Warning in connectivity generation
marci... at gmail.com
Thu Nov 23 09:31:25 UTC 2017
the connectivity is usually not needed for a DFT calculation.
Is there any particular reason why you want cp2k to generate the
Anyway, the input part that is related to that is the SUBSYS section and
not the DFT one.
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:
> GENERATE| WARNING in connectivity generation!
> GENERATE| Two molecules/residues named (MOL1) have different number of
> 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
> 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
> Here's the DFT section of my input:
> CHARGE 1
> BASIS_SET_FILE_NAME BASIS_SET2
> POTENTIAL_FILE_NAME GTH_POTENTIALS2
> NGRIDS 5
> CUTOFF 500
> &END MGRID
> METHOD GPW
> &END QS
> SCF_GUESS RESTART
> EPS_SCF 5.0E-6
> MAX_SCF 150
> ADDED_MOS 100
> METHOD BROYDEN_MIXING
> ALPHA 0.1
> NBROYDEN 8
> &END MIXING
> &END SCF
> &XC_FUNCTIONAL PBE
> &END XC_FUNCTIONAL
> POTENTIAL_TYPE 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,
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