Materials Designer

A standalone React/Redux application for atomistic design of material structures. Deployed within the Mat3ra.com platform as explained in the corresponding part of its documentatation here. Can be used as a library in other applications.

Try Materials Designer in action here

Functionality

As below:

• 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
• 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

Installation

Tested with Node v14.19.3. The corresponding version(s) of npm should be fine, tested with v6.4.19. We recommend using nvm for version management.

From source

Materials Designer can be installed from 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:

cd materials-designer
sh run-application.sh

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
# after successful installation run next command in the root directory of this repository:
git lfs install

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

From Docker

See Docker Files section below.

Development

Execute the following commands when running the application in development mode.

npm install
npm start

Tests

Start the application and then run one of the below commands to run the tests.

This will require proper java v1.8 installed, please verify it with command java -version. If version does not mach use next commands to install (on OSX):

brew tap adoptopenjdk/openjdk
brew install --cask adoptopenjdk8
# set to path
export PATH=/Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home/bin:$PATH

To run all tests:

sh run-tests.sh

To run a specific test feature, pass it's relative path as option:

sh run-tests.sh -f=menu/advanced/create-supercell.feature       # to run a specific test

TODO list

Desirable features/fixes for implementation:

• add tests for all the functionality listed above. We only tests advanced operations at current.
• switch color back to white when the material is back to original after editing
• add logic for Interstitials, Vacancy concentrations in combinatorial sets
• fix modal dialog exceptions for AdvancedGeometryDialog
• add line numbers to SourceEditor
• remove updateIndex action when index is the same
• show the total number of materials in set and the current index
• fix fullscreen support

Dependencies

This package depends on Made.js and Wave.js. See package.json for the full list.

CI Docker files

There are two docker files 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 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

Cove.js local development

In case you need to link Cove.js into the app for local development you need

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

    "@exabyte-io/code.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.

Links

1. Create React App, GitHub Repository