Warning in connectivity generation

Gabriele gabri... at gmail.com
Thu Nov 23 10:33:45 CET 2017


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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