Colins numerical simulator in Elixir/Erlang

COLINS is a concurrent, adaptive, multi-rate, multi-method, numerical solver for dynamical systems.

Dynamical systems are represented as a network of nodes and edges.

Nodes and edges are grouped into independent partitions.

Different partitions can be run with different solver types (ie deterministic ODE, stochastic ODE), with different time-steps.

(Solver types implemented: Basic, Euler, RungeKutta4, RungeKuttaFelhberg, BackwardEuler)

Networks can be defined using SBML or the in-built, domain-agnostic language specification (DaSL), in YAML: (Antimony coming soon)

# dy/dx = (x-y)/2
# Using adaptive deterministic solver (RKF56 and BackwardEuler) 
partitions:
    1:
        solver_type: ODE
        start_step_size: 0.1
        local_error_maximum: 1.0e-6
        local_error_minimum: 1.0e-12
        explicit_implicit_switch_step_size_tolerance: 1.0e-4
nodes:
    :node_y:
        initial_value: 1
    :timepoint:
        initial_value: 0
edges:
    :y_equals_x:
        partition: 1
        inputs:
            input1: :timepoint
            input2: :node_y
        lambda: fn(input1,input2) -> (input1 - input2)/2 end
        outputs:
            :node_y: add

Uses SymPy for calculating Jacobian, and libSBML for parsing SBML.

Installation

If available in Hex, the package can be installed by adding colins to your list of dependencies in mix.exs:

def deps do
  [
    {:colins, "~> 0.1.0"}
  ]
end

Create a python environment containing the following packages:

sympy python-libsbml pyyaml

In your dev.exs or prod.exs file specify the python_path:

config :colins, python_path: "/rds/general/user/ghaggart/home/anaconda3/envs/colins/bin/python"

If you plan to use COLINS as a standalone executable, you must compile into an escript.

To do so, run the following command:

cd colins rm -rf deps && rm -rf _build mix deps.get && MIX_ENV=prod mix compile && MIX_ENV=prod mix escript.build

Usage

Either use as part of another Elixir/Erlang program, or use the command line executable:

./colins -n '/path/to/model_file/' -f '/path/to/results' -l <max_timepoint> -m <mesh_size> -i <sim_name>

gordondavies/colins

Colins numerical simulator in Elixir/Erlang

Installation

Usage

Copyright