# Generate2DAMRDataSetWithPulse

VTKExamples/Cxx/CompositeData/Generate2DAMRDataSetWithPulse

### Description

This utility code generates a simple 2D AMR dataset with a Gaussian pulse at the center. The resulting AMR dataset is written using the vtkXMLHierarchicalBoxDataSetWriter.

Note

This original source code for this example is here.

### Code

Generate2DAMRDataSetWithPulse.cxx

    // .NAME Generate2DAMRDataSetWithPulse.cxx -- Generates sample 2-D AMR dataset
    //
    // .SECTION Description
    //  This utility code generates a simple 2D AMR dataset with a gaussian
    //  pulse at the center. The resulting AMR dataset is written using the
    //  vtkXMLHierarchicalBoxDataSetWriter.

    #include <cmath>
    #include <iostream>
    #include <sstream>

    #include <vtkAMRBox.h>
    #include <vtkAMRUtilities.h>
    #include <vtkCell.h>
    #include <vtkCellData.h>
    #include <vtkCompositeDataWriter.h>
    #include <vtkDataArray.h>
    #include <vtkDoubleArray.h>
    #include <vtkHierarchicalBoxDataSet.h>
    #include <vtkMultiBlockDataSet.h>
    #include <vtkOverlappingAMR.h>
    #include <vtkPointData.h>
    #include <vtkPoints.h>
    #include <vtkSmartPointer.h>
    #include <vtkUniformGrid.h>
    #include <vtkXMLHierarchicalBoxDataReader.h>
    #include <vtkXMLImageDataWriter.h>
    #include <vtkXMLMultiBlockDataWriter.h>

    namespace AMRCommon
    {
      void WriteUniformGrid(vtkUniformGrid* g, const std::string& prefix);
      void WriteAMRData(vtkOverlappingAMR* amrData, const std::string& prefix);
      vtkHierarchicalBoxDataSet* ReadAMRData(const std::string& file);
      void WriteMultiBlockData(vtkMultiBlockDataSet* mbds, const std::string& prefix);
      vtkUniformGrid* GetGrid(double* origin, double* h, int* ndim);
      void ComputeCellCenter(vtkUniformGrid* grid, const int cellIdx, double c[3]);
    }
    namespace
    {
      struct PulseAttributes
      {
        double origin[3]; // xyz for the center of the pulse
        double width[3]; // the width of the pulse
        double amplitude; // the amplitude of the pulse
      } Pulse;
      //
      // Function prototype declarations
      //

      // Description:
      // Sets the pulse attributes
      void SetPulse();

      // Description:
      // Constructs the vtkHierarchicalBoxDataSet.
      vtkOverlappingAMR* GetAMRDataSet();

      // Description:
      // Attaches the pulse to the given grid.
      void AttachPulseToGrid(vtkUniformGrid* grid);
    }

    //
    // Program main
    //
    int main(int, char*[])
    {
      // STEP 0: Initialize gaussian pulse parameters
      SetPulse();

      // STEP 1: Get the AMR dataset
      vtkSmartPointer<vtkOverlappingAMR> amrDataSet = GetAMRDataSet();

      AMRCommon::WriteAMRData(amrDataSet, "Gaussian2D");
      return EXIT_SUCCESS;
    }

    namespace
    {
      //=============================================================================
      //                    Function Prototype Implementation
      //=============================================================================

      void SetPulse()
      {
        Pulse.origin[0] = Pulse.origin[1] = Pulse.origin[2] = -1.0;
        Pulse.width[0] = Pulse.width[1] = Pulse.width[2] = 6.0;
        Pulse.amplitude = 0.0001;
      }

      //------------------------------------------------------------------------------
      void AttachPulseToGrid(vtkUniformGrid* grid)
      {
        vtkSmartPointer<vtkDoubleArray> xyz = vtkSmartPointer<vtkDoubleArray>::New();
        xyz->SetName("GaussianPulse");
        xyz->SetNumberOfComponents(1);
        xyz->SetNumberOfTuples(grid->GetNumberOfCells());

        for (int cellIdx = 0; cellIdx < grid->GetNumberOfCells(); ++cellIdx)
        {
          double center[3];
          AMRCommon::ComputeCellCenter(grid, cellIdx, center);

