<div dir="ltr"><div class="gmail_default" style="font-family:times new roman,serif">Hi,</div><div class="gmail_default" style="font-family:times new roman,serif"><br></div><div class="gmail_default" style="font-family:times new roman,serif">As usual, human error is to blame. I realized that the previous run was input using separate A, B, and C commands, not the ABC command. I did get it to run (although not to converge, probably because the coordinates need to be adjusted). </div><div class="gmail_default" style="font-family:times new roman,serif"><br></div><div class="gmail_default" style="font-family:times new roman,serif">Thanks for all your help,</div><div class="gmail_default" style="font-family:times new roman,serif"><br></div><div class="gmail_default" style="font-family:times new roman,serif">Laszlo</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Feb 17, 2015 at 7:22 PM, Matt W <span dir="ltr"><<a href="mailto:MattWa...@gmail.com" target="_blank">MattWa...@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"><div>Hi,</div><div><br></div><div>Are guys you running the same input on the same machine, with the same executable?</div><div><br></div><div>Then that would be really weird.</div><div><br></div><div><span style="font-family:'times new roman',serif">Laszlo, what I am hinting at is could you try a different cp2k module just to check that it isn't somehow a bug of </span><br></div><div><span style="font-family:'times new roman',serif"><br></span></div><div><div><font face="times new roman, serif"> CP2K| version string: CP2K version 2.6 (Development Version)</font></div><div><font face="times new roman, serif"> CP2K| source code revision number: svn:14482</font></div><div><font face="times new roman, serif"> CP2K| is freely available from <a href="http://www.cp2k.org/" target="_blank">http://www.cp2k.org/</a></font></div><div style="font-family:'times new roman',serif"><br></div></div><div style="font-family:'times new roman',serif">You don't need to run the whole big system, just see if anything with a monoclinic cell gives you the same problems.</div><span class="HOEnZb"><font color="#888888"><div style="font-family:'times new roman',serif"><br></div><div>Matt</div></font></span><div><div class="h5"><br>On Tuesday, February 17, 2015 at 5:28:52 PM UTC, S Ling wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I don't have problem with the latter setting. I am not sure why you didn't get the same.<div><br></div><div>SL<br><div><br></div><div><br><br>On Tuesday, February 17, 2015 at 5:20:04 PM UTC, Laszlo Ryan Seress wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div style="font-family:times new roman,serif">I did the latter before I tried to manually dictate the symmetry, the same issue of changing all angles to 90 occurred. That file is attached here.</div><div style="font-family:times new roman,serif"><br></div><div style="font-family:times new roman,serif">Apropos, I think that using the former would do the calculation on a reflected version of my system (because b and c are the same length, if I switch the y and z coordinates, wouldn't I luck out and still have a functional structure? Maybe I am picturing this in my head wrong). I will still probably have to do the rotation to check.</div><div style="font-family:times new roman,serif"><br></div><div style="font-family:times new roman,serif">Any ideas as to why the latter is failing? I still don't understand why it is overwriting my inputted angles. </div><div style="font-family:times new roman,serif"><br></div><div style="font-family:times new roman,serif">Thanks, as always,</div><div style="font-family:times new roman,serif">Laszlo <br></div><div style="font-family:times new roman,serif"><br></div><div style="font-family:times new roman,serif"><br></div></div><div><br><div class="gmail_quote">On Tue, Feb 17, 2015 at 5:12 PM, S Ling <span dir="ltr"><<a rel="nofollow">ling...@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"><div>Either</div><span><div><br></div><div> &CELL</div><div> ABC 16.000 15.600 15.600</div><div> ALPHA_BETA_GAMMA 90.00000000 86.40000000 90.00000000</div><div> SYMMETRY MONOCLINIC</div><div> &END CELL</div><div><br></div></span><div>or</div><span><div><br></div><div> &CELL</div><div> ABC 16.000 15.600 15.600</div><div> ALPHA_BETA_GAMMA 90.00000000 90.00000000 86.40000000</div></span><div> &END CELL</div><div><br></div><div>should give you correct "BETA" angle. You need to rotate the whole lattice system for the first setting. Since you are not doing a CELL_OPT, I would suggest you to use the second setting, in which you don't need to change the coordinate system.