Merge, but also fix some things (mainly that the geometry reader had …

…the wrong premable length)
hemelb-codes · Jan 9, 2012 · 9cb6a1f · 9cb6a1f
2 parents fa101ec + 6236f6b
commit 9cb6a1f
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Showing 59 changed files with 685 additions and 500 deletions.
diff --git a/.hgsubstate b/.hgsubstate
@@ -1 +1 @@
-84e30137ca192ffd22b2426bc473e547c628311f RegressionTests
+17380f5a9c3c63bf4627e8d86f49232e18e2ead8 RegressionTests
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -20,7 +20,8 @@ option(HEMELB_USE_STREAKLINES "Calculate streakline images" ON)
 option(HEMELB_USE_ALL_WARNINGS_GNU "Show all compiler warnings on development builds (gnu-style-compilers)" ON)
 option(HEMELB_USE_BOOST "Use Boost" OFF)
 set(HEMELB_OPTIMISATION "-O4" CACHE STRING "Optimisation level (can be blank or -O1 to -O4)")
-
+set(HEMELB_STEERING_HOST "CCS" CACHE STRING "Use a default host suffix for steering? (CCS, NGS2Leeds, NGS2Manchester, LONI, NCSA or blank)")
+option(HEMELB_DEPENDENCIES_SET_RPATH "Set runtime RPATH" ON)
 #------- Dependencies -----------
 
 add_subdirectory(dependencies)
@@ -50,6 +51,10 @@ ExternalProject_Add(
 	-DMPI_CXX_NO_INTERROGATE=${MPI_CXX_NO_INTERROGATE}
 	-DHEMELB_USE_ALL_WARNINGS_GNU=${HEMELB_USE_ALL_WARNINGS_GNU}
 	-DHEMELB_USE_BOOST=${HEMELB_USE_BOOST}
+	-DHEMELB_STEERING_HOST=${HEMELB_STEERING_HOST}
+	-DCTEMPLATE_USE_STATIC=${CTEMPLATE_USE_STATIC}
+	-DCPPUNIT_USE_STATIC=${CPPUNIT_USE_STATIC}
+	-DHEMELB_DEPENDENCIES_SET_RPATH=${HEMELB_DEPENDENCIES_SET_RPATH}
 )
 ExternalProject_Get_Property(hemelb install_dir)
 

diff --git a/Code/CMakeLists.txt b/Code/CMakeLists.txt
@@ -10,6 +10,8 @@ option(HEMELB_BUILD_UNITTESTS "Build the unit-tests" ON)
 option(HEMELB_USE_ALL_WARNINGS_GNU "Show all compiler warnings on development builds (gnu-style-compilers)" ON)
 option(HEMELB_USE_STREAKLINES "Calculate streakline images" ON)
 option(HEMELB_USE_BOOST "Use Boost" OFF)
+option(HEMELB_DEPENDENCIES_SET_RPATH "Set runtime RPATH" ON)
+
 set(HEMELB_LOG_LEVEL info
 	CACHE STRING "Log level, choose 'debug', 'warning', or 'info'" )
 set(HEMELB_STEERING_LIB basic
@@ -42,9 +44,10 @@ list(APPEND CMAKE_INCLUDE_PATH ${HEMELB_DEPENDENCIES_INSTALL_PATH}/include)
 list(APPEND CMAKE_LIBRARY_PATH ${HEMELB_DEPENDENCIES_INSTALL_PATH}/lib)
 
 #--- Set up runtime search path for DLLs -----
-
-SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-SET(CMAKE_INSTALL_RPATH "${HEMELB_DEPENDENCIES_PATH}/lib")
+if(HEMELB_DEPENDENCIES_SET_RPATH)
+	SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+	SET(CMAKE_INSTALL_RPATH "${HEMELB_DEPENDENCIES_PATH}/lib")
+endif()
 
