def GetOrbitalIndices(self):
# Determine snr (siesta number) for each label
csl = SIO.GetFDFblock(self.fdf, KeyWord='ChemicalSpeciesLabel')
csl2snr = {}
for set in csl:
csl2snr[set[2]] = set[0]
# Determine nao (number of orbitals) for each snr
ionNCfiles = glob.glob(self.directory + '/*.ion.nc*')
snr2nao = {}
for ionfile in ionNCfiles:
if ionfile.endswith('.gz'):
print('Phonons.GetOrbitalIndices: Unzipping: ' + ionfile)
os.system('gunzip ' + ionfile)
ionfile = ionfile[:-3]
file = NC4.Dataset(ionfile, 'r')
thissnr = int(csl2snr[file.Label])
snr2nao[thissnr] = file.Number_of_orbitals
file.close()
print('Phonons.GetOrbitalIndices: Dictionary snr2nao = ' +
str(snr2nao))
# Determine which orbital indices that belongs to a certain atom
orbitalIndices = []
tmpOrb = 0
for num in self.geom.snr:
nao = snr2nao[num]
orbitalIndices.append([tmpOrb, tmpOrb + int(nao) - 1])
tmpOrb += nao
self.orbitalIndices = N.array(orbitalIndices)
self.nao = tmpOrb # total number of orbitals
self.snr2nao = snr2nao # orbitals per species
return self.orbitalIndices, self.nao
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 __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 == general.NNEB + 1)
if not restart and not self.fixed:
os.makedirs(dirr)
SUR.CopyInputFiles(general.initial + "/CGrun/", dirr,
['.fdf', '.vps', '.psf'])
# Interpolate
ixyz, fxyz = N.array(initial.XVgeom.xyz), N.array(final.XVgeom.xyz)
mix = float(iistep) / (general.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")
# Append lines to RUN.fdf
elm = dirr + "/RUN.fdf"
f = open(elm, 'r')
lines = f.readlines()
f.close()
f = open(elm, 'w')
f.write('### Lines appended %s \n' % time.ctime())
f.write("SolutionMethod diagon\n")
f.write("MD.TypeOfRun CG\n")
f.write("MD.NumCGsteps 0\n")
f.write("TS.SaveHS True\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()
self.const = SIO.GetFDFblock(dirr + "/RUN.fdf", "GeometryConstraints")
def get_elec_vars(lr):
# Look up old format first
TSHS = SIO.GetFDFlineWithDefault(opts.fn, 'TS.HSFile' + lr, str, '',
exe)
NA1 = SIO.GetFDFlineWithDefault(opts.fn, 'TS.ReplicateA1' + lr, int, 1,
exe)
NA2 = SIO.GetFDFlineWithDefault(opts.fn, 'TS.ReplicateA2' + lr, int, 1,
exe)
# default semi-inf direction
semiinf = 2
# Proceed looking up new format, which precedes
belec = 'TS.Elec.' + lr
print('Looking for new electrode format in: %%block {}'.format(belec))
# Default replication stuff
TSHS = SIO.GetFDFlineWithDefault(opts.fn, belec + '.TSHS', str, TSHS,
exe)
NA1 = SIO.GetFDFlineWithDefault(opts.fn, belec + '.Bloch.A1', int, NA1,
exe)
NA2 = SIO.GetFDFlineWithDefault(opts.fn, belec + '.Bloch.A2', int, NA2,
exe)
NA3 = SIO.GetFDFlineWithDefault(opts.fn, belec + '.Bloch.A3', int, 1,
exe)
# Overwrite block
block = SIO.GetFDFblock(opts.fn, KeyWord=belec)
for line in block:
print(line)
# Lower-case, FDF is case-insensitive
key = line[0].lower()
if key in ['tshs', 'tshs-file', 'hs', 'hs-file']:
TSHS = line[1]
elif key in [
'replicate-a', 'rep-a', 'replicate-a1', 'rep-a1',
'bloch-a1'
]:
NA1 = int(line[1])
elif key in [
'replicate-b', 'rep-b', 'replicate-a2', 'rep-a2',
'bloch-a2'
]:
NA2 = int(line[1])
elif key in [
'replicate-c', 'rep-c', 'replicate-a3', 'rep-a3',
'bloch-a3'
]:
NA3 = int(line[1])
elif key in ['replicate', 'rep', 'bloch']:
# We have *at least* 2 integers
NA1 = int(line[1])
NA2 = int(line[2])
NA3 = int(line[3])
elif key in ['semi-inf-direction', 'semi-inf-dir', 'semi-inf']:
# This is lower-case checked
axis = line[1][1:].lower()
if 'a' == axis or 'a1' == axis:
semiinf = 0
elif 'b' == axis or 'a2' == axis:
semiinf = 1
elif 'c' == axis or 'a3' == axis:
semiinf = 2
# Simple check of input, this may be overwritten later
if semiinf != 2 and NA1 * NA2 * NA3 > 1:
raise ValueError(
("Cannot provide semi-infinite directions "
"other than A3-direction with repetition."))
if TSHS[0] != '/':
# path is relative
TSHS = opts.head + '/' + TSHS
return TSHS, NA1, NA2, semiinf
def OptionsCheck(opts):
"""
Generic routine for adjusting most used options for routines.
