--- trunk/src/applications/staticProps/StaticProps.cpp 2006/05/17 21:51:42 963 +++ trunk/src/applications/staticProps/StaticProps.cpp 2010/06/23 19:25:02 1454 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,15 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [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). */ #include @@ -52,162 +52,266 @@ #include "applications/staticProps/StaticPropsCmd.h" #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/RhoZ.hpp" +#include "applications/staticProps/pAngle.hpp" +#include "applications/staticProps/BondAngleDistribution.hpp" +#include "applications/staticProps/NanoVolume.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" -using namespace oopse; +using namespace OpenMD; int main(int argc, char* argv[]){ - //register force fields - registerForceFields(); + //register force fields + registerForceFields(); - gengetopt_args_info args_info; + gengetopt_args_info args_info; - //parse the command line option - if (cmdline_parser (argc, argv, &args_info) != 0) { - exit(1) ; - } + //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; - //get the dumpfile name and meta-data file name - std::string dumpFileName = args_info.input_arg; + // check the first selection argument, or set it to the environment + // variable, or failing that, set it to "select all" - std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md"; - - - std::string sele1; - std::string sele2; - - if (args_info.sele1_given) { - sele1 = args_info.sele1_arg; - }else { - char* sele1Env= getenv("OOPSE_SELE1"); - if (sele1Env) { - sele1 = sele1Env; - }else if (!args_info.scd_given) { - sprintf( painCave.errMsg, - "neither --sele1 option nor $OOPSE_SELE1 is set"); - painCave.severity = OOPSE_ERROR; - painCave.isFatal = 1; - simError(); + if (args_info.sele1_given) { + sele1 = args_info.sele1_arg; + } else { + char* sele1Env= getenv("SELECTION1"); + if (sele1Env) { + sele1 = sele1Env; + } else { + sele1 = "select all"; + } } - } - - if (args_info.sele2_given) { - sele2 = args_info.sele2_arg; - }else { - char* sele2Env = getenv("OOPSE_SELE2"); - if (sele2Env) { - sele2 = sele2Env; - } else if (args_info.density_given) { - sele2 = "select all"; - } else if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) { - sprintf( painCave.errMsg, - "neither --sele2 option nor $OOPSE_SELE2 is set"); - painCave.severity = OOPSE_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 = OOPSE_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 = OOPSE_ERROR; - painCave.isFatal = 1; - simError(); - + // 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"; + } } - } - //parse md file and set up the system - SimCreator creator; - SimInfo* info = creator.createSim(mdFileName); - RealType maxLen; - if (args_info.length_given) { - maxLen = args_info.length_arg; - } else { - Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); - maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; - } + // 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(); +// } +// } - StaticAnalyser* analyser; - if (args_info.gofr_given){ - analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg); - } else if (args_info.r_theta_given) { - analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); - } else if (args_info.r_omega_given) { - analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_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.nrbins_arg); - } else { - sprintf( painCave.errMsg, - "--refsele must set when --gxyz is used"); - painCave.severity = OOPSE_ERROR; - painCave.isFatal = 1; - simError(); - } - } else if (args_info.p2_given) { - analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); - } 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.nrbins_arg); - } else if (args_info.slab_density_given) { - Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); - analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nrbins_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.nrbins_arg); -#endif - } + // 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(); - if (args_info.output_given) { - analyser->setOutputName(args_info.output_arg); - } - if (args_info.step_given) { - analyser->setStep(args_info.step_arg); - } + } + } - analyser->process(); + //parse md file and set up the system + SimCreator creator; + std::cout << "dumpFile = " << dumpFileName << "\n"; + SimInfo* info = creator.createSim(dumpFileName); - delete analyser; - delete info; + 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); + } - return 0; + 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 { + 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){ + 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); + } + + 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; }