Messages

1

General Questions and Answers / Re: VNL 2016.3 stopped working - initializing shaders ....

« on: March 1, 2017, 15:47 »

The following message appeared when I started the vnl from terminal.


setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
setNativeLocks failed: Resource temporarily unavailable
.........
.........



HELP !

2

General Questions and Answers / Re: VNL 2016.3 stopped working - initializing shaders ....

« on: March 1, 2017, 13:30 »

I appreciate if anyone reply. This is very strange problem with VNL. I need it fixed very urgently.

3

General Questions and Answers / VNL 2016.3 stopped working - initializing shaders ....

« on: March 1, 2017, 11:47 »

Dear All,

I was working with VNL on my desktop yesterday when the Linux system of our institute crashed. When I came back this morning to use VNL, it is not opening.

It stopped at the point 'Initializing shaders .....'. 

I re-installed the VNL desktop, but I got the same problem.

Do you have any idea how to fix this problem? please reply.

Thank you
Yasheng

 

4

General Questions and Answers / Re: Extended Huckel Device calculation gets extremely slow

« on: December 12, 2016, 15:36 »

Yes. That is true. But I expected that Extended Huckel method can be much faster than DFT calculations. But it is super slow at this point, and I cannot see that EH is faster than DFT.

5

General Questions and Answers / Re: Extended Huckel Device calculation gets extremely slow

« on: December 12, 2016, 10:43 »

No, that is device calculation. No geometry optimization is performed in this calculation.

6

General Questions and Answers / Extended Huckel Device calculation gets extremely slow

« on: December 9, 2016, 15:31 »

Hi

I am doing some device calculations using extended huckel theory. It was pretty fast in the beginning, but it gets very slow after some time. See the energy below

