--- trunk/src/applications/dynamicProps/DynamicProps.cpp 2011/08/26 17:55:44 1615 +++ trunk/src/applications/dynamicProps/DynamicProps.cpp 2012/11/16 15:12:21 1811 @@ -36,20 +36,21 @@ * [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). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include #include #include -#include "brains/Register.hpp" #include "brains/SimCreator.hpp" #include "brains/SimInfo.hpp" #include "utils/StringUtils.hpp" #include "utils/simError.h" #include "applications/dynamicProps/DynamicPropsCmd.h" +#include "applications/dynamicProps/SelectionCorrFunc.hpp" #include "applications/dynamicProps/DipoleCorrFunc.hpp" #include "applications/dynamicProps/RCorrFunc.hpp" #include "applications/dynamicProps/VCorrFunc.hpp" @@ -62,14 +63,10 @@ #include "applications/dynamicProps/SystemDipoleCorrFunc.hpp" #include "applications/dynamicProps/MomentumCorrFunc.hpp" - using namespace OpenMD; int main(int argc, char* argv[]){ - //register force fields - registerForceFields(); - gengetopt_args_info args_info; //parse the command line option @@ -101,7 +98,7 @@ int main(int argc, char* argv[]){ if (args_info.sele2_given) { sele2 = args_info.sele2_arg; - }else { + } else { char* sele2Env = getenv("SELECTION2"); if (sele2Env) { sele2 = sele2Env; @@ -117,16 +114,17 @@ int main(int argc, char* argv[]){ "Amount of memory being used: %llu bytes\n", memSize); painCave.severity = OPENMD_INFO; painCave.isFatal = 0; - simError(); - + simError(); + //parse md file and set up the system SimCreator creator; SimInfo* info = creator.createSim(dumpFileName, false); - TimeCorrFunc* corrFunc; if(args_info.sdcorr_given){ corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); + } else if (args_info.selecorr_given){ + corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize); } else if (args_info.dcorr_given){ corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); } else if (args_info.rcorr_given) {