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Topics - Roc

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31
General Questions and Answers / the error about the IterationControlParameters.DensityMatrix
« on: March 5, 2009, 12:51 »
when I run the job about the two-probe system, the error happened, as follows, (the script is run in the version of 2008.10)

Traceback (most recent call last):
  File "Au-molecule_script.py", line 218, in ?
    history_steps = 15
NLArgumentNameError: The quantity, NL.DensityFunctionalTheory.ATKParameters.IterationControlParameters.DensityMatrix, is not recognized.

how to resolve it, thanks!

32
General Questions and Answers / some questions about the geometric optimization
« on: February 25, 2009, 04:26 »
Dear everyone,

In order to relax the two-probe system like Au-DTB-Au, could we optimize the struture by ATK more precisely and quickly and how to set it in VNL? It seems that thare are two geometric optimization mothods Steepest decent and Quasi Newton, which method is better for optmizing the two-probe system and what's the  relative merits for these two methods?  how to set the parameter "Geometric Constraints" in VNL

Thanks!

33
General Questions and Answers / some questions about Gate Voltage
« on: February 24, 2009, 08:50 »
Dear everyone,

If we calculate the properties when the gate voltage is used, which atoms will often be applied gate voltage, just the molecule or the central scattering? Are there any special parameters to be set when applying the gate voltage?

Another, It seems diffult for the convergence when the bias voltage between two electrodes is more than +-2V. what about the situation on the gate voltage? In some experments, the gate voltage could be more than 30V, colud the ATK stimulate the situation? Does anyone have the experience, and could you give any advice?

Thanks！

34
General Questions and Answers / some questions about the electrode
« on: February 14, 2009, 08:01 »
Dear everyone,

I try to  produce the electrodes using semi enclosed nanotube or one fullerene like C70, but it seems difficult to get it by VNL because of the periode boundary conditions. Could anybody give me some advice
 to produce these two types of electrode and how to definite the screening layers.
 

thanks,

35
General Questions and Answers / some question about the DOS
« on: January 12, 2009, 01:46 »
Dear everyone,

When I probe my two-probe system, I calculate the "Density of atates", how to understand
 the "Density of atates" (it is of the molecule or central scattering region or....), When I set it from-2eV to 2eV like the attachment1, I get the DOS like attachment2, Does the energy point 0eV mean the Fermi level. Another, my molecule has high symmetry, is the DOS distrustful? 

That seems that the current version couldn't calculate the PDOS, could someone write one script for it.


Thanks!

36
General Questions and Answers / Negative numbers in density of states
« on: January 7, 2009, 02:41 »
Dear everyone,

Error happens in ATK caculation, as follows,


Traceback (most recent call last):
  File "AumolecularAuscript.py", line 291, in ?
    mulliken_population = calculateMullikenPopulation(self_consistent_calculation = scf)
NLTypeError: The population must contain non-negative numbers only.[/b]

that‘s to say, some negetive numbers happen in DOS, the .dat document is that,

# Density Of States
# -----------------------------------------------------------------------------
# Energy (eV)   DOS (1/eV)
        -4.00       0.0001
        -3.90       0.0002
        -3.80       0.0003
          ................
         3.60      -0.0012
         3.70      -0.0012
         3.80      -0.0016
         3.90      -0.0017
         4.00      -0.0016
how to deal with it?
Thanks!

Moderator edit: Changed subject to improve searching

37
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!

38
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!



39
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!

40
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

41
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!
 

42
General Questions and Answers / Some questions about "Color by"
« on: January 2, 2009, 13:58 »
Dear everyone,

When the result document .vnl is visualized by VNL tool, there are three options " Value, Magnitude, Sign" in the "Color by" pull-down menu, how do I choose it, and why is the numerical value different in the "Show colorbar" sometimes when I choose  "Value" or others. Just choose the default? I haven't understood the explanation in the manuscript:
Magnitude: available for all types of functions.
Phase: available for complex functions, such as wave functions.
Sign: available for real functions.
Value: available for real functions.

Thanks.

43
General Questions and Answers / some questions about the geometry optimizing
« on: January 1, 2009, 03:47 »
Dear everyone,

First, Please accept my sincere wishes for the New Year. I hope you will continue to enjoy good health.

Second, I have some questions to consult with you about the geometry optimizing.
As we know, in some other softwares, i.e., Gaussian03,Dmol, after optimizing one molecular or cluster geometry, we could judge the stability of the molucular or cluster through analyzing the vibration frequency. However, if we optimize one molecular or two-probe system in ATK , how do we verify the stability of the optimized structure.

Thanks!

44
General Questions and Answers / some questions about MPSH
« on: December 27, 2008, 09:52 »
Dear everyone,

In this tutorial analyzing the Li-H2-Li two-probe system, a part of one script is that,

# Calculate HOMO and LUMO eigenstates for the H atoms in the two-probe system
eigenstates = calculateProjectedHamiltonianEigenstates(
    scf, projection_atoms = [3,4],
    quantum_numbers = [0,1]
    )

For other two-probe systems, how to decide the "Quantum Numbers " in VNL when I calculate Projected Hamiltonian eigenstates to obtain the HOMO、LUMO、HOMO-N and LUMO+N 

Thanks!

45
General Questions and Answers / how to choose the eigenchannel index
« on: December 26, 2008, 05:40 »
Dear everyone,

There is speaking in VNL mannul"Transmission eigenchannels of doped Al wire":

# Calculate the transmission eigenstates
index_list = [0,1]
kpoint_list = [(0.0,0.0)]
for index in index_list:
    transmission_eigenstate = calculateTransmissionEigenstates(
        scf,
        energy,
        quantum_numbers=(index,kpoint_list)
    )
    results.addToSample(transmission_eigenstate[0],"perfect_alwire")

I have some question about it. When I calculate the transmission eigenstates of the two-probe system, how can I choose eigenchannel index and set it in VNL

Thanks.

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