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]"
To parallelize expensive numpy operations on HPC runs, set OMP_NUM_THREADS to a value compatible with available resources: (be careful not to set too high and oversubscribe)
export OMP_NUM_THREADS=8
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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