--- trunk/src/applications/staticProps/StaticProps.cpp 2010/11/19 20:26:36 1522 +++ trunk/src/applications/staticProps/StaticProps.cpp 2013/01/31 15:55:47 1846 @@ -36,14 +36,14 @@ * [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). + * [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" @@ -69,20 +69,18 @@ #include "applications/staticProps/pAngle.hpp" #include "applications/staticProps/BondAngleDistribution.hpp" #include "applications/staticProps/NanoVolume.hpp" +#include "applications/staticProps/NanoLength.hpp" #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) #include "applications/staticProps/Hxy.hpp" #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" using namespace OpenMD; int main(int argc, char* argv[]){ - //register force fields - registerForceFields(); gengetopt_args_info args_info; @@ -95,8 +93,6 @@ 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" @@ -122,38 +118,21 @@ int main(int argc, char* argv[]){ 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"); @@ -168,14 +147,12 @@ 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; @@ -212,8 +189,8 @@ 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"); @@ -233,7 +210,22 @@ int main(int argc, char* argv[]){ simError(); } } else if (args_info.p2_given) { - analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); + if (args_info.sele1_given) { + if (args_info.sele2_given) + analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); + else + 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"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } } else if (args_info.rp2_given){ analyser = new RippleOP(info, dumpFileName, sele1, sele2); } else if (args_info.bo_given){ @@ -261,6 +253,18 @@ int main(int argc, char* argv[]){ painCave.isFatal = 1; simError(); } + } 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.bor_given){ if (args_info.rcut_given) { analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg, @@ -274,7 +278,8 @@ 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, @@ -282,14 +287,16 @@ 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, @@ -317,10 +324,12 @@ int main(int argc, char* argv[]){ } } else if (args_info.hullvol_given) { analyser = new NanoVolume(info, dumpFileName, sele1); + } else if (args_info.rodlength_given) { + analyser = new NanoLength(info, dumpFileName, sele1); } 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); } @@ -332,7 +341,6 @@ int main(int argc, char* argv[]){ delete analyser; delete info; - + return 0; } -