API Index
EarthSciMLBase.Advection
EarthSciMLBase.ConnectorSystem
EarthSciMLBase.CoupledSystem
EarthSciMLBase.DomainInfo
EarthSciMLBase.ICBCcomponent
EarthSciMLBase.Operator
EarthSciMLBase.SolverIMEX
EarthSciMLBase.SolverStrang
EarthSciMLBase.SolverStrangSerial
EarthSciMLBase.SolverStrangThreads
EarthSciMLBase.SolverStrategy
EarthSciMLBase.constBC
EarthSciMLBase.constIC
EarthSciMLBase.periodicBC
EarthSciMLBase.zerogradBC
Base.convert
Base.convert
EarthSciMLBase.ConstantWind
EarthSciMLBase.MeanWind
EarthSciMLBase.add_dims
EarthSciMLBase.add_metadata
EarthSciMLBase.add_scope
EarthSciMLBase.copy_with_change
EarthSciMLBase.couple
EarthSciMLBase.couple2
EarthSciMLBase.dims
EarthSciMLBase.domains
EarthSciMLBase.dtype
EarthSciMLBase.endpoints
EarthSciMLBase.get_coupletype
EarthSciMLBase.get_dv
EarthSciMLBase.get_needed_vars
EarthSciMLBase.graph
EarthSciMLBase.grid
EarthSciMLBase.icbc
EarthSciMLBase.init_callback
EarthSciMLBase.init_u
EarthSciMLBase.ivar
EarthSciMLBase.observed_expression
EarthSciMLBase.observed_function
EarthSciMLBase.ode_step!
EarthSciMLBase.operator_compose
EarthSciMLBase.param_to_var
EarthSciMLBase.partialderivative_transforms
EarthSciMLBase.partialderivatives
EarthSciMLBase.partialderivatives_δxyδlonlat
EarthSciMLBase.prune_observed
EarthSciMLBase.pvars
EarthSciMLBase.single_ode_step!
EarthSciMLBase.steplength
EarthSciMLBase.stiff_callback
EarthSciMLBase.threaded_ode_step!
EarthSciMLBase.timesteps
EarthSciMLBase.tspan
API Documentation
EarthSciMLBase.Advection
— TypeApply advection to a model.
EarthSciMLBase.ConnectorSystem
— TypeA connector for two systems.
eqs
from
to
EarthSciMLBase.CoupledSystem
— TypeA system for composing together other systems using the couple
function.
systems
: Model components to be composed togetherdomaininfo
: Initial and boundary conditions and other domain informationpdefunctions
: A vector of functions where each function takes as an argument the resulting PDESystem after DomainInfo is added to this system, and returns a transformed PDESystem.
ops
: A vector of operators to run during simulations.
callbacks
: A vector of callbacks to run during simulations.init_callbacks
: Objectsx
with aninit_callback(x, Simulator)::DECallback
method.
Things that can be added to a CoupledSystem
: * ModelingToolkit.ODESystem
s. If the ODESystem has a field in the metadata called :coupletype
(e.g. ModelingToolkit.get_metadata(sys)[:coupletype]
returns a struct type with a single field called sys
) then that type will be used to check for methods of EarthSciMLBase.couple
that use that type. * Operator
s * DomainInfo
s * Callbacks * Types X
that implement a EarthSciMLBase.init_callback(::X, sys::CoupledSystem, sys_mtk, obs_eqs, domain::DomainInfo)::DECallback
method * Other CoupledSystem
s * Types X
that implement a EarthSciMLBase.couple2(::X, ::CoupledSystem)
or EarthSciMLBase.couple2(::CoupledSystem, ::X)
method. * Tuple
s or AbstractVector
s of any of the things above.
EarthSciMLBase.DomainInfo
— TypeDomain information for a ModelingToolkit.jl PDESystem. It can be used with the +
operator to add initial and boundary conditions and coordinate transforms to a ModelingToolkit.jl ODESystem or Catalyst.jl ReactionSystem.
NOTE: The independent variable (usually time) must be first in the list of initial and boundary conditions.
partial_derivative_funcs
: Function that returns spatial derivatives of the partially-independent variables, optionally performing a coordinate transformation first.Current function options in this package are:
partialderivatives_δxyδlonlat
: Returns partial derivatives after transforming any variables namedlat
andlon
from degrees to cartesian meters, assuming a spherical Earth.
