Added ASAGI and the netCDF-writer.

src/examples/swe_mpi.cpp

@@ -23,21 +23,34 @@
  *
  * @section DESCRIPTION
  *
- * Very basic setting of SWE, which uses a wave propagation solver and an artificial scenario on a single block.
+ * Setting of SWE, which uses a wave propagation solver and an artificial or ASAGI scenario on multiple blocks.
  */
 
 #include <mpi.h>
-#include "../tools/help.hh"
+#include <cassert>
+#include <cmath>
 #include <cstdlib>
 #include <string>
 
+#include "../tools/help.hh"
+
 #include "../SWE_Block.hh"
+
 #ifndef CUDA
 #include "../SWE_WavePropagationBlock.hh"
 #else
 #include "../SWE_WavePropagationBlockCuda.hh"
 #endif
+
+#ifdef WRITENETCDF
+#include "../tools/NetCdfWriter.hh"
+#endif
+
+#ifdef ASAGI
+#include "../scenarios/SWE_AsagiScenario.hpp"
+#else
 #include "../scenarios/SWE_simple_scenarios.h"
+#endif
 
 #ifdef READXML
 #include "../tools/CXMLConfig.hpp"
@@ -136,6 +149,7 @@ int main( int argc, char** argv ) {
 
   // read xml file
   #ifdef READXML
+  assert(false); //TODO: not implemented.
   if(argc != 2) {
     l_sweLogger.printString("Aborting. Please provide a proper input file.");
     l_sweLogger.printString("Example: ./SWE_gnu_debug_none_augrie config.xml");
@@ -169,8 +183,34 @@ int main( int argc, char** argv ) {
   l_blockPositionX = l_mpiRank / l_blocksY;
   l_blockPositionY = l_mpiRank % l_blocksY;
 
+  #ifdef ASAGI
+  /*
+   * Pixel node registration used [Cartesian grid]
+   * Grid file format: nf = GMT netCDF format (float)  (COARDS-compliant)
+   * x_min: -500000 x_max: 6500000 x_inc: 500 name: x nx: 14000
+   * y_min: -2500000 y_max: 1500000 y_inc: 500 name: y ny: 8000
+   * z_min: -6.48760175705 z_max: 16.1780223846 name: z
+   * scale_factor: 1 add_offset: 0
+   * mean: 0.00217145586762 stdev: 0.245563641735 rms: 0.245573241263
+   */
+
+  //simulation area
+  float simulationArea[4];
+  simulationArea[0] = -450000;
+  simulationArea[1] = 6450000;
+  simulationArea[2] = -2450000;
+  simulationArea[3] = 1450000;
+
+  //  scenarios::Asagi scene( "/naslx/ptmp/2/di56dok/data/tohoku_gebco_ucsb3_500m_hawaii_bath.nc",
+  //                          "/naslx/ptmp/2/di56dok/data/tohoku_gebco_ucsb3_500m_hawaii_displ.nc",
+  //                          (float) 300., simulationArea);
+  SWE_AsagiScenario l_scenario( "/work/breuera/workspace/geo_information/output/tohoku_gebco_ucsb3_500m_hawaii_bath.nc",
+                                "/work/breuera/workspace/geo_information/output/tohoku_gebco_ucsb3_500m_hawaii_displ.nc",
+                                (float) 14400., simulationArea, true);
+  #else
   // create a simple artificial scenario
   SWE_BathymetryDamBreakScenario l_scenario;
+  #endif
 
   //! number of checkpoints for visualization (at each checkpoint in time, an output file is written).
   int l_numberOfCheckPoints = 40;
@@ -218,7 +258,7 @@ int main( int argc, char** argv ) {
   #endif
 
   // initialize the wave propgation block
-  l_wavePropgationBlock.initScenario(l_scenario);
+  l_wavePropgationBlock.initScenario( l_scenario, true );
 
   //! time when the simulation ends.
   float l_endSimulation = l_scenario.endSimulation();
@@ -330,8 +370,27 @@ int main( int argc, char** argv ) {
 
