<div>Hi Ashley,</div><div> </div><div>For some reason USE_FINER_GRID T in the &XC_GRID causes the internal pressure to explode. Try removing it and maybe increase the CUTOFF instead. </div><div> </div><div>Cheers,</div><div>Fabian </div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 24 October 2023 at 16:48:44 UTC+2 Ashley Dickson wrote: </div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">This is the input file using the crystallography data:<div> </div><div></div><div> &FORCE_EVAL METHOD Quickstep &DFT BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME GTH_POTENTIALS LSD &POISSON POISSON_SOLVER PERIODIC PERIODIC XYZ &END POISSON &MGRID NGRIDS 5 CUTOFF 800 REL_CUTOFF 60 &END MGRID &QS METHOD GPW EPS_PGF_ORB 1E-16 &END QS &SCF &SMEAR ON ELECTRONIC_TEMPERATURE 1000 METHOD FERMI_DIRAC &END SMEAR ADDED_MOS 700 CHOLESKY INVERSE SCF_GUESS RESTART EPS_SCF 1.0E-6 MAX_SCF 250 &DIAGONALIZATION ON ALGORITHM STANDARD &END DIAGONALIZATION &MIXING T METHOD BROYDEN_MIXING ALPHA 0.5 BETA 1.5 NBUFFER 15 &END MIXING &END SCF &KPOINTS SCHEME MONKHORST-PACK 2 2 2 FULL_GRID yes SYMMETRY yes VERBOSE yes PARALLEL_GROUP_SIZE -1 &END KPOINTS &XC &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &XC_GRID USE_FINER_GRID T &END XC_GRID &END XC &END DFT &SUBSYS &COORD </div><div>SCALED Y 0.5 0.5 0.5 Ba 0.5 0.5 0.18393 Cu 0 0 0 Cu 0 0 0.35501 O 0 0.5 0 O 0.5 0 0.37819 O 0 0.5 0.37693 O 0 0 0.15840</div><div> &END COORD &TOPOLOGY &END TOPOLOGY &CELL SYMMETRY ORTHORHOMBIC </div><div> ABC 3.8203 3.88548 11.68349 PERIODIC XYZ &CELL_REF ABC 14 14 28 &END CELL_REF</div><div> &END CELL &KIND O BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q6 &END KIND &KIND Ba BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q10 &END KIND &KIND Y BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q11 &END KIND &KIND Cu BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q11 &END KIND &PRINT &CELL HIGH &END CELL &END PRINT &END SUBSYS STRESS_TENSOR ANALYTICAL &END FORCE_EVAL &GLOBAL PROJECT SZV RUN_TYPE CELL_OPT PRINT_LEVEL MEDIUM &END GLOBAL &MOTION &CELL_OPT KEEP_SYMMETRY .TRUE. </div><div> OPTIMIZER CG</div><div> KEEP_ANGLES EXTERNAL_PRESSURE [Pa] 100000 &END CELL_OPT &END MOTION </div><div>There was no initial warning, the cell just continued to shrink and the SCF did converge. The output file is attached. Thanks Ash </div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 24 October 2023 at 15:41:13 UTC+1 <a href data-email-masked rel="nofollow">fabia...@gmail.com</a> wrote: </div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> <div>The coordinates above are not a super cell from for same crystal as the one from the database. I suggest that you use the correct unit cell again. Did cp2k produce any warning during your initial cell optimization (the one that shrunk)? Did the scf properly converge? Without seeing the output it is difficult to help. You should probably decrease ALPHA to 0.1 or 0.2, ADDED_MOS 700 is excessive, 10 should be enough. </div><div> </div><div>Fabian</div> <div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 24 October 2023 at 16:35:11 UTC+2 Ashley Dickson wrote: </div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I feel like I'm not being very clear here apologies. So, I want to obtain a reasonable value for the lattice parameter of YBCO. Using the current input file but with the coordinates given on the crystallography database website, I run into the issue that the simulation cell volume shrinks and gives unphysical results. To my mind, this means it is not treating the structure I have provided as periodic in space. How can I modify my input such that it appears to cp2k that my unitcell is repeated in space? <div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 24 October 2023 at 15:28:47 UTC+1 Ashley Dickson wrote: </div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><a href="http://www.crystallography.net/cod/1000030.html" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en-GB&q=http://www.crystallography.net/cod/1000030.html&source=gmail&ust=1698318143813000&usg=AOvVaw02eVfOW_bYbxgGQtnG0Xxb">http://www.crystallography.net/cod/1000030.html</a><div> </div><div>This is the unit cell from the database. When I ran the cell optimisations with this structure and cell parameters of ABC 3.8 3.9 11.7, the cell just continually shrunk to an unreasonable size. I then tried opening the cif file in vesta and exporting the whole unit cell as an xyz file, which is where I got the current coordinates from.</div><div> </div><div>Many thanks</div><div>Ash</div><div> </div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 24 October 2023 at 15:24:47 UTC+1 <a rel="nofollow">fabia...@gmail.com</a> wrote: </div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Is this the unit cell from the open crystallography database? If not, how have you modified it?