<div dir="ltr">Hi Juerg<div><br></div><div>Could you explain how the size gonna affect the results and how to choose the cell size? I am trying to calculate the binding energy and the original unit cell is non-orthogonal. I tried several numbers for the cell size of IPA, as long as it's not extremely large, the difference is negligible. </div><div><br></div><div>Thank you very much!</div><div>Xin<br><br>On Tuesday, June 30, 2020 at 5:27:41 AM UTC-4, jgh wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">Hi
<br>
<br>> Will the cell size affect the geometry optimization results for single-molecule in the gas phase?
<br>
<br>Yes
<br>
<br>> and do I have to use a cubic cell?
<br>
<br>Yes, for the wavelet Poisson solver.
<br>
<br>regards
<br>
<br>Juerg Hutter
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<br>Juerg Hutter Phone : ++41 44 635 4491
<br>Institut für Chemie C FAX : ++41 44 635 6838
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<br>From: "Xin Wei"
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<br>Date: 06/30/2020 06:37AM
<br>Subject: [CP2K:13569] Geo-opt for gas molecule (
<br>
<br>Hello everyone,
<br>
<br>I am doing geometry optimization using cp2k for isopropanol alcohol (gas phase). However, I don't know how to fix the error below: Can anyone help me with it? (I centered my molecule using &CENTER_COORDINATES)
<br>*** WARNING in pw/ps_wavelet_methods.F:236 :: Density non-zero on the edges of the unit cell: wrong results in WAVELET solver
<br>
<br>Will the cell size affect the geometry optimization results for single-molecule in the gas phase? and do I have to use a cubic cell?
<br> &CELL
<br> PERIODIC NONE
<br> ABC 14.83 14.83 14.83
<br> ALPHA_BETA_GAMMA 60.0 60.0 60.0
<br> &END CELL
<br>
<br>Here is my input file: (my output file and xyz file are attached)
<br>
<br>&GLOBAL
<br> PROJECT IPA
<br> RUN_TYPE GEO_OPT
<br> PRINT_LEVEL LOW
<br>&END GLOBAL
<br>
<br>&FORCE_EVAL
<br>
<br> METHOD Quickstep
<br> &DFT
<br> BASIS_SET_FILE_NAME /ihome/crc/build/cp2k/cp2k-6.<wbr>1-intel-mkl/data/BASIS_MOLOPT
<br> &POISSON
<br> PERIODIC NONE
<br> PSOLVER WAVELET
<br> &END POISSON
<br> &QS
<br> METHOD GAPW
<br> &END QS
<br>
<br>
<br> &SCF
<br> SCF_GUESS ATOMIC
<br> EPS_SCF 1.0E-05
<br> MAX_SCF 200
<br> &DIAGONALIZATION T
<br> ALGORITHM STANDARD
<br> &END DIAGONALIZATION
<br> &MIXING T
<br> ALPHA 0.5
<br> METHOD PULAY_MIXING
<br> NPULAY 5
<br> &END MIXING
<br> &PRINT
<br> &RESTART OFF
<br> &END RESTART
<br> &END PRINT
<br> &END SCF
<br>
<br>
<br> &XC
<br> &XC_FUNCTIONAL
<br> &PBE
<br> &END
<br> &END XC_FUNCTIONAL
<br> ! add Grimme D3 correction (without C9 terms, default)
<br> &VDW_POTENTIAL
<br> POTENTIAL_TYPE PAIR_POTENTIAL
<br> &PAIR_POTENTIAL
<br> PARAMETER_FILE_NAME dftd3.dat
<br> TYPE DFTD3
<br> REFERENCE_FUNCTIONAL PBE
<br> R_CUTOFF [angstrom] 16
<br> &END
<br> &END VDW_POTENTIAL
<br> &END XC
<br>
<br> &END DFT
<br>
<br>
<br> &SUBSYS
<br> &CELL
<br> PERIODIC NONE
<br> ABC 14.83 14.83 14.83
<br> ALPHA_BETA_GAMMA 60.0 60.0 60.0
<br> &END CELL
<br>
<br> &TOPOLOGY
<br> &CENTER_COORDINATES
<br> &END CENTER_COORDINATES
<br> COORD_FILE_NAME IPA.xyz
<br> COORD_FILE_FORMAT XYZ
<br> &END
<br>
<br> &KIND C
<br> BASIS_SET DZVP-MOLOPT-SR-GTH
<br> POTENTIAL GTH-PBE-q4
<br> &END KIND
<br> &KIND H
<br> BASIS_SET DZVP-MOLOPT-SR-GTH
<br> POTENTIAL GTH-PBE-q1
<br> &END KIND
<br> &KIND O
<br> BASIS_SET DZVP-MOLOPT-SR-GTH
<br> POTENTIAL GTH-PBE-q6
<br> &END KIND
<br> &KIND Zr
<br> BASIS_SET DZVP-MOLOPT-SR-GTH
<br> POTENTIAL GTH-PBE-q12
<br> &END KIND
<br> &END SUBSYS
<br>&END FORCE_EVAL
<br>
<br>&MOTION
<br> &GEO_OPT
<br> OPTIMIZER BFGS
<br> MAX_ITER 1500
<br> MAX_DR [bohr] 0.003
<br> &BFGS
<br> &END
<br> &END
<br> &PRINT
<br> &RESTART
<br> BACKUP_COPIES 0
<br> &END RESTART
<br> &END PRINT
<br>&END
<br>
<br>Thanks!!!
<br>Xin
<br>
<br>
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<br>
<br>
<br>[attachment "simulation 2.out" removed by Jürg Hutter/at/UZH]
<br>[attachment "IPA.xyz" removed by Jürg Hutter/at/UZH]
<br></blockquote></div></div>