Messages

76

General Questions and Answers / Re: some question about the out document

« on: January 7, 2009, 01:48 »

Thanks,

yeah, I just make the script by the VNL tool, I expect the VNL more perfect.

You've had a long day.You've had a long flight. Thanks again!

77

General Questions and Answers / Re: Some questions about "Color by"

« on: January 7, 2009, 01:40 »

Dear everyone,

However, for my same one .vnl result document, I polt it using the three choices, respectively, as follows,(the first one is that when I choose "sign",the second is the situation for "Magnitude").
We can see that, the numbers are different at the "Show colorbar". Especial for the "sign", It seems that only three colors describe the data extent.

So, I'm still confused with that how to decide the choice.
Which is  correct, how to explain it?

Thanks very much!
Regards!

78

General Questions and Answers / some question about the MPSH

« on: January 6, 2009, 12:42 »

Dear everyone,

Like the picture as follows,When  caculating the "Projected Hamiltonian eigenstates" and “Projected Hamiltonian energy spectrum ”，we should choose the projected atoms, do you often just caculate the molecular or the total central scattering region(the molecular and the probe screening layers),  what are the differences between them?

Thanks!

79

General Questions and Answers / Re: Some questions about "MolecularEnergySpectrum"

« on: January 6, 2009, 08:47 »

Thanks!

Regards!

80

Scripts, Tutorials and Applications / Re: Script for calculating the voltage drop.

« on: January 6, 2009, 08:45 »

Thank you, Nordland. I will try again! 

Another，I am confused with that when should I use the new electrode constraint 'DensityMatrix' instead of 'Off' and when not , could you list any examples when you have free time. .

Thanks again!

81

General Questions and Answers / Re: Some questions about "MolecularEnergySpectrum"

« on: January 6, 2009, 04:13 »

Oh, Thank everyone for the discussion!  ,

However, for the two-probe system, when I caculated "Projected Hamiltonian energy spectrum ", I got the results as follows,

# Energy Spectrum
# -----------------------------------------------------------------------------
# Energy (eV)
      ............
        -4.09
        -4.02
        -3.86
        -3.48
        -3.48
        -3.25
        -3.18
        -2.53
        -0.34
        -0.33
         0.35
         0.59
         0.59
         0.84
         1.87

Is here different from the above? The Fermi level is 0eV? The HOMO is -0.33eV, LUMO is 0.35eV? Are all these right?
I am confused with "the single molecular EnergySpectrum" and "two-probe Projected Hamiltonian energy spectrum " , the Fermi level,HOMO and LUMO. Who can explain it .
 
Thanks!

82

Scripts, Tutorials and Applications / Re: Script for calculating the voltage drop.

« on: January 6, 2009, 01:19 »

Thanks

However, I got the questionable result, as follows, The polt descripes the voltage dropt from 0.1V to -0.1V.
All my scripts (Li-H2-Li as the example)are all upload. Moreover, the polt descriping the voltage dropt from 0V to -0.1V has the same curvilinear trend as that from 0.1V to -0.1V. How to explain it, or what's wrong with my scripts?Thanks again!

83

General Questions and Answers / Re: some question about the out document

« on: January 6, 2009, 01:15 »

Thanks, Nordland. You are  very kind!

84

General Questions and Answers / some question about the out document

« on: January 5, 2009, 12:47 »

Dear everyone,

In the out document as follows,

# -----------------------------------------------------------------------------
# Energy Spectrum
# -----------------------------------------------------------------------------
# Energy (eV)
       -21.89
       -19.75
       .........
        83.74
        84.39
        84.39
[array([  1.96681012e-01,   5.99825296e-24,  -2.78097762e-24]), array([  1.96681012e-01,   1.58750525e-24,  -7.23663503e-24])]

What does "[array([  1.96681012e-01,   5.99825296e-24,  -2.78097762e-24]), array([  1.96681012e-01,   1.58750525e-24,  -7.23663503e-24])][/b]" mean?

Thanks!

