def BuildOSstruct(infile,
outfile,
axes=[0, 1, 2],
direction=[-1, 1],
displacement=0.04 * PC.Bohr2Ang):
print('BuildOSstruct: displacement = %.6f Ang' % displacement)
geom = MG.Geom(infile)
for i in axes:
for displdir in direction:
new = MG.Geom(infile)
displ = [0., 0., 0.]
displ[i] = displdir * displacement
new.move(displ)
geom.addGeom(new)
geom.writeFDF(outfile)
def FindElectrodeSep(directory, AtomsPerLayer):
for xvfile in glob.glob(directory + '/*.XV*'):
print(xvfile)
g = MG.Geom(xvfile)
g.findContactsAndDevice(AtomsPerLayer)
DeviceFirst, DeviceLast = g.deviceList[0], g.deviceList[-1]
return g.ContactSeparation, DeviceFirst, DeviceLast
def __init__(self, runfdf):
self.fdf = runfdf
self.directory, self.tail = os.path.split(runfdf)
self.systemlabel = SIO.GetFDFlineWithDefault(runfdf, 'SystemLabel',
str, 'siesta', 'Phonons')
# Read geometry
self.geom = MG.Geom(runfdf)
# Compare with XV file corrected for last displacement
XV = self.directory + '/%s.XV' % self.systemlabel
geomXV = MG.Geom(XV)
natoms = self.geom.natoms
# Determine TSHS files
files = glob.glob(self.directory + '/%s*.TSHS' % self.systemlabel)
# Build dictionary over TSHS files and corresponding displacement amplitudes
self.TSHS = {}
try:
self.TSHS[0] = files[0] # Equilibrium TSHS
except:
sys.exit('Phonons.GetFileLists: No TSHS file found in %s' %
self.directory)
def checkDone(self):
if self.fixed==True:
self.FDFgeom = MG.Geom(self.dir+"/RUN.fdf")
self.XVgeom = readxv(self.dir)
self.forces = SIO.ReadForces(self.dir+"/RUN.out")
self.forces = self.forces[-len(self.XVgeom.xyz):]
self.Ftot = self.forces
self.converged = True
return True
else:
SIO.CheckTermination(self.dir+"/RUN.out")
self.FDFgeom = MG.Geom(self.dir+"/RUN.fdf")
done = False
try:
self.XVgeom = readxv(self.dir)
self.forces = SIO.ReadForces(self.dir+"/RUN.out")
print len(self.forces[0])
if N.allclose(self.XVgeom.xyz, self.FDFgeom.xyz, 1e-6):
done=True
except:
done=False
return done
def checkDone(self):
if self.fixed == True:
self.FDFgeom = MG.Geom(self.dirr + "/" + opts.fn)
self.XVgeom = readxv(self.dirr)
self.forces = SIO.ReadForces(self.dirr + "/RUN.out")
self.forces = self.forces[-len(self.XVgeom.xyz):]
self.F = N.array(self.forces) * 0
self.v = N.array(self.forces) * 0
self.converged = True
return True
else:
done = SIO.CheckTermination(self.dirr + "/RUN.out")
if done:
try:
self.FDFgeom = MG.Geom(self.dirr + "/" + opts.fn)
self.XVgeom = readxv(self.dirr)
self.forces = SIO.ReadForces(self.dirr + "/RUN.out")
if N.allclose(self.XVgeom.xyz, self.FDFgeom.xyz, 1e-6):
done = True
except:
done = False
return done
def readxv(dirpath):
global geom
# Read geometry from first .XV file found in dirpath
fns=glob.glob(dirpath+'/*.XV')
if len(fns)>1:
print "ERROR: NEB: More than one .XV file in dir:%s"%dirpath
sys.exit(1)
elif len(fns)<1:
return None
print('Reading geometry from "%s" file' % fns[0])
geom = MG.Geom(fns[0])
return geom
def cutlayers(infile, nalayer, nl, nr, outfile, ord=None):
"""
cut down some layers for md simulation
infile input STRUCT.fdf file
