<div dir="ltr"><div>Dear Dmitrii,</div><div><br></div><div>how did you obtain the xyz? Did you just export it from CIF? It looks like it is full of disordered hydrogen atoms.<br></div><div><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>MULTIPLICITY 2 <br></div></blockquote><div>Are you sure?</div><div><br></div><div>
<div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>What do you think I need to change for energy calculations, expect of deeper EPS_SCF from 1.0E-6 to 1.0E-7 or -8?</div></blockquote><div>I don't know. AFAIR, the default is 1e-5, I used to lower it to 1e-6, while 1.0e-7 resulted in very slow convergence (I mean that the calculation reached the residues of ca 1e-6 and then started to turning around it, until "accidentally" reached 1e-7 -- I guess that some other parameters are to be tuned to avoid numeric noise). Anyway, you always could check the consistency w.r.t. to the considered parameter by yourself. The key point in your case is to get rid of numeric noise in gradients -- you can assess it via observing the course of your geometry optimization (if you see some random moves around the equilibrium rather than smooth convergence to it, this might be the case).<br></div><div><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>Do
 I need to use spin polarisation for Co and Zn atoms when I calculate 
adsorption energy for ORR reaction coordinate, or I can reach desirably 
accuracy without it? My job is to compare different facets reactivity 
for ORR.</div></blockquote><div>I probably don't understand your question. If your system is paramagnetic, you have to use the spin-unrestricted formalism (LSD aka UKS) anyway.</div><div><br></div><div>I don't think the idea of crystallographic facets makes real sense in the case of MOFs. The active centers in the case of MOFs are either the metal ions with the coordinated atoms, or the fragments of ligands, these centers are unlikely to be affected if you change the facet.</div><div><br></div><div>Yours,</div><div>Anton<br></div>

</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">нд, 27 бер. 2022 р. о 08:47 DMITRII Drugov <<a href="mailto:dresearcher1991@gmail.com">dresearcher1991@gmail.com</a>> пише:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Anton,<div><br></div><div>Thank you for your reply.</div><div>I even did not think about low symmetry of MOFs. Thank you for this point.</div><div>I attach my input file below for cell_opt first, then I will do energy calculation.</div><div>Could you please have a look at my settings and express your opinion on its accuracy?</div><div>What do you think I need to change for energy calculations, expect of deeper EPS_SCF from 1.0E-6 to 1.0E-7 or -8?</div><div>Do I need to use spin polarisation for Co and Zn atoms when I calculate adsorption energy for ORR reaction coordinate, or I can reach desirably accuracy without it? My job is to compare different facets reactivity for ORR.</div><div><br></div><div>Best,</div><div>Dmitrii</div><div><br></div><div>&GLOBAL<br>  PROJECT MOF_011_optimisation_larger_cell <br>  RUN_TYPE CELL_OPT<br>  PRINT_LEVEL MEDIUM<br>  !EXTENDED_FFT_LENGTHS<br>&END GLOBAL<br>&FORCE_EVAL<br>STRESS_TENSOR ANALYTICAL<br>  METHOD QS<br>  &DFT<br>    BASIS_SET_FILE_NAME BASIS_MOLOPT<br>    POTENTIAL_FILE_NAME GTH_POTENTIALS<br>    LSD<br>    CHARGE 0<br>    MULTIPLICITY 2<br>    &MGRID<br>      CUTOFF 800<br>      NGRIDS 5<br>      REL_CUTOFF 70<br>    &END MGRID<br>    &QS<br>      EPS_DEFAULT 1.0E-14<br>      !WF_INTERPOLATION ASPC<br>    &END QS<br>   &SCF<br>      SCF_GUESS ATOMIC<br>      EPS_SCF 1.0E-6<br>      MAX_SCF 300<br>      &OT<br>       MINIMIZER CG<br>       PRECONDITIONER FULL_KINETIC<br>       # ENERGY_GAP 0.01<br>       &END OT<br>      &OUTER_SCF<br>       EPS_SCF 1E-6<br>       MAX_SCF 300<br>      &END <br>      !CHOLESKY INVERSE<br>      !ADDED_MOS 100<br>      !&SMEAR ON<br>       ! METHOD FERMI_DIRAC<br>       ! ELECTRONIC_TEMPERATURE [K] 1000<br>     ! &END SMEAR<br>      !&DIAGONALIZATION<br>       ! ALGORITHM STANDARD<br>      !&END DIAGONALIZATION<br>      !