<div>Hi there,</div><div>I'm a fresh user of CP2K. Planning to use it for MOFs cell optimizations. I have a basic/stupid question regarding the input file. If I wanna optimize the unit cell parameters, does the input file have to include all atoms in a unit cell, or I can minimize the number of atoms in a way?</div><div><br></div><div>Thanks, S</div><div><br></div><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Sunday, February 28, 2021 at 9:44:51 PM UTC-5 Monu Joy wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr"><div dir="ltr">Hi Leo<div><br></div><div>Thanks for the help. I started a CASTEP calculation on the CP2K twisted (relaxed) geometry and it converged as twisted, and this CASTEP relaxed twisted geometry is more stable than the untwisted version by a factor of 0.00030737 eV. Gamma point was used for both twisted and untwisted
calculations.</div><div><br></div><div>Moreover, I have tried the CP2K calculation as you suggested to untwist the geometry but it converged as twisted. I am using CP2K 7.1 and the only change that I have made in the input was the removal of the following lines: </div><div><br></div><div> #COORD_FILE CP2K_Optimzed structure_CIF.cif<br> #COORD_FILE_FORMAT CIF<br></div><div><br></div><div>Are there any significant changes between 7.1 and 8.1 in terms of dealing with symmetry...?</div><div><br></div><div>-Monu</div></div><br><div class="gmail_quote"></div></div><div dir="ltr"><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Feb 24, 2021 at 3:50 AM Leopold Talirz <<a href data-email-masked rel="nofollow">leo...@gmail.com</a>> wrote:<br></div></div></div><div dir="ltr"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Monu,<div><br></div><div>thanks for following up - I did run a CP2K cell optimization starting from your relaxed "twisted" CP2K geometry. You find the trajectory and movie attached</div><div>Does this agree with your results?</div><div><br></div><div>It certainly seems to "untwist" the ligands (see movie) - I had to stop the optimization at some point though because convergence became very slow.</div><div><br></div><div>Some stats from the total energy:<br></div><div><br></div><div>First total energy (single-point): -2160.041714658635101</div><div>First optimization step: -2160.136731180092738</div><div>50th optimization step: -2160.<a href="tel:(281)%20755-1900" value="+12817551900" target="_blank" rel="nofollow">2817551900</a></div><div>100th optimization step: -2160.2996248085</div><div><br></div><div>I.e. after the first "untwisting" that lowers total energy by ~260mHa (quite significant), the final 50 steps lower the total energy by less than 3 mHa.</div><div>This is with cp2k 8.1 [2] and with minimal modifications to the input file (see tar file). It's not clear to me why you would get a different result - both MULTIPLE_UNIT_CELL 1 1 2 and 2 2 2 K-points should give this result.</div><div><br></div><div>As to why the CASTEP gamma point calculation does not yield the twisted structure: it is possible that this involves breaking a symmetry that is for some reason preserved in the CASTEP calculation (don't know).</div><div>Can you try starting your CASTEP calculation from the twisted CP2K geometry and see where it ends up?</div><div>If it remains twisted, you can then compare total energies to the untwisted result, which should tell you which one is the actual minimum.</div><div><br></div><div>Best,</div><div>Leo</div><div><br></div><div>[1] Try "grep i <a href="http://925-pos-1.xyz" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://925-pos-1.xyz&source=gmail&ust=1622832647883000&usg=AFQjCNEfY1oYjggCYBizEX-EaohRE45EaA">925-pos-1.xyz</a>" on the trajectory</div><div>[2] Our previous calculations were with cp2k v5.1 though.</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 23 February 2021 at 05:45:09 UTC+1 Monu Joy wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div style="font-family:verdana,helvetica,sans-serif;font-size:13px"><div><div dir="ltr"><div><div dir="ltr" style="font-family:verdana,helvetica,sans-serif">Even though the doubling of the z-axis (MULTIPLE_UNIT_CELL 1 1 2) seemed fine in the initial cycles, it ended up being twisted on convergence. Then I have tried the K-point scheme (SCHEME MONKHORST-PACK 2 2 2), where the result was the same, twisted. However, the structure seems reasonable (no twisting) in CASTEP even with the gamma point.</div><div dir="ltr" style="font-family:verdana,helvetica,sans-serif"><br clear="none"></div><div dir="ltr" style="font-family:verdana,helvetica,sans-serif">But of course, the culprit could be the small z-axis, but I am not sure how to tackle this in CP2K.</div><div style="font-family:verdana,helvetica,sans-serif"><br clear="none"></div><div style="font-family:verdana,helvetica,sans-serif"><div dir="ltr" style="font-size:small">-Monu</div></div></div></div></div>