   // write the output at time zero
   l_sweLogger.printOutputTime(0);
+  #ifdef WRITENETCDF
+  //boundary size of the ghost layers
+  int l_boundarySize[4];
+  l_boundarySize[0] = l_boundarySize[1] = l_boundarySize[2] = l_boundarySize[3] = 1;
+
+  //construct a NetCdfWriter
+  std::string l_fileName = generateFileName(l_baseName,l_blockPositionX,l_blockPositionY);
+  io::NetCdfWriter l_netCdfWriter( l_fileName, l_nXLocal, l_nYLocal );
+  //create the netCDF-file
+  l_netCdfWriter.createNetCdfFile( l_dX, l_dY,
+                                   l_originX, l_originY );
+  l_netCdfWriter.writeBathymetry( l_wavePropgationBlock.getBathymetry(),
+                                  l_boundarySize );
+  l_netCdfWriter.writeUnknowns( l_wavePropgationBlock.getWaterHeight(),
+                                l_wavePropgationBlock.getDischarge_hu(),
+                                l_wavePropgationBlock.getDischarge_hv(),
+                                l_boundarySize, (float) 0.);
+#else
   l_wavePropgationBlock.writeVTKFileXML( generateFileName(l_baseName,0,l_blockPositionX,l_blockPositionY),
                                          l_nXLocal*l_blockPositionX, l_nYLocal*l_blockPositionY);
+#endif
 
 
   /**
@@ -352,7 +411,6 @@ int main( int argc, char** argv ) {
     // do time steps until next checkpoint is reached
     while( l_t < l_checkPoints[c] ) {
       // exchange ghost and copy layers
-      l_sweLogger.printString("Exchanging ghost and copy layers.");
       exchangeLeftRightGhostLayers( l_leftNeighborRank,  l_leftInflow,  l_leftOutflow,
                       l_rightNeighborRank, l_rightInflow, l_rightOutflow,
                       l_mpiCol );
@@ -364,7 +422,7 @@ int main( int argc, char** argv ) {
       // reset the cpu clock
       l_sweLogger.resetCpuClockToCurrentTime();
 
-      // set values in ghost cells:
+      // set values in ghost cells
       l_wavePropgationBlock.setGhostLayer();
 
       // compute numerical flux on each edge
@@ -396,9 +454,16 @@ int main( int argc, char** argv ) {
     // print current simulation time
     l_sweLogger.printOutputTime(l_t);
 
-    // write vtk output
+    // write output
+    #ifdef WRITENETCDF
+    l_netCdfWriter.writeUnknowns( l_wavePropgationBlock.getWaterHeight(),
+                                  l_wavePropgationBlock.getDischarge_hu(),
+                                  l_wavePropgationBlock.getDischarge_hv(),
+                                  l_boundarySize, l_t);
+    #else
     l_wavePropgationBlock.writeVTKFileXML( generateFileName(l_baseName,c,l_blockPositionX,l_blockPositionY),
                                           l_blockPositionX*l_nXLocal, l_blockPositionY*l_nYLocal);
+    #endif
   }
 
   /**

src/examples/swe_wavepropagation.cpp

@@ -23,21 +23,35 @@
  *
  * @section DESCRIPTION
  *
- * Very basic setting of SWE, which uses a wave propagation solver and an artificial scenario on a single block.
+ * Basic setting of SWE, which uses a wave propagation solver and an artificial or ASAGI scenario on a single block.
  */
 
-#include "../tools/help.hh"
+#include <cassert>
 #include <cstdlib>
 #include <string>
+#include "../tools/help.hh"
 
 #include "../SWE_Block.hh"
+
 #ifndef CUDA
 #include "../SWE_WavePropagationBlock.hh"
 #else
 #include "../SWE_WavePropagationBlockCuda.hh"
 #endif
+
+#ifdef WRITENETCDF
+#include "../tools/NetCdfWriter.hh"
+#endif
+
+#ifdef ASAGI
+#include "../scenarios/SWE_AsagiScenario.hpp"
+#else
 #include "../scenarios/SWE_simple_scenarios.h"
-#include "../tools/Logger.hpp"
+#endif
+
+#ifdef READXML
+#include "../tools/CXMLConfig.hpp"
+#endif
 