&MIXING<br>       ! METHOD BROYDEN_MIXING<br>        !ALPHA 0.4                <br>        !NBROYDEN 8<br>      !&END MIXING<br>    &END SCF<br>    &XC<br>      &XC_FUNCTIONAL<br>        &PBE<br>        &END PBE<br>      &END XC_FUNCTIONAL<br>      &vdW_POTENTIAL<br>            DISPERSION_FUNCTIONAL PAIR_POTENTIAL<br>             &PAIR_POTENTIAL<br>                PARAMETER_FILE_NAME dftd3.dat<br>                       TYPE DFTD3<br>                       REFERENCE_FUNCTIONAL PBE<br>                       R_CUTOFF 8.0<br>            &END PAIR_POTENTIAL<br>     &END vdW_POTENTIAL<br>    &END XC<br>    SURFACE_DIPOLE_CORRECTION T<br>    SURF_DIP_DIR Z<br>    &POISSON<br>      PERIODIC xy<br>      POISSON_SOLVER ANALYTIC<br>    &END POISSON<br>  &END DFT<br>  &SUBSYS<br>    &CELL<br>      ABC 18.55406 16.35222 50<br>      ALPHA_BETA_GAMMA 90.0 90.0 90.0<br>      PERIODIC xy<br>      SYMMETRY ORTHORHOMBIC<br>    &END CELL<br>    &COORD<br>C         2.69109      3.50908       2.31039<br>C         2.69109      12.34314      2.31039<br>C         0.51227      7.92611       3.89871<br>N         5.94837      3.44592       0.26929<br>N         1.20316      9.05092       3.62466<br>N         1.20316      6.8013        3.62466<br>N         5.94837      12.4063       0.26929<br>C         6.87686      10.39498      0<br>C         5.92646      4.78521       0.67203<br>C         2.43496      8.59814       3.1409<br>C         2.43496      7.25408       3.1409<br>C         6.87686      5.45724       0<br>C         5.92646      11.06701      0.67203<br>H         7.0639       9.48822       0.08937<br>H         5.34848      5.15102       1.30235<br>H         3.13933      9.1391        2.86446<br>H         3.13933      6.71312       2.86446<br>H         7.0639       6.364         0.08937<br>H         5.34848      10.7012       1.30235<br>C         2.26139      4.168         1.04379<br>C         2.26139      11.68422      1.04379<br>H         1.56208      4.79832       1.23086<br>H         2.83938      11.95708      0.32767<br>H         1.56208      11.0539       1.23086<br>H         2.83938      3.89514       0.32767<br>H         3.00789      4.62555       0.65058<br>H         2.30689      10.73099      1.14626<br>H         3.00789      11.22667      0.65058<br>H         2.30689      5.12123       1.14626<br>H         1.93449      3.50312       0.43134<br>H         1.35819      11.94159      0.83884<br>H         1.93449      12.3491       0.43134<br>H         1.35819      3.91063       0.83884<br>O         5.79166      7.92611       2.27822<br>Zn        4.81431      13.8838       0.89604<br>Zn        0.60158      10.90496      3.87488<br>C         6.93752      15.29816      2.4367<br>C         0.69089      10.88113      6.85373<br>N         3.68024      13.25705      2.37354<br>N         2.08951      12.13224      3.49836<br>N         0            11.15518      5.72892<br>N         5.94837      15.36131      1.52279<br>C         3.70215      13.65979      3.71283<br>C         2.75175      12.98777      4.38486<br>H         4.28013      14.29012      4.07864<br>H         6.48928      15.85222      5.64074<br>H         2.56471      13.07713      5.29162<br>C         7.36722      14.03155      3.09562<br>C         2.05244      10.27344      6.85373<br>H         2.83938      15.81052      1.4644<br>H         8.06653      14.21863      3.72594<br>H         2.36587      10.18765      5.95054<br>H         6.78923      13.31544      2.82276<br>H         6.62072      13.63835      3.55317<br>H         2.65402      10.83346      6.35805<br>H         7.32172      14.13403      4.04885<br>H         1.35819      15.82601      0.95323<br>H         1.93449      15.4185       1.36074<br>H         7.69412      13.4191       2.43074<br>H         2.01537      9.40362       6.44622<br>H         8.27042      13.82661      2.83825<br>O         3.83695      15.26599      6.85373<br>O         5.92646      12.31097      6.85373<br>Co        0.60158      4.94726       3.87488<br>Zn        4.81431      1.96842       0.89604<br>C         6.93752      0.55406       