[CP2K-user] [CP2K:16705] AIMD Simulation of water: Attn: Dvelopers

[Jürg Hutter]

Hi

from the release notes of Version 8.1 (Dec. 2020)

mGGA: Add stress tensor and fix bug (#1116)

regards

Juerg Hutter

________________________________________
From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Niharendu Choudhury <niharc2007 at gmail.com>
Sent: Monday, March 14, 2022 5:05 AM
To: cp2k
Subject: Re: [CP2K:16704] AIMD Simulation of water: Attn: Dvelopers

Dear Developers,
I am using cp2k-7.1.0 version and it is showing stress tensor, analytical, is not available for meta functional.
Does newer version contain stress tensor, analytical ?

As I mentioned I found with scan npt simulation is running too slowly to have a meaningful simulation run.

Any other help. See the inp and out file in my earlier post.

Best regards
Niharendu Choudhury


On Friday, March 11, 2022 at 11:47:27 AM UTC+5:30 Niharendu Choudhury wrote:
Dear users,
I am using cp2k-7.1.0 version and it is showing stress tensor, analytical, is not available for meta functional.
Does newer version contain stress tensor, analytical ?

As I mentioned I found with scan npt simulation is running too slowly to have a meaningful simulation run.

Any other help. See the inp and out file in my earlier post.

Best regards
Niharendu Choudhury

On Thursday, March 10, 2022 at 11:03:32 PM UTC+5:30 Niharendu Choudhury wrote:
Dear Lucas,
I tried with stress tensor, analytical, but gave error. Then I changed it to numerical. Regarding your other suggestions, I'll try
implementing then and update you the result. By the way, today I ran the same system in VASP with SCAN functional, it is running 50 steps
in 2 hours (i.e. 500 steps in 20 hrs) and the same 40 cores are used.
What should be the typical thermostat timeconand barostat timecon?
Regards
Nihar

On Thursday, March 10, 2022 at 1:14:58 AM UTC+5:30 Lucas Lodeiro wrote:
Hi Niharendu Choudhury,

If I understand correctly, your commented (!) lines are the PBE input which are changed for SCAN input. Taking this into account, the main change is the way you are calculating the stress tensor, analytically in PBE and numerically in SCAN. Numerical computation is in most cases a very demanding calculator in terms of time, due to it needs to run many static calculations (20) for each step/frame of MD to compute the stress tensor. If analytical stress tensor is available for SCAN functional, use it.
Also, you compute the energy of 4 lowest unoccupied orbitals per 10 MD frames, this uses an extra amount of time... if you do not need it, delete it to speed up your AIMD a little. Finally, your thermostat timecon and region is weird to me. First, usually the timecon of the thermostat is set to 1/10 of barosthat timecon. Secondly, for production MD the global region is the adequate, but to for equilibration MD molecule or even massive regions could be used, but with a little timecon, and then flip to global region for production MD.

Regards - Lucas


El mié, 9 mar 2022 a las 14:42, Niharendu Choudhury (<nihar... at gmail.com>) escribió:
Dear Experts,
I have tried to run 64 water molecules in a box of 12.24 Angstrom (bulk water)
using SCAN functional without vdW correction in NPT ensemble. Problem is, it is
taking long time to complete 1 MD step. For example, while running in 40 cores, it takes about 20 hours to
complete 10 MD steps (whereas in normal PBE calculation, it is more than 700 MD steps
running in the same number of cores in 20 hours). I have attached the .inp as well as output file for the same.
Please go through these files and point out if there is any mistake or any modification by which I can make it run faster.

Hoping to get encouraging reply.

Best regards
Niharendu Choudhury

On Monday, March 7, 2022 at 9:45:25 AM UTC+5:30 Niharendu Choudhury wrote:
Thanks Prof. Kühne  for your valuable comments.

Regards
Niharendu Choudhury

On Sunday, March 6, 2022 at 9:38:04 PM UTC+5:30 tkuehne wrote:
Dear Niharendu Choudhury,

the bare SCAN functional (without Grimme’s dispersion correction) is able to reasonable well describe intermediate-ranged vdW interactions.
A manifestation of that is the particle density is already rather well reproduced contrary to most other semi-local XC functional. Since IMHO,
the impact of Grimme’s dispersion correction is mainly on water’s density, it’s relevance when using the SCAN functional and obviously also
for NVT simulations is much reduced. The good agreement with joint x-ray/neutron diffraction experiments, however, is mainly due to the use
of elevated temperature, which is rather well known to mimic nuclear quantum effects.

