Thermal transport in MOFs (thermof)

Investigating thermal transport in metal-organic frameworks.

• a) Idealized porous crystal (8 × 8 × 8 cubic unit cells), single unit cell highlighted in red
• b) Bonding arrangement for single unit cell using Morse potential (red bonds are modeled stronger than blue bonds)
• c) Doubly interpenetrated unit cells with framework depicted as red and blue (initial frameworks in each simulation are 5 Å apart in each dimension
• d) Interpenetrated idealized porous crystal (8 × 8 × 8 cubic unit cells).

Installation

Clone the repository, enter the main repository directory and run setup:

git clone https://github.com/kbsezginel/thermof.git
cd thermof
python setup.py install

Usage

thermof library can be used to initialize, run, and analyze simulation results to investigate thermal transport in porous crytals. Here sample files for an idealized cubic MOF along with an interpenetrated version are provided (see Figure 1). Using these files Molecular Dynamics simulations can be run with Lammps.

Command-line interface

TherMOF can be used with the command-line interface (CLI) provided in this repository. The CLIs are given in CLI directory.

Initializing LAMMPS simulations

A thermal conductivity calculation input files for LAMMPS can be generated for a cif file with the thermof_write CLI as follows:

python thermof_write.py MOF5.cif

Using the --help flag more information about the CLI (such as selecting force field, cell size) can be obtained:

python thermof_write.py --help

Analyzing LAMMPS simulations

After running LAMMPS simulations the resuts can be analyzed and plotted with the thermof_read CLI as follows:

python thermof_read.py /path/to/simulation

Here /path/to/simulation is the name of the directory that contains simulation results.

Using the --help flag more information about the CLI (such as selecting plots, parameters) can be obtained:

python thermof_read.py --help

Sample

Sample Lammps input files for thermal conductivity calculations can be found in thermof/sample

• in3_ipmof.cond.sample: Interpenetrated MOF simulation parameters with 3D thermal flux
• in3_single.cond.sample: Single MOF simulation parameters with 3D thermal flux
• in_ipmof.cond.sample: Interpenetrated MOF simulation parameters with 1D thermal flux
• lammps_ipmof.data.sample: Interpenetrated MOF structure file
• lammps_ipmof_metal.data.sample: Interpenetrated MOF with differemt corner atoms structure file
• lammps_single.data.sample: Single MOF structure file
• lammps_single_metal.data.sample: Single MOF with differemt corner atoms structure file
• lammps_qsub.sh.sample: Job submission script for lammps simulations on Frank

Notebooks

Example jupyter notebooks can be found in /notebooks

• change_trajectory: Change xyz trajectory atoms names
• initialize: Initialize Lammps simulation files according to selected simulation parameters
• interpenetrate: Create interpenetrated structure
• read_simulation: Read and plot thermal conductivity Lammps simulation results

Methods

Methods for thermal conductivity calculation and more.

Lammps benchmarking

Results

Preliminary results are presented here.