** Reference to paper:

https://aip.scitation.org/doi/abs/10.1063/1.5070129

** DOI:

10.1063/1.5070129

** Title:

An AIMD study of dissociative chemisorption of methanol on Cu(111) with implications for formaldehyde formation

** Authors:

Gerrits, Nick; Kroes, Geert-Jan

** Contact e-mail:

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

** Abstract:

An important industrial process is methanol steam reforming, which is typically used in conjunction with copper catalysts. How-
ever, little agreement exists on the reaction mechanisms involved on a copper catalyst. Therefore, we have performed research
yielding additional insight into the reaction mechanism for dissociative chemisorption of methanol on Cu(111) using ab initio
molecular dynamics, supported by static calculations of the molecule-surface interaction with density functional theory. Our
work predicts that after the initial dissociation, formaldehyde is formed through three different mechanisms. Additionally, it
is observed that at high energy, CH cleavage is the dominant pathway instead of the formerly presumed OH cleavage pathway.
Finally, in order to describe the interaction of methanol with the metal surface, the SRP32-vdW functional is used, which has been
previously developed and tested for CHD3 on Ni(111), Pt(111), and Pt(211) using the Specific Reaction Parameter (SRP) approach. In
this work, the SRP32-vdW functional is applied to methanol on Cu(111) as well, in the hope that future experiments can validate
the transferability of the SRP32-vdW functional to chemically related molecule-metal surface systems.

** Description per file:
pdf_archiveJCPSA6vol_150iss_2024706_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.

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 InitialConditionsMethanol_SRP032:
The program used to generate the initial conditions for methanol.
MainInput.inp contains all the parameters needed to set up the conditions.

** 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 273, if ShouldIWrite = True), it will produce files that contain the surface positions and velocities used in AIMD. Make sure that lines 241 and 243 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:
Analysis_ET.py - Python script to analyze the energy transfer (average and width)
checker - Script to run periodically the check script during calculations
check-methanol.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.
dynamics-sub.py - Python script that submits jobs
ET_INCAR - Input file for VASP for the energy transfer calculations. Note that the energy cut off is 350 eV instead of 400 eV. This should not affect the results for the energy transfer.
Job-car - Initial job file using the Slurm submission system instead of Torque. Makes sure that the correct velocities are in the POSCAR due to the leap frog algorithm of VASP
Job-ET - Job file to perform calculations for the energy transfer
Job-restart - Job file for restarts
Job-restart-propagation - Job file for propagating reacted trajectories further
generate_ET.py - Python script to submit the energy transfer calculations
longpropagation.py - Python script to submit reacted trajectories to propagate further (to investigate formation of formaldehyde)
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