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<p>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.<br>
</p>
<p>Thanks,</p>
<p>Alex<br>
</p>
<p>p.s. Complete file below:<br>
</p>
&GLOBAL<br>
PROJECT opt<br>
PRINT_LEVEL MEDIUM <br>
RUN_TYPE GEO_OPT<br>
&END GLOBAL<br>
&MOTION<br>
&GEO_OPT<br>
MAX_ITER 400<br>
OPTIMIZER BFGS <br>
&END<br>
&END MOTION <br>
&FORCE_EVAL<br>
METHOD QS<br>
STRESS_TENSOR ANALYTICAL<br>
&DFT<br>
# CHARGE 1 <br>
BASIS_SET_FILE_NAME BASIS_SET2<br>
POTENTIAL_FILE_NAME GTH_POTENTIALS2<br>
&MGRID<br>
NGRIDS 5<br>
CUTOFF 500<br>
&END MGRID<br>
&QS<br>
METHOD GPW<br>
&END QS<br>
&SCF<br>
SCF_GUESS RESTART <br>
EPS_SCF 5.0E-6<br>
MAX_SCF 150<br>
ADDED_MOS 100 <br>
&MIXING<br>
METHOD BROYDEN_MIXING<br>
ALPHA 0.1<br>
NBROYDEN 8<br>
&END MIXING<br>
&END SCF<br>
&XC<br>
&XC_FUNCTIONAL PBE<br>
&END XC_FUNCTIONAL<br>
&VDW_POTENTIAL<br>
POTENTIAL_TYPE PAIR_POTENTIAL<br>
&PAIR_POTENTIAL<br>
TYPE DFTD3<br>
PARAMETER_FILE_NAME dftd3.dat<br>
REFERENCE_FUNCTIONAL PBE<br>
CALCULATE_C9_TERM T<br>
&END PAIR_POTENTIAL<br>
&END VDW_POTENTIAL<br>
&END XC<br>
&END DFT<br>
&SUBSYS<br>
&CELL<br>
ABC 22.087 21.859 50.000<br>
ANGLES 90.000 90.000 90.000<br>
PERIODIC XYZ <br>
MULTIPLE_UNIT_CELL 1 1 1 <br>
&END<br>
&TOPOLOGY<br>
&CENTER_COORDINATES TRUE<br>
&END<br>
COORD_FILE_NAME pore3_potassium4.pdb<br>
COORD_FILE_FORMAT PDB<br>
MULTIPLE_UNIT_CELL 1 1 1<br>
&END<br>
&KIND S<br>
BASIS_SET DZVP-MOLOPT-SR-GTH<br>
POTENTIAL GTH-PBE-q6<br>
&END KIND<br>
&KIND MO<br>
BASIS_SET DZVP-MOLOPT-SR-GTH<br>
POTENTIAL GTH-PBE-q14<br>
&END KIND<br>
&KIND O<br>
BASIS_SET DZVP-MOLOPT-SR-GTH<br>
POTENTIAL GTH-PBE-q6<br>
&END KIND<br>
&KIND K <br>
BASIS_SET DZVP-MOLOPT-SR-GTH<br>
POTENTIAL GTH-PBE-q9<br>
&END KIND<br>
&END SUBSYS<br>
&END<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 11/23/2017 2:33 AM, Gabriele wrote:<br>
</div>
<blockquote type="cite"
cite="mid:34cc39e3-80ff-4d...@googlegroups.com">
<div dir="ltr">Hi Alex,
<div><br>
</div>
<div>It looks like the error comes from the SUBSYS section
in <a class="moz-txt-link-freetext" href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/">https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/</a>
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. </div>
<div><br>
</div>
<div>Cheers,</div>
<div>Gabriele</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div><br>
On Thursday, November 23, 2017 at 3:02:52 AM UTC+1, Alex
wrote:
<blockquote class="gmail_quote" style="margin:
0;margin-left: 0.8ex;border-left: 1px #ccc
solid;padding-left: 1ex;">
<div dir="ltr">Hi all,
<div><br>
</div>
<div>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: </div>
<div><br>
</div>
<div>
<div><br>
</div>
<div> GENERATE| Preliminary Number of Bonds
generated: 360</div>
<div><br>
</div>
<div> GENERATE| WARNING in connectivity generation!</div>
<div> GENERATE| Two molecules/residues named (MOL1)
have different number of atoms.</div>
<div> GENERATE| Molecule starting at position (13) has
Nr. <0> of atoms.</div>
<div> GENERATE| while the other same molecules have
Nr. <162> of atoms!</div>
<div> GENERATE| Increasing bondparm_factor by 1.05..
An error was found in the generated</div>
<div> GENERATE| connectivity. Retry...</div>
<div> GENERATE| Present value of BONDPARM_FACTOR (
Infinity ).</div>
</div>
<div><br>
</div>
<div>When I replace the potassium ion with e.g. a
proton, everything is back to normal.</div>
<div><br>
</div>
<div>Here's the DFT section of my input:</div>
<div><br>
</div>
<div>
<div> &DFT</div>
<div> CHARGE 1</div>
<div> BASIS_SET_FILE_NAME BASIS_SET2</div>
<div> POTENTIAL_FILE_NAME GTH_POTENTIALS2</div>
<div> &MGRID</div>
<div> NGRIDS 5</div>
<div> CUTOFF 500</div>
<div> &END MGRID</div>
<div> &QS</div>
<div> METHOD GPW</div>
<div> &END QS</div>
<div> &SCF</div>
<div> SCF_GUESS RESTART</div>
<div> EPS_SCF 5.0E-6</div>
<div> MAX_SCF 150</div>
<div> ADDED_MOS 100</div>
<div> &MIXING</div>
<div> METHOD BROYDEN_MIXING</div>
<div> ALPHA 0.1</div>
<div> NBROYDEN 8</div>
<div> &END MIXING</div>
<div> &END SCF</div>
<div> &XC</div>
<div> &XC_FUNCTIONAL PBE</div>
<div> &END XC_FUNCTIONAL</div>
<div> &VDW_POTENTIAL</div>
<div> POTENTIAL_TYPE PAIR_POTENTIAL</div>
<div> &PAIR_POTENTIAL</div>
<div> TYPE DFTD3</div>
<div> PARAMETER_FILE_NAME dftd3.dat</div>
<div> REFERENCE_FUNCTIONAL PBE</div>
<div> CALCULATE_C9_TERM T</div>
<div> &END PAIR_POTENTIAL</div>
<div> &END VDW_POTENTIAL</div>
<div> &END XC</div>
<div> &END DFT</div>
</div>
<div><br>
</div>
<div>Any suggestions? If you need further info, please
let me know. </div>
<div><br>
</div>
<div>Thank you,</div>
<div><br>
</div>
<div>Alex</div>
</div>
</blockquote>
</div>
</div>
</div>
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