** Reference to paper:

https://doi.org/10.1021/acs.jpcc.9b09121

** DOI:

10.1021/acs.jpcc.9b09121

** Title:

Curious Mechanism of the Dissociative Chemisorption of Ammonia on Ru(0001)

** Authors:

Gerrits, Nick; Kroes, Geert-Jan

** Contact e-mail:

n.gerrits@lic.leidenuniv.nl
g.j.kroes@chem.leidenuniv.nl

** Abstract:

Dissociative chemisorption of polyatomic molecules on metals, which is relevant to heterogeneous catalysis, usually proceeds through a rotationally adiabatic or rotational sudden mechanism.
The reaction is usually either direct or proceeds through a trapped molecular chemisorbed state.
Here, ab initio molecular dynamics is used to model the dissociative chemisorption of ammonia on Ru(0001).
The reaction mechanism is neither rotationally adiabatic nor rotational sudden, with clearly distinct and nonstatistical initial and time-of-reaction orientation distributions.
A reasonably good agreement is obtained between the computed and previously measured sticking probabilities.
Under the conditions investigated, the reaction of NH3 goes through a molecular chemisorption-like state, but the reaction is direct.

** Description per file:
Note that many files/scripts are missing for how to perform the calculations as they are the same as the ones provided in 2018_jcp_CHD3_cu_alloys.
Therefore, in this folder mainly the results and new scripts are provided.
Furthermore, not all analysis scripts are included, as they essentially just gather data generated by check-CHD3.py contained in the PostAnalysis.dat

The program used for DFT is VASP v5.3.5 with a special modification in order to use a SRP functional and with VTST (http://theory.cm.utexas.edu/vtsttools/index.html).
Of course, since RPBE is used in this work, the "SRP100" is employed, which is essentially RPBE.

** Folder Barrier:
The barrier and asymptotic geometries are provided.

** Folder Equilibrated_slabs:
Contains the equilibrated slabs and their snapshots that have been used in the AIMD.

** Folder InitialConditionsNH3_100_general:
Contains the code to generate the initial conditions of NH3.

All figures are made with matplotlib 1.5.1, except figures of the molecule which was made with Blender 1.79 and annoted with GIMP.

** Folder Figure01:
angles.pdf
Analysis_angle_jpcc.py - generates the plot and yields averages and their errors, but requires the AIMD data.
HODNi111.dat ni_angles_reac.dat - data files of HOD and CHD3 + Ni(111)

** Folder Figure02:
F3_annoted.pdf - made in Blender and annoted with GIMP.

** Folder Figure03:
reactionprobability.pgf - should be compiled in a latex document to obtain the figure
plotsticking.py - generates the plot

** Folder Figure04:
snapshots.pdf - made in Blender and annoted with GIMP.

** Folder Figure05:
energytransfer.pdf
plotenergytransfer.py - generates the plot

** Folder Figure06:
energytrapping.pdf - Note the comments at check-NH3.py, which should be re-run for all AIMD trajectories and a new plot should be generated (would yield a slightly different parallel energy).
plotenergytrapping.py - generates the plot

** Folder Figure07:
reactionsite_p.pdf
plotreactionsite_p.py - generates the plot

** Folder Figure08:
Zn_ts_site.pdf
plotr_ts_site.py - generates the plot

** Folder Figure09:
xysteering.pdf
Analysis_xysteering.py - generates the plot but requires the AIMD data

** Folder Figure10:
site.pdf
Analysis_dist_plot.py - generates the plot but requires the AIMD data

** Folder FigureS01:
convergence.pdf
plotconvergence.py - generates the plot

** Folder FigureS02:
vdwwell.pdf
plotvdwwell.py - generates the plot

** Folder FigureS03:
elbow_f3.pdf - see 2018_jcp_CHD3_cu_alloys for how to generate the plot
energy.dat - data file

** Folder FigureS04:
reactionprobability_SI.pdf
plotsticking_SI.py - generates the plot

** Folder FigureS05:
reactionprobability_v0.pgf - should be compiled in a latex document to obtain the figure
plotsticking_v0.py - generates the plot

Other files:
check-NH3.py - analysis the trajectories. Note that there was a bug at linenumber 220 where the norm was taken, even though it should have been the sum. This is also present in the article, however, results should not be affected significantly in Figure 6. This bug is fixed in the version here (see also the source code).
MakeSlab-Temperature-100.py - Generates a thermally distorted surface that can used in equilibration runs.