//
public void MonteCarloSimlation(RadiationSchema rs)
{
for (int i = 0; i < rs.MChistories; i++)
{
TimeOperator timeOperator = new TimeOperator();
switch (RadiationSchema.rad_repair_action) // zzz-- enable only DNA breakage
{
case 0:
{
timeOperator.DoTimeEvolution(rs, listObjs); // recursion creates time loop
}
break;
// case 1:
// {
//// timeOperator.ApplyBreakage(rs, listObjs);
// }
// break;
// default:
// {
// // timeOperator.ApplyRadAndRepair(rs, listObjs);
// }
// break;
}
}
}
public Work(int thread, int n, RadiationSchema r, DSBs dd)
{
nThread = thread;
nThreads = n;
rs = r;
DSBdata = dd;
}
//
public bool ApplyRadiation(RadiationSchema rs)
{
if (CreateRadBreaks(rs))
{
return(true);
}
else
{
return(false);
}
}
//
public bool DoTimeEvolution(RadiationSchema rs, List <Object> listObjs)
{
if (ApplyRadAndRepair(rs, listObjs))
{
return(true);
}
else
{
return(false);
}
}
//
public bool CreateRadBreaks(RadiationSchema rs)
{
//DSBdata = new DSBs("default");
//return true;
if (DNAbreakage.PrepairDSBpositionsInGenome(rs, DSBdata))
{
return(true);
}
else
{
return(false);
}
}
//
public bool ApplyBreakage(RadiationSchema rs)
{
if (ApplyRadiation(rs))
{
if (ApplyBystanderEffect())
{
return(true);
}
else
{
return(false);
}
}
else
{
return(false);
}
}
//
public bool ApplyRadAndRepair(RadiationSchema rs, List <Object> listObjs)
{
if (ApplyBreakage(rs))
{
if (RestitutionKinetics(listObjs))
{
return(true);
}
else
{
return(false);
}
}
else
{
return(false);
}
}
//
public static bool ApplyRad2RWs(RadiationSchema rs, RandomWalk rw, DSBs DSBdata)
{
int ndsb = 0;
try
{
double dose;
double dose_total = 0.0;
for (int nb = 0; nb < rs.nBeams; nb++) // iterate over all beams
{
foreach (int j in rw.nmonomer)
{
dose = Dconst;
dose_total += Dconst;
try
{
for (int i = 0; i < amorphous_partile_tracks[nb].track_struct.ntracks; i++)
{
int x = amorphous_partile_tracks[nb].track_struct.X[i];
int y = amorphous_partile_tracks[nb].track_struct.Y[i];
int dist2 = (x - rw.LL[j].X) * (x - rw.LL[j].X) + (y - rw.LL[j].Y) * (y - rw.LL[j].Y);
if (dist2 < Convert.ToInt32((RadiationSchema.Pr / lattice_dim) * (RadiationSchema.Pr / lattice_dim)))
{
int t = Convert.ToInt32(MainForm.Particle.Tracks.grid * lattice_dim * Math.Sqrt(dist2) / RadiationSchema.Pr); // microns
dose += amorphous_partile_tracks[nb].track_struct.dose[t];
dose_total += amorphous_partile_tracks[nb].track_struct.dose[t];
}
}
}
catch { return(false); }
double Q = 0.812 * 35.0 / 25.0; // multiply by 35./25. for high/low LET; also 1e-5 is factored out
if (amorphous_partile_tracks[nb].p_t == MainForm.Radiation.p_type.photon)
{
Q = 0.812; // multiply by 35./25. for high LET
}
else
{
Q = 0.812 * 35.0 / 25.0; // multiply by 35./25. for high LET
}
Q *= 1.0e-5; // Q is determined from PFGE experiments
Random random = new Random();
try
{
if (SimpleRNG.GetUniform() < 1.0 - Math.Exp(-Q * dose))
{
ndsb++;
DSBs.DSBstruct new_dsb = new DSBs.DSBstruct
{
ndsb = ndsb,
L = rw.LL[j],
position = rw.nmonomer[j],
entry_time = rs.entryTime[nb],
exit_time = rs.exitTime[nb]
};
new_dsb.random_time = SimpleRNG.GetUniform() * (new_dsb.exit_time - new_dsb.entry_time) + new_dsb.entry_time; // a DSB is created sometime during the fractionation interval
