<div dir="ltr">Hi Ralph,<div><br></div><div>Thanks for your insightful (and quite creative!) reply. It looks like a great starting point for what I intend to do so I can replicate the paper. I followed your suggestion, and I generated xc.spl, cx.spl and xx.spl files. I also made the xx.spl file all zeros essentially. I also added them to the scc_parameter file (which I renamed parameter_table some time ago). I'm attaching the files here. Then, I adjusted my geometry to have two X atoms in the XYZ input (which is attached too) to represent my initial break or crack.</div><div><br></div><div>When I tried to run my job, it wouldn't start as the KIND X was not defined in the input. I defined the KIND X using:</div><div><br></div><div><div> &KIND X</div><div> ELEMENT C</div><div> &END KIND</div></div><div><br></div><div>But when CP2K runs it says:</div><div><br></div><div><div> *** 00:18:09 WARNING in atomic_kind_types:read_atomic_kind :: Information ***</div><div> *** provided in the input file regarding POTENTIAL for KIND <X> will be ***</div><div> *** ignored!atomic_kind_types.F line 2341 </div></div><div><br></div><div>And the results look extremely unphysical (3 carbon atoms collapsing essentially one into the other). I thought that removing xx.spl, xc.spl and cx.spl would perhaps make it work, but it didn't work either. When I make change X atoms to C atoms in the input structure, everything is back to normal. This makes me think the problem is related to how KIND is working when selecting parameters to use (treating them as if they weren't there?). When I print their charges and mass, it all looks right. Do you have any idea if I am defining my KIND incorrectly, or what could be my issue?</div><div><br></div><div>I've also attached my input, to keep the mailing list clean.</div><div><br></div><div>Thanks,</div><div>Rafael</div><div><br>On Wednesday, November 5, 2014 11:25:14 AM UTC-6, Ralph wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi,<div><br></div><div>I think it should be feasible to do this without changes to the code. In your DFTB calculation, find the Slater-Koster parameter file for Carbon, should be something like '<font face="courier new, monospace">cc.spl</font>', make three copies of that file '<font face="courier new, monospace">cx.spl</font>', '<font face="courier new, monospace">xc.spl</font>', '<font face="courier new, monospace">xx.spl</font>'. Then edit the file that assigns parameters to atoms ('<font face="courier new, monospace">scc_parameter</font>' ?), it contains a list of what spl file to use for which interaction. Add the following lines:</div><div><font face="courier new, monospace"> C X cx.spl</font></div><div><font face="courier new, monospace"> X C xc.spl</font></div><div><font face="courier new, monospace"> X X xx.spl</font></div><div>(the C C interaction should already be there).</div><div><br></div><div>You can then replace your two desired carbons in graphene by atoms of type X, and tune their interaction by modifying the <font face="courier new, monospace">xx.spl</font> file. In the simplest case, set all columns to zero to turn off all interactions. You can also scale the interaction, or turn off orbital-specific components.</div><div>X atoms will still behave like C atoms to other C atoms.<br><div><br></div><div>See my slides from the cp2k tutorial for details on setting up a dftb calculation and on the format of the .spl files.</div><div> <a href="http://ralph.koitz.info/doc/dftb_cp2k.pdf" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fralph.koitz.info%2Fdoc%2Fdftb_cp2k.pdf\46sa\75D\46sntz\0751\46usg\75AFQjCNEP68TPzBao_x_ACq_yHBzz5BIjBw';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fralph.koitz.info%2Fdoc%2Fdftb_cp2k.pdf\46sa\75D\46sntz\0751\46usg\75AFQjCNEP68TPzBao_x_ACq_yHBzz5BIjBw';return true;">http://ralph.koitz.info/doc/<wbr>dftb_cp2k.pdf</a><br></div></div><div><br></div><div>Hope that helps,</div><div>Ralph</div></div><div><br><div class="gmail_quote">On Wed, Nov 5, 2014 at 4:35 PM, Rafael Soler-Crespo <span dir="ltr"><<a href="javascript:" target="_blank" gdf-obfuscated-mailto="UchkX9Zh2roJ" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">raso...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi all,<div><br></div><div>I'm trying to perform a calculation to replicate a MD paper on CP2K using DFTB to see if the findings still hold (out of curiosity). In this paper, a crack is imposed on graphene by removing explicitly atoms from the material. I want to do this a little differently by turning off interactions between two neighboring carbon atoms. My system has around 7000 carbon atoms, and I want to forcefully zero any interactions between two adjacent C atoms. I searched around the documentation, but I couldn't find a great way to do this. Is it possible for someone to let me know if this is possible in CP2K, and if it is not, if it could be coded in principle?</div><div><br></div><div>Thanks,</div><div>Rafael</div></div><span><font color="#888888">
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