2.4367<br>C         0.69089      4.97109       6.85373<br>N         2.08951      3.71998       3.49836<br>N         3.68024      2.59517       2.37354<br>N         5.94837      0.49091       1.52279<br>N         0            4.69704       5.72892<br>C         2.75175      2.86445       4.38486<br>C         3.70215      2.19243       3.71283<br>H         2.56471      2.77509       5.29162<br>H         6.48928      0             5.64074<br>H         4.28013      1.5621        4.07864<br>C         7.36722      1.82067       3.09562<br>C         2.05244      5.57878       6.85373<br>H         2.83938      0.0417        1.4644<br>H         6.78923      2.53678       2.82276<br>H         2.36587      5.66457       5.95054<br>H         8.06653      1.63359       3.72594<br>H         7.32172      1.71819       4.04885<br>H         2.65402      5.01876       6.35805<br>H         6.62072      2.21387       3.55317<br>H         1.93449      0.43372       1.36074<br>H         1.35819      0.02621       0.95323<br>H         8.27042      2.02561       2.83825<br>H         2.01537      6.4486        6.44622<br>H         7.69412      2.43312       2.43074<br>O         3.83695      0.58623       6.85373<br>O         5.92646      3.54125       6.85373<br>C         17.36317     7.92611       3.89871<br>N         15.96455     4.57074       2.6476<br>N         14.37382     12.4063       1.52279<br>N         15.96455     11.28148      2.6476<br>N         14.37382     3.44592       1.52279<br>N         18.05406     9.05092       3.62466<br>N         18.05406     6.8013        3.62466<br>C         15.30231     5.45724       1.79207<br>C         14.35191     11.06701      1.12005<br>C         15.30231     10.39498      1.79207<br>C         14.35191     4.78521       1.12005<br>H         15.48935     6.364         1.70271<br>H         13.77393     10.7012       0.48972<br>H         15.48935     9.48822       1.70271<br>H         13.77393     5.15102       0.48972<br>C         10.68684     11.68422      0.74829<br>C         10.68684     4.168         0.74829<br>C         16.00162     7.92611       4.5064<br>H         9.98753      11.0539       0.56121<br>H         11.26483     3.89514       1.4644<br>H         15.68819     8.8293        4.59219<br>H         15.68819     7.02292       4.59219<br>H         9.98753      4.79832       0.56121<br>H         11.26483     11.95708      1.4644<br>H         11.43334     11.22667      1.14149<br>H         10.73234     5.12123       0.64581<br>H         15.40004     7.43043       3.94638<br>H         15.40004     8.42179       3.94638<br>H         11.43334     4.62555       1.14149<br>H         10.73234     10.73099      0.64581<br>H         10.35994     12.3491       1.36074<br>H         9.78364      3.91063       0.95323<br>H         16.03869     7.5186        5.37622<br>H         16.03869     8.33362       5.37622<br>H         10.35994     3.50312       1.36074<br>H         9.78364      11.94159      0.95323<br>O         12.1276      7.92611       2.46887<br>Zn        13.23976     13.8838       0.89604<br>Zn        17.45248     10.90496      3.87488<br>C         15.36297     12.46945      2.4367<br>C         11.11654     15.42446      2.31039<br>C         17.54179     10.88113      6.85373<br>N         14.37382     15.36131      0.26929<br>N         10.51496     15.63536      3.49836<br>N         16.8509      11.15518      5.72892<br>N         12.10569     14.51055      2.37354<br>C         11.1772      14.77984      4.38486<br>C         15.6191      11.63894      6.1817<br>C         12.1276      14.10781      3.71283<br>H         10.99016     14.69047      5.29162<br>H         14.91473     11.91538      5.64074<br>H         12.70558     13.47749      4.07864<br>C         15.79267     13.73605      3.09562<br>H         15.21468     14.45217      2.82276<br>H         16.49198     13.54898      3.72594<br>H         11.26483     15.81052      0.32767<br>H         15.74717     13.63358      4.04885<br>H         15.04617     14.12926      3.55317<br>H         16.69587     13.941        2.83825<br>H         16.11957     