std::string ParserMgr::AnnotateErrMsg(const std::string& err_mesg, const mu::Parser& parser) const { #ifdef DEBUG_PM_FUNC ScopeTracker st("ParserMgr::AnnotateErrMsg", std::this_thread::get_id()); #endif const char* pos_str = "position "; size_t pos = err_mesg.find(pos_str); if (pos!=std::string::npos) { size_t spc = err_mesg.find_first_of(' ', pos); std::string s = err_mesg.substr(spc); int errpos = std::stoi(s); std::string pstr = parser.GetExpr(); std::string small = "..." + pstr.substr(errpos, 20) + "..."; return err_mesg + " " + small; } return err_mesg; }
int Network3::run_PLA(double& time, double maxTime, double sampleTime, double& step, double maxStep, double stepInterval, mu::Parser& stop_condition, bool print_on_stop, char* prefix, bool print_cdat, bool print_func, bool print_save_net, bool print_end_net, bool additional_pla_output, bool verbose){ // Output files string outpre(prefix); bool print_classif = additional_pla_output; // ... // Species file (must exist) FILE* cdat = NULL; string cFile = outpre + ".cdat"; if ((cdat = fopen(cFile.c_str(),"r"))){ fclose(cdat); cdat = fopen(cFile.c_str(),"a"); } else { cout << "Error in Network3::run_PLA(): Concentrations file \"" << cFile << "\" doesn't exist. Exiting." << endl; exit(1); } // Observables file (optional) FILE* gdat = NULL; string gFile = outpre + ".gdat"; if ((gdat = fopen(gFile.c_str(),"r"))){ fclose(gdat); gdat = fopen(gFile.c_str(),"a"); } else{ // cout << "Warning: Groups file \"" << gFile << "\" doesn't exist." << endl; } // Functions file (optional) /* FILE* fdat = NULL; string fFile = outpre + ".fdat"; if ((fdat = fopen(fFile.c_str(),"r"))){ fclose(fdat); fdat = fopen(fFile.c_str(),"a"); } else{ // cout << "Warning: Functions file \"" << fFile << "\" doesn't exist." << endl; }*/ // PLA-specific output files FILE* classif = NULL; if (print_classif){ if ((classif = fopen((outpre+"_classif.pla").c_str(),"r"))){ fclose(classif); classif = fopen((outpre+"_classif.pla").c_str(),"a"); } else{ cout << "Error in Network3::run_PLA(): 'print_classif' flag set but classifications file \"" << (outpre+"_classif.pla") << "\" doesn't exist. Exiting." << endl; exit(1); } } // ... // Identify observables involved in functions vector<unsigned int> funcObs; for (unsigned int i=0;i < FUNCTION.size();i++){ map<string,double*> var = FUNCTION[i]->first->p->GetUsedVar(); for (unsigned int j=0;j < OBSERVABLE.size();j++){ if (var.find(OBSERVABLE[j]->first->name) != var.end()){ bool already = false; for (unsigned int k=0;k < funcObs.size() && !already;k++){ if (funcObs[k] == j){ already = true; } } if (!already){ // add to the list funcObs.push_back(j); } } } } // Prepare for simulation double nextOutputTime = time + sampleTime; double nextOutputStep = stepInterval; while (nextOutputStep <= step) nextOutputStep += stepInterval; bool lastOut = true; // Simulation loop // PLA_SIM->rc.forceClassifications(RxnClassifier::EXACT_STOCHASTIC); string print_net_message; while (time < maxTime && step < maxStep && !stop_condition.Eval()) { // Next step step++; PLA_SIM->nextStep(); if (PLA_SIM->tau < INFINITY && PLA_SIM->tau > -INFINITY){ time += PLA_SIM->tau; } else break; // Error check if (PLA_SIM->tau <= 0.0){ cout << "Error in Network3::run_PLA(): tau = " << PLA_SIM->tau << ". Shouldn't happen. Exiting." << endl; exit(1); } // Is it time to output? lastOut = false; if (time >= nextOutputTime || step >= nextOutputStep) // YES { // Update all observables for (unsigned int i=0;i < OBSERVABLE.size();i++){ OBSERVABLE[i]->second = OBSERVABLE[i]->first->getValue(); } // Update all functions for (unsigned int i=0;i < FUNCTION.size();i++){ FUNCTION[i]->second = FUNCTION[i]->first->Eval(); } // Output to file if (print_cdat) Network3::print_species_concentrations(cdat,time); if (gdat) Network3::print_observable_concentrations(gdat,time,print_func); if (print_func) Network3::print_function_values(gdat,time); if (print_save_net){ // Write current system state to .net file // Collect species populations and update network concentrations vector