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On Friday, 19 February, 2021, 05:25:24 pm GMT-5, Leopold Talirz <<a rel="nofollow">leo...@gmail.com</a>> wrote:
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</div></div></div><div><div><div style="font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:13px;color:rgb(38,40,42)"><div><div><div><div><div>Since Andres Ortega from our group noticed this with a similar Al MOF, I just wanted to confirm:</div><div><br clear="none"></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div style="font-family:verdana,helvetica,sans-serif;font-size:13px"><div><div dir="ltr">Thanks, Marcella, for the suggestions. I just increased the Z direction by <span>MULTIPLE_UNIT_CELL 1 1 2. Albeit it's not yet converged, the intermediate geometries are reasonable (no twisting so far). </span></div></div></div></div></blockquote><div>This is indeed the source of the issue here - doubling the cell along z results in a reversal of the twisting of the ligands, even when starting from the twisted geometry (I checked).</div><div><br clear="none"></div><div>In our case, the twisted structure was the correct minimum for the unit-cell only calculation, with a substantially lower energy (~250meV per twisted phenyl), while for the doubled cell the twisted structure was slightly higher in energy (order of 10meV per twisted phenyl).</div><div><br clear="none"></div><div>This then re-raises the original question of the thread, which is why CASTEP seems to yield a different result. I believe the answer is in the CASTEP output:</div><div><br clear="none"></div><div><div> -------------------------------</div><div> k-Points For BZ Sampling</div><div> -------------------------------</div><div> MP grid size for SCF calculation is 1 1 2</div><div> with an offset of 0.000 0.000 0.000</div><div> Number of kpoints used = 1</div></div><div><br clear="none"></div><div>CASTEP chooses a 2-kpoint grid along z (which reduced to just a single k-point calculation through symmetry).</div><div><br clear="none"></div><div>From the CASTEP manual [1]:</div><div><br clear="none"></div><div><div>> For cubic cells and for the C direction of hexagonal cells the even and odd grids for the Monkhorst-Pack scheme give the same number of k-points. However, the even grid provides better sampling and will always be used automatically under these conditions. This ensures that a good grid with k-point separation at (or less than) the specified target can be achieved more economically. As a consequence, such lattices may have much finer separations than requested as odd grids have been excluded - even though they would have been closer to the specified separation - and the better even grids have been taken in preference.</div><div><br clear="none"></div><div>I suspect that forcing CASTEP to do a Gamma-point calculation would result in the same twisting as seen in CP2K (in our case, we checked with CRYSTAL).</div><div>For our MOF, just to exclude any possibility of issues with OT, we also tested this with DIAGONALIZATION and KPOINTS in cp2k and got the same result as with the 1x1x2 supercell.</div><div><br clear="none"></div><div>The lesson is simply that ~6.5A can be too short along the direction of these inorganic chains/rods in MOFs.</div><div><br clear="none"></div><div>Best,</div><div>Leopold</div></div><div><br clear="none"></div><div>[1] <a href="http://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/CASTEP.html#modules/castep/dlgcastepelecoptkpoints.htm?Highlight=monkhorst" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/CASTEP.html%23modules/castep/dlgcastepelecoptkpoints.htm?Highlight%3Dmonkhorst&source=gmail&ust=1622832647884000&usg=AFQjCNGab1-u6xERWqg9BH1B7Y6ahSt6Yg">http://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/CASTEP.html#modules/castep/dlgcastepelecoptkpoints.htm?Highlight=monkhorst</a></div><div><div> </div></div></div></div></div></div></div></div></div><div><div><div style="font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:13px;color:rgb(38,40,42)"><div><div><div><div>
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