14.3485       2.43074<br>H         10.35994     15.4185       0.43134<br>H         9.78364      15.82601      0.83884<br>O         12.2624      12.50162      6.85373<br>O         14.35191     15.45663      6.85373<br>Zn        17.45248     4.94726       3.87488<br>Zn        13.23976     1.96842       0.89604<br>C         15.36297     3.38277       2.4367<br>C         11.11654     0.42776       2.31039<br>C         17.54179     4.97109       6.85373<br>N         14.37382     0.49091       0.26929<br>N         12.10569     1.34167       2.37354<br>N         16.8509      4.69704       5.72892<br>N         10.51496     0.21686       3.49836<br>C         12.1276      1.74441       3.71283<br>C         15.6191      4.21328       6.1817<br>C         11.1772      1.07238       4.38486<br>H         12.70558     2.37473       4.07864<br>H         14.91473     3.93684       5.64074<br>H         10.99016     1.16175       5.29162<br>C         15.79267     2.11617       3.09562<br>H         16.49198     2.30324       3.72594<br>H         15.21468     1.40005       2.82276<br>H         11.26483     0.0417        0.32767<br>H         15.04617     1.72296       3.55317<br>H         15.74717     2.21864       4.04885<br>H         16.11957     1.50372       2.43074<br>H         16.69587     1.91122       2.83825<br>H         9.78364      0.02621       0.83884<br>H         10.35994     0.43372       0.43134<br>O         12.2624      3.3506        6.85373<br>O         14.35191     0.39559       6.85373<br>   &END COORD<br>    &KIND Co <br>      BASIS_SET DZVP-MOLOPT-SR-GTH <br>      POTENTIAL GTH-PBE-q17<br>    &END KIND<br>    &KIND Zn <br>      BASIS_SET DZVP-MOLOPT-SR-GTH<br>      POTENTIAL GTH-PBE-q12<br>    &END KIND<br>    &KIND O<br>      BASIS_SET TZVP-MOLOPT-GTH<br>      POTENTIAL GTH-PBE-q6<br>    &END KIND<br>    &KIND C<br>      BASIS_SET TZVP-MOLOPT-GTH<br>      POTENTIAL GTH-PBE-q4<br>    &END KIND<br>    &KIND H                              <br>      BASIS_SET TZVP-MOLOPT-GTH<br>      POTENTIAL GTH-PBE-q1<br>    &END KIND<br>    &KIND N<br>      BASIS_SET TZVP-MOLOPT-GTH<br>      POTENTIAL GTH-PBE-q5<br>    &END KIND<br>   &END SUBSYS<br>&END FORCE_EVAL<br>&MOTION<br>  &GEO_OPT<br>   OPTIMIZER LBFGS<br>   MAX_ITER 300<br>  &END GEO_OPT<br>  &CELL_OPT<br>    EXTERNAL_PRESSURE [bar] 0.0<br>    KEEP_ANGLES TRUE<br>    KEEP_SYMMETRY TRUE<br>    OPTIMIZER LBFGS<br>  &END<br> &END MOTION<br>&END<br>  <br></div><div><br></div><div> </div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Friday, March 25, 2022 at 8:32:42 PM UTC+10 <a href="mailto:anton.s.l...@gmail.com" target="_blank">anton.s.l...@gmail.com</a> 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 dir="ltr"><div>Dear Dmitrii,</div><div><br></div><div>CP2k has implementation of k-points, but it could be incompatible with some methods and features.</div><div><br></div><div>But why do you need it? MOFs cells are typically large and have low symmetry.</div><div><br></div><div>Yours,</div><div>Anton<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">пт, 25 бер. 2022 р. о 10:38 DMITRII Drugov <<a rel="nofollow">dresear...@gmail.com</a>> пише:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"></blockquote></div><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">Dear CP2K users, <div><br></div><div>Could you please share your thoughts on correct CP2K settings to study oxygen reaction reaction on MOFs surface (186 atoms, C, H, O, N, Zn)? I used to conduct similar job on Quantum Espresso for to study HER on graphite slab (86 atoms) and it took ages to finish single energy calculation with soft potentials (ecutrho =   0.4000000000d+03</div>  ecutwfc =   0.5000000000d+02). According to my experience at gamma point CP2K is much faster but I never added k-point mesh to CP2K.<div>Could you please let me know what my CP2K should be? Does CP2K allow to set up k-points for energy calculation? My system is a slab with vacuum of 2*x or y in z dimension.</div><div><br></div><div>Best regards,</div><div>Dmitrii</div>

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