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/main.cpp

@@ -11,6 +11,17 @@
 #include <algorithm>
 #include <stdarg.h>
 #include "my_glut.h"
+#include <iomanip>
+
+inline static unsigned int flip(const unsigned int * fp)
+{
+	unsigned int mask = -((int)(*fp >> 31)) | 0x80000000;
+	return *fp ^ mask;
+}
+#define _0(x)	(x & 0x7FF)
+#define _1(x)	(x >> 11 & 0x7FF)
+#define _2(x)	(x >> 22 )
+
 
 
 using namespace INMOST;
@@ -21,7 +32,7 @@ int width = 800, height = 800;
 double sleft = 1e20, sright = -1e20, sbottom = 1e20, stop = -1e20, sfar = -1e20, snear = 1e20;
 double shift[3] = {0,0,0};
 bool perspective = false;
-bool boundary = true, planecontrol = false, clipupdate = false, bndupdate = true, clipboxupdate = false;
+bool boundary = true, planecontrol = false, clipupdate = false, bndupdate = true, clipboxupdate = false, draw_volumetric = false;
 
 Mesh::GeomParam table;
 
@@ -38,6 +49,13 @@ Mesh::GeomParam table;
 Storage::real p[3] = {0,0,0}, n[3] = {0,0,1};
 ElementArray<Element> boundary_faces;
 
+double amplitude = 10;
+double radius = 25;
+char visualization_prompt[8192];
+bool visualization_prompt_active = false;
+Tag visualization_tag;
+ElementType visualization_type;
+
 void printtext(const char * fmt, ... )
 {
 	
@@ -55,18 +73,216 @@ void printtext(const char * fmt, ... )
 	}
 }
 
+const int name_width = 32;
+const int type_width = 14;
+const int elems_width = 10;
+const int sparse_width = 10;
+const int length_width = 10;
+
+void PrintTag(Tag t)
+{
+	std::cout << std::setw(name_width) << t.GetTagName() << std::setw(type_width) << DataTypeName(t.GetDataType());
+	int num = 0;
+	char elems[7] = "NEFCSM";
+	std::string print = "";
+	for(ElementType etype = NODE; etype <= MESH; etype = etype << 1)
+	{
+		if( t.isDefined(etype) )
+		{
+			print = print + elems[ElementNum(etype)];
+			num++;
+		}
+	}
+	std::cout << std::setw(elems_width) << print;
+	print = "";
+	for(ElementType etype = NODE; etype <= MESH; etype = etype << 1)
+	{
+		if( t.isSparse(etype) )
+		{
+			print = print + elems[ElementNum(etype)];
+			num++;
+		}
+	}
+	std::cout << std::setw(sparse_width) << print;
+	if( t.GetSize() == ENUMUNDEF )
+		std::cout << std::setw(length_width) << "VAR" << std::endl;
+	else
+		std::cout << std::setw(length_width) << t.GetSize() << std::endl;
+}
+
+void PrintTags(Mesh * m, ElementType etypes)
+{
+	std::cout << std::setw(name_width) << "Name" << std::setw(type_width) << "Type" << std::setw(elems_width) << "Element" << std::setw(sparse_width) << "Sparse" << std::setw(length_width) << "Length" << std::endl;
+	for(Mesh::iteratorTag t = m->BeginTag(); t != m->EndTag(); ++t )
+	{
+		bool print = false;
+		for(ElementType etype = NODE; etype <= MESH; etype = etype << 1) if( (etype&etypes) && t->isDefined(etype) ) {print = true; break;}
+		if( print ) PrintTag(*t);
+	}
+}
+
+struct color_t
+{
+	float c[4];
+	color_t() {memset(c,0,sizeof(float)*4);}
+	color_t(float r, float g, float b)
+	{
+		c[0] = r;
+		c[1] = g;
+		c[2] = b;
+		c[3] = 1.0;
+	}
+	color_t(float r, float g, float b, float a)
+	{
+		c[0] = r;
+		c[1] = g;
+		c[2] = b;
+		c[3] = a;
+	}
+	color_t(const color_t & other) {memcpy(c,other.c,sizeof(float)*4);}
+	color_t & operator =(color_t const & other)
+	{
+		memmove(c,other.c,sizeof(float)*4);
+		return *this;
+	}
+	void set_color() const {glColor4fv(c);}
+	float & r() {return c[0];}
+	float & g() {return c[1];}
+	float & b() {return c[2];}
+	float & a() {return c[3];}
+	float r() const {return c[0];}
+	float g() const {return c[1];}
+	float b() const {return c[2];}
+	float a() const {return c[3];}
+	color_t operator *(float mult){return color_t(c[0]*mult,c[1]*mult,c[2]*mult,c[3]*mult);}
+	color_t operator +(color_t other){return color_t(c[0]+other.c[0],c[1]+other.c[1],c[2]+other.c[2],c[3]+other.c[3]);}
+};
+
+class color_bar
+{
+	float min, max;
+	std::vector<float> ticks; //ticks from 0 to 1 for each color
+	std::vector<color_t> colors; //4 floats for each tick
+	std::string comment;
+public:
+	color_bar()
+	{
+		min = 0;
+		max = 1;
+		comment = "";
+		ticks.push_back(0.f);
+		ticks.push_back(0.2f);
+		ticks.push_back(0.4f);
+		ticks.push_back(0.6f);
+		ticks.push_back(0.8f);
+		ticks.push_back(1.f);
+		colors.push_back(color_t(1,0,0));
+		colors.push_back(color_t(1,1,0));
+		colors.push_back(color_t(0,1,0));
+		colors.push_back(color_t(0,1,1));
+		colors.push_back(color_t(0,0,1));
+		colors.push_back(color_t(1,0,1));
+		
+		
+		
+		
+		//colors.push_back(color_t(1,0,0));
+	}
+	void set_comment(std::string text) {comment = text;}
+	void set_min(float newmin) { min = newmin;}
+	void set_max(float newmax) { max = newmax;}
+	color_t pick_color(float value) 
+	{
+		float t = (value-min)/(max-min);
+		std::vector<float>::iterator it = std::lower_bound(ticks.begin(),ticks.end(),t);
+		size_t pos = it-ticks.begin();
+		if( it == ticks.end() || pos >= ticks.size() ) 
+		{
+			return colors.back();
+		}
+		if( pos == 0 ) 
+		{
+			return colors[0];
+		}
+		float interp = (t-ticks[pos-1])/(ticks[pos]-ticks[pos-1]);
+		return (colors[pos]*interp+colors[pos-1]*(1-interp));
+	}
+	void Draw()
+	{
+		float text_pos = -0.89;
+		float left = -0.95;
+		float right = -0.9;
+		float bottom = -0.75;
+		float top = 0.75;
+		glBegin(GL_QUADS);
+		for(int i = 0; i < ticks.size()-1; ++i)
+		{
+			colors[i].set_color();
+			glVertex2f(left,bottom+ticks[i]*(top-bottom));
+			glVertex2f(right,bottom+ticks[i]*(top-bottom));
+			colors[i+1].set_color();
+			glVertex2f(right,bottom+ticks[(i+1)]*(top-bottom));
+			glVertex2f(left,bottom+ticks[(i+1)]*(top-bottom));
+		}
+		glEnd();
+		
+		glColor4f(0,0,0,1);
+		for(int i = 0; i < ticks.size(); ++i)
+		{
+			glRasterPos2f(text_pos,bottom+ticks[i]*(top-bottom));
+			printtext("%f",min+ticks[i]*(max-min));
+		}
+		if( comment != "")
+		{
+			glRasterPos2f(left,bottom-0.04);
+			printtext("%s",comment.c_str());
+		}
+	}
+} CommonColorBar;
+
 
