[CP2K-user] [CP2K:19834] Help: cp2k vibration analysis stopped in the middle, how to renew the calculation?

Mikhail Povarnitsyn povarnitsynme at gmail.com
Sun Jan 28 23:31:31 UTC 2024

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Dear Leili,

Sorry for the late reply. Two files for you version 2022.1 are attached.
You have to make substitution into src/motion and recompile the code:
make ARCH=local VERSION="psmp".

To specify the range of atoms to shift from equilibrium positions, just add
the keywords START_ATOM_ID and END_ATOM_ID:

&VIBRATIONAL_ANALYSIS
DX 0.005
START_ATOM_ID 1
END_ATOM_ID 100
.....................
.....................

For instance, you can split the task of 600 atoms into 6 parts
1-100,101-200, etc and then gather the force derivatives into the dynamical
matrix.
If you need further assistance, please let me know.

Best regards,
Mikhail

On Wednesday, January 3, 2024 at 4:47:41 AM UTC+1 Leili Rassouli wrote:

Thank you, Eric. I made a new inquiry.

On Tuesday, January 2, 2024 at 1:50:00 PM UTC-5 Eric Patterson wrote:

Dear Lili,

I suggest you make your TDDFT inquiry a new thread since it is a separate
issue. I have no experience with TDDFT in CP2K, so I’m afraid I’m of no use
in this case..

Best,
Eric

On Jan 2, 2024, at 1:34 PM, Leili Rassouli <rassoul... at gmail.com> wrote:

Dear Mikhail and Eric,

Thank you for your responses. My job is completed after 10 days, but to
enhance the computational efficiency, I am considering the use of a
mode-selective method or the dividing the full range into several parts to
potentially expedite the calculation process. Mikhail, I would be
appreciative if you could provide me access to the source files, given that
I am currently utilizing CP2K v2022.1.

I'm currently facing an issue with negative frequencies. While using the
ground state wavefunction in the ground state geometry, frequencies are
positive and within the expected range. However, switching to the first
excited wavefunction yields a significant number of negative frequencies.

Enclosed is my input file for 221 supercells of Fe2O3 with 120 atoms. Your
insights and recommendations on this matter would be greatly valued.

I've explored various parameters, including:

Adjusting the CUTOFF value of TDDFPT from 300 to 600 and 700
Refining the optimized geometry
Increasing the TDDFT convergence from 1.0e-5 to 1.0e-6 and 1.0e-7
Despite these efforts, a notable proportion of frequencies persist as
negative values.

I express my gratitude in advance for your time and assistance.

Best regards,
Lili

On Tuesday, January 2, 2024 at 11:21:34 AM UTC-5 Eric Patterson wrote:

Hello Lili,

I did do a little bit of testing of the mode-selective method vs the normal
method. The results are comparable if I choose all atoms and restart until
all modes are converged (or at least nearly so — I didn’t care vey much
about low energy modes).

However, I’ve also managed to compile a working MPI version on my HPC, so I
am able to run on enough nodes to get through a default vibrational
analysis before the queue kills the job.

Best,
Eric

On Dec 31, 2023, at 3:24 PM, Leili Rassouli <rassoul... at gmail.com> wrote:

Hi Eric,

I've faced a similar issue and was considering the approach you suggested.
Have you had a chance to try it, and does it work well in your case? Your
insights would be greatly appreciated.

Thank you for your assistance.
Lili Rassouli

On Friday, February 10, 2023 at 11:32:16 AM UTC-5 Eric Patterson wrote:

On a closely-related note…

Since normal vibrational analysis is not restartable, but mode-selective
vibrational analysis is… Is there any drawback to using mode-selective and
choosing all atoms, and then restarting as necessary until all modes have
converged? Given the queue time limit imposed by my HPC resources, this
seems to me the only way to get the job done. Are there any pitfalls one
should bear in mind?

Thanks,
Eric

On Feb 9, 2023, at 6:03 AM, Krack Matthias <matthia... at psi.ch> wrote:

It is not possible to restart a vibrational analysis run. Such a
functionality is not implemented.

*From: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Zac
Smith <qingxi... at gmail.com>
*Date: *Thursday, 9 February 2023 at 02:54
*To: *cp2k <cp... at googlegroups.com>
*Subject: *[CP2K:18425] Help: cp2k vibration analysis stopped in the
middle, how to renew the calculation?
Hello cp2k users,
I used a virtual machine to do vibration analysis with cp2k, but the task
was killed when the hard disk was full, and the output file only contains
out, molden, cube, and the eig file of size 0. Can the calculation be
continued in this case?
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<Fe2O3_vib.inp>

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