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exercises:2017_ethz_mmm:qmmm

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Validation of a KCl QMMM model

(exercise by Matthew Watkins, University college, London)

In this exercise you will validate the mixed quamtum/classical model for a KCl slab. Hte : 10.1021%2Fja505936b.

  • In the first part of the exercise you will consider the optimized configuration (already in the directory) and study the pure electronic adsorption energy, namely the difference between the total energy of the surface-molecule system and the energy of the molecule alone and surface alone in the same geometry as the surface-molecule system minimum structure. This will allow to show the binding pattern of the electronic density.
  • In the second part, you will optimize the surface and the molecule separately; this will allow to compute the total adsorption energy.

1. Task: Familiarize yourself

The coordinates of the optimized configuration are provided to you as S_M.opt.xyz (S stands for “Substrate”, M for “Molecule”, opt for “optimized”). Visualize the geometry with VMD and familiarize yourself with the system.

2. Task: Bond induced density differences

Compute the density difference induced by the adsorption bonding. For this you will have to run three separate energy calculations, using the *.ene.inp files.

  1. combined system (file S_M.opt.xyz)
  2. lone acetylene (file M.S_M.xyz)
  3. lone slab (file S.S_M.xyz)

In order to output the electronic densities as cube files, your input file has to contain the following snipped:

&DFT
  &PRINT
    &E_DENSITY_CUBE
    &END E_DENSITY_CUBE
  &END
&END DFT
The calculations involving the slab should be run on at least 16 cores with qsub run -v INP=prefix. Check the run file for the number of nodes.

To process the cube files we are going to use the cubecruncher tool. It is part of CP2K and is in your exercise directory.

you@eulerX ~$ ./cubecruncher.x -i S_M-ELECTRON_DENSITY-1_0.cube -subtract S-ELECTRON_DENSITY-1_0.cube -o tmp.cube
you@eulerX ~$ ./cubecruncher.x -i tmp.cube -subtract M-ELECTRON_DENSITY-1_0.cube -o Delta_ads.cube

The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool:

you@eulerX ~$ ./cubecruncher.x -center geo -i Delta_ads.cube -o Delta_ads-centered.cube

You can visualize the resulting file delta_ads-centered.cube with VMD. This has been covered in a previous exercise.

What you get should look similar to this:

3. Task: Bonding energies

Compute the binding energy:

\[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \]

For this you will need the energy values of three systems:

  1. lone acetylene molecule (run geometry optimization, use energy of last step)
  2. lone slab (you can use the already geometry optimized coordinates from S.opt.xyz at the end of the exercise)
  3. combined system adsorbed (can be reused from previous task)
You can not reuse the energy values for the lone sub-systems from the previous task. Since the unbound subsystems might relax into a different geometry, they have to be geometry optimized first.

Questions

  • Sketch briefly the geometry of the molecule when adsorbed and in the gas phase.
  • Report the system energy for the bonded system, lone slab, and lone molecule.
  • Can you estimate the contribution due to the geometry relaxation?
  • Briefly report the bond induced density difference on the system.

Required Files

When you are dealing with big systems and multiple atomic species, the input can be simplified by splitting it into multiple files. We are going to use separate files for the coordinates, the basis-sets, and the pseudo-potentials. All these files should reside in the same directory as the main input file.
The provided files are all in the directory /home/psd/Exercise_9. Change the name of the xyz file accordingly in the input files.
input.inp
@SET METHOD = QMMM # FIST all classical treatment # QS all quantum treatment
 
&GLOBAL
  FLUSH_SHOULD_FLUSH
  PRINT_LEVEL LOW
  PROJECT KCl
  RUN_TYPE GEO_OPT
&END GLOBAL
 
&FORCE_EVAL
  METHOD $METHOD
  @include QS.inc
  @include MM.inc
  &QMMM
    #this defines the QS cell in the QMMM calc
    &CELL
      ABC 12.6 15.0 12.6
      PERIODIC XZ
    &END CELL
    ECOUPL GAUSS # use GEEP method
    NOCOMPATIBILITY
    USE_GEEP_LIB 6  # use GEEP method
    &PERIODIC # apply periodic potential
      #in this case QM box = MM box in XZ so turn
      #off coupling/recoupling of the QM multipole
      &MULTIPOLE OFF
      &END
    &END PERIODIC
    #these are just the ionic radii of K Cl
    #but should be treated as parameters in general
    #fit to some physical property
    &MM_KIND K
      RADIUS 1.52
    &END MM_KIND
    &MM_KIND Cl
      RADIUS 1.67
    &END MM_KIND
    #define the model
    &QM_KIND K
      MM_INDEX 25..32 41..48
    &END QM_KIND
        &MM_KIND Cl
      RADIUS 1.67
    &END MM_KIND
    #define the model
    &QM_KIND K
      MM_INDEX 25..32 41..48
    &END QM_KIND
    &QM_KIND Cl
      MM_INDEX 17..24 33..40
    &END QM_KIND
  &END QMMM
 
  &SUBSYS
    #this defines the cell of the whole system
    #must be orthorhombic, I think
    &CELL
      ABC 12.6 100.0 12.6
    &END CELL
    &TOPOLOGY
      COORD_FILE_NAME kcl.xyz
      COORD_FILE_FORMAT XYZ
      &GENERATE
         &ISOLATED_ATOMS
         #ignores bonds dihedrals etc in classical part
            LIST 1..48
         &END
      &END
    &END
    &KIND K
      ELEMENT K
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q9
    &END KIND
    &KIND Cl
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q7
    &END
  &END SUBSYS
&END FORCE_EVAL
 
