--- trunk/src/applications/staticProps/StaticProps.cpp	2005/02/16 20:30:50	354
+++ trunk/src/applications/staticProps/StaticProps.cpp	2006/09/19 21:14:11	1039
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -50,102 +50,195 @@
 #include "utils/simError.h"
 
 #include "applications/staticProps/StaticPropsCmd.h"
+#include "applications/staticProps/StaticAnalyser.hpp"
 #include "applications/staticProps/GofR.hpp"
 #include "applications/staticProps/GofRAngle.hpp"
 #include "applications/staticProps/GofAngle2.hpp"
 #include "applications/staticProps/GofXyz.hpp"
+#include "applications/staticProps/P2OrderParameter.hpp"
+#include "applications/staticProps/BondOrderParameter.hpp"
+#include "applications/staticProps/RippleOP.hpp"
+#include "applications/staticProps/SCDOrderParameter.hpp"
+#include "applications/staticProps/DensityPlot.hpp"
+#include "applications/staticProps/RhoZ.hpp"
+#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
+#include "applications/staticProps/Hxy.hpp"
+#endif
 
 using namespace oopse;
 
 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;
+
+  // 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("OOPSE_SELE1");
+    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"
+  
+  if (args_info.sele2_given) {
+    sele2 = args_info.sele2_arg;
+  } else {
+    char* sele2Env = getenv("OOPSE_SELE2");
+    if (sele2Env) {
+      sele2 = sele2Env;            
+    } else { 
+      sele2 = "select all";
+    }
+  }
 
-    //get the dumpfile name and meta-data file name
-    std::string dumpFileName = args_info.input_arg;
 
-    std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
+  // Problems if sele1 wasn't specified, but 
+// if (!args_info.scd_given) {
+//       sprintf( painCave.errMsg,
+//                "neither --sele1 option nor $OOPSE_SELE1 is set");
+//       painCave.severity = OOPSE_ERROR;
+//       painCave.isFatal = 1;
+//       simError();
+//     }
+//   }
 
-    
-    std::string sele1;
-    std::string sele2;
+  // Problems if sele1 wasn't specified
 
-    if (args_info.sele1_given) {
-        sele1 = args_info.sele1_arg;
-    }else {
-        char*  sele1Env= getenv("OOPSE_SELE1");
-        if (sele1Env) {
-            sele1 = sele1Env;
-        }else {
-            sprintf( painCave.errMsg,
-               "neither --sele1 option nor $OOPSE_SELE1 is set");
-            painCave.severity = OOPSE_ERROR;
-            painCave.isFatal = 1;
-            simError();
-        }
-    }
+//     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();        
     
-    if (args_info.sele2_given) {
-        sele2 = args_info.sele2_arg;
-    }else {
-        char* sele2Env = getenv("OOPSE_SELE2");
-        if (sele2Env) {
-            sele2 = sele2Env;            
-        } else {
-            sprintf( painCave.errMsg,
-               "neither --sele2 option nor $OOPSE_SELE2 is set");
-            painCave.severity = OOPSE_ERROR;
-            painCave.isFatal = 1;
-            simError();        
-        }
     }
+  }
 
-    //parse md file and set up the system
-    SimCreator creator;
-    SimInfo* info = creator.createSim(mdFileName);
+  //parse md file and set up the system
+  SimCreator creator;
+  SimInfo* info = creator.createSim(dumpFileName);
 
-    double 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;
+  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;        
+  }    
 
-    RadialDistrFunc* rdf;
-    if (args_info.gofr_given){
-        rdf= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);        
-    } else if (args_info.r_theta_given) {
-        rdf  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
-    } else if (args_info.r_omega_given) {
-        rdf  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg);
-    } else if (args_info.theta_omega_given) {
-        rdf  = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg);
-    } else if (args_info.xyz_given) {
-        rdf= new GofXyz(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg);        
+  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();  
     }
-    
-    if (args_info.output_given) {
-        rdf->setOutputName(args_info.output_arg);
+  } 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 && args_info.LegendreL_given) {
+      analyser = new BondOrderParameter(info, dumpFileName, sele1, 
+                                        args_info.rcut_arg, 
+                                        args_info.LegendreL_arg);
+    } else {
+      sprintf( painCave.errMsg,
+               "Both the cutoff radius (rcut) and LegendreL must be specified when calculating Bond Order Parameters");
+      painCave.severity = OOPSE_ERROR;
+      painCave.isFatal = 1;
+      simError();
     }
-    if (args_info.step_given) {
-        rdf->setStep(args_info.step_arg);
+  } 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
+  }
+  
+  if (args_info.output_given) {
+    analyser->setOutputName(args_info.output_arg);
+  }
+  if (args_info.step_given) {
+    analyser->setStep(args_info.step_arg);
+  }
 
-    rdf->process();
+  analyser->process();
 
-    delete rdf;    
-    delete info;
+  delete analyser;    
+  delete info;
 
-    return 0;   
+  return 0;   
 }