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<p>Hi Gabriele,</p>
<p>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!</p>
<p>Alex<br>
</p>
<br>
<div class="moz-cite-prefix">On 11/23/2017 4:11 AM, Gabriele wrote:<br>
</div>
<blockquote type="cite"
cite="mid:4c9ed083-07e4-47...@googlegroups.com">
<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;" moz-do-not-send="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>
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