double r = SimpleRNG.GetUniform();
if (r < DSBs.DSBcomplP[0])
{
new_dsb.DSBcmplx = DSBs.DSBstruct.DSBcomplexity.simpleDSB;
}
else
{
if (r >= DSBs.DSBcomplP[0] && r < DSBs.DSBcomplP[1]) // zzz can a DSB appear more than 1 time at the same monomer
{
new_dsb.DSBcmplx = DSBs.DSBstruct.DSBcomplexity.DSBplus;
}
else
{
new_dsb.DSBcmplx = DSBs.DSBstruct.DSBcomplexity.DSBplusplus;
}
}
DSBdata.listDSBs.Add(new_dsb);
}
}
catch { return(false); }
}
}
dose_total /= Convert.ToDouble(rw.nmonomer.Length); // total dose integrated over all monomers // zzz might wanna output somewhere
return(true);
}
catch { return(false); }
}
//
public bool PrepairDSBpositionsInGenome(RadiationSchema rs, DSBs DSBdata)
{
bool bParallel = false; // zzz666
try
{
RandomWalk rw = new RandomWalk();
int nmonomers = IntactHumanGenome.WholeGenome();
rw.LL = new Location[nmonomers];
rw.nmonomer = new int[nmonomers];
Random random = new Random();
int rnucleus = Convert.ToInt32(R / lattice_dim);
int j = 0;
if (!bParallel)
{
for (int chn = 0; chn < IntactHumanGenome.nObjs; chn++) // zzz666 split these into subtasks
{
while (true)
{
rw.LL[j].X = random.Next(0, 2 * rnucleus) - rnucleus; // RW random origin
rw.LL[j].Y = random.Next(0, 2 * rnucleus) - rnucleus;
rw.LL[j].Z = random.Next(0, 2 * rnucleus) - rnucleus;
if (InsideEllipsoid(rw.LL[j]))
{
break;
}
} // zzz666 these RWs don't have loops or domains yet
rw.nmonomer[j] = j;
j++;
for (int i = 0; i < Convert.ToInt32(IntactHumanGenome.NC[chn] / IntactHumanGenome.monomerSize) - 1; i++)
{
Location l_temp;
switch (random.Next(0, 3))
{
case 0:
{
l_temp.X = rw.LL[j - 1].X + (2 * random.Next(0, 2) - 1);
l_temp.Y = rw.LL[j - 1].Y;
l_temp.Z = rw.LL[j - 1].Z;
if (InsideEllipsoid(l_temp))
{
rw.LL[j] = l_temp;
}
}
break;
case 1:
{
l_temp.X = rw.LL[j - 1].X;
l_temp.Y = rw.LL[j - 1].Y + (2 * random.Next(0, 2) - 1);
l_temp.Z = rw.LL[j - 1].Z;
if (InsideEllipsoid(l_temp))
{
rw.LL[j] = l_temp;
}
}
break;
case 2:
{
l_temp.X = rw.LL[j - 1].X;
l_temp.Y = rw.LL[j - 1].Y;
l_temp.Z = rw.LL[j - 1].Z + (2 * random.Next(0, 2) - 1);
if (InsideEllipsoid(l_temp))
{
rw.LL[j] = l_temp;
}
}
break;
default:
break;
}
rw.nmonomer[j] = j;
j++;
}
}
if (ApplyRad2RWs(rs, rw, DSBdata)) // collect all sets of DSBs and put them into a list
{
return(true);
}
else
{
return(false);
}
}
else
{
//foreach (var item in new ManagementObjectSearcher("Select * from Win32_ComputerSystem").Get())
//{
// Console.WriteLine("Number Of Physical Processors: {0} ", item["NumberOfProcessors"]);
//}
int coreCount = 0;
foreach (var item in new ManagementObjectSearcher("Select * from Win32_Processor").Get())
{
coreCount += int.Parse(item["NumberOfCores"].ToString());
}
//Console.WriteLine("Number Of Cores: {0}", coreCount);
//Console.WriteLine("Number Of Logical Processors: {0}", Environment.ProcessorCount);
int processorCount = Environment.ProcessorCount;
int logicalprocessorCount = 0;
foreach (var item in new ManagementObjectSearcher("Select * from Win32_ComputerSystem").Get())
{
//Console.WriteLine("Number Of Logical Processors: {0}", item["NumberOfLogicalProcessors"]);
logicalprocessorCount += int.Parse(item["NumberOfLogicalProcessors"].ToString());
}
int nThreads = coreCount; // zzz ? or logicalprocessorCount?
