--- trunk/src/applications/staticProps/StaticProps.cpp 2010/06/23 19:25:02 1454 +++ trunk/src/applications/staticProps/StaticProps.cpp 2014/10/02 14:35:14 2023 @@ -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" @@ -64,254 +64,385 @@ #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" #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" +#include "applications/staticProps/TetrahedralityParamXYZ.hpp" +#include "applications/staticProps/RNEMDStats.hpp" +#include "applications/staticProps/NitrileFrequencyMap.hpp" +#include "applications/staticProps/MultipoleSum.hpp" using namespace OpenMD; 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; + + 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; + std::string sele3; + + // 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("SELECTION1"); + if (sele1Env) { + sele1 = sele1Env; } else { - char* sele1Env= getenv("SELECTION1"); - if (sele1Env) { - sele1 = sele1Env; - } else { - sele1 = "select all"; - } + sele1 = "select all"; } - - // check the second selection argument, or set it to the environment - // variable, or failing that, set it to "select all" + } - if (args_info.sele2_given) { - sele2 = args_info.sele2_arg; - } else { - char* sele2Env = getenv("SELECTION1"); - if (sele2Env) { - sele2 = sele2Env; - } else { - sele2 = "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("SELECTION2"); + if (sele2Env) { + sele2 = sele2Env; + } else { + //If sele2 is not specified, then the default behavior + //should be what is already intended for sele1 + sele2 = sele1; } + } + // check the third selection argument, which is only set if + // requested by the user - // 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.sele3_given) sele3 = args_info.sele3_arg; - // 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) { - 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) { - sprintf( painCave.errMsg, - "below conditions are not satisfied:\n" - "0 <= begin && 0<= end && begin <= end-2\n"); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - batchMode = true; - } else{ - sprintf( painCave.errMsg, - "either --sele1, --sele2, --sele3 are specified," - " or --molname, --begin, --end are specified\n"); - 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; - zmaxLen = hmat(2,2); - } - - StaticAnalyser* analyser; - if (args_info.gofr_given){ - analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, - args_info.nbins_arg); - } 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); - } else if (args_info.r_omega_given) { - analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, - 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); - } 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); - } else { - sprintf( painCave.errMsg, - "--refsele must set when --gxyz is used"); - painCave.severity = OPENMD_ERROR; - 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 { + bool batchMode; + if (args_info.scd_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) { sprintf( painCave.errMsg, - "A slab width (dz) must be specified when calculating TwoDGofR"); + "below conditions are not satisfied:\n" + "0 <= begin && 0<= end && begin <= end-2\n"); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; - simError(); + simError(); } - } else if (args_info.p2_given) { - analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); - } 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); - } 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.bor_given){ - if (args_info.rcut_given) { - analyser = new BOPofR(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.bad_given){ - if (args_info.rcut_given) { - analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg, - args_info.nbins_arg); - } else { - sprintf( painCave.errMsg, - "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); - } 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); - } else if (args_info.slab_density_given) { - analyser = new RhoZ(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 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); -#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)"); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - }else if (args_info.hullvol_given) { - analyser = new NanoVolume(info, dumpFileName, sele1); + batchMode = true; + } else{ + sprintf( painCave.errMsg, + "either --sele1, --sele2, --sele3 are specified," + " or --molname, --begin, --end are specified\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); } + } - if (args_info.output_given) { - analyser->setOutputName(args_info.output_arg); + //parse md file and set up the system + SimCreator creator; + 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; } - if (args_info.step_given) { - analyser->setStep(args_info.step_arg); - } + } else { + Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); + 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); + } 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) { + if (args_info.sele3_given) + analyser = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen, + args_info.nbins_arg, args_info.nanglebins_arg); + else + analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, + args_info.nbins_arg, args_info.nanglebins_arg); + } else if (args_info.r_omega_given) { + if (args_info.sele3_given) + analyser = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen, + args_info.nbins_arg, args_info.nanglebins_arg); + else + analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, + args_info.nbins_arg, args_info.nanglebins_arg); - analyser->process(); - - delete analyser; - delete info; - - return 0; + } else if (args_info.theta_omega_given) { + if (args_info.sele3_given) + analyser = new GofAngle2(info, dumpFileName, sele1, sele2, sele3, + args_info.nanglebins_arg); + else + analyser = new GofAngle2(info, dumpFileName, sele1, sele2, + 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); + } else { + sprintf( painCave.errMsg, + "--refsele must set when --gxyz is used"); + painCave.severity = OPENMD_ERROR; + 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) { + 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){ + if (args_info.rcut_given) { + analyser = new BondOrderParameter(info, dumpFileName, sele1, + args_info.rcut_arg, + args_info.nbins_arg); + } 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.multipole_given){ + analyser = new MultipoleSum(info, dumpFileName, sele1, + maxLen, args_info.nbins_arg); + } 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, 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.tet_param_xyz_given) { + if (!args_info.rcut_given) { + sprintf( painCave.errMsg, + "A cutoff radius (rcut) must be specified when calculating" + " Tetrahedrality Parameters"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + if (!args_info.voxelSize_given) { + sprintf( painCave.errMsg, + "A voxel size must be specified when calculating" + " volume-resolved Tetrahedrality Parameters"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + if (!args_info.gaussWidth_given) { + sprintf( painCave.errMsg, + "A gaussian width must be specified when calculating" + " volume-resolved Tetrahedrality Parameters"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2, + args_info.rcut_arg, + args_info.voxelSize_arg, + args_info.gaussWidth_arg); + } else if (args_info.ior_given){ + if (args_info.rcut_given) { + 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, + "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } 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); + } else { + sprintf( painCave.errMsg, + "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); + } else{ + 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); + } 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.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) { + 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, + 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)"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } 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; + + return 0; } -