[CP2K:9723] Re: Warning in connectivity generation

Alex nedo... at gmail.com
Thu Nov 23 20:19:36 CET 2017


Hi Gabriele,

I wish I looked at the TOPOLOGY section description more carefully -- 
apparently CONN_FILE_FORMAT (with the alias you mentioned) is indeed the 
key. Why it sets the default to generating a topology when DFT is used 
to calculate interactions is a bit beyond me. In any case, thank you!

Alex


On 11/23/2017 4:11 AM, Gabriele wrote:
> 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/
>>>     <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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>>
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