--- trunk/src/applications/dynamicProps/DynamicProps.cpp 2012/08/22 02:28:28 1782 +++ trunk/src/applications/dynamicProps/DynamicProps.cpp 2013/10/29 16:02:58 1937 @@ -35,7 +35,7 @@ * * [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). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ @@ -50,10 +50,12 @@ #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" #include "applications/dynamicProps/LegendreCorrFunc.hpp" +#include "applications/dynamicProps/LegendreCorrFuncZ.hpp" #include "applications/dynamicProps/RadialRCorrFunc.hpp" #include "applications/dynamicProps/ThetaCorrFunc.hpp" #include "applications/dynamicProps/DirectionalRCorrFunc.hpp" @@ -61,9 +63,8 @@ #include "applications/dynamicProps/StressCorrFunc.hpp" #include "applications/dynamicProps/SystemDipoleCorrFunc.hpp" #include "applications/dynamicProps/MomentumCorrFunc.hpp" +#include "applications/dynamicProps/cOHz.hpp" - - using namespace OpenMD; int main(int argc, char* argv[]){ @@ -75,35 +76,38 @@ int main(int argc, char* argv[]){ exit(1) ; } - //get the dumpfile name and meta-data file name std::string dumpFileName = args_info.input_arg; std::string sele1; std::string sele2; - + + // check the first selection argument, or set it to the environment + // variable, or failing that, set it to "select all" + if (args_info.sele1_given) { sele1 = args_info.sele1_arg; - }else { + } else { char* sele1Env= getenv("SELECTION1"); if (sele1Env) { sele1 = sele1Env; - }else { - sprintf( painCave.errMsg, - "neither --sele1 option nor $SELECTION1 is set"); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); + } else { + sele1 = "select all"; } } - + + // check the second selection argument, or set it to the environment + // variable, or failing that, set it to the first selection + if (args_info.sele2_given) { sele2 = args_info.sele2_arg; - }else { + } else { char* sele2Env = getenv("SELECTION2"); if (sele2Env) { sele2 = sele2Env; - } else { + } else { + //If sele2 is not specified, then the default behavior + //should be what is already intended for sele1 sele2 = sele1; } } @@ -121,10 +125,11 @@ int main(int argc, char* argv[]){ 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) { @@ -149,15 +154,44 @@ int main(int argc, char* argv[]){ order = args_info.order_arg; else { sprintf( painCave.errMsg, - "--order must be set if --lcoor is set\n"); + "--order must be set if --lcorr is set\n"); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); + } else if (args_info.lcorrZ_given) { + int order; + if (args_info.order_given) + order = args_info.order_arg; + else { + sprintf( painCave.errMsg, + "--order must be set if --lcorrZ is set\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + + corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); + + } else if (args_info.cohZ_given) { + int order; + if (args_info.order_given) + order = args_info.order_arg; + else { + sprintf( painCave.errMsg, + "--order must be set if --cohZ is set\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + + corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); + } + if (args_info.output_given) { corrFunc->setOutputName(args_info.output_arg); }