Cell Optimization does not work in QM

[Pierre-André Cazade]

Hello,

I am rather new to CP2K though I am experienced with molecular modelling both quantum and classical, and with a wide range of software. It is quite frustrating that it seems impossible to get CP2K to perform a simple CELL_OPT of a beta glycine crystal (20 atoms, monoclinic) with PBE. Such a calculation works fine with VASP, so I am quite surprised the same calculation goes astray with CP2K. Basically, the B unit cell vector increases drastically up to absurd values. Needless to say, this is a test system as I wish to use CP2K for its linear scaling DFT to model protein crystals. I have tried to play with CUTOFF and REL_CUTOFF in the MGRID section up to 1400 and 80 respectively. I also tried GPW and GAPW methods, all electrons or GTH pseudo. Nothing works. Please, if anyone could have a look at the attached input file "cell_opt_qm.inp" and point what's wrong in it, I would be grateful.

Furthermore, I have tried LS approach with DFTB on a 5x5x5 crystal of beta glycine and do not have much more success. First, the pressure in the crystal is insanely high and will lead again to a 20 folds increase of the lattice vectors (with CG). Then, with LBFGS method, the system stops after 3 to 4 cycles with a message telling LBFGS convergence criteria were reached, whereas the system is clearly not. Again, I would be grateful if anyone could tell me what's wrong with my system ("cell_opt2_qm.inp" with "betacry.pdb" for the coordinates). Ideally, my goal would be to be able to run large complex systems with the LS approach and with any DFT/DFTB method.

Thank you in advance for your help.

Regards,

Pierre

[Dr. Dirk Buddensiek]

Dear Pierre,

at first glance the CUTOFF and RELCUTOFF seem to be a lttle bit unbalanced. Maybe it would help to take a look in the tutorial hpw to get optimised cuttof values. https://www.cp2k.org/howto:converging_cutoff

[Pierre Cazade]

Dear Dirk,

Thank you for your answer. I went through the tutorial about CUTOFF and RELCUTOFF. That's how I came up with CUTOFF=1400 and RELCUTOFF=80. I also tried CUTOFF=400 and RELCUTOFF=60. It does not change the problem when it comes to the cell optimization. Furthermore, I have, to some extend, a similar issue on the large crystal using DFTB. Please have a look at the input files, there might be a silly mistake I make or a missing keyword, I am not aware of.

Regarding the tutorial, it is far from being helpful as the criterion to decide if CUTOFF and RELCUTOFF are appropriate is rather undefined/unspecific. Anyway, I have exhausted the resources available on CP2K website before asking on the forum.

Thanks again,
Pierre

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Dr Pierre Cazade, PhD
AD3-023, Bernal Institute,
University of Limerick,
Plassey Park Road,
Castletroy, co. Limerick,
Ireland

[Dr. Dirk Buddensiek]

Good morning Pierre,

please find enclosed an example which at least worked for computation of the unit cell of p-Dimethylaminothiopivalophenone. Unfortunately the Online-Manual of CP2K is not self-explanatory. But there is a lot of material (Tutorials, Excercises from summer Schools etc.) available which might help.

Hope you succeed with the input file. Don´t worry. I had some similar experience in the beginning.

Kind regards 

Dirk

PS: In really difficult cases I guess Juerg Hutter and / or Marcella Ianuzzi can help.

Am Mittwoch, 7. August 2019 17:05:56 UTC+2 schrieb Pierre-André Cazade:

[Pierre Cazade]

Hello Dirk,

Thank you for the files. I will have a careful look at them and give them a try. I will test the MP2 method on my small crystal and see if it gives the correct optimization.

What bothers me with my systems is that it is not only the crystal which is expending but also the inter atomic distance, by which I mean, the distance between two atoms that are part of the same molecule. For example, the N-H bond length of the -NH3+ group of my glycine molecule increases from 0.98 A to 1.4 A, at the point where I stopped the calculation. It feels like there is a problem with the input coordinates or that they are understood by cp2k as been in Bohr whereas they are in Angstrom.

Thanks again,
Pierre

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[Dr. Dirk Buddensiek]

Hi Pierre,

good luck. Concerning distance units: It might be that there are in Bohr for MP2. But you can set the units explicitly in the input deck.

Dirk

Am Mittwoch, 7. August 2019 17:05:56 UTC+2 schrieb Pierre-André Cazade:

[Matt W]

Standard inputs are in Angstroms for a coord section.

The most common problem is that the planewave basis changes as the cell optimizes. You can use a constant size of plane wave basis by specifying a reference cell, something like this. Where the CELL_REF contains a reference cell that should be a bit bigger that the expected largest cell after optimization.

    &CELL
      ABC 5.620 5.620 5.620
      &CELL_REF
        ABC 5.620*1.1 5.620*1.1 5.620*1.1
      &END
    &END CELL

If your cell has symmetry (orthorhombic, hexagonal etc) you can specify this to be kept. Similarly first optimizing just the volume and keeping the angles constant, then relaxing everything can be more efficient.

Also I'd stick with BFGS rather than LBFGS unless you system is huge (> 2000 atoms)

Maybe this helps a little, 

Matt

[Pierre Cazade]

Hi Matt,

Thanks for the tip about the cell_ref, I'll give it a try. Otherwise, I define the symmetry and I keep it fixed. I also keep the angles fixed for the first optimization.

A new calculation I've just run with the DFT parameters from Dirk's input file yields similar results as I obtained before:

 CELL| Vector a [angstrom]:       4.251     0.000     0.000    |a| =       4.251
 CELL| Vector b [angstrom]:       0.000     7.405     0.000    |b| =       7.405
 CELL| Vector c [angstrom]:      -2.287     0.000     5.298    |c| =       5.771

I started with this however:

&CELL
      ABC [angstrom]   5.078       6.192     5.387
      ALPHA_BETA_GAMMA [deg] 90.00 113.35  90.00
      SYMMETRY MONOCLINIC
      PERIODIC XYZ
&END CELL

I know from VASP the optimized unit cell is:

   a                  b             c         alpha          beta          gamma
 5.12269  6.41270  5.41981   90.0000    112.7275     90.0000

Of course, I do not expect two different software using different methods and different pseudopotentials to give the exact same result but they should be close enough. The contraction of the A vector and the expansion of the B vector are absurd. I will try the ref_cell, it might help.

Regards,
Pierre

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[Matt W]

You are not using K points, so you will need a 2x2x2 cell to get something sensible.

Matt

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[Marcella Iannuzzi]

Dear Pierre,

the attached input for geometry optimisation seems to work fine. 

According to the resulting stress tensor, the given cell is too small in all directions and a cell_opt simulation should lead to a larger cell.

I did not run a cell_opt though. 

Regards,

Marcella

[Pierre-André Cazade]

Dear Marcella,

Thank you for the input file. I will give it a try right away and see how things goes.

Regards,

Pierre

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From: cp...@googlegroups.com on behalf of Marcella Iannuzzi <marci...@gmail.com>
Sent: Thursday, August 8, 2019 1:45 p.m.
To: cp2k
Subject: [CP2K:12063] Re: Cell Optimization does not work in QM

 

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