Bug? The conserved quantity is NOT conserved after flexible cell MD is restarted
MattWa... at gmail.com
Tue Aug 16 10:36:45 CEST 2016
(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
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
>>> <https://groups.google.com/forum/#!topic/cp2k/mwieBkpEjns>the 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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