theochem / nice.jl Goto Github PK

Description

Add an exact non-linear solver for systems of simultaneous equilibria to the NICE (“N-species ICE-table”) Julia module.

📚 Package Description and Impact

A system of simultaneous equilibria’s steady state can be computed by solving a system of nonlinear equations, although for non-trivial systems, a very good guess at the equilibrium reaction extents is required for this. Kinetic Monte Carlo (KMC) methods are often used, then, to stochastically solve this type of system. The KMC method is slow, however, and cannot arrive at the exact solution, although the result of a KMC computation can be used as an initial guess to then solve the system exactly. Currently, NICE features the KMC method, but not the exact method. This project will entail writing the exact method’s objective function and its Jacobian, and then making use of a nonlinear solver Julia module to program the exact method into NICE.

👷 What will you do?

Using the existing NICE reaction system structure, you will write the objective and Jacobian function for the exact equilibrium solution. You will also find a suitable Julia module for nonlinear optimization, and using this, write the function that runs the exact method. You will also write a method that first runs the KMC method, and then uses its output as an initial guess to the exact solver. Finally, you must test these methods.

🏁 Expected Outcomes

1. Implement exact solver objective and Jacobian functions
2. Use a nonlinear optimizer library to program the exact method
3. Write a hybrid method using the result of the KMC method as the guess for the exact method
4. Test each new function and method you have implemented

🙋 Mentors

https://github.com/QuantumElephant/NICE/blob/master/nice/exact.py

Based on Hasan's tests, NICE and NICE.jl give different results.

We should figure out what's going on. His presentation is Thursday, and I doubt I'll have time to look at it before then. @msricher do you think you could see what's off? @mmg870630 might be helpful too.

Marco, this is a net-event kinetic-Monte-Carlo code we've been working on in the group.