jtsun/tmd

Utilities for transition metal dichalcogenide DFT and Wannier analysis

Workflow description

Running the calculation:

python3 tmd/bilayer/dgrid.py: prepare inputs for grid of d's (interlayer shifts) and submit DFT calculation for all d's (scf, nscf bands, nscf).

python3 tmd/bilayer/submit_pw_post.py: submit post-processing calculation for all d's (make bands data file, run pw2wannier90).

sbatch work_base/global_prefix_launcher: run Wannier90 for all d's

Analysis of results:

python3 tmd/bilayer/gaps.py: used to obtain the gap as a function of d for states localized in a given layer. This is the only analysis tool in this repository used for the results in "Topological Exciton Bands in Moiré Heterojunctions".

python3 tmd/bilayer/plot_ds.py: plot properties (energy, overall gap, matrix elements) as function of d

python3 tmd/bilayer/plotBands.py: plot bands as function of d

python3 tmd/bilayer/dfourier.py: plot matrix elements as function of G (the Fourier transform of d)

Dependencies and installation: LS5

Install python3:

cd ~
wget https://www.python.org/ftp/python/3.5.1/Python-3.5.1.tar.xz
unxz Python-3.5.1.tar.xz
tar -xvf Python-3.5.1.tar
cd Python-3.5.1
./configure --prefix=$HOME/python3.5
make
make install

Add to .bashrc:

export PATH=$HOME/python3.5/bin
export PYTHONPATH=$HOME/python3.5/lib/python3.5/site-packages:$PYTHONPATH
export CPATH=$HOME/local:$CPATH
export LIBRARY_PATH=$HOME/local:$LIBRARY_PATH

Restart bash. Get virtualenv (not required due to installation in $HOME/python3.5):

easy_install-3.5 virtualenv

Get libyaml and make:

cd ~
wget http://pyyaml.org/download/libyaml/yaml-0.1.5.tar.gz
cd yaml-0.1.5
./configure --prefix=$HOME/local
make
make install

Set up virtualenv (not required due to installation in $HOME/python3.5):

cd ~/tmd
virtualenv -p python3 tmd_env
source tmd_env/bin/activate

When finished with tmd, can use deactivate to leave virtualenv. Install tmd:

python3 setup.py develop

Dependencies and installation: local

Uses pyyaml which requires libyaml:

sudo apt-get install libyaml-dev

Uses ASE and the 2D materials repository.

Create a virtualenv:

sudo apt-get install python-virtualenv
virtualenv -p python3 tmd_env
source tmd_env/bin/activate

Install:

python3 setup.py install

or:

python3 setup.py develop

For making plots, need cwannier:

git submodule init
git submodule update
cd cwannier
git submodule init
git submodule update
cd ctetra
make
cd ..
make