#should be able to use most motion sections
#analytic stress tensor not available, I think
@include motion.inc

and includes as separate files, using the @include macro, for the QS, MM and motion sections

QS.inc
  &DFT
    BASIS_SET_FILE_NAME BASIS_MOLOPT
    POTENTIAL_FILE_NAME GTH_POTENTIALS
    &MGRID
      COMMENSURATE
      CUTOFF 150
    &END MGRID
    &QS
      EPS_DEFAULT 1.0E-12
    &END QS
    &SCF
      EPS_SCF 1.0E-06
      MAX_SCF 26
      SCF_GUESS RESTART
      &OT
        MINIMIZER CG
        PRECONDITIONER FULL_SINGLE_INVERSE
        ENERGY_GAP 0.001
      &END OT
      &OUTER_SCF
        EPS_SCF 1.0E-05
      &END OUTER_SCF
    &END SCF
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC
    &PRINT
       &MO_CUBES
           NLUMO 10
           WRITE_CUBE T
       &END MO_CUBES
       &V_HARTREE_CUBE
           STRIDE 2 2 2
       &END
    &END PRINT
  &END DFT
MM.inc
  &MM
    &FORCEFIELD
      &CHARGE
         ATOM K
         CHARGE 1.0
      &END CHARGE
      &CHARGE
         ATOM Cl
         CHARGE -1.0
      &END CHARGE
      &NONBONDED
        &WILLIAMS
          atoms K   Cl
          A [eV] 4117.9
          B [angstrom^-1] 3.2808
          C [eV*angstrom^6] 0.0
          RCUT [angstrom] 3.0
        &END WILLIAMS
        &WILLIAMS
          atoms Cl  Cl
          A [eV] 1227.2
          B [angstrom^-1] 3.1114
          C [eV*angstrom^6] 124.0
          RCUT [angstrom] 3.0
        &END WILLIAMS
        &WILLIAMS
          atoms K   K
          A [eV] 3796.9
          B [angstrom^-1] 3.84172
          C [eV*angstrom^6] 124.0
          RCUT [angstrom] 3.0
        &END WILLIAMS
      &END NONBONDED
    &END FORCEFIELD
    &POISSON
      &EWALD
        EWALD_TYPE spme
        ALPHA .44
        GMAX  40
      &END EWALD
    &END POISSON
  &END MM
motion.inc
&MOTION
  &GEO_OPT
     OPTIMIZER LBFGS
  &END
  &CONSTRAINT
     &FIXED_ATOMS
     LIST 1..16
     EXCLUDE_MM .FALSE.
     EXCLUDE_QM .TRUE.
     &END FIXED_ATOMS
  &END CONSTRAINT
&END MOTION
kcl.xyz
48
 
Cl         0.00000       15.00000        0.00000
Cl         3.15000       15.00000        3.15000
Cl         0.00000       15.00000        6.30000
Cl         3.15000       15.00000        9.45000
Cl         6.30000       15.00000        0.00000
Cl         9.45000       15.00000        3.15000
Cl         6.30000       15.00000        6.30000
Cl         9.45000       15.00000        9.45000
K          3.15000       15.00000        0.00000
K          0.00000       15.00000        3.15000
K          3.15000       15.00000        6.30000
K          0.00000       15.00000        9.45000
K          9.45000       15.00000        0.00000
K          6.30000       15.00000        3.15000
K          9.45000       15.00000        6.30000
K          6.30000       15.00000        9.45000
Cl         3.15000       18.15000        0.00000
Cl         0.00000       18.15000        3.15000
Cl         3.15000       18.15000        6.30000
Cl         0.00000       18.15000        9.45000
Cl         9.45000       18.15000        0.00000
Cl         6.30000       18.15000        3.15000
Cl         9.45000       18.15000        6.30000
Cl         6.30000       18.15000        9.45000
K          0.00000       18.15000        0.00000
K          3.15000       18.15000        3.15000
K          0.00000       18.15000        6.30000
K          3.15000       18.15000        9.45000
K          6.30000       18.15000        0.00000
K          9.45000       18.15000        3.15000
K          6.30000       18.15000        6.30000
K          9.45000       18.15000        9.45000
Cl         0.00000       21.30000        0.00000
Cl         3.15000       21.30000        3.15000
Cl         0.00000       21.30000        6.30000
Cl         3.15000       21.30000        9.45000
Cl         6.30000       21.30000        0.00000
Cl         9.45000       21.30000        3.15000
Cl         6.30000       21.30000        6.30000
Cl         9.45000       21.30000        9.45000
K          3.15000       21.30000        0.00000
K          0.00000       21.30000        3.15000
K          3.15000       21.30000        6.30000
K          0.00000       21.30000        9.45000
K          9.45000       21.30000        0.00000
K          6.30000       21.30000        3.15000
K          9.45000       21.30000        6.30000
K          6.30000       21.30000        9.45000
exercises/2017_ethz_mmm/qmmm.1496370507.txt.gz · Last modified: 2017/06/02 02:28 by dpasserone