Messages

136

Installation and License Questions / is there a way to install the ATK12.2.8 in a command line

« on: May 14, 2013, 04:08 »

i want to install the demo version in a remote server  machine.
i find the graphic interface presented in Xshell window is rarther slow. and the instaling propcess  is not 1% within 2 hours, so i am wondering is there a way to install it in a command line?

137

General Questions and Answers / Re: how to set the initial spin of left and right electrode in the 12.2.8 version

« on: May 13, 2013, 04:31 »

thank you very much . i got it

138

General Questions and Answers / how to set the initial spin of left and right electrode in the 12.2.8 version

« on: May 10, 2013, 11:45 »

i saw the example in the http:// http://quantumwise.com/publications/tutorials/mini-tutorials/94-transmission-spectrum-of-a-spin-polarized-atomic-chain.
and found in the step of initial spin setup, the initial spin can only be setted in the interaction region including scatter region and left(right) eletrode copy.

as i know, the left and right electrodes are exactly the same with the corresponding copies in the interaction region.

so it means if i set the initial spin of the electrode copy, there  is no need to set the electrode again?

is that so?

139

General Questions and Answers / A demo version 12.8 can run parallel in linux platform

« on: May 8, 2013, 13:53 »

i download the demo version 12.8 (without trial license)
it can run parallel in  linux platform?

140

General Questions and Answers / in the latest ATK 12.8,2, the relax problem

« on: May 3, 2013, 15:07 »

i just do a test calculation in the new version 12.8.2
i have a question about the relax process.

as i know, in the older 2008 version, along the transport direction, i.e z direction, the device region is not relaxed.

in other word, the distance along z direction between the right and left electrode is fixed.

so i am wondering the new version 12.8.2, the device region can relaxed in the z direction? 

141

General Questions and Answers / Re: ATK error of a spin configration of carbon chain-gnrs system

« on: May 3, 2013, 14:53 »

the error is not caused the atomic position <0.
because i just put all the atom inside the cell.
the error is the same.

so any one could help me put this structure into the latest version,and see the result?

thanks very much!   

142

General Questions and Answers / ATK error of a spin configration of carbon chain-gnrs system

« on: May 2, 2013, 04:54 »

i am doing a scf calcualtion of a carbon chain-gnrs sysyem with spin-configuration. but the error comes :


# sc 15 : Fermi Energy =   -0.29591 Ry  Etot = -3923.57173 Ry  dRho =  4.5092E-03  dEtot =  7.4271E-06 Ry
# ----------------------------------------------------------------
# TwoProbe Calculation
# ----------------------------------------------------------------
# sc  0 : q =  858.01144 e
# sc  1 : q =  862.08559 e  dRho =  1.6332E+02
Traceback (most recent call last):
  File "<string>", line 632, in ?
ATKError: inverse(DZMatrix const &) : Could not LU factorize!
Traceback (most recent call last):
  File "<string>", line 632, in ?
ATKError: inverse(DZMatrix const &) : Could not LU factorize!
Traceback (most recent call last):
  File "<string>", line 632, in ?
ATKError: inverse(DZMatrix const &) : Could not LU factorize!
Traceback (most recent call last):
  File "<string>", line 632, in ?
ATKError: inverse(DZMatrix const &) : Could not LU factorize!
Traceback (most recent call last):
  File "<string>", line 632, in ?
ATKError: inverse(DZMatrix const &) : Could not LU factorize!
Traceback (most recent call last):

i tried to find the reasons as mentioned before in the forum. firstly the geometry configurations, so i do a test calcualtion without spin. but the results is : 
ATKError: Exceeded maximum number of self-consistent iterations.   But the scf step is setted
200, it is enough. so  i think it is the geometry problem. the central scatter region and electrode are both relaxed   

but i check the geometry in  the vnl, it is ok.
so i can not find what is the problem  with this configuration.

i attacked the script  in the scf  calculation without spin, anyone would help me, i would be aprreciated. i used the version is ATK 2008

thanks very much                             

143

General Questions and Answers / how to know or print the finally spin of every atom

« on: January 20, 2011, 07:44 »

hi, after spin-polarized scf calculation, i want to know the finally spin orientiation of every atom, or the majority spin or some related information,
how to get this information, is there any sample script code here?
thanks a lot

144

General Questions and Answers / Re: how to write correctly a script to output SPIN-POLARIZED transport spectrum

« on: January 17, 2011, 14:55 »

thank you very  much. Anders Blom

145

General Questions and Answers / how to write correctly a script to output SPIN-POLARIZED transport spectrum

« on: January 17, 2011, 13:40 »

hi, i have a script to calculate and print the transport spectrum for the non-spin-polarized system.
now, i have add a liitle in script for the spin-polarized system.but it errors.