nalayer number of atoms per layer
nl nl layers from left
nr nr layers from left
ord atom lists in new order
"""
print "reading ", infile
geom = MG.Geom(infile)
xyz = geom.xyz
snr = geom.snr
anr = geom.anr
pbc = geom.pbc
if ord is not None:
anr, xyz = reordxyz(anr, xyz, ord)
zs = [a[2] for a in xyz]
olen = max(zs) - min(zs)
na = len(xyz)
nal = nl * nalayer
nar = nr * nalayer
if (nal + nar >= na):
print "Cuting too many atoms"
sys.exit(0)
nna = int(na - nal - nar)
nxyz = [xyz[nal + i] for i in range(nna)]
nsnr = [snr[nal + i] for i in range(nna)]
nanr = [anr[nal + i] for i in range(nna)]
nzs = [a[2] for a in nxyz]
nlen = max(nzs) - min(nzs)
pbc[2][2] = pbc[2][2] - (olen - nlen)
geom.xyz = nxyz
geom.pbc = pbc
geom.snr = nsnr
geom.anr = nanr
geom.natoms = nna
geom.writeFDF(outfile)
geom.writeXYZ(os.path.splitext(outfile)[0] + ".xyz")
return geom
def __init__(self, dirr, restart, iistep, initial=None, final=None):
self.dirr = dirr
self.converged, self.Fmax = False, 0.0
self.ii = iistep
self.fixed = (iistep == 0) or (iistep == opts.NNEB + 1)
if restart or self.fixed:
self.FDFgeom = MG.Geom(self.dirr + "/" + opts.fn)
self.XVgeom = readxv(self.dirr)
self.v = N.array(self.FDFgeom.xyz) * 0
if not restart and not self.fixed:
os.makedirs(dirr)
SUR.CopyInputFiles(opts.initial+"/CGrun/", dirr,\
['.fdf', '.vps', '.psf'])
# Interpolate
ixyz, fxyz = N.array(initial.XVgeom.xyz), N.array(final.XVgeom.xyz)
mix = float(iistep) / (opts.NNEB + 1.0)
xyz = (1 - mix) * ixyz + mix * fxyz
self.FDFgeom = copy.copy(initial.XVgeom)
self.FDFgeom.xyz = [xyz[ii, :] for ii in range(len(xyz))]
self.FDFgeom.writeFDF(self.dirr + "/STRUCT.fdf")
self.v = N.array(self.FDFgeom.xyz) * 0
# Append lines to RUN.fdf
elm = dirr + "/" + opts.fn
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 CG\n")
f.write("MD.NumCGsteps 0\n")
f.write("MD.UseSaveXV False\n")
f.write("MD.UseSaveCG False\n")
f.write('# end of lines appended %s \n' % time.ctime())
for line in lines:
f.write(line)
f.close()
self.done = self.checkDone()
const = SIO.GetFDFblock(dirr + "/" + opts.fn, "GeometryConstraints")
if opts.const2 != None:
self.const = [[opts.const2[0], opts.const2[0]]]
else:
self.const = []
for ii in const:
self.const += [[int(ii[2]) - 1, int(ii[4]) - 1]]
def readxv():
global geom
# Read geometry from first .XV file found in dir
fns = glob.glob('*.XV')
if len(fns) > 1:
print "ERROR: BandStruct: More than one .XV file ... which geometry to choose???"
sys.exit(1)
elif len(fns) < 1:
print "ERROR: BandStruct: Error ... No .XV file found!"
sys.exit(1)
print('Reading geometry from "%s" file' % fns[0])
geom = MG.Geom(fns[0])
geom.sym = SYM.Symmetry(fns[0], onlyLatticeSym=True)
if geom.sym.NNbasis != geom.natoms:
print "ERROR: Siesta cell does not contain one unit cell"
sys.exit(1)
def RunTBT(TSrun,
Emin,
Emax,
NPoints,
NumKxy_A1=1,
NumKxy_A2=1,
AtomsPerLayer=0,
DeviceLayerInclLeft=0,
DeviceLayerInclRight=0,
PBStemplate=None,
PBSsubs=None,
submitJob=False):
"""
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?
