--- trunk/src/applications/dynamicProps/DynamicProps.cpp 2011/08/26 17:55:44 1615 +++ trunk/src/applications/dynamicProps/DynamicProps.cpp 2014/06/01 19:28:44 2003 @@ -35,25 +35,27 @@ * * [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). + * [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" #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" @@ -61,15 +63,14 @@ #include "applications/dynamicProps/StressCorrFunc.hpp" #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; int main(int argc, char* argv[]){ - //register force fields - registerForceFields(); - gengetopt_args_info args_info; //parse the command line option @@ -77,35 +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 { + } 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; } } @@ -117,16 +121,17 @@ 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) { @@ -139,27 +144,60 @@ int main(int argc, char* argv[]){ 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.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; if (args_info.order_given) 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); }