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Generate3DAMRDataSetWithPulse

vtk-examples/Cxx/CompositeData/Generate3DAMRDataSetWithPulse

Description

This utility code generates a simple 3D AMR dataset with a Gaussian pulse at the center. The resulting AMR dataset is written using the vtkXMLHierarchicalBoxDataSetWriter.

Note

The original source code for this example is here.

Question

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Code

Generate3DAMRDataSetWithPulse.cxx

// .NAME Generate3DAMRDataSetWithPulse.cxx -- Generated sample 3D AMR dataset
//
// .SECTION Description
//  This utility code generates a simple 3D 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 <vtkMultiBlockDataSet.h>
#include <vtkNew.h>
#include <vtkOverlappingAMR.h>
#include <vtkPointData.h>
#include <vtkPoints.h>
#include <vtkUniformGrid.h>
#include <vtkXMLImageDataWriter.h>
#include <vtkXMLMultiBlockDataWriter.h>
#include <vtkXMLUniformGridAMRReader.h>

namespace {
namespace AMRCommon {
void WriteUniformGrid(vtkUniformGrid* g, const std::string& prefix);
void WriteAMRData(vtkOverlappingAMR* amrData, const std::string& prefix);
vtkSmartPointer<vtkOverlappingAMR> ReadAMRData(const std::string& file);
void WriteMultiBlockData(vtkMultiBlockDataSet* mbds, const std::string& prefix);
vtkSmartPointer<vtkUniformGrid> GetGrid(double* origin, double* h, int* ndim);
void ComputeCellCenter(vtkUniformGrid* grid, const int cellIdx, double c[3]);
} // namespace AMRCommon
} // namespace
namespace {
static 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 vtkOverlappingAMR.
vtkSmartPointer<vtkOverlappingAMR> GetAMRDataSet();

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

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

  // STEP 1: Get the AMR dataset
  auto amrDataSet = GetAMRDataSet();
  AMRCommon::WriteAMRData(amrDataSet, "Gaussian3D");
  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)
{
  vtkNew<vtkDoubleArray> xyz;
  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);

    auto r = 0.0;
    for (auto i = 0; i < 3; ++i)
    {
      auto dx = center[i] - Pulse.origin[i];
      r += (dx * dx) / (Pulse.width[i] * Pulse.width[i]);
    }
    auto f = Pulse.amplitude * std::exp(-r);

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

  grid->GetCellData()->AddArray(xyz);
}
//------------------------------------------------------------------------------
vtkSmartPointer<vtkOverlappingAMR> GetAMRDataSet()
{
  vtkNew<vtkOverlappingAMR> data;
  int blocksPerLevel[2] = {1, 3};
  double globalOrigin[3] = {-2.0, -2.0, -2.0};
  data->Initialize(2, blocksPerLevel);
  data->SetOrigin(globalOrigin);
  data->SetGridDescription(VTK_XYZ_GRID);

  // Root Block -- Block 0
  double origin[3] = {-2.0, -2.0, -2.0};
  double h[3] = {1.0, 1.0, 1.0};
  int ndim[3] = {6, 5, 5};

  auto blockId{0};
  auto level{0};
  auto 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
  ndim[0] = 3;
  ndim[1] = ndim[2] = 5;
  h[0] = h[1] = h[2] = 0.5;
  origin[0] = origin[1] = origin[2] = -2.0;
  blockId = 0;
  level = 1;
  auto 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 2
  ndim[0] = 3;
  ndim[1] = ndim[2] = 5;
  h[0] = h[1] = h[2] = 0.5;
  origin[0] = 0.0;
  origin[1] = origin[2] = -1.0;
  blockId = 1;
  level = 1;
  auto grid2 = AMRCommon::GetGrid(origin, h, ndim);
  vtkAMRBox box2(origin, ndim, h, data->GetOrigin(),
                 data->GetGridDescription());
  AttachPulseToGrid(grid2);
  data->SetSpacing(level, h);
  data->SetAMRBox(level, blockId, box2);
  data->SetDataSet(level, blockId, grid2);

  // Block 3
  ndim[0] = 3;
  ndim[1] = ndim[2] = 7;
  h[0] = h[1] = h[2] = 0.5;
  origin[0] = 2.0;
  origin[1] = origin[2] = -1.0;
  blockId = 2;
  level = 1;
  auto 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);
  return (data);
}
} // namespace
namespace {
namespace AMRCommon {

//------------------------------------------------------------------------------
// Description:
// Writes a uniform grid as a structure grid
void WriteUniformGrid(vtkUniformGrid* g, const std::string& prefix)
{
  vtkNew<vtkXMLImageDataWriter> imgWriter;
  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)
{
  vtkNew<vtkCompositeDataWriter> writer;
  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.
vtkSmartPointer<vtkOverlappingAMR> ReadAMRData(const std::string& file)
{
  vtkNew<vtkXMLUniformGridAMRReader> myAMRReader;

  std::ostringstream oss;
  oss << file << ".vthb";

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

  myAMRReader->SetFileName(oss.str().c_str());
  myAMRReader->Update();
  return vtkOverlappingAMR::SafeDownCast(myAMRReader->GetOutput());
}

//------------------------------------------------------------------------------
// 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
  vtkNew<vtkXMLMultiBlockDataWriter> writer;
  std::ostringstream oss;
  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.
vtkSmartPointer<vtkUniformGrid> GetGrid(double* origin, double* h, int* ndim)
{
  vtkNew<vtkUniformGrid> grd;
  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;
}
} // namespace AMRCommon
} // namespace

CMakeLists.txt

cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

project(Generate3DAMRDataSetWithPulse)

find_package(VTK COMPONENTS 
  vtkCommonCore
  vtkCommonDataModel
  vtkIOLegacy
  vtkIOXML
  QUIET
)

if (NOT VTK_FOUND)
  message("Skipping Generate3DAMRDataSetWithPulse: ${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(Generate3DAMRDataSetWithPulse MACOSX_BUNDLE Generate3DAMRDataSetWithPulse.cxx )
  target_link_libraries(Generate3DAMRDataSetWithPulse PRIVATE ${VTK_LIBRARIES})
else ()
  # include all components
  add_executable(Generate3DAMRDataSetWithPulse MACOSX_BUNDLE Generate3DAMRDataSetWithPulse.cxx )
  target_link_libraries(Generate3DAMRDataSetWithPulse PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS Generate3DAMRDataSetWithPulse
    MODULES ${VTK_LIBRARIES}
    )
endif ()

Download and Build Generate3DAMRDataSetWithPulse

Click here to download Generate3DAMRDataSetWithPulse and its CMakeLists.txt file. Once the tarball Generate3DAMRDataSetWithPulse.tar has been downloaded and extracted,

cd Generate3DAMRDataSetWithPulse/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:

./Generate3DAMRDataSetWithPulse

WINDOWS USERS

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