"""
# Remove old Green's functions
for elm in glob.glob(TSrun + '/*GF'):
print('SetupRuns.RunTBT: Removing *.GF')
if os.path.isfile(elm):
print(' Deleting %s' % elm)
os.remove(elm)
# Determine Device PDOS?
if AtomsPerLayer > 0:
for elm in glob.glob(TSrun + '/*XV'):
if os.path.isfile(elm):
geom = MG.Geom(elm)
geom.findContactsAndDevice(AtomsPerLayer)
PDOSfirst = min(
geom.deviceList) - DeviceLayerInclLeft * AtomsPerLayer
PDOSlast = max(
geom.deviceList) + DeviceLayerInclRight * AtomsPerLayer
else:
PDOSfirst, PDOSlast = 0, 0
# Prepend lines to TBTRANS.fdf
tbtfile = TSrun + '/TBTRANS.fdf'
f = open(tbtfile, 'r')
lines = f.readlines()
f.close()
f = open(tbtfile, 'w')
f.write('### Lines appended %s \n' % time.ctime())
if PDOSfirst > 0 and PDOSlast > 0:
print('SetupRuns.RunTBT: Prepending PDOS = [%i,%i] to %s' \
%(PDOSfirst, PDOSlast, tbtfile))
f.write('TS.TBT.PDOSFrom %i\n' % PDOSfirst)
f.write('TS.TBT.PDOSTo %i\n' % PDOSlast)
print('SetupRuns.RunTBT: Writing Emin=%f, Emax=%f, NPoints=%i to %s' \
%(Emin, Emax, NPoints, tbtfile))
f.write('TS.TBT.Emin %f eV\n' % Emin)
f.write('TS.TBT.Emax %f eV\n' % Emax)
f.write('TS.TBT.NPoints %i\n' % NPoints)
f.write('TS.NumKxy_A1 %i\n' % NumKxy_A1)
f.write('TS.NumKxy_A2 %i\n' % NumKxy_A2)
f.write('pyTBT.K_A1 %i\n' % NumKxy_A1)
f.write('pyTBT.K_A2 %i\n\n' % NumKxy_A2)
for line in lines:
f.write(line)
f.close()
# PBS files
MakePBS(PBStemplate,
newTSrun + '/RUN.pyTBT.pbs',
PBSsubs,
submitJob,
rtype='PY')
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', '.slurm', '.TSHS'])
# 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 = input(' ... select file:')
geom = MG.Geom(XVfiles[int(select)])
else:
print('No XV file was found in folder %s:' % templateCGrun)
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 SetupFCrun(CGrun,
newFCrun,
FCfirst,
FClast,
displacement=0.02,
overwrite=False,
PBStemplate=None,
PBSsubs=None,
submitJob=False,
main_fdf="RUN.fdf"):
"""
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', '.slurm', '.TSDE',
'.TSHS'
])
# 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 = input(' ... select file:')
geom = MG.Geom(XVfiles[int(select)])
else:
print('No XV file was found in folder %s:' % CGrun)
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])
if os.path.isfile(CGrun + "/STRUCT.fdf"):
copy_chemical_info(CGrun + "/STRUCT.fdf", newFCrun + "/STRUCT.fdf")
# Prepend lines to RUN.fdf
elm = newFCrun + '/' + main_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)
f.write('%include STRUCT.fdf\n')
f.writelines(lines)
f.close()
else:
print("{} was not found, so it cannot be edited."
