QMMM setting up

[Matt W]

Hi,

the MM_index is just the number of the atom in the coordinate file (by 
default), so you give 

$QM_KIND Pt
   LIST 104 105 106
&END
 
in your example.

The need for a topology depends on the classical part of the calculation. 
So in your case, if Al2O3 is just charges and non bonding parameters then 
no topology is needed. If you had a forcefield with say Al-O-Al bend 
parameters you would need a topology that specified those.

Matt



On Friday, August 28, 2015 at 9:40:36 AM UTC+1, Geng Sun wrote:
>
> Hello CP2K users,
>
>          I am trying to study the Pt6 clusters adsorption on the Al2O3 
> surface, using the QMMM  method in CP2K.  
>          In this study, I want to simulate the Al2O3 surface by classical 
> forcefield assuming that the Al2O3 interacts with Pt clusters only by 
> electrostatic interaction and Van der Waals' source. 
>          The Pt cluster is studied by GPW method.  In the structure 
> optimization, all the Al and O atoms are fixed. 
>          
>         And assuming that, Al  are all the atoms whose ID from 1    to  40
>                                      O   are all the atoms whose ID from 
> 41  to 100
>                                      Pt  are all the atoms whose ID from 
> 101 to 106
>
>          So, there is something which is not clear for me:
>    
>          1) How to appoint the QM atoms and MM atoms? There are two 
> subsections, QM_KIND and MM_KIND,  in the FORCE_EVAL 
> <http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL.html> / QMMM 
> <http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/QMMM.html>  
> section. But I don't know what are  the MM_indexs in QM_KIND section ?
>               Are they the atoms ID in the  FORCE_EVAL 
> <http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL.html> / 
> SUBSYS 
> <http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS.html>
>  / COORD 
> <http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/COORD.html> section 
> ?  And why there are no keyword for assign the Index for MM_KIND ?
>          2 )  I think I don't need to specify the topology structure for 
> my systems,  so could I just leave this section empty ?
>
>
>      A trial input is shown below which is written according to my 
> understanding and the examples in test folders. 
>      
>      I know my questions are quite silly for my poor understanding of the 
> philosophy in QMMM settings in CP2K.  So any suggestions and advices would 
> be much appreciated.
>
>      Geng Sun
>
> &FORCE_EVAL
>   METHOD QMMM
>   &DFT
>     BASIS_SET_FILE_NAME BASIS_SET
>     POTENTIAL_FILE_NAME GTH_POTENTIALS
>     &MGRID
>       COMMENSURATE
>       CUTOFF 20
>     &END MGRID
>     &QS
>     &END QS
>     &SCF
>       SCF_GUESS atomic
>     &END SCF
>     &XC
>       &XC_FUNCTIONAL PADE
>       &END XC_FUNCTIONAL
>     &END XC
>   &END DFT
>   &MM
>     &FORCEFIELD
>       IGNORE_MISSING_CRITICAL_PARAMS T
>       &CHARGE
>         ATOM Al
>         CHARGE 1.4175
>       &END CHARGE
>       &CHARGE
>         ATOM O
>         CHARGE -0.9450
>       &END CHARGE
>     &END FORCEFIELD
>     &POISSON
>       &EWALD
>         EWALD_TYPE ewald
>         ALPHA .44 
>         GMAX 21
>       &END EWALD
>     &END POISSON
>   &END MM
>   &QMMM
>     USE_GEEP_LIB 10
>     CENTER NEVER
>     &CELL
>       ABC 16.8260 16.1360 25.0003
>     &END CELL
>     ECOUPL GAUSS
>     NOCOMPATIBILITY
>     &INTERPOLATOR
>       EPS_R 1.0e-14
>       EPS_X 1.0e-14
>       MAXITER 100 
>     &END INTERPOLATOR
>     &QM_KIND Pt
>              MM_INDEX  101..106
>     &END QM_KIND
>     &MM_KIND Al
>     &END MM_KIND
>     &MM_KIND O
>     &END MM_KIND 
>   &END QMMM
>   &SUBSYS
>     &CELL
>       ABC 16.8260 16.1360 25.0003
>     &END CELL
>     &COORD
> .................many O and Al positions, not shown here.
> O     16.24701734      14.39169840       5.63706764 
> O     16.24701734      14.31456832       2.94428533
> O     16.24701734      14.25696280       8.53085237
> Al     12.04034908      13.30606832       2.94428533
> Al     12.04034908      13.24846280       8.53085237
> O     12.04034908      12.14588992       4.36330236
> O     12.04034908      12.08828440       9.94986940
> O     12.04034908      12.28046416       1.46926763
> O     12.04034908      12.22285864       7.05608467
> Pt      8.14041880       4.95391336      12.72190266
> Pt     10.22314108       4.88420584      12.97940575
> Pt      6.98161218       7.10855344      12.92565511
> Pt      8.98171880       7.10855344      12.92565511
> Pt     11.31195154       7.17826096      12.66815202
> Pt      5.81018606       4.88420584      12.97940575
>     &END COORD
>     &KIND Pt
>          BASIS_SET DZV-GTH-PADE
>          POTENTIAL GTH-PADE-q10
>     &END KIND
>     &TOPOLOGY
>     &END TOPOLOGY
>   &END SUBSYS
> &END FORCE_EVAL
> &GLOBAL
>   PROJECT qmmm_test
>   PRINT_LEVEL MEDIUM
>   RUN_TYPE ENERGY
> &END GLOBAL
>
>     
>
>
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