[CP2K-user] [CP2K:16687] AIMD Simulation of water

[Lucas Lodeiro]

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 (<niharc2007 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
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