Model for bacteria mixing in three-dimensions using random walker agents

This repository has the code to run a model of bacteria mixing in three-dimensions using random walker agents. The model is written in Rust and uses Atrix to run the server. The client is using the svelte framework to render the model.

[SERVER] Running the model

To run the model, you need to have Rust installed. You can install Rust by following the instructions on the Rust website. Once you have Rust installed, you can run the model by running the following command in the terminal:

cd server
cargo watch -x run

This will start up a server on the port 8080. You can then open up a browser and go to the address localhost:8080/2d to see the state of the model.

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[SERVER] Endpoints

WARNING: For now only the CPU endpoint is implemented. The GPU endpoint is still in development.

The server has two main endpoints

GET alive

Returns for each universe dimension if it is Some or None. If it is Some, then the universe is alive and can be used. If it is None, then the universe is dead and cannot be used.

GET [1d|2d|3d]

Get current state of the model as JSON Object. State includes:

• size: NUMBER - The size of the model
• agents: [NUMBER, NUMBER] - The number of agents in the model
• seed: NUMBER - The seed used to generate the model
• iteration: NUMBER - Number of updates the model has gone through
• params: JSON - The parameters of the model
  • gamma: NUMBER - TODO
  • lambda: TODO
  • beta: TODO
• nodes: ARRAY[JSON] - A list of nodes where each node is defined by
  • index: NUMBER - The index of the node
  • neighbours: ARRAY[NUMBER] - The indices of the neighbours of the node
  • grafitti: [NUMBER, NUMBER]- The amount of red and blue grafitti in the node
  • red_agents: NUMBER - The number of red agents in the node
  • blue_agents: NUMBER - The number of blue agents in the node

GET [1d|2d|3d]/agent-nodes

Get current state of the model as JSON Object. Is identical to the GET [1d|2d|3d] endpoint except that the nodes field is a list of agent nodes instead of nodes. Agent nodes are defined by:

• nodes: [{agents_red: NUMBER, agents_blue: NUMBER}]

POST [1d|2d|3d]/setup/<size>/<agents>?seed=<NUMBER>

Setup the model with a lattice size of <size>x<size> for 2d and <size>x<size>x<size> for 3d and <agents> agents. The seed is optional and will default to 100 if not provided.

• size: NUMBER - The size of the lattice
• agents: NUMBER - The number of agents in the model for each species
• seed?: NUMBER - The seed used to generate the model

POST [1d|2d|3d]/set_params?gamma=<NUMBER>&lambda=<NUMBER>&beta=<NUMBER>

Set the parameters of the model

• gamma: NUMBER - TODO
• lambda: NUMBER - TODO
• beta: NUMBER - TODO

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PATCH [1d|2d|3d]/iterate?amount=<NUMBER>

Iterate the model <amount> times

[SERVER] Example sequence

# Create a 2d model with a size of 10x10 and 100 agents with a seed of 1234
POST localhost:8080/2d/10/100?seed=1234 

# Set the parameters of the model
POST localhost:8080/2d/set_params?beta=0.1

# Iterate the model 100 times
PATCH localhost:8080/2d/iterate?amount=100

# Get the current state of the model as a json object 
GET localhost:8080/2d