[CP2K-user] [CP2K:13450] Visualize electron density during formation of a water molecule

[Michael Hale]

Well I filled out the input file as well as I could figure out from your 
tips. CP2K runs for a few minutes and then aborts with the error "KS energy 
is an abnormal value (NaN/Inf)". I tried setting a small MAX_SCF value, but 
it still hits that error. Any other tips? Here is my input file:

&GLOBAL
  PROJECT water-formation
  RUN_TYPE MD
  PRINT_LEVEL LOW
&END GLOBAL
&MOTION
  &MD
    ENSEMBLE NVT
    &THERMOSTAT
      TYPE CSVR
    &END THERMOSTAT
  &END MD
&END MOTION
&FORCE_EVAL
  &SUBSYS
    &KIND H
      BASIS_SET DZVP-GTH-PADE
      POTENTIAL GTH-PADE-q1
    &END KIND
    &KIND O
      BASIS_SET DZVP-GTH-PADE
      POTENTIAL GTH-PADE-q6
    &END KIND
    &CELL
      ABC 10 10 10
      PERIODIC NONE
    &END CELL
    &COORD
      H    4.0    4.0    4.66667
      H    6.0    6.0    4.66667
      O    5.0    5.0    5.66667
    &END COORD
  &END SUBSYS
  &DFT
    BASIS_SET_FILE_NAME  data/BASIS_SET
    POTENTIAL_FILE_NAME  data/POTENTIAL
    LSD
    &SCF
      ADDED_MOS 10
      &DIAGONALIZATION
      &END DIAGONALIZATION
      &MIXING
        METHOD BROYDEN_MIXING
      &END MIXING
      &SMEAR
        METHOD FERMI_DIRAC
      &END SMEAR
    &END SCF
    &XC
      &XC_FUNCTIONAL PADE
      &END XC_FUNCTIONAL
    &END XC
    &PRINT
      &E_DENSITY_CUBE
        &EACH
          MD 1
        &END EACH
        FILENAME CUBE
      &END E_DENSITY_CUBE
    &END PRINT
  &END DFT
&END FORCE_EVAL

On Thursday, June 4, 2020 at 10:10:06 AM UTC-4, Michael Hale wrote:
>
> Great! Thank you. I'll look into those options and hopefully mess with it 
> some more this weekend.
>
> Is there much of a hobbyist community around computational chemistry? I'm 
> a pretty experienced software developer, but still new to this. I know 
> there are projects like Folding at Home which don't give you much control, and 
> Chemistry Stack Exchange which is more just traditional Q&A. But I'd love 
> to find community projects to help enhance digital chemistry textbooks with 
> ab initio quantum MD animations of common reactions and such.
>
> I actually first tried this during a weekend a couple of years ago. Here 
> was the result:
> https://www.youtube.com/watch?v=foG5LgFYb2o
>
> I finally revisited it a week or two ago. I thought maybe just my initial 
> conditions needed to be tweaked, but then I realized my simulation set up 
> had deeper problems, haha. Thanks again for your help. I hope to post an 
> update again soon. 
>
> On Thursday, June 4, 2020 at 9:26:25 AM UTC-4, jgh wrote:
>>
>> Hi 
>>
>> What I would do: 
>>
>> Small basis e.g. DZVP 
>> LSD 
>> SCF with Diagonalization and Broyden mixing, use all MOs 
>> Fermi-Dirac Smearing with high temperature 
>> NVT MD with velocity rescaling to get rid of excessive energy 
>> Print CUBE file automatically during MD 
>>
>> regards 
>>
>> Juerg Hutter 
>> -------------------------------------------------------------- 
>> Juerg Hutter                         Phone : ++41 44 635 4491 
>> Institut für Chemie C                FAX   : ++41 44 635 6838 
>> Universität Zürich                   E-mail: h... at chem.uzh.ch 
>> Winterthurerstrasse 190 
>> CH-8057 Zürich, Switzerland 
>> --------------------------------------------------------------- 
>>
>> -----c... at googlegroups.com wrote: ----- 
>> To: "cp2k" <c... at googlegroups.com> 
>> From: "Michael Hale" 
>> Sent by: c... at googlegroups.com 
>> Date: 06/04/2020 05:08AM 
>> Subject: [CP2K:13450] Visualize electron density during formation of a 
>> water molecule 
>>
>> Hey, sorry for the basic question. I've skimmed some computational 
>> chemistry books, but I still find the CP2K documentation a bit 
>> overwhelming. I'm trying to put two hydrogens an an oxygen atom near each 
>> other and watch the spontaneous assembly of a water molecule. I can make 
>> the input file and have CP2K output the forces on the atoms and a cube file 
>> that I can use to make a 3D visualization of the electron density in 
>> Mathematica. Then I update the atom positions with a simple velocity Verlet 
>> update and run CP2K again. The resulting animation looks how I want 
>> stylistically, but the behavior is clearly not accurate. The atoms come 
>> together and bounce off of each other and come back together and bounce off 
>> harder. They keep getting more energy and bouncing farther and farther away 
>> until they fly apart instead of bonding together. 
>>
>> Is the error that the energy calculation for the forces and electron 
>> density isn't converging and causing the erratic behavior? Is the error 
>> probably in the way I'm updating the atom positions manually? Can I use the 
>> CP2K molecular dynamics functionality to do multiple steps of the 
>> simulation at once while also outputting the cube file of the electron 
>> density for each step? Is this type of simulation of the formation of small 
>> molecules within the scope of CP2K? It seems most people typically assume 
>> the molecules are already formed and they just want to simulate how those 
>> molecules interact, not how atoms come together to form the small 
>> molecules. 
>>
>> This is all just for fun. I just want to watch the animations and see how 
>> "sticky" the atoms and molecules are. Thanks for any help and guidance you 
>> might provide.   
>>   -- 
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>>
>>   
>>
>
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