</div><span><font color="#888888"><div><br></div><div>SL</div></font></span><div><span><br>On Tuesday, February 17, 2015 at 4:50:12 PM UTC, Laszlo Ryan Seress 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"><div style="font-family:'times new roman',serif">Hi,</div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif">I've attached my input and coordinate files. There is some "overflow" beyond the edges of the box, but I have been told this is ok because of periodic boundary conditions. I got the coordinates from the SI of a paper, which I have not attached due to size, but can be found at this link, in case it is of interest. <a href="http://dx.doi.org/10.1021/ma100551m" rel="nofollow" target="_blank">dx.doi.org/10.1021/ma100551m</a> In the SI, they have gamma = 86.4, which is why I have it set up that way. </div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif">I am aware that since I didn't rotate the coordinates yet there could be (i.e. almost definitely are) issues with the accuracy of the results, but I suppose I'm surprised that the geometry is still being set to 90 degrees. From what I understand, the program is immediately setting it to an orthorhomic box and so the errors are occurring on calculations that aren't in the right symmetry anyways. </div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif">Thanks again for taking the time to help out with this.</div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif">Laszlo</div></div></span><div><br><div class="gmail_quote"><span>On Tue, Feb 17, 2015 at 4:38 PM, S Ling <span dir="ltr"><<a rel="nofollow">ling...@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">It would be more useful if you can provide your full input file.<div><br></div><div>As I said in the first post, you need to rotate your lattice if you swap BETA and GAMMA angles, i.e. you need to change the whole coordinate system and coordiantes of all the atoms. The "ERRORL2 in cp_fm_cholesky:cp_fm_cholesky_<u></u><u></u>decompose processor" error message might mean you have a very bad geometry, which is related to the way you set your CELL section.</div><span><font color="#888888"><div><br></div><div>SL</div><div><br></div><div><br></div></font></span></div></span><div><div><div><br><div class="gmail_quote"><div><div>On 17 February 2015 at 16:11, Laszlo Ryan Seress <span dir="ltr"><<a rel="nofollow">lasz...@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div style="font-family:'times new roman',serif">Thank you again for the reply. I thought this was a really good suggestion so I was surprised to see that it didn't work (and also felt silly that I didn't think of it myself).</div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif">I ran the program twice, with inputs:</div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif">(run *759)</div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif"><div> &CELL</div><div> ABC 16.000 15.600 15.600</div><div> ALPHA_BETA_GAMMA 90.00000000 86.40000000 90.00000000</div><div> SYMMETRY MONOCLINIC</div><div> &END CELL</div><div><br></div><div>and</div><div><br></div><div>(run *762)</div><div><br></div><div><div> &CELL</div><div> ABC 16.000 15.600 15.600</div><div> ALPHA_BETA_GAMMA 90.00000000 90.00000000 86.40000000</div><div> SYMMETRY MONOCLINIC</div><div> &END CELL</div><div><br></div><div>Both runs ended with errors. </div><div><br></div><div>Interestingly, in both cases, the output has the following information in the beginning:</div><div><br></div><div><div>CELL_TOP| Volume [angstrom^3]: 3886.077</div><div> CELL_TOP| Vector a [angstrom 16.000 0.000 0.000 |a| = 16.000</div><div> CELL_TOP| Vector b [angstrom 0.000 15.600 0.000 |b| = 15.600</div><div> CELL_TOP| Vector c [angstrom 0.000 0.000 15.600 |c| = 15.600</div><div> CELL_TOP| Angle (b,c), alpha [degree]: 90.000</div><div> CELL_TOP| Angle (a,c), beta [degree]: 90.000</div><div> CELL_TOP| Angle (a,b), gamma [degree]: 90.000</div><div> CELL_TOP| Requested initial symmetry: MONOCLINIC</div><div> CELL_TOP| Numerically orthorhombic: YES</div><div><br></div><div>So still the angles are being overwritten. However, something else is clearly breaking because the program is ending with errors. I don't really know how to interpret the error reports in great detail, but I have attached them in case they prove useful.</div><div><br></div><div>Any thoughts?</div><div><br></div><div>Laszlo</div><div><br></div></div></div></div></div></div></div><div><div><div><br><div class="gmail_quote">On Tue, Feb 17, 2015 at 2:32 PM, S Ling <span dir="ltr"><<a rel="nofollow">ling...