--- trunk/src/applications/staticProps/StaticProps.cpp	2010/06/08 18:35:22	1444
+++ trunk/src/applications/staticProps/StaticProps.cpp	2010/06/08 20:26:50	1445
@@ -76,53 +76,53 @@ int main(int argc, char* argv[]){
 
 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
+    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"
+    // 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;
+    if (args_info.sele1_given) {
+	sele1 = args_info.sele1_arg;
     } else {
-      sele1 = "select all";
+	char*  sele1Env= getenv("SELECTION1");
+	if (sele1Env) {
+	    sele1 = sele1Env;
+	} else {
+	    sele1 = "select all";
+	}
     }
-  }
 
-  // check the second selection argument, or set it to the environment
-  // variable, or failing that, set it to "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";
+    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 
+    // Problems if sele1 wasn't specified, but 
 // if (!args_info.scd_given) {
 //       sprintf( painCave.errMsg,
 //                "neither --sele1 option nor $SELECTION1 is set");
@@ -132,7 +132,7 @@ int main(int argc, char* argv[]){
 //     }
 //   }
 
-  // Problems if sele1 wasn't specified
+    // Problems if sele1 wasn't specified
 
 //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
 //       sprintf( painCave.errMsg,
@@ -143,158 +143,163 @@ int main(int argc, char* argv[]){
 //     }
 //   }
 
-  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();        
+    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);
+    //parse md file and set up the system
+    SimCreator creator;
+    std::cout << "dumpFile = " << dumpFileName << "\n";
+    SimInfo* info = creator.createSim(dumpFileName);
 
-  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;        
-  }    
+    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, 
+    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.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);
+    } 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.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);
+    }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.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.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);
-  }
+    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;   
 }