Merge branch 'master' of https://github.com/INMOST-DEV/INMOST

Conflicts:
	solver.cpp

CMakeLists.txt

@@ -101,6 +101,7 @@ option(COMPILE_TESTS "Compile some tests" OFF)
 option(USE_PARTITIONER_PARMETIS "Use ParMetis partitioner" OFF)
 option(USE_PARTITIONER_ZOLTAN "Use Zoltan partitioner" OFF)
 option(USE_SOLVER_METIS "Use METIS for matrix reordering" OFF)
+option(USE_SOLVER_MONDRIAAN "Use Mondriaan for matrix reordering" OFF)
 option(USE_SOLVER_PETSC "Use PETSc solvers" OFF)
 option(USE_SOLVER_TRILINOS "Use Trilinos solvers" OFF)
 #option(USE_AUTODIFF_OPENCL "Use OpenCL for automatic differentiation (under work)" OFF)
@@ -174,6 +175,20 @@ if(USE_SOLVER_METIS)
 	endif()
 endif()
 
+if(USE_SOLVER_MONDRIAAN)
+	find_package(MONDRIAAN)
+	if(NOT MONDRIAAN_FOUND)
+		set(USE_SOLVER_MONDRIAAN OFF)
+		message("Mondriaan NOT FOUND")
+	else()
+		link_directories(${MONDRIAAN_LIBRARY_DIRS})
+		include_directories(${MONDRIAAN_INCLUDE_DIRS})
+		set(USE_SOLVER_MONDRIAAN ON)
+		message("Mondriaan FOUND")
+	endif()
+endif()
+
+
 if(USE_PARTITIONER_ZOLTAN)
 	find_package(ZOLTAN)
 	if(NOT ZOLTAN_FOUND)

Debuggers/VisualStudio/readme.txt

@@ -2,6 +2,6 @@ Copy and paste contents of autoexp.dat into
 C:\Program Files (x86)\Microsoft Visual Studio 10.0\Common7\Packages\Debugger\autoexp.dat 
 or the directry where Visual Studio was installed.
 
-In future capabilities will grove.
+In future capabilities will grow.
 
 Tested with Visual studio 2010.

cmake_find/LICENSE

+Copyright (c) 2014-2015
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

cmake_find/readme.txt

+This folder contains scripts for CMake that aid in compilation of the INMOST library with third party libraries.
+
+The original files were obtained through internet from the following projects:
+- PETSc
+- MSTK
+- FindOpenCL
+
+And may appear in original or modified form.
\ No newline at end of file

examples/DrawMatrix/CMakeLists.txt

@@ -34,6 +34,10 @@ if(OPENGL_FOUND)
         message("linking DrawMatrix with Metis")
         target_link_libraries(DrawMatrix ${METIS_LIBRARIES})
       endif()
+      if(USE_SOLVER_MONDRIAAN)
+        message("linking DrawMatrix with Mondriaan")
+        target_link_libraries(DrawMatrix ${MONDRIAAN_LIBRARIES})
+      endif()
     endif()
 
 

examples/FVDiscr/CMakeLists.txt

@@ -25,6 +25,10 @@ if(USE_SOLVER)
     message("linking FVDiscr with Metis")
     target_link_libraries(FVDiscr ${METIS_LIBRARIES})
   endif()
+  if(USE_SOLVER_MONDRIAAN)
+    message("linking FVDiscr with Mondriaan")
+    target_link_libraries(FVDiscr ${MONDRIAAN_LIBRARIES})
+  endif()
 endif()
 
 

examples/FVDiscr/main.cpp

@@ -128,6 +128,7 @@ int main(int argc,char ** argv)
 		
 		ttt = Timer();
 		Solver S(Solver::INNER_ILU2); // Specify the linear solver to ASM+ILU2+BiCGStab one
+		S.SetParameterReal("absolute_tolerance",1e-8);
 		Solver::Matrix A; // Declare the matrix of the linear system to be solved
 		Solver::Vector x,b; // Declare the solution and the right-hand side vectors
 		
@@ -242,6 +243,8 @@ int main(int argc,char ** argv)
 
 		ttt = Timer();
 
+    Tag error = m->CreateTag("error",DATA_REAL,CELL,NONE,1);
+
 		Storage::real err_C = 0.0, err_L2 = 0.0;
 		for( Mesh::iteratorCell cell = m->BeginCell(); cell != m->EndCell(); ++cell )
 			if( cell->GetStatus() != Element::Ghost )
@@ -251,6 +254,7 @@ int main(int argc,char ** argv)
 				if (err > err_C)
 					err_C = err;
 				err_L2 += err * err * cell->Volume();
+        cell->Real(error) = err;
 // 				x[cell->Integer(id)] = err;
 			}
 		err_C = m->AggregateMax(err_C); // Compute the maximal C norm for the error

examples/MatSolve/CMakeLists.txt

@@ -33,6 +33,10 @@ if(USE_SOLVER)
     message("linking MatSolve with Metis")
     target_link_libraries(MatSolve ${METIS_LIBRARIES})
   endif()
+  if(USE_SOLVER_MONDRIAAN)
+    message("linking MatSolve with Mondriaan")
+    target_link_libraries(MatSolve ${MONDRIAAN_LIBRARIES})
+  endif()
 endif()
 
 

examples/OctreeCutcell/octgrid.cpp

@@ -538,6 +538,7 @@ class incident_matrix
 		}
 		return success;
 	}
+/*
 	Storage::real compute_measure(dynarray<T,64> & data)
 	{
 		Storage::real measure = 0;
@@ -622,6 +623,7 @@ class incident_matrix
 		}
 		return measure;
 	}
+*/
 	void recursive_find(unsigned node, unsigned length)
 	{
 		if( !min_loop.empty() && length > min_loop.size() ) return;
@@ -851,7 +853,7 @@ public:
 			}
 		} while( min_loop.empty() && first != UINT_MAX );
 		
-		for(dynarray<T,64>::iterator it = min_loop.begin(); it != min_loop.end(); ++it)
+		for(typename dynarray<T,64>::iterator it = min_loop.begin(); it != min_loop.end(); ++it)
 			ret.push_back(it->self());
 		//ret.insert(ret.end(),min_loop.begin(),min_loop.end());
 		min_loop.clear();

examples/OldDrawGrid/rotate.cpp

@@ -168,6 +168,46 @@ void rotatevector(double * vec)
 	vec[2] = ret[2]/ret[3];
 }
 
+void reverse_rotatevector(double * vec)
+{
+	int i;
+	double rot[16];
+	double temp[4] = {vec[0],vec[1],vec[2],1.0};
+	double ret[4];
+	q.x = -q.x;
+	q.y = -q.y;
+	q.z = -q.z;
+	rot[ 0] = (q.w*q.w + q.x*q.x - q.y*q.y - q.z*q.z);
+	rot[ 1] = 2.*(q.x*q.y - q.w*q.z);
+	rot[ 2] = 2.*(q.x*q.z + q.w*q.y);
+	rot[ 3] = 0.0;
+	rot[ 4] = 2.*(q.x*q.y + q.w*q.z);
+	rot[ 5] = (q.w*q.w - q.x*q.x + q.y*q.y - q.z*q.z);
+	rot[ 6] = 2.*(q.y*q.z - q.w*q.x);
+	rot[ 7] = 0.0;
+	rot[ 8] = 2.*(q.x*q.z - q.w*q.y);
+	rot[ 9] = 2.*(q.y*q.z + q.w*q.x);
+	rot[10] = (q.w*q.w - q.x*q.x - q.y*q.y + q.z*q.z);
+	rot[11] = 0.0;
+	rot[12] = 0.0;
+	rot[13] = 0.0;
+	rot[14] = 0.0;
+	rot[15] = (q.w*q.w + q.x*q.x + q.y*q.y + q.z*q.z);
+	for(i=0; i < 4; i++)
+	{
+		ret[i]  = temp[0] * rot[i*4];
+		ret[i] += temp[1] * rot[i*4+1];
+		ret[i] += temp[2] * rot[i*4+2];
+		ret[i] += temp[3] * rot[i*4+3];
+	}
+	vec[0] = ret[0]/ret[3];
+	vec[1] = ret[1]/ret[3];
+	vec[2] = ret[2]/ret[3];
+	q.x = -q.x;
+	q.y = -q.y;
+	q.z = -q.z;
+}
+
 void revrotatevector(double * vec)
 {
 	int i;
@@ -240,6 +280,51 @@ void rotatevector_from_stack(double * vec)
 	vec[2] = ret[2]/ret[3];
 }
 
+void quatget(double *vec)
+{
+	vec[0] = q.x / q.w;
+	vec[1] = q.y / q.w;
+	vec[2] = q.z / q.w;
+}
+
+void reverse_rotatevector_from_stack(double * vec)
+{
+	int i;
+	struct quaternion q = storage.back();
+	q.x = -q.x;
+	q.y = -q.y;
+	q.z = -q.z;
+	double rot[16];
+	double temp[4] = {vec[0],vec[1],vec[2],1.0};
+	double ret[4];
+	rot[ 0] = (q.w*q.w + q.x*q.x - q.y*q.y - q.z*q.z);
+	rot[ 1] = 2.*(q.x*q.y - q.w*q.z);
+	rot[ 2] = 2.*(q.x*q.z + q.w*q.y);
+	rot[ 3] = 0.0;
+	rot[ 4] = 2.*(q.x*q.y + q.w*q.z);
+	rot[ 5] = (q.w*q.w - q.x*q.x + q.y*q.y - q.z*q.z);
+	rot[ 6] = 2.*(q.y*q.z - q.w*q.x);
+	rot[ 7] = 0.0;
+	rot[ 8] = 2.*(q.x*q.z - q.w*q.y);
+	rot[ 9] = 2.*(q.y*q.z + q.w*q.x);
+	rot[10] = (q.w*q.w - q.x*q.x - q.y*q.y + q.z*q.z);
+	rot[11] = 0.0;
+	rot[12] = 0.0;
+	rot[13] = 0.0;
+	rot[14] = 0.0;
+	rot[15] = (q.w*q.w + q.x*q.x + q.y*q.y + q.z*q.z);
+	for(i=0; i < 4; i++)
+	{
+		ret[i]  = temp[0] * rot[i*4];
+		ret[i] += temp[1] * rot[i*4+1];
+		ret[i] += temp[2] * rot[i*4+2];
+		ret[i] += temp[3] * rot[i*4+3];
+	}
+	vec[0] = ret[0]/ret[3];
+	vec[1] = ret[1]/ret[3];
+	vec[2] = ret[2]/ret[3];
+}
+
 void rotate()
 {
 	double rot[16];

examples/OldDrawGrid/rotate.h

@@ -20,13 +20,16 @@
 void clickmotion(int nmx, int nmy);
 void motion(int nmx, int nmy);
 void click(int b, int s, int nmx, int nmy);
+void quatget(double * vec);
 void quatinit();
 void quatpush();
 void quatpop();
 void rotate();
 void rotate_from_stack();
 void rotatevector(double * vec);
+void reverse_rotatevector(double * vec);
 void revrotatevector(double * vec);
 void rotatevector_from_stack(double * vec);
+void reverse_rotatevector_from_stack(double * vec);
 
 #endif

examples/Solver/CMakeLists.txt

@@ -25,6 +25,10 @@ if(USE_SOLVER)
     message("linking Solver with Metis")
     target_link_libraries(Solver ${METIS_LIBRARIES})
   endif()
+  if(USE_SOLVER_MONDRIAAN)
+    message("linking Solver with Mondriaan")
+    target_link_libraries(Solver ${MONDRIAAN_LIBRARIES})
+  endif()
 endif(USE_SOLVER)
 
 if(USE_PARTITIONER)

geometry.cpp

@@ -529,6 +529,9 @@ namespace INMOST
 	
 	void Mesh::GetGeometricData(HandleType e, GeometricData type, Storage::real * ret)
 	{
+		assert(e != InvalidHandle());
+		assert(ret != NULL);
+		assert(type == MEASURE || type == CENTROID || type == BARYCENTER || type == NORMAL);
 		ElementType etype = GetHandleElementType(e);
 		integer edim = Element::GetGeometricDimension(GetGeometricType(e));
 		integer mdim = GetDimensions();

inmost-config.cmake.in

@@ -27,6 +27,8 @@ set(INMOST_LIBRARIES inmost)
 set(USE_MPI @USE_MPI@)
 set(USE_PARTITIONER_ZOLTAN @USE_PARTITIONER_ZOLTAN@)
 set(USE_PARTITIONER_PARMETIS @USE_PARTITIONER_PARMETIS@)
+set(USE_SOLVER_MONDRIAAN @USE_SOLVER_MONDRIAAN@)
+set(USE_SOLVER_METIS @USE_SOLVER_METIS@)
 set(USE_SOLVER_TRILINOS @USE_SOLVER_TRILINOS@)
 set(USE_SOLVER_PETSC @USE_SOLVER_PETSC@)
 
@@ -49,6 +51,16 @@ if( USE_PARTITIONER_PARMETIS )
 	list(APPEND INMOST_INCLUDE_DIRS "@METIS_INCLUDE_DIR@")
 endif( USE_PARTITIONER_PARMETIS )
 
+if( USE_SOLVER_MONDRIAAN )
+	list(APPEND INMOST_LIBRARIES "@MONDRIAAN_LIBRARIES@")
+	list(APPEND INMOST_INCLUDE_DIRS "@MONDRIAAN_INCLUDE_DIRS@")
+	list(APPEND INMOST_LIBRARY_DIRS "@MONDRIAAN_LIBRARY_DIRS@")
+endif( USE_SOLVER_MONDRIAAN )
+
+if( USE_SOLVER_METIS )
+	list(APPEND INMOST_LIBRARIES "@METIS_LIBRARIES@")
+	list(APPEND INMOST_INCLUDE_DIRS "@METIS_INCLUDE_DIR@")
+endif( USE_SOLVER_METIS )
 
 if( USE_SOLVER_TRILINOS )
 	list(APPEND INMOST_LIBRARIES "@Trilinos_LIBRARIES@")

inmost_mesh.h

@@ -137,7 +137,7 @@ namespace INMOST
 	__INLINE INMOST_DATA_INTEGER_TYPE        GetHandleElementNum  (HandleType h) {return h >> handle_etype_shift;}
 	__INLINE ElementType                     GetHandleElementType (HandleType h) {return 1 << GetHandleElementNum(h);}
 	__INLINE HandleType                      ComposeHandle        (ElementType etype, INMOST_DATA_INTEGER_TYPE ID) {return ID == -1 ? InvalidHandle() : ((ElementNum(etype) << handle_etype_shift) + (1+ID));}
-	__INLINE HandleType                      ComposeHandle        (INMOST_DATA_INTEGER_TYPE etypenum, INMOST_DATA_INTEGER_TYPE ID) {return ID == -1 ? InvalidHandle() : ((etypenum << handle_etype_shift) + (1+ID));}
+	__INLINE HandleType                      ComposeHandleNum     (INMOST_DATA_INTEGER_TYPE etypenum, INMOST_DATA_INTEGER_TYPE ID) {return ID == -1 ? InvalidHandle() : ((etypenum << handle_etype_shift) + (1+ID));}
 	__INLINE bool                            isValidHandle        (HandleType h) {return h != 0;}
 	
 
@@ -2356,7 +2356,7 @@ namespace INMOST
 		void                              Exit               ();
 		int &                             GetFuncID          () {return func_id;}
 		std::fstream &                    GetStream          ();
-		std::fstream &                    WriteTab           (std::fstream & f);
+		std::ostream &                    WriteTab           (std::ostream & f);
 		void                              FinalizeFile       ();
 		static void                       AtExit             (void);
 #endif
@@ -2933,7 +2933,7 @@ namespace INMOST
 		void                              EndSequentialCode  ();
 		//iterator.cpp::::::::::::::::::::::::::::::::::::::::::::::::::
 	public:
-		Element                           ElementByLocalID   (integer etypenum, integer lid) {assert(etypenum < 5 && (lid >= 0 && lid < static_cast<integer>(links[etypenum].size())) || (etypenum == 5 && lid == 0)); return Element(this,ComposeHandle(etypenum,lid));}
+		Element                           ElementByLocalID   (integer etypenum, integer lid) {assert(etypenum < 5 && (lid >= 0 && lid < static_cast<integer>(links[etypenum].size())) || (etypenum == 5 && lid == 0)); return Element(this,ComposeHandleNum(etypenum,lid));}
 		Element                           ElementByLocalID   (ElementType etype, integer lid) {return ElementByLocalID(ElementNum(etype),lid);}
 		Element                           ElementByHandle    (HandleType h) {return Element(this,h);}
 		
@@ -2941,16 +2941,16 @@ namespace INMOST
 		HandleType                        PrevHandle         (HandleType h) const; //returns InvalidHandle() when go beyond first element
 		HandleType                        NextHandle         (HandleType h, ElementType mask) const;
 		HandleType                        PrevHandle         (HandleType h, ElementType mask) const; //returns InvalidHandle() when go beyond first element
-		HandleType                        FirstHandle        () const {return ComposeHandle(ElementNum(NODE),0);}
-		HandleType                        LastHandle         () const {return ComposeHandle(ElementNum(MESH),1);} 
-		HandleType                        FirstHandle        (ElementType etype) const {return ComposeHandle(ElementNum(etype),0);}
-		HandleType                        LastHandle         (ElementType etype) const  {integer num = ElementNum(etype); return ComposeHandle(num,static_cast<integer>(links[num].size()));}
+		HandleType                        FirstHandle        () const {return ComposeHandleNum(ElementNum(NODE),0);}
+		HandleType                        LastHandle         () const {return ComposeHandleNum(ElementNum(MESH),1);} 
+		HandleType                        FirstHandle        (ElementType etype) const {return ComposeHandleNum(ElementNum(etype),0);}
+		HandleType                        LastHandle         (ElementType etype) const  {integer num = ElementNum(etype); return ComposeHandleNum(num,static_cast<integer>(links[num].size()));}
 
-		Node                              NodeByLocalID      (integer lid) { assert(lid >= 0 && lid < static_cast<integer>(links[0].size())); return Node(this,ComposeHandle(0,lid)); }
-		Edge                              EdgeByLocalID      (integer lid) { assert(lid >= 0 && lid < static_cast<integer>(links[1].size())); return Edge(this,ComposeHandle(1,lid)); }
-		Face                              FaceByLocalID      (integer lid) { assert(lid >= 0 && lid < static_cast<integer>(links[2].size())); return Face(this,ComposeHandle(2,lid));}
-		Cell                              CellByLocalID      (integer lid) { assert(lid >= 0 && lid < static_cast<integer>(links[3].size())); return Cell(this,ComposeHandle(3,lid)); }
-		ElementSet                        EsetByLocalID      (integer lid) { assert(lid >= 0 && lid < static_cast<integer>(links[4].size())); return ElementSet(this,ComposeHandle(4,lid)); }
+		Node                              NodeByLocalID      (integer lid) { assert(lid >= 0 && lid < static_cast<integer>(links[0].size())); return Node(this,ComposeHandleNum(0,lid)); }
+		Edge                              EdgeByLocalID      (integer lid) { assert(lid >= 0 && lid < static_cast<integer>(links[1].size())); return Edge(this,ComposeHandleNum(1,lid)); }
+		Face                              FaceByLocalID      (integer lid) { assert(lid >= 0 && lid < static_cast<integer>(links[2].size())); return Face(this,ComposeHandleNum(2,lid));}
+		Cell                              CellByLocalID      (integer lid) { assert(lid >= 0 && lid < static_cast<integer>(links[3].size())); return Cell(this,ComposeHandleNum(3,lid)); }
+		ElementSet                        EsetByLocalID      (integer lid) { assert(lid >= 0 && lid < static_cast<integer>(links[4].size())); return ElementSet(this,ComposeHandleNum(4,lid)); }
 		
 		integer                           NodeNextLocalID    (integer lid) const {++lid; while(lid < static_cast<integer>(links[0].size()) && links[0][lid] == -1) ++lid; return lid;}
 		integer                           EdgeNextLocalID    (integer lid) const {++lid; while(lid < static_cast<integer>(links[1].size()) && links[1][lid] == -1) ++lid; return lid;}

inmost_options_cmake.h

@@ -15,6 +15,7 @@
 #cmakedefine USE_PARTITIONER_PARMETIS
 
 #cmakedefine USE_SOLVER
+#cmakedefine USE_SOLVER_MONDRIAAN
 #cmakedefine USE_SOLVER_METIS
 #cmakedefine USE_SOLVER_PETSC
 #cmakedefine USE_SOLVER_TRILINOS

iterator.cpp

@@ -50,7 +50,7 @@ namespace INMOST
 			else break;
 		}
 		if( num == 5 && id > 0 ) id = 1;
-		return ComposeHandle(num,id);
+		return ComposeHandleNum(num,id);
 	}
 
 	HandleType  Mesh::PrevHandle(HandleType h) const 
@@ -61,7 +61,7 @@ namespace INMOST
 		{
 			if( id < 0 )
 				num = 4;
-			else return ComposeHandle(ElementNum(MESH),0);
+			else return ComposeHandleNum(ElementNum(MESH),0);
 		}
 		while( num >= 0 )
 		{
@@ -74,7 +74,7 @@ namespace INMOST
 			else break;
 		}
 		if( num < 0 ) return InvalidHandle();
-		return ComposeHandle(num,id);
+		return ComposeHandleNum(num,id);
 	}
 
 	HandleType  Mesh::NextHandle(HandleType h, ElementType etype) const 
@@ -102,7 +102,7 @@ namespace INMOST
 			else break;
 		}
 		if( num == 5 && id > 0 ) id = 1;
-		return ComposeHandle(num,id);
+		return ComposeHandleNum(num,id);
 	}
 
 	HandleType  Mesh::PrevHandle(HandleType h, ElementType etype) const 
@@ -127,7 +127,7 @@ namespace INMOST
 				}
 				if( stop ) return InvalidHandle();
 			}
-			else return ComposeHandle(ElementNum(MESH),0);
+			else return ComposeHandleNum(ElementNum(MESH),0);
 		}
 		while( num >= 0 )
 		{
@@ -150,7 +150,7 @@ namespace INMOST
 			else break;
 		}
 		if( num < 0 ) return InvalidHandle();
-		return ComposeHandle(num,id);
+		return ComposeHandleNum(num,id);
 	}
 
 	Storage::integer  Mesh::FirstLocalID(ElementType etype) const 

mesh.cpp

@@ -440,7 +440,7 @@ namespace INMOST
 #endif //USE_MPI
 #if defined(USE_PARALLEL_WRITE_TIME)
 		FinalizeFile();
-		out_time.close();
+		
 		for(size_t q = 0; q < allocated_meshes.size(); ++q)
 			if (allocated_meshes[q] == this)
 				allocated_meshes[q] = NULL;
@@ -862,7 +862,7 @@ namespace INMOST
 	Node Mesh::CreateNode(const real * coords)
 	{
 		integer id = TieElement(0);
-		HandleType h = ComposeHandle(0,id);
+		HandleType h = ComposeHandleNum(0,id);
 		SetGeometricType(h,Element::Vertex);
 		real * v = static_cast<Storage::real *>(MGetDenseLink(h,CoordsTag()));
 		for(integer i = 0; i < dim; i++) v[i] = coords[i];
@@ -912,7 +912,7 @@ namespace INMOST
 				if (test != InvalidHandle()) return std::make_pair(Edge(this,test),false);
 			}
 			integer id = TieElement(1);
-			he = ComposeHandle(1,id);
+			he = ComposeHandleNum(1,id);
 			for(ElementArray<Node>::size_type i = 0; i < nodes.size(); i++)
 			{
 				Element::adj_type & hc = HighConn(nodes.at(i));
@@ -1004,7 +1004,7 @@ namespace INMOST
 				if (test != InvalidHandle()) return std::make_pair(Face(this,test),false);
 			}
 			integer id = TieElement(2);
-			he = ComposeHandle(2,id);
+			he = ComposeHandleNum(2,id);
 			for(ElementArray<Edge>::size_type i = 0; i < f_edges.size(); i++)
 			{
 				Element::adj_type & hc = HighConn(f_edges.at(i));
@@ -1374,7 +1374,7 @@ namespace INMOST
 				if (test != InvalidHandle()) return std::make_pair(Cell(this,test),false);
 			}
 			integer id = TieElement(3);
-			he = ComposeHandle(3,id);
+			he = ComposeHandleNum(3,id);
 			for(ElementArray<Face>::size_type i = 0; i < c_faces.size(); i++)
 			{
 				Element::adj_type & hc = HighConn(c_faces.at(i));
@@ -1476,7 +1476,7 @@ namespace INMOST
 			if( e->GetName() == name )
 				return std::make_pair(e->self(),false);
 		}
-		HandleType he = ComposeHandle(4,TieElement(4));
+		HandleType he = ComposeHandleNum(4,TieElement(4));
 		bulk_array set_name = BulkArrayDV(he,SetNameTag());
 		set_name.resize(static_cast<bulk_array::size_type>(name.size()));
 		memcpy(set_name.data(),name.c_str(),name.size());
@@ -1498,7 +1498,7 @@ namespace INMOST
 			Storage::integer j = 0;
 			for(Storage::integer k = 0; k < NodeLastLocalID(); ++k) if( isValidElement(0,k) )
 			{
-				memcpy(temp.data()+j,MGetDenseLink(ComposeHandle(0,k),CoordsTag()),sizeof(Storage::real)*dims);
+				memcpy(temp.data()+j,MGetDenseLink(ComposeHandleNum(0,k),CoordsTag()),sizeof(Storage::real)*dims);
 				j+=dims;
 			}
 			
@@ -1507,7 +1507,7 @@ namespace INMOST
 			j = 0;
 			for(Storage::integer k = 0; k < NodeLastLocalID(); ++k) if( isValidElement(0,k) )
 			{
-				memcpy(MGetDenseLink(ComposeHandle(0,k),CoordsTag()),temp.data()+j,sizeof(Storage::real)*dims);
+				memcpy(MGetDenseLink(ComposeHandleNum(0,k),CoordsTag()),temp.data()+j,sizeof(Storage::real)*dims);
 				j+=dims;
 			}
 			dim = dims;
@@ -1536,7 +1536,7 @@ namespace INMOST
 			back_links[etypenum][ADDR] = -1;
 			empty_space[etypenum].push_back(ADDR);
 			empty_links[etypenum].push_back(ID);
-			//REPORT_VAL("destroyed",ComposeHandle(etypenum,ID) << " " << etypenum << " " << ADDR << " " << ID);
+			//REPORT_VAL("destroyed",ComposeHandleNum(etypenum,ID) << " " << etypenum << " " << ADDR << " " << ID);
 		}
 	}
 	
@@ -1576,7 +1576,7 @@ namespace INMOST
 			new_size = GetArrayCapacity(etypenum);
 			if( new_size != old_size ) ReallocateData(etypenum,new_size);
 			back_links[etypenum][ADDR] = ID;
-			last_created = ComposeHandle(etypenum,ID);
+			last_created = ComposeHandleNum(etypenum,ID);
 			//REPORT_VAL("created",last_created << " " << etypenum << " " << ADDR << " " << ID);
 		}
 		return ID;

partitioner.cpp

@@ -346,9 +346,17 @@ namespace INMOST
 						{
 							queue.push_back(*it);
 							m->Integer(queue.back(),index) = visited++;
+
+							if( visited % chunk == 0 ) 
+							{
+								queue.clear();
+								break;
+							}
+
 						}
 					}
-					if( visited % chunk == 0 ) queue.clear();
+					//this may not fire properly
+					//if( visited % chunk == 0 ) queue.clear();
 				}
 			}
 			m->DeleteTag(order);

solver.cpp

+#define _CRT_SECURE_NO_WARNINGS
 #include "inmost_solver.h"
 #if defined(USE_SOLVER)
 #include "solver_petsc.h"
@@ -1337,37 +1338,47 @@ namespace INMOST
 		(void)argv;
 		if( database != NULL )
 		{
-			std::fstream file(database,std::ios::in);
-			char str[4096];
-			while( !file.eof() && file.getline(str,4096) )
-			{
-				int k = 0, l;
-				for(k = 0; k < (int)strlen(str); ++k)
-				{
-					if( str[k] == ':' ) break;
-				}
-				if( k == strlen(str) ) continue; //invalid line
-				for(l = 0; l < k; ++l) str[l] = tolower(str[l]);
-				l = k+1;
-				while(l < (int)strlen(str) && isspace(str[l]) ) ++l;
-				if( l == strlen(str) ) continue; //skip empty entry
-				if( !strncmp(str,"petsc",k) )
-					petsc_database_file = std::string(str+l);
-				else if( !strncmp(str,"trilinos_ifpack",k) )
-					trilinos_ifpack_database_file = std::string(str+l);
-				else if( !strncmp(str,"trilinos_aztec",k) )
-					trilinos_aztec_database_file = std::string(str+l);
-				else if( !strncmp(str,"trilinos_ml",k) )
-					trilinos_ml_database_file = std::string(str+l);
-				else if( !strncmp(str,"trilinos_belos",k) )
-					trilinos_belos_database_file = std::string(str+l);
-				else if( !strncmp(str,"ani",k) )
-					ani_database_file = std::string(str+l);
-				else if( !strncmp(str,"fcbiilu2",k) )
-					fcbiilu2_database_file = std::string(str+l);
-				else if( !strncmp(str,"k3biilu2",k) )
-					k3biilu2_database_file = std::string(str+l);
-			}
+      FILE * f = fopen(database,"r");
+      if( f )
+      {
+			  //std::fstream file(database,std::ios::in);
+			  char str[4096];
+			  //while( !file.eof() && file.getline(str,4096) )
+        while( !feof(f) && fgets(str,4096,f) )
+			  {
+				  int k = 0, l;
+				  for(k = 0; k < (int)strlen(str); ++k)
+				  {
+					  if( str[k] == ':' ) break;
+				  }
+				  if( k == strlen(str) ) continue; //invalid line
+				  for(l = 0; l < k; ++l) str[l] = tolower(str[l]);
+				  l = (int)strlen(str)-1; // Right-trim string
+				  while(l > 0 && isspace(str[l]) ) --l;
+				  str[l+1] = 0;
+				  l = k+1;
+				  while(l < (int)strlen(str) && isspace(str[l]) ) ++l;
+				  if( l == strlen(str) ) continue; //skip empty entry
+				  if( !strncmp(str,"petsc",k) )
+					  petsc_database_file = std::string(str+l);
+				  else if( !strncmp(str,"trilinos_ifpack",k) )
+					  trilinos_ifpack_database_file = std::string(str+l);
+				  else if( !strncmp(str,"trilinos_aztec",k) )
+					  trilinos_aztec_database_file = std::string(str+l);
+				  else if( !strncmp(str,"trilinos_ml",k) )
+					  trilinos_ml_database_file = std::string(str+l);
+				  else if( !strncmp(str,"trilinos_belos",k) )
+					  trilinos_belos_database_file = std::string(str+l);
+				  else if( !strncmp(str,"ani",k) )
+					  ani_database_file = std::string(str+l);
+				  else if( !strncmp(str,"fcbiilu2",k) )
+				 	  fcbiilu2_database_file = std::string(str+l);
+				  else if( !strncmp(str,"k3biilu2",k) )
+					  k3biilu2_database_file = std::string(str+l);
+			  }
+			  //file.close();
+        fclose(f);
+      }
 		}
 		//std::cout << "PETSc \"" << petsc_database_file << "\"" << std::endl;
 		//std::cout << "Trilinos_Ifpack \"" << trilinos_ifpack_database_file << "\"" << std::endl;

solver_bcgsl.hpp

@@ -46,13 +46,15 @@ namespace INMOST
 		shell<INMOST_DATA_REAL_TYPE> u(pu,n*n);
 		shell<INMOST_DATA_REAL_TYPE> v(pv,n*n);
 		shell<INMOST_DATA_REAL_TYPE> w(pw,n);
-		std::copy(a.begin(),a.end(),u.begin());
+		//std::copy(a.begin(),a.end(),u.begin());
 		//memcpy(u,a,sizeof(INMOST_DATA_REAL_TYPE)*n*n);
 		int flag, i, its, j, jj, k, l, nm;
 		INMOST_DATA_REAL_TYPE c, f, h, s, x, y, z;
 		INMOST_DATA_REAL_TYPE anorm = 0.0, g = 0.0, scale = 0.0;
-		static std::vector<INMOST_DATA_REAL_TYPE> rv1(n);
+		dynarray<INMOST_DATA_REAL_TYPE,64> rv1;
+    rv1.resize(n);
 		// Householder reduction to bidiagonal form
+		for (i = 0; i < n*n; ++i) u[i] = a[i];
 		for (i = 0; i < n; i++) 
 		{
 			// left-hand reduction
@@ -624,13 +626,13 @@ namespace INMOST
 			}
 #endif
 			INMOST_DATA_ENUM_TYPE i = 0;
-
 			bool halt = false;
 			if( last_resid < atol || last_resid < rtol*resid0 ) 
 			{
 				reason = "initial solution satisfy tolerances";
-				goto exit;
+				halt = true;
 			}
+
 #if defined(USE_OMP)
 #pragma omp parallel
 #endif
@@ -826,17 +828,24 @@ namespace INMOST
 						sigma[j-1] = sigma_sum;
 					}
 #if defined(CONVEX_COMBINATION)
-					INMOST_DATA_REAL_TYPE lagrangian = 0.0;
-					for(INMOST_DATA_ENUM_TYPE j = 0; j < l; j++) lagrangian += tau[j+size*j];
-					sigma[l] = lagrangian;
-					tau[(l+1)*(l+1)-1] = 0.0;
-					for(INMOST_DATA_ENUM_TYPE j = 0; j < l; j++)
+#if defined(USE_OMP)
+#pragma omp single
+#endif
 					{
-						tau[l + j*(l+1)] = -lagrangian;
-						tau[l*(l+1)+j] = lagrangian;
+						INMOST_DATA_REAL_TYPE lagrangian = 0.0;
+						for(INMOST_DATA_ENUM_TYPE j = 0; j < l; j++) lagrangian += tau[j+size*j];
+						sigma[l] = lagrangian;
+						tau[(l+1)*(l+1)-1] = 0.0;
+						for(INMOST_DATA_ENUM_TYPE j = 0; j < l; j++)