Bug? The conserved quantity is NOT conserved after flexible cell MD is restarted
rusta... at gmail.com
Wed Aug 17 06:54:30 UTC 2016
I hope you are right and the dynamics is correct even though there are
discontinuities in the conserved quantity after restarts. Unfortunately,
Nose thermostat has the same problem (see the new figure) so there is no
way so far to tell if the dynamics is correct.
On Tuesday, August 16, 2016 at 4:36:45 AM UTC-4, Matt W wrote:
> (I could well be wrong here, this is sort of anecdotal rather than
> rigorously checking the details) I think that the conserved quantity for
> the CSVR thermostat is quite a complicated thing compared to other
> thermostats. To my memory, the proper conserved quantity requires sums over
> information from all previous states in a non-trivial way that is tough to
> implement efficiently (i.e. adding new information at every step without
> complete recomputation).
> After all that waffle, I suspect the 'problem' is the CSVR thermostat, and
> it is not actually an indication of bad behaviour, but a question of
> efficiency in calculating the conserved quantity (i.e. dynamics are
> correct, but it is hard to be sure without a conserved quantity). Maybe try
> Nose-Hoover after equilibriating with CSVR to be sure?
> On Sunday, August 14, 2016 at 4:41:29 AM UTC+1, Rustam wrote:
>> Hi Matthias,
>> Thanks for the great advice! I tried changing the basis set to the one
>> compatible with Mg q2 and low cutoff. Unfortunately, the problem remains as
>> shown in the new figure.
>> On a different note, what basis sets would you recommend for solid state
>> systems? All-electron basis sets? Or do you think I should generate a pair
>> of potential/basis for the problem at hand?
>> Thanks again,
>> PS. The input file is also attached.
>> On Saturday, August 13, 2016 at 2:34:04 AM UTC-4, Matthias Krack wrote:
>>> Hi Rustam
>>> in the first place I would suggest to use a compatible pair of basis set
>>> and potential for Mg. The Mg TZV2P-GTH basis set was generated for a Mg
>>> GTH-*-q10, but a GTH-BLYP-q2 is employed. Unfortunately, the GTH_BASIS_SET
>>> file provides only generic labels. I will fix that. Please, run the case
>>> with a valid combinations of potential and basis set and report if the
>>> error persists. Note, that the Mg q10 potential requires a very large
>>> cutoff and for the Mg q2 potential there is only a DZVP basis set available
>>> in the file BASIS_SET.
>>> Best regards
>>> PS: The basis sets in GTH_BASIS_SETS are usually not well suited for
>>> (dense) solid state systems as they have been generated mainly for
>>> molecular systems.
>>> On Saturday, 13 August 2016 07:56:39 UTC+2, Rustam wrote:
>>>> Hi guys,
>>>> As Amandine Chouanard mentioned in a recent post
>>>> conserved quantity shows discontinuities when a flexible cell MD simulation
>>>> is restarted. I used her input file and found that restart works fine with
>>>> NVT and NPT_I simulations, but NOT with NPT_F (see attached figure). The
>>>> discontinuities in NVT_F the conserved quantity are larger if restarts are
>>>> less frequent (i.e. trajectory pieces are longer).
>>>> It seems that the conserved quantities in NPT_I and NPT_F simulations
>>>> are computed by the same subroutine in
>>>> motion/md_conserved_quantities.F:390. So it seems that the restart file
>>>> contains ALL data on the current state of the barostat and thermostat to
>>>> ensure a smooth restart.
>>>> Is it possible that this has something to do with the CELL_REF setting?
>>>> Something along the lines that the grids before and after the restart are
>>>> different? I tried printing the GRID info but it seems to keep the number
>>>> of points constant...
>>>> I will appreciate any suggestions/comments,
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