<div dir="ltr">Hi,<div><br></div><div>The atoms have to have the same ordering in i.xyz and f.xyz. You have NCH in one and NHC in the other.</div><div><br></div><div>-T</div><div><br><br>On Tuesday, February 4, 2020 at 7:37:46 AM UTC-5, Jacob Jensen wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><font face="arial, sans-serif">Dear all,</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">I'm doing CI-NEB calculations for a set of reactions on different metal surfaces. During my calculations I encountered a very bizarre behavior of the code which I haven't been able to find a reason for it.</font></div><div><font face="arial, sans-serif">The problem is: I give starting (<a href="http://i.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fi.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG8E7ipZiX0LOe-snzV9VYr6iLytQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fi.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG8E7ipZiX0LOe-snzV9VYr6iLytQ';return true;">i.xyz</a>) and end points (<a href="http://f.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ff.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEgwd9kPFExbLobIdhccdRrAtDoaQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ff.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEgwd9kPFExbLobIdhccdRrAtDoaQ';return true;">f.xyz</a>) to the CP2K to do a simple CI-NEB calculation, but in a completely random way (only happens to some reactions) the code exchanges the last two lines of the final configuration (<a href="http://f.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ff.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEgwd9kPFExbLobIdhccdRrAtDoaQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ff.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEgwd9kPFExbLobIdhccdRrAtDoaQ';return true;">f.xyz</a>) and starts the calculation with wrong coordinates. It has happened also for more than two lines in some structures.</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">For instance in the coordinates provided below, "tail <a href="http://f.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ff.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEgwd9kPFExbLobIdhccdRrAtDoaQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ff.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEgwd9kPFExbLobIdhccdRrAtDoaQ';return true;">f.xyz</a>" shows this:</font></div><div><font face="arial, sans-serif"><br></font></div><div><div><font face="arial, sans-serif"> Cu 2.5607522840 3.6179848259 10.2114493134</font></div><div><font face="arial, sans-serif"> Cu 5.1090632775 3.6199416787 10.2213122857</font></div><div><font face="arial, sans-serif"> Cu 7.6670721044 3.6155408617 10.2040766974</font></div><div><font face="arial, sans-serif"> Cu 0.0000430330 7.2313188455 10.2023231891</font></div><div><font face="arial, sans-serif"> Cu 2.5586830958 7.2299962241 10.2055589609</font></div><div><font face="arial, sans-serif"> Cu 5.1117660386 7.2291476249 10.2075861138</font></div><div><font face="arial, sans-serif"> Cu 7.6675778217 7.2313677337 10.2036234566</font></div><div><font face="arial, sans-serif"> N 6.0791607429 5.3490729602 14.3227064450</font></div><div><span style="background-color:rgb(255,255,0)"><font face="arial, sans-serif"> C 5.1523694228 5.0243296300 14.0410514879</font></span></div><div><span style="background-color:rgb(255,255,0)"><font face="arial, sans-serif"> H 4.1418019657 4.6566468208 13.6463880308</font></span></div></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">But once the job starts to run, CP2K exchanges the last two atoms (C and H) and starts with: </font></div><div><font face="arial, sans-serif"><br></font></div><div><div><font face="arial, sans-serif"> NEB|*************************<wbr>******************************<wbr>********************</font></div><div><font face="arial, sans-serif"> NEB| Geometry for Replica Nr. 2 in Angstrom</font></div><div><font face="arial, sans-serif"> NEB| Cu 1.278231000 1.807692000 1.278231000</font></div></div><div><font face="arial, sans-serif">.</font></div><div><font face="arial, sans-serif">.</font></div><div><font face="arial, sans-serif">.</font></div><div><div><font face="arial, sans-serif"> NEB| Cu 5.112380330 -0.000210681 10.202471653</font></div><div><font face="arial, sans-serif"> NEB| Cu 7.667615495 -0.000585929 10.201760866</font></div><div><font face="arial, sans-serif"> NEB| Cu 0.000556842 3.615646368 10.203009475</font></div><div><font face="arial, sans-serif"> NEB| Cu 2.560752284 3.617984826 10.211449313</font></div><div><font face="arial, sans-serif"> NEB| Cu 5.109063277 3.619941679 10.221312286</font></div><div><font face="arial, sans-serif"> NEB| Cu 7.667072104 3.615540862 10.204076697</font></div><div><font face="arial, sans-serif"> NEB| Cu 0.000043033 7.231318845 10.202323189</font></div><div><font face="arial, sans-serif"> NEB| Cu 2.558683096 7.229996224 10.205558961</font></div><div><font face="arial, sans-serif"> NEB| Cu 5.111766039 7.229147625 10.207586114</font></div><div><font face="arial, sans-serif"> NEB| Cu 7.667577822 7.231367734 10.203623457</font></div><div><font face="arial, sans-serif"> NEB| N 6.079160743 5.349072960 14.322706445</font></div><div><span style="background-color:rgb(255,255,0)"><font face="arial, sans-serif"> NEB| H 5.152369423 5.024329630 14.041051488</font></span></div><div><span style="background-color:rgb(255,255,0)"><font face="arial, sans-serif"> NEB| C 4.141801966 4.656646821 13.646388031</font></span></div></div><div><font face="arial, sans-serif">.</font></div><div><font face="arial, sans-serif">.</font></div><div><font face="arial, sans-serif">.</font></div><div><font face="arial, sans-serif">This happens without any error or warning and as you can imagine, the result of this calculation would be nothing but garbage. I have provided my input file, initial and final configurations together with the required basis sets and pseudopotentials to provide a possibility of simple test run (even with one core, cause the interpolation is at the very beginning of the output file).</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">I would be grateful if you can take a look and let me know about the possible reason. Or if you have had the same experience with other structures that would be beneficial for me to know.</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">I have tried with different versions of CP2K (e.g. 5.1 and 7.0) and the result is the same. Also, whenever I change <a href="http://i.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fi.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG8E7ipZiX0LOe-snzV9VYr6iLytQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fi.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG8E7ipZiX0LOe-snzV9VYr6iLytQ';return true;">i.xyz</a> to <a href="http://f.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ff.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEgwd9kPFExbLobIdhccdRrAtDoaQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ff.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEgwd9kPFExbLobIdhccdRrAtDoaQ';return true;">f.xyz</a> in :</font></div><div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif"> &TOPOLOGY</font></div><div><font face="arial, sans-serif"> COORD_FILE_FORMAT XYZ</font></div><div><font face="arial, sans-serif"> COORD_FILE_NAME <a href="http://i.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fi.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG8E7ipZiX0LOe-snzV9VYr6iLytQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fi.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG8E7ipZiX0LOe-snzV9VYr6iLytQ';return true;">i.xyz</a></font></div><div><font face="arial, sans-serif"> &END,</font></div></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">the same exchange of lines happens to <a href="http://i.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fi.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG8E7ipZiX0LOe-snzV9VYr6iLytQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fi.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG8E7ipZiX0LOe-snzV9VYr6iLytQ';return true;">i.xyz</a> and final replica (<a href="http://f.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ff.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEgwd9kPFExbLobIdhccdRrAtDoaQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ff.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEgwd9kPFExbLobIdhccdRrAtDoaQ';return true;">f.xyz</a>) stays intact! This really baffles me a lot. </font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Any remark or sharing of experience is highly appreciated.</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Kind regards,</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Jacob Jensen</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif"><br></font></div><div><br></div></div></blockquote></div></div>