|   0 E = -10007.2 dE =  2.372717e+00 dM =  3.881271e+00 dH =  2.766148e+00    |
|   1 E =  -9647.9 dE =  5.044531e-01 dM =  8.826795e-01 dH =  1.263772e+01    |
|   2 E = -9699.78 dE =  2.108909e-01 dM =  1.167843e+00 dH =  5.148475e+00    |
|   3 E = -9803.43 dE =  8.707716e-02 dM =  5.143593e-01 dH =  7.848367e-01    |
|   4 E = -9822.94 dE =  3.082800e-02 dM =  2.266662e-01 dH =  1.002323e+00    |
|   5 E = -9873.88 dE =  4.537150e-02 dM =  6.728930e-02 dH =  4.481365e-01    |
|   6 E = -9905.77 dE =  5.128498e-02 dM =  7.364029e-02 dH =  2.391064e-01    |
|   7 E = -9888.47 dE =  3.357228e-02 dM =  8.941489e-02 dH =  1.079357e-01    |
|   8 E = -9878.69 dE =  1.354342e-02 dM =  5.635861e-02 dH =  1.311752e-01    |
|   9 E = -9863.55 dE =  8.930520e-03 dM =  1.878326e-02 dH =  1.391255e-01    |
|  10 E = -9808.44 dE =  2.425624e-02 dM =  1.748760e-02 dH =  1.516485e-01    |
|  11 E = -9779.94 dE =  2.019184e-02 dM =  4.813811e-02 dH =  6.752169e-02    |
|  12 E = -9700.18 dE =  4.412686e-02 dM =  2.669891e-02 dH =  5.040059e-02    |
|  13 E = -9687.98 dE =  1.553101e-02 dM =  9.136254e-02 dH =  2.393973e-02    |
|  14 E = -9675.29 dE =  4.491408e-03 dM =  9.358001e-03 dH =  1.728568e-02    |
|  15 E = -9653.48 dE =  8.449555e-03 dM =  1.304811e-02 dH =  1.931539e-02    |
|  16 E = -9657.06 dE =  6.636468e-03 dM =  2.398464e-02 dH =  2.166887e-02    |
|  17 E = -9656.72 dE =  5.926826e-03 dM =  2.333166e-02 dH =  1.594946e-02    |
|  18 E = -9649.38 dE =  2.057189e-03 dM =  1.157775e-02 dH =  1.221886e-02    |
|  19 E =  -9649.8 dE =  9.569909e-04 dM =  8.755228e-03 dH =  1.364530e-02    |
|  20 E = -9650.44 dE =  4.131596e-04 dM =  2.258146e-03 dH =  8.320241e-03    |
|  21 E =  -9651.2 dE =  7.876470e-04 dM =  1.094355e-03 dH =  3.545779e-03    |
|  22 E = -9650.42 dE =  3.944362e-04 dM =  2.924421e-03 dH =  1.437835e-03    |
|  23 E = -9650.59 dE =  2.561794e-04 dM =  7.892831e-04 dH =  1.264300e-03    |
|  24 E = -9650.55 dE =  1.269612e-04 dM =  5.339099e-04 dH =  3.232002e-04    |
|  25 E = -9650.53 dE =  5.716055e-05 dM =  2.470325e-04 dH =  3.040669e-04    |
|  26 E = -9650.51 dE =  3.487375e-05 dM =  1.424110e-04 dH =  2.824968e-04    |
|  27 E =  -9650.5 dE =  3.046916e-05 dM =  9.223943e-05 dH =  1.448771e-04    |
|  28 E = -9650.49 dE =  4.055575e-05 dM =  1.324895e-04 dH =  1.066330e-04    |
|  29 E = -9650.49 dE =  3.746318e-05 dM =  1.685873e-04 dH =  4.697196e-05    |
|  30 E = -9650.49 dE =  7.948944e-06 dM =  3.468878e-05 dH =  1.020323e-04    |
|  31 E = -9650.48 dE =  7.207351e-06 dM =  2.625369e-05 dH =  7.815433e-05    |
|  32 E = -9650.47 dE =  9.508154e-06 dM =  2.164556e-05 dH =  3.843625e-05    |
|  33 E = -9650.47 dE =  1.048967e-05 dM =  5.130989e-05 dH =  3.154927e-05    |
|  34 E = -9650.47 dE =  5.263989e-06 dM =  2.555428e-05 dH =  1.370972e-05    |
|  35 E = -9650.47 dE =  1.897275e-06 dM =  1.002230e-05 dH =  1.006073e-05    |
|  36 E = -9650.48 dE =  9.147661e-07 dM =  5.963234e-06 dH =  7.529066e-06    |
|   0 E = -9972.47 dE =  2.396304e+00 dM =  3.882094e+00 dH =  3.051248e+00    |
|   1 E = -9664.55 dE =  5.067676e-01 dM =  8.794833e-01 dH =  1.228658e+01    |
|   2 E = -9735.68 dE =  2.127791e-01 dM =  1.179770e+00 dH =  5.818448e+00    |
