[CP2K-user] [CP2K:19580] MOF optimization

[K.AK]

Dear cp2k experts

In addition, the cif  files have been attached below.

Please advice me what I should modify in the input file? 


Many thanks,
K.AK


2023年11月27日月曜日 9:13:32 UTC+9 K.AK:

> Dear cp2k experts
>
> Thank you for your reply, Gupta Dhananjay.
>
> I would try to change CIF to XYZ by mercury etc.software, and I simulated 
> it.
>
> Also, under previous conditions, SCF did not converge, and energy change 
> was approximately -1.0E-07-1.0E06.
>
> The input and output files (Default conditions & FULL_SINGLE_INVERSE )have 
> been attached below.
> Could you advice me what I should modify in the input file? Should I 
> change the cell structure and how do I modify it?
>
>
> Many thanks,
> K.AK
>
> 2023年11月27日月曜日 2:04:58 UTC+9 Gupta Dhananjay:
>
>> Dear K.AK,
>> If possible use any other software to change CIF to XYZ, sometimes VESTA 
>> gives wrong XYZ file (sometimes it happened with me while dealing with 
>> MOFs).
>>
>> Thanks 
>>
>> On Fri, 24 Nov, 2023, 21:10 K.AK, <kosh... at gmail.com> wrote:
>>
>>> Dear cp2k experts
>>>
>>> Thank you for your advice, Anton Lytvynenko.
>>>
>>> In this case, CIF file which I used was converted from real CIF to XYZ 
>>> coordinations by VESTA.
>>>
>>> UiO-66 was a miswritten, I would like to optimize different MOF 
>>> structure.
>>>
>>> Also, I have simulated MOF optimization under suggested conditions.
>>>
>>> But, the SCF did not converged for 400 cycles.
>>>
>>> Could you advice me what I should modify in the input file?
>>>
>>> The input and output files have been attached below.
>>>
>>> Many thanks,
>>> K.AK
>>>
>>> 2023年11月24日金曜日 0:27:52 UTC+9 Anton Lytvynenko:
>>>
>>>> Dear K.AK,
>>>> Am 23.11.2023 um 15:04 schrieb K.AK:
>>>>
>>>> Also, this is a general question, but what should I do if the 
>>>> calculation does not converge in the periodic boundary calculation?
>>>>
>>>> I wonder if this question can be answered shortly and via definitive 
>>>> set of instructions, it worth a long manual addressing various sources of 
>>>> the solution instability.
>>>>
>>>> In your case, you should first start with OT optimizer, it is quite 
>>>> robust algorithm and should converge reasonably for your system. 
>>>>
>>>> If you see any problems, try to check your geometry first - it can be 
>>>> tricky to prepare input files from real CIF data for a number of reasons. 
>>>> If there are still problems, please show us the problematic output.
>>>>
>>>> By the way, UiO-66 is a Zr MOF, isn't it? But I can't see Zr atoms in 
>>>> your input. Is it correct?
>>>>
>>>> Yours,
>>>>
>>>> Anton
>>>>
>>>>
>>>> 2023年11月23日木曜日 22:53:56 UTC+9 Jürg Hutter:
>>>>
>>>>> Hi 
>>>>>
>>>>> Use GPW not GAPW for this setup. 
>>>>> Use DZVP-MOLOPT-SR-GTH for all elements (SR!) 
>>>>>
>>>>> regards 
>>>>> JH 
>>>>>
>>>>> ________________________________________ 
>>>>> From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of 
>>>>> K.AK <kosh... at gmail.com> 
>>>>> Sent: Thursday, November 23, 2023 2:48 PM 
>>>>> To: cp2k 
>>>>> Subject: Re: [CP2K:19556] MOF optimization 
>>>>>
>>>>> Thank you for your helps, Anton Lytvynenko and Jürg Hutter. 
>>>>>
>>>>>
>>>>> Following your advices, I have reviewed the calculation conditions. I 
>>>>> have created a new input file, and Could you please verify this? 
>>>>>
>>>>> I would proceed with the calculation under these conditions. Now, the 
>>>>> calculation time is approximately 120 s per step. 
>>>>>
