Tutorial 4: Working with Multiple Grids

Input File Setup

The previous tutorial was based on working with multiple adsorbates. However, different adsorbates do not always prefer the same adsorption sites. Therefore, multiple grids are necessasry to offer different adsorption sites. In this tutorial we will work with methanesulfonic acid (MSA) and pyrrole as our adsorbates as these molecules prefer to adsorb at the hollow and on-top site, respectively. Create xyz files with the provided coordinates:

8
xyz file for deprotonated MSA
S   7.55175   5.84738    8.82304
C   7.54062   5.87192   10.59489
H   6.63347   5.35940   10.93177
H   8.43980   5.35291   10.94313
H   7.54197   6.91971   10.91366
O   6.31967   6.55908    8.39407
O   7.55093   4.41761    8.42300
O   8.78986   6.55470    8.40759

10
xyz file for pyrrole
N   7.56794   8.33034   9.01478
C   8.70449   7.55773   8.93506
C   8.30387   6.22604   8.84668
C   6.86940   6.21305   8.85184
C   6.44501   7.53688   8.94245
H   7.55869   9.34894   8.96275
H   9.69526   7.99974   8.99005
H   8.96215   5.36132   8.87377
H   6.22759   5.33612   8.88089
H   5.44698   7.96111   9.00395

As we work with two adsorbates, again two molecule blocks are needed in the main input file.

# Adsorption on Cu(111)
Molecule
    rotationmodus = angle
    rotationangle = 120.0
    fixpointtype = atoms
    fixpointatoms = 1
    structure = ...ADJUST-YOUR-PATH.../msa.xyz
End

Molecule
    rotationmodus = angle
    rotationangle = 60.0
    fixpointtype = atoms
    fixpointatoms = 1
    structure = ...ADJUST-YOUR-PATH.../pyrrole.xyz
End

We use the lattice of the Cu(111) surface. It is important to note that the lattice must be the same for any grids as only one lattice can be defined in every simulation.

# Lattice of the Cu(111) surface
Lattice
    transx = 30
    transy = 18
    
    vectors
        2.51883   0.00000   0.00000
        0.00000   4.36274   0.00000
        0.00000   0.00000   1.00000
    end
End

To introduce multiple adsorption sites, multiple grid blocks are defined:

# On-top grid points of the Cu(111) surface
Grid
    points
        0.00000   0.00000   0.00000
        1.25942   2.18137   0.00000
    end
End

# Hollow grid points of the Cu(111) surface
Grid
    points
        0.00000   1.45518   0.00000
        0.00000   2.90908   0.00000
        1.25942   0.72771   0.00000
        1.25942   3.63655   0.00000  
    end
End

Finally, as MSA (adsorbate 1) is adsorbing on the hollow sites (grid 2) and pyrrole (adsorbate 2) is adsorbing on the on-top sites (grid 1) the following event list is defined:

# General settings for adsorption  
Events
    steps = 1000

    eventlist
        1 ads 2 1.0
        2 ads 1 1.0
    end
End

Running the Simulation

To start the simulations use the perform_multiple_rsa_runs function. Again, you should get a message that the RSA simulations are done after some time.

NRuns = 1000
inputfile_path = "...ADJUST-YOUR-PATH.../input.inp"
rsa_results, Nmolecules, molecules, Ngrids, grids, lattice, events, timings = perform_multiple_rsa_runs(NRuns, inputfile_path);

Evaluation

The plot_count_area_histograms and the plot_RSA_run functions are our main tools to evaluate the RSA simulations.

histo, mean, variance, minvalue, minvalue_id, maxvalue, maxvalue_id, avgvalue, avgvalue_id = plot_count_area_histograms(NRuns, rsa_results, Nmolecules, molecules, lattice, plotonly = false, area = 0.6);

avgvalue_id[6]
surfaceplot = plot_RSA_run(rsa_results[ID of most average run].status, Ngrids, grids, Nmolecules, molecules, lattice)