Tutorial 8: Mimic Reactions

Input File Setup

For this tutorial you can use the coordinates of diethylsulfite and its thiolate from the Molecule Library. The largest part of the main input file is identical to previous tutorials:

# Adsorption on Cu(111)
Molecule
    rotationmodus = angle
    rotationangle = 60.0
    fixpointtype = atoms
    fixpointatoms = 1
    structure = ...ADJUST-YOUR-PATH.../des.xyz
End

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

# 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

# Bridge grid points of the Cu(111) surface
Grid
    points
        0.00000   2.18137   0.00000
        0.62971   1.09068   0.00000
        0.62971   3.27205   0.00000
        1.25942   0.00000   0.00000
        1.88912   1.09068   0.00000
        1.88912   3.27205   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

This time, the eventlist contains several "chained" events: Adsorption events are only possible for molecule 1 - which should be DES. DES can "decompose" and form a thiolate fragment - that should be molecule 2. This conversion takes place only on grid points of the first grid (bridge grid points). The third event contains the diffusion of the thiolate fragment from grid 1 to grid 2 (hollow grid points). Usually a realistic description would always combine the decomposition of DES and the diffsuion of its fragments to their prefered adsorption site. Within our RSA simulation we have to separate these steps and use the weigths to make sure that both events usually happen in succession. That is why the weigth for the diffusion step is so large. As a final event the diffusion of molecule 2 on grid 2 is added as we assume the thiolate fragment to be mobile.

# General settings for adsorption of DES  
Events
    steps = 2500
    coverageconvergence = 100
    forceadsorption = 25

    eventlist
	    1 ads 1 1.0
        1 con 2 1 5.0
        2 dif 1 2 1000.0 2.6
        2 dif 2 2 10.0 2.6
    end
End

Running the Simulation

To start the simulations use the perform_multiple_rsa_runs function:

NRuns = 100
inputfile_path = "...ADJUST-YOUR-PATH.../input.inp"
rsa_results, Nmolecules, molecules, Ngrids, grids, lattice, events, timings = perform_multiple_rsa_runs(NRuns, inputfile_path);

Evaluation

As a first step of the evaluation you should check how your input keywords affected the simulations. Here, you can check how many steps were performed by using the Nsteps field, how often a certain event was performed by using the Nevents field, or which event was still possible at the end of the simulation by using the stepinfo field.

• Nsteps: Check whether the maximum allowed number of steps or the surface coverage convergence was reached.
• Nevents: Check how many adsorption events (firt value) and how many conversion events (fourth number) were performed.
• stepinfo: Check the last columns of this matrix. The first value within each column tells you how many events in total were possible while the second and fifth value tell you how many adsorption and conversion events were possible, respectively. What type of events were performed at the end of the simulation?

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]

rsa_results[ID of most average run].Nsteps
rsa_results[ID of most average run].Nevents
rsa_results[ID of most average run].stepinfo

As usual the plot_RSA_run function can be used to visualize the final state of a simulation. In addition, it might be interesting to use the animate_RSA_run function to create an animation of the RSA simulation:

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

anim = animate_RSA_run(rsa_results[ID of most average run].stepinfo, Ngrids, grids, Nmolecules, molecules, lattice)
gif(anim, "...ADJUST-YOUR-PATH.../rsa_animation.gif", fps = 10, loop = -1)