Thread[] oThread = null;
for (thread = 0; thread < nThreads; thread++)
{
Work w = new Work(thread, nThreads, rs, DSBdata);
ThreadStart threadDelegate = new ThreadStart(Work.DoWork);
oThread[thread] = new Thread(threadDelegate);
oThread[thread].Start();
}
}
return(true);
// zzz666 run subtask all the way here, so that every CPU would produce DSBdata for each own RW, which has 46/nCPU chromosomes; meaure time with and w/o parallelization
}
catch { return(false); }
}
public NASARTI_original(RadiationSchema rs)
{
amorphous_partile_tracks = new MainForm.Particle[rs.nBeams];
SimpleRNG.SetSeedFromSystemTime(); // setting seed from computer time
for (int nb = 0; nb < rs.nBeams; nb++) // iterate over all beams
{
amorphous_partile_tracks[nb] = new MainForm.Particle(rs.pt[nb])
{
track_struct = new MainForm.Particle.Tracks()
};
amorphous_partile_tracks[nb].track_struct.distance = new List <double>();
amorphous_partile_tracks[nb].track_struct.dose = new List <double>();
string appPath = Application.StartupPath;
string trackData;
string[] RDinput;
double LET;
double LET1;
double fraction_of_energy_lost = 0.0;
if (rs.pt[nb] == MainForm.Radiation.p_type.photon)
{
Dconst += rs.D[nb];
}
else
{
if (File.Exists(appPath + @"\RD\RD.dat"))
{
trackData = File.ReadAllText(appPath + @"\RD\RD.dat");
RDinput = trackData.Split((char[])null, StringSplitOptions.RemoveEmptyEntries);
// define particles with track properties
LET = Convert.ToDouble(RDinput[0]);
LET1 = Convert.ToDouble(RDinput[1]);
fraction_of_energy_lost = Convert.ToDouble(RDinput[2]);
Dconst += rs.D[nb] * fraction_of_energy_lost;
for (int i = 0; i < RDinput.Length - 3; i++)
{
switch (i % 5)
{
case 0:
{
amorphous_partile_tracks[nb].E = amorphous_partile_tracks[nb].track_struct.energy = Convert.ToInt32(Convert.ToDouble(RDinput[i + 3]));
}
break;
case 1:
{
amorphous_partile_tracks[nb].A = amorphous_partile_tracks[nb].track_struct.mass = Convert.ToInt32(Convert.ToDouble(RDinput[i + 3]));
}
break;
case 2:
{
amorphous_partile_tracks[nb].Z = amorphous_partile_tracks[nb].track_struct.charge = Convert.ToInt32(Convert.ToDouble(RDinput[i + 3]));
}
break;
case 3:
{
amorphous_partile_tracks[nb].track_struct.distance.Add(Convert.ToDouble(RDinput[i + 3]));
}
break;
case 4:
{
amorphous_partile_tracks[nb].track_struct.dose.Add(Convert.ToDouble(RDinput[i + 3]));
}
break;
default:
break;
}
}
string source = appPath + @"\RD\RD.dat";
string destination = appPath + @"\RD\RD_" + Convert.ToInt32(amorphous_partile_tracks[nb].track_struct.mass).ToString() + "_"
+ Convert.ToInt32(amorphous_partile_tracks[nb].track_struct.charge).ToString() + "_"
+ Convert.ToInt32(amorphous_partile_tracks[nb].track_struct.energy).ToString() + ".dat";
try
{
File.Copy(source, destination, true);
File.Delete(source);
}
catch
{
