Messages

1

General Questions and Answers / Re: Fermi level position for a semiconductor (SnO2) as an electrode

« on: September 5, 2014, 11:00 »

I think this was a problem in 13.8 which is fixed in 2014. You should check that. But yes, if you use 13.8, the Fermi level will be in that position in the electrodes.

Update: Ok I see you did run 2014. Can you post the script, I think it's odd, the Fermi level should be in the middle of the gap. We can investigate a bit. But also try an odd k-point mesh - ATK doesn't have even Gamma-centered meshes, so if you exclude the Gamma point by using an even mesh, perhaps this can happen also...

Hi Anders,
Thank you very much for your reply.

You are right, when an odd k-point mech was used for SnO2, the Fermi level locates in the middle of the gap. It happens also in version 13.8.2

Best regards,
Qiang

2

General Questions and Answers / CPU still running after MPI job exited

« on: September 4, 2014, 17:18 »

Dear Experts,

Recently we encounter a problem when performing parallel ATK calculations. When the job does not finish successfully (be killed or exit due to time limit), it may leave all processes still running, and cause CPU overloading for the next job, no matter if it is an ATK job.

Could you please give us some advice to fix the problem? Thank you very much!
(Please find a job info in the attachment. A ATK job was killed due to convergence issue and then a VASP job started)

Best regards,
Qiang Fu

3

General Questions and Answers / Re: Fermi level position for a semiconductor (SnO2) as an electrode

« on: September 4, 2014, 16:30 »

I have seen this effect when you have too few k-points, try to increase that. Also, which version of ATK? We have improved the accuracy of the Fermi function in ATK 2014.

Hi, Anders,
Thank you very much for your reply.

We have performed a new calculation for SnO2 bulk, with an increased k-points grid (12x12x18, in previous calculation, it is 8x8x12), and the newest version (2014.c1, in previous calculation, it is 13.8 ). Both calculations give the same bandgap value. The only difference is that in the new calculation, the Fermi level locates a bit lower (0.136 eV below the conduction band minimum; in previous calculation, it is 0.054 eV below), but still around the conduction band minimum.

My question is: when the SnO2 bulk is used as an electrode, will the Fermi level locate at the same place, i.e. a bit below the conduction band minimum?

Thank you for the answer.
Best regards,
Qiang

4

General Questions and Answers / Fermi level position for a semiconductor (SnO2) as an electrode

« on: September 2, 2014, 15:00 »

Dear Experts,

I have a question about the Fermi level position for a semiconductor (SnO2) as an electrode.

For metallic system, the position of Fermi level is determined by the filling of electrons, since Fermi level crosses  the Density of State. For semiconductor, in principle, the position of Fermi level could be placed at any place between valence band maximum and conduction band minimum. But when the semiconductor is used as an electrode, its Fermi level should be equal to that of another electrode (a metallic system in our studies) when the bias is zero. In this case, the Fermi level position of the semiconductor is important.

From band structure calculations of SnO2 bulk, we found that the Fermi level of SnO2 is put at the conduction band minimum (in attached figure). Could you please tell me whether the Fermi level will be placed at the same position, i.e. the conduction band minimum of the electrode, in a transmission calculation (Bias = 0V)?

Thank you very much for your answer.

Best regards,
Qiang

5

General Questions and Answers / Re: Problem: Singular value decomposition failed

« on: July 23, 2014, 14:27 »

I'm not so sure about that. The abort of the MPIs is caused but the C++ runtime error, which is an unusual one. Try keeping a fixed value of the c parameter in the TB09 functional instead, and see if that helps. It would be most appropriate to do so anyway. The value should be found from the bulk calculation of the material, or the most important material in the system in case you have several.

Thank you very much for your suggestion, Anders. I did not have a good understanding until yesterday. Your advice is very insightful. Now I realize that our setting for mGGA calculations was not appropriate. We will make the correction.

6

General Questions and Answers / Re: Problem: Singular value decomposition failed

« on: July 16, 2014, 10:22 »

It seems like a network error.

Thank you very much 

7

General Questions and Answers / Problem: Singular value decomposition failed

« on: July 15, 2014, 10:18 »

Dear Experts,

We performed a mGGA(TB09LDA) calculation for the transport properties of a doped-semiconductor/metal interface. The basis set of the metallic element was set to be LDABasis.Element_DoubleZeta, while for other elements LDABasis.Element_DoubleZetaPolarized were used. The bias was set to be 1.0V(Left electrode: +0.5V and Right electrode: -0.5V).

In the calculation, the three parts: Left Electrode Calculation, Right Electrode Calculation, and Equivalent Bulk finished well. However, in the following part, we encounter the following error message:

in the output file:
--------------------------------------------------------------------------------
rank 15 in job 1  g071.dcsc.fysik.dtu.dk_39347   caused collective abort of all ranks
  exit status of rank 15: killed by signal 9
rank 13 in job 1  g071.dcsc.fysik.dtu.dk_39347   caused collective abort of all ranks
  exit status of rank 13: return code 134
rank 10 in job 1  g071.dcsc.fysik.dtu.dk_39347   caused collective abort of all ranks
  exit status of rank 10: return code 134
rank 9 in job 1  g071.dcsc.fysik.dtu.dk_39347   caused collective abort of all ranks
  exit status of rank 9: return code 134
rank 6 in job 1  g071.dcsc.fysik.dtu.dk_39347   caused collective abort of all ranks
  exit status of rank 6: killed by signal 9
rank 5 in job 1  g071.dcsc.fysik.dtu.dk_39347   caused collective abort of all ranks
  exit status of rank 5: return code 134
rank 3 in job 1  g071.dcsc.fysik.dtu.dk_39347   caused collective abort of all ranks
  exit status of rank 3: return code 134
rank 2 in job 1  g071.dcsc.fysik.dtu.dk_39347   caused collective abort of all ranks
  exit status of rank 2: return code 134
rank 0 in job 1  g071.dcsc.fysik.dtu.dk_39347   caused collective abort of all ranks
  exit status of rank 0: return code 134
--------------------------------------------------------------------------------

in the log.err file
-----------------------------------------------------------------------------------------------------------------------------------
** Back Engine Exception : Singular value decomposition failed
** Location of Exception : mathutils.cpp:870


/home/opt/common/QuantumWise/atk-13.8.0/atkpython/bin/atkpython: line 7:  7673 Aborted                 $EXEC_DIR/atkpython_exec $*
/home/opt/common/QuantumWise/atk-13.8.0/atkpython/bin/atkpython: line 7:  7670 Aborted                 $EXEC_DIR/atkpython_exec $*
-----------------------------------------------------------------------------------------------------------------------------------

Could you please give us some advice to fix the problem? Many thanks in advance.

It is worth noting that calculations at a lower bias is running well now (has not finished). In addition, calculation at the same bias (1.0V) but using PBE functional finished successfully.
We use Atomistix ToolKit 13.8.0 for our calculations.

Have a nice day!
Best regards,
Qiang