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Topics - jjhskang

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1
General Questions and Answers / How can I interprete the result of Mulliken population analysis?
« on: November 10, 2011, 00:55 »
Hi!

I have difficulty in interprteting Mulliken polulation result. For example, what does each line in the following example correspond to? Why are there 6 lines ? The last two lines seem to correspond to P orbitals. Are they for 5p and 4p?
What is order? "4d, 4s,....."

I would appreciate if somebody can explain this.





Mulliken Population Report                                                   |
|                                                                              |
| ---------------------------------------------------------------------------- |
|                        |                                                     |
| Element   Total  Shell | Orbitals                                            |
|                        |                                                     |
|                        |     xy     zy  zz-rr     zx  xx-yy                  |
|      0  Ag   11.005  1.267 |  0.253  0.253  0.255  0.253  0.253                 |
|                        |      s                                              |
|                 -0.014 | -0.014                                              |
|                        |     xy     zy  zz-rr     zx  xx-yy                  |
|                  8.202 |  1.638  1.650  1.627  1.650  1.638                  |
|                        |      s                                              |
|                  0.801 |  0.801                                              |
|                        |      y      z      x                                |
|                  0.011 |  0.004  0.002  0.004                                |
|                        |      y      z      x                                |
|                  0.740 |  0.246  0.247  0.247   

2
General Questions and Answers / VNL in ATK 11.2 fails to display contour plot
« on: July 5, 2011, 14:07 »
Hi!


I am a valid ATK 11.2 user.
When I try to display contour plot, it gives error messages below:

---------------------------------------------------
X Error: GLXBadContext 149
  Extension:    143 (Uknown extension)
  Minor opcode: 5 (Unknown request)
  Resource id:  0x200546
QGLContext::makeCurrent(): Failed.
X Error: GLXBadContext 149
  Extension:    143 (Uknown extension)
  Minor opcode: 5 (Unknown request)
  Resource id:  0x200548
.....................(omitted).......

QGLContext::makeCurrent(): Failed.
X Error: GLXBadDrawable 151
  Extension:    143 (Uknown extension)
  Minor opcode: 11 (Unknown request)
  Resource id:  0x2004bf

--------------------------------------------------------

I am using X-manager on windows XP system to run vnl.

How can I solve this problem?

3
General Questions and Answers / Error in Nanolanguage in writing Mulliken charge
« on: May 11, 2011, 14:11 »
Hi!

I am trying to calculate Mulliken charge of each atom in bulk configuration. For that, I first made a calculation with "atk_setup.py " attached. It generates a file "mulliken.nc". Next, I tried to print the Mulliken charge of each atom by running the file "mulliken.py".

However, it gives an error message:
---------------------------------------------------
Traceback (most recent call last):
  File "mulliken.py", line 6, in <module>
    mulliken_up = mulliken_pop.atoms(0)
AttributeError: 'list' object has no attribute 'atoms'
Traceback (most recent call last):
  File "mulliken.py", line 6, in <module>
    mulliken_up = mulliken_pop.atoms(0)
AttributeError: 'list' object has no attribute 'atoms'
----------------------------------------------------------------

Can you let me know what the problem is? Why does it say that there exist no attribute 'atoms'? What's wrong with this?
I am pretty new for ATK2011.02.


4
General Questions and Answers / "new" Nanolanguage for "calculateProjectedHamiltonianEnergySpectrum()" ??
« on: April 25, 2011, 14:42 »
I am trying to switch over to ATK 2011.02 from 2008.10.

For that, I want to know what is the "new" Nanolanguage for "calculateProjectedHamiltonianEnergySpectrum()" in ATK 2008.10 ?

I cannot find it.

5
General Questions and Answers / total Charge is not conserved in two probe SCF calculation
« on: April 9, 2011, 04:05 »
Hi!

I am making two probe calculations using atk2008.10.

In one of them, I find that the SCF calculation at zero bias gives
 
 q =  412.42189 e  Etot = -2064.51856  ...... at the end of the convergence iteration.

However, the total # of electrons in the scattering region should be 413, and some electrons disappeared.
What is the problem here and how can I solve this problem?



6
General Questions and Answers / Possible Bug in the code: dips in the transmittance
« on: March 17, 2010, 10:04 »
Hi!

I have calculated the transmittance of (5,5) carbon nanotube at zero bias. The ATK version I used for that calculation is 2008.10.  See the file attached. There you can find that the transmiitance is zero at E = 0 (Fermi energy), which is certainly incorrect! It should be 2, since there are two conducting channels at the Fermi level. I addition, you will also find many dips at other energies in the plot. This is a problem.

I used 4-4-4 primitive cells in the left electrode, scattering region, and the right electrode. Since the lattice constant for a primitive cell along the tube axis is 2.45A, each region is 2.45*4 = 9.8A, which seems to be large enough to exclude any appreciable overlap between nonadjacent units. I used DZP basis set, and 80 k-points.

Please answer the following questions:

(1) Is  this problem fixed in the newer version, i.e., in version "2010.02 bug fixed release (= 2010_fixed)" ?
(2) In the quantumwise home page, you mentioned that

  As before noted for the 2009.11 release, ATK-DFT 2010.02 is not a complete replacement of ATK 2008.10, as it is still missing a few key features. Therefore it is considered an alpha-version, while VNL hereby is released in another beta-version.

