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

Alex nedo... at gmail.com
Thu Oct 8 01:58:26 CEST 2015


Thanks, that is really useful, but still not much of a gain in terms of 
speed. 

I was also looking at trying D3, but the examples from slide #14 are 
definitely missing from my CP2K installation. I suppose I will stick with 
PBE + NON_LOCAL VDW for the moment, just to get some idea, but then consult 
with the cited paper.

Alex

On Wednesday, October 7, 2015 at 5:42:20 PM UTC-6, S Ling wrote:
>
> 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 <ned... at gmail.com <javascript:>> 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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>
>
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