          double r = 0.0;
          for (int i = 0; i < 2; ++i)
          {
            double dx = center[i] - Pulse.origin[i];
            r += (dx * dx) / (Pulse.width[i] * Pulse.width[i]);
          }
          double f = Pulse.amplitude * std::exp(-r);

          xyz->SetTuple1(cellIdx, f);
        } // END for all cells

        grid->GetCellData()->AddArray(xyz);
      }

      //------------------------------------------------------------------------------
      vtkOverlappingAMR* GetAMRDataSet()
      {
        int NumLevels = 2;
        int BlocksPerLevel[2] = { 1, 2 };
        double origin[3];
        origin[0] = origin[1] = -2.0;
        origin[2] = 0.0;

        vtkOverlappingAMR* data = vtkOverlappingAMR::New();
        data->Initialize(NumLevels, BlocksPerLevel);
        data->SetOrigin(origin);
        data->SetGridDescription(VTK_XY_PLANE);

        double h[3];
        int ndim[3];

        // Root Block -- Block 0,0
        ndim[0] = 6;
        ndim[1] = 5;
        ndim[2] = 1;
        h[0] = h[1] = h[2] = 1.0;

        int blockId = 0;
        int level = 0;
        vtkSmartPointer<vtkUniformGrid> root = AMRCommon::GetGrid(origin, h, ndim);
        vtkAMRBox box(origin, ndim, h, data->GetOrigin(), data->GetGridDescription());
        AttachPulseToGrid(root);

        data->SetSpacing(level, h);
        data->SetAMRBox(level, blockId, box);
        data->SetDataSet(level, blockId, root);

        // Block 1,0
        ndim[0] = ndim[1] = 9;
        ndim[2] = 1;
        h[0] = h[1] = h[2] = 0.25;
        origin[0] = origin[1] = -2.0;
        origin[2] = 0.0;
        blockId = 0;
        level = 1;
        vtkSmartPointer<vtkUniformGrid> grid1 = AMRCommon::GetGrid(origin, h, ndim);
        vtkAMRBox box1(origin, ndim, h, data->GetOrigin(),
          data->GetGridDescription());
        AttachPulseToGrid(grid1);

        data->SetSpacing(level, h);
        data->SetAMRBox(level, blockId, box1);
        data->SetDataSet(level, blockId, grid1);

        // Block 1,1
        ndim[0] = ndim[1] = 9;
        ndim[2] = 1;
        h[0] = h[1] = h[2] = 0.25;
        origin[0] = 1.0;
        origin[1] = origin[2] = 0.0;
        blockId = 1;
        level = 1;
        vtkSmartPointer<vtkUniformGrid> grid3 = AMRCommon::GetGrid(origin, h, ndim);
        vtkAMRBox box3(origin, ndim, h, data->GetOrigin(),
          data->GetGridDescription());

        AttachPulseToGrid(grid3);
        data->SetSpacing(level, h);
        data->SetAMRBox(level, blockId, box3);
        data->SetDataSet(level, blockId, grid3);

        vtkAMRUtilities::BlankCells(data);
        data->Audit();
        return (data);
      }
    }
    namespace AMRCommon
    {

      //------------------------------------------------------------------------------
      // Description:
      // Writes a uniform grid as a structure grid
      void WriteUniformGrid(vtkUniformGrid* g, const std::string& prefix)
      {
        vtkSmartPointer<vtkXMLImageDataWriter> imgWriter =
          vtkSmartPointer<vtkXMLImageDataWriter>::New();

        std::ostringstream oss;
        oss << prefix << "." << imgWriter->GetDefaultFileExtension();
        imgWriter->SetFileName(oss.str().c_str());
        imgWriter->SetInputData(g);
        imgWriter->Write();
      }

      //------------------------------------------------------------------------------
      // Description:
      // Writes the given AMR dataset to a *.vth file with the given prefix.
      void WriteAMRData(vtkOverlappingAMR* amrData, const std::string& prefix)
      {
        vtkSmartPointer<vtkCompositeDataWriter> writer =
          vtkSmartPointer<vtkCompositeDataWriter>::New();

        std::ostringstream oss;
        oss << prefix << ".vthb";
        writer->SetFileName(oss.str().c_str());
        writer->SetInputData(amrData);
        writer->Write();
      }

