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Re: [lammps-users] Pressure induced phase transition Metadynamics with PLUMED
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Re: [lammps-users] Pressure induced phase transition Metadynamics with PLUMED


From: Matej Badin <matej.badin@...24...>
Date: Thu, 19 Apr 2018 20:57:45 +0200

Well that's the exactly the behavior which is counter-intuitive since we would expect that the box starts to actually sample higher coordination numbers (>4), so there should not be a reason
to sample significantly lower areas of CV space under the value 4. Yes therefore, I agree that it probably causes box to exhibit strange deformations in order to maintain a high pressure but sample
low coordination number, however I do not see a reason system has to do so.

2018-04-18 17:10 GMT+02:00 David Stelter <dstelter@...5214...>:
I tried to implement metadynamics at 500 kBar and try to reconstruct Gibbs free energy profile based on simple coordination number between Na-Cl ions, which differs between B1 and B2 phase (6 and 8 respectively)

I would take a look at the lower wall of your CV, it is set to 2, yet you want to sample phases that have coordination numbers of 6 & 8. It seems that the deformations start when you begin to sample low coordination numbers (<4), is this what you expect? I think it makes some sense that your box could exhibit strange deformations in order to sample low coordination number and maintain high pressure.

David

 

On Tue, Apr 17, 2018 at 3:23 PM, Matej Badin <matej.badin@...24...> wrote:
Yes, I have asked in PLUMED mailinglist the same question, but I was still interested if someone try to use the metadynamics
in the same way in LAMMPS (pressure induced phase transitions) in order to see if there not some possible issues with implementation.

Matej
 

2018-04-17 16:34 GMT+02:00 Steve Plimpton <sjplimp@...24...>:
Someone more familiar with PLUMED or the use of metadyanmics for this
kind of model would need to answer.  Maybe there is a mail list for PLUMED
where you can ask these Qs?

Steve


On Fri, Apr 13, 2018 at 7:12 AM, Matej Badin <matej.badin@...24...> wrote:
Dear all,

I am trying to use LAMMPS (v17 Aug 2017) together with PLUMED (2.3.2) to study pressure induced phase transitions.

I try to applicate (continuous) Metadynamics, to pressure induced phase transition in NaCl from B1 to B2 phase.

From simple unbiased simulations in NPT ensemble using fully anisotropic unit cell (structure transformation needs to deformate the cell on relatively small system - 1024 particles preparted
in B1 phase) I now that such transitions occur around 550 - 600 kbar (obviously the precise value suffers from hysterics effects which came from relaxation).
This value I took as a reference value for further study.

Then, I tried to implement metadynamics at 500 kBar and try to reconstruct Gibbs free energy profile based on simple coordination number between Na-Cl ions,
which differs between B1 and B2 phase (6 and 8 respectively). To to this, as a common rule of thumb, I guessed expected barrier height and took a fraction of it
to set the gaussian height, using fluctuations of coordination number in unbiased simulation and the gaussian deposit rate was chosen the closest to the
barostat relaxation time, so that the system should still have enough time between successive deposits to equilibrate. The cutoff for switch function which is used
in calculating coordination number was chosen in the middle between the first two maxima in radial distribution function for Na-Cl in unbiased simulation
at given pressure.

Typical example of system parameters are 300 K, 550 kbar, 0.25 ps for thermostat relaxation time, 0.5 ps for barostat relaxation time using Nose-Hoover
anisotropic barostat in LAMMPS with MTK term. As force field I have a standard used Born-Mayers-Huggins potential for NaCl.

However, regardless of tunning MetaD parameters, changing the times of barostat I observe a common strange behavior that system successfully escapes from B1 phase
to B2 phase, however it is not able to fully return to the B1 phase, instead the unit cell starts to deform in some strange fashion. The crystallization of the new phase
proceed through layering and deformation of the unit cell which resembles Burgers mechanism.

Do you have any suggestion how can be this behavior suppressed, in order to correct sample both phases?
Here I attached the figures to illustrate the issue:


Fig.1: Time evolution of coordination number which shows a strange behavior - the system does not return to the B1 phase.



Fig.2: Time evolution of cell size.




Fig. 3: Time evolution of cell angles - showing strange deformation of unit cell.

 
The input files for LAMMPS and PLUMED from which the issue can be reconstructed are attached.
Thank you for your answer in advance!

Best,
Matej Badin

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--
David Stelter
Graduate Student
Department of Chemistry
Boston University