ontology.qe.yml

---
version: "0.1"
namespace: "QE"
author: "Mathias Driesse"

ontology:

    ############################ Relationships
    
    HAS_PART:
        description: "default relationship"
        subclass_of:
            - CUBA.activeRelationship
        inverse: QE.IS_PART_OF
        default_rel: true

    IS_PART_OF:
        description: "inverse of the default relationship"
        subclass_of:
            -  CUBA.passiveRelationship
        inverse: QE.HAS_PART
        
    ############################ Framework
    
    QEWrapper:
        description: "The quantum espresso wrapper"
        subclass_of:
            - CUBA.Wrapper
            - QE.HAS_PART:
                cardinality: 1
                exclusive: true
                range: QE.SIMULATION
    
    Simulation:
        description: "All components of the simulation that are needed to run the model"
        subclass_of:
            - CUBA.Entity
            - QE.HAS_PART:
                cardinality: 1
                exclusive: false
                range: QE.Cell
            - QE.HAS_PART:
                cardinality: 1
                exclusive: false
                range: QE.TotalEnergy


    ############################ Physical objects

    Cell:
        subclass_of:
            - CUBA.Entity
            - QE.HAS_PART:
                range: QE.Atom
                cardinality: 1+
            - QE.HAS_PART:
                range: QE.CellParams
        
    Atom:
        subclass_of:
            - CUBA.Entity
            - QE.HAS_PART:
                range: QE.Position
                cardinality: 1

    Element:
        subclass_of:
            - CUBA.Entity
            - QE.HAS_PART:
                range: QE.Mass
                cardinality: 1
            - QE.HAS_PART:
                range: QE.Atom
                cardinality: 1+
            - QE.HAS_PART:
                range: QE.PSEUDOPOTENTIAL
                cardinality: 1
        attributes:
            QE.name:



    ############################ Physical quantities

    PhysicalQuantity:
        attributes:
            QE.value:
            QE.unit:
        subclass_of:
            - CUBA.Entity

    PhysicalQuantityVector:
        attributes:
            QE.vector:
            QE.unit:
        subclass_of:
            - CUBA.Entity

    PhysicalQuantityVector6:
        attributes:
            QE.vector6:
            QE.unit:
        subclass_of:
            - CUBA.Entity

    PhysicalQuantityTensor2:
        attributes:
            QE.tensor2:
            QE.unit:
        subclass_of:
            - CUBA.Entity

    Position:
        description: "Position of an entity"
        subclass_of: 
            - QE.PhysicalQuantityVector

    IfPos:
        description: "Multiplier of a force in a particular direction. Each component can be 0 or 1, with 0 fixed and 1 variable"
        subclass_of:
            - QE.PhysicalQuantityVector

    Mass:
        description: "Mass of an entity"
        subclass_of:
            - QE.PhysicalQuantity

    CellParams:
        subclass_of:
            - QE.PhysicalQuantityTensor2

    TotalEnergy:
        subclass_of:
            - QE.PhysicalQuantity

    StressTensor:
        subclass_of:
            - QE.PhysicalQuantityTensor2

    Celldm1:
        description: Placeholder
        subclass_of:
            - QE.PhysicalQuantity

    BulkModulus:
        description: The bulk modulus of the cell
        subclass_of:
            - QE.PhysicalQuantity

    Force:
        description: A force
        subclass_of:
            - QE.PhysicalQuantityVector

    Pressure:
        subclass_of:
            - QE.PhysicalQuantity

    K_POINTS:
        description: Placeholder
        subclass_of:
            - QE.PhysicalQuantityVector6

    K_POINT:
        description: Vector is the location in the Brillouin zone. Value is the weight of the K Point.
        subclass_of:
            - CUBA.Entity
        attributes:
            QE.vector:
            QE.value:
            QE.unit:

    Volume:
        subclass_of:
            - QE.PhysicalQuantity

    EquilibriumVolume:
        subclass_of:
            - QE.PhysicalQuantity

    Frequency:
        subclass_of:
            - QE.PhysicalQuantity
    
    QPoint:
        subclass_of:
            - QE.PhysicalQuantityVector
        attributes:
            QE.calculate:

    Mode:
        attributes:
            QE.number:
        subclass_of:
            - CUBA.Entity

    DielectricTensor:
        subclass_of:
            - QE.PhysicalQuantityTensor2

    IfPos:
        subclass_of:
            - QE.PhysicalQuantityVector

    # Constraint:
    #     subclass_of:
    #         - CUBA.Entity
    #     attributes:
    #         QE.name:
    #         QE.vector4

    ############################ Attributes

    value:
        subclass_of:
            - CUBA.attribute
        datatype: FLOAT

    unit:
        subclass_of:
            - CUBA.attribute
        datatype: STRING

    vector:
        subclass_of:
            - CUBA.attribute
        datatype: VECTOR:3

    vector6:
        subclass_of:
            - CUBA.attribute
        datatype: VECTOR:6

    tensor2:
        subclass_of:
            - CUBA.attribute
        datatype: VECTOR:3:3

    name:
        subclass_of:
            - CUBA.attribute
        datatype: STRING

    number:
        subclass_of:
            - CUBA.attribute
        datatype: INT

    calculate:
        subclass_of:
            - CUBA.attribute
        datatype: BOOL

    ############################ Files

    PSEUDOPOTENTIAL:
        subclass_of:
            - CUBA.File

    Outfile:
        subclass_of:
            - CUBA.File
    
    BandsDat:
        subclass_of:
            - CUBA.File

    PwOut:
        subclass_of:
            - CUBA.File

    DosDat:
        subclass_of:
            - CUBA.File

    XSF:
        subclass_of:
            - CUBA.File

    PhOut:
        subclass_of:
            - CUBA.File
    
    EvOut:
        subclass_of:
            - CUBA.File

    A2fDat:
        subclass_of:
            - CUBA.File

    DynMat:
        subclass_of:
            - CUBA.File