Class: Continuation

Complete specification of a numerical continuation / bifurcation analysis. All universal solver settings live directly here. Toolkit-specific string options go in the options slot. When used inside a BranchSwitch, only explicitly set attributes override the parent’s values.

URI: tvbo:class/Continuation

 classDiagram
    class Continuation
    click Continuation href "./Continuation.html"
      Continuation : algorithm
        
          
    
        
        
        Continuation --> "0..1" ContinuationAlgorithm : algorithm
        click ContinuationAlgorithm href "../../enums/ContinuationAlgorithm.html"
    

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

        
      Continuation : branches
        
          
    
        
        
        Continuation --> "*" BranchSwitch : branches
        click BranchSwitch href "./BranchSwitch.html"
    

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

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

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

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

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

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

        
      Continuation : dynamics
        
          
    
        
        
        Continuation --> "0..1" Dynamics : dynamics
        click Dynamics href "./Dynamics.html"
    

        
      Continuation : execution
        
          
    
        
        
        Continuation --> "0..1" ExecutionConfig : execution
        click ExecutionConfig href "./ExecutionConfig.html"
    

        
      Continuation : free_parameters
        
          
    
        
        
        Continuation --> "*" Parameter : free_parameters
        click Parameter href "./Parameter.html"
    

        
      Continuation : initial_state
        
          
    
        
        
        Continuation --> "0..1" InitialState : initial_state
        click InitialState href "./InitialState.html"
    

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

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

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

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

        
      Continuation : name
        
          
    
        
        
        Continuation --> "1" String : name
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

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

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

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

        
      Continuation : options
        
          
    
        
        
        Continuation --> "*" Option : options
        click Option href "./Option.html"
    

        
      Continuation : software
        
          
    
        
        
        Continuation --> "0..1" SoftwareRequirement : software
        click SoftwareRequirement href "./SoftwareRequirement.html"
    

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

        
      

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 xsd:string		direct
label	0..1 xsd:string		direct
description	0..1 xsd:string		direct
dynamics	0..1 Dynamics	Reference to the dynamical system model (by name)	direct
free_parameters	* Parameter	Parameters to vary	direct
ds	0..1 xsd:float	Initial arc-length step size	direct
ds_min	0..1 xsd:float	Minimum adaptive step size	direct
ds_max	0..1 xsd:float	Maximum adaptive step size	direct
max_steps	0..1 xsd:integer	Maximum continuation steps	direct
newton_tol	0..1 xsd:float	Absolute tolerance for Newton corrector convergence	direct
newton_max_iterations	0..1 xsd:integer	Maximum Newton corrector iterations per step	direct
nev	0..1 xsd:integer	Number of eigenvalues to compute	direct
tol_stability	0..1 xsd:float	Tolerance on real part of eigenvalue for stability boundary	direct
detect_bifurcation	0..1 xsd:integer	Bifurcation detection level	direct
detect_fold	0..1 xsd:boolean	Enable fold (limit point) detection	direct
n_inversion	0..1 xsd:integer	Number of eigenvalue sign inversions to flag a bifurcation	direct
max_bisection_steps	0..1 xsd:integer	Maximum bisection steps for bifurcation point localization	direct
algorithm	0..1 ContinuationAlgorithm	Predictor-corrector algorithm	direct
initial_state	0..1 InitialState	How to obtain the initial equilibrium	direct
branches	* BranchSwitch	Child branches to continue from detected bifurcation points (PO from Hopf, fo…	direct
bothside	0..1 xsd:boolean	Continue in both directions from the starting point	direct
execution	0..1 ExecutionConfig	Per-analysis execution configuration	direct
software	0..1 SoftwareRequirement	Backend engine (BifurcationKit, AUTO-07p, MatCont, etc	direct
options	* Option	Toolkit-specific string options (tangent method, solver name, etc	direct

Usages

used by	used in	type	used
BranchSwitch	continuation	range	Continuation
SimulationExperiment	continuations	range	Continuation

