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Messages - jjhskang

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1
General Questions and Answers / Re: How can I interprete the result of Mulliken population analysis?
« on: November 10, 2011, 05:13 »
Yes, that for DZDP basis set.
So, do they represent 4d 5s 4d 5s .... in sequence ?

2
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   

3
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?

4
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.


5
General Questions and Answers / Re: "new" Nanolanguage for "calculateProjectedHamiltonianEnergySpectrum()" ??
« on: April 25, 2011, 14:46 »
It's very difficult to find a new nanolanguage for ATK2011.02 corresponding to that in ATK 2008.10. Where can I find it? Does anyone know ?

6
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.

7
General Questions and Answers / Re: total Charge is not conserved in two probe SCF calculation
« on: April 9, 2011, 04:14 »
(1) Is it because I have not included all the poles in the calculation?
I used the default value of  integral_lower_bound, i.e., 3eV.
 
(2) I believe that I have inlcuded farely large number of atoms in the scattering region in order to ensure completel screening in the scattering.

Quote from: jjhskang 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?




8
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?



9
General Questions and Answers / Re: Possible Bug in the code: dips in the transmittance
« on: April 10, 2010, 08:49 »
Hi

I found that (5,5) CNT has  10 atoms with the same z coordinates. In my old runs, some of their z coordinates are different by 0.001 or 0.002A. [In this case, note that coordinates for 4 cells which constitute the eelctrode  still have exact replication of those for the primitive cell.] Therefore, I reoptimized the structure with those z coordinates the same, which resulted in changes in only X and Y coordinates, leaving the Z coordinates the same one another. I guess that this is a well-known problem of the mimimizer when the number of atoms is large. Now, the zero transmittance at E = 0 is solved. However, there are still dips in other energies.

It seems that the transmittance is quite senstive to small errors in the coordinates.

10
General Questions and Answers / Re: Possible Bug in the code: dips in the transmittance
« on: April 4, 2010, 08:02 »
Hi!

If I look at Nori's python script, I find that he supplied very accurae atomic corrdinates. However, I usually do not use Nanoscript to build my python script, but rely on my own way of converting a pdb file(which is accurate up to 3 decial digits) whose coordinate are optimized using some other method to a pyton script.

One of the possible source of the problem could be the limited  number of digits in atomic coordinates. Do you agree with this? If then, I might have to device some other of writing the script which includes more than 3 decimal digits in the atmic coordinates.

Thanks!

11
General Questions and Answers / Re: Possible Bug in the code: dips in the transmittance
« on: April 4, 2010, 07:51 »
Hi

I used 80 and 200 k-points along the Z-axis, both of which give zero tranmittance at E = 0.
For your convenience, I attach three python scripts for that using 200 k-poinhts.

Youc an run

set_up.py -> scf_dm.py -> tspec_bias_0p0.py ins equence.

I hope to hear from you very soon.

Thanks!

12
General Questions and Answers / Re: Possible Bug in the code: dips in the transmittance
« on: April 2, 2010, 04:13 »
Hi!

It's possible that it is due to the number of k-points along the Z axis. I used 80 points, which might not be large enough to describe the band crossing at the Fermi level. I am currently running with more k-points.

13
General Questions and Answers / Re: Possible Bug in the code: dips in the transmittance
« on: April 1, 2010, 07:31 »
Hi

Following your suggestions in your previous reply to this question, I have calculated the transmission at zero bias using real_axis_infinitesial = 0.004eV (default = 0.01) at every 0.001eV (very cvompact !), again finding dips around E= 0!

Below you will find nunerical values for the trasnmissiona round E = 0.

--------------------------------------
           E(eV)            Transmittance
--------------------------------------
           -0.010          1.999754
           -0.009          1.999750
           -0.008          1.999745
           -0.007          1.999736
           -0.006          1.999719
           -0.005          1.999681
           -0.004          1.999502
           -0.003          0.000542
           -0.002          0.000044
           -0.001          0.000022
            0.000          0.000019
            0.001          0.000024
            0.002          0.000056
            0.003          0.003167
            0.004          1.999573
            0.005          1.999692
            0.006          1.999724
            0.007          1.999738
            0.008          1.999746
            0.009          1.999751
            0.010          1.999755
            0.011          1.999757
            0.012          1.999759
-----------------------------------------

Obviously something is wrong!
I hope that you could consider this problem serioulsy, checking possible bugs in the code.

I hope to hear from you very soon.

Thanks!

14
General Questions and Answers / Re: Possible Bug in the code: dips in the transmittance
« on: March 29, 2010, 08:14 »
Hi

I have made extensive calculations for pristine (5,5) CNT by changing the electrode length,  Lx, and the length of the scattering region. Lz = 2.45A for a primitive cell.

(a) 4-4-4 cells in the left electrode, scattering region, and the right electrode. Lx-Ly = 25A, Lz = 2.45*4
(b) 4-4-4 cells, Lx = Ly = 32A (much larger than that for (a)), Lz = 2.45*4
(c) 5-5-5 cells, Lx=Ly = 25A. Lz = 2.45*5

For all of the runs above, I still get a very sharp dip (Transmission = 0) in the transmission at E=0.

Also note that I find that T = 2.0 (correct answer) at E = 0.005 eV !!!

I guess I have tried all your suggestions in your previous reply,and I still get a wrong answer!

What can you suggest me next to get the right answer? Does't this mean that there's a bug in the code?
I hope that I would have your reply very soon.

Thanks!
 


15
General Questions and Answers / Re: Possible Bug in the code: dips in the transmittance
« on: March 18, 2010, 10:02 »
Some more questions:

(1) Does the size of the system along X and Y axes affect the computational time ? If I increase them, does the calcultion require much more CPU time? The CNT systems, i.e., both of pristine and CNT+molecule,  I have considere are alreay too big, which required more than three days for the calculation of zero-bias tranmittance only.

(2) That makes me hesitate to use larger supercell sizes of X and Y axes as well as using more atoms in the scattering region so that the perfect screening is guaranteed. Can you suggest me any possible solution for this kind of timing problem? How many cores of Zeon CPU would you recommend to use for the calculation of the zero-bias transmittance ?

(3)  Since dips at E=0 appears for both of pristine (5,5) CNT [which uses 4 prim cells for the scattering region] and CNT+molecule [which uses much longer tube for the scattering region], I doubt that the problem is originated from the short size of Lz for the scattering region. This is puzzling to me, unless this is due to the supercell-supercell interaction along X and Y axes.

Thanks!


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