +
(maxz - minz + dz) * N.array([0, 0, 1], N.float)),
geom.snr[0], geom.anr[0])
geom.pbc[2][2] += len(AddRightList) / AtomsPerLayer * dz
# Write structure to files
geom.writeFDF(newTSrun + '/STRUCT.fdf')
geom.writeXYZ(newTSrun + '/STRUCT.xyz')
geom.writeXYZ(newTSrun + '/STRUCT2.xyz', rep=[2, 2, 2])
# Find device atoms
geom.findContactsAndDevice(AtomsPerLayer)
PDOSfirst = min(geom.deviceList) - DeviceLayerInclLeft * AtomsPerLayer
PDOSlast = max(geom.deviceList) + DeviceLayerInclRight * AtomsPerLayer
# Prepend lines to TBTRANS.fdf
for elm in glob.glob(newTSrun + '/TBTRANS.fdf'):
if os.path.isfile(elm):
print 'SetupRuns.SetupTSrun: Prepending PDOS = [%i,%i] to %s' \
%(PDOSfirst, PDOSlast, elm)
f = open(elm, 'r')
lines = f.readlines()
f.close()
f = open(elm, 'w')
f.write('### Lines appended %s \n' % time.ctime())
f.write('TS.TBT.PDOSFrom %i\n' % PDOSfirst)
f.write('TS.TBT.PDOSTo %i\n\n' % PDOSlast)
for line in lines:
f.write(line)
f.close()
# PBS files
MakePBS(PBStemplate, newTSrun + '/RUN.pbs', PBSsubs, submitJob, rtype='TS')
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)
def SetupFCrun(CGrun,
newFCrun,
FCfirst,
FClast,
displacement=0.02,
overwrite=False,
PBStemplate=None,
PBSsubs=None,
submitJob=False):
"""
CGrun : Path+foldername to a relaxed structure CGrun folder on
which to perform a FCrun calculation. This folder must
contain an *.XV file
newFCrun : Path+foldername for the FCrun to be created
FCfirst : Number of the first atom to displace (SIESTA numbering)
FClast : Number of the last atom to displace (SIESTA numbering)
displacement : Displacement
overwrite : (True/False) Specifies if one is allowed to write in existing
directories
PBStemplate : Path+foldername to a template RUN.pbs file for PBS queueing
PBSsubs : A list of string substitutions to be applied to the template
PBS script in order to generate a new PBS script
(e.g., PBSsubs=[['JOBNAME','newjobname'],...]' will replace
any JOBNAME string with newjobname)
submitJob : (True/False) Submit to batch queue via qsub command?
"""
# Make new directory
if not os.path.isdir(newFCrun):
print '\nSetupRuns.SetupFCrun: Creating folder %s' % newFCrun
os.mkdir(newFCrun)
elif not overwrite:
print '\nSetupRuns.SetupFCrun: %s already exists. No further actions taken.'\
%newFCrun
return '' # Quit script
else:
print '\nSetupRuns.SetupFCrun: %s already exists. OVERWRITING FILES!!!'\
%newFCrun
# Copy template files
CopyInputFiles(CGrun, newFCrun,
['.fdf', '.vps', '.psf', '.DM', '.XV', '.pbs', '.TSDE'])
# Read relaxed geometry and overwrite STRUCT files
XVfiles = glob.glob(CGrun + '/*.XV*')
if len(XVfiles) == 1:
geom = MG.Geom(XVfiles[0])
elif len(XVfiles) > 1:
print 'More than one XV file was found in folder %s:' % CGrun
for i, xvfile in enumerate(XVfiles):
print ' No. %i :' % i, xvfile
select = raw_input(' ... select file:')
geom = MG.Geom(XVfiles[int(select)])
else:
print 'No XV file was found in folder %s:' % CGrun
raw_input(' ... Continue reading geometry from RUN.fdf?')
geom = MG.Geom(CGrun + '/RUN.fdf')
geom.writeFDF(newFCrun + '/STRUCT.fdf')
geom.writeXYZ(newFCrun + '/STRUCT.xyz')
geom.writeXYZ(newFCrun + '/STRUCT2.xyz', rep=[2, 2, 2])
# Prepend lines to RUN.fdf
for elm in glob.glob(newFCrun + '/RUN.fdf'):
if os.path.isfile(elm):
print 'SetupRuns.SetupFCrun: Modifying %s' % elm
f = open(elm, 'r')
lines = f.readlines()
f.close()
f = open(elm, 'w')
f.write('### Lines appended %s \n' % time.ctime())
f.write('MD.TypeOfRun FC\n')
f.write('MD.FCfirst %i\n' % FCfirst)
f.write('MD.FClast %i\n' % FClast)
f.write('TS.HS.Save True\n')
f.write('TS.SaveHS True\n')
f.write('MD.FCDispl %.8f Ang\n' % displacement)
for line in lines:
f.write(line)
f.close()
# PBS files
MakePBS(PBStemplate, newFCrun + '/RUN.pbs', PBSsubs, submitJob, rtype='TS')
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)