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_"));
}