--- trunk/src/applications/staticProps/StaticProps.cpp	2010/06/23 19:25:02	1454
+++ trunk/src/applications/staticProps/StaticProps.cpp	2010/10/19 18:40:54	1513
@@ -64,6 +64,7 @@
 #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"
@@ -77,241 +78,243 @@ int main(int argc, char* argv[]){
 
 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;
+  //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;
+  } 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 "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";
     }
-
-
-    // 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) {
-	    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 {
+  }
+  
+  
+  // 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) {
+      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;
+  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;
     }
-    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) {
+    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.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.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();
+  analyser->process();
 
-    delete analyser;    
-    delete info;
+  delete analyser;    
+  delete info;
 
-    return 0;   
+  return 0;   
 }