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/tvbo

Mappings

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

LinkML Source

Direct

name: Continuation
description: Complete specification of a numerical continuation / bifurcation analysis.
  All universal solver settings live directly here. Toolkit-specific string options
  go in the options slot. When used inside a BranchSwitch, only explicitly set attributes
  override the parent's values.
from_schema: https://w3id.org/tvbo
slots:
- name
- label
- description
attributes:
  dynamics:
    name: dynamics
    description: Reference to the dynamical system model (by name). Resolved from
      the experiment's dynamics dict at runtime.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Network
    - Node
    - Edge
    - Continuation
    - SimulationExperiment
    range: Dynamics
    inlined: false
  free_parameters:
    name: free_parameters
    description: Parameters to vary. First parameter is primary (codim-1); second
      enables codim-2 continuation. Each Parameter has name + domain (Range with lo/hi
      bounds).
    from_schema: https://w3id.org/tvbo
    domain_of:
    - OptimizationStage
    - Continuation
    range: Parameter
    multivalued: true
    inlined: true
  ds:
    name: ds
    description: Initial arc-length step size.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: float
  ds_min:
    name: ds_min
    description: Minimum adaptive step size.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: float
  ds_max:
    name: ds_max
    description: Maximum adaptive step size.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: float
  max_steps:
    name: max_steps
    description: Maximum continuation steps.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: integer
  newton_tol:
    name: newton_tol
    description: Absolute tolerance for Newton corrector convergence.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: float
  newton_max_iterations:
    name: newton_max_iterations
    description: Maximum Newton corrector iterations per step.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: integer
  nev:
    name: nev
    description: Number of eigenvalues to compute. Must be >= number of state variables
      for reliable Hopf detection.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: integer
  tol_stability:
    name: tol_stability
    description: Tolerance on real part of eigenvalue for stability boundary.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: float
  detect_bifurcation:
    name: detect_bifurcation
    description: Bifurcation detection level. 0 = off, 1 = eigenvalues only, 2 = detect,
      3 = locate precisely.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: integer
  detect_fold:
    name: detect_fold
    description: Enable fold (limit point) detection.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: boolean
  n_inversion:
    name: n_inversion
    description: Number of eigenvalue sign inversions to flag a bifurcation. Must
      be even. Higher = fewer false positives.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: integer
  max_bisection_steps:
    name: max_bisection_steps
    description: Maximum bisection steps for bifurcation point localization.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: integer
  algorithm:
    name: algorithm
    description: Predictor-corrector algorithm.
    from_schema: https://w3id.org/tvbo
    ifabsent: string(PALC)
    domain_of:
    - OptimizationStage
    - AlgorithmInclude
    - Continuation
    range: ContinuationAlgorithm
  initial_state:
    name: initial_state
    description: 'How to obtain the initial equilibrium. Default: time integration
      to steady state.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: InitialState
    inlined: true
  branches:
    name: branches
    description: Child branches to continue from detected bifurcation points (PO from
      Hopf, fold continuation, etc.).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Continuation
    range: BranchSwitch
    multivalued: true
    inlined: true
  bothside:
    name: bothside
    description: Continue in both directions from the starting point.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - BranchSwitch
    - Continuation
    range: boolean
  execution:
    name: execution
    description: Per-analysis execution configuration.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Optimization
    - Exploration
    - Algorithm
    - Continuation
    - SimulationExperiment
    range: ExecutionConfig
    inlined: true
  software:
    name: software
    description: Backend engine (BifurcationKit, AUTO-07p, MatCont, etc.).
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Callable
    - Continuation
    - SimulationExperiment
    range: SoftwareRequirement
    inlined: true
  options:
    name: options
    description: Toolkit-specific string options (tangent method, solver name, etc.).
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Discretization
    - BranchSwitch
    - Continuation
    range: Option
    multivalued: true
    inlined: true

