--- trunk/src/applications/dynamicProps/DynamicProps.cpp 2013/08/26 14:15:09 1934 +++ trunk/src/applications/dynamicProps/DynamicProps.cpp 2015/03/07 21:41:51 2071 @@ -64,6 +64,8 @@ #include "applications/dynamicProps/SystemDipoleCorrFunc.hpp" #include "applications/dynamicProps/MomentumCorrFunc.hpp" #include "applications/dynamicProps/cOHz.hpp" +#include "applications/dynamicProps/BondCorrFunc.hpp" +#include "applications/dynamicProps/FreqFlucCorrFunc.hpp" using namespace OpenMD; @@ -76,35 +78,38 @@ 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 { 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; } } @@ -122,9 +127,10 @@ int main(int argc, char* argv[]){ SimCreator creator; SimInfo* info = creator.createSim(dumpFileName, false); - TimeCorrFunc* corrFunc; + TimeCorrFunc* corrFunc = NULL; if(args_info.sdcorr_given){ - corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); + 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){ @@ -136,17 +142,26 @@ int main(int argc, char* argv[]){ } else if (args_info.thetacorr_given) { corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize); } else if (args_info.drcorr_given) { - corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize); + corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, + memSize); } else if (args_info.vcorr_given) { corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize); + } else if (args_info.vcorrZ_given) { + corrFunc = new VCorrFuncZ(info, dumpFileName, sele1, sele2, memSize); + } else if (args_info.vcorrR_given) { + corrFunc = new VCorrFuncR(info, dumpFileName, sele1, sele2, memSize); + } else if (args_info.bondcorr_given) { + corrFunc = new BondCorrFunc(info, dumpFileName, sele1, memSize); } else if (args_info.helfandEcorr_given){ corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize); } else if (args_info.stresscorr_given){ corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize); } else if (args_info.momentum_given){ corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize); + } else if (args_info.freqfluccorr_given){ + corrFunc = new FreqFlucCorrFunc(info, dumpFileName, sele1, sele2, memSize); } else if (args_info.lcorr_given) { - int order; + int order(0); if (args_info.order_given) order = args_info.order_arg; else { @@ -157,9 +172,10 @@ int main(int argc, char* argv[]){ simError(); } - corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); + corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, + memSize); } else if (args_info.lcorrZ_given) { - int order; + int order(0); if (args_info.order_given) order = args_info.order_arg; else { @@ -170,10 +186,11 @@ int main(int argc, char* argv[]){ simError(); } - corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); + corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, + args_info.nzbins_arg, memSize); } else if (args_info.cohZ_given) { - int order; + int order(0); if (args_info.order_given) order = args_info.order_arg; else { @@ -184,12 +201,12 @@ int main(int argc, char* argv[]){ simError(); } - corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); + corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, + args_info.nzbins_arg, memSize); } - if (args_info.output_given) { corrFunc->setOutputName(args_info.output_arg); }