Materials Designer

A standalone React application for atomistic structural design. Deployed within the Mat3ra.com platform as documented here and can be used as a library in any web/Node.js application.

Try Materials Designer in action here

1. Installation

1.1. From source

Materials Designer can be installed from the source as follows:

git clone [email protected]:Exabyte-io/materials-designer.git

Or use https, if no SSH authentication is set up with GitHub:

git clone https://github.com/Exabyte-io/materials-designer.git

then start the application using Node v14.19:

cd materials-designer
npm install
npm start

Some files might not be downloaded by git clone or git pull commands if your system doesn't have git-lfs installed. To fix this run (on OSX):

brew install git-lfs
git lfs pull

Open http://localhost:3001 to view the application in the browser.

1.2. Using Docker

See the Docker Files section below.

2. Functionality

2.1. Current Functionality

As below and further documented here:

• Input/Output Menu
  • Export materials in JSON/POSCAR formats
• Edit Menu
  • Undo/Redo/Reset/Clone operations
• View
  • Fullscreen mode
  • Multi-material Editor (combining multiple materials into one)
• Advanced Menu
  • Creating supercells
  • Creating surfaces/slabs
  • Creating combinatorial sets
  • Creating interpolated sets
  • Run Python Script
  • Launch a Jupyter Lite session
• Basis Editor
  • Adding/Removing/Modifying sites
  • Adding/Removing/Modifying atomic constraints
  • Switching Crystal/Cartesian units
• Lattice Editor
  • Adjusting lattice units/types/parameters
• 3D Editor
  • Visualizing materials
    • Rotation
    • Repetition/Radius
    • Toggle axes
  • Adjusting materials
    • add/remove/select atoms
    • multiple selection with drag-and-drop

2.2. TODO list

Desirable features/fixes for implementation.

General Improvements:

• switch the color back to white when the material is back to the original after editing
• show the total number of materials in the list and the current index
• fix fullscreen support
• add lattice vectors form to change lattice vectors in a 3x3 matrix with all components explicitly:
• highlight atoms that are selected in the source editor in the 3D editor and vice versa
• add the ability to drop files with material structural data to the materials list
  • ESSE JSON and POSCAR parsers already implemented in made.js
  • add a skeleton material with (+) button to the materials list (combines functionality of "Edit" -> "Clone" and "I/O" -> "Import...")
• save the state of Materials Designer to share materials and exact visualization via URL link.
  • the idea is to be able to share an exact copy of the state of the application
  • materials data is stored in the redux store
  • visualization settings stored in wave.js components, via useState() hook

Specific features:

• add logic for Interstitials and vacancy concentrations in combinatorial sets

Developer Experience:

• add tests for all the functionality listed above. We only test advanced operations at current.
• fix modal dialog exceptions for AdvancedGeometryDialog
• remove the updateIndex action when the index is the same

3. Development

3.1. Run the application

Execute the following commands when running the application in development mode. Use Node v14.19

npm install
npm start

3.2. Tests

Tests are implemented using Cypress. To launch it use Node v20 and run:

cd tests
npm install
npm test

To run a specific test feature, pass its relative path as an option:

sh run-tests.sh -f=menu/advanced/create-supercell.feature

3.3. Dependencies

This package depends on Made, Wave, and Cove.js among other packages. For the full list, see package.json.

3.4. CI Docker files

Two docker files were used for testing in CI. In principle, we could use more targeted base images for the use case (e.g. node or selenium images), but we want to verify the correct behavior on a specific CentOS version. The first dockerfiles/centos/Dockerfile builds and runs the application. The second dockerfiles/test/Dockerfile provisions and runs the tests. The test image uses the centos image as a base and is related by the entrypoint.sh script. It is targeted for CI so if you are editing the entrypoint.sh you may need to re-build both containers for your changes to work. It can also be useful to comment out the ENTRYPOINT in the centos dockerfile as well as the CMD in the test dockerfile in order to easily run and debug both containers. There is also a docker-compose.yml file, which can be used for local building and testing. Provided docker-compose is installed, it can be used like so:

docker-compose build materials-designer
docker-compose build materials-designer-test

docker-compose up -d materials-designer
sleep 30  # let the app actually start
docker-compose run materials-designer-test

To run tests in the container use default profile by not specifying it:

docker-compose up -d --build

For debugging purposes, Materials Designer and test container can be run interactively with access via VNC:

docker-compose --profile use-vnc up -d --build

Then connect to vnc://localhost:5920 with a VNC client. The password is 123. (Port set in .env file.) Make sure to have VNC client installed on the system, when address is typed in the Chrome browser, the VNC prompt will appear.

3.5. Using Cove.js for local development

If need to link Cove.js into the app for local development, you need

1. Add the local path of Cove.js to package.json

    "@exabyte-io/cove.js": "file:../../cove.js"

2. Run the app

    npm start

If you need to re-link it again, remove node_modules in cove.js and the app, run npm install, then run npm start again.

4. Links

1. Create React App, GitHub Repository
2. Mat3ra Platform documentation for materials designer.