[CP2K-user] [CP2K:14828] Re: Conflict of results
Sarah-K
sarah.kar... at gmail.com
Thu Jun 3 18:54:54 UTC 2021
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
>>>
>>>
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>>>
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