Does this mean that you do not recommend to use 2010_fixed instead of 2008.10?

(3) Do you have any other suggestion to solve this probelm?

Thanks!

7
General Questions and Answers / How can I get rid of noisy dips in the tranmission curve?
« on: March 13, 2010, 03:06 »
Hi!

I have calculated the zero-bias tranmission for (5,5) carbon nanotube with a molecule adsorbed on it. I find many dips in the transmission. For example, you will find a dip which shows that the tranmittance is zero at E=0 (Fermi energy). I do not know if it is a noise or not. Is there any way in which I can check if it's noise?

I used 80 k-points, 300K, DZP basis set, and default values for other parameters.

For your convenience, I  attach the script for the cvalculation and the tranmission curve resulting from the calculation.

Thanks!

8
General Questions and Answers / Scientific questions regarding ATK
« on: February 27, 2010, 20:24 »
Hi

I have two scientific questions for ATK.

(1) ATK does not take into account the energy dissipation. An incoming electron from an electrode preserves the same energy until it enters the other electrode. Does ATK assume that energy of hot electons are disspated after it enters there?

(2) Does ATK have the term in the Hamiltonian for electrons which explicitly depend on the applied E-field so that Stark effect is correctly treated?

I would appreciat you if you could answer these questions.

Thanks.


9
General Questions and Answers / the bulk density of states (DOS) for 1D system?
« on: December 16, 2009, 23:12 »
Hi!

Do you have a script to calculate 1-dimensional bulk density of states (DOS)? I find that you've written a script for 3D DOS, but not for 1D.

Thanks!

10
General Questions and Answers / Is Milliken Charge transfer physically correct?
« on: December 6, 2009, 00:12 »
Hi
 
With density matrix option, I made I(V)  claculation for a perfect Au(111) wire, which is composed of [3,4,3] layers in [left electorde, scattering region, right electrode] and each layer consits of 7 atoms.

I find that total Mulliken charge decreases from 923.99 to 923.89 when V changes from 0.1 to 0.6 Volt. I wonder if this much decrease (= 0.1) at 0.6V is physically correct or meaningless. namely, is charge transfer really involved at 0.6V from the scattering region to the electrode for this perfect Au wire?

Thanks 

11
General Questions and Answers / 'constraint DensityMatrix' for Voltage drop
« on: December 2, 2009, 20:36 »
In the past question, I found that I need to use 'constraint DensityMatrix' means for the voltage drop calculation.
I do not know what it means.

(1) How and where do I use the new "constraint DensityMatrix" to calculate potential drop? Can anyone give me an example of the python script for it ? In which ATK command is it used?

(2)  Do I also need to use the 'constraint DensityMatrix' to calculate the effective potential itself ?

Thanks!

12
General Questions and Answers / Is MPSH energy given w.r.t. the average fermi energy?
« on: November 30, 2009, 06:04 »
Hi

Is MPSH energy returned from "calculateProjectedHamiltonianEnergySpectrum()" function defined w.r.t the average fermi energy of the electrode at a given bias, so that energy zero means the fermi level ? I once checked this long time agao, but I forgot what it was. I want to make sure this.

Thanks

13
General Questions and Answers / Convergece problem in tw probe calculation
« on: November 17, 2009, 03:46 »
Hi

I am trying to calculate I-V characteristics for a two-probe system of an organometallic molecule between Au111 wires. I used PBE XC functional. I was able get the curren I between -1.5 < V < 1.6 Volt. I want t extend the caculation at least up to +2.5V and down to -2.5V.

(1) For this, I have tried to calculate the current gradually lowering temperature from a high (say, > 1000K) T to 300K at several steps. That does not work and scf calculton diverged when V >= 1.6 or V <= -1.5. It even diverges at a very high Temp !

(2) I also tried to adjust mixing parameter (from 0.1 to 0.05) and history steps, which do not solve the problem.

Can you give me a suggestion to this probelm?


14
General Questions and Answers / charge density rho(x,y,z) at an external bias??
« on: November 7, 2009, 23:32 »
Hi!

I wonder how I can get the numerical values of charge density rho(x,y,z) in the scattering region as a function of x, y, z  or rho(z) along the current flow at a specific external bias.

I would appreciate you if somebody can answer this question.

15
General Questions and Answers / Two Questions for calculateDenistyOfStates() function
« on: November 7, 2009, 02:48 »
Hi!

I have difficulty in understanding the parameters of calculateDenistyOfStates(self_consistent_calculation, energies,.......) function.
Here, does 'energies' argument mean energy interval in which DOS is calculated?

As an example,

density_of_states= calculateDenistyOfStates{
 self_const_cal = scf,
 energies = [0.*electronVolt]
}
energies2 = density_of_states.energies()
dos = density_of_states.densityOfStates()


.....

You wil  find that there are two 'energies' in the above example: One  (i.e., 'energies') for a paramater for calculateDenistyOfStates() function, and the other (i.e., 'energies2') is a method of the output of the function.

For this, I have two questions:


(1) How are thoe two energies different?
(2) How do I specifiy energy range in which DOS is to be calculated? For example, if I want to calculate DOS in (=-10, 2)eV at every 0.01eV, how can I achieve it?

I appreciate if somebody can give me an answer to this question.

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