Thermal transport in MOFs (thermof)

Investigating thermal transport in metal-organic frameworks.

Installation

First, install lammps_interface Python package:

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

Then, clone and install the TherMOF repository:

git clone https://github.com/kbsezginel/thermof.git
cd thermof
pip install -e .

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 installed as console scripts by default. Alternatively, you can find the scripts in thermof/cli.

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:

thermof_write myMOF.cif

This would create a directory, myMOF, containing LAMMPS input files in the same directory as the cif file . Currently only P1 symmetry is accepted. An example cif file can be found in thermof/sample/MOF5.cif.

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

thermof_write --help

Analyzing LAMMPS simulations

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

thermof_read /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:

thermof_read --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

Publications

Babaei, Hasan, and Christopher E. Wilmer. "Mechanisms of heat transfer in porous crystals containing adsorbed gases: Applications to metal-organic frameworks." Physical review letters 116.2 (2016): 025902.
Babaei, Hasan, Alan JH McGaughey, and Christopher E. Wilmer. "Effect of pore size and shape on the thermal conductivity of metal-organic frameworks." Chemical Science 8.1 (2017): 583-589.
Sezginel, Kutay B., Patrick Asinger, Hasan Babaei, and Christopher E. Wilmer. "Effect of interpenetration on the thermal conductivity of metal-organic frameworks." submitted

kbsezginel / thermof