cubie
Contents
Getting Started with Cubie
Tutorials
Tutorial 1: Your First Parameter Sweep
Tutorial 2: Summaries Instead of Trajectories
Tutorial 3: Stiff Systems, Implicit Methods, and Drivers
User Manual
Creating a “System” of Differential Equations
Solving ODEs
Coming from SciPy
Coming from MATLAB
Configuration Reference
Batching and Parameter Sweeps
Working with Results
Drivers (Time-dependent functions)
Timing Parameters
Choosing an Algorithm
Solver Options Reference
User functions and derivatives
CellML Models
GPU Memory Management
Caching and Recompilation
Making it Faster (basic)
Troubleshooting
Theory
Numerical Integration
Nonlinear Solvers
Jacobians and Symbolic Differentiation
CUDA and GPU Computing
Developer Guide
Architecture Overview
Adding Algorithms
Code Generation Pipeline
Buffer Registry
Adding Summary Metrics
Testing Guide
Reference Manual
Batch solving
Solver
solve_ivp
SolveResult
SolveSpec
Calibration
Optimisation
Candidate comparison
BatchSolverConfig
BatchSolverKernel
SystemInterface
Arrays
ArrayContainer
BaseArrayManager
ManagedArray
InputArrayContainer
InputArrays
OutputArrayContainer
ActiveOutputs
OutputArrays
ODE systems
create_ODE_system
SymbolicODE
BaseODE
ODEData
Variables
SystemLayout
SystemSizes
ODECache
Symbolic
Integrators
SingleIntegratorRun
IntegratorReturnCodes
Algorithms
BaseStepConfig
BaseAlgorithmStep
StepCache
ExplicitStepConfig
ExplicitEulerStep
ImplicitStepConfig
BackwardsEulerStep
BackwardsEulerPCStep
CrankNicolsonStep
ERKStep
ERK tableau registry
DIRKStep
DIRK tableau registry
FIRKStep
FIRK tableau registry
GenericRosenbrockWStep
Rosenbrock tableau registry
get_algorithm_step
Loops
IVPLoop
ODELoopConfig
Matrix-free solvers
LinearSolver
NewtonKrylov
SolverRetCodes
Step control
get_controller
BaseStepController
BaseAdaptiveStepController
FixedStepController
AdaptiveIController
AdaptivePIController
AdaptivePIDController
GustafssonController
BaseStepControllerConfig
AdaptiveStepControlConfig
FixedStepControlConfig
PIStepControlConfig
PIDStepControlConfig
GustafssonStepControlConfig
Output handling
OutputFunctions
OutputConfig
OutputCompileFlags
OutputArrayHeights
SingleRunOutputSizes
BatchInputSizes
BatchOutputSizes
OutputFunctionCache
summary_metrics
register_metric
Summary metrics
summary_metrics
register_metric
SummaryMetric
SummaryMetrics
MetricFuncCache
Mean
Max
RMS
Peaks
Std
Min
MaxMagnitude
Extrema
NegativePeaks
MeanStdRms
DxdtMax
DxdtMin
DxdtExtrema
D2xdt2Max
D2xdt2Min
D2xdt2Extrema
Memory
default_memmgr
MemoryManager
ArrayRequest
ArrayResponse
StreamGroups
GUI Editors
ParametersEditor
StatesEditor
PreParseEditor
cubie
Reference Manual
GUI Editors
ParametersEditor
View page source
ParametersEditor