public void TestWithParameters()
{
// Create a model
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Parameter parameter = new MuCell.Model.SBML.Parameter();
parameter.ID = "k_1";
parameter.Value = 0.07d;
model.listOfParameters = new List<MuCell.Model.SBML.Parameter>();
model.listOfParameters.Add(parameter);
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
// Set some values for species1
species1.ID = "s1";
species1.InitialAmount = 1.0d;
// Set some values for species2
species2.ID = "s2";
species2.InitialAmount = 12.0d;
model.AddId("s1", species1);
model.AddId("s2", species2);
model.AddId("k_1", parameter);
// Set up the reaction
MuCell.Model.SBML.Reaction reaction1 = new MuCell.Model.SBML.Reaction("reaction1");
// Set up the kinetic law
reaction1.KineticLaw = new MuCell.Model.SBML.KineticLaw(model);
reaction1.KineticLaw.Formula = "s1*s2*k_1";
// set up the species reference for the reactants
MuCell.Model.SBML.SpeciesReference ref1 = new MuCell.Model.SBML.SpeciesReference(species1, 1);
// set up the species references for the products
MuCell.Model.SBML.SpeciesReference ref2 = new MuCell.Model.SBML.SpeciesReference(species2, 3);
// Add the references
reaction1.Reactants.Add(ref1);
reaction1.Products.Add(ref2);
// set up the cell definition
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("cell1");
celldef1.addSBMLModel(model);
// set up a cell
MuCell.Model.CellInstance cell1 = celldef1.createCell();
cell1.localSpeciesDelta.Add("s1", 0.0d);
cell1.localSpeciesDelta.Add("s2", 0.0d);
cell1.localSpeciesVariables.Add("s1", 1.0d);
cell1.localSpeciesVariables.Add("s2", 12.0d);
// set up the statesnaphost
MuCell.Model.StateSnapshot state1 = new MuCell.Model.StateSnapshot();
state1.Cells.Add(cell1);
// get the eval function
MuCell.Model.EffectReactionEvaluationFunction fun1 = reaction1.ToEffectReactionEvaluationFunction();
// Evaluate
fun1(state1, cell1);
cell1.setSpeciesAmount("s1", cell1.UnitTestGetSpeciesAmountsAndDeltas("s1"));
cell1.setSpeciesAmount("s2", cell1.UnitTestGetSpeciesAmountsAndDeltas("s2"));
cell1.UnitTestClearDeltas();
AssertDouble.AreEqual(1.0d-0.84d, cell1.getLocalSimulationSpeciesAmount("s1"));
AssertDouble.AreEqual(12.0d+0.84d*3.0d, cell1.getLocalSimulationSpeciesAmount("s2"));
System.Console.WriteLine("about to eval");
// Evaluate again
fun1(state1, cell1);
cell1.setSpeciesAmount("s1", cell1.UnitTestGetSpeciesAmountsAndDeltas("s1"));
cell1.setSpeciesAmount("s2", cell1.UnitTestGetSpeciesAmountsAndDeltas("s2"));
cell1.UnitTestClearDeltas();
AssertDouble.AreEqual(0.16d-0.162624d, cell1.getLocalSimulationSpeciesAmount("s1"));
AssertDouble.AreEqual(14.52d+0.162624d*3.0d, cell1.getLocalSimulationSpeciesAmount("s2"));
// Check the param is the same
Assert.AreEqual(0.07m, parameter.Value);
}
public void TestWithSpecies()
{
// Create a model
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
// Set some values for species1
species1.ID = "s1";
species1.InitialAmount = 4.0d;
// Set some values for species2
species2.ID = "s2";
species2.InitialAmount = 0.1d;
model.AddId("s1", species1);
model.AddId("s2", species2);
// Set up the reaction
MuCell.Model.SBML.Reaction reaction1 = new MuCell.Model.SBML.Reaction("reaction1");
model.listOfReactions = new List<MuCell.Model.SBML.Reaction>();
model.listOfReactions.Add(reaction1);
// Set up the kinetic law
reaction1.KineticLaw = new MuCell.Model.SBML.KineticLaw(model);
reaction1.KineticLaw.Formula = "(s1)*2";
// set up the species reference for the reactants
MuCell.Model.SBML.SpeciesReference ref1 = new MuCell.Model.SBML.SpeciesReference(species1, 1);
// set up the species references for the products
MuCell.Model.SBML.SpeciesReference ref2 = new MuCell.Model.SBML.SpeciesReference(species1, 0.75);
MuCell.Model.SBML.SpeciesReference ref3 = new MuCell.Model.SBML.SpeciesReference(species2, 2);
// Add the references
reaction1.Reactants.Add(ref1);
reaction1.Products.Add(ref2);