</div><div> </div><div>Cheers,</div><div>Fabian </div> <div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 24 October 2023 at 16:16:45 UTC+2 Ashley Dickson wrote: </div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Fabian <div> </div><div>I think this is the main issue that's confusing me. I have a unit cell of YBCO with lattice parameters 3.8 3.9 11.7 (roughly), however increased the cell size as it was not working. I realise my mistake is that the periodicity of the cell results in the atoms being on top of each other. In order that I can retrieve accurate lattice parameters for the bulk crystal how should I modify the coordinates? </div><div> </div><div>Many thanks </div><div>Ash </div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 24 October 2023 at 15:10:24 UTC+1 <a rel="nofollow">fabia...@gmail.com</a> wrote: </div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Hi Ashley,</div><div> </div><div>The ABC 4 4 12 seems a bit strange, are you sure this is correct? Two of the atoms are Cu 0 0 0Cu 3.820300 0.000000 11.683490 </div><div>if your lattice is indeed 4 4 12 these two are almost on top of each other. I expect the cell is much too small which is why its size keeps increasing. </div><div> </div><div>Also, did your scf converge and are there any warnings in the output?</div><div> </div><div>Cheers,</div><div>Fabian</div><div> </div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 24 October 2023 at 15:50:28 UTC+2 Ashley Dickson wrote: </div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I'm trying to perform a cell optimisation on a crystal of YBCO however the calculations always seem to spit out nonsense (the cell volume continually increases). I am using the structural data found on the open crystallography database which should be accurate. Is there perhaps something wrong with the unit cell I've chosen? The input is provided below:<div> </div> &FORCE_EVAL METHOD Quickstep &DFT BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME GTH_POTENTIALS LSD &POISSON POISSON_SOLVER PERIODIC PERIODIC XYZ &END POISSON &MGRID NGRIDS 5 CUTOFF 800 REL_CUTOFF 60 &END MGRID &QS METHOD GPW EPS_PGF_ORB 1E-16 &END QS &SCF &SMEAR ON ELECTRONIC_TEMPERATURE 1000 METHOD FERMI_DIRAC &END SMEAR ADDED_MOS 700 CHOLESKY INVERSE SCF_GUESS RESTART EPS_SCF 1.0E-6 MAX_SCF 250 &DIAGONALIZATION ON ALGORITHM STANDARD &END DIAGONALIZATION &MIXING T METHOD BROYDEN_MIXING ALPHA 0.5 BETA 1.5 NBUFFER 15 &END MIXING &END SCF &KPOINTS SCHEME MONKHORST-PACK 2 2 2 FULL_GRID yes SYMMETRY yes VERBOSE yes PARALLEL_GROUP_SIZE -1 &END KPOINTS &XC &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &XC_GRID USE_FINER_GRID T &END XC_GRID &END XC &END DFT &SUBSYS &COORD Cu 0 0 0 Y 1.910150 1.942740 5.841745 Ba 1.910150 1.942740 2.148944 Ba 1.910150 1.942740 9.534546 Cu 0.000000 0.000000 11.683490 Cu 0.000000 3.885480 0.000000 Cu 0.000000 3.885480 11.683490 Cu 3.820300 0.000000 0.000000 Cu 3.820300 0.000000 11.683490 Cu 3.820300 3.885480 0.000000 Cu 3.820300 3.885480 11.683490 Cu 0.000000 0.000000 4.147756 Cu 0.000000 3.885480 4.147756 Cu 3.820300 0.000000 4.147756 Cu 3.820300 3.885480 4.147756 Cu 0.000000 0.000000 7.535734 Cu 0.000000 3.885480 7.535734 Cu 3.820300 0.000000 7.535734 Cu 3.820300 3.885480 7.535734 O 0.000000 1.942740 0.000000 O 0.000000 1.942740 11.683490 O 3.820300 1.942740 0.000000 O 3.820300 1.942740 11.683490 O 1.910150 0.000000 4.418579 O 1.910150 3.885480 4.418579 O 1.910150 0.000000 7.264911 O 1.910150 3.885480 7.264911 O 0.000000 1.942740 4.403858 O 3.820300 1.942740 4.403858 O 0.000000 1.942740 7.279632 O 3.820300 1.942740 7.279632 O 0.000000 0.000000 1.850665 O 0.000000 3.885480 1.850665 O 3.820300 0.000000 1.850665 O 3.820300 3.885480 1.850665 O 0.000000 0.000000 9.832825 O 0.000000 3.885480 9.832825 O 3.820300 0.000000 9.832825 O 3.820300 3.885480 9.832825 &END COORD &TOPOLOGY &END TOPOLOGY &CELL SYMMETRY ORTHORHOMBIC ABC 4 4 12 PERIODIC XYZ &END CELL &KIND O BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q6 &END KIND &KIND Ba BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q10 &END KIND &KIND Y BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q11 &END KIND &KIND Cu BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q11 &END KIND &PRINT &CELL HIGH &END CELL &END PRINT &END SUBSYS STRESS_TENSOR ANALYTICAL &END FORCE_EVAL &GLOBAL PROJECT SZV RUN_TYPE CELL_OPT PRINT_LEVEL MEDIUM &END GLOBAL &MOTION &CELL_OPT KEEP_SYMMETRY .TRUE. OPTIMIZER BFGS KEEP_ANGLES EXTERNAL_PRESSURE [Pa] 100000 &END CELL_OPT <div>&END MOTION </div><div> </div><div> </div><div>Many thanks for any help,</div><div>Ash</div></blockquote></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div> -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>. To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/a33a6e30-8647-4787-af7f-7873e60d8210n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/a33a6e30-8647-4787-af7f-7873e60d8210n%40googlegroups.com</a>.