--- trunk/src/applications/staticProps/StaticProps.cpp 2010/10/19 18:40:54 1513 +++ trunk/src/applications/staticProps/StaticProps.cpp 2012/08/22 18:43:27 1785 @@ -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" @@ -69,17 +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/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; @@ -92,8 +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" @@ -119,7 +118,11 @@ int main(int argc, char* argv[]){ if (sele2Env) { sele2 = sele2Env; } else { - sele2 = "select all"; + //It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior + //should not be 'select all' but rather what is already intended for sele1 + //JRM 8/22/12 + sele2 = sele1; + //sele2 = "select all"; } } @@ -187,33 +190,33 @@ int main(int argc, char* argv[]){ maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; zmaxLen = hmat(2,2); } - + StaticAnalyser* analyser; if (args_info.gofr_given){ analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, - args_info.nbins_arg); + args_info.nbins_arg); } else if (args_info.gofz_given) { analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen, - args_info.nbins_arg); + 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); + 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); + args_info.nbins_arg, args_info.nanglebins_arg); } else if (args_info.r_omega_given) { analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, - args_info.nbins_arg, args_info.nanglebins_arg); + args_info.nbins_arg, args_info.nanglebins_arg); } else if (args_info.theta_omega_given) { analyser = new GofAngle2(info, dumpFileName, sele1, sele2, - args_info.nanglebins_arg); + 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); + maxLen, args_info.nbins_arg); } else { sprintf( painCave.errMsg, - "--refsele must set when --gxyz is used"); + "--refsele must set when --gxyz is used"); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); @@ -221,37 +224,73 @@ int main(int argc, char* argv[]){ } 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); + args_info.dz_arg, args_info.nbins_arg); } else { sprintf( painCave.errMsg, - "A slab width (dz) must be specified when calculating TwoDGofR"); + "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); + if (args_info.sele1_given) { + if (args_info.sele2_given) + analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); + 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){ if (args_info.rcut_given) { analyser = new BondOrderParameter(info, dumpFileName, sele1, - args_info.rcut_arg, - args_info.nbins_arg); + args_info.rcut_arg, + args_info.nbins_arg); } else { sprintf( painCave.errMsg, - "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); + "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } + + } else if (args_info.tet_param_given) { + if (args_info.rcut_given) { + analyser = new TetrahedralityParam(info, dumpFileName, sele1, + 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.tet_param_z_given) { + if (args_info.rcut_given) { + analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, + 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, - 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"); + "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); @@ -259,25 +298,25 @@ 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"); + "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions"); 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, - args_info.begin_arg, args_info.end_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); } }else if (args_info.density_given) { analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, - args_info.nbins_arg); + args_info.nbins_arg); } else if (args_info.count_given) { analyser = new ObjectCount(info, dumpFileName, sele1 ); } else if (args_info.slab_density_given) { @@ -287,31 +326,35 @@ int main(int argc, char* argv[]){ #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, - args_info.nbins_y_arg, args_info.nbins_arg); + args_info.nbins_y_arg, args_info.nbins_arg); #endif }else if (args_info.rho_r_given) { if (args_info.radius_given){ analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg); }else{ sprintf( painCave.errMsg, - "A particle radius (radius) must be specified when calculating Rho(r)"); + "A particle radius (radius) must be specified when calculating Rho(r)"); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } - }else if (args_info.hullvol_given) { + } 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); } if (args_info.step_given) { analyser->setStep(args_info.step_arg); } - + analyser->process(); - + delete analyser; delete info;