Welcome to JEDI, the Judgement of Energy Distribution Analysis
The JEDI (Judgement of Energy DIstribution) analysis is a quantum chemical analysis tool for the distribution of strain mechanically deformed systems. JEDI is implemented in Python. Currently, the main contributor to JEDI is the AG Neudecker from the University of Bremen.
Introduction and Overview
Based on the harmonic approximation, the JEDI analysis calculates the strain energy for each bond, bending and torsion in a molecule or an extended system, thus allowing the identification of the mechanically most strained regions in the system as well as the rationalization of mechanochemical processes.
Usage
JEDI can be used in various application scenarios, some of which are:
Mechanically Deformed Molecules
When a molecule or a periodic system is deformed, e.g., due to mechanical stretching or hydrostatic compression, some internal coordinates store more energy than others. This leads to particularly large displacements of certain coordinates such as the stretching of bond lengths, and to the preconditioning of selected bonds for rupture. Using the JEDI analysis the mechanochemical properties of the system can be investigated.
Adsorbed molecules
When a molecule adsorbs onto a surface, the geometry of the adsorbate changes as compared to the relaxed molecule in the gas phase. As JEDI allows strain analysis for only a subset of atoms, it is possible to quantify the strain due to adsorbtion.
Dynamical Strain Analyses
During an Ab Initio Molecular Dynamics (AIMD) simulation, JEDI can quantify the potential energy part of the strain due to, e.g., stretching and compression. In this scenario, each time step is considered as a deformed geometry. Dynamical strain analyses using JEDI enable the creation of color-coded movies showing the propagation of strain in dynamical mechanochemical processes.
How to Cite JEDI
When using JEDI, please cite the following papers:
Stauch, A. Dreuw, J. Chem. Phys. 140, 134107 (2014)
Stauch, A. Dreuw, Acc. Chem. Res. 50, 1041-1048 (2017)
Details on the theoretical background of JEDI are given in
Stauch, A. Dreuw, J. Chem. Phys. 143, 074118 (2015)
Documentation
Set Up:
User Guide