Warning in connectivity generation

Marcella Iannuzzi marci... at gmail.com
Thu Nov 23 10:31:25 CET 2017


Hi Alex, 

the connectivity is usually not needed for a DFT calculation.
Is there any particular reason why you want cp2k to generate the 
connectivity?
Anyway, the input part that is related to that is the SUBSYS section and 
not the DFT one.
Regards
Marcella


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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