I.e. Inelastica/EigenChannels/pyTBT.
"""
import Inelastica.io.siesta as SIO
import os
import os.path as osp
# Module name
exe = opts.module
# Destination directory
if not osp.isdir(opts.DestDir):
print('\n' + exe + ': Creating folder {0}'.format(opts.DestDir))
os.mkdir(opts.DestDir)
if not osp.isfile(opts.fn):
raise IOError("FDF-file not found: " + opts.fn)
# Read SIESTA files
opts.head = osp.split(opts.fn)[0]
if opts.head == '': # set filepath if missing
opts.head = '.'
print(exe + ": Reading keywords from {0} \n".format(opts.fn))
opts.systemlabel = SIO.GetFDFlineWithDefault(opts.fn, 'SystemLabel', str,
'siesta', exe)
opts.TSHS = '%s/%s.TSHS' % (opts.head, opts.systemlabel)
# These first keys can be used, but they are superseeded by keys in the TS.Elec.<> block
# Hence if they are read in first it will do it in correct order.
if opts.UseBulk < 0:
# Note NRP:
# in principle this is now a per-electrode setting which
# may be useful for certain systems...
opts.UseBulk = SIO.GetFDFlineWithDefault(opts.fn,
'TS.UseBulkInElectrodes',
bool, True, exe)
opts.UseBulk = SIO.GetFDFlineWithDefault(opts.fn, 'TS.Elecs.Bulk',
bool, opts.UseBulk, exe)
def get_elec_vars(lr):
# Look up old format first
TSHS = SIO.GetFDFlineWithDefault(opts.fn, 'TS.HSFile' + lr, str, '',
exe)
NA1 = SIO.GetFDFlineWithDefault(opts.fn, 'TS.ReplicateA1' + lr, int, 1,
exe)
NA2 = SIO.GetFDFlineWithDefault(opts.fn, 'TS.ReplicateA2' + lr, int, 1,
exe)
# default semi-inf direction
semiinf = 2
# Proceed looking up new format, which precedes
belec = 'TS.Elec.' + lr
print('Looking for new electrode format in: %%block {}'.format(belec))
# Default replication stuff
TSHS = SIO.GetFDFlineWithDefault(opts.fn, belec + '.TSHS', str, TSHS,
exe)
NA1 = SIO.GetFDFlineWithDefault(opts.fn, belec + '.Bloch.A1', int, NA1,
exe)
NA2 = SIO.GetFDFlineWithDefault(opts.fn, belec + '.Bloch.A2', int, NA2,
exe)
NA3 = SIO.GetFDFlineWithDefault(opts.fn, belec + '.Bloch.A3', int, 1,
exe)
# Overwrite block
block = SIO.GetFDFblock(opts.fn, KeyWord=belec)
for line in block:
print(line)
# Lower-case, FDF is case-insensitive
key = line[0].lower()
if key in ['tshs', 'tshs-file', 'hs', 'hs-file']:
TSHS = line[1]
elif key in [
'replicate-a', 'rep-a', 'replicate-a1', 'rep-a1',
'bloch-a1'
]:
NA1 = int(line[1])
elif key in [
'replicate-b', 'rep-b', 'replicate-a2', 'rep-a2',
'bloch-a2'
]:
NA2 = int(line[1])
elif key in [
'replicate-c', 'rep-c', 'replicate-a3', 'rep-a3',
'bloch-a3'
]:
NA3 = int(line[1])
elif key in ['replicate', 'rep', 'bloch']:
# We have *at least* 2 integers
NA1 = int(line[1])
NA2 = int(line[2])
NA3 = int(line[3])
elif key in ['semi-inf-direction', 'semi-inf-dir', 'semi-inf']:
# This is lower-case checked
axis = line[1][1:].lower()
if 'a' == axis or 'a1' == axis:
semiinf = 0
elif 'b' == axis or 'a2' == axis:
semiinf = 1
elif 'c' == axis or 'a3' == axis:
semiinf = 2
# Simple check of input, this may be overwritten later
if semiinf != 2 and NA1 * NA2 * NA3 > 1:
raise ValueError(
("Cannot provide semi-infinite directions "
"other than A3-direction with repetition."))
