--- trunk/src/applications/staticProps/StaticProps.cpp 2011/06/19 17:51:15 1585 +++ trunk/src/applications/staticProps/StaticProps.cpp 2014/04/30 18:50:45 1994 @@ -35,15 +35,15 @@ * * [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 "io/DumpReader.hpp" @@ -75,15 +75,15 @@ #endif #include "applications/staticProps/RhoR.hpp" #include "applications/staticProps/AngleR.hpp" -#include "applications/staticProps/RhoAngleR.hpp" #include "applications/staticProps/TetrahedralityParam.hpp" +#include "applications/staticProps/TetrahedralityParamZ.hpp" +#include "applications/staticProps/RNEMDStats.hpp" +#include "applications/staticProps/NitrileFrequencyMap.hpp" using namespace OpenMD; int main(int argc, char* argv[]){ - //register force fields - registerForceFields(); gengetopt_args_info args_info; @@ -96,8 +96,6 @@ int main(int argc, char* argv[]){ std::string dumpFileName = args_info.input_arg; std::string sele1; std::string sele2; - bool userSpecifiedSelect1; - bool userSpecifiedSelect2; // check the first selection argument, or set it to the environment // variable, or failing that, set it to "select all" @@ -114,47 +112,30 @@ int main(int argc, char* argv[]){ } // check the second selection argument, or set it to the environment - // variable, or failing that, set it to "select all" + // variable, or failing that, set it to the first selection if (args_info.sele2_given) { sele2 = args_info.sele2_arg; } else { - char* sele2Env = getenv("SELECTION1"); + char* sele2Env = getenv("SELECTION2"); if (sele2Env) { sele2 = sele2Env; } else { - sele2 = "select all"; + //If sele2 is not specified, then the default behavior + //should be what is already intended for sele1 + sele2 = sele1; } } - - - // Problems if sele1 wasn't specified, but - // if (!args_info.scd_given) { - // sprintf( painCave.errMsg, - // "neither --sele1 option nor $SELECTION1 is set"); - // painCave.severity = OPENMD_ERROR; - // painCave.isFatal = 1; - // simError(); - // } - // } - - // Problems if sele1 wasn't specified - - // if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) { - // sprintf( painCave.errMsg, - // "neither --sele2 option nor $SELECTION1 is set"); - // painCave.severity = OPENMD_ERROR; - // painCave.isFatal = 1; - // simError(); - // } - // } - + bool batchMode; if (args_info.scd_given){ - if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) { + if (args_info.sele1_given && + args_info.sele2_given && args_info.sele3_given) { batchMode = false; - } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) { - if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) { + } else if (args_info.molname_given && + args_info.begin_given && args_info.end_given) { + if (args_info.begin_arg < 0 || + args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) { sprintf( painCave.errMsg, "below conditions are not satisfied:\n" "0 <= begin && 0<= end && begin <= end-2\n"); @@ -169,14 +150,12 @@ int main(int argc, char* argv[]){ " or --molname, --begin, --end are specified\n"); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; - simError(); - + simError(); } } //parse md file and set up the system SimCreator creator; - std::cout << "dumpFile = " << dumpFileName << "\n"; SimInfo* info = creator.createSim(dumpFileName); RealType maxLen; @@ -213,8 +192,8 @@ int main(int argc, char* argv[]){ args_info.nanglebins_arg); } else if (args_info.gxyz_given) { if (args_info.refsele_given) { - analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, - maxLen, args_info.nbins_arg); + analyser= new GofXyz(info, dumpFileName, sele1, sele2, + args_info.refsele_arg, maxLen, args_info.nbins_arg); } else { sprintf( painCave.errMsg, "--refsele must set when --gxyz is used"); @@ -238,7 +217,11 @@ int main(int argc, char* argv[]){ if (args_info.sele2_given) analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); else - analyser = new P2OrderParameter(info, dumpFileName, sele1); + if (args_info.seleoffset_given) + analyser = new P2OrderParameter(info, dumpFileName, sele1, + args_info.seleoffset_arg); + else + analyser = new