--- trunk/src/applications/randomBuilder/randomBuilder.cpp 2010/05/10 17:28:26 1442 +++ trunk/src/applications/randomBuilder/randomBuilder.cpp 2014/03/13 13:03:11 1978 @@ -34,10 +34,10 @@ * * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). - * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). - * [4] Vardeman & Gezelter, in progress (2009). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * * - * * randomBuilder.cpp * * Created by Charles F. Vardeman II on 10 Apr 2006. @@ -77,8 +77,6 @@ int main(int argc, char *argv []) { int main(int argc, char *argv []) { - // register force fields - registerForceFields(); registerLattice(); gengetopt_args_info args_info; @@ -233,8 +231,8 @@ int main(int argc, char *argv []) { for (int i=0; i < nComponents; i++) { molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; totalMolecules += nMol.at(i); - molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i), - oldInfo->getForceField())); + molecularMasses.push_back(MoLocator::getMolMass(oldInfo->getMoleculeStamp(i), + oldInfo->getForceField())); totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i); } RealType avgMass = totalMass / (RealType) totalMolecules; @@ -285,8 +283,7 @@ int main(int argc, char *argv []) { createMdFile(inputFileName, outputFileName, nMol); - if (oldInfo != NULL) - delete oldInfo; + delete oldInfo; // We need to read in the new SimInfo object, then Parse the // md file and set up the system @@ -317,7 +314,7 @@ int main(int argc, char *argv []) { // Randomize a vector of ints: vector ids; - for (int i = 0; i < sites.size(); i++) ids.push_back(i); + for (unsigned int i = 0; i < sites.size(); i++) ids.push_back(i); std::random_shuffle(ids.begin(), ids.end()); Molecule* mol; @@ -351,6 +348,7 @@ int main(int argc, char *argv []) { sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " "generated.\n", outputFileName.c_str()); painCave.isFatal = 0; + painCave.severity = OPENMD_INFO; simError(); return 0; } @@ -370,12 +368,12 @@ void createMdFile(const std::string&oldMdFileName, oldMdFile.getline(buffer, MAXLEN); - int i = 0; + unsigned int i = 0; while (!oldMdFile.eof()) { //correct molecule number if (strstr(buffer, "nMol") != NULL) { - if(i