Warning in connectivity generation
gabri... at gmail.com
Thu Nov 23 10:33:45 CET 2017
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.
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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