README.md

Code used in: Learning moment closure in reaction-diffusion systems with spatial dynamic Boltzmann distributions

• Phys. Rev. E 99, 063315
• arXiv:1808.08630

Requirements / libraries used

Dependenices are handled using the CPM.cmake manager. There is no need to download and install any libraries manually, simply proceed to the contents below.

For reference, the libraries downloaded by the package manager are:

• Dynamic Boltzmann library, specifically v3.1 here.
  • This further requires (also automatically managed):
  • Q3C1 library, specifically v2.0 here.
  • Armadillo, specifically v9.300.2 here.
• LatticeGillespie library for stochastic simulations, specifically v1.0 here.

Contents

Folders:

• hermite: this generates a simple figure of the Hermite polynomials.
• bimol_train_stoch_sim: generates training data for the A+A->0 reaction.
• bimol_train: trains the hidden & visible layer models for the A+A->0 reaction.
• bimol_test_stoch_sim: generates testing data for the A+A->0 reaction.
• bimol_test: tests the learned differential equations system for visible & hidden layer models for the A+A->0 reaction.
• rossler_stoch_sims: generates training data for the Rossler system.
• rossler_dynamic_3sp: learns and tests the Rossler system.