if TSHS[0] != '/':
# path is relative
TSHS = opts.head + '/' + TSHS
return TSHS, NA1, NA2, semiinf
# Look up electrode block
block = SIO.GetFDFblock(opts.fn, KeyWord='TS.Elecs')
if len(block) == 0:
# Did not find the electrode block, defaults to old naming scheme
opts.fnL, opts.NA1L, opts.NA2L, opts.semiinfL = get_elec_vars('Left')
opts.fnR, opts.NA1R, opts.NA2R, opts.semiinfR = get_elec_vars('Right')
elif len(block) == 2:
# NB: The following assumes that the left electrode is the first in the block!
opts.fnL, opts.NA1L, opts.NA2L, opts.semiinfL = get_elec_vars(
block[0][0])
opts.fnR, opts.NA1R, opts.NA2R, opts.semiinfR = get_elec_vars(
block[1][0])
else:
print(block)
raise IOError('Currently only two electrodes are supported')
# Read in number of buffer atoms
opts.buffer, L, R = SIO.GetBufferAtomsList(opts.TSHS, opts.fn)
opts.bufferL = L
opts.bufferR = R
if 'maxBias' in opts.__dict__:
# Bias range
opts.maxBias = abs(opts.maxBias)
opts.minBias = -abs(opts.maxBias)
# Device region
if opts.DeviceFirst <= 0:
opts.DeviceFirst = SIO.GetFDFlineWithDefault(opts.fn,
'TS.TBT.PDOSFrom', int, 1,
exe)
opts.DeviceFirst -= L
if opts.DeviceLast <= 0:
opts.DeviceLast = SIO.GetFDFlineWithDefault(opts.fn, 'TS.TBT.PDOSTo',
int, 1e10, exe)
opts.DeviceLast -= L
opts.NumberOfAtoms = SIO.GetFDFlineWithDefault(opts.fn, 'NumberOfAtoms',
int, 1e10, exe)
opts.NumberOfAtoms -= L + R
if opts.DeviceLast < opts.DeviceFirst:
print(
exe +
' error: DeviceLast<DeviceFirst not allowed. Setting DeviceLast=DeviceFirst'
)
opts.DeviceLast = opts.DeviceFirst
opts.DeviceAtoms = [
max(opts.DeviceFirst, 1),
min(opts.DeviceLast, opts.NumberOfAtoms)
]
# Voltage
opts.voltage = SIO.GetFDFlineWithDefault(opts.fn, 'TS.Voltage', float, 0.0,
exe)
#############
# Here comes some specifics related to different executables:
#############
if "VfracL" in opts.__dict__:
if opts.VfracL < 0.0 or opts.VfracL > 1.0:
raise RuntimeError(
'Option VfracL must be a value in the range [0,1].')
if "PhononNetCDF" in opts.__dict__:
if not osp.isfile(opts.PhononNetCDF):
raise IOError("Electron-phonon coupling NetCDF file not found: " +
opts.PhononNetCDF)
if "eta" in opts.__dict__:
if opts.eta < 0:
raise RuntimeError("eta must be a posivite number")
if "etaLead" in opts.__dict__:
if opts.etaLead < 0:
raise RuntimeError("etaLead must be a posivite number")
if "PhExtDamp" in opts.__dict__:
if opts.PhExtDamp < 0:
raise RuntimeError("PhExtDamp must be a posivite number")
if "biasPoints" in opts.__dict__:
if opts.biasPoints < 6:
raise AssertionError("BiasPoints must be larger than 5")
if "iSpin" in opts.__dict__:
if not opts.iSpin in [0, 1]:
raise AssertionError("Spin must be either 0 or 1")
if "Emin" in opts.__dict__:
if opts.Emin == 1e10:
opts.Emin = SIO.GetFDFlineWithDefault(opts.fn, 'TS.TBT.Emin',
float, 0.0, 'pyTBT')
if "Emax" in opts.__dict__:
if opts.Emax == 1e10:
opts.Emax = SIO.GetFDFlineWithDefault(opts.fn, 'TS.TBT.Emax',
float, 1.0, 'pyTBT')
if "NPoints" in opts.__dict__:
if opts.NPoints <= 0:
opts.NPoints = SIO.GetFDFlineWithDefault(opts.fn, 'TS.TBT.NPoints',
int, 1, 'pyTBT')
# Create list of energies
try:
opts.Elist
# Do not overwrite if some Elist is already specified
except:
if opts.NPoints == 1:
opts.Elist = _np.array((opts.Emin, ), _np.float)
else:
# Linspace is just what we need
opts.Elist = _np.linspace(opts.Emin, opts.Emax, opts.NPoints)