Greetings,
Thomas Kühne

Am 06.03.2022 um 08:41 schrieb Niharendu Choudhury <nihar... at gmail.com>:

Thanks Prof. Hutter for your interesting reply. My basic question is whether vdW correction  is required at all with the SCAN
functional? Why I am asking this is because, even without using vdW correction, SCAN gives (see  PNAS 114, 10846-10851 (2017)) exceptionally
good g(r) and other properties of water at 330K.

Isn't it that SCAN already includes vdW correction  required for at least water an aqueous systems?
Please comment.

Best regards
Niharendu Choudhury

On Friday, March 4, 2022 at 2:32:08 PM UTC+5:30 jgh wrote:
Hi

There are by now many variations of the SCAN functional, some use an empirical vdW correction,
some don't. Many different variations have already be used for water simulations.
You need to go through the literature and pick the one you prefer.

regards

Juerg Hutter

________________________________________
From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Niharendu Choudhury <nihar... at gmail.com>
Sent: Friday, March 4, 2022 7:59 AM
To: cp2k
Subject: [CP2K:16665] Re: AIMD Simulation of water

Any update about using following vdW potential with scan functional and scan PP?

&vdW_POTENTIAL
Dear All Experts,

DISPERSION_FUNCTIONAL PAIR_POTENTIAL

&PAIR_POTENTIAL

R_CUTOFF 40.0

TYPE DFTD3

D3_SCALING 1.0 1.324 0.0

PARAMETER_FILE_NAME dftd3.dat

! REFERENCE_FUNCTIONAL SCAN

&END PAIR_POTENTIAL

&END vdW_POTENTIAL


Please comment if it is okay or any better way dir vdW is required for water with SCAN?

Best regards

Niharendu Choudhury




On Tuesday, March 1, 2022 at 1:55:09 PM UTC+5:30 Niharendu Choudhury wrote:

Dear All Experts,
For bulk water I want to use GPW with SCAN and SCAN optimized pp as found at
https://github.com/juerghutter/GTH/blob/master/SCAN/POTENTIAL.

What should be the vdW potential? Is the following ok?

&vdW_POTENTIAL

DISPERSION_FUNCTIONAL PAIR_POTENTIAL

&PAIR_POTENTIAL

R_CUTOFF 40.0

TYPE DFTD3

D3_SCALING 1.0 1.324 0.0

PARAMETER_FILE_NAME dftd3.dat

! REFERENCE_FUNCTIONAL SCAN

&END PAIR_POTENTIAL

&END vdW_POTENTIAL


Please comment if it is okay or any better way dir vdW is required for water with SCAN?

Best regards

Niharendu Choudhury


On Thursday, February 17, 2022 at 2:51:45 PM UTC+5:30 Niharendu Choudhury wrote:
Thanks Ivan, for your prompt help and for referring to such an excellent review, which currently I am going through.
I'll try to run with SCAN and if any further difficulty appears, I will write to the list again.

Best regards
Niharendu Choudhury

On Wednesday, February 16, 2022 at 12:21:05 PM UTC+5:30 igladi... at gmail.com wrote:
Hi
yes CP2K with SCAN is possible, see

https://groups.google.com/g/cp2k/c/hKU0yMZXzfU/m/HxaWxHx9BwAJ

There are also the pseudopotential for SCAN

https://groups.google.com/g/cp2k/c/k0M3XuOdIHI/m/TEeDFRMwAAAJ

Regarding DFT for water, you can start from here

https://doi.org/10.1063/1.4944633

Hope it helps

Ivan


On Tuesday, February 15, 2022 at 2:47:00 PM UTC+3 nihar... at gmail.com wrote:
Dear experts,
I found (PNAS 114, 10846-10851 (2017)) that SCAN (strongly constrained and appropriately normed) functional is very good for water properties. Do we have this option in CP2K?

Can anybody suggest me (any review or so) regarding which functional is the best for water simulations?

Warm regards
Niharendu Choudhury

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==============================
Thomas D. Kühne
Dynamics of Condensed Matter
Chair of Theoretical Chemistry
University of Paderborn
Warburger Str. 100
D-33098 Paderborn
Germany
thomas... at upb.de
+49/(0)5251/60-5726<tel:+49%205251%20605726>


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