[CP2K-user] [CP2K:12023] PIMD with CP2K

[Jinggang Lan]

Constraint atoms lead to nonphysical velocity assignment. It has been fixed 
in I-PI but not in CP2K as Thomas mentioned.

On Monday, 12 August 2019 16:23:42 UTC+2, Yun An wrote:
>
> Dear Thomas,
>
> Thank you very much for the kind reply.  I tried with PINT module in cp2k, 
> the weird thing is,  I want to fix some atoms during the calculations, but 
> it seems that the "CONSTRAINT" section didn't work, because the atoms which 
> are supposed to be fixed moves a lot according to the structures it gives 
> out. Do you know what is the problem and how to fix it?
>
> I attached the input file, thanks a lot in advance.
>
> Best regards,
> Yun 
>
> Thomas Kühne <t... at gmail.com <javascript:>> 于2019年8月1日周四 下午10:55写道：
>
>> Dear Yun, 
>>
>> yes the trajectories of the individual beads are in H2O-pos-*-1.xyz, 
>> whereas the 
>> centroid, which corresponds to the center of mass of the closed 
>> ring-polymer made 
>> up of the imaginary-time replica, is in centroid-pos-1.xyz. 
>> Conceptually, conducting PIMD-based metadynamics should be rather 
>> straightforward, 
>> however, since there is some bookkeeping is necessary to apply the bias 
>> potential 
>> to the individual beads I suspect it not to directly work as is. Yet, via 
>> i-Pi v2 in conjunction 
>> with PLUMED it is advertised to work: 
>> http://ipi-code.org/assets/pdf/manual.pdf
>>
>> Best, 
>> Thomas
>>
>> Am 01.08.2019 um 19:19 schrieb Yun An <an... at gmail.com <javascript:>>:
>>
>> Dear Thomas,
>>
>> Thank you for the kind reply, it helps a lot. I still have some questions:
>>
>> I use 4 beads to test h2o molecule, is it means  the trajectory is 
>> represented by the average replica positions of each atom, in the current 
>> case, is the all the atom positions of these four H2O-pos-?-1.xyz file?
>>
>> Anther question is if I want to run MD simulations to see the quantum 
>> effects, for example, H2 and D2 diffusion in the metal surface, is it 
>> possible that cp2k combines PINT and metadynamics? Because the RUN_TYPE 
>> section to me is like either one can choose MD to perform normal MD or PINT 
>> to run PIMD, but not both at one calculations. So in such case, how should 
>> I consider quantum effects?
>>
>> Thank you again for your help.
>>
>> Best regards,
>> Yun 
>>
>> Thomas Kühne <t... at gmail.com <javascript:>> 于2019年7月31日周三 下午4:16写道：
>>
>>> Dear Yun, 
>>>
>>> you can indeed conduct PIMD using the CP2K built-in PINT module, or 
>>> using the driver mode 
>>> via the i-Pi program. The latter more functionality for more 
>>> sophisticated PIMD simulations, 
>>> though the former already permits to conduct all sort of conventional 
>>> PIMD simulations and has 
>>> the advantage of having everything in one package. 
>>> The centroid-pos-1.xyz contains not the coordinates of every bead, but 
>>> only the ones of the centroid, 
>>> i.e. the center of mass of the closed ring-polymer. The 
>>> centroid-vel-1.xyz contains the corresponding 
>>> velocities, but be aware that except the when centroid molecular 
>>> dynamics is used, the dynamics of 
>>> the ring-polymer is unphysical, only static ensemble averages are. 
>>>
>>> Best, 
>>> Thomas
>>>
>>> Am 30.07.2019 um 18:39 schrieb Yun An <an... at gmail.com <javascript:>>:
>>>
>>> Dear all,
>>>
>>>
>>> I want to perform PIMD with cp2k, according to the manual, one can add a 
>>> PINT session to run path integral simulations; also, can use i-PI mode  
>>> DRIVER. What is the difference between those two, is that in principle they 
>>> both can do PIMD? I tried a H2O molecule with run_type of PINT, then I got 
>>> centroid-pos-1.xyz and centroid-vel.xyz, I thought the 
>>> centroid-pos-1.xyz  is the atom positions of each replica, but what is 
>>> the meaning of centroid-vel.xyz?  Also, I want to see the trajectories, 
>>> is this directly given in centroid-pos-1.xyz or one need to use some 
>>> script to transform, because from current centroid-pos-1.xyz , the 
>>> atoms are not quantum at all.
>>>
>>>
>>> Thank you all in advance for any help.
>>>
>>>
>>> Best regards,
>>>
>>> Yun
>>>
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>>> .
>>> <H2O-centroid-pos-1.xyz><H2O-centroid-vel-1.xyz>
>>>
>>>
>>>
>>>
>>> ==============================
>>> Thomas D. Kühne
>>> Dynamics of Condensed Matter
>>> Chair of Theoretical Chemistry
>>> University of Paderborn
>>> Warburger Str. 100
>>> D-33098 Paderborn
>>> Germany
>>> td... at mail.upb.de <javascript:>
>>> +49/(0)5251/60-5726
>>>
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>>> .
>>>
>>
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>> .
>> <H2O-pos-1-1.xyz><H2O-pos-2-1.xyz><H2O-pos-3-1.xyz><H2O-pos-4-1.xyz>
>> <h2o_test.inp>
>>
>>
>>
>>
>>
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>> .
>>
>
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