|   3 E = -9873.96 dE =  1.056756e-01 dM =  5.449805e-01 dH =  9.256945e-01    |
|   4 E = -9900.72 dE =  4.139485e-02 dM =  2.481530e-01 dH =  1.154714e+00    |
|   5 E =  -9969.8 dE =  5.756637e-02 dM =  7.480533e-02 dH =  5.133595e-01    |
|   6 E = -9976.85 dE =  6.533643e-02 dM =  2.718134e-01 dH =  1.425417e-01    |
|   7 E = -9957.92 dE =  5.258978e-02 dM =  3.909658e-01 dH =  3.307109e-01    |
|   8 E = -9932.17 dE =  2.945179e-02 dM =  2.657950e-01 dH =  1.316867e-01    |
|   9 E = -9921.46 dE =  2.947370e-02 dM =  1.628053e-01 dH =  3.419604e-01    |
|  10 E = -9901.14 dE =  2.249100e-02 dM =  1.715336e-01 dH =  3.123765e-01    |
|  11 E = -9803.81 dE =  4.051056e-02 dM =  1.757609e-01 dH =  2.160042e-01    |
|  12 E = -9768.73 dE =  3.337533e-02 dM =  2.745907e-01 dH =  1.832847e-01    |
|  13 E = -9753.33 dE =  1.278105e-02 dM =  4.559303e-02 dH =  1.634954e-01    |
|  14 E = -9738.67 dE =  6.697541e-03 dM =  1.585258e-02 dH =  1.454397e-01    |
|  15 E = -9723.08 dE =  7.016223e-03 dM =  1.036462e-02 dH =  1.370453e-01    |
|  16 E =  -9710.5 dE =  8.441387e-03 dM =  1.674829e-02 dH =  1.278319e-01    |
|  17 E = -9711.24 dE =  1.103741e-02 dM =  3.331772e-02 dH =  9.347300e-02    |
|  18 E = -9710.51 dE =  1.430376e-02 dM =  5.546725e-02 dH =  3.832660e-02    |
|  19 E = -9705.64 dE =  1.043261e-02 dM =  5.771637e-02 dH =  2.055331e-02    |
|  20 E = -9704.09 dE =  1.517789e-03 dM =  7.250730e-03 dH =  1.422365e-02    |
|  21 E = -9704.25 dE =  6.092258e-04 dM =  4.573158e-03 dH =  8.808351e-03    |
|  22 E = -9703.45 dE =  5.262796e-04 dM =  3.780297e-03 dH =  1.060313e-02    |
|  23 E = -9702.27 dE =  7.224439e-04 dM =  2.300360e-03 dH =  7.719219e-03    |
|  24 E = -9701.98 dE =  9.999892e-04 dM =  6.052943e-03 dH =  1.106367e-03    |
|  25 E = -9701.86 dE =  1.693533e-04 dM =  6.722706e-04 dH =  8.378249e-04    |
|  26 E = -9701.77 dE =  2.337466e-04 dM =  8.310487e-04 dH =  7.761768e-04    |
|  27 E = -9701.79 dE =  1.500651e-04 dM =  1.362241e-03 dH =  1.280371e-03    |
|  28 E = -9701.73 dE =  2.289511e-04 dM =  1.569001e-03 dH =  2.215329e-04    |
|  29 E = -9701.74 dE =  5.490650e-05 dM =  3.694301e-04 dH =  1.984777e-04    |
|  30 E = -9701.74 dE =  2.505310e-05 dM =  1.249585e-04 dH =  1.533695e-04    |
|  31 E = -9701.75 dE =  1.905561e-05 dM =  5.049472e-05 dH =  1.232262e-04    |
|  32 E = -9701.74 dE =  2.630230e-05 dM =  1.329433e-04 dH =  5.317673e-05    |
|  33 E = -9701.74 dE =  1.562071e-05 dM =  5.118395e-05 dH =  5.218829e-05    |
|  34 E = -9701.75 dE =  1.263054e-05 dM =  7.951046e-05 dH =  6.459322e-05    |
|  35 E = -9701.75 dE =  7.727156e-06 dM =  3.191942e-05 dH =  3.316060e-05    |
|  36 E = -9701.75 dE =  5.153394e-06 dM =  3.623935e-05 dH =  1.594992e-05    |
|  37 E = -9701.75 dE =  2.231581e-06 dM =  1.423721e-05 dH =  1.180548e-05    |
|  38 E = -9701.75 dE =  1.755838e-06 dM =  5.739102e-06 dH =  6.154657e-06    |
|   0 E = -23987.4 dE =  2.594486e+00 dM =  3.881963e+00 dH =  1.677087e+01    |
|   1 E =   -24409 dE =  2.893981e-01 dM =  1.304877e+00 dH =  8.072611e+00    |
|   2 E = -24721.6 dE =  5.519631e-01 dM =  2.036661e+00 dH =  2.578159e+00    |
|   3 E = -24619.4 dE =  1.789553e-01 dM =  7.836281e-01 dH =  1.425827e+00    |


