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. Thank you 
). So, this approach will possibly not hold for metal-decorated CNTs as there is scattering. And I fully agree, that ideal systems are some kind of "uninteresting". Nevertheless, the following question:
from NanoLanguange
from numpy import * # sorry for this dirty import of numpy
from NanoLanguage import *
def create_transmission_atk(band, emin = -4, emax = 4, npoints = 1000):
# create transmission function, band is an ATK-bandstructure object
# [emin, emax] define the energy interval
# npoints gives the resolution of the interval (+1 is added to this value, later on)
energies = array(band.evaluate()) # all the energy points of the bandstructure in an array
return create_transmission(energies, emin = emin, emax = emax, npoints = npoints)
# the next function may be used also with other programs than ATK, no nano languange is needed
def create_transmission(energies, emin = -4, emax = 4, npoints = 1000):
# create transmission function
# energies = the energy points of the bandstructure in an array, each band separated
epoints = linspace(emin, emax, npoints+1)
transmission = zeros(npoints+1)
nbands = size(energies[0,:])
for i in range(nbands): # loop over bands
tmp = energies[:,i] # band number i
# print tmp
l = size(tmp)
nextreme = [0] # minima and maxima of the band
de2 = 0; de = 0;
for j in range(1,l-1):
de2 = de
de = tmp[j]-tmp[j-1]
if (de2*de < 0):
# does the sign of the energy difference change? (local extremum)
nextreme.append(j-1)
nextreme.append(l-1)
for k in range(size(nextreme)-1):
# all the minima and maxima
istart = int((tmp[nextreme[k]]-emin) / (emax - emin) * npoints)
iend = int((tmp[nextreme[k+1]]-emin) / (emax - emin) * npoints)
if (istart < 0):
istart = 0
if (iend < 0):
iend = 0
if (istart > npoints ):
istart = npoints
if (iend > npoints ):
iend = npoints
if istart > iend:
istart, iend = iend, istart
transmission[istart:iend] = transmission[istart:iend] + ones(iend - istart)
return array([epoints, transmission])
# reading input and so on...
master = processIsMaster()
for k in arange(kstart,kend,kstep): # (1,52,5)
# Define nanotube
NT = NanoTube(n,m,element1,element2,bond_length*Units.Ang,vacuum*Units.Ang) # given parameters
NT = NT.center()
if master:
print "k-number: %d" % (k)
# Basis Set and basic calculator config
basis_set = LDABasis.DoubleZetaPolarized
numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling = (1, 1, int(k)),
grid_mesh_cutoff = 40.0*Rydberg,
)
calculator = LCAOCalculator(
basis_set=basis_set,
numerical_accuracy_parameters=numerical_accuracy_parameters,
)
NT.setCalculator(calculator)
t1 = time()
force = Forces(NT)
t2 = time()
if master:
print "time for DFT + Forces: %fs" % (t2-t1)
desc = "Nanotube-%d-%d" % (n,m)
nlsave(filename + ".nc", NT, desc)
print "structure \"%s\" successfully written to %.nc" % (desc,filename)
# program stucks here! why?
print >> "%s epsilon %f" % ('%',epsilon)
f = open(filename + "_forces_NT.txt", 'w')
print >> f,"%s epsilon %f" % ('%',epsilon)
force.nlprint(f)
print >> f,""
f.close()
[...]
+------------------------------------------------------------------------------+
| Calculation Converged in 13 steps |
| |
| Fermi Level = -0.131172 Ha |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| DFT Calculation [Finished Wed Aug 17 11:50:15 2011] |
| |
+------------------------------------------------------------------------------+
|--------------------------------------------------|
Calculating Eigenvalues : ==================================================
Calculating Density Matrix : ==================================================
time for DFT + Forces: 92.478966s