Messages

1

General Questions and Answers / Distinguishing branches of phonon dispersion exported to .txt file

« on: May 9, 2017, 07:56 »

Dear all,

I calculated phonon dispersion of graphene and exported data to .txt file. (attached .txt file)
In the .txt file, data are separated and labeled as "Band0"~"Band5", and I plotted them. (attached .jpg file)
In the graph, 6 different colors are corresponding to "Band0"~"Band5".

However, I want the data points to be distinguished by phonon modes (LA,TA,ZA,LO,TO,ZO),
so that 6 different colors represent each phonon mode and phonon branches with different colors can cross each other.

How can I do that?
Any advice would be appreciated.

2

General Questions and Answers / Re: Error message: "unknown software exception" when using larger # of processors

« on: February 23, 2017, 03:41 »

The script you attached works if executed in serial and in parallel. A few comments:
- The chosen convergence threshold for the unit cell stress is 0.001 GPa, which is extremely low (below the level on numerical noise). This causes the geometry optimization algorithm to take many more steps than needed. I suggest to increase that tolerance to 0.01 GPa, which is still very low, so that only 4 BFGS steps are needed. The full calculation then finishes in 10 seconds if executed in serial!
- Your graphene unit cell is small, and the chosen ATK-DFT calculator settings are not "heavy". There is therefore no need for advanced MPI parallelization with odd numbers of processes. As mentioned above, the calculation should not take much more than 10 seconds if executed in serial on a modern laptop.

Oh, it seems my unit cell stress setting was too high. The calculation is finished in a few seconds. Thanks a lot!

3

General Questions and Answers / Re: Error message: "unknown software exception" when using larger # of processors

« on: February 20, 2017, 07:20 »

And one more thing, I do not get this error message when I'm running other python scripts.
Somehow, the attached .py file might have problem.

4

General Questions and Answers / Re: Error message: "unknown software exception" when using larger # of processors

« on: February 20, 2017, 07:10 »

You may run out of memory... You really have 28 cores on that Windows machine? How much RAM?

My windows machine has 56 cores (in 2 sockets) and my ATK licence is for 28 cores (to meet a budget)
In case of RAM, I have 128GB in total.
And when running calculation, the amount of memory usage is only about 10~15GB

5

General Questions and Answers / Error message: "unknown software exception" when using larger # of processors

« on: February 17, 2017, 05:28 »

Dear All,

My calculation is optimizing the structure of graphene, and "the number of k points" are 85.
I'm trying to compare the time taken for calculation when "the number of processors" are 5 and 17 (I have 28 processors in total).

I got the calculation result when using 5 processors,
but I got the error message ".... unknown software exception (0xc000417)......" when using 17 processors.
(please see the attached img file. Error message is written in Korean partially, but I hope you can guess.)

I do not get this error message when the number of processors is below 8,
but when the number of processor is more than 8, say "N" number of processors,
N-8 number of atkpython.exe is forcibly closed about 1 minute after starting calculation.

Please help me solving this problem.
Thank you in advance.

6

General Questions and Answers / Re: Change in "number of processors per kpoint" doesn't seem to be applied.

« on: February 17, 2017, 04:42 »

Thank you for your reply
It really helps.

7

General Questions and Answers / Change in "number of processors per kpoint" doesn't seem to be applied.

« on: February 16, 2017, 10:39 »

Dear all,

I'm a quite new to VNL-ATK and I'm trying to optimize the structure of graphene.
I changed "number of processor per kpoint" from default value to 4 (using "scriptor" or "editor") and checked log file after calculation.
But in the log file, I got the warning message like below,

+------------------------------------------------------------------------------+
| DiagonalizationSolver parallelization report.                                |
+------------------------------------------------------------------------------+
| Total number of processes: 4                                                 |
| Total number of k-points: 85                                                 |
| Processes per k-point: 1                                                     |
| Number of process groups: 4                                                  |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| 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.             |
| 3 process(es) have fewer k-points assigned than others                       |
| and will be partially idle.                                                  |
+------------------------------------------------------------------------------+
| WARNING: Sub-optimal process distribution for the DiagonalizationSolver.     |
| Number of processes per k-point has been adapted for better performance.     |
| For an optimal process distribution, use 4 MPI process(es),                  |
| and set processes_per_kpoint=1                                               |
+------------------------------------------------------------------------------+

Calculation is finished anyway, but the changed value of "number of processors per kpoint" is not reflected.
Is this a bug or am I making mistake?
Any help or comments would be greatly appreciated.