 #ifndef STATICLOGGER
 #define STATICLOGGER
@@ -53,12 +67,14 @@ int main( int argc, char** argv ) {
    * Initialization.
    */
   // check if the necessary command line input parameters are given
+  #ifndef READXML
   if(argc != 4) {
     std::cout << "Aborting ... please provide proper input parameters." << std::endl
               << "Example: ./SWE_parallel 200 300 /work/openmp_out" << std::endl
               << "\tfor a single block of size 200 * 300" << std::endl;
     return 1;
   }
+  #endif
 
   //! number of grid cells in x- and y-direction.
   int l_nX, l_nY;
@@ -67,15 +83,58 @@ int main( int argc, char** argv ) {
   std::string l_baseName;
 
   // read command line parameters
+  #ifndef READXML
   l_nY = l_nX = atoi(argv[1]);
   l_nY = atoi(argv[2]);
   l_baseName = std::string(argv[3]);
+  #endif
 
-  //create a simple artificial scenario
+  // read xml file
+  #ifdef READXML
+  assert(false); //TODO: not implemented.
+  if(argc != 2) {
+    s_sweLogger.printString("Aborting. Please provide a proper input file.");
+    s_sweLogger.printString("Example: ./SWE_gnu_debug_none_augrie config.xml");
+    return 1;
+  }
+  s_sweLogger.printString("Reading xml-file.");
+
+  std::string l_xmlFile = std::string(argv[1]);
+  s_sweLogger.printString(l_xmlFile);
+
+  CXMLConfig l_xmlConfig;
+  l_xmlConfig.loadConfig(l_xmlFile.c_str());
+  #endif
+
+  #ifdef ASAGI
+  /* Information about the example bathymetry grid (tohoku_gebco_ucsb3_500m_hawaii_bath.nc):
+   *
+   * Pixel node registration used [Cartesian grid]
+   * Grid file format: nf = GMT netCDF format (float)  (COARDS-compliant)
+   * x_min: -500000 x_max: 6500000 x_inc: 500 name: x nx: 14000
+   * y_min: -2500000 y_max: 1500000 y_inc: 500 name: y ny: 8000
+   * z_min: -6.48760175705 z_max: 16.1780223846 name: z
+   * scale_factor: 1 add_offset: 0
+   * mean: 0.00217145586762 stdev: 0.245563641735 rms: 0.245573241263
+   */
+
+  //simulation area
+  float simulationArea[4];
+  simulationArea[0] = -450000;
+  simulationArea[1] = 6450000;
+  simulationArea[2] = -2450000;
+  simulationArea[3] = 1450000;
+
+  SWE_AsagiScenario l_scenario( "/work/breuera/workspace/geo_information/output/tohoku_gebco_ucsb3_500m_hawaii_bath.nc",
+                                "/work/breuera/workspace/geo_information/output/tohoku_gebco_ucsb3_500m_hawaii_displ.nc",
+                                (float) 28800., simulationArea, true);
+  #else
+  // create a simple artificial scenario
   SWE_BathymetryDamBreakScenario l_scenario;
+  #endif
 
   //! number of checkpoints for visualization (at each checkpoint in time, an output file is written).
-  int l_numberOfCheckPoints = 40;
+  int l_numberOfCheckPoints = 20;
 
   //! size of a single cell in x- and y-direction
   float l_dX, l_dY;
@@ -116,8 +175,27 @@ int main( int argc, char** argv ) {
      l_checkPoints[cp] = cp*(l_endSimulation/l_numberOfCheckPoints);
   }
 
+
   // write the output at time zero
+  s_sweLogger.printOutputTime((float) 0.);
+  #ifdef WRITENETCDF
+  //boundary size of the ghost layers
+  int l_boundarySize[4];
+  l_boundarySize[0] = l_boundarySize[1] = l_boundarySize[2] = l_boundarySize[3] = 1;
+
+  //construct a NetCdfWriter
+  std::string l_fileName = l_baseName;
+  io::NetCdfWriter l_netCdfWriter( l_fileName, l_nX, l_nY );
+  //create the netCDF-file
+  l_netCdfWriter.createNetCdfFile(l_dX, l_dY, l_originX, l_originY);
+  l_netCdfWriter.writeBathymetry(l_wavePropgationBlock.getBathymetry(), l_boundarySize);
+  l_netCdfWriter.writeUnknowns( l_wavePropgationBlock.getWaterHeight(),
+                                l_wavePropgationBlock.getDischarge_hu(),
+                                l_wavePropgationBlock.getDischarge_hv(),
+                                l_boundarySize, (float) 0.);
+  #else
   l_wavePropgationBlock.writeVTKFileXML(generateFileName(l_baseName,0,0,0), l_nX, l_nY);
+  #endif
 