 #-------Check for platform dependent features ----
 
@@ -162,7 +165,8 @@ if(HEMELB_BUILD_UNITTESTS)
 		${TINYXML_LIBRARIES}
 		${CPPUNIT_LIBRARY}
 		${Boost_LIBRARIES}
-		${CTEMPLATE_LIBRARIES})
+		${CTEMPLATE_LIBRARIES}
+		${CMAKE_DL_LIBS}) #Because on some systems CPPUNIT needs to be linked to libdl
 	INSTALL(TARGETS unittests_hemelb RUNTIME DESTINATION bin)
 	list(APPEND RESOURCES unittests/resources/four_cube.dat unittests/resources/four_cube.xml unittests/resources/config.xml)
 endif()

diff --git a/Code/D3Q15.cc b/Code/D3Q15.cc
@@ -25,4 +25,42 @@ namespace hemelb
                                            1.0 / 72.0 };
 
   const int D3Q15::INVERSEDIRECTIONS[] = { 0, 2, 1, 4, 3, 6, 5, 8, 7, 10, 9, 12, 11, 14, 13 };
+
+  /*
+   *  Kinetic moments defined in d'Humieres 2002. To get the matrix below, columns 8 and 9 are respectively permuted
+   *  with columns 14 and 11 to match HemeLB's lattice velocitiy ordering.
+   *
+   *  See publication for  meaning of e, epsilon, etc. Other moments definitions are possible.
+   */
+  const distribn_t D3Q15::REDUCED_MOMENT_BASIS[NUM_KINETIC_MOMENTS][NUMVECTORS] = {{ -2, -1, -1, -1, -1, -1, -1,  1,  1,  1,  1,  1,  1,  1,  1}, // e
+                                                                                   { 16, -4, -4, -4, -4, -4, -4,  1,  1,  1,  1,  1,  1,  1,  1}, // epsilon
+                                                                                   {  0, -4,  4,  0,  0,  0,  0,  1, -1,  1, -1,  1, -1,  1, -1}, // q_x
+                                                                                   {  0,  0,  0, -4,  4,  0,  0,  1, -1,  1, -1, -1,  1, -1,  1}, // q_y
+                                                                                   {  0,  0,  0,  0,  0, -4,  4,  1, -1, -1,  1,  1, -1, -1,  1}, // q_z
+                                                                                   {  0,  2,  2, -1, -1, -1, -1,  0,  0,  0,  0,  0,  0,  0,  0}, // 3*p_xx
+                                                                                   {  0,  0,  0,  1,  1, -1, -1,  0,  0,  0,  0,  0,  0,  0,  0}, // p_ww = p_yy - p_zz
+                                                                                   {  0,  0,  0,  0,  0,  0,  0,  1,  1,  1,  1, -1, -1, -1, -1}, // p_xy
+                                                                                   {  0,  0,  0,  0,  0,  0,  0,  1,  1, -1, -1, -1, -1,  1,  1}, // p_yz
+                                                                                   {  0,  0,  0,  0,  0,  0,  0,  1,  1, -1, -1,  1,  1, -1, -1}, // p_zx
+                                                                                   {  0,  0,  0,  0,  0,  0,  0,  1, -1, -1,  1, -1,  1,  1, -1}  // m_xyz
+                                                                                  };
+
+  const distribn_t D3Q15::BASIS_TIMES_BASIS_TRANSPOSED[NUM_KINETIC_MOMENTS] = {18., 360., 40., 40., 40., 12., 4., 8., 8., 8., 8.};
+
+
+
+  void D3Q15::ProjectVelsIntoMomentSpace(const distribn_t * const velDistributions,
+                                         distribn_t * const moments)
+  {
+    for (unsigned momentIndex = 0; momentIndex < NUM_KINETIC_MOMENTS; momentIndex++)
+    {
+      moments[momentIndex] = 0.;
+      for (unsigned velocityIndex = 0; velocityIndex < NUMVECTORS; velocityIndex++)
+      {
+        moments[momentIndex] += REDUCED_MOMENT_BASIS[momentIndex][velocityIndex]
+            * velDistributions[velocityIndex];
+      }
+    }
+  }
+
 }
diff --git a/Code/D3Q15.h b/Code/D3Q15.h
@@ -21,6 +21,24 @@ namespace hemelb
 
