[CP2K:9720] Re: Warning in connectivity generation

Gabriele gabri... at gmail.com
Thu Nov 23 12:11:23 CET 2017


Hi Alex,

You can use the topology section to import the coordinates from an external 
pdb or xyz file, which may be useful especially for large systems. Try to 
insert CONNECTIVITY OFF inside the TOPOLOGY section. You should have no 
issues associated with the generation of the connectivity...

Cheers,
Gabriele

On Thursday, November 23, 2017 at 11:14:04 AM UTC+1, Alex wrote:
>
> 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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