COGITO - Crystal Orbital Guided Iteration To atomic-Orbitals
This repository hosts the code for COGITO, a tool for obtaining quantum chemistry from plane wave DFT calculations. The main codes modules are COGITO, COGITOpost, COGITOanalyze, and COGITOico.
Installation
pip install --upgrade pip
pip install cogito-dft
To install optional dependences (scikit-image, dash, dash-ag-grid) that are used in some COGITOpost functions:
pip install "cogito-dft[plot]"
Running on HPC
As of verison 0.3.2, compute heavy sections of COGITO.py are parallelized. Control the number of jobs and avoid thread oversubscription with:
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --cpus-per-task=4
export OMP_NUM_THREADS=1
Quick Start
Visit the live website: cogito-dft.readthedocs.io
| Section | Description |
|---|---|
| Tutorial | Step-by-step analysis workflow |
| File Guide | Interactive guide of inputs and outputs |
| API Docs | Complete function reference |
Basic Workflow:
- Run VASP - Static calculation with saved wavefunctions and high NBANDS
- Generate COGITO model - Creates COGITO basis functions and tight binding parameters
- Verify quality - Check convergence, charge spilling, orbital mixing, and band interpolation
- Analyze chemistry - COHP, bonding, charge analysis
# Run VASP
vasp_std
# See 'COGITO --help' for variable options
COGITO --dir './'
# Check that quality metrics are within range (check band interpolation after COGITOpost)
COGITOanalyze --dir './'
# Generate atom and bond partition of charge / band energies, make bond plots, and more
COGITOpost --dir './'
# Customize a runTBmodel.py file to get specific plots
python runTBmodel.py
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