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

Chenghan lch0... at gmail.com
Wed Aug 26 20:07:28 UTC 2020


Hi,

This is Chenghan. Thank Thomas and Jinggang for the information. That's 
very helpful!
I also want to use PLUMED in PIMD. A question I have:
Does i-Pi act on the bias forces from PLUMED on the centroid position or 
treat each bead independently and calculate bias forces for each bead 
seperately?

Best Regards,
Chenghan

On Wednesday, August 14, 2019 at 7:52:24 AM UTC-5 Jinggang Lan wrote:

> 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> 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>:
>>>
>>> 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> 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>:
>>>>
>>>> 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
>>>>
>>>> -- 
>>>> 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 c... at googlegroups.com.
>>>>
>>>>
>>>> To view this discussion on the web visit 
>>>> https://groups.google.com/d/msgid/cp2k/3aa5af5d-4b37-471b-ae2b-18dc83d0b3b5%40googlegroups.com 
>>>> <https://groups.google.com/d/msgid/cp2k/3aa5af5d-4b37-471b-ae2b-18dc83d0b3b5%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>> <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
>>>> +49/(0)5251/60-5726 <+49%205251%20605726>
>>>>
>>>>
>>>> -- 
>>>> You received this message because you are subscribed to a topic in the 
>>>> Google Groups "cp2k" group.
>>>> To unsubscribe from this topic, visit 
>>>> https://groups.google.com/d/topic/cp2k/CKzhBph4yFc/unsubscribe.
>>>>
>>> To unsubscribe from this group and all its topics, send an email to 
>>>> c... at googlegroups.com.
>>>
>>>
>>>> To view this discussion on the web visit 
>>>> https://groups.google.com/d/msgid/cp2k/C543F0FA-BD29-4238-B04B-C4E0CDAB9E00%40gmail.com 
>>>> <https://groups.google.com/d/msgid/cp2k/C543F0FA-BD29-4238-B04B-C4E0CDAB9E00%40gmail.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 c... at googlegroups.com.
>>>
>>>
>>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/cp2k/CA%2BSzDiPznCF4%3Do%2BNOkE8x_Lau3ScWFHDjDYje05-ZJGT-SS68Q%40mail.gmail.com 
>>> <https://groups.google.com/d/msgid/cp2k/CA%2BSzDiPznCF4%3Do%2BNOkE8x_Lau3ScWFHDjDYje05-ZJGT-SS68Q%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>> .
>>> <H2O-pos-1-1.xyz><H2O-pos-2-1.xyz><H2O-pos-3-1.xyz><H2O-pos-4-1.xyz>
>>> <h2o_test.inp>
>>>
>>> -- 
>>> You received this message because you are subscribed to a topic in the 
>>> Google Groups "cp2k" group.
>>> To unsubscribe from this topic, visit 
>>> https://groups.google.com/d/topic/cp2k/CKzhBph4yFc/unsubscribe.
>>>
>> To unsubscribe from this group and all its topics, send an email to 
>>> c... at googlegroups.com.
>>
>>
>>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/cp2k/AF2E4F64-1C56-4B51-9B8C-0CB8120FAE3C%40gmail.com 
>>> <https://groups.google.com/d/msgid/cp2k/AF2E4F64-1C56-4B51-9B8C-0CB8120FAE3C%40gmail.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20200826/58be1fbe/attachment.htm>


More information about the CP2K-user mailing list