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

[Yun An]

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 <tku... at gmail.com> 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 <anyu... at gmail.com>:
>
> 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 <tku... at gmail.com> 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 <anyu... at gmail.com>:
>>
>> 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
>> tdku... at mail.upb.de
>> +49/(0)5251/60-5726
>>
>>
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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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