Thank you a lot for all your advices. I am knew to CP2K and any solid state DFT software. Could you please help me to create right cell dimension in CP2K for my system?<div>I built Au(111) slab with a= 4.07825 and I repeated this unit 3 times in xy and only 1 in z dimension.</div><div>So, this gave me </div><div>
<p>created 36 atom sample</p>
<p>(super)cell vectors</p>
<p>a1 = array([ 12.23, 0.00, 0.00])</p>
<p>a2 = array([ 0.00, 12.23, 0.00])</p>
<p>a3 = array([ 0.00, 0.00, 4.08])</p>
<p>-----------------------------------------</p>
<p>cell for VMD : pbc set { 12.235 12.235 4.078 90.00 90.00 90.00 }; pbc box</p><p>However, in my CP2K optimization input with organic molecules I specify everything in the way listed bellow.</p><p>Could you please help me to choose right PBC settings with cell dimension parameters?</p><p><br></p><p>&GLOBAL</p><p> PROJECT Au_optimisation </p><p> RUN_TYPE GEO_OPT</p><p> PRINT_LEVEL MEDIUM</p><p>&END GLOBAL</p><p>&FORCE_EVAL</p><p> METHOD QS</p><p> &DFT</p><p> BASIS_SET_FILE_NAME BASIS_MOLOPT</p><p> POTENTIAL_FILE_NAME GTH_POTENTIALS</p><p> CHARGE +1</p><p> MULTIPLICITY 1</p><p> &MGRID</p><p> CUTOFF 800</p><p> NGRIDS 5</p><p> REL_CUTOFF 70</p><p> &END MGRID</p><p> &QS</p><p> EPS_DEFAULT 1.0E-12</p><p> WF_INTERPOLATION ASPC</p><p> &END QS</p><p> &SCF</p><p> SCF_GUESS ATOMIC</p><p> EPS_SCF 1.0E-7</p><p> MAX_SCF 1000</p><p> CHOLESKY INVERSE</p><p> ADDED_MOS 20</p><p> &SMEAR ON</p><p> METHOD FERMI_DIRAC</p><p> ELECTRONIC_TEMPERATURE [K] 300</p><p> &END SMEAR</p><p> &DIAGONALIZATION</p><p> ALGORITHM STANDARD</p><p> &END DIAGONALIZATION</p><p> &MIXING</p><p> METHOD BROYDEN_MIXING</p><p> ALPHA 0.4<span style="white-space:pre"> </span> </p><p> NBROYDEN 8</p><p> &END MIXING</p><p> &END SCF</p><p> &XC</p><p> &XC_FUNCTIONAL</p><p><span style="white-space:pre"> </span>&PBE</p><p><span style="white-space:pre"> </span>&END PBE</p><p> &END XC_FUNCTIONAL</p><p> &vdW_POTENTIAL</p><p> <span style="white-space:pre"> </span>DISPERSION_FUNCTIONAL PAIR_POTENTIAL</p><p> <span style="white-space:pre"> </span> &PAIR_POTENTIAL</p><p> <span style="white-space:pre"> </span> PARAMETER_FILE_NAME dftd3.dat</p><p> <span style="white-space:pre"> </span>TYPE DFTD3</p><p> <span style="white-space:pre"> </span>REFERENCE_FUNCTIONAL PBE</p><p> <span style="white-space:pre"> </span>R_CUTOFF 15.0</p><p> <span style="white-space:pre"> </span>&END PAIR_POTENTIAL</p><p> &END vdW_POTENTIAL</p><p> &END XC</p><p> &POISSON</p><p> PERIODIC xyz</p><p> POISSON_SOLVER WAVELET</p><p> &END POISSON</p><p> &END DFT</p><p> &SUBSYS</p><p> &CELL</p><p> ABC 15.00000 15.00000 26.00000 </p><p> PERIODIC xyz</p><p> &END CELL</p><p> &COORD</p><p>&END COORD<br></p><div> &KIND Au</div><div> BASIS_SET DZVP-MOLOPT-SR-GTH </div><div> POTENTIAL GTH-PBE-q11</div><div> &END KIND</div><div> &KIND C</div><div> BASIS_SET TZV2P-MOLOPT-GTH</div><div> POTENTIAL GTH-PBE-q4</div><div> &END KIND</div><div> &KIND H</div><div> BASIS_SET TZV2P-MOLOPT-GTH</div><div> POTENTIAL GTH-PBE-q1</div><div> &END KIND</div><div> &KIND N</div><div> BASIS_SET TZV2P-MOLOPT-GTH</div><div> POTENTIAL GTH-PBE-q5</div><div> &END KIND</div><div> &END SUBSYS</div><div>&END FORCE_EVAL</div><div>&MOTION</div><div> &CONSTRAINT</div><div> &FIXED_ATOMS</div><div> COMPONENTS_TO_FIX XYZ</div><div> LIST 1..54 </div><div> &END FIXED_ATOMS</div><div> &END CONSTRAINT</div><div> &GEO_OPT</div><div> TYPE MINIMIZATION</div><div> MAX_DR 1.0E-03</div><div> MAX_FORCE 1.0E-03</div><div> RMS_DR 1.0E-03</div><div> RMS_FORCE 1.0E-03</div><div> MAX_ITER 300</div><div> OPTIMIZER CG</div><div> &CG</div><div> MAX_STEEP_STEPS 0</div><div> RESTART_LIMIT 9.0E-01</div><div> &END CG</div><div> &END GEO_OPT</div><div> &END MOTION</div></div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, November 17, 2020 at 7:47:47 AM UTC+11 ant...@gmail.com 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;">Dear Dmitrii,
<br>
<br>in addition to the suggestions you've already received from Dr.
<br>Iannuzzi, I could append the following comments.
<br>
<br>16.11.20 03:48, DMITRII Drugov пише:
<br>> I expected organic molecule moves more from it's initial position.
<br>> Otherwise it's almost same as I built in avogadro software.
<br>
<br>As far as I can see from your files, you have pre-optimized your system
<br>via MM(UFF) in Avogadro. The molecule actually "lays" on the surface
<br>(take a look on the structure in the "van der Waals spheres" mode in
<br>Avogadro). Bearing that in mind, I see no reasons to expect any
<br>significant movements in so heavily constrained system. You effectively
<br>allow only movements relevant to intramolecular interactions in your
<br>adsorbate and van der Waals interactions between the molecule and the
<br>surface -- both of them are reasonably well described within MM approach
<br>(due to the adsorbate structure, no specific covalent bonding between
<br>this molecule and the surface is to be expected).
<br>
<br>> Do you think while optimization I should keep system non periodic with
<br>> poison wavelet or periodic in xy or xyz with poison analytic?
<br>
<br>You may want to consider this paper: Phys. Chem. Chem. Phys., 2018, 20,
<br>8456.
<br>
<br>Yours,
<br>Anton
<br></blockquote></div>