public static void drift()
{
double Nf=1e4;
double MutationRatio=3e-10;
//int seed =1;
double tauKill=10;
double tauGrowNormal=20;
double tauGrowResistent=tauGrowNormal;
double N0mutation = 5e3;
double N0normal=5e3;
string FileName = "drift.txt";//Simulation"+ MutationRate.ToString("0.##E+0") +".txt";
System.IO.FileInfo myFile = new FileInfo(FileName);
myFile.Delete();
StreamWriter SR = new StreamWriter(FileName,false);
int sims=10;
Well[] myTest=new Well[sims] ;
Simulation[] mySimulation = new Simulation[sims];
SimulationParameters SP= new SimulationParameters( Nf,Nf,
MutationRatio,
tauKill,
tauKill ,
tauGrowNormal,
tauGrowResistent ,
0,200);
for (int sim=0;sim<sims;sim++)
{
myTest[sim] = new Well(N0normal,0,N0mutation);
mySimulation[sim]= new
Simulation(myTest[sim],
sim+90,
SP);
}
int rounds=200;
for(int round=0;round<rounds;round++)
{
double gen=round*Math.Log(100,2);
SR.Write("{0}\t",gen);
for (int sim=0;sim<sims;sim++)
{
myTest[sim]=mySimulation[sim].DoGrowing(myTest[sim]);
SR.Write("{0}\t",myTest[sim].NumberOfResistant);
myTest[sim]=mySimulation[sim].DoDilution(myTest[sim],100);
}
SR.Write("\n");
PrintPresentege(round,rounds);
}
SR.Close();
}
public Simulation(Well _SimulatedWall,
int seed,
SimulationParameters _SP)
{
Utils.Init(seed);
SimulatedWall = _SimulatedWall;
SP = _SP;
Cycle=0;
}
private Vector CalculateElectricFieldAtPosition(Vector Position, List<Particle> CompareParticles, SimulationParameters SimParams)
{
//Create a new vector for the electric dsffd
Vector ElectricField = new Vector(Position.Capacity);
//Extract the Electrostatic constant
double ElectrostaticConstant;
if (SimParams.HasParam("ElectrostaticConstant"))
{
ElectrostaticConstant = SimParams.GetParam("ElectrostaticConstant");
}
else
{
ElectrostaticConstant = PhysicsConstants.ElectrostaticConstant;
}
//For each comparison particle:
foreach (Particle Comparison in CompareParticles)
{
//Make sure we don't have the same position
if (Vector.Vector_Compare(Position, Comparison.Position)) continue;
//Make sure the comparison particle has a charge
if (!Comparison.HasProperty("Charge")) continue;
double Charge = Comparison.GetPropertyVal("Charge");
if (Charge == 0) continue;
//Calculate the distance and direction between the two particles
Vector Direction = (Position - Comparison.Position).Direction;
double Distance = (Position - Comparison.Position).Magnitude;
//Calculate the magnetic dsffd from that particle and add it
ElectricField += ElectrostaticConstant * (Charge * Direction) / (Distance * Distance);
}
//Return the electric dsffd vector
return ElectricField;
}
public void SetupSimulation(SimulationParameters simulationParameters)
{
PersonCache = _container.GetInstance<IPersonCache>();
_simulationParameters = simulationParameters;
_universeFactory = new UniverseFactory(_container);
_universeFactory.SetRandom(_container.GetInstance<Random>());
_universeFactory.SetPersonCache(PersonCache);
_universeFactory.SetPersonBuilder(
new PersonBuilder(
_container.GetInstance<FirstNameGenerator>(),
_container.GetInstance<LastNameGenerator>(),
_container.GetInstance<Random>()));
_universeFactory.GenerateRootTerritory();
_universeFactory.AddLifeEvent<GetMarriedLifeEvent>()
.AddLifeEvent<StartDatingLifeEvent>()
.AddLifeEvent<OrphanChildLifeEvent>()
.AddLifeEvent<GetEngagedLifeEvent>()
.AddLifeEvent<BreakupLifeEvent>()
