Supplementary data for "Molecular dynamics study of confined water in the periclase-brucite system under conditions of reaction-induced fracturing"

In this dataset you can find sample data from periclase and brucite simulations and python scripts that can be used to confirm the plots in the paper.

• "bruciteSimualtions" and "periclaseSimualtions" contains the simulations where the mineral in contact with water is either brucite or periclase. Within each of these two folders, there are two subfolders, "waterProperties" and "waterThickness". 
  • The data in "waterProperties" is used to calculate water properties. Each folder inside "simulations" represent one simulation.
  • The data in "waterThickness" is used to calculate the change in water film thickness with time under different conditions. The simulations are run for either 3 ns or 10 ns. Each folder inside "simulations_Xns" represent one simulation.
• For each folder containing one simulations, we provide:
  • NAME.run: The input script
  • NAME.data: The input data
  • job.sh: Script to run the simulation
  • log.lammps: Thermodynamic output from the simulation
  • Note that the pressures given in the folder names and in the simulations are in atm, not MPa.

• "bruciteSimulations" and "periclaseSimualtions" are in zip containers. In order to use them, please unzip them and leave the resulting folders in the same directory as this README file. 

• The python scripts shows how to extract the relevant data from the lammps log files, which enables reproduction of the figures in the paper. See instructions below to use the scripts.

Installation instructions to make the python plot scripts working, assuming you already have numpy and matplotlib:

> pip3 install git+https://github.com/henriasv/regex-file-collector.git

> pip3 install git+https://github.com/henriasv/lammps-logfile.git
 

If this does not work, please contact Marthe Grønlie Guren, m.g.guren@geo.uio.no