Other packages may implement additional functions. They are encouraged to use function names starting with
partialderivatives_
.
grid_spacing
: The discretization intervals for the partial independent variables.icbc
: The sets of initial and/or boundary conditions.spatial_ref
: The spatial reference system for the domain.time_offset
: The time offset for the domain.
EarthSciMLBase.ICBCcomponent
— TypeInitial and boundary condition components that can be combined to create an DomainInfo object.
EarthSciMLBase.Operator
— TypeOperators are objects that modify the current state of a Simulator
system. Each operator should be define a function with the signature:
`EarthSciMLBase.get_scimlop(::Operator, csys::CoupledSystem, mtk_sys, domain::DomainInfo, obs_functions, coordinate_transform_functions, u0, p)::AbstractSciMLOperator`
which should return a SciMLOperators.AbstractSciMLOperator. Refer to the SciMLOperators.jl documentation for more information on how to define operators.
EarthSciMLBase.SolverIMEX
— TypeA solver strategy based on implicit-explicit (IMEX) time integration. See here for additional information.
kwargs for ODEProblem constructor:
- stiff_scimlop: Whether the stiff ODE function should be implemented as a SciMLOperator.
- stiff_sparse: Whether the stiff ODE function should use a sparse Jacobian.
- stiff_jac: Whether the stiff ODE function should use an analytical Jacobian.
- stiffjacscimlop: Whether the stiff ODE function Jacobian should be implemented as a SciMLOperator. (Ignored if
stiff_jac==false
.) - stiff_tgrad: Whether the stiff ODE function should use an analytical time gradient.
- u0: initial condtions; if "nothing", default values will be used.
- p: parameters; if "nothing", default values will be used.
EarthSciMLBase.SolverStrang
— TypeA simulator strategy based on Strang splitting. Choose either SimulatorStrangThreads
or SimulatorStrangSerial
to run the simulation.
kwargs for ODEProblem constructor:
- u0: initial condtions; if "nothing", default values will be used.
- p: parameters; if "nothing", default values will be used.
- nonstiff_params: parameters for the non-stiff ODE system.
- name: name of the system.
EarthSciMLBase.SolverStrangSerial
— Type# Specify the stiff ODE solver algorithm.
# `timestep` is the length of time for each splitting step.
SimulatorStrangSerial(stiffalg, timestep; kwargs...)
Perform a simulation using Strang splitting, where the MTK system is assumed to be stiff and the operators are assumed to be non-stiff. The solution will be calculated in serial.
stiffalg
: Stiff solver algorithm to use (see https://docs.sciml.ai/DiffEqDocs/stable/solvers/ode_solve/)timestep
: Length of each splitting time stepstiff_kwargs
: Keyword arguments for the stiff ODEProblem constructor and solver.
EarthSciMLBase.SolverStrangThreads
— Type# Specify the number of threads and the stiff ODE solver algorithm.
# `timestep` is the length of time for each splitting step.
SimulatorStrangThreads(threads, stiffalg, timestep; kwargs...)
# Use the default number of threads.
SimulatorStrangThreads(stiffalg, timestep; kwargs...)
Perform a simulation using Strang splitting, where the MTK system is assumed to be stiff and the operators are assumed to be non-stiff. The solution of the stiff ODE system is parallelized across grid cells using the specified number of threads.
threads
: Number of threads to usestiffalg
: Stiff solver algorithm to use (see https://docs.sciml.ai/DiffEqDocs/stable/solvers/ode_solve/)timestep
: Length of each splitting time stepstiff_kwargs
: Keyword arguments for the stiff ODEProblem constructor and solver.
EarthSciMLBase.SolverStrategy
— TypeSolverStrategy is an abstract type that defines the strategy for running a simulation.
EarthSciMLBase.constBC
— TypeConstruct constant boundary conditions equal to the value specified by val
.
val
: The value of the constant boundary conditions.partialdomains
: The partial domains, e.g.[x ∈ Interval(x_min, x_max), y ∈ Interval(y_min, y_max)]
.
EarthSciMLBase.constIC
— TypeConstruct constant initial conditions equal to the value specified by val
.
val
: The value of the constant initial conditions.indepdomain
: The independent domain, e.g.t ∈ Interval(t_min, t_max)
.
EarthSciMLBase.periodicBC
— TypeConstruct periodic boundary conditions for the given partialdomains
. Periodic boundary conditions are defined as when the value at one side of the domain is set equal to the value at the other side, so that the domain "wraps around" from one side to the other.
partialdomains
: The partial domains, e.g.[x ∈ Interval(x_min, x_max), y ∈ Interval(y_min, y_max)]
.
