[CP2K:9723] Re: Warning in connectivity generation
Alex
nedo... at gmail.com
Thu Nov 23 19:19:36 UTC 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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