Traceback (most recent call last):
  File "two-my-own-tran.py", line 35, in ?
    print '%17.3f %17.6f %17.6f' %(
TypeError: coefficients() takes exactly 1 argument (2 given)
Mon Jan 17 18:17:48 CST 2011
                 
 i can not find what is wrong?

from ATK.TwoProbe import *
from ATK.MPI import *
# Restoring the SCF from the previous calculation
scf = restoreSelfConsistentCalculation('GNR-four-C-GNR-opt-all-szp.nc')
# Specify the range of energies
energy_scan = [ i/200.0*Units.eV for i in range(-1601,601)]
# Calculate the Transmission Spectrum
bz_int_parm = brillouinZoneIntegrationParameters( (1,1,100) )
spectrum = calculateTransmissionSpectrum(
self_consistent_calculation=scf,
energies = energy_scan,
#energies = energy_list*electronVolt,
brillouin_zone_integration_parameters=bz_int_parm)
# Save the Transmission Spectrum to VNL file
if ( processIsMaster() ):
  vnlfile = VNLFile("GNR-four-C-GNR-_trans.vnl")
  vnlfile.addToSample(spectrum,'GNR-four-C-GNR-_trans')
 
 
  print 'Transmission Spectrum'
  print '-----------------------------------------------------------------------'
  print 'Energies(eV) Coefficients'
  for i in range(len(spectrum.energies())):
      print '%17.3f %17.6f %17.6f' %(
      spectrum.energies().inUnitsOf(Units.eV),
     spectrum.coefficients(0),spectrum.coefficients(1))
                                                                     

  
 

146

General Questions and Answers / Re: the SPIN-POLARIZED orientiation of GNR electrode

« on: January 16, 2011, 12:58 »

thank you zh. i know it.

147

General Questions and Answers / Re: hard to convergence for the SPIN-POLARIZED transport of GNR-wires-GNR two probe

« on: January 16, 2011, 12:57 »

hi,
thank you zh,
i have check the spin configuration for carbon atoms in the left electrode should be exactly same with the one for carbon atoms in the left screening layers in scattering region. Also for the right side.
yes they are, because i use a small code below to make sure above the situation , but the error still exsits. i do not know why. would you  give me further hints, thanks  a lot !

scattering_region_initial_scaled_spin = [0,]*len(scattering_elements)
 
for index in range(len(scattering_elements)):
        if (scattering_elements[index]==Carbon) :
                if (scattering_coordinates[index][1]> y1):
                      scattering_region_initial_scaled_spin[index]=0.5
                elif  (scattering_coordinates[index][1]< y2):
                       scattering_region_initial_scaled_spin[index]=-0.5......
electrode_region_initial_scaled_spin = [0,]*len(electrode_elements)
for index in range(len(electrode_elements)):
       if (electrode_elements[index]==Carbon) :
                if (electrode_coordinates[index][1]> y1):
                       electrode_region_initial_scaled_spin[index]=0.5
                elif  (electrode_coordinates[index][1]< y2):
                       electrode_region_initial_scaled_spin[index]=-0.5

148

General Questions and Answers / hard to convergence for the SPIN-POLARIZED transport of GNR-wires-GNR two probe

« on: January 16, 2011, 03:11 »

hi , i have read a paper appl.phys.lett.96.042104 (2010),
before, i have run non-spin transport calculation, it goes well, but when try to study the spin-polarized transport of GNR-nanowires-GNR two probe system, it has errors:
it is a problem that is disscussed in this forum before. 1)structure geometry problem, but it seems that my system has not,for non-spin transport calculation, it goes well 2)
the initial_spin  problem, i am  not sure my system has or not, but i change the initical spin from 1~0.5, the error still came out as below.so i don not where is my problem.
my input script is in attatchment. in fact my non-spin script is revised by zh last time, i only add the spin related part in the sript.
any suggestion is apppreciated. thanks a lot !!!!!!

