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Inc."},"license":"Apache-2.0","homepage":"http://.","repository":{"type":"git","url":"git+https://github.com/mat3ra/materials-designer.git"},"description":"Materials Designer","maintainers":[{"name":"exabyte-io","email":"info@exabyte.io"}],"readme":"[![npm version](https://badge.fury.io/js/%40mat3ra%2Fmaterials-designer.svg)](https://badge.fury.io/js/%40mat3ra%2Fmaterials-designer)\n[![License: Apache](https://img.shields.io/badge/License-Apache-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0)\n\n# Materials Designer\n\nA standalone React application for atomistic structural design. Deployed within the Mat3ra.com platform as\ndocumented [here](https://docs.mat3ra.com/materials-designer/overview/) and can be used as a library in any web/Node.js\napplication.\n\n[Try Materials Designer in action here](https://mat3ra-materials-designer.netlify.app/)\n\n![Materials Designer in action](https://i.imgur.com/f7NvNNl.png)\n\n## 1. Installation\n\n### 1.1. From source\n\nMaterials Designer can be installed from the source as follows:\n\n```bash\ngit clone git@github.com:mat3ra/materials-designer.git\n```\n\nOr use https, if no SSH authentication is set up with GitHub:\n\n```bash\ngit clone https://github.com/mat3ra/materials-designer.git\n```\n\nthen start the application using Node v20.18:\n\n```bash\ncd materials-designer\nnpm install\nnpm start\n```\n\n> Some files might not be downloaded by `git clone` or `git pull` commands if your system doesn't have `git-lfs`\n> installed.\n> To fix this run (on OSX):\n> ```\n> brew install git-lfs\n> git lfs pull\n> ```\n\nOpen http://localhost:3001 to view the application in the browser.\n\n### 1.2. Using Docker\n\nSee the Docker Files section below.\n\n## 2. Functionality\n\n### 2.1. Current Functionality\n\nAs documented [here](https://docs.mat3ra.com/materials-designer/overview/):\n\n- Input/Output Menu\n    - Export materials in JSON/POSCAR formats\n- Edit Menu\n    - Undo/Redo/Reset/Clone operations\n- View\n    - Fullscreen mode\n    - Multi-material Editor (combining multiple materials into one)\n- Advanced Menu\n    - Creating supercells\n    - Creating surfaces/slabs\n    - Creating combinatorial sets\n    - Creating interpolated sets\n    - Run Python Script\n    - Launch a Jupyter Lite session\n- Basis Editor\n    - Adding/Removing/Modifying sites\n    - Adding/Removing/Modifying atomic constraints\n    - Switching Crystal/Cartesian units\n- Lattice Editor\n    - Adjusting lattice units/types/parameters\n- 3D Editor\n    - Visualizing materials\n        - Rotation\n        - Repetition/Radius\n        - Toggle axes\n    - Adjusting materials\n        - add/remove/select atoms\n        - multiple selection with drag-and-drop\n\n### 2.2. TODO list\n\nDesirable features/fixes for implementation.\n\nGeneral Improvements:\n\n- switch the color back to white when the material is back to the original after editing\n- show the total number of materials in the list and the current index\n- fix fullscreen support\n- add lattice vectors form to change lattice vectors in a 3x3 matrix with all components explicitly:\n- highlight atoms that are selected in the source editor in the 3D editor and vice versa\n- add the ability to drop files with material structural data to the materials list\n    - ESSE JSON and POSCAR parsers already implemented in made.js\n    - add a skeleton material with (+) button to the materials list (combines functionality of \"Edit\" -> \"Clone\" and \"\n      I/O\" -> \"Import...\")\n- save the state of Materials Designer to share materials and exact visualization via URL link.\n    - the idea is to be able to share an exact copy of the state of the application\n    - materials data is stored in the redux store\n    - visualization settings stored in wave.js components, via `useState()` hook\n\nSpecific features:\n\n- add logic for Interstitials and vacancy concentrations in combinatorial sets\n\nDeveloper Experience:\n\n- add tests for all the functionality listed above. We only test advanced operations at current.\n- fix modal dialog exceptions for AdvancedGeometryDialog\n- remove the `updateIndex` action when the index is the same\n\n## 3. Development\n\n### 3.1. Run the application\n\nExecute the following commands when running the application in development mode. Use Node v14.19\n\n```bash\nnpm install\nnpm start\n```\n\n### 3.2. Tests\n\nTests are implemented using Cypress. To launch it use Node v20 and run:\n\n```bash\ncd tests\nnpm install\nnpm test\n```\n\nTo run a specific test feature, pass its relative path as an option:\n\n```bash\nsh run-tests.sh -f=menu/advanced/create-supercell.feature\n```\n\n### 3.3. Dependencies\n\nThis package depends on [Made](https://github.com/mat3ra/made), [Wave](https://github.com/mat3ra/wave.js),\nand [Cove.js](https://github.com/mat3ra/cove) among other packages. For the full list,\nsee [package.json](package.json).\n\n### 3.4. CI Docker files\n\nThe first `dockerfiles/app/Dockerfile` builds and runs the application. The second `dockerfiles/tests/Dockerfile` provisions and runs the tests. \n\nProvided `docker compose` is installed, it can be used like so:\n\n```bash\ndocker compose build materials-designer\ndocker compose build materials-designer-test\n\ndocker compose up -d materials-designer\nsleep 30  # let the app actually start\ndocker compose run materials-designer-test\n```\n\nTo run tests in the container use default profile by not specifying it:\n\n```bash\ndocker compose up -d --build\n```\n\nTo run on MacOS, add CYPRESS_BASE_URL=http://host.docker.internal:3001 to the environment variables in the test container\n\n```\nCYRPRESS_BASE_URL=http://host.docker.internal:3001 docker compose run materials-designer-test\n```\n\nTo run both services and execute tests:\n\n```\nCYPRESS_BASE_URL=http://host.docker.internal:3001 docker compose up --abort-on-container-exit --exit-code-from materials-designer-test\n```\n\nFor debugging purposes, Materials Designer and test container can be run interactively with access via VNC:\n\n```bash\ndocker compose --profile use-vnc up -d --build\n```\n\nThen connect to `vnc://localhost:5920` with a VNC client. The password is `123`. (Port set in `.env` file.)\nMake sure to have VNC client installed on the system, when address is typed in the Chrome browser, the VNC prompt will\nappear.\n\n### 3.5. Using Cove.js for local development\n\nIf need to link Cove.js into the app for local development, you need\n\n1. Add the local path of Cove.js to package.json\n\n```bash\n    \"@mat3ra/cove\": \"file:../../cove.js\"\n```\n\n2. Run the app\n\n```bash\n    npm start\n```\n\nIf you need to re-link it again, remove node_modules in cove.js and the app, run npm install, then run npm start again.\n### 3.6. Running tests for JupyterLite Notebooks\n\nTo run tests for JupyterLite Notebooks, set the environment variable in `.env` file.\nAnd update the URL for JL dev distribution by getting the URL from the JupyterLite PR preview.\n\n```bash\nVITE_USE_JUPYTERLITE_DEV_URL=true\nVITE_JUPYTERLITE_DEVELOPMENT_URL=\"https://deploy-preview-56--mat3ra-jupyterlite.netlify.app\"\n```\n\nThis should source JL from the development distribution and run only notebook healthcheck tests.\n\n## 4. Links\n\n1. [Create React App, GitHub Repository](https://github.com/facebook/create-react-app)\n2. [Mat3ra Platform documentation for materials designer](https://docs.mat3ra.com/materials-designer/overview/).\n","readmeFilename":"README.md"}