[CP2K:9720] Re: Warning in connectivity generation

Alex nedo... at gmail.com
Thu Nov 23 10:46:06 CET 2017


See, but that's the funny part. I absolutely DO NOT want any topologies 
created and I did not think there was any need for it in this type of 
simulations. Other than using a PDB file with coordinates as input as 
part TOPOLOGY section, I am not asking (not explicitly, anyway) for any 
connectivity tables. should I just convert to xyz and dump the whole 
TOPOLOGY section? All suggestions are very welcome.

Thanks,

Alex

p.s. Complete file below:

&GLOBAL
   PROJECT opt
   PRINT_LEVEL MEDIUM
   RUN_TYPE GEO_OPT
&END GLOBAL
  &MOTION
   &GEO_OPT
     MAX_ITER 400
     OPTIMIZER BFGS
   &END
&END MOTION
&FORCE_EVAL
   METHOD QS
   STRESS_TENSOR ANALYTICAL
   &DFT
#    CHARGE 1
     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 150
       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
           POTENTIAL_TYPE  PAIR_POTENTIAL
           &PAIR_POTENTIAL
             TYPE  DFTD3
             PARAMETER_FILE_NAME dftd3.dat
            REFERENCE_FUNCTIONAL PBE
            CALCULATE_C9_TERM  T
           &END PAIR_POTENTIAL
         &END VDW_POTENTIAL
       &END XC
   &END DFT
   &SUBSYS
     &CELL
      ABC    22.087 21.859 50.000
     ANGLES    90.000 90.000 90.000
         PERIODIC XYZ
         MULTIPLE_UNIT_CELL 1 1 1
     &END
     &TOPOLOGY
        &CENTER_COORDINATES TRUE
        &END
        COORD_FILE_NAME pore3_potassium4.pdb
        COORD_FILE_FORMAT PDB
        MULTIPLE_UNIT_CELL 1 1 1
     &END
     &KIND S
       BASIS_SET  DZVP-MOLOPT-SR-GTH
       POTENTIAL  GTH-PBE-q6
     &END KIND
     &KIND MO
       BASIS_SET  DZVP-MOLOPT-SR-GTH
       POTENTIAL  GTH-PBE-q14
     &END KIND
     &KIND O
       BASIS_SET  DZVP-MOLOPT-SR-GTH
       POTENTIAL  GTH-PBE-q6
     &END KIND
     &KIND K
       BASIS_SET  DZVP-MOLOPT-SR-GTH
       POTENTIAL  GTH-PBE-q9
     &END KIND
&END SUBSYS
&END



On 11/23/2017 2:33 AM, Gabriele wrote:
> Hi Alex,
>
> It looks like the error comes from the SUBSYS section 
> in https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/ and not 
> from the DFT section. If you are using just DFT there is no need to 
> generate the connectivity, which is where you get the warning. We can 
> have a closer look if you upload the whole input file.
>
> Cheers,
> Gabriele
>
>
>
> On Thursday, November 23, 2017 at 3:02:52 AM UTC+1, Alex wrote:
>
>     Hi all,
>
>     I have a system that contains a molybdenum disulfide (MoS2) sample
>     and a charged (+1) potassium ion. The MoS2 structure itself gets
>     energy-minimized without any issues, but in combination with this
>     ion I get a nonstop stream of GENERATE warnings like this:
>
>
>      GENERATE|  Preliminary Number of Bonds generated:               
>                360
>
>      GENERATE| WARNING in connectivity generation!
>      GENERATE| Two molecules/residues named (MOL1) have different 
>     number of atoms.
>      GENERATE| Molecule starting at position (13) has Nr. <0> of atoms.
>      GENERATE| while the other same molecules have Nr. <162> of atoms!
>      GENERATE| Increasing bondparm_factor by 1.05.. An error was found
>     in the generated
>      GENERATE| connectivity. Retry...
>      GENERATE| Present value of BONDPARM_FACTOR (  Infinity ).
>
>     When I replace the potassium ion with e.g. a proton, everything is
>     back to normal.
>
>     Here's the DFT section of my input:
>
>       &DFT
>         CHARGE 1
>         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 150
>           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
>               POTENTIAL_TYPE  PAIR_POTENTIAL
>               &PAIR_POTENTIAL
>                 TYPE  DFTD3
>                 PARAMETER_FILE_NAME dftd3.dat
>                REFERENCE_FUNCTIONAL PBE
>                CALCULATE_C9_TERM  T
>               &END PAIR_POTENTIAL
>             &END VDW_POTENTIAL
>           &END XC
>       &END DFT
>
>     Any suggestions? If you need further info, please let me know.
>
>     Thank you,
>
>     Alex
>
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