mat3ra-standata 2024.10.29.post0

Standard data for digital Materials R&D.

Standata

Standard data for digital materials R&D entities in the ESSE data format.

1. Installation

1.1. Python

The package is compatible with Python 3.8+. It can be installed as a Python package either via PyPI:

pip install mat3ra-standata

Or as an editable local installation in a virtual environment after cloning the repository:

virtualenv .venv
source .venv/bin/activate
pip install -e PATH_TO_STANDATA_REPOSITORY

1.2. JavaScript

Standata can be installed as a Node.js package via NPM (node package manager).

npm install @mat3ra/standata

2. Usage

2.1. Python

from mat3ra.standata.materials import materials_data
# This returns a list of JSON configs for all materials.
materialConfigs = materials_data["filesMapByName"].values();

2.2. JavaScript

// Direct import can be used to avoid importing all data at once.
import data from "@mat3ra/standata/lib/runtime_data/materials";
// This creates a list of JSON configs for all materials.
const materialConfigs = Object.values(data.filesMapByName);

3. Conventions

3.1. Runtime Modules

To avoid file system calls on the client, the entity categories and data structures are made available at runtime via the files in src/js/runtime_data. These files are generated automatically using the following command:

npm run build:runtime-data

3.2. CLI Scripts for Creating Symlinks

3.2.1. Python

The Python package adds a command line script create-symlinks that creates a category-based file tree where entity data files are symbolically linked in directories named after the categories associated with the entity. The resulting file tree will be contained in a directory names by_category. The script expects the (relative or absolute) path to an entity config file (categories.yml). The destination of the file tree can be modified by passing the --destination/-d option.

# consult help page to view all options
create-symlinks --help
# creates symbolic links in materials/by_category
create-symlinks materials/categories.yml
# creates symbolic links for materials in tmp/by_category
create-symlinks materials/categories.yml -d tmp

3.2.1 JavaScript/Node

Analogous to the command line script in Python, the repository also features a script in TypeScript (src/js/cli.ts) and (after transpiling) in JavaScript (lib/cli.js). The script takes the entity config file as a mandatory positional argument and the alternative location for the directory containing the symbolic links (--destination/-d).

# creates symbolic links in materials/by_category (node)
node lib/cli.js materials/categories.yml
# creates symbolic links in materials/by_category (ts-node)
ts-node src/js/cli.ts materials/categories.yml
# creates symbolic links for materials in tmp/by_category
ts-node src/js/cli.ts -d tmp materials/categories.yml
# run via npm
npm run build:categories -- materials/categories.yml

4. Development

See ESSE for the notes about development and testing.

To develop, first, create a virtual environment and install the dev dependencies:

python -m venv .venv
source .venv/bin/activate
pip install ".[dev]"

4.1. Materials Source

The materials data is sourced from the Materials Project for 3D materials and 2dmatpedia for 2D materials. The structural data in POSCAR format is stored in the materials/sources directory alongside the manifest.yml file that contains the additional description and metadata for each material.

To add new materials to Standata, place the POSCAR file in the materials/sources directory and update the manifest.yml file with the new material's metadata. Then run to create the materials data:

python create_materials.py

4.2. Materials Naming Conventions

Our dataset's naming convention for materials is designed to provide a comprehensive description of each material, incorporating essential attributes such as chemical composition, common name, crystal structure, and unique identifiers.

4.2.1. Name Property Format

The format for the material name property is a structured representation that includes the chemical formula, common name, crystal system, space group, dimensionality, specific structure details, and a unique identifier. Each element in the name is separated by a comma and space.

Format:

{Chemical Formula}, {Common Name}, {Crystal System} ({Space Group}) {Dimensionality} ({Structure Detail}), {Unique Identifier}

Examples:

• Ni, Nickel, FCC (Fm-3m) 3D (Bulk), mp-23
• ZrO2, Zirconium Dioxide, MCL (P2_1/c) 3D (Bulk), mp-2858
• C, Graphite, HEX (P6_3/mmc) 3D (Bulk), mp-48
• C, Graphene, HEX (P6/mmm) 2D (Monolayer), mp-1040425

4.2.2. Filename Format

Filenames are derived from the name property through a slugification process, ensuring they are filesystem-friendly and easily accessible via URLs or command-line interfaces. This process involves converting the structured name into a standardized, URL-safe format that reflects the material's attributes.

Format:

{Chemical_Formula}-[{Common_Name}]-{Crystal_System}_[{Space_Group}]_
{Dimensionality}_[{Structure_Detail}]-[{Unique_Identifier}]

Transformation Rules:

Commas and Spaces: Replace , (comma and space) with - (hyphen) and (space) with _ (underscore). Parentheses: Convert ( and ) into [ and ] respectively. Special Characters: Encode characters such as / into URL-safe representations (e.g., %2F). Brackets: Wrap common name and identifier parts in square brackets [].

Filename Examples:

• Ni-[Nickel]-FCC_[Fm-3m]3D[Bulk]-[mp-23]
• ZrO2-[Zirconium_Dioxide]-MCL_[P2_1%2Fc]3D[Bulk]-[mp-2858]
• C-[Graphite]-HEX_[P6_3%2Fmmc]3D[Bulk]-[mp-48]
• C-[Graphene]-HEX_[P6%2Fmmm]2D[Monolayer]-[mp-1040425]

5. Links

To be added here.