Tutorial 7: Including Conformer Changes

Input File Setup

For this tutorial you can use the coordinates of Pyridine 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.../pyridine-upright.xyz
End

Molecule
    rotationmodus = angle
    rotationangle = 60.0
    fixpointtype = atoms
    fixpointatoms = 1
    structure = ...ADJUST-YOUR-PATH.../pyridine-tilted.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

# 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

The major difference in the input file is the presence of conversion events for the adsorbate in the eventlist. In our case we enable the conversion from adsorbate 1 to adsorbate 2 (a reverse reaction could be added as an additional entry in the eventlist). Furthermore coverageconvergence and forceadsorption are added. The first keyword will stop the RSA simulation once the given number of steps were performed without the occurence of an adsorption event - thereby the surface coverage is assumed to be converged. The second keyword will try to force an adsorption event once the given the given number of steps were performed without the occurence of an adsorption event.

# General settings for adsorption of pyridine  
Events
    steps = 1000
    #coverageconvergence = 100
    #forceadsorption = 25

    eventlist
	    1 ads 1 1.0
        2 ads 1 1.0
        1 con 2 1 10.0
    end
End

Running the Simulation

To start the simulations use the perform_multiple_rsa_runs function:

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

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)