** Reference to paper:

https://aip.scitation.org/doi/10.1063/1.5053990

** DOI:

10.1063/1.5053990

** Title:

Dissociation of CHD3 on Cu(111), Cu(211), and single atom alloys of Cu(111)

** Authors:

Gerrits, Nick; Migliorini, Davide; Kroes, Geert-Jan

** Contact e-mail:

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

** Abstract:

In order to model accurately reactions of polyatomic molecules with metal surfaces important for
heterogeneous catalysis in industry, the Specific Reaction Parameter (SRP) approach to density func-
tional theory has been developed. This approach has been shown to describe the dissociation of
CHD3 on Ni(111), Pt(111), and Pt(211) with chemical accuracy. In this work, predictions have been
made for the reaction of CHD3 on Cu(111) and Cu(211) using barriers, elbow plots, and ab initio
molecular dynamics. Future experiments could hopefully prove the transferability of the SRP func-
tional to systems in which methane reacts with flat and stepped surfaces of adjacent groups of the
periodic table, by comparison with our predictions. Moreover, the effect of a so-called single atom
alloy on the reactivity of methane is investigated by making predictions for CHD3 on Pt–Cu(111) and
Pd–Cu(111). It is found that the reactivity is only increased for Pt–Cu(111) near the alloyed atom,
which is not only caused by the lowering of the barrier height but also by changes in the dynamical
pathway and reduction of energy transfer from methane to the surface.

** Description per file:
pdf_archiveJCPSA6vol_149iss_22224701_1_am.pdf - Preprint of the accepted manuscript

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).

** Folder Barrier:
Two folders exist within barrier: asymptotic and dimer.
These two give examples of how to calculate the asymptotic configuration (methane halfway between the slabs) and the barrier configuration for an arbitrary functional, number of layers, supercell size, etc.

The files:
INCAR - Input for VASP
Job - The job file to run the calculation on a cluster using Torque
KPOINTS - Input for VASP describing the k-point grid
POSCAR - Input for the positions of the atoms

Missing files due to copyright:
POTCAR - The PAW pseudo potentials from VASP v5.2. If one wants to adjust the atomic mass, one needs to adjust the tag POMASS
vdw_kernel.bindat - The vdW kernel generated by VASP. If none is supplied VASP will recalculate the kernel. One can then reuse the resulting kernel for other calculations.

** Folder Frequency:
An example of how a frequency analysis is performed using finite differences.
File descriptions are the same as the folder Barrier.

** Folder NEB:
An example of how a NEB calculations is performed.
File descriptions are the same as the folder Barrier.

From vasputil (https://github.com/jabl/vasputil) the interpolate script is used to generate the initial configurations along the reaction path.
The resulting POSCARs need to be in the folders 01..NIMAGES.

** Folder Slab:
An example of how a slab equilibration is performed.
File descriptions are the same as the folder Barrier.

** Folder Bulk:
An example of how a bulk equilibration is performed.
File descriptions are the same as the folder Barrier.

** Folder Elbow:
An example of how the contour/elbow plots are made. The interpolation routine used to find the MEP is also included.
The energies obtained from VASP are single point calculations as described in the main article.
Typically, the single point calculations are the barrier geometry where the height of the carbon and the bond distance of CH are varied.

draw_elbow.py - Script to generate the elbow plot
energy.dat - Data file containing Z, r and the total free energy (F in VASP output)
phi_scan.py - Script to find the minimum energy path (MEP)

** Folder InitialConditionsCHD3_SRP032:
The program used to generate the initial conditions for CHD3.
MainInput.inp contains all the parameters needed to set up the conditions.
There is one small error in the potentials causing the minimum of vibrational modes to be slightly next to the minimum, i.e. for Q=0 the energy is slightly too high.
However, this error is very small and should not affect the calculations since the rest of the vibrational potentials are correct.
In the CHD3 paper on Cu(111) with the neural network this error is fixed.

** Folder Slab_equilibration:
Scripts to run slab equilibration according to a surface temperature.
Typically first a 1 ps run is performed to equilibrate the slabs, then another 1 ps run is performed which serves as a basis for the snapshots that are used for the initial conditions.
File descriptions in the subfolder INPUTS are the same as the folder Barrier.

Additional files:
generator.e - Bash script that runs MakeSlab-Temperature-032.py and checks whether both the potential and kinetic energy are within the set range, and submits the jobs
MakeSlab-Temperature-032.py - Python script that generates positions and velocities according to the provided parameters such as temperature, unit cell vectors and lattice expansion due to surface temperature
TemperatureCheck.py - Python script that compares the VASP temperature with the values obtained from Temperature-interlayer-check.py
Temperature-interlayer-check.py - Python script that obtains average interlayer distances and temperature. If writing is enabled (see line 272, if ShouldIWrite = True), it will produce files that contain the surface positions and velocities used in AIMD. Make sure that lines 240 and 242 contain the correct output paths. The script is run with the input folders in the command line (e.g. `python Temperature-interlayer-check.py 1/dyn 2/dyn 3/dyn 4/dyn`).
Subfolder EQUILIBRATED - Contains the collected positions and velocities used in the AIMD

** Folder AIMD
The input files for the AIMD trajectories, which use the initial conditions generated from the program in the folder InitialConditionsCHD3_SRP032 and the equilibrated slabs.
File descriptions are the same as the folder Barrier.

Additional files:
check-CHD3.py - Python script to check whether a trajectory is scattered, reacted or trapped, and relevant dynamical data such as angles and velocities. Stops calculations by writing a STOPCAR when an outcome is reached.
checker - Script to run periodically the check script during calculations
dynamics-sub.py - Python script that submits jobs
Job-erc - Initial job file. Makes sure that the correct velocities are in the POSCAR due to the leap frog algorithm of VASP
Job-restart - Job file for restarts
restart.py - Python script that restarts jobs
submitter.sh - Bash script that makes sure that jobs are (re)started according to queue size, what's already in the queue, and how many nodes are free (can be disabled)
Traj_Analysis.py - Python script that collects all outcomes and generates a summary file