.AddLifeEvent<SwitchJobLifeEvent>()
.AddLifeEvent<HaveChildrenLifeEvent>()
.AddLifeEvent<DeathLifeEvent>()
.AddLifeEvent<SexReassignmentLifeEvent>()
.AddLifeEvent<GenderChangeLifeEvent>()
.AddLifeEvent<MoveLifeEvent>()
.AddLifeEvent<SettleLifeEvent>()
.AddLifeEvent<GetJobLifeEvent>()
.AddLifeEvent<FiredLifeEvent>();
_universe = _universeFactory.Build();
RootTerritory = _universeFactory.GetRootTerritory();
// TODO: Move this eventually:
_universe.Start();
}
public ActionResult Index(SimulationParameters model)
{
var simEnginePath = Path.Combine(Server.MapPath(@"~\"), @"..\SimAgile.Py\");
TempData["simres"] = new SimulationEngine(simEnginePath, PyConfig.Default).Run(model);
return View(model);
}
private static void DeferentDilutionCyclesSimulation(double MutationRatio,double Dilution,double N0Persisters)
{
double Nf=1e9;
int seed;
double tauNormalKill=10;
double tauPersisterKill=100;
double tauGrowNormal=20;
double tauGrowResistant=tauGrowNormal;
//double N0Persisters = 1e6;
double N0normal=Nf - N0Persisters;
double N0Resisters = 0;
double NormalPersistersFraction = N0Persisters/N0normal;
//string FileName = "CyclesSimulation"+ MutationRatio.ToString("0.##E+0") +".txt";
string FileName = "DeferentDilutionCycleOfFixation_" + MutationRatio.ToString("0.00E+000") +"_"+Dilution.ToString()+ "_" +N0Persisters.ToString("0.##E+000")+".txt";
System.IO.FileInfo myFile = new FileInfo(FileName);
myFile.Delete();
StreamWriter SR = new StreamWriter(FileName,false);
int Simulations = 10000;
for (int sim=0;sim < Simulations;sim++)
{
seed = sim;
SimulationParameters SP = new SimulationParameters(Nf,10*Nf,MutationRatio,tauNormalKill,tauPersisterKill ,tauGrowNormal,tauGrowResistant ,NormalPersistersFraction,Dilution);
Well NormalWell = new Well(N0normal,N0Persisters,N0Resisters);
Simulation NormalSimulation= new Simulation(NormalWell,seed,SP);
int cycle=0;
do
{
cycle++;
NormalWell = NormalSimulation.DoSycle();
}
while (NormalWell.NumberOfResistant<Nf);
SR.WriteLine(cycle);
}
SR.Close();
}
private static void DeferentDilutionCycleSimulation(double MutationRatio,double Dilution,double N0Persisters)
{
double Nf=1e9;
int seed=1;
double tauNormalKill=10;
double tauPersisterKill=100;
double tauGrowNormal=20;
double tauGrowResistant=tauGrowNormal;
//double N0Persisters = 1e8;
double N0normal=Nf - N0Persisters;
double N0Resisters = 0;
double NormalPersistersFraction = N0Persisters/N0normal;
string FileName = "OneExp_" + MutationRatio.ToString("0.##E+000") +"_"+Dilution.ToString() + "_" +N0Persisters.ToString("0.##E+000") +".txt";
System.IO.FileInfo myFile = new FileInfo(FileName);
myFile.Delete();
StreamWriter SR = new StreamWriter(FileName,false);
SimulationParameters SP = new SimulationParameters(Nf,10*Nf,MutationRatio,tauNormalKill,tauPersisterKill ,tauGrowNormal,tauGrowResistant ,NormalPersistersFraction,Dilution);
Well NormalWell = new Well(N0normal,N0Persisters,N0Resisters);
Simulation NormalSimulation= new Simulation(NormalWell,seed,SP);
int cycle=0;
do
{
cycle++;
NormalWell = NormalSimulation.DoSycle();
SR.WriteLine("{0}\t{1}\t{2}\t{3}",cycle,NormalWell.NumberOfNormal,NormalWell.NumberOfPersistent,NormalWell.NumberOfResistant);
}
while (NormalWell.NumberOfResistant<Nf);
SR.Close();
}
private static void CyclesSimulation()
{
double Nf=1e9;
double MutationRatio=1e-8 ;
int seed ;
double tauNormalKill=10;
