--- trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp 2004/07/29 03:31:50 1432 +++ trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp 2004/07/29 19:12:00 1436 @@ -31,9 +31,7 @@ int main( int argc, char* argv[]){ string outMdFileName; string outInitFileName; SimInfo* oldInfo; - SimInfo* newInfo; SimSetup* oldSimSetup; - SimSetup* newSimSetup; BaseLattice* simpleLat; int numMol; double latticeConstant; @@ -53,24 +51,9 @@ int main( int argc, char* argv[]){ // parse command line arguments if (cmdline_parser (argc, argv, &args_info) != 0) exit(1) ; + + density = args_info.density_arg; - //process density - if(!args_info.density_given && !args_info.ndensity_given){ - cerr << "SimpleBuilder Error: density or number density must be given" << endl; - cmdline_parser_print_help(); - exit(1); - } - else if(args_info.density_given){ - if( args_info.ndensity_given) - cerr << "SimpleBuilder Warning: both of density and number density are given, use density" << endl; - - density = args_info.density_arg; - } - else if(args_info.ndensity_given){ - //convert number density to density - } - - //get lattice type latticeType = UpperCase(args_info.latticetype_arg); if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){ @@ -107,17 +90,7 @@ int main( int argc, char* argv[]){ exit(1); } - //determine the output file names - if (args_info.output_given){ - outPrefix = args_info.output_arg; - } - else - outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; - - outMdFileName = outPrefix + ".md"; - outInitFileName = outPrefix + ".in"; - //parse md file and set up the system oldInfo = new SimInfo; if(oldInfo == NULL){ @@ -130,15 +103,16 @@ int main( int argc, char* argv[]){ cerr << "error in creating SimSetup" << endl; exit(1); } - + + oldSimSetup->suspendInit(); oldSimSetup->setSimInfo(oldInfo ); oldSimSetup->parseFile(&inputFileName[0] ); oldSimSetup->createSim(); + if(oldInfo->nComponents >=2){ cerr << "can not build the system with more than two components" << endl; exit(1); } - //get mass of molecule. //Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass @@ -161,51 +135,50 @@ int main( int argc, char* argv[]){ simpleLat->setLatticeConstant(lc); //calculate the total number of molecules - numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell; - - //creat new .md file on fly - createMdFile(inputFileName, outMdFileName, numMol); + numMol = nx * ny * nz * numMolPerCell; - //parse new .md file and set up the system - newInfo = new SimInfo; - if(newInfo == NULL){ - cerr << "error in creating SimInfo" << endl; - exit(1); - } - - newSimSetup = new SimSetup(); - if(newSimSetup == NULL){ - cerr << "error in creating SimSetup" << endl; - exit(1); - } - - newSimSetup->setSimInfo(newInfo ); - newSimSetup->parseFile(&outMdFileName[0] ); - newSimSetup->createSim(); + if (oldInfo->n_mol != numMol){ + outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; + outMdFileName = outPrefix + ".md"; + + //creat new .md file on fly which corrects the number of molecule + createMdFile(inputFileName, outMdFileName, numMol); + cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <getConfiguration()->createArrays(newInfo->n_atoms); - for (int i = 0; i < newInfo->n_atoms; i++) - newInfo->atoms[i]->setCoords(); + oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms); + for (int i = 0; i < oldInfo->n_atoms; i++) + oldInfo->atoms[i]->setCoords(); //creat Molocator - locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField()); + locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField()); //fill Hmat Hmat[0][0] = nx * latticeConstant; Hmat[0][1] = 0.0; Hmat[0][2] = 0.0; - Hmat[1][0] = ny * latticeConstant; - Hmat[1][1] = 0.0; + Hmat[1][0] = 0.0; + Hmat[1][1] = ny * latticeConstant; Hmat[1][2] = 0.0; - Hmat[2][0] = nz * latticeConstant; + Hmat[2][0] = 0.0; Hmat[2][1] = 0.0; - Hmat[2][2] = 0.0; + Hmat[2][2] = nz * latticeConstant ; //set Hmat - newInfo->setBoxM(Hmat); + oldInfo->setBoxM(Hmat); //place the molecules @@ -223,32 +196,29 @@ int main( int argc, char* argv[]){ simpleLat->getLatticePointsPos(latticePos, i, j, k); for(int l = 0; l < numMolPerCell; l++) - locator->placeMol(latticePos[l], latticeOrt[l], &(newInfo->molecules[curMolIndex++])); + locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++])); } } } //create dumpwriter and write out the coordinates - writer = new DumpWriter( newInfo ); + oldInfo->finalName = outInitFileName; + writer = new DumpWriter( oldInfo ); if(writer == NULL){ cerr << "error in creating DumpWriter" << endl; exit(1); } writer->writeFinal(0); - + cout << "new initial configuration file: " << outInitFileName <<" is generated." << endl; //delete objects - if(!oldInfo) + + //delete oldInfo and oldSimSetup + if(oldInfo != NULL) delete oldInfo; - if(!oldSimSetup) - delete oldSimSetup; - - if(!newInfo) - delete newInfo; + if(oldSimSetup != NULL) + delete oldSimSetup; - if(!newSimSetup) - delete newSimSetup; - if (writer != NULL) delete writer; return 0; @@ -259,7 +229,6 @@ void createMdFile(const string& oldMdFileName, const s ofstream newMdFile; const int MAXLEN = 65535; char buffer[MAXLEN]; - string line; //create new .md file based on old .md file oldMdFile.open(oldMdFileName.c_str()); @@ -268,8 +237,8 @@ void createMdFile(const string& oldMdFileName, const s oldMdFile.getline(buffer, MAXLEN); while(!oldMdFile.eof()){ - if(line.find("nMol") < line.size()){ - + //correct molecule number + if(strstr(buffer, "nMol") !=NULL){ sprintf(buffer, "\t\tnMol = %d;", numMol); newMdFile << buffer << endl; }