These highlighted steps are very slow. I noticed that there is the discontinuity in the energy here.

Let me know if you knw why this happens.

Thank you,
Yasheng

7

General Questions and Answers / Re: Huckel basis set

« on: December 5, 2016, 13:09 »

Thanks for your reply.

 For oxygen, only Hoffmann.Oxygen Huckel Basis set available. If we want to do calculations for oxides, we are restrained to use Hoffmann basis sets only, if we cannot mix different basis sets.

In my experience, Hoffman basis sets are giving wrong band gap. (I mean totally unreasonable)

8

General Questions and Answers / Huckel basis set

« on: December 2, 2016, 16:39 »

Hi All,

I have a question about Huckel basis set. is it ok to mix different Huckel basis sets in one calculation? for example, If I have copper and oxygen in my system, can I use Cerda.Copper and Muller.Oxygen ?

Thanks,
Yasheng

9

General Questions and Answers / Re: Polycrystal Builder

« on: December 2, 2016, 16:35 »

Thank you. the attached document helps a lot.

10

General Questions and Answers / Polycrystal Builder

« on: November 29, 2016, 13:25 »

Hi All,

I wonder if there is a detailed documentation/manual available for Polycrystal Builder. I know that there is only one tutorial is about how to use this tool.

Specifically, what is the seed file in Polycrystal builder ? how do we use it ?  what are Grid points and Jitter ?  etc

Thank you,
Yasheng

 

 

11

General Questions and Answers / Building grain boundaries

« on: October 10, 2016, 12:11 »

Hi,

I was wondering if VNL has any dedicated grain boundary builder Addon feature?  Something like this would be very helpful: https://staff.aist.go.jp/h.ogawa/GBstudio/indexE.html 


Regards,
Yasheng

12

General Questions and Answers / Re: number of K points vs number of cpus

« on: September 7, 2016, 11:58 »

That is more clear now. Thank you all.

13

General Questions and Answers / number of K points vs number of cpus

« on: September 3, 2016, 21:53 »

Hi All,

I am using 2016 ATK. In one of my calculation, the number or symmetry reduced k-points is 50, and I used 24 cpus for doing the calculation.

And I got this warning in my output file:

+------------------------------------------------------------------------------+
| DiagonalizationSolver parallelization report.                                |
+------------------------------------------------------------------------------+
| Total number of processes: 24                                                |
| Total number of k-points: 50                                                 |
| Processes per k-point: 1                                                     |
| Number of process groups: 24                                                 |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| WARNING: Sub-optimal distribution of processes over k-points.                |
| For optimal performance make sure the number of processes is                 |
| a multiple of the number of k-points times processes_per_kpoint.             |
| 22 process(es) have fewer k-points assigned than others                      |
| and will be partially idle.                                                  |
+------------------------------------------------------------------------------+


Does this mean that I am only using 2 cpus? and 22 others are idle and wasted?
Should I use 50 cpus for this calculation to do 1 cpu for 1 kpoint?   What if I don't have that many cpus available ?

Can you explain in detail how to do this and not wasting our time and computational resources?

Thank you,

Yasheng

14

General Questions and Answers / processes_per_kpoint in 2016 version

« on: August 25, 2016, 11:59 »

Hi,

In 2016 version, the default value of processes_per_kpoint=None. what does this setting mean? If we want to run parallel calculations, let say using 64 cpu, what should be the value of processes_per_kpoint ? 

Thank you,
Yasheng

15

General Questions and Answers / Re: "IndentationError: unexpected indent" with ATK 2016

« on: August 17, 2016, 11:45 »

That is a good news! I look forward the release of 2016.1 and fixing all these bugs.

I used OMX basis sets for my previous calculations, and I think I should probably stick to that for the sake of consistency.