[CP2K:7031] Re: Molecular crystal in a triclinic cell

S Ling lingsa... at gmail.com
Thu Oct 8 01:42:16 CEST 2015


Hi

Please replace your &SCF section with the following settings, which should
significantly accelerate your SCF calculations:

     &SCF
       MAX_SCF  20
       EPS_SCF     1.000E-06
       SCF_GUESS  RESTART
       &OT  T
         MINIMIZER  DIIS
         PRECONDITIONER  FULL_ALL
         ENERGY_GAP 0.001
       &END OT
       &OUTER_SCF  T
         EPS_SCF     1.000E-06
         MAX_SCF  20
       &END OUTER_SCF
     &END SCF

You can use PBE pseudopotential for BEEF functional. It takes time to
generate and test the performance of new basis sets and pseudopotentials.
The PBE pseudopotential is perhaps the "closest" choice you have for BEEF
functional, and it should be good enough for BEEF functional, but you need
to test it.

In terms of choice of XC functional, please note BEEF functional contains
parameters which were optimised for several data sets chosen by the
original authors. There is no guarantee that it is good for your system. So
you need to test the functional on your specific system. You may want to
try PBE+D3 which I mentioned in the slides. Generally speaking, D2/D3
should be cheaper than non-local vdW based methods, but they may have their
own advantages and disadvantages.

With respect to the supercell sizes, please keep in mind CP2K uses
Gamma-point approximation. I am not sure whether you will be able to get
correct electronic structure of your system if you use a 1x1x1 cell with
cell dimensions smaller than 5 A. If the electronic structure is wrong,
then the forces, stress tensor and optimised lattice parameters will also
be wrong. You will be more likely to get better electronic structure if you
use bigger supercells.

SL


On 7 October 2015 at 19:34, Alex <nedo... at gmail.com> wrote:

> Thanks Matt.
>
> I enforced the angles and changed my SCF section to, hope this looks
> reasonable:
>
>     &SCF
>       &OT ON
>        MINIMIZER DIIS
>        PRECONDITIONER FULL_ALL
>        ENERGY_GAP 0.001
>       &END OT
>       SCF_GUESS RESTART
>       EPS_SCF 5.0E-6
>       MAX_SCF 300
>     &END SCF
>
> Given the above, I do not see much of an improvement speed-wise, to be
> honest. The memory footprint is about half of what it was, I can see that
> much.
>
> Your comment regarding XC is definitely well taken, we here don't believe
> PBE+VDW out of the box should be accurate. I am tempted to try the setup
> from p. 21 of the pdf you suggested, but does this BEEF work in stock CP2K
> and does one need to change the potentials (I am using GTH potentials). I
> suppose this boils down to whether there is an input file from the authors
> for others to try...
>
> Alex
>
>
> On Wednesday, October 7, 2015 at 2:37:42 AM UTC-6, Matt W wrote:
>>
>> Hi Alex,
>>
>> one concern would be the XC functional. There are some slides from a
>> recent CECAM meeting at
>> http://www.cp2k.org/_media/events:2015_cecam_tutorial:ling_vdw.pdf with
>> some partial inputs of setting up DFT-vdw functionals. I'm not sure PBE+vdw
>> is great.
>>
>> Otherwise, there are some things that might be a bit more efficient:
>>
>> Changing to the OT method instead of using diagonalization would give you
>> a very large speed up, I would think (order of magnitude probably here).
>>
>> It might be a good idea to fix the angles of the cell and do an
>> optimization (CELL_OPT/KEEP_ANGLES) then optimize again without the
>> constraint.
>>
>> Matt
>>
>> On Tuesday, October 6, 2015 at 7:35:18 PM UTC+1, Alex wrote:
>>>
>>> Hi all,
>>>
>>> We're trying to simulate an n-octane crystal (triclinic, coordinates and
>>> cell vectors from literature) -- just a static cell + geometry
>>> optimization. Here's the issue: when simulating a single cell (1 1 1), the
>>> crystal cohesive energy is far above the experiment -- an order of
>>> magnitude larger in absolute value. As a vacuum ref we're simulating an
>>> isolated octane molecule. In all cases, a NON_LOCAL vdw energy correction
>>> is used.
>>>
>>> When simulating a total of eight cells (2 2 2), and the simulation is
>>> still running, so the results are preliminary, things appear to be much
>>> more reasonable. The input file is below (I can provide the coordinates as
>>> well, if needed). Can you just by simple inspection tell me if anything is
>>> obviously wrong?
>>>
>>> Thanks a lot,
>>>
>>> Alex
>>>
>>> **********************************
>>> &GLOBAL
>>>   PROJECT opt
>>>   PRINT_LEVEL MEDIUM
>>>   RUN_TYPE CELL_OPT
>>> &END GLOBAL
>>>  &MOTION
>>>   &GEO_OPT
>>>     OPTIMIZER BFGS
>>>   &END
>>>   &CELL_OPT
>>>     EXTERNAL_PRESSURE [bar] 1.0
>>>     OPTIMIZER BFGS
>>>   &END
>>> &END MOTION
>>>
>>> &FORCE_EVAL
>>>   METHOD QS
>>>   STRESS_TENSOR ANALYTICAL
>>>   &DFT
>>>     BASIS_SET_FILE_NAME BASIS_SET2
>>>     POTENTIAL_FILE_NAME GTH_POTENTIALS2
>>>     &MGRID
>>>       NGRIDS 5
>>>       CUTOFF 500
>>>     &END MGRID
>>>     &QS
>>>       METHOD GPW
>>>     &END QS
>>>     &SCF
>>>       SCF_GUESS RESTART
>>>       EPS_SCF 5.0E-6
>>>       MAX_SCF 300
>>>       ADDED_MOS  100
>>>       &MIXING
>>>           METHOD BROYDEN_MIXING
>>>           ALPHA    0.1
>>>           NBROYDEN   8
>>>       &END MIXING
>>>     &END SCF
>>>     &XC
>>>       &XC_FUNCTIONAL PBE
>>>       &END XC_FUNCTIONAL
>>>       &VDW_POTENTIAL NON_LOCAL
>>>       &END VDW_POTENTIAL
>>>     &END XC
>>>   &END DFT
>>>   &SUBSYS
>>>     &CELL
>>>   ABC 4.160 4.750 11.000
>>> ANGLES 94.80  84.50 105.10
>>>         PERIODIC XYZ
>>> SYMMETRY TRICLINIC
>>>         MULTIPLE_UNIT_CELL 2 2 2
>>>     &END
>>>     &TOPOLOGY
>>>        COORD_FILE_NAME noct_2mol.pdb
>>>        COORD_FILE_FORMAT PDB
>>>        MULTIPLE_UNIT_CELL  2 2 2
>>>     &END
>>>     &KIND C
>>>       BASIS_SET  DZVP-MOLOPT-SR-GTH
>>>       POTENTIAL  GTH-PBE-q4
>>>     &END KIND
>>>     &KIND H
>>>       BASIS_SET  DZVP-MOLOPT-SR-GTH
>>>       POTENTIAL  GTH-PBE-q1
>>>     &END KIND
>>> &END SUBSYS
>>> &END
>>>
>>> --
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