@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">Please remove the three A/B/C cell vectors, and set your CELL section like this:<div><br></div><div><div>&CELL</div><div><span style="white-space:pre-wrap"> </span>ABC 16.0 15.6 15.6</div><span><div><span style="white-space:pre-wrap"> </span>ALPHA_BETA_GAMMA 90.00000000 86.40000000 90.00000000</div><div><span style="white-space:pre-wrap"> </span>SYMMETRY MONOCLINIC</div><div>&END CELL</div></span></div><div><br></div><div>SL<span><br><br>On Tuesday, February 17, 2015 at 2:18:00 PM UTC, Laszlo Ryan Seress wrote:</span><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><span><div style="font-family:'times new roman',serif">Thank you for your reply. </div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif">I tried the following input:</div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif"><div> &CELL</div><div> A 16.00000000 0.000000000 0.000000000</div><div> B 0.000000000 15.60000000 0.000000000</div><div> C 0.000000000 0.000000000 15.60000000</div><div> ALPHA_BETA_GAMMA 90.00000000 86.40000000 90.00000000</div><div> SYMMETRY MONOCLINIC</div><div> &END CELL</div></div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif">but still got this output:</div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif"><div> CELL| Volume [angstrom^3]: 3893.760</div><div> CELL| Vector a [angstrom]: 16.000 0.000 0.000 |a| = 16.000</div><div> CELL| Vector b [angstrom]: 0.000 15.600 0.000 |b| = 15.600</div><div> CELL| Vector c [angstrom]: 0.000 0.000 15.600 |c| = 15.600</div><div> CELL| Angle (b,c), alpha [degree]: 90.000</div><div> CELL| Angle (a,c), beta [degree]: 90.000</div><div> CELL| Angle (a,b), gamma [degree]: 90.000</div><div> CELL| Requested initial symmetry: MONOCLINIC</div><div> CELL| Numerically orthorhombic: YES</div></div><div><br></div><div><div style="font-family:'times new roman',serif">It seems to be overwriting my inputted angles and replacing them with 90 degrees.</div><div style="font-family:'times new roman',serif"><br></div><div style="font-family:'times new roman',serif">Best,</div><div style="font-family:'times new roman',serif">Laszlo</div><br></div><div><br></div></span><div><br><div class="gmail_quote"><div><div>On Tue, Feb 17, 2015 at 2:02 PM, S Ling <span dir="ltr"><<a rel="nofollow">ling...@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">You need to rotate your lattice so that your beta=86.4, not gamma=86.4. This is the requirement of MONOCLINIC space symmetry in CP2K, see <a href="http://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#desc_SYMMETRY" rel="nofollow" target="_blank">http://manual.cp2k.org/<u></u>tru<u></u><u></u>nk/CP2K_INPUT/FORCE_EVAL/<u></u>SUBSY<u></u><u></u>S/CELL.html#desc_SYMMETRY</a><span><font color="#888888"><div><br></div></font></span><div><span><font color="#888888">SL</font></span><div><div><br><br>On Tuesday, February 17, 2015 at 1:15:44 PM UTC, Laszlo Ryan Seress wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear All,<div><br></div><div>I have been having an issue with the symmetry command in the CELL section. My input has:</div><div><br></div><div><div> &CELL</div><div> A 16.00000000 0.000000000 0.000000000</div><div> B 0.000000000 15.60000000 0.000000000</div><div> C 0.000000000 0.000000000 15.60000000</div><div> ALPHA_BETA_GAMMA 90.00000000 90.00000000 86.40000000</div><div> SYMMETRY MONOCLINIC</div><div> &END CELL</div></div><div><br></div><div>but the output has:</div><div><br></div><div><div> CELL_TOP| Volume [angstrom^3]: 3893.760</div><div> CELL_TOP| Vector a [angstrom 16.000 0.000 0.000 |a| = 16.000</div><div> CELL_TOP| Vector b [angstrom 0.000 15.600 0.000 |b| = 15.600</div><div> CELL_TOP| Vector c [angstrom 0.000 0.000 15.600 |c| = 15.600</div><div> CELL_TOP| Angle (b,c), alpha [degree]: 90.000</div><div> CELL_TOP| Angle (a,c), beta [degree]: 90.000</div><div> CELL_TOP| Angle (a,b), gamma [degree]: 90.000</div><div> CELL_TOP| Requested initial symmetry: MONOCLINIC</div><div> CELL_TOP| Numerically orthorhombic: YES</div></div><div><br></div><div>Has anyone had a similar issue with getting the angles changed and the program changing the symmetry from monoclinic to orthorhombic?</div><div><br></div><div>Thanks for any help you may be able to provide.</div><div><br></div><div>Best regards,</div><div>Laszlo </div></div></blockquote></div></div></div></div></div></div><div><div><div><div>
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