Supporting dataset for "Understanding the entanglement between diffusion and reaction by probing the mobility of ketene in chabazites"

Dataset Description: Ketene Diffusion in Chabazite Materials (CP2K + PLUMED Umbrella Sampling)

This dataset includes all input files and analysis scripts used for umbrella sampling simulations of ketene diffusion in chabazite materials, conducted using CP2K and PLUMED. It is organized as follows:

1. CP2K Input Files

• Format: .inp

• Naming Convention:
  SSZ-13-0BAS-Ketene_<coord>.inp
  Example: SSZ-13-0BAS-Ketene_0.0.inp

• Description:
  Each file corresponds to a specific umbrella sampling window at a given diffusion coordinate (in Å).

  • 0BAS indicates the absence of Brønsted acid sites.

2. PLUMED Input Files

• Located in the same folder as the corresponding CP2K .inp file.

• Default File Name: PLUMED.inp

• Special Cases (e.g., in cases 4-9):
  Additional PLUMED input files apply specific constraints to control the chemical state of ketene and its derivatives:

• PLUMED_KT.inp: Ketene (KT)

• PLUMED_AY.inp: Acylium ion (AY)

• PLUMED_SA.inp: Surface acetate (SA)

• PLUMED_AcOH.inp: Acetic acid (AcOH)

• PLUMED_MA.inp: Methyl acetate (MA)

3. Free Energy Surface Analysis

• Python Scripts (.py):

  • Located in the root directory

  • Used to generate 1D and 2D free energy surfaces from the simulation data by Thermolib code.

4. Thermolib Input

• File: wham_input.txt

• Used for WHAM (Weighted Histogram Analysis Method) post-processing.

• Present in each case-specific folder.

5. Collective Variable (Colvar) Files

• Naming Convention: colvar_xx_xx.dat

• Contain the collective variable data from PLUMED simulations.

• Located in the corresponding simulation folders.