"Rerun with main_fdf set correctly.".format(elm))
# PBS files
MakePBS(PBStemplate, newFCrun + '/RUN.pbs', PBSsubs, submitJob, rtype='TS')
def __init__(self, runfdf):
self.fdf = runfdf
self.directory, self.tail = os.path.split(runfdf)
self.systemlabel = SIO.GetFDFlineWithDefault(runfdf, 'SystemLabel',
str, 'siesta', 'Phonons')
FCfirst = SIO.GetFDFlineWithDefault(runfdf, 'MD.FCfirst', int, 0,
'Phonons')
FClast = SIO.GetFDFlineWithDefault(runfdf, 'MD.FClast', int, 0,
'Phonons')
# Finite-displacement amplitude
ampl, unit = SIO.GetFDFline(runfdf, KeyWord='MD.FCDispl')
if unit.upper() == 'ANG':
self.Displ = float(ampl)
elif unit.upper() == 'BOHR':
self.Displ = float(ampl) * PC.Bohr2Ang
print('Displacement = %.6f Ang' % self.Displ)
# Read geometry
self.geom = MG.Geom(runfdf)
# Compare with XV file corrected for last displacement
XV = self.directory + '/%s.XV' % self.systemlabel
geomXV = MG.Geom(XV)
geomXV.xyz[FClast - 1, 2] -= self.Displ
if not N.allclose(geomXV.xyz, self.geom.xyz):
sys.exit('Error: Geometries %s and %s should differ ONLY by displacement of atom %s in z'\
%(runfdf, XV, FClast))
# Set up FC[i,a,j,b]: Force constant (eV/A^2) from moved atom i, axis a to atom j, axis b
natoms = self.geom.natoms
self.m = N.zeros((FClast - FCfirst + 1, 3, natoms, 3), N.float)
self.p = N.zeros((FClast - FCfirst + 1, 3, natoms, 3), N.float)
fc = N.array(
SIO.ReadFCFile(self.directory + '/%s.FC' % self.systemlabel))
for i in range(FClast - FCfirst + 1):
for j in range(3):
self.m[i, j] = fc[2 * (3 * i + j) *
natoms:(2 * (3 * i + j) + 1) * natoms]
self.p[i, j] = fc[(2 * (3 * i + j) + 1) *
natoms:(2 * (3 * i + j) + 2) * natoms]
# Correct force constants for the moved atom
# Cf. Eq. (13) in Frederiksen et al. PRB 75, 205413 (2007)
for i in range(FClast - FCfirst + 1):
for j in range(3):
self.m[i, j, FCfirst - 1 + i, :] = 0.0
self.m[i, j, FCfirst - 1 + i, :] = -N.sum(self.m[i, j], axis=0)
self.p[i, j, FCfirst - 1 + i, :] = 0.0
self.p[i, j, FCfirst - 1 + i, :] = -N.sum(self.p[i, j], axis=0)
self.DynamicAtoms = list(range(FCfirst, FClast + 1))
# Determine TSHS files
files = glob.glob(self.directory + '/%s*.TSHS' % self.systemlabel)
files.sort()
if self.directory + '/%s.TSHS' % self.systemlabel in files:
# If present, ignore this file which does not origninate from the FCrun
files.remove(self.directory + '/%s.TSHS' % self.systemlabel)
if (FClast - FCfirst + 1) * 6 + 1 != len(files):
warnings.warn(
'Phonons.GetFileLists: WARNING - Inconsistent number of *.TSHS files in %s'
% self.directory)
return
# Build dictionary over TSHS files and corresponding displacement amplitudes
self.TSHS = {}
self.TSHS[0] = files[0] # Equilibrium TSHS
for i, v in enumerate(self.DynamicAtoms):
for j in range(3):
# Shifted TSHS files (atom,axis,direction)
self.TSHS[v, j, -1] = files[1 + 6 * i + 2 * j]
self.TSHS[v, j, 1] = files[1 + 6 * i + 2 * j + 1]
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
from __future__ import print_function
import glob
import os
import Inelastica.MakeGeom as MG
import numpy as N
import numpy.linalg as LA
# Find geometries
fns = glob.glob('NEB*/CGrun/RUN.fdf')
# Fix order
indx = [int(ii.split('_')[1].split('/')[0]) for ii in fns]
fns = [fns[ii] for ii in N.argsort(indx)]
geoms = [MG.Geom(ii) for ii in fns]
xyz = [N.array(ii.xyz) for ii in geoms]
# Find bond length
d = LA.norm(xyz[0][37] - xyz[0][36])
# Move in z to keep bond length
for ii in xyz:
ii[37, 2] = ii[36, 2] + N.sqrt(d**2 - (ii[36, 0] - ii[37, 0])**2 -
(ii[36, 1] - ii[37, 1])**2)
# Redistribute points
xyz, nxyz = N.array(xyz), N.array(xyz) # Two copies
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', '.slurm'])
# 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 = input(' ... select file:')
geom = MG.Geom(XVfiles[int(select)])
else:
print('No XV file was found in folder %s:' % CGrun)
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(list(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 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 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)