MessageBox.Show("File RD.dat with the amorphous track structure was not processed!");
}
}
else
{
try
{ // parse file name
trackData = File.ReadAllText(appPath + @"\RD\RD_" + Convert.ToInt32(amorphous_partile_tracks[nb].A).ToString() + "_"
+ Convert.ToInt32(amorphous_partile_tracks[nb].Z).ToString() + "_" + Convert.ToInt32(amorphous_partile_tracks[nb].E).ToString() + ".dat");
RDinput = trackData.Split((char[])null, StringSplitOptions.RemoveEmptyEntries);
// define particles with track properties
LET = Convert.ToDouble(RDinput[0]);
LET1 = Convert.ToDouble(RDinput[1]);
fraction_of_energy_lost = Convert.ToDouble(RDinput[2]);
Dconst += rs.D[nb] * fraction_of_energy_lost;
for (int i = 0; i < RDinput.Length - 3; i++)
{
switch (i % 5)
{
case 0:
{
amorphous_partile_tracks[nb].E = amorphous_partile_tracks[nb].track_struct.energy = Convert.ToInt32(Convert.ToDouble(RDinput[i + 3]));
}
break;
case 1:
{
amorphous_partile_tracks[nb].A = amorphous_partile_tracks[nb].track_struct.mass = Convert.ToInt32(Convert.ToDouble(RDinput[i + 3]));
}
break;
case 2:
{
amorphous_partile_tracks[nb].Z = amorphous_partile_tracks[nb].track_struct.charge = Convert.ToInt32(Convert.ToDouble(RDinput[i + 3]));
}
break;
case 3:
{
amorphous_partile_tracks[nb].track_struct.distance.Add(Convert.ToDouble(RDinput[i + 3]));
}
break;
case 4:
{
amorphous_partile_tracks[nb].track_struct.dose.Add(Convert.ToDouble(RDinput[i + 3]));
}
break;
default:
break;
}
}
amorphous_partile_tracks[nb].p_t = GetPtype(amorphous_partile_tracks[nb].A, amorphous_partile_tracks[nb].Z, amorphous_partile_tracks[nb].E);
amorphous_partile_tracks[nb].track_struct.X = new List <int>();
amorphous_partile_tracks[nb].track_struct.Y = new List <int>();
amorphous_partile_tracks[nb].lambda = rs.D[nb] / (LET * 1.6021 / 10.0) * (Math.PI * (R + RadiationSchema.Pr) * (R + RadiationSchema.Pr));
amorphous_partile_tracks[nb].nParticles = Convert.ToInt32(amorphous_partile_tracks[nb].lambda);
amorphous_partile_tracks[nb].track_struct.ntracks = SimpleRNG.GetPoisson(amorphous_partile_tracks[nb].lambda); // Poisson dist. ntracks
Random random = new Random();
for (int i = 0; i < amorphous_partile_tracks[nb].track_struct.ntracks; i++)
{
int cell_r = Convert.ToInt32(R / lattice_dim);
amorphous_partile_tracks[nb].track_struct.X.Add(random.Next(0, 2 * cell_r) - cell_r);
amorphous_partile_tracks[nb].track_struct.Y.Add(random.Next(0, 2 * cell_r) - cell_r);
}
}
catch
{
MessageBox.Show("Input file with the radial dose could not be found!");
}
}
}
}
}
//
public void Do()
{
RadiationSchema rs = new RadiationSchema();
MonteCarloSimlation(rs);
}
public readonly double sigma2 = 2.0e3; // get it from fits to the experiment; sigma2 parameter in the distance exp.
//
public TimeOperator()
{
rs = new RadiationSchema();
DNAbreakage = new NASARTI_original(rs);
DSBdata = new DSBs();
}