 
   /**
@@ -159,11 +237,18 @@ int main( int argc, char** argv ) {
     // update the cpu time in the logger
     s_sweLogger.updateCpuTime();
 
-    // print current simulation time
+    // print current simulation time of the output
     s_sweLogger.printOutputTime(l_t);
 
-    // write vtk output
+    // write output
+#ifdef WRITENETCDF
+    l_netCdfWriter.writeUnknowns( l_wavePropgationBlock.getWaterHeight(),
+                                  l_wavePropgationBlock.getDischarge_hu(),
+                                  l_wavePropgationBlock.getDischarge_hv(),
+                                  l_boundarySize, l_t);
+#else
     l_wavePropgationBlock.writeVTKFileXML(generateFileName(l_baseName,c,0,0), l_nX, l_nY);
+#endif
   }
 
   /**
@@ -173,7 +258,7 @@ int main( int argc, char** argv ) {
   s_sweLogger.printStatisticsMessage();
 
   // print the cpu time
-  s_sweLogger.printCpuTime("CPU/GPU time");
+  s_sweLogger.printCpuTime();
 
   // print the wall clock time (includes plotting)
   s_sweLogger.printWallClockTime(time(NULL));

src/scenarios/SWE_AsagiScenario.hpp

@@ -25,19 +25,15 @@
  * Access to bathymetry and displacement files with ASAGI.
  */
 
-#ifndef ASAGI_HPP_
-#define ASAGI_HPP_
+#ifndef SWEASAGISCENARIO_HPP_
+#define SWEASAGISCENARIO_HPP_
 
 #include <cassert>
 #include <string>
 #include <asagi.h>
 #include "SWE_Scenario.h"
 
-namespace scenarios {
-  class Asagi;
-}
-
-class scenarios::Asagi: public SWE_Scenario {
+class SWE_AsagiScenario: public SWE_Scenario {
 //private:
     //! pointer to the Asagi bathymetry grid
     asagi::Grid* bathymetryGrid;
@@ -75,17 +71,17 @@ class scenarios::Asagi: public SWE_Scenario {
      * @param i_displacementFile path to the netCDF-displacement file
      * @param i_duration time the simulation runs (in seconds)
      */
-    Asagi ( const std::string i_bathymetryFile,
-            const std::string i_displacementFile,
-            const float i_duration,
-            const float i_simulationArea[4],
-            const bool i_dynamicDisplacement = false ):
-              dynamicDisplacement(i_dynamicDisplacement),
-              duration(i_duration) {
-      //create the bathymetry grid
-      bathymetryGrid = asagi::Grid::create( asagi::Grid::FLOAT );
-      //create the displacement grid
-      displacementGrid = asagi::Grid::create( asagi::Grid::FLOAT );
+   SWE_AsagiScenario ( const std::string i_bathymetryFile,
+                       const std::string i_displacementFile,
+                       const float i_duration,
+                       const float i_simulationArea[4],
+                       const bool i_dynamicDisplacement = false ):
+                       dynamicDisplacement(i_dynamicDisplacement),
+                       duration(i_duration) {
+                       //create the bathymetry grid
+                       bathymetryGrid = asagi::Grid::create( asagi::Grid::FLOAT );
+                       //create the displacement grid
+                       displacementGrid = asagi::Grid::create( asagi::Grid::FLOAT );
 
       int l_asagiOpen = bathymetryGrid->open(i_bathymetryFile.c_str());
       //open the bathymetry grid
@@ -154,7 +150,7 @@ class scenarios::Asagi: public SWE_Scenario {
 
     }
 
-    virtual ~Asagi() {
+    virtual ~SWE_AsagiScenario() {
     }
 
     void deleteGrids() {
@@ -287,4 +283,4 @@ class scenarios::Asagi: public SWE_Scenario {
     };
 };
 
-#endif /* ASAGI_HPP_ */
+#endif /* SWEASAGISCENARIO_HPP_ */