Nanomaterials Discovery

Software for the paper "A Nanomaterials Discovery Robot for the Darwinian Evolution of Shape Programmable Gold Nanoparticles" as published in Nature Communications.

Software Requirements

This software requires the following:

• Python >= 3.6 (Linux / Windows)
• Arduino IDE
• Arduino Command Handler
• Arduino Command Tools

Python Libraries

To install all rquired Python libraries, run the following command: pip install -r requirements.txt

Running The System

Information on firmware setup can be found here

The majority of the execution paramters for this platform are all defined in the platform's info.json file. This defined how many generations of experiments to perform as well as which pumps to use, what parameters to use for the GA etc.

Initial Start

• Make appropriate changes to the info.json file
• Navigate to nanobot_analysis
• Run the heimddall.py file
  • This will create the appropriate folders and populate them depending on algorithm type
  • Leave this window running if using GA mode

Execution

• Navigate to nanobot_run
• Run either the experiment.py or ga_experiment.py file depending on your experiment mode
  • This will look in the appropriate filepaths set up by the heimdall.py script and begin to load and execute experiments
• Leave this to run and process experiments
  • heimdall.py will automatically process and store experimental data in the appropriate locations
  • This wil lalso update the GA algorithm with fitness values as the generations proceed.
• Once the generations are finished, the experiment has concluded.

Arduino Firmware Setup

The following is a description of how to set up the Arduino firmware for use with Commanduino.

Installation

Clone the following repositories and follow the basic set up instructions within (Works with Windows/Linux)

• Arduino Command Handler
• Arduino Command Tools

Basic Setup

• Include the Command Handler and Command Manager at the top of your file and create a CommandManager instance

#include <CommandHandler.h>
#include <CommandManager.h>
CommandManager cmdMgr;

• Include the basic Arduino devices you will be using e.g. AccelSteppers, Servos, etc.

#include <AccelStepper.h>
#include <LinearAccelStepperActuator.h>

/* Additional Modules if necessary */

• Next, include the "Command" version of all your included devices from above

#include <CommandAccelStepper.h>
#include <CommandLinearAccelStepperActuator.h>

• Now instantiate the Arduino device objects and their Command equivalents
  • Note: The numbers are pins and these may change depending on your setup

AccelStepper stepper1(AccelStepper::DRIVER, 54, 55);
CommandLinearAccelStepperActuator cmdStepper(stepper1, 3, 38);

/* Additional Object creation */

Setup Function

Within the setup function, we use the created CommandDevice objects and add them to the manager. Each object is given a unique ID that the user specifies.

void setup() {
    /* Here, "drive_wheel" is the unique ID */
    cmdStepper.registerToCommandManager(cmdMgr, "drive_wheel");

    /* Register the remaining devices in a similar fashion */
}

Loop Function

The loop function only contains single call for the manager to update. Nothing else is required here.

void loop() {
    cmdMgr.update();
}

Pin Mappings

One of the most common uses of Commanduino is controlling stepper motors for movement, pumps, etc. To be able to use multiple stepper motors on a single Arduino board, a RAMPS shield is used, giving access to 5 possible motor locations and a collection of pins for other devices. Below is a list of pin mappings for using multiple stepper motors on a single RAMPS shield.

X_STEP_PIN         54
X_DIR_PIN          55
X_ENABLE_PIN       38

Y_STEP_PIN         60
Y_DIR_PIN          61
Y_ENABLE_PIN       56

Z_STEP_PIN         46
Z_DIR_PIN          48
Z_ENABLE_PIN       62

E0_STEP_PIN         26
E0_DIR_PIN          28
E0_ENABLE_PIN       24

E1_STEP_PIN         36
E1_DIR_PIN          34
E1_ENABLE_PIN       30

X_MIN_PIN          3
X_MAX_PIN          2
Y_MIN_PIN          14
Y_MAX_PIN          15
Z_MIN_PIN          18
Z_MAX_PIN          19

Commanduino Setup

This platform uses the COmmanduino library to facilitate all communication between the Arduino board and our Python interface. More examples can be found here.

Configuration File

Example config file:

{
    "ios": [
        {
            "port": "/dev/ttyACM0"
        },
        {
            "port": "/dev/ttyACM1"
        },
        {
            "port": "/dev/ttyACM2"
        }
    ],
    "devices": {
        "wheel": {
            "command_id": "wheel",
            "config": {
                "reverted_switch": true,
                "revereted_driection": true,
                "enabled_acceleration": false,
                "speed": 12000,
                "homing_speed": 12000,
                "acceleration": 2000
            }
        },
        "module1": {
            "command_id": "modY",
            "config": {
                "add_whats_necessary_for_device": true
            }
        },
        ...

    }
}

IOS

The ios key represents the USB port the Arduino port is connected to. Commanduino will scan these ports to find the appropriate Arduino attached. For a single arduino attached, the above setup for ios is sufficient but for multiple Arduinos, it is best to assign them to a single port only. This prevents clashes.
For port names:

• Linux
  • "/dev/ttyACM{number}"
• Windows
  • "COM{number}"

Devices

The devices key holds all the information for the devices attached to the Arduino board. In the example above, wheel and module1 are the names Commanduino will use to access them. Inside the devices, we have the command_id and config.

• command_id
  • This is unique ID given in the Arduino file. (See Arduino Setup)
• config
  • Dependent on the device type. (See Commanduino Device Examples)

Commanduino File

Example Commanduino file:

import os
import sys
import json
import time
import inspect

from commanduino import CommandManager # <-- Important!

class CoreDevice(object):
    """
    Class representing a core Commanduino system.
    Allows access to the modules attached

    Args:
        config (str): path to the Commanduino config file
    """
    def __init__(self, config):
        self.mgr = CommandManager.from_configfile(config) # Creates the CommandManager with JSON configuration file

        # Can now access devices attached e.g.
        self.wheel = self.mgr.wheel
        self.module1 = self.mgr.module1
        # etc. etc.

    ...

Authors

• Daniel Salley
• Graham Keenan
• Abhishek Sharma
• Jonathan Grizou
• Sergio Martin Marti
• Leroy Cronin

All software and designs were developed as members of the Cronin Group (University of Glasgow)