Class: Integrator

Fixed-step or adaptive ODE integrator with TVB-specific extensions (noise, transient time, etc.). Inherits abs_tol, rel_tol from Solver. Overrides method default to ‘euler’.

URI: tvbo:Integrator

 classDiagram
    class Integrator
    click Integrator href "./Integrator.html"
      Solver <|-- Integrator
        click Solver href "./Solver.html"
      
      Integrator : abs_tol
        
          
    
        
        
        Integrator --> "0..1" Float : abs_tol
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : delayed
        
          
    
        
        
        Integrator --> "0..1" Boolean : delayed
        click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
    

        
      Integrator : description
        
          
    
        
        
        Integrator --> "0..1" String : description
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Integrator : differentiation
        
          
    
        
        
        Integrator --> "0..1" Differentiation : differentiation
        click Differentiation href "./Differentiation.html"
    

        
      Integrator : duration
        
          
    
        
        
        Integrator --> "0..1" Float : duration
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : intermediate_expressions
        
          
    
        
        
        Integrator --> "*" DerivedVariable : intermediate_expressions
        click DerivedVariable href "./DerivedVariable.html"
    

        
      Integrator : method
        
          
    
        
        
        Integrator --> "0..1" String : method
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Integrator : noise
        
          
    
        
        
        Integrator --> "0..1" Noise : noise
        click Noise href "./Noise.html"
    

        
      Integrator : number_of_stages
        
          
    
        
        
        Integrator --> "0..1" Integer : number_of_stages
        click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
    

        
      Integrator : parameters
        
          
    
        
        
        Integrator --> "*" Parameter : parameters
        click Parameter href "./Parameter.html"
    

        
      Integrator : rel_tol
        
          
    
        
        
        Integrator --> "0..1" Float : rel_tol
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : scipy_ode_base
        
          
    
        
        
        Integrator --> "0..1" Boolean : scipy_ode_base
        click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
    

        
      Integrator : state_wise_sigma
        
          
    
        
        
        Integrator --> "*" Float : state_wise_sigma
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : step_size
        
          
    
        
        
        Integrator --> "0..1" Float : step_size
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : steps
        
          
    
        
        
        Integrator --> "0..1" Integer : steps
        click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
    

        
      Integrator : time_scale
        
          
    
        
        
        Integrator --> "0..1" UnitEnum : time_scale
        click UnitEnum href "../../enums/UnitEnum.html"
    

        
      Integrator : transient_time
        
          
    
        
        
        Integrator --> "0..1" Float : transient_time
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      Integrator : unit
        
          
    
        
        
        Integrator --> "0..1" UnitEnum : unit
        click UnitEnum href "../../enums/UnitEnum.html"
    

        
      Integrator : update_expression
        
          
    
        
        
        Integrator --> "0..1" DerivedVariable : update_expression
        click DerivedVariable href "./DerivedVariable.html"

Inheritance

Class Properties

Property Value
Class URI tvbo:Integrator

Slots

Name Cardinality and Range Description Inheritance
time_scale 0..1
UnitEnum		 Time unit for the integration / simulation direct
unit 0..1
UnitEnum		 Physical unit of measurement direct
parameters *
Parameter		 direct
duration 0..1
xsd:float		 direct
description 0..1
xsd:string		 direct
method 0..1
xsd:string		 Integration method (euler, heun, rk4, etc direct
step_size 0..1
xsd:float		 direct
steps 0..1
xsd:integer		 direct
noise 0..1
Noise		 direct
state_wise_sigma *
xsd:float		 direct
transient_time 0..1
xsd:float		 direct
scipy_ode_base 0..1
xsd:boolean		 direct
number_of_stages 0..1
xsd:integer		 direct
intermediate_expressions *
DerivedVariable		 direct
update_expression 0..1
DerivedVariable		 direct
delayed 0..1
xsd:boolean		 direct
differentiation 0..1
Differentiation		 Backend-neutral strategy for propagating gradients through the temporal integ… direct
abs_tol 0..1
xsd:float		 Absolute tolerance for adaptive solvers Solver
rel_tol 0..1
xsd:float		 Relative tolerance for adaptive solvers Solver

Usages

used by used in type used
Optimization integration range Integrator
Inference integration range Integrator
SimulationExperiment integration range Integrator

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/tvbo

Mappings

Mapping Type Mapped Value
self tvbo:Integrator
native tvbo:Integrator

LinkML Source

Direct

name: Integrator
description: Fixed-step or adaptive ODE integrator with TVB-specific extensions (noise,
  transient time, etc.). Inherits abs_tol, rel_tol from Solver. Overrides method default
  to 'euler'.
from_schema: https://w3id.org/tvbo
is_a: Solver
slots:
- time_scale
- unit
- parameters
- duration
- description
attributes:
  method:
    name: method
    description: Integration method (euler, heun, rk4, etc.)
    from_schema: https://w3id.org/tvbo
    ifabsent: string(euler)
    domain_of:
    - Discretization
    - InitialState
    - Solver
    - Integrator
    range: string
  step_size:
    name: step_size
    from_schema: https://w3id.org/tvbo
    aliases:
    - dt
    rank: 1000
    ifabsent: float(0.01220703125)
    domain_of:
    - Integrator
    range: float
  steps:
    name: steps
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Procedure
    - Integrator
    range: integer
  noise:
    name: noise
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Stimulus
    - StateVariable
    - Integrator
    range: Noise
    inlined: true
  state_wise_sigma:
    name: state_wise_sigma
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Integrator
    range: float
    multivalued: true
  transient_time:
    name: transient_time
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: float(0)
    domain_of:
    - Integrator
    range: float
  scipy_ode_base:
    name: scipy_ode_base
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'False'
    domain_of:
    - Integrator
    range: boolean
  number_of_stages:
    name: number_of_stages
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(1)
    domain_of:
    - Integrator
    range: integer
  intermediate_expressions:
    name: intermediate_expressions
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Integrator
    range: DerivedVariable
    multivalued: true
    inlined: true
  update_expression:
    name: update_expression
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Integrator
    range: DerivedVariable
    inlined: true
  delayed:
    name: delayed
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'True'
    domain_of:
    - Integrator
    - Coupling
    range: boolean
  differentiation:
    name: differentiation
    description: Backend-neutral strategy for propagating gradients through the temporal
      integration (e.g. truncated backprop-through-time).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Integrator
    range: Differentiation
    inlined: true
class_uri: tvbo:Integrator

