aryaghan-mutum / moleculardynamics

Javascript implementation of ReaxFF potential functions

Molecular Dynamics Simulation

MD is an atomistic simulation technique used to study broad set of biomolecules in diverse conditions.

Description

It is a project to implemet ReaxFF Reactive Force Field potential functions for Molecular Dynamics Simulations of Hydrocarbon Oxidation in JavaScript.

This project comprises the general ReaxFF-potential functions. They are as follows:

1. Bond Order
2. Bond Energy
3. Lone pair energy 
4. Over Coordination
5. Under Coordination
6. Valence energy 
7. Penalty energy
8. Coalition energy
9. Torison energy 
10. Four-body conjugation term
11. Hydrogen body interaction
12. C2 Correction
13. Triple bond energy correction
14. Non bonded interactions
15. Taper correction
16. Van der Waals interactions
17. Coulomb interactions
18. Overall system energy

Download node.js and npm

• Download the node.js .pkg installer from: https://nodejs.org/en/download/
• Verify version: node --version
• Run node.js installer
• Verify version: node -v or node --version
• Update npm version: npm install

Contributors

• Jeffrey Comer ([email protected])
• Anurag Muthyam ([email protected])

moleculardynamics's Issues

sum_ovun2 value is incorrect needs to fix

Fix NaN problem

Implementation of the Lone pair energy, Over and Under coordination are completed. However, some of the variables inside these functions are displaying "NaN". Needs to fix!

var delta_lpcorr in overCoordination() is showing NaN

Remove the parseFloat() in the molecular_dynamics.js

parse the values of the input file before the values are used in the molecular_dynamics.js