[CP2K-user] [CP2K:14828] Re: Conflict of results

[Sarah-K]

Hi there,
I'm a fresh user of CP2K. Planning to use it for MOFs cell optimizations. I 
have a basic/stupid question regarding the input file. If I wanna optimize 
the unit cell parameters, does the input file have to include all atoms in 
a unit cell, or I can minimize  the number of atoms in a way?

Thanks, S


On Sunday, February 28, 2021 at 9:44:51 PM UTC-5 Monu Joy wrote:

> Hi Leo
>
> Thanks for the help. I started a CASTEP calculation on the CP2K twisted 
> (relaxed) geometry and it converged as twisted, and this CASTEP relaxed 
> twisted geometry is more stable than the untwisted version by a factor of 
> 0.00030737 eV. Gamma point was used for both twisted and untwisted 
> calculations.
>
> Moreover, I have tried the CP2K calculation as you suggested to untwist 
> the geometry but it converged as twisted. I am using CP2K 7.1 and the only 
> change that I have made in the input was the removal of the following 
> lines:  
>
>         #COORD_FILE CP2K_Optimzed structure_CIF.cif
>         #COORD_FILE_FORMAT CIF
>
> Are there any significant changes between 7.1 and 8.1 in terms of dealing 
> with symmetry...?
>
> -Monu
>
> On Wed, Feb 24, 2021 at 3:50 AM Leopold Talirz <leo... at gmail.com> 
> wrote:
>
>> Hi Monu,
>>
>> thanks for following up - I did run a CP2K cell optimization starting 
>> from your relaxed "twisted" CP2K geometry. You find the trajectory and 
>> movie attached
>> Does this agree with your results?
>>
>> It certainly seems to "untwist" the ligands (see movie) - I had to stop 
>> the optimization at some point though because convergence became very slow.
>>
>> Some stats from the total energy:
>>
>> First total energy (single-point): -2160.041714658635101
>> First optimization step: -2160.136731180092738
>> 50th optimization step: -2160.2817551900 <(281)%20755-1900>
>> 100th optimization step: -2160.2996248085
>>
>> I.e. after the first "untwisting" that lowers total energy by  ~260mHa 
>> (quite significant), the final 50 steps lower the total energy by less than 
>> 3 mHa.
>> This is with cp2k 8.1 [2] and with minimal modifications to the input 
>> file (see tar file). It's not clear to me why you would get a different 
>> result - both MULTIPLE_UNIT_CELL 1 1 2 and 2 2 2 K-points should give this 
>> result.
>>
>> As to why the CASTEP gamma point calculation does not yield the twisted 
>> structure: it is possible that this involves breaking a symmetry that is 
>> for some reason preserved in the CASTEP calculation (don't know).
>> Can you try starting your CASTEP calculation from the twisted CP2K 
>> geometry and see where it ends up?
>> If it remains twisted, you can then compare total energies to the 
>> untwisted result, which should tell you which one is the actual minimum.
>>
>> Best,
>> Leo
>>
>> [1] Try  "grep i 925-pos-1.xyz" on the trajectory
>> [2] Our previous calculations were with cp2k v5.1 though.
>>
>> On Tuesday, 23 February 2021 at 05:45:09 UTC+1 Monu Joy wrote:
>>
>>> Even though the doubling of the z-axis (MULTIPLE_UNIT_CELL 1 1 2) seemed 
>>> fine in the initial cycles, it ended up being twisted on convergence. Then 
>>> I have tried the K-point scheme (SCHEME MONKHORST-PACK 2 2 2), where the 
>>> result was the same, twisted. However, the structure seems reasonable (no 
>>> twisting) in CASTEP even with the gamma point.
>>>
>>> But of course, the culprit could be the small z-axis, but I am not sure 
>>> how to tackle this in CP2K.
>>>
>>> -Monu
>>>
>>>
>>> On Friday, 19 February, 2021, 05:25:24 pm GMT-5, Leopold Talirz <
>>> leo... at gmail.com> wrote: 
>>>
>>>
>>> Since Andres Ortega from our group noticed this with a similar Al MOF, I 
>>> just wanted to confirm:
>>>
>>> Thanks, Marcella, for the suggestions. I just increased the Z direction 
>>> by MULTIPLE_UNIT_CELL  1 1 2. Albeit it's not yet converged, the 
>>> intermediate geometries are reasonable (no twisting so far). 
>>>
>>> This is indeed the source of the issue here - doubling the cell along z 
>>> results in a reversal of the twisting of the ligands, even when starting 
>>> from the twisted geometry (I checked).
>>>
>>> In our case, the twisted structure was the correct minimum for the 
>>> unit-cell only calculation, with a substantially lower energy (~250meV per 
>>> twisted phenyl), while for the doubled cell the twisted structure was 
>>> slightly higher in energy (order of 10meV per twisted phenyl).
>>>
>>> This then re-raises the original question of the thread, which is why 
>>> CASTEP seems to yield a different result. I believe the answer is in the 
>>> CASTEP output:
>>>
>>>                            -------------------------------
>>>                               k-Points For BZ Sampling
>>>                            -------------------------------
>>>                        MP grid size for SCF calculation is  1  1  2
>>>                             with an offset of   0.000  0.000  0.000
>>>                        Number of kpoints used =             1
>>>
>>> CASTEP chooses a 2-kpoint grid along z (which reduced to just a single 
>>> k-point calculation through symmetry).
>>>
>>> From the CASTEP manual [1]:
>>>
>>> > For cubic cells and for the C direction of hexagonal cells the even 
>>> and odd grids for the Monkhorst-Pack scheme give the same number of 
>>> k-points. However, the even grid provides better sampling and will always 
>>> be used automatically under these conditions. This ensures that a good grid 
>>> with k-point separation at (or less than) the specified target can be 
>>> achieved more economically. As a consequence, such lattices may have much 
>>> finer separations than requested as odd grids have been excluded - even 
>>> though they would have been closer to the specified separation - and the 
>>> better even grids have been taken in preference.
>>>
>>> I suspect that forcing CASTEP to do a Gamma-point calculation would 
>>> result in the same twisting as seen in CP2K (in our case, we checked with 
>>> CRYSTAL).
>>> For our MOF, just to exclude any possibility of issues with OT, we also 
>>> tested this with DIAGONALIZATION and KPOINTS in cp2k and got the same 
>>> result as with the 1x1x2 supercell.
>>>
>>> The lesson is simply that ~6.5A can be too short along the direction of 
>>> these inorganic chains/rods in MOFs.
>>>
>>> Best,
>>> Leopold
>>>
>>> [1] 
>>> http://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/CASTEP.html#modules/castep/dlgcastepelecoptkpoints.htm?Highlight=monkhorst
>>>  
>>>
>>> -- 
>>> 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 cp... at googlegroups.com.
>>> To view this discussion on the web visit 
>>>
>>> https://groups.google.com/d/msgid/cp2k/a018da49-5c42-4ade-b9f5-1c1b68579a91n%40googlegroups.com 
>>> <https://groups.google.com/d/msgid/cp2k/a018da49-5c42-4ade-b9f5-1c1b68579a91n%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 cp... at googlegroups.com.
>>
> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/cp2k/1240ce91-eb54-48ff-9c13-0e4e1f6ce735n%40googlegroups.com 
>> <https://groups.google.com/d/msgid/cp2k/1240ce91-eb54-48ff-9c13-0e4e1f6ce735n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20210603/e0f079eb/attachment.htm>