# sc 26 : Fermi Energy =   -0.29992 Ry  Etot = -1084.00920 Ry  dRho =  4.6250E-03  dEtot = -3.6937E-04 Ry
# sc 27 : Fermi Energy =   -0.29992 Ry  Etot = -1084.00932 Ry  dRho =  1.2625E-03  dEtot = -1.2192E-04 Ry
# sc 28 : Fermi Energy =   -0.29994 Ry  Etot = -1084.00941 Ry  dRho =  8.9892E-04  dEtot = -9.1762E-05 Ry
# sc 29 : Fermi Energy =   -0.29996 Ry  Etot = -1084.00950 Ry  dRho =  9.6766E-04  dEtot = -8.7967E-05 Ry
# sc 30 : Fermi Energy =   -0.29999 Ry  Etot = -1084.00956 Ry  dRho =  6.1229E-04  dEtot = -6.0620E-05 Ry
# sc 31 : Fermi Energy =   -0.29998 Ry  Etot = -1084.00962 Ry  dRho =  7.9344E-04  dEtot = -6.1285E-05 Ry
# sc 32 : Fermi Energy =   -0.29998 Ry  Etot = -1084.00962 Ry  dRho =  6.7926E-05  dEtot =  1.0508E-06 Ry
# ----------------------------------------------------------------
# TwoProbe Calculation
# ----------------------------------------------------------------
# sc  0 : q =  322.00362 e
# sc  1 : q =  341.96025 e  dRho =  3.5328E+01
Traceback (most recent call last):
  File "<string>", line 365, in ?
ATKError: inverse(DZMatrix const &) : Could not LU factorize!

149

General Questions and Answers / Re: how should i write a script to specify the different initial_scaled_spin

« on: January 16, 2011, 02:46 »

thank you it is the problem exists
and another problem is the 17, it should be written 17ang , including the unit.

150

General Questions and Answers / Re: how should i write a script to specify the different initial_scaled_spin

« on: January 15, 2011, 08:31 »

thank you Anders Blom
i have revised my code following you suggestion.
scattering_region_initial_scaled_spin = [0,]*len(scattering_elements)
 
for index in range(len(scattering_elements)):
        if (scattering_elements[index]=="Carbon") :
                if (scattering_coordinates[index][2]> 17):
                      scattering_region_initial_scaled_spin[index]=1
                elif  (scattering_coordinates[index][2]< 13):
                       scattering_region_initial_scaled_spin[index]=1
but a strange things happed. the for ...if ... language does not work. all the scattering_region_initial_scaled_spin are set to 0 in my output
Initial Scaled Spin = (0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)

my scattering_elements and corresponding scattering_coordinates are following, i can make sure there are atoms fit the if condition (the atoms are carbon and their y coordinates are larger than 17 or less than 13), and of course, these atoms initial_scaled_spin should be labled 1. but the output shows not. i do not know why? please give me some hints. thanks a lot!!!!
scattering_elements = [Hydrogen, Carbon,   Carbon,   Carbon,
                       Carbon,   Hydrogen, Carbon,   Carbon,
                       Carbon,   Carbon,   Hydrogen, Carbon,
                       Carbon,   Carbon,   Carbon,   Hydrogen,
                       Carbon,   Carbon,   Carbon,   Carbon,
                       Hydrogen, Carbon,   Carbon,   Carbon,
                       Carbon,   Hydrogen, Carbon,   Carbon,
                       Carbon,   Carbon,   Hydrogen, Carbon,
                       Carbon,   Carbon,   Carbon,   Hydrogen,
                       Carbon,   Carbon,   Carbon,   Carbon,
                       Hydrogen, Hydrogen, Carbon,   Hydrogen,

,,,,,
and scattering_coordinates = [[  0.00000000e+00+5.0,   0.00000000e+00+20.0,   9.83800000e+00],
                          [ -1.22989401e-15+5.0,  -1.12843802e+00+20.0,   9.85067344e+00],
                          [ -2.94995475e-15+5.0,  -3.92924460e+00+20.0,   9.85627415e+00],
                          [ -4.66985681e-15+5.0,  -5.36743000e+00+20.0,   9.86150159e+00],
                          [ -5.47776181e-16+5.0,  -8.20440839e+00+20.0,   9.84598938e+00],
                          [  7.14895909e-16+5.0,  -9.36487852e+00+20.0,   9.81171705e+00],
                          [ -2.17900005e-15+5.0,  -1.78728400e+00+20.0,   1.10995077e+01],
                          [ -2.86524241e-15+5.0,  -3.23383319e+00+20.0,   1.11043162e+01],
                          [ -2.38880286e-15+5.0,  -6.08197662e+00+20.0,   1.11053456e+01],
                          [  1.62864277e-15+5.0,  -7.53795350e+00+20.0,   1.10969972e+01],
                          [ -1.10737121e-15+5.0,   9.41494265e-02+20.0,   1.23040920e+01],
                          [ -3.10119238e-15+5.0,  -1.06706289e+00+20.0,   1.23230761e+01],
                          [ -2.21118463e-15+5.0,  -3.93739872e+00+20.0,   1.23453547e+01],
                          [  9.63002055e-16+5.0,  -5.37828650e+00+20.0,   1.23518140e+01],
.......