Induced

name: Continuation
description: Complete specification of a numerical continuation / bifurcation analysis.
  All universal solver settings live directly here. Toolkit-specific string options
  go in the options slot. When used inside a BranchSwitch, only explicitly set attributes
  override the parent's values.
from_schema: https://w3id.org/tvbo
attributes:
  dynamics:
    name: dynamics
    description: Reference to the dynamical system model (by name). Resolved from
      the experiment's dynamics dict at runtime.
    from_schema: https://w3id.org/tvbo
    alias: dynamics
    owner: Continuation
    domain_of:
    - Network
    - Node
    - Edge
    - Continuation
    - SimulationExperiment
    range: Dynamics
    inlined: false
  free_parameters:
    name: free_parameters
    description: Parameters to vary. First parameter is primary (codim-1); second
      enables codim-2 continuation. Each Parameter has name + domain (Range with lo/hi
      bounds).
    from_schema: https://w3id.org/tvbo
    alias: free_parameters
    owner: Continuation
    domain_of:
    - OptimizationStage
    - Continuation
    range: Parameter
    multivalued: true
    inlined: true
  ds:
    name: ds
    description: Initial arc-length step size.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: ds
    owner: Continuation
    domain_of:
    - Continuation
    range: float
  ds_min:
    name: ds_min
    description: Minimum adaptive step size.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: ds_min
    owner: Continuation
    domain_of:
    - Continuation
    range: float
  ds_max:
    name: ds_max
    description: Maximum adaptive step size.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: ds_max
    owner: Continuation
    domain_of:
    - Continuation
    range: float
  max_steps:
    name: max_steps
    description: Maximum continuation steps.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: max_steps
    owner: Continuation
    domain_of:
    - Continuation
    range: integer
  newton_tol:
    name: newton_tol
    description: Absolute tolerance for Newton corrector convergence.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: newton_tol
    owner: Continuation
    domain_of:
    - Continuation
    range: float
  newton_max_iterations:
    name: newton_max_iterations
    description: Maximum Newton corrector iterations per step.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: newton_max_iterations
    owner: Continuation
    domain_of:
    - Continuation
    range: integer
  nev:
    name: nev
    description: Number of eigenvalues to compute. Must be >= number of state variables
      for reliable Hopf detection.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: nev
    owner: Continuation
    domain_of:
    - Continuation
    range: integer
  tol_stability:
    name: tol_stability
    description: Tolerance on real part of eigenvalue for stability boundary.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: tol_stability
    owner: Continuation
    domain_of:
    - Continuation
    range: float
  detect_bifurcation:
    name: detect_bifurcation
    description: Bifurcation detection level. 0 = off, 1 = eigenvalues only, 2 = detect,
      3 = locate precisely.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: detect_bifurcation
    owner: Continuation
    domain_of:
    - Continuation
    range: integer
  detect_fold:
    name: detect_fold
    description: Enable fold (limit point) detection.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: detect_fold
    owner: Continuation
    domain_of:
    - Continuation
    range: boolean
  n_inversion:
    name: n_inversion
    description: Number of eigenvalue sign inversions to flag a bifurcation. Must
      be even. Higher = fewer false positives.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: n_inversion
    owner: Continuation
    domain_of:
    - Continuation
    range: integer
  max_bisection_steps:
    name: max_bisection_steps
    description: Maximum bisection steps for bifurcation point localization.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: max_bisection_steps
    owner: Continuation
    domain_of:
    - Continuation
    range: integer
  algorithm:
    name: algorithm
    description: Predictor-corrector algorithm.
    from_schema: https://w3id.org/tvbo
    ifabsent: string(PALC)
    alias: algorithm
    owner: Continuation
    domain_of:
    - OptimizationStage
    - AlgorithmInclude
    - Continuation
    range: ContinuationAlgorithm
  initial_state:
    name: initial_state
    description: 'How to obtain the initial equilibrium. Default: time integration
      to steady state.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: initial_state
    owner: Continuation
    domain_of:
    - Continuation
    range: InitialState
    inlined: true
  branches:
    name: branches
    description: Child branches to continue from detected bifurcation points (PO from
      Hopf, fold continuation, etc.).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: branches
    owner: Continuation
    domain_of:
    - Continuation
    range: BranchSwitch
    multivalued: true
    inlined: true
  bothside:
    name: bothside
    description: Continue in both directions from the starting point.
    from_schema: https://w3id.org/tvbo
    alias: bothside
    owner: Continuation
    domain_of:
    - BranchSwitch
    - Continuation
    range: boolean
  execution:
    name: execution
    description: Per-analysis execution configuration.
    from_schema: https://w3id.org/tvbo
    alias: execution
    owner: Continuation
    domain_of:
    - Optimization
    - Exploration
    - Algorithm
    - Continuation
    - SimulationExperiment
    range: ExecutionConfig
    inlined: true
  software:
    name: software
    description: Backend engine (BifurcationKit, AUTO-07p, MatCont, etc.).
    from_schema: https://w3id.org/tvbo
    alias: software
    owner: Continuation
    domain_of:
    - Callable
    - Continuation
    - SimulationExperiment
    range: SoftwareRequirement
    inlined: true
  options:
    name: options
    description: Toolkit-specific string options (tangent method, solver name, etc.).
    from_schema: https://w3id.org/tvbo
    alias: options
    owner: Continuation
    domain_of:
    - Discretization
    - BranchSwitch
    - Continuation
    range: Option
    multivalued: true
    inlined: true
  name:
    name: name
    from_schema: https://w3id.org/tvbo
    rank: 1000
    key: true
    alias: name
    owner: Continuation
    domain_of:
    - BrainAtlas
    - CommonCoordinateSpace
    - ParcellationEntity
    - DBSProtocol
    - ClinicalScale
    - ClinicalScore
    - Event
    - Tractogram
    - GraphGenerator
    - File
    - StateValue
    - Observation
    - Dynamics
    - StateVariable
    - Distribution
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - Algorithm
    - Option
    - BranchSwitch
    - Continuation
    - Coupling
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    range: string
    required: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: label
    owner: Continuation
    domain_of:
    - ParcellationTerminology
    - Dataset
    - Contact
    - Equation
    - Stimulus
    - Event
    - Parcellation
    - Tractogram
    - Matrix
    - Network
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - TuningObjective
    - Continuation
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - DifferentialOperator
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: description
    owner: Continuation
    domain_of:
    - ClinicalScore
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - Network
    - GraphGenerator
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - TuningObjective
    - Algorithm
    - BranchSwitch
    - Continuation
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string