Can CP2K fixed part of atoms when perform CI-NEB?

Matthias Krack matthia... at psi.ch
Tue Nov 8 17:33:25 CET 2016


Hi

I did not suggest to perform a QM/MM at all. Your original request referred 
to a TS seach using the CI-NEB method. I just suggested to use DIIS and not 
MD for the BAND optimisation to determine the minimum energy path for your 
reaction at 0K, i.e. excluding temperature effects. The CP2K reference 
manual provides links to the publications the NEB implementation is based 
on. These references should also be printed at the end of each CP2K output.

Best regards

Matthias

On Tuesday, 8 November 2016 16:32:49 UTC+1, J. Ye wrote:
>
> Hi Matthias, 
>
> I am working on a catalyst material that has metal nanoparticles supported 
> on a porous material.  This porous material which is a big system that has 
> about 600 atoms, however the catalytic reaction process only on the metal 
> clusters. We want to study the effect of the pore size on the catalytic 
> reaction. So I want to perform a periodic calculations and compare with 
> cluster model. If the barriers are similar, then I could perform for 
> cluster model instead. 
>
> Your suggestion is peroform QM/MM? 
>
> What's the difference between DIIS and MD? Why DIIS is more efficient? Do 
> you have any books or papers recommend for us to read? 
>
> Thanks very much!
>
> Best regards,
>  
> J. Ye
>
> On Tuesday, November 8, 2016 at 2:12:42 AM UTC-6, Matthias Krack wrote:
>>
>> Hi
>>
>> do you have any special reason to use the OPT_TYPE MD? Otherwise I 
>> suggest to try the default OPT_TYPE DIIS which should be much more 
>> efficient. Moreover, if you want to fix some atoms only because of the 
>> computational cost caused by the large size of your system then there will 
>> be most likely not much benefit doing so, because the forces for all atoms 
>> are calculated anyway and then set to zero for the fixed atoms afterwards. 
>> You should rather check if fixing atoms is really needed as a boundary for 
>> a realistic modelling of the reaction you are interested in.
>>
>> Best regards
>>
>> Matthias
>>
>> On Tuesday, 8 November 2016 07:01:18 UTC+1, J. Ye wrote:
>>>
>>>  Hi Fabio, 
>>>
>>> I indeed included both "ALIGN_FRAMES FALSE" and "ROTATE_FRAMES FALSE" in 
>>> my input(Please see the attachment). But I still found the atoms moves. The 
>>> methods we use are different. I don't know how does this affect the fixed 
>>> atoms. Do you have any idea? 
>>>
>>> I have tested your input. Atom 1 and 3 indeed do not move. I also tried 
>>> to switch TI-NEB to CI-NEB, the atoms are not move. So this should not be 
>>> affected by BAND_TYPE. 
>>>
>>> Can any expert of CP2K give us some hints on this problem? 
>>>
>>> Thanks very much!
>>> Best,
>>>
>>> J. Ye
>>>
>>> On Monday, November 7, 2016 at 2:02:05 PM UTC-6, elb... at gmail.com 
>>> wrote:
>>>>
>>>> Hello J. Ye!
>>>>
>>>> Yes, I have checked. If you use only the constraint flag, indeed the 
>>>> fixed atoms move for the other images. But if you include both 
>>>> "ALIGN_FRAMES FALSE" and "ROTATE_FRAMES FALSE" flags in the BAND section, 
>>>> that does not happen anymore, at least in the calculations I have performed 
>>>> so far. Check for example the NEB input attached to this e-mail. It is very 
>>>> simple and it runs very fast (it has no meaning, it is just an example), 
>>>> but you can check that atoms 1 and 3, that are asked to be fixed, do not 
>>>> move for all NEB images. Let me know if you get the same behavior as me!
>>>>
>>>> All the best!
>>>>
>>>
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