[CP2K-user] [CP2K:16704] AIMD Simulation of water: Attn: Dvelopers

Niharendu Choudhury niharc2007 at gmail.com
Mon Mar 14 04:05:13 UTC 2022
Previous message (by thread): [CP2K-user] [CP2K:16695] AIMD Simulation of water
Next message (by thread): [CP2K-user] [CP2K:16705] AIMD Simulation of water: Attn: Dvelopers
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
 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 
>>>>>>>
>>>>>>> -- 
>>>>>>> You received this message because you are subscribed to the Google 
>>>>>>> Groups "cp2k" group. 
>>>>>>> To unsubscribe from this group and stop receiving emails from it, 
>>>>>>> send an email to cp2k+uns... at googlegroups.com<mailto:
>>>>>>> cp2k+uns... at googlegroups.com>. 
>>>>>>> To view this discussion on the web visit 
>>>>>>> https://groups.google.com/d/msgid/cp2k/37d17193-3905-4185-94a9-4f43376a7c09n%40googlegroups.com
>>>>>>> <
>>>>>>> https://groups.google.com/d/msgid/cp2k/37d17193-3905-4185-94a9-4f43376a7c09n%40googlegroups.com?utm_medium=email&utm_source=footer>. 
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> -- 
>>>>>> You received this message because you are subscribed to the Google 
>>>>>> Groups "cp2k" group.
>>>>>>
>>>>>> To unsubscribe from this group and stop receiving emails from it, 
>>>>>> send an email to cp2k+uns... at googlegroups.com.
>>>>>> To view this discussion on the web visit 
>>>>>> https://groups.google.com/d/msgid/cp2k/23a442ff-6c65-4a60-a8b6-54fbb79038f1n%40googlegroups.com 
>>>>>> <https://groups.google.com/d/msgid/cp2k/23a442ff-6c65-4a60-a8b6-54fbb79038f1n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>>> .
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ==============================
>>>>>> 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>
>>>>>>
>>>>>> -- 
>>>> You received this message because you are subscribed to the Google 
>>>> Groups "cp2k" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send 
>>>> an email to cp2k+uns... at googlegroups.com.
>>>>
>>> To view this discussion on the web visit 
>>>> https://groups.google.com/d/msgid/cp2k/d904de46-c6ed-4b52-a0a8-2ca871e1716cn%40googlegroups.com 
>>>> <https://groups.google.com/d/msgid/cp2k/d904de46-c6ed-4b52-a0a8-2ca871e1716cn%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/09e403d3-61cb-4887-8f87-3880c70cb210n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20220313/51975833/attachment-0001.htm>
Previous message (by thread): [CP2K-user] [CP2K:16695] AIMD Simulation of water
Next message (by thread): [CP2K-user] [CP2K:16705] AIMD Simulation of water: Attn: Dvelopers
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
More information about the CP2K-user mailing list