>>>>> Also, this is a general question, but what should I do if the 
>>>>> calculation does not converge in the periodic boundary calculation? 
>>>>>
>>>>>
>>>>> Many thanks, 
>>>>>
>>>>> K.AK 
>>>>>
>>>>> 2023年11月23日木曜日 22:07:19 UTC+9 Jürg Hutter: 
>>>>> Hi 
>>>>>
>>>>> a few general remarks: 
>>>>>
>>>>> For the use of hybrid functionals in PBC, you should use an 
>>>>> interaction 
>>>>> potential with a cutoff (6 Angstrom should be ok). 
>>>>>
>>>>> Make sure that you have enough memory to keep the integrals in core 
>>>>> (print HF_INFO, set MEMORY). 
>>>>>
>>>>> EPS_SCHWARZ can most likely be set to 1.E-08. 
>>>>>
>>>>> Restart from a GGA wavefunction and set SCREEN_ON_INITIAL_P true. 
>>>>>
>>>>> EPS_DEFAULT 1.E-10 is most likely good enough. 
>>>>>
>>>>> Don't set EPS_FIT and EPS_PGF_ORB, defaults will be good enough. 
>>>>> Ignore the HFX warning about occupation or follow advice in comment. 
>>>>>
>>>>> REL_CUTOFF should be 60 
>>>>>
>>>>> GAPW with 6-31G basis might not be a good choice. Consider GPW/MOLOPT 
>>>>> basis sets. In the latter case use ADMM! 
>>>>>
>>>>> For MOFs I would advice to use vdW corrections. 
>>>>>
>>>>> I don't know what the reason behind the fixed K atom is. But this will 
>>>>> cause 
>>>>> convergence problems in the geometry optimization. It might also 
>>>>> interfere with CENTER_COORDINATES (why use it for a periodic system?). 
>>>>>
>>>>> regards 
>>>>> JH 
>>>>>
>>>>> ________________________________________ 
>>>>> From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of 
>>>>> K.AK <kosh... at gmail.com> 
>>>>> Sent: Thursday, November 23, 2023 10:10 AM 
>>>>> To: cp2k 
>>>>> Subject: [CP2K:19549] MOF optimization 
>>>>>
>>>>> Dear experts, 
>>>>>
>>>>> I try to optimize MOF structure by performing periodic DFT 
>>>>> calculations. 
>>>>>
>>>>> I have performed the calculations under the periodic conditions of the 
>>>>> attached input file. 
>>>>>
>>>>> But, the computation time is very long and the convergence is not 
>>>>> good. 
>>>>>
>>>>> Please advise about the cp2k simulation method and input file. 
>>>>>
>>>>> The input files have been attached below. 
>>>>>
>>>>>
>>>>> Many thanks, 
>>>>> K.AK 
>>>>>
>>>>> -- 
>>>>> 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/ac837fd8-7833-4871-a8b1-acf6099ccee5n%40googlegroups.com
>>>>> <
>>>>> https://groups.google.com/d/msgid/cp2k/ac837fd8-7833-4871-a8b1-acf6099ccee5n%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<mailto:
>>>>> cp2k+uns... at googlegroups.com>. 
>>>>> To view this discussion on the web visit 
>>>>> https://groups.google.com/d/msgid/cp2k/0c14f2c9-3fe3-441b-853c-ef037665fdbcn%40googlegroups.com
>>>>> <
>>>>> https://groups.google.com/d/msgid/cp2k/0c14f2c9-3fe3-441b-853c-ef037665fdbcn%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/9ba670b6-c5bc-4b0e-89c9-d6db28733753n%40googlegroups.com 
>>>> <https://groups.google.com/d/msgid/cp2k/9ba670b6-c5bc-4b0e-89c9-d6db28733753n%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/277b24d4-dca6-4ce7-b40d-cc9c14fcfe36n%40googlegroups.com 
>>> <https://groups.google.com/d/msgid/cp2k/277b24d4-dca6-4ce7-b40d-cc9c14fcfe36n%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/eb4d4887-20af-4045-a078-26caa727daf2n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20231126/924d2a40/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: cp2k.cif
Type: chemical/x-cif
Size: 4924 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20231126/924d2a40/attachment-0001.cif>