Class: SimulationBox¶

Simulation box information

URI: https://CCPBioSim.ac.uk/biosim-schema/SimulationBox

         classDiagram
    class SimulationBox
    click SimulationBox href "../../classes/SimulationBox/"
      SimulationBox : box_angles
        
          
    
        
        
        SimulationBox --> "0..1" VectorAngleQuantity : box_angles
        click VectorAngleQuantity href "../../classes/VectorAngleQuantity/"
    

        
      SimulationBox : box_dimensions
        
          
    
        
        
        SimulationBox --> "0..1" VectorLengthQuantity : box_dimensions
        click VectorLengthQuantity href "../../classes/VectorLengthQuantity/"
    

        
      SimulationBox : box_type
        
          
    
        
        
        SimulationBox --> "0..1" BoxType : box_type
        click BoxType href "../../enums/BoxType/"
    

        
      SimulationBox : periodic_boundary_conditions
        
          
    
        
        
        SimulationBox --> "0..1" PeriodicBoundaryConditions : periodic_boundary_conditions
        click PeriodicBoundaryConditions href "../../enums/PeriodicBoundaryConditions/"

Slots¶

Name	Cardinality and Range	Description	Inheritance
box_dimensions	0..1 VectorLengthQuantity	The lengths/dimensions of the box used to simulate the system	direct
box_angles	0..1 VectorAngleQuantity	The angles of the box used to simulate the system	direct
box_type	0..1 BoxType	The type of box used to simuluate the system	direct
periodic_boundary_conditions	0..1 PeriodicBoundaryConditions	What directions in a simulation cell periodic boundaries are set if they are …	direct

Usages¶

used by	used in	type	used
TrajectoryMetadata	simulation_box	range	SimulationBox

Identifier and Mapping Information¶

Schema Source¶

from schema: https://CCPBioSim.ac.uk/biosim-schema/

Mappings¶

Mapping Type	Mapped Value
self	https://CCPBioSim.ac.uk/biosim-schema/SimulationBox
native	https://CCPBioSim.ac.uk/biosim-schema/SimulationBox

LinkML Source¶

Direct¶

name: SimulationBox
description: Simulation box information
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
slots:
- box_dimensions
- box_angles
- box_type
- periodic_boundary_conditions

Induced¶

name: SimulationBox
description: Simulation box information
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
attributes:
  box_dimensions:
    name: box_dimensions
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: box_dimensions
          unit: Ang
    description: The lengths/dimensions of the box used to simulate the system.
    examples:
    - value: '[10, 10, 10]'
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: SimulationBox
    domain_of:
    - SimulationBox
    range: VectorLengthQuantity
  box_angles:
    name: box_angles
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: box_angles
          unit: degree
    description: The angles of the box used to simulate the system.
    examples:
    - value: '[90, 90, 90]'
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: SimulationBox
    domain_of:
    - SimulationBox
    range: VectorAngleQuantity
  box_type:
    name: box_type
    description: The type of box used to simuluate the system.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: SimulationBox
    domain_of:
    - SimulationBox
    range: BoxType
  periodic_boundary_conditions:
    name: periodic_boundary_conditions
    description: What directions in a simulation cell periodic boundaries are set
      if they are turned on.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: SimulationBox
    domain_of:
    - SimulationBox
    range: PeriodicBoundaryConditions