EarthSciMLBase.zerogradBC
— TypeConstruct zero-gradient boundary conditions for the given partialdomains
.
partialdomains
: The partial domains, e.g.[x ∈ Interval(x_min, x_max), y ∈ Interval(y_min, y_max)]
.
Base.convert
— Methodconvert(, sys; name, simplify, kwargs...)
Get the ODE ModelingToolkit ODESystem representation of a CoupledSystem
.
kwargs:
- name: The desired name for the resulting ODESystem
- simplify: if true, the observed variables that are not needed to specify the state variables will be pruned and returned as a second return value after the ODESystem, which will be structurally simplified.
Base.convert
— Methodconvert(, sys; name, kwargs...)
Get the ModelingToolkit PDESystem representation of a CoupledSystem
.
EarthSciMLBase.ConstantWind
— MethodConstantWind(t, vals; name)
Construct a constant wind velocity model component with the given wind speed(s), which should include units. For example, ConstantWind(t, 1u"m/s", 2u"m/s")
.
EarthSciMLBase.MeanWind
— MethodMeanWind(t, domain)
A model component that represents the mean wind velocity, where pvars
is the partial dependent variables for the domain.
EarthSciMLBase.add_dims
— Methodadd_dims(expression, vars, dims)
add_dims(equation, vars, dims)
Add the given dimensions to each variable in vars
in the given expression or equation. Each variable in vars
must be unidimensional, i.e. defined like @variables u(t)
rather than @variables u(..)
.
Example:
using EarthSciMLBase, ModelingToolkit
@parameters x y k t
@variables u(t) q(t)
exp = 2u + 3k*q + 1
EarthSciMLBase.add_dims(exp, [u, q], [x, y, t])
# output
1 + 2u(x, y, t) + 3k*q(x, y, t)
EarthSciMLBase.add_metadata
— MethodAdd the units and description in the variable from
to the variable to
.
EarthSciMLBase.add_scope
— Methodadd_scope(sys, v, iv)
Add a system scope to a variable name, for example so that x
in system sys1
becomes sys1₊x
. iv
is the independent variable.
EarthSciMLBase.copy_with_change
— Methodcopy_with_change(
sys;
eqs,
name,
metadata,
continuous_events,
discrete_events
)
Create a copy of an ODESystem with the given changes.
EarthSciMLBase.couple
— Methodcouple(systems...) -> CoupledSystem
Couple multiple ModelingToolkit systems together.
The systems that are arguments to this system can be of type ModelingToolkit.AbstractSystem
, CoupledSystem
, DomainInfo
, or any type T
that has a method couple(::CoupledSystem, ::T)::CoupledSystem
or a method couple(::T, ::CoupledSystem)::CoupledSystem
defined for it.
EarthSciMLBase.couple2
— Methodcouple2()
Perform bi-directional coupling for two equation systems.
To specify couplings for system pairs, create methods for this function with the signature:
EarthSciMLBase.couple2(a::ACoupler, b::BCoupler)::ConnectorSystem
where ACoupler
and BCoupler
are :coupletype
s defined like this:
struct ACoupler sys end
@named asys = ODESystem([], t, metadata=Dict(:coupletype=>ACoupler))
EarthSciMLBase.dims
— Methoddims(
icbc::EarthSciMLBase.ICcomponent
) -> Vector{Symbolics.Num}
Returns the dimensions of the independent and partial domains associated with these initial or boundary conditions.
EarthSciMLBase.domains
— Methoddomains(icbc::EarthSciMLBase.ICcomponent) -> Vector
Returns the domains associated with these initial or boundary conditions.
EarthSciMLBase.dtype
— Methoddtype(_)
Return the data type of the state variables for this domain, based on the data types of the boundary conditions domain intervals.
EarthSciMLBase.endpoints
— Methodendpoints(d)
Return the endpoints of the partial independent variables for this domain.
EarthSciMLBase.get_coupletype
— MethodReturn the coupling type associated with the given system.
EarthSciMLBase.get_dv
— MethodReturn the dependent variable, which is the first argument of the term, unless the term is a time derivative, in which case the dependent variable is the argument of the time derivative.
EarthSciMLBase.get_needed_vars
— Methodget_needed_vars(sys)
Return the indexes of the system variables that the state variables of the final simplified system depend on. This should be done before running structural_simplify
on the system.
