[CP2K-user] [CP2K:16695] AIMD Simulation of water

Niharendu Choudhury niharc2007 at gmail.com
Fri Mar 11 06:17:26 UTC 2022
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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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>>>>>> <
>>>>>> https://groups.google.com/d/msgid/cp2k/37d17193-3905-4185-94a9-4f43376a7c09n%40googlegroups.com?utm_medium=email&utm_source=footer>. 
>>>>>>
>>>>>>
>>>>>
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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 <+49%205251%20605726>
>>>>>
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>>> .
>>>
>>

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