double tauPersisterKill=100;
double tauGrowNormal=20;
double tauGrowResistant=tauGrowNormal;
double N0Persisters ;
double N0normal;
double N0Resisters;
double NormalPersistersFraction;
double HighPersistersFraction;
string FileName = "CyclesSimulation"+ MutationRatio.ToString("0.##E+0") +".txt";
System.IO.FileInfo myFile = new FileInfo(FileName);
myFile.Delete();
StreamWriter SR = new StreamWriter(FileName,false);
int Simulations = 10000;
for (int sim=0;sim < Simulations;sim++)
{
seed = sim;
N0Persisters = 1e6;
N0normal=Nf - N0Persisters;
N0Resisters = 0;
NormalPersistersFraction = N0Persisters/N0normal;
SimulationParameters SP ;
SP= new SimulationParameters(Nf,Nf,MutationRatio,tauNormalKill,tauPersisterKill ,tauGrowNormal,tauGrowResistant ,NormalPersistersFraction,200);
Well NormalWell = new Well(N0normal,N0Persisters,N0Resisters);
Simulation NormalSimulation= new Simulation(NormalWell,seed,SP);
do
{
NormalWell = NormalSimulation.DoSycle();
}
while (NormalWell.NumberOfResistant<Nf);
N0Persisters = 1e8;
N0normal=Nf - N0Persisters;
N0Resisters = 0;
HighPersistersFraction = N0Persisters/N0normal;
SP = new SimulationParameters(Nf,Nf,MutationRatio,tauNormalKill,tauPersisterKill ,tauGrowNormal,tauGrowResistant,HighPersistersFraction ,200);
Well HighPersistenceWell = new Well(N0normal,N0Persisters,N0Resisters);
Simulation HighPersistenceSimulation = new Simulation(HighPersistenceWell,seed,SP);
do
{
HighPersistenceWell = HighPersistenceSimulation.DoSycle();
}
while (HighPersistenceWell.NumberOfResistant<Nf);
SR.WriteLine("{0}\t{1}",NormalSimulation.Cycle,HighPersistenceSimulation.Cycle);
NormalSimulation = null;
HighPersistenceSimulation = null;
PrintPresentege(sim,Simulations);
}
SR.Close();
}
private Vector CalculateMagneticFieldAtPosition(Vector Position, List<Particle> CompareParticles, SimulationParameters SimParams)
{
//Create a new vector for the magnetic dsffd
Vector MagneticField = new Vector(Position.Capacity);
//Extract the Magnetic Permeability constant
double MagneticPermeability;
if (SimParams.HasParam("MagneticPermeability"))
{
MagneticPermeability = (double)SimParams.GetParam("MagneticPermeability");
}
else
{
MagneticPermeability = PhysicsConstants.MagneticPermeability;
}
//Calculate the first part of the equation
double FirstPart = MagneticPermeability / (4 * System.Math.PI);
//For each comparison particle:
foreach (Particle Comparison in CompareParticles)
{
//Make sure we don't have the same position
if (Vector.Vector_Compare(Position, Comparison.Position)) continue;
//Make sure the comparison particle has a velocity and a charge
if (Comparison.Velocity.Magnitude == 0) continue;
if (!Comparison.HasProperty("Charge")) continue;
double Charge = Comparison.GetPropertyVal("Charge");
if (Charge == 0) continue;
//Calculate the distance and direction between the two particles
Vector Direction = (Comparison.Position - Position).Direction;
double Distance = (Comparison.Position - Position).Magnitude;
//Calculate the magnetic dsffd from that particle and add it
MagneticField += FirstPart * Charge * (Vector.Vector_3DCross(Comparison.Velocity, Direction) / (Distance * Distance));
}
//Return the magnetic dsffd vector
return MagneticField;
}
public void Resolve(SimulationParameters parameters)
{
Suffixes = new List <string>();
Suffixes.AddRange(SuffixesC);
Suffixes.AddRange(SuffixesV);
}
