Exact solver translate to Julia

theochem / NICE.jl

https://theochem.github.io/NICE.jl/

MIT License

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Exact solver translate to Julia #2

Open PaulWAyers opened 1 year ago

PaulWAyers commented 1 year ago

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

PaulWAyers commented 1 year ago

Here are some notes on the method (as I recall). examples.pdf Simultaneous Chemical Equilibria.pdf Simultaneous Chemical Equilibria.docx 11Systems of Nonlinear Equations from Simultaneous Equilibria.docx

PaulWAyers commented 1 year ago

The constraint is that there can never be a negative amount of a reactant. So for reaction R, $\xi_R$ is greater than the -1 times the smallest positive stoichiometric coefficient and larger than the -1 times the largest negative stoichiometric coefficient.

PaulWAyers commented 1 year ago

Initial guess:

specified by user.
from net-event KMC run.
randomly selected in the allowed interval of $\xi_R$ for each reaction.
selected to be zero.
more sophisticated choices are possible but perhaps not worthwhile. E.g., you could choose $xi_R$ to be greater than zero when $K_R > 1$ and less than zero otherwise.

PaulWAyers commented 1 year ago

I'd probably give two options:

User specified (can include user passing result from a previous simulation).
Zero (if user doesn't specify).

PaulWAyers commented 1 year ago

It may be worth using the optim.jl package, as it doesn't require building the sum-of-squares objective function.

https://github.com/JuliaNLSolvers/Optim.jl

PaulWAyers commented 1 year ago

It looks like there is a high-level interface with the Neqproblem keyword https://github.com/JuliaNLSolvers/NLSolvers.jl

NamanKothari5 commented 6 months ago

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

@PaulWAyers as of now the URL is not working I wanted to attempt on the exact solver implementation can you point me to some relevant materials to get started with this.

Also, I wish to connect with you mentors and other members of the community, so, it would be beneficial if you can provide Slack, Element, Discord or any other communication channel link.

PaulWAyers commented 6 months ago

Some notes on simultaneous equilibria are here. The first is the general framework, then a set of notes that has a lot of examples. General Notes General + Specific Examples

The supplementary material from J. Mol. Modelling v23, 155, (2017) is also relevant.

magnamad commented 5 months ago

Hi,

I am Madhavan, currently pursuing my masters from IISc Bangalore, India in the department of Chemical Engineering. @PaulWAyers First of all, thank you for the resources shared regarding the setting up of nonlinear equations. Additionally, can you also provide some resources pointing to how the KMC simulations needs to be implemented. It would be great if you could share the link for some contact channel so that I can connect with the members of your community.

Thanks again! Madhavan