Schemas

PDI NOMAD Plugin

The PDI NOMAD Plugin contains schemas for different synthesis methods. An overview of the package structure is shown below.

Technical description

There are some technical aspects to understand the Python package built for this plugin, they are not crucial for the data model understanding itself:

• It is structured according to the src layout.
• It is a regular Python package, i. e., the structure is defined by the presence of __init__.py files. Each of these files contains one or multiple entry points. These are used to load a portion of the code within your NOMAD through a specific section in the nomad.yaml file.
• It is pip installable. The project.toml file defines what will be installed, the dependencies, further details. The entry points included are listed in this file.

nomad-material-processing/
├── docs
├── pyproject.toml
├── README.md
├── src
│   └── pdi_nomad_plugin
│       ├── __init__.py
│       ├── utils.py
│       ├── general
│       │   └── schema.py
│       ├── mbe
│       │   ├── __init__.py
│       │   ├── instrument.py
│       │   ├── materials.py
│       │   ├── processes.py
│       │   ├── epic_parser
│       │   │   ├── __init__.py
│       │   │   └── parser.py
│       │   └── mbe_app
│       │       └── __init__.py
│       └── characterization
│           ├── __init__.py
│           └── schema.py
└── tests
    └── data
        └── mbe

Data model description

Each method has a dedicated module, i. e., a python file.

Dependencies

This plugin uses the NOMAD community plugins. Check the repos and their documentations:

• nomad-material-processing repo, nomad-material-processing docs
• nomad-measurements repo, nomad-measurements docs

mbe.materials

mbe.processes

mbe.instrument

nomad_material_processing.solution.general

solution.general module contains the following entry sections (used to create NOMAD entries):

Solution

Describes liquid solutions by extending the CompositeSystem with quantities: pH, mass, calculated_volume, measured_volume, density, and sub-sections: solvents, solutes, and solution_storage.

# pseudocode for `Solution` datamodel
class Solution(CompositeSystem, EntryData):
    ph_value: float
    mass: float
    calculated_volume: float
    measured_volume: float
    density: float
    components: list[
        Union(
            SolutionComponent,
            SolutionComponentReference,
        )
    ]
    solutes: list[SolutionComponent]
    solvents: list[SolutionComponent]
    solution_storage: SolutionStorage

Hint

The measured_volume field is user-defined. By default, the automation in Solution uses calculated_volume, but if measured_volume is provided, it will take precedence. This is useful when the final solution volume differs from the sum of its component volumes, and should be specified by the user.

The components sub-section, inherited from CompositeSystem and re-defined, is used to describe a list of components used in the solution. Each of them contributes to the mass and calculated_volume of the solution. The component can either nest a sub-section describing its composition, or can be another Solution entry connected via reference. These options are are handled by SolutionComponent and SolutionComponentReference sections respectively.

Let's take a closer look at each of them.

SolutionComponent extends PureSubstanceComponent with quantities: component_role, mass, volume, density, and sub-section: molar_concentration. The pure_substance sub-section inherited from PureSubstanceComponent specifies the chemical compound. This information along with the mass of the component and total volume of the solution is used to automatically determine the molar concentration of the component, populating the corresponding sub-section. Based on the component_role, the components are copied over to either Solution.solvents or Solution.solutes.

class SolutionComponent(PureSubstanceComponent):
    component_role: Enum('Solvent', 'Solute')
    mass: float
    volume: float
    density: float
    molar_concentration: MolarConcentration

SolutionComponentReference makes a reference to another Solution entry and specifies the amount used. Based on this, solutes and solvents of the referenced solution are copied over to the first solution. Their mass and volume are adjusted based on the amount of the referenced solution used.

class SolutionComponentReference(SystemComponent):
    mass: float
    volume: float
    system: Solution

Both Solution.solvents and Solution.solutes are a list of SolutionComponent. The molar concentration of each of them is automatically determined. Additionally, if the list has multiple SolutionComponent representing the same chemical entity, there are combined into one.

The solution_storage uses SolutionStorage section to describe storage conditions , i.e., temperature and atmosphere, along with preparation and expiry dates.

SolutionPreparation

Extends Process to describe the recipe for solution preparation. It generates a Solution entry based on the data added to it.