EarthSciMLBase.graph
— MethodCreate a graph from a CoupledSystem using the MetaGraphsNext package.
EarthSciMLBase.grid
— Methodgrid(d)
Return the ranges representing the discretization of the partial independent variables for this domain, based on the discretization intervals given in Δs
.
EarthSciMLBase.icbc
— Methodicbc(di, states)
Return a vector of equations that define the initial and boundary conditions for the given state variables.
EarthSciMLBase.init_callback
— MethodTypes that implement an:
init_callback(x, sys::CoupledSystem, obs_eqs, domain::DomainInfo)::DECallback
method can also be coupled into a CoupledSystem
. The init_callback
function will be run before the simulator is run to get the callback.
EarthSciMLBase.init_u
— MethodInitialize the state variables.
EarthSciMLBase.ivar
— Methodivar(di::DomainInfo) -> Any
Return the independent variable associated with these initial and boundary conditions.
EarthSciMLBase.observed_expression
— Methodobserved_expression(eqs, x)
Return an expression for the observed value of a variable x
after substituting in the constants observed values of other variables. extra_eqs
is a list of additional equations to use in the substitution.
EarthSciMLBase.observed_function
— Methodobserved_function(eqs, x, coords)
Return a function to for the observed value of a variable x
based on the input arguments in coords
. extra_eqs
is a list of additional equations to use to determine the value of x
.
EarthSciMLBase.ode_step!
— MethodTake a step using the ODE solver.
EarthSciMLBase.operator_compose
— Functionoperator_compose(a, b)
operator_compose(a, b, translate)
Compose to systems of equations together by adding the right-hand side terms together of equations that have matching left-hand sides. The left hand sides of two equations will be considered matching if:
- They are both time derivatives of the same variable.
- The first one is a time derivative of a variable and the second one is the variable itself.
- There is an entry in the optional
translate
dictionary that maps the dependent variable in the first system to the dependent variable in the second system, e.g.Dict(sys1.sys.x => sys2.sys.y)
. - There is an entry in the optional
translate
dictionary that maps the dependent variable in the first system to the dependent variable in the second system, with a conversion factor, e.g.Dict(sys1.sys.x => sys2.sys.y => 6)
.
EarthSciMLBase.param_to_var
— MethodReplace the parameter p
in the system sys
with a new variable that has the same name, units, and description as p
.
param_to_var(sys, ps)
This can be useful to replace a parameter that does not change in time in a model component with one specified by another system that does change in time (or space). For example, the code below specifies a first-order loss equation, and then changes the temperature (which determines the loss rate) with a temperature value that varies in time. ```
EarthSciMLBase.partialderivative_transforms
— Methodpartialderivative_transforms(di::DomainInfo) -> Vector{Any}
Return transform factor to multiply each partial derivative operator by, for example to convert from degrees to meters.
EarthSciMLBase.partialderivatives
— Methodpartialderivatives(di::DomainInfo) -> Any
Return the partial derivative operators for the given domain.
EarthSciMLBase.partialderivatives_δxyδlonlat
— Methodpartialderivatives_δxyδlonlat(pvars; default_lat)
Return partial derivative operator transform factors corresponding for the given partial-independent variables after converting variables named lon
and lat
from degrees to x and y meters, assuming they represent longitude and latitude on a spherical Earth.
EarthSciMLBase.prune_observed
— Methodprune_observed(sys)
Remove equations from an ODESystem where the variable in the LHS is not present in any of the equations for the state variables. This can be used to remove computationally intensive equations that are not used in the final model.
EarthSciMLBase.pvars
— Methodpvars(di::DomainInfo) -> Any
Return the partial independent variables associated with these initial and boundary conditions.
EarthSciMLBase.single_ode_step!
— MethodTake a step using the ODE solver with the given IIchunk (grid cell interator) and integrator.
EarthSciMLBase.steplength
— Methodsteplength(timesteps)
Return the time step length common to all of the given timesteps
. Throw an error if not all timesteps are the same length.
EarthSciMLBase.stiff_callback
— MethodA callback to periodically run the stiff solver.
EarthSciMLBase.threaded_ode_step!
— MethodTake a step using the ODE solver.
EarthSciMLBase.timesteps
— Methodtimesteps(tsteps)
Return the time points during which integration should be stopped to run the operators.
EarthSciMLBase.tspan
— Methodtspan(d)
Return the time range associated with this domain.