<div dir="ltr">Well I filled out the input file as well as I could figure out from your tips. CP2K runs for a few minutes and then aborts with the error "KS energy is an abnormal value (NaN/Inf)". I tried setting a small MAX_SCF value, but it still hits that error. Any other tips? Here is my input file:<br><br><div>&GLOBAL</div><div> PROJECT water-formation</div><div> RUN_TYPE MD</div><div> PRINT_LEVEL LOW</div><div>&END GLOBAL</div><div>&MOTION</div><div> &MD</div><div> ENSEMBLE NVT</div><div> &THERMOSTAT</div><div> TYPE CSVR</div><div> &END THERMOSTAT</div><div> &END MD</div><div>&END MOTION</div><div>&FORCE_EVAL</div><div> &SUBSYS</div><div> &KIND H</div><div> BASIS_SET DZVP-GTH-PADE</div><div> POTENTIAL GTH-PADE-q1</div><div> &END KIND</div><div> &KIND O</div><div> BASIS_SET DZVP-GTH-PADE</div><div> POTENTIAL GTH-PADE-q6</div><div> &END KIND</div><div> &CELL</div><div> ABC 10 10 10</div><div> PERIODIC NONE</div><div> &END CELL</div><div> &COORD</div><div> H 4.0 4.0 4.66667</div><div> H 6.0 6.0 4.66667</div><div> O 5.0 5.0 5.66667</div><div> &END COORD</div><div> &END SUBSYS</div><div> &DFT</div><div> BASIS_SET_FILE_NAME data/BASIS_SET</div><div> POTENTIAL_FILE_NAME data/POTENTIAL</div><div> LSD</div><div> &SCF</div><div> ADDED_MOS 10</div><div> &DIAGONALIZATION</div><div> &END DIAGONALIZATION</div><div> &MIXING</div><div> METHOD BROYDEN_MIXING</div><div> &END MIXING</div><div> &SMEAR</div><div> METHOD FERMI_DIRAC</div><div> &END SMEAR</div><div> &END SCF</div><div> &XC</div><div> &XC_FUNCTIONAL PADE</div><div> &END XC_FUNCTIONAL</div><div> &END XC</div><div> &PRINT</div><div> &E_DENSITY_CUBE</div><div> &EACH</div><div> MD 1</div><div> &END EACH</div><div> FILENAME CUBE</div><div> &END E_DENSITY_CUBE</div><div> &END PRINT</div><div> &END DFT</div><div>&END FORCE_EVAL</div><br>On Thursday, June 4, 2020 at 10:10:06 AM UTC-4, Michael Hale wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Great! Thank you. I'll look into those options and hopefully mess with it some more this weekend.<div><br></div><div>Is there much of a hobbyist community around computational chemistry? I'm a pretty experienced software developer, but still new to this. I know there are projects like Folding@Home which don't give you much control, and Chemistry Stack Exchange which is more just traditional Q&A. But I'd love to find community projects to help enhance digital chemistry textbooks with ab initio quantum MD animations of common reactions and such.</div><div><br></div><div>I actually first tried this during a weekend a couple of years ago. Here was the result:<br><a href="https://www.youtube.com/watch?v=foG5LgFYb2o" target="_blank" rel="nofollow" onmousedown="this.href='https://www.youtube.com/watch?v\x3dfoG5LgFYb2o';return true;" onclick="this.href='https://www.youtube.com/watch?v\x3dfoG5LgFYb2o';return true;">https://www.youtube.com/watch?<wbr>v=foG5LgFYb2o</a><br><br>I finally revisited it a week or two ago. I thought maybe just my initial conditions needed to be tweaked, but then I realized my simulation set up had deeper problems, haha. Thanks again for your help. I hope to post an update again soon. <br><br>On Thursday, June 4, 2020 at 9:26:25 AM UTC-4, jgh wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi
<br>
<br>What I would do:
<br>
<br>Small basis e.g. DZVP
<br>LSD
<br>SCF with Diagonalization and Broyden mixing, use all MOs
<br>Fermi-Dirac Smearing with high temperature
<br>NVT MD with velocity rescaling to get rid of excessive energy
<br>Print CUBE file automatically during MD
<br>
<br>regards
<br>
<br>Juerg Hutter
<br>------------------------------<wbr>------------------------------<wbr>--
<br>Juerg Hutter Phone : ++41 44 635 4491
<br>Institut für Chemie C FAX : ++41 44 635 6838
<br>Universität Zürich E-mail: <a rel="nofollow">h...@chem.uzh.ch</a>
<br>Winterthurerstrasse 190
<br>CH-8057 Zürich, Switzerland
<br>------------------------------<wbr>------------------------------<wbr>---
<br>
<br>-----<a rel="nofollow">c...@googlegroups.com</a> wrote: -----
<br>To: "cp2k" <<a rel="nofollow">c...@googlegroups.com</a>>
<br>From: "Michael Hale"
<br>Sent by: <a rel="nofollow">c...@googlegroups.com</a>
<br>Date: 06/04/2020 05:08AM
<br>Subject: [CP2K:13450] Visualize electron density during formation of a water molecule
<br>
<br>Hey, sorry for the basic question. I've skimmed some computational chemistry books, but I still find the CP2K documentation a bit overwhelming. I'm trying to put two hydrogens an an oxygen atom near each other and watch the spontaneous assembly of a water molecule. I can make the input file and have CP2K output the forces on the atoms and a cube file that I can use to make a 3D visualization of the electron density in Mathematica. Then I update the atom positions with a simple velocity Verlet update and run CP2K again. The resulting animation looks how I want stylistically, but the behavior is clearly not accurate. The atoms come together and bounce off of each other and come back together and bounce off harder. They keep getting more energy and bouncing farther and farther away until they fly apart instead of bonding together.
<br>
<br>Is the error that the energy calculation for the forces and electron density isn't converging and causing the erratic behavior? Is the error probably in the way I'm updating the atom positions manually? Can I use the CP2K molecular dynamics functionality to do multiple steps of the simulation at once while also outputting the cube file of the electron density for each step? Is this type of simulation of the formation of small molecules within the scope of CP2K? It seems most people typically assume the molecules are already formed and they just want to simulate how those molecules interact, not how atoms come together to form the small molecules.
<br>
<br>This is all just for fun. I just want to watch the animations and see how "sticky" the atoms and molecules are. Thanks for any help and guidance you might provide.
<br> --
<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 rel="nofollow">c...@googlegroups.com</a>.
<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/e90450de-cd30-4bad-ae96-96779a50764e%40googlegroups.com" rel="nofollow" target="_blank" onmousedown="this.href='https://groups.google.com/d/msgid/cp2k/e90450de-cd30-4bad-ae96-96779a50764e%40googlegroups.com';return true;" onclick="this.href='https://groups.google.com/d/msgid/cp2k/e90450de-cd30-4bad-ae96-96779a50764e%40googlegroups.com';return true;">https://groups.google.com/d/<wbr>msgid/cp2k/e90450de-cd30-4bad-<wbr>ae96-96779a50764e%<wbr>40googlegroups.com</a>.
<br>
<br></blockquote></div></div></blockquote></div>