       // The index of the inverse direction of each discrete velocity vector
       static const int INVERSEDIRECTIONS[NUMVECTORS];
+
+      /** Moments can be separated into two groups: a) hydrodynamic (conserved) and b) kinetic (non-conserved). */
+      static const unsigned NUM_KINETIC_MOMENTS = 11;
+
+      /** Matrix used to convert from the velocities space to the reduced moment space containing only kinetic moments. */
+      static const double REDUCED_MOMENT_BASIS[NUM_KINETIC_MOMENTS][NUMVECTORS];
+
+      /** Diagonal matrix REDUCED_MOMENT_BASIS * REDUCED_MOMENT_BASIS'. See #61 for the MATLAB code used to compute it (in case REDUCED_MOMENT_BASIS is modified). */
+      static const double BASIS_TIMES_BASIS_TRANSPOSED[NUM_KINETIC_MOMENTS];
+
+      /**
+       * Projects a velocity distributions vector into the (reduced) MRT moment space.
+       *
+       * @param velDistributions velocity distributions vector
+       * @param moments equivalent vector in the moment space
+       */
+      static void ProjectVelsIntoMomentSpace(const distribn_t * const velDistributions,
+                                             distribn_t * const moments);
   };
 }
 #endif /* HEMELB_D3Q15_H */
diff --git a/Code/SimulationMaster.cc b/Code/SimulationMaster.cc
@@ -125,16 +125,12 @@ void SimulationMaster::Initialise()
 
   simulationState = new hemelb::lb::SimulationState(simConfig->StepsPerCycle, simConfig->NumCycles);
 
-  // TODO The way we initialise LbmParameters is not great.
-  hemelb::lb::LbmParameters params(1000, 0.1);
-
   hemelb::log::Logger::Log<hemelb::log::Warning, hemelb::log::Singleton>("Initialising LatticeData.");
 
   timings[hemelb::reporting::Timers::netInitialise].Start();
   latticeData
       = hemelb::geometry::LatticeData::Load(hemelb::steering::SteeringComponent::RequiresSeparateSteeringCore(),
                                             simConfig->DataFilePath,
-                                            &params,
                                             timings);
   timings[hemelb::reporting::Timers::netInitialise].Stop();
 
@@ -145,8 +141,6 @@ void SimulationMaster::Initialise()
                                               simulationState,
                                               timings[hemelb::reporting::Timers::lb]);
 
-  latticeBoltzmannModel->GetLbmParams()->StressType = params.StressType;
-
   // Initialise and begin the steering.
   if (hemelb::topology::NetworkTopology::Instance()->IsCurrentProcTheIOProc())
   {

diff --git a/Code/configuration/SimConfig.cc b/Code/configuration/SimConfig.cc
@@ -60,6 +60,9 @@ namespace hemelb
       TiXmlElement* lSimulationElement = GetChild(iTopNode, "simulation", iIsLoading);
       DoIO(lSimulationElement, "cycles", iIsLoading, NumCycles);
       DoIO(lSimulationElement, "cyclesteps", iIsLoading, StepsPerCycle);
+      long dummyStress = -1;
+      DoIO(lSimulationElement, "stresstype", iIsLoading, dummyStress);
+      StressType = (lb::StressTypes) dummyStress;
 
       TiXmlElement* lGeometryElement = GetChild(iTopNode, "geometry", iIsLoading);
 

diff --git a/Code/configuration/SimConfig.h b/Code/configuration/SimConfig.h
@@ -34,6 +34,7 @@ namespace hemelb
         float MaxStress;
         unsigned long NumCycles;
         long StepsPerCycle;
+        lb::StressTypes StressType;
 
         void DoIO(TiXmlElement *iXmlNode,
                   bool iIsLoading,

diff --git a/Code/debug/common/ActiveDebugger.cc b/Code/debug/common/ActiveDebugger.cc
@@ -57,7 +57,7 @@ namespace hemelb
       if (mAmAttached)
         return;
 
-      int amWaiting = 1;
+      volatile int amWaiting = 1;
       int rank;
       MPI_Comm_rank(MPI_COMM_WORLD, &rank);
       int nProcs;

diff --git a/Code/debug/linux/resume.gdb b/Code/debug/linux/resume.gdb
@@ -1,7 +1,7 @@
 # Get out of sleep and disable the waiting flag
 up
 up
-set var amWaiting = 0
+set amWaiting = 0
 
 # Set up a breakpoint for our break function and a command to finish
 # it automatically