reaction1.Products.Add(ref3);
// set up the cell definition
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("cell1");
celldef1.addSBMLModel(model);
// set up a cell
MuCell.Model.CellInstance cell1 = celldef1.createCell();
cell1.localSpeciesDelta.Add("s1", 0.0d);
cell1.localSpeciesDelta.Add("s2", 0.0d);
cell1.localSpeciesVariables.Add("s1", 4.0d);
cell1.localSpeciesVariables.Add("s2", 0.1d);
// set up the statesnaphost
MuCell.Model.StateSnapshot state1 = new MuCell.Model.StateSnapshot();
state1.Cells.Add(cell1);
// get the eval function
MuCell.Model.EffectReactionEvaluationFunction fun1 = reaction1.ToEffectReactionEvaluationFunction();
// Evaluate
fun1(state1, cell1);
cell1.setSpeciesAmount("s1", cell1.UnitTestGetSpeciesAmountsAndDeltas("s1"));
cell1.setSpeciesAmount("s2", cell1.UnitTestGetSpeciesAmountsAndDeltas("s2"));
cell1.UnitTestClearDeltas();
Assert.AreEqual(2.0d, cell1.getLocalSimulationSpeciesAmount("s1"));
Assert.AreEqual(16.1d, cell1.getLocalSimulationSpeciesAmount("s2"));
// Evaluate again
fun1(state1, cell1);
cell1.setSpeciesAmount("s1", cell1.UnitTestGetSpeciesAmountsAndDeltas("s1"));
cell1.setSpeciesAmount("s2", cell1.UnitTestGetSpeciesAmountsAndDeltas("s2"));
cell1.UnitTestClearDeltas();
Assert.AreEqual(1.0d, cell1.getLocalSimulationSpeciesAmount("s1"));
Assert.AreEqual(24.1d, cell1.getLocalSimulationSpeciesAmount("s2"));
}
public void TestGenerateTimeSeries()
{
// simulation
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
// experiment
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experiment1");
// Hopf model
MuCell.Model.SBML.Reader.SBMLReader s = new MuCell.Model.SBML.Reader.SBMLReader("../../UnitTests/smallest.Hopf.level2.xml");
List<MuCell.Model.SBML.Model> models = new List<MuCell.Model.SBML.Model>();
models.Add(s.model);
// Cell definition
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("celldef1");
celldef1.addSBMLModel(s.model);
experiment.addCellDefinition(celldef1);
// Cells
List<MuCell.Model.CellInstance> cells = new List<MuCell.Model.CellInstance>();
for(int i=0;i<5;i++)
{
cells.Add(celldef1.createCell());
}
// StateSnapshot for intial state
MuCell.Model.StateSnapshot initialState = new MuCell.Model.StateSnapshot(cells);
MuCell.Model.Vector3 size = new MuCell.Model.Vector3(1, 1, 1);
initialState.SimulationEnvironment = new MuCell.Model.Environment(size);
// trime series
MuCell.Model.TimeSeries ts1 = new MuCell.Model.TimeSeries("Average X", "X/celldef1", 0.01001d);
ts1.Initialize(models, experiment, simulation);
MuCell.Model.TimeSeries ts2 = new MuCell.Model.TimeSeries("Total X", "X", 0.01001d);
ts2.Initialize(models, experiment, simulation);
// Parameters
MuCell.Model.SimulationParameters parameters = new MuCell.Model.SimulationParameters();
parameters.TimeSeries.Add(ts1);
parameters.TimeSeries.Add(ts2);
parameters.InitialState = initialState;
parameters.SimulationLength = 0.04004d;
parameters.SnapshotInterval = 1;
parameters.StepTime = 0.01001d;
parameters.RelativeTolerance = 1E-8;
parameters.SolverMethod = MuCell.Model.Solver.SolverMethods.RungeKutta;
// Simulation
simulation.Parameters = parameters;
// Start simulation
simulation.StartSimulation();
// Now check the results
Assert.AreEqual(5, ts1.Series.Count);
Assert.AreEqual(5, ts2.Series.Count);
double[] ts = ts1.Series.ToArray();
double[] tst = ts2.Series.ToArray();
Assert.AreEqual(2.5d, ts[0]);
AssertDouble.AreEqual(rk_x_t1, ts[1]);
AssertDouble.AreEqual(rk_x_t2, ts[2]);
AssertDouble.AreEqual(rk_x_t3, ts[3]);
AssertDouble.AreEqual(rk_x_t4, ts[4]);
Assert.AreEqual(5*2.5d, tst[0]);
AssertDouble.AreEqual(5*rk_x_t1, tst[1]);
AssertDouble.AreEqual(5*rk_x_t2, tst[2]);
AssertDouble.AreEqual(5*rk_x_t3, tst[3]);
AssertDouble.AreEqual(5*rk_x_t4, tst[4]);
}
public void InvalidTimeSeriesEquation()
{
// simulation
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
// experiment
MuCell.Model.Experiment experiment = new MuCell.Model.Experiment("experiment1");
