--- trunk/src/applications/dynamicProps/DynamicProps.cpp 2005/04/15 22:04:00 507 +++ trunk/src/applications/dynamicProps/DynamicProps.cpp 2015/03/07 21:41:51 2071 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,29 +28,49 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [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, 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" +#include "applications/dynamicProps/EnergyCorrFunc.hpp" +#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 oopse; +using namespace OpenMD; int main(int argc, char* argv[]){ - //register force fields - registerForceFields(); - gengetopt_args_info args_info; //parse the command line option @@ -67,57 +78,135 @@ 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 mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md"; - 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 { - char* sele1Env= getenv("OOPSE_SELE1"); + } else { + char* sele1Env= getenv("SELECTION1"); if (sele1Env) { sele1 = sele1Env; - }else { - sprintf( painCave.errMsg, - "neither --sele1 option nor $OOPSE_SELE1 is set"); - painCave.severity = OOPSE_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("OOPSE_SELE2"); + } 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; } } + // use the memory string to figure out how much memory we can use: + char *end; + long long int memSize = memparse(args_info.memory_arg, &end); + sprintf( painCave.errMsg, + "Amount of memory being used: %llu bytes\n", memSize); + painCave.severity = OPENMD_INFO; + painCave.isFatal = 0; + simError(); + //parse md file and set up the system SimCreator creator; - SimInfo* info = creator.createSim(mdFileName, false); + SimInfo* info = creator.createSim(dumpFileName, false); - - TimeCorrFunc* corrFunc; - if (args_info.dcorr_given){ - corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2); + TimeCorrFunc* corrFunc = NULL; + 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) { - corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2); + corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize); + } else if (args_info.r_rcorr_given) { + corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize); + } 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); + } 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(0); + if (args_info.order_given) + order = args_info.order_arg; + else { + sprintf( painCave.errMsg, + "--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(0); + 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(0); + 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); + } - else if (args_info.vcorr_given) { - corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2); - } + if (args_info.output_given) { corrFunc->setOutputName(args_info.output_arg); }