--- trunk/src/applications/staticProps/StaticProps.cpp 2010/03/22 19:21:22 1413 +++ trunk/src/applications/staticProps/StaticProps.cpp 2010/10/19 18:40:54 1513 @@ -53,15 +53,18 @@ #include "applications/staticProps/StaticAnalyser.hpp" #include "applications/staticProps/GofR.hpp" #include "applications/staticProps/GofZ.hpp" +#include "applications/staticProps/GofRZ.hpp" #include "applications/staticProps/GofRAngle.hpp" #include "applications/staticProps/GofAngle2.hpp" #include "applications/staticProps/GofXyz.hpp" +#include "applications/staticProps/TwoDGofR.hpp" #include "applications/staticProps/P2OrderParameter.hpp" #include "applications/staticProps/BondOrderParameter.hpp" #include "applications/staticProps/BOPofR.hpp" #include "applications/staticProps/RippleOP.hpp" #include "applications/staticProps/SCDOrderParameter.hpp" #include "applications/staticProps/DensityPlot.hpp" +#include "applications/staticProps/ObjectCount.hpp" #include "applications/staticProps/RhoZ.hpp" #include "applications/staticProps/pAngle.hpp" #include "applications/staticProps/BondAngleDistribution.hpp" @@ -77,24 +80,24 @@ int main(int argc, char* argv[]){ //register force fields registerForceFields(); - + gengetopt_args_info args_info; - + //parse the command line option if (cmdline_parser (argc, argv, &args_info) != 0) { exit(1) ; } - + //get the dumpfile name 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" - + if (args_info.sele1_given) { sele1 = args_info.sele1_arg; } else { @@ -105,7 +108,7 @@ int main(int argc, char* argv[]){ sele1 = "select all"; } } - + // check the second selection argument, or set it to the environment // variable, or failing that, set it to "select all" @@ -119,29 +122,29 @@ int main(int argc, char* argv[]){ sele2 = "select all"; } } - - + + // 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(); -// } -// } - + // 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(); -// } -// } - + + // 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) { @@ -163,21 +166,26 @@ int main(int argc, char* argv[]){ painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); - + } } - + //parse md file and set up the system SimCreator creator; std::cout << "dumpFile = " << dumpFileName << "\n"; SimInfo* info = creator.createSim(dumpFileName); RealType maxLen; + RealType zmaxLen; if (args_info.length_given) { maxLen = args_info.length_arg; + if (args_info.zlength_given){ + zmaxLen = args_info.zlength_arg; + } } else { Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); - maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; + maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; + zmaxLen = hmat(2,2); } StaticAnalyser* analyser; @@ -187,6 +195,9 @@ int main(int argc, char* argv[]){ } else if (args_info.gofz_given) { analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen, args_info.nbins_arg); + } else if (args_info.r_z_given) { + analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen, + args_info.nbins_arg, args_info.nbins_z_arg); } else if (args_info.r_theta_given) { analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nbins_arg, args_info.nanglebins_arg); @@ -207,6 +218,17 @@ int main(int argc, char* argv[]){ painCave.isFatal = 1; simError(); } + } else if (args_info.twodgofr_given){ + if (args_info.dz_given) { + analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen, + args_info.dz_arg, args_info.nbins_arg); + } else { + sprintf( painCave.errMsg, + "A slab width (dz) must be specified when calculating TwoDGofR"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } } else if (args_info.p2_given) { analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); } else if (args_info.rp2_given){ @@ -226,7 +248,7 @@ int main(int argc, char* argv[]){ } else if (args_info.bor_given){ if (args_info.rcut_given) { analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg, - args_info.nbins_arg, maxLen); + args_info.nbins_arg, maxLen); } else { sprintf( painCave.errMsg, "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); @@ -237,7 +259,7 @@ 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, - args_info.nbins_arg); + args_info.nbins_arg); } else { sprintf( painCave.errMsg, "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions"); @@ -256,6 +278,8 @@ int main(int argc, char* argv[]){ }else if (args_info.density_given) { analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nbins_arg); + } else if (args_info.count_given) { + 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.p_angle_given) { @@ -275,7 +299,7 @@ int main(int argc, char* argv[]){ painCave.isFatal = 1; simError(); } - }else if (args_info.hullvol_given) { + }else if (args_info.hullvol_given) { analyser = new NanoVolume(info, dumpFileName, sele1); }