// Hopf model
MuCell.Model.SBML.Reader.SBMLReader s = new MuCell.Model.SBML.Reader.SBMLReader("../../UnitTests/smallest.Hopf.level2.xml");
List<MuCell.Model.SBML.Model> models = new List<MuCell.Model.SBML.Model>();
models.Add(s.model);
// Cell definition
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("celldef1");
celldef1.addSBMLModel(s.model);
experiment.addCellDefinition(celldef1);
// Cells
List<MuCell.Model.CellInstance> cells = new List<MuCell.Model.CellInstance>();
for(int i=0;i<5;i++)
{
cells.Add(celldef1.createCell());
}
// StateSnapshot for intial state
MuCell.Model.StateSnapshot initialState = new MuCell.Model.StateSnapshot(cells);
MuCell.Model.Vector3 size = new MuCell.Model.Vector3(1, 1, 1);
initialState.SimulationEnvironment = new MuCell.Model.Environment(size);
// Parameters
simulation.Parameters.InitialState = initialState;
simulation.Parameters.SimulationLength = 3;
simulation.Parameters.SnapshotInterval = 1;
simulation.Parameters.StepTime = 1;
// Time series
MuCell.Model.TimeSeries ts1 = new MuCell.Model.TimeSeries("Average A", "(A)", 1.0);
ts1.Initialize(models, experiment, simulation);
}
public void RunHopfSimulationRK(MuCell.Model.SBML.Reader.SBMLReader s)
{
// Cell definition
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("celldef1");
celldef1.addSBMLModel(s.model);
// Cells
List<MuCell.Model.CellInstance> cells = new List<MuCell.Model.CellInstance>();
MuCell.Model.CellInstance cell1 = celldef1.createCell();
cells.Add(cell1);
// StateSnapshot for intial state
MuCell.Model.StateSnapshot initialState = new MuCell.Model.StateSnapshot(cells);
MuCell.Model.Vector3 size = new MuCell.Model.Vector3(1, 1, 1);
initialState.SimulationEnvironment = new MuCell.Model.Environment(size);
// Parameters
MuCell.Model.SimulationParameters parameters = new MuCell.Model.SimulationParameters();
parameters.InitialState = initialState;
parameters.SimulationLength = 0.01001d;
parameters.SnapshotInterval = 2;
parameters.StepTime = 0.01001d;
parameters.SolverMethod = MuCell.Model.Solver.SolverMethods.RungeKutta;
// Simulation
MuCell.Model.Simulation simulation = new MuCell.Model.Simulation("simulation1");
simulation.Parameters = parameters;
// Assert that is not complete at all
Assert.AreEqual(0.0d, simulation.SimulationProgress());
// Test the initial conditions
Assert.AreEqual(1.0d, cell1.getSpeciesAmount("A"));
Assert.AreEqual(2.5d, cell1.getSpeciesAmount("X"));
Assert.AreEqual(2.5d, cell1.getSpeciesAmount("Y"));
Assert.AreEqual(2.5d, cell1.getSpeciesAmount("Z"));
Assert.AreEqual(0.0d, cell1.getSpeciesAmount("_void_"));
// Start simulation
simulation.StartSimulation();
// Assert that is complete
Assert.AreEqual(1.0d, simulation.SimulationProgress());
// Test the results (test generated from the Python model)
AssertDouble.AreEqual(1.0d, cell1.getSpeciesAmount("A"));
AssertDouble.AreEqual(rk_x_t1, cell1.getSpeciesAmount("X"));
AssertDouble.AreEqual(rk_y_t1, cell1.getSpeciesAmount("Y"));
AssertDouble.AreEqual(rk_z_t1, cell1.getSpeciesAmount("Z"));
Assert.AreEqual(0.0d, cell1.getSpeciesAmount("_void_"));
// Make the simulation run a bit longer
parameters.SimulationLength = 0.02002;
simulation.UnPauseSimulation();
AssertDouble.AreEqual(1.0d, cell1.getSpeciesAmount("A"));
AssertDouble.AreEqual(rk_x_t2, cell1.getSpeciesAmount("X"));
AssertDouble.AreEqual(rk_y_t2, cell1.getSpeciesAmount("Y"));
AssertDouble.AreEqual(rk_z_t2, cell1.getSpeciesAmount("Z"));
Assert.AreEqual(0.0d, cell1.getSpeciesAmount("_void_"));
// Make the simulation run a bit longer
parameters.SimulationLength = 0.03003;
simulation.UnPauseSimulation();
AssertDouble.AreEqual(1.0d, cell1.getSpeciesAmount("A"));
AssertDouble.AreEqual(rk_x_t3, cell1.getSpeciesAmount("X"));
AssertDouble.AreEqual(rk_y_t3, cell1.getSpeciesAmount("Y"));
AssertDouble.AreEqual(rk_z_t3, cell1.getSpeciesAmount("Z"));
Assert.AreEqual(0.0d, cell1.getSpeciesAmount("_void_"));
}