      //------------------------------------------------------------------------------
      // Description:
      // Reads AMR data to the given data-structure from the prescribed file.
      vtkHierarchicalBoxDataSet* ReadAMRData(const std::string& file)
      {
        vtkXMLHierarchicalBoxDataReader* myAMRReader =
          vtkXMLHierarchicalBoxDataReader::New();

        std::ostringstream oss;
        oss.str("");
        oss.clear();
        oss << file << ".vthb";

        std::cout << "Reading AMR Data from: " << oss.str() << std::endl;
        std::cout.flush();

        myAMRReader->SetFileName(oss.str().c_str());
        myAMRReader->Update();

        vtkHierarchicalBoxDataSet* amrData =
          vtkHierarchicalBoxDataSet::SafeDownCast(myAMRReader->GetOutput());
        return (amrData);
      }

      //------------------------------------------------------------------------------
      // Description:
      // Writes the given multi-block data to an XML file with the prescribed prefix
      void WriteMultiBlockData(vtkMultiBlockDataSet* mbds, const std::string& prefix)
      {
        // Sanity check
        vtkSmartPointer<vtkXMLMultiBlockDataWriter> writer =
          vtkSmartPointer<vtkXMLMultiBlockDataWriter>::New();

        std::ostringstream oss;
        oss.str("");
        oss.clear();
        oss << prefix << "." << writer->GetDefaultFileExtension();
        writer->SetFileName(oss.str().c_str());
        writer->SetInputData(mbds);
        writer->Write();
      }

      //------------------------------------------------------------------------------
      // Constructs a uniform grid instance given the prescribed
      // origin, grid spacing and dimensions.
      vtkUniformGrid* GetGrid(double* origin, double* h, int* ndim)
      {
        vtkUniformGrid* grd = vtkUniformGrid::New();
        grd->Initialize();
        grd->SetOrigin(origin);
        grd->SetSpacing(h);
        grd->SetDimensions(ndim);
        return grd;
      }

      //------------------------------------------------------------------------------
      // Computes the cell center for the cell corresponding to cellIdx w.r.t.
      // the given grid. The cell center is stored in the supplied buffer c.
      void ComputeCellCenter(vtkUniformGrid* grid, const int cellIdx, double c[3])
      {
        vtkCell* myCell = grid->GetCell(cellIdx);

        double pCenter[3];
        double* weights = new double[myCell->GetNumberOfPoints()];
        int subId = myCell->GetParametricCenter(pCenter);
        myCell->EvaluateLocation(subId, pCenter, c, weights);
        delete[] weights;
      }

    } // END namespace

### CMakeLists.txt

    cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

    project(Generate2DAMRDataSetWithPulse)

    find_package(VTK COMPONENTS
      vtkCommonCore
      vtkCommonDataModel
      vtkIOLegacy
      vtkIOXML QUIET)
    if (NOT VTK_FOUND)
      message("Skipping Generate2DAMRDataSetWithPulse: ${VTK_NOT_FOUND_MESSAGE}")
      return ()
    endif()
    message (STATUS "VTK_VERSION: ${VTK_VERSION}")
    if (VTK_VERSION VERSION_LESS "8.90.0")
      # old system
      include(${VTK_USE_FILE})
      add_executable(Generate2DAMRDataSetWithPulse MACOSX_BUNDLE Generate2DAMRDataSetWithPulse.cxx )
      target_link_libraries(Generate2DAMRDataSetWithPulse PRIVATE ${VTK_LIBRARIES})
    else ()
      # include all components
      add_executable(Generate2DAMRDataSetWithPulse MACOSX_BUNDLE Generate2DAMRDataSetWithPulse.cxx )
      target_link_libraries(Generate2DAMRDataSetWithPulse PRIVATE ${VTK_LIBRARIES})
      # vtk_module_autoinit is needed
      vtk_module_autoinit(
        TARGETS Generate2DAMRDataSetWithPulse
        MODULES ${VTK_LIBRARIES}
        )
    endif ()

### Download and Build Generate2DAMRDataSetWithPulse

Click here to download Generate2DAMRDataSetWithPulse and its CMakeLists.txt file. Once the tarball Generate2DAMRDataSetWithPulse.tar has been downloaded and extracted,

    cd Generate2DAMRDataSetWithPulse/build

If VTK is installed:

    cmake ..

If VTK is not installed but compiled on your system, you will need to specify the path to your VTK build:

    cmake -DVTK_DIR:PATH=/home/me/vtk_build ..

Build the project:

    make

and run it:

    ./Generate2DAMRDataSetWithPulse

WINDOWS USERS

Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.