double* pops = new double[SPECIES.size()]; for (unsigned int j=0;j < SPECIES.size();j++){ pops[j] = SPECIES[j]->population; } set_conc_network(pops); delete pops; // Print network w/ current species populations using network::print_network() char buf[1000]; sprintf(buf, "%s_save.net", prefix); FILE* out = fopen(buf, "w"); print_network(out); fclose(out); print_net_message = " Wrote NET file to " + (string)buf; // fprintf(stdout, " Wrote NET file to %s", buf); } if (print_classif){ fprintf(classif,"%19.12e",time); fprintf(classif," %19.19g",step); for (unsigned int v=0;v < PLA_SIM->classif.size();v++){ fprintf(classif, " %10d", PLA_SIM->classif[v]); } fprintf(classif,"\n"); fflush(classif); } // Output to stdout if (verbose){ cout << "\t" << fixed << setprecision(6) << time << "\t" << setprecision(0) << step; // for (unsigned int i=0;i < OBSERVABLE.size();i++){ // cout << "\t" << OBSERVABLE[i]->second; // } if (print_save_net){ fprintf(stdout, "%s", print_net_message.c_str()); } cout << endl; } // Get next output time and step if (time >= nextOutputTime) nextOutputTime += sampleTime; if (step >= nextOutputStep) nextOutputStep += stepInterval; lastOut = true; } else{ // NO // Only update observables that are involved in functions for (unsigned int i=0;i < funcObs.size();i++){ OBSERVABLE[funcObs[i]]->second = OBSERVABLE[funcObs[i]]->first->getValue(); } // Update all functions for (unsigned int i=0;i < FUNCTION.size();i++){ FUNCTION[i]->second = FUNCTION[i]->first->Eval(); } } } // Final output if (!lastOut) { // Update all observables for (unsigned int i=0;i < OBSERVABLE.size();i++){ OBSERVABLE[i]->second = OBSERVABLE[i]->first->getValue(); } // Update all functions for (unsigned int i=0;i < FUNCTION.size();i++){ FUNCTION[i]->second = FUNCTION[i]->first->Eval(); } // Output to file if (print_cdat) Network3::print_species_concentrations(cdat,time); // Don't print if stopping condition met and !print_on_stop (must print to CDAT) if (!(stop_condition.Eval() && !print_on_stop)){ if (gdat) Network3::print_observable_concentrations(gdat,time,print_func); if (print_func) Network3::print_function_values(gdat,time); string print_net_message; if (print_save_net){ // Write current system state to .net file // Collect species populations and update network concentrations vector double pops[SPECIES.size()]; for (unsigned int j=0;j < SPECIES.size();j++){ pops[j] = SPECIES[j]->population; } set_conc_network(pops); // Print network w/ current species populations using network::print_network() char buf[1000]; sprintf(buf, "%s_save.net", prefix); FILE* out = fopen(buf, "w"); print_network(out); fclose(out); print_net_message = " Wrote NET file to " + (string)buf; } if (print_classif){ fprintf(classif,"%19.12e",time); for (unsigned int v=0;v < PLA_SIM->classif.size();v++){ fprintf(classif, " %10d", PLA_SIM->classif[v]); } fprintf(classif,"\n"); fflush(classif); } } // Output to stdout if (verbose){ cout << "\t" << fixed << setprecision(6) << time << "\t" << setprecision(0) << step; // for (unsigned int i=0;i < OBSERVABLE.size();i++) cout << "\t" << OBSERVABLE[i]->second; if (print_save_net) fprintf(stdout, "%s", print_net_message.c_str()); cout << endl; } } // Messages if stopping conditions met if (stop_condition.Eval()){ // Stop condition satisfied cout << "Stopping condition " << stop_condition.GetExpr() << "met in PLA simulation." << endl; } // else if (step >= startStep + maxSteps){ // maxSteps limit reached // cout << "Maximum step limit (" << maxSteps << ") reached in PLA simulation." << endl; // } // If print_end_net = true, collect species populations and update network concentrations vector if (print_end_net){ double pops[SPECIES.size()]; for (unsigned int j=0;j < SPECIES.size();j++){ pops[j] = SPECIES[j]->population; } set_conc_network(pops); } // Close files fclose(cdat); if (gdat) fclose(gdat); // if (fdat) fclose(fdat); if (classif) fclose(classif); // Return value if (time >= maxTime) return 0; else if (step >= maxStep) return -1; else return -2; // stop condition met }