Electron Phonon Coupling for Molecular Crystals

Installation:

Requirement: Gaussian 09 or 16

We recommend using conda to create virtual environment.

    git clone https://github.com/moule-group/ElPh.git

    conda create -n elph
    cd Elph
    pip install .

Environment variables in .bashrc

export PATH="your_path/catnip/build/":$PATH
export GAUSS_EXEDIR="your_path/g16"
export GAUSS_SCRDIR="$your_path/GaussianScratch"
export PATH="$GAUSS_EXEDIR:$PATH"
export PATH="$GAUSS_SCRDIR:$PATH"

For installing Catnip (ChArge TraNsfer Integral Package), please refer to https://joshuasbrown.github.io/docs/CATNIP/catnip_downloads.html

Make scripts in src/elph executable.

chmod +x * 

We recommend users set the environment variable

export ELPH=/pscratch/sd/r/.../ElPh/src/elph
export PATH=$ELPH:$PATH

Example code

$ELPH/create_jo_input.py 

Usage:

Optimized Structure Transfer Integral Simulation

First step: Prepare input files in the folder: CONTCAR or POSCAR (VASP structure format) ; FORCE_SETS and phonopy_disp.yaml from Phonopy simulation.

Second step: Run create_j0_input.py, which will generate the input files to calculate transfer integral J at reference state. Then loop through every subfolder to execute run.bash. This will conduct gaussian simulation.

Third step: Run j0.py. This will call Catnip to calculate transfer integral based on Gaussian output files. the result will be written into j0.json.

Displaced Structure Transfer Integral Simulation

First step: Run create_disp_input.py. This will generate displaced structures in "displacements" folder. It will also return "run_all.sh" script for users to conduct Gaussian simulations.

Second step: User should finish all Gaussian simulations for 1 dimer and 2 monomers. (Ex: dimer A; monomer 1 and 2. dimer B; monomer 1 and 3). Then run disp_j.py, which will generate a run script for user to run catnip calculations.

Note: User can also utilize xTB package for transfer integral simulation

Electron-Phonon Coupling (EPC) and Singular Value Decomposition (SVD) Analysis

Please check the example folder, there is a tutorial of BTBT dimer.

Theory:

This will divide into two parts. First part is transfer integral J, electron phonon coupling (EPC), and singular value decomposition (SVD) analysis. The second part is transient localization theory.

Transfer integral J, Electron-Phonon Coupling (EPC), Variance, and Singular Value Decomposition (SVD)

We refer the user to the research article we are preparing.

Transient Localization Theory (TLT)

The mobility equation is shown below: $\mu = \frac{e}{kT} \frac{L^2_{x(y)}}{2\tau}$

where $\tau$ is the relaxation time, $L^2_{x(y)}$ is squared localization length, e is the charge, T is the temperature in K, k is the Boltzmann constant. The mobility unit is in $\frac{cm^2}{Vs}$