public void SolverFactoryTest()
{
var model = EmodlLoader.LoadEMODLModel(_sirModel);
ISolver solver = SolverFactory.CreateSolver("SSA", model, 1, 2.0, 3);
Assert.IsTrue(solver is Gillespie);
solver = SolverFactory.CreateSolver("FIRST", model, 1, 2.0, 3);
Assert.IsTrue(solver is GillespieFirstReaction);
solver = SolverFactory.CreateSolver("NEXT", model, 1, 2.0, 3);
Assert.IsTrue(solver is GibsonBruck);
solver = SolverFactory.CreateSolver("HYBRID", model, 1, 2.0, 3);
Assert.IsTrue(solver is HybridSSA);
solver = SolverFactory.CreateSolver("TAU", model, 1, 2.0, 3);
Assert.IsTrue(solver is TauLeaping);
solver = SolverFactory.CreateSolver("MID", model, 1, 2.0, 3);
Assert.IsTrue(solver is MidPoint);
solver = SolverFactory.CreateSolver("R", model, 1, 2.0, 3);
Assert.IsTrue(solver is RLeaping);
solver = SolverFactory.CreateSolver("RFAST", model, 1, 2.0, 3);
Assert.IsTrue(solver is RLeapingFast);
solver = SolverFactory.CreateSolver("BLEAP", model, 1, 2.0, 3);
Assert.IsTrue(solver is BLeaping);
solver = SolverFactory.CreateSolver("TSSA", model, 1, 2.0, 3);
Assert.IsTrue(solver is TransportSSA);
solver = SolverFactory.CreateSolver("DFSP", model, 1, 2.0, 3);
Assert.IsTrue(solver is DFSP);
solver = SolverFactory.CreateSolver("OTSSA", model, 1, 2.0, 3);
Assert.IsTrue(solver is OptimalTransportSSA);
/* Fractional diffusion solver doesn't handle single node models gracefully.
* solver = SolverFactory.CreateSolver("LEVY", model, 1, 2.0, 3);
* Assert.IsTrue(solver is FractionalDiffusion);
*/
/* Exit times solver doesn't handle missing target condition gracefully.
* solver = SolverFactory.CreateSolver("EXITTIMES", model, 1, 2.0, 3);
* Assert.IsTrue(solver is ExitTimes);
*/
/* dwSSA solver automatically starts solving
* Configuration.CurrentConfiguration = Configuration.ConfigurationFromString("{\"dwSSA\":{\"re_name\":\"I\",\"re_val\":500}}");
* solver = SolverFactory.CreateSolver("DWSSA", model, 1, 2.0, 3);
* Assert.IsTrue(solver is dwSSA);
*/
}
public void MigrationReactions()
{
const string modelDescription = @"
; migration model
(import (rnrs) (emodl cmslib))
(start-model ""migration"")
(locale site-a)
(set-locale site-a)
(species A::S 990)
(species A::E)
(species A::I 10)
(species A::R)
;(observe susceptibleA A::S)
;(observe exposedA A::E)
;(observe infectiousA A::I)
;(observe recoveredA A::R)
(observe populationA (sum A::S A::E A::I A::R))
;(observe prevalenceA (/ A::I (sum A::S A::E A::R)))
(param Ki 0.0005)
(param Kl 0.2)
(param Kr (/ 1 7))
(param Kw (/ 1 135))
(reaction exposureA (A::S) (A::E) (* Ki A::S A::I))
(reaction infectionA (A::E) (A::I) (* Kl A::E))
(reaction recoveryA (A::I) (A::R) (* Kr A::I))
(reaction waningA (A::R) (A::S) (* Kw A::R))
(locale site-b)
(set-locale site-b)
(species B::S 100)
(species B::E)
(species B::I)
(species B::R)
;(observe susceptibleB B::S)
;(observe exposedB B::E)
;(observe infectiousB B::I)
;(observe recoveredB B::R)
(observe populationB (sum B::S B::E B::I B::R))
;(observe prevalenceB (/ B::I (sum B::S B::E B::R)))
(reaction exposureB (B::S) (B::E) (* Ki B::S B::I))
(reaction infectionB (B::E) (B::I) (* Kl B::E))
(reaction recoveryB (B::I) (B::R) (* Kr B::I))
(reaction waningB (B::R) (B::S) (* Kw B::R))
; migration
(param Km 0.01)
(reaction SA->SB (A::S) (B::S) (* Km A::S))
(reaction EA->EB (A::E) (B::E) (* Km A::E))
(reaction IA->IB (A::I) (B::I) (* Km A::I))
(reaction RA->RB (A::R) (B::R) (* Km A::R))
(reaction SB->SA (B::S) (A::S) (* Km B::S 10))
(reaction EB->EA (B::E) (A::E) (* Km B::E 10))
(reaction IB->IA (B::I) (A::I) (* Km B::I 10))
(reaction RB->RA (B::R) (A::R) (* Km B::R 10))
(end-model)
";
Console.WriteLine("Building model with local and migratory/diffusive reactions...");
ModelInfo modelInfo = EmodlLoader.LoadEMODLModel(modelDescription);
var local = from reaction in modelInfo.Reactions where reaction.IsLocal select reaction;
var migration = from reaction in modelInfo.Reactions where reaction.IsDiffusion select reaction;
Console.WriteLine("Checking model for local reactions...");
Expect(local.Count() == 8);
Console.WriteLine("Checking model for migratory/diffusive reactions...");
Expect(migration.Count() == 8);
Console.WriteLine("");
}