<div dir="ltr">Hi Alex,<div><br></div><div>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...</div><div><br></div><div>Cheers,</div><div>Gabriele<br><br>On Thursday, November 23, 2017 at 11:14:04 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 text="#000000" bgcolor="#FFFFFF">
<p>Okay, nevermind. Indeed, it was the TOPOLOGY section. By simply
invoking it to supply the coordinates, I asked cp2k to create,
well, the topology. :) <br>
</p>
<p>All fixed by converting coordinates to xyz and sticking them into
the input file.</p>
<p>Thanks!</p>
<p>Alex<br>
</p>
<br>
<div>On 11/23/2017 2:46 AM, Alex wrote:<br>
</div>
<blockquote type="cite">
<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>On 11/23/2017 2:33 AM, Gabriele
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Alex,
<div><br>
</div>
<div>It looks like the error comes from the SUBSYS section in <a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fmanual.cp2k.org%2Ftrunk%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWUPIHoS90TeE7dh2eTzJws1vQuA';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fmanual.cp2k.org%2Ftrunk%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGWUPIHoS90TeE7dh2eTzJws1vQuA';return true;">https://manual.cp2k.org/<wbr>trunk/CP2K_INPUT/FORCE_EVAL/<wbr>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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