<div dir="ltr">Hi,<div><br></div><div>Yes, using boron as a "fake carbon" will most likely lead cp2k to use the mass of actual boron in MD simulations.</div><div>I'd try the following: In your input, in &SUBSYS, put</div><div><font face="courier new, monospace"> &KIND B</font></div><div><font face="courier new, monospace"> MASS 12.0107 !desired mass of carbon</font></div><div><font face="courier new, monospace"> &END KIND</font></div><div><br></div><div>You can also (re)define numerous other atomic properties [1], but mass should be the only parameter relevant for MD runs, as the forces are taken from the DFTB part of the code with all parameters defined there.</div><div><br></div><div>Let me know if this works out for you,</div><div>Ralph</div><div><br></div><div><br></div><div>[1] <a href="http://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/KIND.html#desc_MASS">http://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/KIND.html#desc_MASS</a></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Nov 7, 2014 at 4:44 PM, Rafael Soler-Crespo <span dir="ltr"><<a href="mailto:rasole...@gmail.com" target="_blank">rasole...@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">Dear Ralph,<div><br></div><div>Thanks! Your suggestion seems to have done the trick, and everything is looking great. I did a quick simulation with a couple of these B-B bonds monotonically straining the box, and the system seems to be following fracture mechanics quite well. Nonetheless, I have a quick question regarding classifying the atom as a real element (in this case, boron) and some problems that may cause in actual implementations. </div><div><br></div><div>If I run molecular mechanics and/or molecular dynamics informed with DFTB energies and, consequently, forces, will the mass, atomic radii and stored information for boron be used in the calculation instead of carbon's for B atoms? I bring this up because when I print with one B atom present in my input, using a HIGH level of output, the output contains the mass of a boron atom (and its relevant information) when printing the structure initially. However, in xx.spl, xc.spl and cx.spl we have forcefully defined the mass of the system as that of a C atom. I'm just worried doing molecular mechanics and/or molecular dynamics with this setup will end up giving wrong mechanics/dynamics, as the atomic information for the B atoms in the "cracked bond" are incorrect so as to circumvent CP2K and use our own parameter sets.</div><div><br></div><div>What do you think?</div><div><br></div><div>Thanks for both your time and patience,</div><div>Rafael<span class=""><br><br>On Thursday, November 6, 2014 4:37:20 AM UTC-6, Ralph wrote:</span><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=""><div dir="ltr"><div>Dear Rafael,<br><br></div>Thanks for trying my suggestion. I played around with it some more and got something more reasonable after making the following changes:<br><ul><li>Instead of using atom symbol X, you have to use a 'real' element for your non-interacting carbons. I called it B.</li><li>Drop the KIND X // ELEMENT C ... part in &SUBSYSTEMS. <br></li><li>In the xc.spl and cx.spl files, remove lines 2 and 3. (The format is different for homo- and heteronuclear interactions, compare e.g. oo.spl and oh.spl in a water setup).</li><li>In the xx.spl, in the spline section, leave the first two columns as is, set the others to zero. The first line after Spline should be "0 0 -1" to turn off also the very short-range repulsion.</li></ul><p>I attached the xx.spl file and param_table files.</p><p></p><p>Using these settings the following things work seemingly fine:</p><ul><li>A graphene sheet with only one "B" atom behaves like an unmodified graphene sheet</li><li>A graphene sheet with two adjacent "B" still looks physical, but the B-B bond compresses, presumably because all repulsion has been turned off. C-C and C-"B" bonds remain mostly unperturbed.</li></ul><p>Let me know how this works out for you.<br></p><p><br></p><p>Ralph<br></p></div></span><div><div class="h5"><div><br><div class="gmail_quote">On Thu, Nov 6, 2014 at 12:42 AM, Rafael Soler-Crespo <span dir="ltr"><<a>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 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_<u></u>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><span><br>On Wednesday, November 5, 2014 11:25:14 AM UTC-6, Ralph wrote:</span><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><span><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">http://ralph.koitz.info/doc/<u></u>df<u></u>tb_cp2k.pdf</a><br></div></div><div><br></div><div>Hope that helps,</div><div>Ralph</div></div></span><div><br><div class="gmail_quote"><span>On Wed, Nov 5, 2014 at 4:35 PM, Rafael Soler-Crespo <span dir="ltr"><<a>raso...@gmail.com</a>></span> wrote:<br></span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span><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><span><font color="#888888"><span> <p></p> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br></span> To unsubscribe from this group and stop receiving emails from it, send an email to <a>cp2k+uns...@googlegroups.<u></u>com</a>.<br> To post to this group, send email to <a>cp...@googlegroups.com</a>.<span><br> Visit this group at <a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/<u></u>group<u></u>/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/<u></u>op<u></u>tout</a>.<br> </span></font></span></blockquote></div><br></div> </blockquote></div></div><div><div> <p></p> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a>cp2k+uns...@googlegroups.<u></u>com</a>.<br> To post to this group, send email to <a>cp...@googlegroups.com</a>.<br> Visit this group at <a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/<u></u>group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/<u></u>optout</a>.<br> </div></div></blockquote></div><br></div> </div></div></blockquote></div></div><div class="HOEnZb"><div class="h5"> <p></p> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> Visit this group at <a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br> </div></div></blockquote></div><br></div>