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How to Use This Plugin

This guide explains how to use the AIF parser plugin within a NOMAD environment.

Adding the Plugin to NOMAD

The AIF parser plugin can be integrated into NOMAD in two main ways depending on your setup:

For NOMAD Oasis Users

  1. Follow the NOMAD plugin documentation for detailed instructions
  2. Add the plugin to your NOMAD Oasis instance
  3. Restart your NOMAD service to load the new plugin

For Local NOMAD Installations

  1. Install the plugin in your local NOMAD environment: 

    # Navigate to your NOMAD installation directory
cd /path/to/nomad

# Install the AIF parser plugin
uv pip install -e 'path/to/aifparser/[dev]'

  2. Configure NOMAD to recognize the plugin by ensuring the plugin entry points are registered

Parsing AIF Files

Once the plugin is installed and configured, you can parse AIF files in several ways:

Using the NOMAD GUI

Please see the Tutorial.

Using the NOMAD CLI

# Parse a single AIF file
nomad parse tests/data/dut_134_scd_n2_77k.aif > parsed.json

# Parse multiple files
nomad parse *.aif

Using Python API

import nomad

# Parse an AIF file programmatically
with open('path/to/file.aif', 'r') as f:
    content = f.read()

# Process using NOMAD's parsing infrastructure

Data Access and Querying

After parsing, the AIF data becomes accessible through NOMAD's data model:

Searching Data

You can search for specific AIF data using NOMAD's query language:

# Find all experiments with a specific operator
data.aif_operator#aifparser.schema_packages.aif_schema_package.AdsorptionInformationFile == "TU DD"

# Search for experiments with specific adsorptive
aif_adsorptive == N2

# Find experiments with temperature data
data.aif_temperature = *

# Find experiments with a range
60 mg <= data.aif_sample_mass <= 140 mg

Data Structure

Parsed AIF data follows this structure in NOMAD:

  • Main Section: AdsorptionInformationFile containing metadata
  • Data Subsections: AdsorptionInformationFileData for adsorption/desorption data
  • Units: All physical quantities are properly converted and annotated with units

Visualization

The plugin generates visualizations of adsorption data:

  1. Semilog plots of adsorption/desorption data
  2. Lin-lin plots of adsorption/desorption data
  3. Support for relative pressure calculations when saturation pressure data is available

Example Workflow

Here's a typical workflow for using the AIF parser:

  1. Prepare AIF files with proper metadata
  2. Parse files using nomad parse
  3. Upload to NOMAD for storage and sharing
  4. Query and analyze data using NOMAD's search capabilities
  5. Visualize adsorption isotherms through NOMAD's GUI

Testing the Plugin

To verify that your installation works correctly:

# Run the test suite
python -m pytest -sv tests

# Run tests with coverage
uv pip install pytest-cov
python -m pytest --cov=src tests

Troubleshooting

Common Issues

  1. Plugin not recognized: Ensure the plugin is properly installed and registered in NOMAD
  2. Parsing errors: Verify that AIF files are properly formatted according to the AIF specification
  3. Missing data: Check that required metadata fields are populated in AIF files

Contact Information

If you encounter issues during usage, please contact: