Nathan Goldbaum avatar Nathan Goldbaum committed 60c72bb Merge

Merged in MatthewTurk/enzo-3.0 (pull request #24)

Comments (0)

Files changed (68)

 doc/manual/build
 
 run/results.js
+j
+src/enzo/build/generated_code/*

input/GMCtable.in

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run/Hydro/Hydro-3D/CollapseTestAccretingParticleAMR/user_script.py

+from yt.mods import *
+
+def main():
+    import enzo
+    import message_passing
+    print dir(message_passing)
+    pf = EnzoStaticOutputInMemory()
+    total_cells = sum(g.ActiveDimensions.prod() for g in pf.h.grids)
+    message_passing.test_event(total_cells)

src/enzo/Makefile

 ENZO_DIR = .
 CONFIG_DIR = build/config
 BUILD_DIR = build/objects
+GEN_DIR = build/generated_code
 UTILS_DIR = build/utilities
 MODULES  = 
 VERBOSE  = 0
 
 SVN      = hg
 
+vpath %.o $(BUILD_DIR)/
+vpath %.C $(GEN_DIR)/
+vpath %.h $(GEN_DIR)/
+
 #-----------------------------------------------------------------------
 # Make.config.settings is used for setting default values to all compile-time 
 # configuration settings.
 # OBJECT FILES
 #=======================================================================
 
+include io/python_bridge/Make.module.objects
 include communication/Make.module.objects
 include control/Make.module.objects
 include grid/Make.module.objects
 include solvers/Make.module.objects
 include utilities/Make.module.objects
 
-vpath %.o $(BUILD_DIR)/
-
 OBJS_CONFIG_LIB=$(ENZO_OBJS)
 OBJS_LINK=$(addprefix $(BUILD_DIR)/, $(OBJS_LIB))
 
 #-----------------------------------------------------------------------
 
 all: MKDIR MACHNOTES MAKETAGS $(EXE).exe
+.DEFAULT_GOAL: all
 
 # I believe this has to be done here, as it is target-specific.
 lib: CFLAGS   += $(MACH_SHARED_FLAGS) 
 #-----------------------------------------------------------------------
 
 .PHONY: MKDIR
-MKDIR: $(BUILD_DIR)
+MKDIR: $(BUILD_DIR) $(GEN_DIR)
 
 $(BUILD_DIR):
 	mkdir -p $(BUILD_DIR)
 
+$(GEN_DIR):
+	mkdir -p $(GEN_DIR)
+
 MAKETAGS:
 	@(if [ "$(ETAGS_COMMAND)" != "0" ]; then \
 	   	echo -e "Making Tags with $(ETAGS_COMMAND)" ; \
 	   echo "Failed! See $(OUTPUT) for error messages"; \
 	fi)
 
-.pyx.C: 
-	@cython --cplus $*.pyx -o $< 
-ProblemType_Python.o: python_bridge/problemtype_handler.o
-InitializePythonInterface.C: $(PYTHON_INTERFACE_TARGETS)
-InitializePythonInterface_finderfunctions.inc: global_data.h
+io/InitializePythonInterface.C: io/InitializePythonInterface_finderfunctions.inc
+io/InitializePythonInterface_finderfunctions.inc: headers/global_data.h
 	@python $(UTILS_DIR)/create_dictionary_mapping.py 
 
 #-----------------------------------------------------------------------
 	  fi ; \
 	fi)
 
+.pyx.o:
+	@rm -f $(BUILD_DIR)/$@
+	@echo "Compiling $<"
+	@cython --cplus $< -o $(GEN_DIR)/$*.C
+	@(if [ $(VERBOSE) -eq 0 ]; then \
+	  $(CXX) -c -o $(BUILD_DIR)/$@ $(DEFINES) $(CXXFLAGS) $(INCLUDES) $(GEN_DIR)/$*.C \
+	    >& $(OUTPUT) ; \
+	  if [ ! -e $(BUILD_DIR)/$@ ]; then \
+             echo; \
+             echo "$(CXX) -c -o $(BUILD_DIR)/$@ $(DEFINES) $(CXXFLAGS) $(INCLUDES) $*.C"; \
+             echo; \
+             $(CXX) -c -o $(BUILD_DIR)/$@ $(DEFINES) $(CXXFLAGS) $(INCLUDES) $<;\
+             echo; \
+             exit 1; \
+          fi ; \
+	else \
+	  $(CXX) -c -o $(BUILD_DIR)/$@ $(DEFINES) $(CXXFLAGS) $(INCLUDES) $(GEN_DIR)/$*.C \
+	    >> $(OUTPUT) 2>&1 ; \
+	  if [ ! -e $(BUILD_DIR)/$@ ]; then \
+	     echo "See $(OUTPUT) for error messages"; \
+	     exit 1; \
+	  fi ; \
+	fi)
+
 .C.o:
 	@rm -f $(BUILD_DIR)/$@
 	@echo "Compiling $<"
 .PHONY: dep
 dep:
 	@echo "Updating DEPEND"
-	-@(makedepend $(DEFINES) $(INCLUDES) -fDEPEND -o.o -m -- -- */*.C  *.C *.c *.F *.F90 */*.h *.h) >& out.make.DEPEND
+	-@(makedepend $(DEFINES) $(INCLUDES) -fDEPEND -o.o -m -- -- */*.C  ) >& out.make.DEPEND	
+	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- *.C) >> out.make.DEPEND 2>&1
+	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- *.c) >> out.make.DEPEND 2>&1	
+	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- *.F) >> out.make.DEPEND 2>&1
+	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- *.F90) >> out.make.DEPEND 2>&1
+	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- */*.h) >> out.make.DEPEND 2>&1
+	-@(makedepend $(DEFINES) $(INCLUDES) -a -fDEPEND -o.o -m -- -- *.h) >> out.make.DEPEND 2>&1
 
 include DEPEND
 
 clean:
 	-@rm -f *.so *.o uuid/*.o *.mod *.f *.f90 DEPEND.bak *~ $(OUTPUT) *.exe \
           $(BUILD_DIR)/*.o \
+          $(BUILD_DIR)/*.C \
+          $(BUILD_DIR)/*.h \
+          $(GEN_DIR)/*.C $(GEN_DIR)/*.h \
           io/auto_show*.C hydro_rk/*.o *.oo hydro_rk/*.oo \
           uuid/*.oo DEPEND TAGS \
-          libconfig/*.o \
-          python_bridge/problemtype_handler.C \
-          python_bridge/problemtype_handler.h \
-          python_bridge/problemtype_handler.o
+          libconfig/*.o 
 	-@touch DEPEND
 
 #-----------------------------------------------------------------------

src/enzo/build/config/Make.config.assemble

         ASSEMBLE_NEW_PROBLEM_TYPES_INCLUDES = $(MACH_INCLUDES_NEW_PROBLEM_TYPES)
         ASSEMBLE_NEW_PROBLEM_TYPES_LIBS     = $(MACH_LIBS_NEW_PROBLEM_TYPES)
         ifeq ($(CONFIG_PYTHON),yes)
-            OBJS_PYTHON += python_bridge/problemtype_handler.o
-            OBJS_PYTHON += ProblemType_Python.o
+            OBJS_PYTHON += problemtype_handler.o message_passing.o enzo_includes.o
         endif
     endif
 
                $(ASSEMBLE_PYTHON_INCLUDES) \
                $(ASSEMBLE_NEW_PROBLEM_TYPES_INCLUDES) \
                $(ASSEMBLE_PAPI_INCLUDES) \
-               $(MAKEFILE_INCLUDES)   -I. -Iheaders/
+               $(MAKEFILE_INCLUDES)   -I. -Iheaders/ -Ibuild/generated_code/
 
-    OBJS_LIB = $(OBJS_CONFIG_LIB) \
-    	       $(OBJS_PHOTON_LIB) \
-    	       $(OBJS_LCAPERF_LIB) \
-	       $(OBJS_HYDRO_RK) \
-	       $(OBJS_ECUDA_LIB) \
-	       $(OBJS_PYTHON) 
+    OBJS_LIB = \
+           $(OBJS_PYTHON) \
+           $(OBJS_CONFIG_LIB) \
+           $(OBJS_PHOTON_LIB) \
+           $(OBJS_LCAPERF_LIB) \
+           $(OBJS_HYDRO_RK) \
+           $(OBJS_ECUDA_LIB)
 
     LIBS = $(MACH_LIBS) \
            $(ASSEMBLE_MPI_LIBS) \

src/enzo/build/utilities/create_dictionary_mapping.py

-import sys, glob
+import sys, glob, os
 
 # Enzo's configuration simply does not scale.  There's no schema, there's no
 # correlation between writing and reading, and there's no mechanism for
     return vn.replace(";","").replace(",","")
 
 def parse_file(fn):
+    if not os.path.exists(fn):
+        fn = os.path.join("headers", fn)
+    if not os.path.exists(fn):
+        print "SKIPPING", fn
+        return
     all_vars = []
     for line in open(fn):
         line = line[:line.rfind("//")]
 
 if __name__ == "__main__":
     results = parse_file("global_data.h")
-    output = open("InitializePythonInterface_finderfunctions.inc", "w")
+    output = open("io/InitializePythonInterface_finderfunctions.inc", "w")
     for vn, vt in results:
         a = finder_function(vn, vt)
         output.write(a)

src/enzo/communication/CommunicationShareActiveParticles.C

       mpi_recv_buffer_size = new int[NumberOfProcessors];
 
       // First determine the buffer size, then we can fill it.
-      header_size = ap_info->return_header_size();
-      element_size = ap_info->return_element_size();
+      header_size = sizeof(int);
+      element_size = ap_info->ReturnElementSize();
       size = 0;
       for (i = 0; i < TotalNumberToMove; i++)
 	if (SendList[i]->ReturnType() == type) size++;
 
       // Pack the buffer, ordered by destination processor
       position = 0;
-      for (proc = 0; proc < NumberOfProcessors; proc++)
-	ap_info->allocate_buffer(SendList, size, mpi_buffer, 
-				 total_buffer_size, mpi_buffer_size[proc], 
-				 position, ap_id, proc);
-
+      char *pack_buffer = mpi_buffer;
+      int offset = 0;
+      for (proc = 0; proc < NumberOfProcessors; proc++) {
+	    mpi_buffer_size[proc] = ap_info->FillBuffer(SendList, size, mpi_buffer + offset);
+        offset += size*element_size + header_size;
+      }
       /* Get counts from each processor to allocate buffers. */
 
       MPI_Arg *MPI_SendListCount = new MPI_Arg[NumberOfProcessors];
       for (proc = 0; proc < NumberOfProcessors; proc++) {
 	NumberOfNewParticlesThisProcessor = (MPI_RecvListCount[proc] - header_size) / element_size;
 	if (NumberOfNewParticlesThisProcessor > 0)
-	  ap_info->unpack_buffer(mpi_recv_buffer + MPI_RecvListDisplacements[proc], 
-				 MPI_RecvListCount[proc],
-				 NumberOfNewParticlesThisProcessor,
-				 SharedList, count);
+	  ap_info->UnpackBuffer(mpi_recv_buffer + MPI_RecvListDisplacements[proc], 
+                 count, SharedList, MPI_RecvListCount[proc]);
+      count += MPI_RecvListCount[proc];
       }
 
       NumberOfReceives = NumberOfNewParticles;
     NumberOfReceives = TotalNumberToMove;
     SharedList = SendList;
   }
-  
+
   // First sort the list by destination grid, so the searching for
   // grids is more efficient.
   //qsort(SharedList, NumberOfReceives, star_data_size, compare_star_grid);

src/enzo/control/EventHooks.C

 
 #include "ProblemType.h"
 #include "EventHooks.h"
+#include "EventDataContainers.h"
 
 void RunEventHooks(std::string event_name, HierarchyEntry *Grids[],
-                    TopGridData &MetaData)
+                    TopGridData &MetaData, EventDataContainer *LocalData)
 {
     if (event_hooks.empty()) {
         return;
     }
+
+    EnzoPluginMap *plugins = get_plugins();
+
     std::pair<std::multimap<std::string, std::string>::iterator,
-              std::multimap<std::string, std::string>::iterator> it;
+              std::multimap<std::string, std::string>::iterator> range;
 
-    it = event_hooks.equal_range(event_name);
+    range = event_hooks.equal_range(event_name);
 
-    std::multimap<std::string, std::string>::iterator itr = it.first;
-
-    if (itr == event_hooks.end())
+    if (range.first == range.second)
     {
         /* This is commented out until further notice */
-        /*std::cout << "Event plugin for hook " << event_name;
-        std::cout << " not found." << std::endl;*/
-        return;
+        std::cout << "Event plugins for hook " << event_name;
+        std::cout << " not found." << std::endl;
+        ENZO_FAIL("Event hook not found!");
     }
-    for (; itr != it.second ; itr++)
+    for (std::multimap<std::string, std::string>::iterator itr = range.first;
+         itr != range.second;
+         ++itr)
     {
         std::string plugin_name = (*itr).second;
         /* Debugging statement is next */
-        /*std::cout << "Loading event plugin for hook " << event_name;
+        /*std::cout << "Loading event plugin for hook " << (*itr).first;
         std::cout << " with name " << plugin_name << std::endl;*/
-        plugin_function the_plugin = plugins[plugin_name];
-        the_plugin(Grids, MetaData);
+        if ((*plugins).count(plugin_name) == 0) {
+            std::cout << "Could not find the plugin " << plugin_name << std::endl;
+            std::cout << "But found " << (*plugins).count(plugin_name) << " values." << std::endl;
+            std::cout << "Found:" << std::endl;
+            std::map<std::string, plugin_function>::iterator pit;
+            for (pit = (*plugins).begin() ; pit != (*plugins).end() ; ++pit) {
+                std::cout << "    " << pit->first << std::endl;
+            }
+            std::cout << std::endl;
+            ENZO_FAIL("Could not find the plugin!");
+        }
+        plugin_function the_plugin = (*plugins)[plugin_name];
+        the_plugin(Grids, MetaData, LocalData);
     }
 
 }
     event_hooks.insert(std::pair<std::string, std::string>
                     (event_name, plugin_name));
                     
-    if (event_hooks.empty()) {
-        std::cout << "EVENT HOOKS IS EMPTY1" << std::endl;
-    }
-    if (event_hooks.empty()) {
-        std::cout << "EVENT HOOKS IS EMPTY2" << std::endl;
-    }
 }
 
-void RegisterEventPlugin(std::string plugin_name, plugin_function the_plugin)
+int RegisterEventPlugin(std::string plugin_name, plugin_function the_plugin)
 {
-    std::cout << "Registering plugin " << plugin_name << std::endl;
+    
+    if (the_plugin == NULL) ENZO_FAIL("Plugin is null!");
 
-    plugins.insert(std::pair<std::string, plugin_function >
-                    (plugin_name, the_plugin));
+    EnzoPluginMap *plugins = get_plugins();
+    std::cout << "Registering plugin " << plugin_name << " so we have " 
+              << (*plugins).size() << " plugins. " << std::endl;
+
+    (*plugins)[plugin_name] = the_plugin;
+    return (*plugins).size();
+}
+
+EnzoPluginMap *get_plugins()
+{
+    static EnzoPluginMap the_plugins;
+    return &the_plugins;
 }
 
 #endif

src/enzo/control/EvolveHierarchy.C

 Eint64 mused(void);
 #endif
 #ifdef USE_PYTHON
-int CallPython(LevelHierarchyEntry *LevelArray[], TopGridData *MetaData,
+int CallPython(LevelHierarchyEntry *LevelArray[],
+               HierarchyEntry *Grids[],
+               TopGridData *MetaData,
                int level, int from_topgrid);
 #endif
 
 
 #ifdef USE_PYTHON
     LCAPERF_START("CallPython");
-    CallPython(LevelArray, &MetaData, 0, 1);
+    CallPython(LevelArray, NULL, &MetaData, 0, 1);
     LCAPERF_STOP("CallPython");
 #endif
 

src/enzo/control/EvolveLevel.C

 #endif
 #ifdef NEW_PROBLEM_TYPES
 #include "EventHooks.h"
+#include "EventDataContainers.h"
 #else
-void RunEventHooks(char *, HierarchyEntry *Grid[], TopGridData &MetaData) {}
+void RunEventHooks(char *, HierarchyEntry *Grids[],
+                   TopGridData &MetaData, void *) {};
 #endif
  
 /* function prototypes */
 
 void my_exit(int status);
  
-int CallPython(LevelHierarchyEntry *LevelArray[], TopGridData *MetaData,
+int CallPython(LevelHierarchyEntry *LevelArray[],
+               HierarchyEntry *Grids[],
+               TopGridData *MetaData,
                int level, int from_topgrid);
 int MovieCycleCount[MAX_DEPTH_OF_HIERARCHY];
 double LevelWallTime[MAX_DEPTH_OF_HIERARCHY];
 {
   /* Declarations */
 
+#ifdef NEW_PROBLEM_TYPES
+  EvolveLevelEventDataContainer *LocalData = new EvolveLevelEventDataContainer;
+  EventDataContainer *LocalDataP = static_cast<EventDataContainer*>(LocalData);
+#else
+  void *LocalDataP = NULL;
+  void *Localata = NULL;
+#endif
+
   int dbx = 0;
 
   FLOAT When, GridTime;
   int *NumberOfSubgrids = new int[NumberOfGrids];
   fluxes ***SubgridFluxesEstimate = new fluxes **[NumberOfGrids];
   int *TotalActiveParticleCountPrevious = new int[NumberOfGrids];
-  RunEventHooks("EvolveLevelTop", Grids, *MetaData);
+  /*RunEventHooks("EvolveLevelTop", Grids, *MetaData, LocalDataP);*/
 
 #ifdef FLUX_FIX
   /* Create a SUBling list of the subgrids */
 			  );
 #ifdef USE_PYTHON
     LCAPERF_START("CallPython");
-    CallPython(LevelArray, MetaData, level, 0);
+    CallPython(LevelArray, Grids, MetaData, level, 0);
     LCAPERF_STOP("CallPython");
 #endif
 

src/enzo/control/SetDefaultGlobalValues.C

   H2StarMakerH2FloorInColdGas = 0.0;
   H2StarMakerColdGasTemperature = 1e4;
 
+  GMCParticleRNGSeed               = INT_UNDEFINED;
+  GMCParticleRNGCalls              = 0;
+
   NumberOfParticleAttributes       = INT_UNDEFINED;
   AddParticleAttributes            = FALSE;
   LastSupernovaTime                = FLOAT_UNDEFINED;

src/enzo/grid/Make.module.objects

 	Grid_ComputeCellCenteredField.o \
 	Grid_ComputeConductionTimeStep.o \
 	Grid_ComputeCoolingTime.o \
+	Grid_ComputeDarkMatterDensity.o \
 	Grid_ComputeDustTemperatureField.o \
 	Grid_ComputeElementalDensity.o \
 	Grid_ComputeEnergy.o \

src/enzo/grid/communication/Grid_CommunicationSendActiveParticles.C

       // determine the number of active particles with this type on
       // the other processor.
 
-      header_size = ap_info->return_header_size();
-      element_size = ap_info->return_element_size();
       if (MyProcessorNumber == ProcessorNumber) {
 	size = 0;
 	for (i = 0; i < NumberOfActiveParticles; i++)
       } else {
 	size = NumberOfActiveParticles;
       }
-      TransferSize = header_size + size*element_size;
 
 #ifdef USE_MPI
       if (CommunicationDirection == COMMUNICATION_RECEIVE)
   if (MyProcessorNumber == ProcessorNumber) {
     position = 0;
     ap_id = ap_info->GetEnabledParticleID();
-    ap_info->allocate_buffer(ActiveParticles, NumberOfActiveParticles,
-			     buffer, TransferSize, buffer_size, position, ap_id, -1);
+    ap_info->FillBuffer(ActiveParticles, NumberOfActiveParticles, buffer);
     if (DeleteParticles == true) {
       for (i = 0; i < NumberOfActiveParticles; i++)
 	if (ActiveParticles[i]->ReturnType() == type) {
     NewParticles = new ActiveParticleType*[NumberOfNewParticles];
     buffer_size = header_size + NumberOfNewParticles*element_size;
     npart = 0;
-    ap_info->unpack_buffer(buffer, buffer_size, NumberOfNewParticles,
+    ap_info->UnpackBuffer(buffer, NumberOfNewParticles,
 			   NewParticles, npart);
 
     for (i = 0; i < NumberOfNewParticles; i++)

src/enzo/grid/particles/Grid_ActiveParticleHandler.C

   for (i = 0; i < EnabledActiveParticlesCount; i++)
   {
     ActiveParticleType_info *ActiveParticleTypeToEvaluate = EnabledActiveParticles[i];
-    ActiveParticleTypeToEvaluate->describe_data_flags(flags);
+    ActiveParticleTypeToEvaluate->DescribeSupplementalData(flags);
   }
 
   struct ActiveParticleFormationData supplemental_data = data_default;
   for (i = 0; i < EnabledActiveParticlesCount; i++)
   {
     ActiveParticleType_info *ActiveParticleTypeToEvaluate = EnabledActiveParticles[i];
-    ActiveParticleTypeToEvaluate->formation_function(
+    ActiveParticleTypeToEvaluate->EvaluateFormation(
                                 this, supplemental_data);
     NumberOfNewParticles += supplemental_data.NumberOfNewParticles;
     
     for (i = 0; i < EnabledActiveParticlesCount; i++)
       {
 	ActiveParticleType_info *ActiveParticleTypeToEvaluate = EnabledActiveParticles[i];
-	ActiveParticleTypeToEvaluate->feedback_function(this, supplemental_data);
+	ActiveParticleTypeToEvaluate->EvaluateFeedback(this, supplemental_data);
       }
   
   ActiveParticleType::DestroyData(this, supplemental_data);

src/enzo/grid/solvers/Grid_ComputeDarkMatterDensity.C

+/***********************************************************************
+/
+/  GRID CLASS (COMPUTE THE DARK MATTER DENSITY)
+/
+/  written by: Stephen Skory
+/  date:       August, 2012
+/  modified1:
+/
+/  PURPOSE:
+/
+/  RETURNS:
+/
+************************************************************************/
+
+#include "preincludes.h"
+#include "ErrorExceptions.h"
+#include "macros_and_parameters.h"
+#include "typedefs.h"
+#include "global_data.h"
+#include "Fluxes.h"
+#include "GridList.h"
+#include "ExternalBoundary.h"
+#include "fortran.def"
+#include "Grid.h"
+
+int grid::ComputeDarkMatterDensity(float *DarkMatterDensity)
+{
+    /* Return if this doesn't concern us. */
+    
+    if (ProcessorNumber != MyProcessorNumber)
+      return SUCCESS;
+
+    int i, j, k, dim;
+    int ActiveDim[MAX_DIMENSION];
+
+    /* Compute the size of the field. */
+    
+    int size = 1;
+    for (dim = 0; dim < GridRank; dim++)
+      size *= GridDimension[dim];
+    
+    /* Get grid particle density field */
+    float SaveGravityResolution = GravityResolution;
+    GravityResolution = 1;
+    this->InitializeGravitatingMassFieldParticles(RefineBy);
+    this->ClearGravitatingMassFieldParticles();
+    this->DepositParticlePositions(this, Time,
+                     GRAVITATING_MASS_FIELD_PARTICLES);
+    GravityResolution = SaveGravityResolution;
+    
+    /* If present, write out the GravitatingMassFieldParticles. */
+    
+    for (dim = 0; dim < 3; dim++)
+      ActiveDim[dim] = GridEndIndex[dim] - GridStartIndex[dim] +1;
+    
+    if (GravitatingMassFieldParticles != NULL) {
+      
+      /* Set dimensions. */
+      
+      int StartIndex[] = {0,0,0}, EndIndex[] = {0,0,0};
+      for (dim = 0; dim < GridRank; dim++) {
+        StartIndex[dim] = nint((GridLeftEdge[dim] -
+                   GravitatingMassFieldParticlesLeftEdge[dim])/
+                   GravitatingMassFieldParticlesCellSize);
+        EndIndex[dim] = nint((GridRightEdge[dim] -
+                   GravitatingMassFieldParticlesLeftEdge[dim])/
+                   GravitatingMassFieldParticlesCellSize) - 1;
+      }
+        
+      /* Copy active part of field into grid */
+      
+      for (k = StartIndex[2]; k <= EndIndex[2]; k++)
+        for (j = StartIndex[1]; j <= EndIndex[1]; j++)
+          for (i = StartIndex[0]; i <= EndIndex[0]; i++)
+            DarkMatterDensity[(i-StartIndex[0]) +
+             (j-StartIndex[1])*ActiveDim[0] +
+             (k-StartIndex[2])*ActiveDim[0]*ActiveDim[1] ] =
+              GravitatingMassFieldParticles[ i +
+              j*GravitatingMassFieldParticlesDimension[0] +
+              k*GravitatingMassFieldParticlesDimension[0]*
+              GravitatingMassFieldParticlesDimension[1]];
+