NOMAD Material Processing: a Community plugin¶

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

Technical description¶

This section introduces some aspects of the Python package built for this plugin. Despite not being crucial for the understanding of the data model, they can help installing or developing it.

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.
The __init__.py files contain 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. If this section is not specified, all the entry points are loaded by default.
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
│   └── nomad_material_processing
│       ├── __init__.py
│       ├── utils.py
│       ├── general.py
│       ├── vapor_deposition
│       │   ├── __init__.py
│       │   ├── general.py
│       │   ├── cvd
│       │   │   ├── __init__.py
│       │   │   ├── general.py
│       │   │   └── movpe.py
│       │   └── pvd
│       │       ├── __init__.py
│       │       ├── general.py
│       │       ├── mbe.py
│       │       ├── pld.py
│       │       ├── sputtering.py
│       │       └── thermal.py
│       └── solution
│           ├── __init__.py
│           ├── general.py
│           └── utils.py
└── tests

Data model description¶

Each method is separated in a dedicated module, i. e., a python file.

General¶

The nomad_material_processing.general module contains several general categories of classes:

an abstract process class SampleDeposition that is inherited in the specific processes such as MOVPE, MBE, PLD, etc.
Substrate and CrystallineSubstrate entities, the support used in SampleDeposition activities.
ThinFilm entity, usually created during SampleDeposition activities.
ThinFilmStack in case of processes producing multilayer samples. This class also contains a reference to the Substrate.
Geometry and its subclasses, defining the commonly found macroscopic shapes of a sample. It is a subsection composed within the Substrate. They include Parallelepiped, SquareCuboid, RectangleCuboid, TruncatedCone, Cylinder, CylinderSector, IrregularParallelSurfaces.
Miscut another subsection of Substrate to specify the miscut of the orientation of the surface in terms of angular deviation toward crystallographic directions.
CrystalProperties and ElectronicProperties, found as subsection of sample entities that need these parameters.
simple activities performed on samples: Etching, Annealing, Cleaning. They also include a Recipe that can be referenced inside to avoid repetition for routine tasks.
TimeSeries a general class that shapes every kind of parameters logged along a time window. The quantities referring to the measured parameter are value and time. set_value and set_time can also be specified, as they usually differ from the measured ones. Several subclasses inheriting from this one can be found nested in the package.

Vapor Deposition¶

The nomad_material_processing.vapor_deposition.general module contains classes describing a general vapor deposition process. The master class in this module is VaporDeposition, inheriting from SampleDeposition.

The other classes found here are specifying the subsections found in the steps of the VaporDeposition process. VaporDepositionStep contains three subsections allowing to describe the parameters usually recorded during an experiment:

VaporDepositionSource the metadata on which kind of source will bring the raw material in the reaction chamber. This class is in turn composed by three distinct elements, namely the Component material to be evaporated, the EvaporationSource that is the element that produces the vapor, and MolarFlowRate that is a time series recording the molar flux exiting the source. This is used as a list within the VaporDepositionStep because many sources can be present at the same time.
SampleParameter this subsection hosts the references to the ThinFilm deposited and the ThinFilmStack or Substrate used as support of the deposition. This subsection is also used to record sample-specific parameters in the process, such as temperature, or growth rate. This is a list because many samples can be grown at the same time.
ChamberEnvironment collects the metadata connected to the whole reaction chamber that cannot be linked to one single sample. It usually contains temperature or GasFlow subsections.

These three subsections are the backbone of the VaporDeposition process and they are usually inherited whenever a specific experiment requires to extend them.

Chemical Vapor Deposition¶

The nomad_material_processing.vapor_deposition.cvd.general module contains specifications of VaporDepositionSource and TimeSeries commonly adopted in CVD techniques:

Sources for CVD are inheriting from CVDSource, that is in turn a VaporDepositionSource.

BubblerSource defines a bubbler commonly used in CVD for liquid precursors.
FlashSource the vapor is generated by a FlashEvaporator.
MistSource another kind of source adopted in CVD.
GasCylinderSource a simple cylinder containing some gas phase precursor. In this case the EvaporationSource subclass, called GasCylinderEvaporator, is not really evaporating as the precursor is already at the gas state.
GasLineSource used for gaseous precursors that are provided through a stable installation sourcing gas from facilities external to the lab.

TimeSeries used in CVD are:

Rotation specifies rotation frequency of the substrate holder in the chamber
PartialVaporPressure as subclass of Pressure
PushPurgeGasFlow contains two VolumetricFlowRate subsections that record the source and drain fluxes of the carries gas in the chamber.

Metal-organic Vapor Phase Epitaxy (MOVPE)¶

The nomad_material_processing.vapor_deposition.cvd.movpe module contains classes dedicated to the Metal-organic Vapor Phase Epitaxy (MOVPE) technique.

Physical Vapor Deposition (PVD)¶

The nomad_material_processing.vapor_deposition.pvd.general module contains classes describing a general Physical Vapor Deposition (PVD) process. This adopts the three general concepts from the vapor deposition above (the chamber, the sources, and the substrates) and specializes them for various PVD techniques:

Pulsed Laser Deposition (PLD)¶

The nomad_material_processing.vapor_deposition.pvd.pld module adds a specialized laser source with its corresponding parameters.

Sputtering¶

The nomad_material_processing.vapor_deposition.pvd.sputtering module adds a specialized sputtering source with its corresponding parameters.

Thermal Evaporation¶

The nomad_material_processing.vapor_deposition.pvd.thermal module adds a specialized thermal evaporation source with its corresponding parameters.

Molecular Beam Epitaxy (MBE)¶

The nomad_material_processing.vapor_deposition.pvd.mbe module uses the thermal evaporation source and also adds a plasma source.

Solutions¶

nomad_material_processing.solution.general provides Solution and SolutionPreparation entry sections which can be used to create NOMAD entries. It also contains other auxiliary sections supporting these entry section which can be accessed in the metainfo browser by searching for: "nomad_material_processing.solution.general"

Solution¶

nomad_material_processing.solution.general.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.

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

Info

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, amount_of_substance (in moles), and sub-section: molar_concentration. The pure_substance sub-section inherited from PureSubstanceComponent specifies the chemical compound. This information along with the amount 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.

If not provided, amount_of_substance can be determined from mass and pure_substance.molecular_mass. On other hand, if amount_of_substance is available, but mass is missing, it can be determined using amount_of_substance and pure_substance.molecular_mass. mass can also be determined if volume and density are available.

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
    amount_of_substance: 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¶

nomad_material_processing.solution.general.SolutionPreparation describes the steps of solution preparation by extending Process. Based on the steps added, it also creates a Solution entry and references it under the solution sub-section.

class SolutionPreparation(Process, EntryData):
    solution_name: str
    solution: SolutionReference
    step: list[SolutionPreparationStep]

The generated Solution entry picks its name from solution_name, if specified. Otherwise, it will be uniquely named as "unnamed_solution_{i}", where i will be an integer starting from 0. Currently, the following SolutionPreparationStep are defined:

AddSolutionComponent: Adds a SolutionComponent or SolutionComponentReference to components list of the generated Solution entry. It also contains a sub-section measurement which can be used to specify the methodology used for measuring the component like pipetting and scaling.
```
class AddSolutionComponent(SolutionPreparationStep):
    solution_component: Union(
        SolutionComponent,
        SolutionComponentReference,
    )
    measurement: MeasurementMethodology
```
Agitation: Specifies the process of agitating the solution. There are more sections inheriting this class and describing specific techniques: MechanicalStirring(Agitation) and Sonication(Agitation).