[CP2K:9720] Re: Warning in connectivity generation

Alex nedo... at gmail.com
Thu Nov 23 11:14:06 CET 2017


Okay, nevermind. Indeed, it was the TOPOLOGY section. By simply invoking 
it to supply the coordinates, I asked cp2k to create, well, the 
topology. :)

All fixed by converting coordinates to xyz and sticking them into the 
input file.

Thanks!

Alex


On 11/23/2017 2:46 AM, Alex wrote:
>
> 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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