Created new tool for plotting scatter plots names scatterplot.cpp

Src/GNUmakefile

@@ -10,7 +10,6 @@ USE_OMP       = FALSE
 #EBASE         = combinePlts
 #EBASE         = isosurface
 #EBASE         = stream
-EBASE         = stream2plt
 #EBASE         = sampleStreamlines
 #EBASE         = streamScatter
 #EBASE         = streamSub

Src/integrateNonEBUpdate.cpp

@@ -0,0 +1,153 @@
+/*
+ * =====================================================================================
+ *
+ *       Filename:  integrateNonEBUpdate
+ *
+ *    Description:  Integral tool that takes variables from a plotfile and returns volume integral of that variable(s)-can run in parallel
+ *
+ *        Version:  1.0
+ *        Created:  03/10/2020 01:37:30 PM
+ *       Revision:  none
+ *       Compiler:  gcc
+ *
+ *         Author:  Victor H. Zendejas Lopez 
+ *   Organization:  CCSE @LBL
+ *
+ * =====================================================================================
+ */
+
+
+#include <AMReX_ParmParse.H>
+#include <AMReX_MultiFab.H>
+#include <AMReX_DataServices.H>
+#include <AMReX_ParallelDescriptor.H>
+#include <AMReX_VisMF.H>
+
+using namespace amrex;
+using namespace std;
+
+static void PrintUsage (char* progName)
+{
+   cout << "\nUsage:\n"
+         << progName
+         << "\n\tinfile = inputFileName comps=[n1 n2 ...]"
+         << "\n\t[-help]"
+         << "\n\n";
+    exit(1);
+}
+
+
+static Real SumThisComp(AmrData &amrData, string whichVar , int finestLevel)
+{
+
+   Real sum(0.0);
+
+   // Get levels of refinement 
+   int nLevels = finestLevel+1;
+   // Intersect variablenumber (must come after stoichiometry)
+   Vector<unique_ptr< MultiFab>> mf(nLevels);
+   for (int iLevel=0; iLevel < nLevels; iLevel++){
+      Print()<< "Reading Level " << iLevel << "\n";
+      int ngrow(0);
+
+      // Make space for each component and one for the intersect flag
+      DistributionMapping dm(amrData.boxArray(iLevel));
+      mf[iLevel].reset(new MultiFab(amrData.boxArray(iLevel), dm, 1, ngrow));
+      amrData.FillVar(*mf[iLevel], iLevel, whichVar);      
+   }
+
+   for (int iLevel=0; iLevel<finestLevel; iLevel++) {
+      BoxArray baf = mf[iLevel+1]->boxArray();
+      baf.coarsen(amrData.RefRatio()[iLevel]);   
+
+      for (MFIter mfi(*mf[iLevel]); mfi.isValid(); ++mfi) {
+         FArrayBox& myFab = (*mf[iLevel])[mfi]; 
+         int idx = mfi.index();
+         const Box& bx = mfi.validbox();
+
+         vector < pair < int,Box > > isects = baf.intersections(mf[iLevel]->boxArray()[idx]); 
+         for (int ii = 0; ii < isects.size(); ii++){
+            myFab.setVal(0,isects[ii].second,0,1);
+         }
+
+         sum +=myFab.sum(0,1);
+      }
+   }
+
+   ParallelDescriptor::ReduceRealSum(sum);
+   amrData.FlushGrids(amrData.StateNumber(whichVar));
+   return sum;
+}
+
+
+int main(int argc, char* argv[])
+{
+    Initialize(argc,argv);
+    {
+    if(argc == 1){
+    //   PrintUsage(argv[0]);
+    }     
+
+    ParallelDescriptor::StartParallel(&argc, &argv);
+    ParmParse pp;
+
+    string Output_Variables;
+    //Count the number of terms in the Output_Varibales 
+    int nOutput_Variables = (pp.countval("Output_Variables"));
+    Vector < string > Out_Var(nOutput_Variables); // Creates a vector Out_var length  
+      // Loop over Output_Variables to extract information from each element in Out_Var
+
+    for(int ivarOut = 0; ivarOut < nOutput_Variables; ++ivarOut){ 
+       pp.get("Output_Variables", Out_Var[ivarOut],ivarOut);
+    }
+    string Output_Format; 
+    pp.get("Output_Format", Output_Format); 
+    string Plot_File; 
+    pp.get("Plot_File", Plot_File);
+    string Output_File; 
+    pp.get("Output_File", Output_File); 
+
+    // Extract Plot data
+    DataServices::SetBatchMode();
+    Amrvis::FileType fileType(Amrvis::NEWPLT);    
+    DataServices plotDataType(Plot_File, fileType);
+
+    if (!plotDataType.AmrDataOk()) // If nothing is stored within plotDataType then run this loop
+       DataServices::Dispatch(DataServices::ExitRequest, NULL);
+    AmrData& amrData = plotDataType.AmrDataRef(); 
+    cout << "   ...done." << endl;
+
+    // Most likely, the variable was averaged down conservatively, lev 0 may be all that is reqd
+    int finestLevel = amrData.FinestLevel();
+
+    Vector<string> whichVar(nOutput_Variables);
+    // Read in variable list - adjusting for stoichiometry
+    for(int v = 0; v < nOutput_Variables; v++) {
+       pp.get("Output_Variables", whichVar[v], v);
+    }
+
+    // Check the names of the variables are present in the plotfile
+    Vector < int > destFills(nOutput_Variables);
+    for (int v = 0; v < nOutput_Variables; v++){
+       destFills[v] = v;
+       if (amrData.StateNumber(whichVar[v])<0) {
+          string message="Bad variable name ("+whichVar[v]+")";
+          Error(message.c_str());
+       }
+    } 
+
+     if (ParallelDescriptor::IOProcessor()){
+       cout << "TIME = " << setw(15) << amrData.Time();
+    }
+
+    for (int v = 0; v<whichVar.size(); ++v){
+          Real sumComp = SumThisComp(amrData, whichVar[v] ,finestLevel);
+          if (ParallelDescriptor::IOProcessor()){
+             cout << " int(" << whichVar[v] << ") = "
+              << sumComp << '\n';
+       }
+    }
+      }
+       Finalize();
+       return 0;
+}