85

Scripts, Tutorials and Applications / Re: Script for calculating the voltage drop.

« on: January 5, 2009, 12:32 »

Dear Nordland,

If I want to calculate the voltage drop from 2V to -2V, could I do it using the followed script(just part of it and some changs from your script), is it right? (probe-molecular-probeHV2.nc is the .nc document at 2V, and the probe-molecular-probeLV-2.nc is at -2V)  Thanks!(Sorry, I am new to the Python Language )

high_bias_filename = 'probe-molecular-probeHV2.nc'
low_bias_filename = 'probe-molecular-probeLV-2.nc'
vnl_filename = 'voltage_drop.vnl'


""" ------------ No need to modify anything below this point --------------------- """
# Implementation of the voltage drop.
from ATK.TwoProbe import *; import numpy

# High bias calculation.
high_bias = restoreSelfConsistentCalculation(high_bias_filename )
# Low bias calculation.
low_bias = restoreSelfConsistentCalculation(low_bias_filename)
# Calculate the voltage drop.
voltage_drop = calculateEffectivePotential(low_bias) - calculateEffectivePotential(high_bias)


Thanks for your script again!

86

General Questions and Answers / Re: Some questions about "MolecularEnergySpectrum"

« on: January 5, 2009, 12:21 »

Thanks, Nordland

87

General Questions and Answers / Some questions about "MolecularEnergySpectrum"

« on: January 5, 2009, 04:15 »

Dear everyone,

In the topic about"Calculating molecular properties" of the VNL manuscript, the results "The Kohn-Sham eigenvalue spectrum" of water molecular is that:

Energy eigenvalues for water (in eV)

-----------------------------------------
  LDA             GGA             diff
-----------------------------------------
-24.243         -24.376           0.133
-12.470         -12.442          -0.028
 -8.187          -8.129          -0.058
 -6.140          -5.988          -0.152
  1.811           1.977          -0.166
  4.195           4.342          -0.147
 11.994          12.330          -0.336

The manuscript says：the energy level of -6.140 eV is the HOMO ，the energy level of 1.811 eV  is the LUMO,

when I caculate the "Fermi energy" and "MolecularEnergySpectrum" of my single molecular, the result is that:

Fermi energy
-3.70010920918 eV
# -----------------------------------------------------------------------------
# Energy Spectrum
# -----------------------------------------------------------------------------
# Energy (eV)
        -6.54
        -6.50
        -6.38
        -6.38
        -6.05
        -3.93
        -3.39
        -3.39
        -3.32
        -2.41
        -2.41
        -2.29
        -1.34
        -1.19
        -1.19
        -0.94
         1.93
         1.94
         2.63
         4.63
what't the  HOMO and LUMO energy of the molecular, -3.93 and -3.39? or -0.94 and 1.93?

Thanks!

88

General Questions and Answers / NLInputOutputError: Unable to access file

« on: January 5, 2009, 02:44 »

Dear everyone,

During two-probe calculation ATK gives the error:

Traceback (most recent call last):
  File "Au-molecular-Au_script.py", line 283, in ?
    if processIsMaster(): file.addToSample(transmission_eigenvalue, 'Linear Chain-molecular-Linear Chain', label)
NLInputOutputError: Unable to access file Au-molecular-Au.vnl

In my script, line283 is that:

if processIsMaster(): file.addToSample(transmission_eigenvalue, 'Linear Chain-molecular-Linear Chain', label)

How to deal with it?
Thanks, regards!


Moderator edit: Clarified subject for searching

89

General Questions and Answers / Re: Mulliken population

« on: January 4, 2009, 05:26 »

Thank you, Nordland 

Regards!

90

General Questions and Answers / Mulliken population

« on: January 3, 2009, 04:22 »

Dear everyone,

When I figure out the charge transfer between the molecular and the two probes through analyzing the Mulliken population at zero bias, I find that the molecular loses 0.3225e, however, the two probes just get 0.231e totally, where is the remanent 0.0915e(0.3225e-0.231e), how to explain it?

Thanks!