neumannrf / electronic-structure-experiment

Uses the CP2K software package to run DFT simulations on nanoporous materials.

Electronic Structure Experiment

Automated virtual experiment that uses the CP2K software package to run DFT simulations of materials.

Prerequisites

General Prerequisites

• CP2K
• Chargemol
• Conda

Python Prerequisites

• jupyter
• jupyterlab
• numpy
• pandas
• pip
• python>=3.10
• ase
• gemmi
• pymatgen
• cp2k-input-tools

Currently the Electronic Structure Experiment is only supported on Linux operating systems.

Installation

1. Install CP2K, Chargemol, and Conda.
2. Clone this repository.
3. Create a Conda environment using the environment.yml file in the root directory of this repository. The environment can be created using the following command: conda env create -f environment.yml.
4. Activate the Conda environment.

Usage

Currently the Electronic Structure Experiment package can be used to perform the following tasks:

• Band gap calculation
• HOMO and LUMO orbital plots
• Partial charges calculation
• Geometry optimization
• Vibrational frequencies calculation and FTIR/Raman spectra simulation.

To a list of examples of how to use this repository, see the docs directory.

electronic-structure-experiment's Issues

Add the possibility restart the vibrational modes calculation

Motivation

The current version of the workflow uses CP2K to calculate the vibrational modes and FTIR and Raman spectra of a material. Unfortunately, it does not allow this calculation to be restarted if it is not completed. As the number of steps required for the calculation is considerably large (6N where N is the number of atoms) it is extremely likely that it will be necessary to restart the calculations for some materials.

What should be done

Implement an alternative for calculating the vibrational modes and the FTIR/Raman spectra that allows the correct restart at any stage of the simulation.

Add the possibility to restart the geometry optimization

Motivation

The current version of the code does not allow the restart of the geometry optimization or charge density calculation.

What should be done

Add a new option --Restart to both structure_optimization.py and charge_density.py that will add the commands required for restarting a simulation.