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added this prefixes and cleaned up appearence
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@CodeByDrescher
CodeByDrescher committed Jan 26, 2024
1 parent 7be1b2d commit 495b57f
Showing 1 changed file with 48 additions and 57 deletions.
105 changes: 48 additions & 57 deletions Stochastic/VCellStoch/src/Gibson.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -570,8 +570,7 @@ int Gibson::finalizeSampleRow(int savedSampleCount,double simtime){
/*
*This method is the control of trials, which will be called for Gibson simulation.
*/
void Gibson::march()
{
void Gibson::march(){
#ifdef DEBUG
// Count performance time in milliseconds for the simulation
int ntime=0;
Expand All @@ -582,87 +581,81 @@ void Gibson::march()
#endif

//prepare for writing the results to output file
outfile.open (outfilename);//"c:/gibson_deploy/gibson_deploy/output/gibson_singleTrial.txt"
outfile << setprecision(10); // set precision to output file
if(bMultiButNotHisto)
{
this->outfile.open (this->outfilename, ofstream::out);//"c:/gibson_deploy/gibson_deploy/output/gibson_singleTrial.txt"
this->outfile << setprecision(10); // set precision to output file
if(this->bMultiButNotHisto){
// char thebyte[1];
// thebyte[0]=49;//progress char "1"
// string ofProg(outfilename);
// ofProg.append("_progress");
// ofstream outfileProg;
// outfileProg.open (ofProg.c_str(),ios::out | ios::app | ios::binary);

numMultiNonHisto = NUM_TRIAL;
NUM_TRIAL = 1;//set to 1 to use single trajectory logic in 'core'
this->numMultiNonHisto = this->NUM_TRIAL;
this->NUM_TRIAL = 1;//set to 1 to use single trajectory logic in 'core'

//output file header description for time and variable names
outfile << "t:";
for (int i = 0; i < listOfVarNames.size(); i++) {
outfile << listOfVarNames.at(i) << ":";
this->outfile << "t:";
for (const auto & varName : this->listOfVarNames) {
this->outfile << varName << ":";
}
outfile << endl;
this->outfile << endl;

//Execute NUM_TRIALS of core and accumulate the results
for (currMultiNonHistoIter=0; currMultiNonHistoIter < numMultiNonHisto; currMultiNonHistoIter++)
{
generator->seed(currMultiNonHistoIter+SEED);
for (this->currMultiNonHistoIter = 0; this->currMultiNonHistoIter < this->numMultiNonHisto; this->currMultiNonHistoIter++){
this->generator->seed(this->currMultiNonHistoIter+SEED);
//run the simulation
core();
this->core();
//reset to initial values before next simulation
savedSampleCount = 1;
for(int i=0;i<listOfIniValues.size();i++){
listOfVars[i]->setCurr(listOfIniValues.at(i));
this->savedSampleCount = 1;
for(int i = 0; i < this->listOfIniValues.size(); i++){
this->listOfVars[i]->setCurr(this->listOfIniValues.at(i));
}
for(int i=0;i<listOfProcesses.size();i++){
Tree->setProcess(i,listOfProcesses.at(i));
for(int i = 0; i < this->listOfProcesses.size(); i++){
this->Tree->setProcess(i, this->listOfProcesses.at(i));
}
// outfileProg.write((char *)&thebyte,1);
// outfileProg.flush();
}
// outfileProg.close();

//Calc and save averages of accumulated data
for (int timeIndex = 0; timeIndex < multiTrialStats->getNumTimePoints(); ++timeIndex) {
for (int timeIndex = 0; timeIndex < this->multiTrialStats->getNumTimePoints(); ++timeIndex) {
//timepoint
outfile << multiTrialStats->getTimePoint(timeIndex) << "\t";
for (int varIndex = 0; varIndex < multiTrialStats->getNumVars(); ++varIndex) {
outfile << multiTrialStats->getMean(varIndex, timeIndex) << "\t";
this->outfile << this->multiTrialStats->getTimePoint(timeIndex) << "\t";
for (int varIndex = 0; varIndex < this->multiTrialStats->getNumVars(); ++varIndex) {
this->outfile << this->multiTrialStats->getMean(varIndex, timeIndex) << "\t";
}
outfile << endl;
this->outfile << endl;
}

multiTrialStats->writeHDF5(outfilename, listOfVarNames);
this->multiTrialStats->writeHDF5(this->outfilename, this->listOfVarNames);

}
else if(NUM_TRIAL==1)
{
generator->seed(SEED);
} else if(this->NUM_TRIAL==1){
this->generator->seed(this->SEED);
//output file header
outfile << "t:";
for(int i=0;i<listOfVarNames.size();i++){
outfile<< listOfVarNames.at(i) << ":";
this->outfile << "t:";
for(const auto & listOfVarName : this->listOfVarNames){
this->outfile << listOfVarName << ":";
}
outfile <<endl;
this->outfile << endl;
//output initial condition at STARTING_TIME
outfile << STARTING_TIME << "\t";
for(int i=0;i<listOfIniValues.size();i++){
outfile<< listOfIniValues.at(i) << "\t";
this->outfile << this->STARTING_TIME << "\t";
for(const unsigned long long listOfIniValue : this->listOfIniValues){
this->outfile << listOfIniValue << "\t";
}
outfile << endl;
//run the simulation
core();

}
else if (NUM_TRIAL > 1)
{
} else if (this->NUM_TRIAL > 1){
//output file header
outfile << "TrialNo:";
for(int i=0;i<listOfVarNames.size();i++){
outfile<< listOfVarNames.at(i) << ":";
this->outfile << "TrialNo:";
for(const auto & listOfVarName : this->listOfVarNames){
this->outfile<< listOfVarName << ":";
}
outfile <<endl;
for (long j=SEED;j<NUM_TRIAL+SEED;j++)
this->outfile << endl;
for (long j = this->SEED; j < this->NUM_TRIAL + this->SEED; j++)
{
#ifdef USE_MESSAGING
if (SimulationMessaging::getInstVar()->isStopRequested()) {
Expand All @@ -673,21 +666,19 @@ void Gibson::march()
#ifdef DEBUG
cout << "Trial No. " << j <<endl;
#endif
generator->seed(j);
this->generator->seed(j);
//output trial number. PS:results after each trial are printed in core() function.
outfile << j-SEED+1;//this expression should evaluate equal to 'savedSampleCount'
core();//this will save 1 row of data (
this->outfile << j - this->SEED + 1;//this expression should evaluate equal to 'savedSampleCount'
this->core();//this will save 1 row of data (
//reset to initial values before next simulation
for(int i=0;i<listOfIniValues.size();i++){
listOfVars[i]->setCurr(listOfIniValues.at(i));
for(int i=0; i < this->listOfIniValues.size();i++){
this->listOfVars[i]->setCurr(this->listOfIniValues.at(i));
}
for(int i=0;i<listOfProcesses.size();i++){
Tree->setProcess(i,listOfProcesses.at(i));
for(int i=0;i < this->listOfProcesses.size();i++){
this->Tree->setProcess(i, this->listOfProcesses.at(i));
}
}
}
else
{
} else {
VCELL_EXCEPTION(invalid_argument, "Number of trial smaller than 1!");
}
#ifdef DEBUG
Expand All @@ -697,7 +688,7 @@ void Gibson::march()
ntime = (ntime2.QuadPart-ntime1.QuadPart)/(freq.QuadPart/1000);
cout << endl << "Total time used(ms): " << ntime;
#endif
outfile.close();
this->outfile.close();

#ifdef USE_MESSAGING
if (!SimulationMessaging::getInstVar()->isStopRequested()) {
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