[CP2K-user] [CP2K:13569] Geo-opt for gas molecule (

[Xin Wei]

Hi Juerg

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. 

Thank you very much!
Xin

On Tuesday, June 30, 2020 at 5:27:41 AM UTC-4, jgh wrote:
>
> Hi 
>
> > Will the cell size affect the geometry optimization results for 
> single-molecule in the gas phase?   
>
> Yes 
>
> > and do I have to use a cubic cell? 
>
> Yes, for the wavelet Poisson solver. 
>
> regards 
>
> Juerg Hutter 
> -------------------------------------------------------------- 
> Juerg Hutter                         Phone : ++41 44 635 4491 
> Institut für Chemie C                FAX   : ++41 44 635 6838 
> Universität Zürich                   E-mail: h... at chem.uzh.ch 
> <javascript:> 
> Winterthurerstrasse 190 
> CH-8057 Zürich, Switzerland 
> --------------------------------------------------------------- 
>
> -----c... at googlegroups.com <javascript:> wrote: ----- 
> To: "cp2k" <c... at googlegroups.com <javascript:>> 
> From: "Xin Wei" 
> Sent by: c... at googlegroups.com <javascript:> 
> Date: 06/30/2020 06:37AM 
> Subject: [CP2K:13569] Geo-opt for gas molecule ( 
>
> Hello everyone, 
>
> 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) 
> *** WARNING in pw/ps_wavelet_methods.F:236 :: Density non-zero on the 
> edges of the unit cell: wrong results in WAVELET solver 
>
> 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? 
>        &CELL                         
>        PERIODIC NONE                 
>        ABC 14.83 14.83 14.83 
>        ALPHA_BETA_GAMMA 60.0 60.0 60.0 
>       &END CELL 
>
> Here is my input file: (my output file and xyz file are attached) 
>
> &GLOBAL 
>   PROJECT IPA 
>   RUN_TYPE GEO_OPT 
>   PRINT_LEVEL LOW 
> &END GLOBAL 
>
> &FORCE_EVAL                           
>   
>    METHOD Quickstep                   
>    &DFT 
>     BASIS_SET_FILE_NAME 
> /ihome/crc/build/cp2k/cp2k-6.1-intel-mkl/data/BASIS_MOLOPT 
>     &POISSON                       
>       PERIODIC NONE 
>       PSOLVER  WAVELET             
>     &END POISSON 
>     &QS                             
>       METHOD GAPW               
>     &END QS 
>       
>       
>     &SCF 
>       SCF_GUESS ATOMIC 
>       EPS_SCF 1.0E-05 
>       MAX_SCF 200 
>       &DIAGONALIZATION T 
>         ALGORITHM STANDARD 
>       &END DIAGONALIZATION 
>       &MIXING T 
>         ALPHA 0.5 
>         METHOD PULAY_MIXING 
>         NPULAY 5 
>       &END MIXING 
>       &PRINT 
>         &RESTART OFF 
>         &END RESTART 
>       &END PRINT 
>     &END SCF 
>     
>     
>     &XC 
>       &XC_FUNCTIONAL 
>         &PBE 
>         &END 
>       &END XC_FUNCTIONAL 
>       ! add Grimme D3 correction (without C9 terms, default) 
>       &VDW_POTENTIAL 
>         POTENTIAL_TYPE PAIR_POTENTIAL 
>         &PAIR_POTENTIAL 
>           PARAMETER_FILE_NAME dftd3.dat 
>           TYPE DFTD3 
>           REFERENCE_FUNCTIONAL PBE 
>           R_CUTOFF [angstrom] 16 
>         &END 
>       &END VDW_POTENTIAL 
>     &END XC 
>   
>    &END DFT 
>   
>   
>    &SUBSYS                             
>      &CELL                         
>        PERIODIC NONE                 
>        ABC 14.83 14.83 14.83 
>        ALPHA_BETA_GAMMA 60.0 60.0 60.0 
>       &END CELL 
>
>       &TOPOLOGY 
>         &CENTER_COORDINATES 
>         &END CENTER_COORDINATES 
>         COORD_FILE_NAME IPA.xyz 
>         COORD_FILE_FORMAT XYZ 
>       &END 
>
>       &KIND C 
>         BASIS_SET DZVP-MOLOPT-SR-GTH 
>         POTENTIAL GTH-PBE-q4 
>       &END KIND 
>       &KIND H 
>         BASIS_SET DZVP-MOLOPT-SR-GTH 
>         POTENTIAL GTH-PBE-q1 
>       &END KIND 
>       &KIND O 
>         BASIS_SET DZVP-MOLOPT-SR-GTH 
>         POTENTIAL GTH-PBE-q6 
>       &END KIND 
>       &KIND Zr 
>         BASIS_SET DZVP-MOLOPT-SR-GTH 
>         POTENTIAL GTH-PBE-q12 
>       &END KIND 
>     &END SUBSYS 
> &END FORCE_EVAL 
>
> &MOTION 
>   &GEO_OPT 
>     OPTIMIZER BFGS 
>     MAX_ITER 1500 
>     MAX_DR  [bohr] 0.003 
>     &BFGS 
>     &END 
>   &END 
>   &PRINT 
>     &RESTART 
>       BACKUP_COPIES 0 
>     &END RESTART 
>   &END PRINT 
> &END 
>
> Thanks!!! 
> Xin 
>
>   
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>   
>
> [attachment "simulation 2.out" removed by Jürg Hutter/at/UZH] 
> [attachment "IPA.xyz" removed by Jürg Hutter/at/UZH] 
>
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