Induced

name: Integrator
description: Fixed-step or adaptive ODE integrator with TVB-specific extensions (noise,
  transient time, etc.). Inherits abs_tol, rel_tol from Solver. Overrides method default
  to 'euler'.
from_schema: https://w3id.org/tvbo
is_a: Solver
attributes:
  method:
    name: method
    description: Integration method (euler, heun, rk4, etc.)
    from_schema: https://w3id.org/tvbo
    ifabsent: string(euler)
    owner: Integrator
    domain_of:
    - Discretization
    - InitialState
    - Solver
    - Integrator
    range: string
  step_size:
    name: step_size
    from_schema: https://w3id.org/tvbo
    aliases:
    - dt
    rank: 1000
    ifabsent: float(0.01220703125)
    owner: Integrator
    domain_of:
    - Integrator
    range: float
  steps:
    name: steps
    from_schema: https://w3id.org/tvbo
    owner: Integrator
    domain_of:
    - Procedure
    - Integrator
    range: integer
  noise:
    name: noise
    from_schema: https://w3id.org/tvbo
    owner: Integrator
    domain_of:
    - Stimulus
    - StateVariable
    - Integrator
    range: Noise
    inlined: true
  state_wise_sigma:
    name: state_wise_sigma
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: float
    multivalued: true
  transient_time:
    name: transient_time
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: float(0)
    owner: Integrator
    domain_of:
    - Integrator
    range: float
  scipy_ode_base:
    name: scipy_ode_base
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'False'
    owner: Integrator
    domain_of:
    - Integrator
    range: boolean
  number_of_stages:
    name: number_of_stages
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(1)
    owner: Integrator
    domain_of:
    - Integrator
    range: integer
  intermediate_expressions:
    name: intermediate_expressions
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: DerivedVariable
    multivalued: true
    inlined: true
  update_expression:
    name: update_expression
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: DerivedVariable
    inlined: true
  delayed:
    name: delayed
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: 'True'
    owner: Integrator
    domain_of:
    - Integrator
    - Coupling
    range: boolean
  differentiation:
    name: differentiation
    description: Backend-neutral strategy for propagating gradients through the temporal
      integration (e.g. truncated backprop-through-time).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Integrator
    domain_of:
    - Integrator
    range: Differentiation
    inlined: true
  time_scale:
    name: time_scale
    description: Time unit for the integration / simulation. Determines the physical
      time meaning of one model time-step.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: ms
    owner: Integrator
    domain_of:
    - Observation
    - Integrator
    range: UnitEnum
  unit:
    name: unit
    description: Physical unit of measurement. Values are drawn from the QUDT ontology
      (http://qudt.org/vocab/unit/) with UO cross-references where available.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: qudt:unit
    owner: Integrator
    domain_of:
    - CommonCoordinateSpace
    - MeasureSpec
    - NamedArray
    - Edge
    - StateVariable
    - Parameter
    - Argument
    - DerivedParameter
    - DerivedVariable
    - ExplorationAxis
    - Integrator
    - TimeSeries
    - NDArray
    - SpatialField
    range: UnitEnum
  parameters:
    name: parameters
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Integrator
    domain_of:
    - Equation
    - Stimulus
    - Event
    - TemporalApplicableEquation
    - Network
    - GraphGenerator
    - Node
    - Edge
    - Observation
    - Analysis
    - Dynamics
    - Distribution
    - Noise
    - Exploration
    - Discretization
    - BranchSwitch
    - Integrator
    - Coupling
    - PDE
    range: Parameter
    multivalued: true
    inlined: true
  duration:
    name: duration
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: float(1000)
    owner: Integrator
    domain_of:
    - Stimulus
    - Event
    - InitialState
    - Integrator
    range: float
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: Integrator
    domain_of:
    - Dataset
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - Phenotype
    - MeasureSpec
    - NamedArray
    - Network
    - GraphGenerator
    - ProcedureStep
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - ExplorationAxis
    - FreeParameter
    - Inference
    - Prior
    - Likelihood
    - UpdateRule
    - AlgorithmStage
    - TuningObjective
    - Algorithm
    - BranchSwitch
    - Continuation
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - Study
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  abs_tol:
    name: abs_tol
    description: Absolute tolerance for adaptive solvers.
    from_schema: https://w3id.org/tvbo
    ifabsent: float(1e-10)
    owner: Integrator
    domain_of:
    - InitialState
    - Solver
    range: float
  rel_tol:
    name: rel_tol
    description: Relative tolerance for adaptive solvers.
    from_schema: https://w3id.org/tvbo
    ifabsent: float(1e-10)
    owner: Integrator
    domain_of:
    - InitialState
    - Solver
    range: float
class_uri: tvbo:Integrator