P2OrderParameter(info, dumpFileName, sele1); } else { sprintf( painCave.errMsg, "At least one selection script (--sele1) must be specified when calculating P2 order parameters"); @@ -273,9 +256,33 @@ int main(int argc, char* argv[]){ painCave.isFatal = 1; simError(); } - } else if (args_info.bor_given){ + } else if (args_info.tet_param_z_given) { + if (args_info.rcut_given) { + analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2, + args_info.rcut_arg, + args_info.nbins_arg); + } else { + sprintf( painCave.errMsg, + "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } else if (args_info.ior_given){ if (args_info.rcut_given) { - analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg, + analyser = new IcosahedralOfR(info, dumpFileName, sele1, + args_info.rcut_arg, + args_info.nbins_arg, maxLen); + } else { + sprintf( painCave.errMsg, + "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } else if (args_info.for_given){ + if (args_info.rcut_given) { + analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg, args_info.nbins_arg, maxLen); } else { sprintf( painCave.errMsg, @@ -286,7 +293,8 @@ int main(int argc, char* argv[]){ } } else if (args_info.bad_given){ if (args_info.rcut_given) { - analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg, + analyser = new BondAngleDistribution(info, dumpFileName, sele1, + args_info.rcut_arg, args_info.nbins_arg); } else { sprintf( painCave.errMsg, @@ -294,14 +302,16 @@ int main(int argc, char* argv[]){ painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); - } + } } else if (args_info.scd_given) { if (batchMode) { - analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg, + analyser = new SCDOrderParameter(info, dumpFileName, + args_info.molname_arg, args_info.begin_arg, args_info.end_arg); } else{ std::string sele3 = args_info.sele3_arg; - analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3); + analyser = new SCDOrderParameter(info, dumpFileName, + sele1, sele2, sele3); } }else if (args_info.density_given) { analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, @@ -310,8 +320,44 @@ int main(int argc, char* argv[]){ analyser = new ObjectCount(info, dumpFileName, sele1 ); } else if (args_info.slab_density_given) { analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg); + } else if (args_info.rnemdz_given) { + analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg); + } else if (args_info.rnemdr_given) { + analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg); + } else if (args_info.rnemdrt_given) { + analyser = new RNEMDRTheta(info, dumpFileName, sele1, + args_info.nbins_arg, args_info.nanglebins_arg); + } else if (args_info.nitrile_given) { + analyser = new NitrileFrequencyMap(info, dumpFileName, sele1, + args_info.nbins_arg); } else if (args_info.p_angle_given) { - analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg); + if (args_info.sele1_given) { + if (args_info.sele2_given) + analyser = new pAngle(info, dumpFileName, sele1, sele2, + args_info.nbins_arg); + else + if (args_info.seleoffset_given) { + if (args_info.seleoffset2_given) { + analyser = new pAngle(info, dumpFileName, sele1, + args_info.seleoffset_arg, + args_info.seleoffset2_arg, + args_info.nbins_arg); + } else { + analyser = new pAngle(info, dumpFileName, sele1, + args_info.seleoffset_arg, + args_info.nbins_arg); + } + } else + analyser = new pAngle(info, dumpFileName, sele1, + args_info.nbins_arg); + } else { + sprintf( painCave.errMsg, + "At least one selection script (--sele1) must be specified when " + "calculating P(angle) distributions"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) }else if (args_info.hxy_given) { analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, @@ -334,7 +380,7 @@ int main(int argc, char* argv[]){ } else if (args_info.angle_r_given) { analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg); } - + if (args_info.output_given) { analyser->setOutputName(args_info.output_arg); } @@ -346,7 +392,6 @@ int main(int argc, char* argv[]){ delete analyser; delete info; - + return 0; } -