--- trunk/src/applications/staticProps/StaticProps.cpp 2013/01/31 15:55:47 1846 +++ trunk/src/applications/staticProps/StaticProps.cpp 2014/10/31 18:40:40 2031 @@ -35,7 +35,7 @@ * * [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). + * [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). */ @@ -77,6 +77,12 @@ #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" +#include "applications/staticProps/SurfaceDiffusion.hpp" + using namespace OpenMD; int main(int argc, char* argv[]){ @@ -93,6 +99,7 @@ int main(int argc, char* argv[]){ 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" @@ -109,12 +116,12 @@ 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 { @@ -124,6 +131,11 @@ int main(int argc, char* argv[]){ } } + // check the third selection argument, which is only set if + // requested by the user + + if (args_info.sele3_given) sele3 = args_info.sele3_arg; + bool batchMode; if (args_info.scd_given){ if (args_info.sele1_given && @@ -179,14 +191,27 @@ int main(int argc, char* argv[]){ 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); + 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) { - analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, - args_info.nbins_arg, args_info.nanglebins_arg); + 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); + } else if (args_info.theta_omega_given) { - analyser = new GofAngle2(info, dumpFileName, sele1, sele2, - args_info.nanglebins_arg); + 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, @@ -240,7 +265,9 @@ int main(int argc, char* argv[]){ 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, @@ -265,9 +292,50 @@ int main(int argc, char* argv[]){ painCave.isFatal = 1; simError(); } - } else if (args_info.bor_given){ + } 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 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, @@ -294,7 +362,6 @@ int main(int argc, char* argv[]){ 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); } @@ -305,13 +372,51 @@ 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, args_info.nbins_y_arg, args_info.nbins_arg); #endif + }else if (args_info.surfDiffusion_given){ + analyser = new SurfaceDiffusion(info, dumpFileName, sele1, maxLen); }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);