 class face2gl
 {
-	double dist;
+	float dist;
 	double c[4];
 	double cnt[3];
 	bool flag;
 	ElementType etype;
 	Storage::integer id;
 	std::vector<double> verts;
+	std::vector<color_t> colors;
+	color_t cntcolor;
 public:
-	face2gl():verts() {etype = NONE; id = 0; dist = 0; flag = false; memset(c,0,sizeof(double)*4);}
+	static void radix_sort_dist(std::vector<face2gl> & set)
+	{
+		static std::vector<face2gl> tmp;
+		tmp.resize(set.size());
+		unsigned int i;
+		const unsigned int kHist = 2048;
+		unsigned int  b0[kHist * 3];
+		unsigned int *b1 = b0 + kHist;
+		unsigned int *b2 = b1 + kHist;
+		memset(b0,0,sizeof(unsigned int)*kHist*3);
+		for (i = 0; i < set.size(); i++) 
+		{
+			unsigned int fi = flip((unsigned int *)&set[i].dist);
+			++b0[_0(fi)]; ++b1[_1(fi)]; ++b2[_2(fi)];
+		}
+		{
+			unsigned int sum0 = 0, sum1 = 0, sum2 = 0;
+			for (i = 0; i < kHist; i++) 
+			{
+				b0[kHist-1] = b0[i] + sum0; b0[i] = sum0 - 1; sum0 = b0[kHist-1];
+				b1[kHist-1] = b1[i] + sum1; b1[i] = sum1 - 1; sum1 = b1[kHist-1];
+				b2[kHist-1] = b2[i] + sum2; b2[i] = sum2 - 1; sum2 = b2[kHist-1];
+			}
+		}
+		for (i = 0; i < set.size(); i++) tmp[++b0[_0(flip((unsigned int *)&set[i].dist))]] = set[i];
+		for (i = 0; i < set.size(); i++) set[++b1[_1(flip((unsigned int *)&tmp[i].dist))]] = tmp[i];
+		for (i = 0; i < set.size(); i++) tmp[++b2[_2(flip((unsigned int *)&set[i].dist))]] = set[i];
+		for (i = 0; i < set.size(); i++) set[i] = tmp[set.size()-1-i];
+	}
+	face2gl():verts(),colors() {etype = NONE; id = 0; dist = 0; flag = false; memset(c,0,sizeof(double)*4);}
 	face2gl(const face2gl & other) :verts(other.verts) 
 	{
 		etype = other.etype;
@@ -80,6 +296,8 @@ public:
 		c[2] = other.c[2];
 		c[3] = other.c[3];
 		flag = other.flag;
+		colors = other.colors;
+		cntcolor = other.cntcolor;
 	}
 	face2gl & operator =(face2gl const & other) 
 	{ 
@@ -95,10 +313,14 @@ public:
 		c[2] = other.c[2];
 		c[3] = other.c[3];
 		flag = other.flag;
+		colors = other.colors;
+		cntcolor = other.cntcolor;
 		return *this;
 	}
 	~face2gl() {}
 	void draw_colour() const
+	{
+		if( colors.empty() )
 		{
 			glColor4dv(c); 
 			for(unsigned k = 0; k < verts.size(); k+=3) 
@@ -108,6 +330,51 @@ public:
 				glVertex3dv(&verts[(k+3)%verts.size()]);
 			}
 		}
+		else
+		{
+			for(unsigned k = 0; k < verts.size(); k+=3) 
+			{
+				cntcolor.set_color();
+				glVertex3dv(cnt);
+				colors[k/3].set_color();
+				glVertex3dv(&verts[k]);
+				colors[(k/3+1)%colors.size()].set_color();
+				glVertex3dv(&verts[(k+3)%verts.size()]);
+			}
+		}
+	}
+	void draw_colour_alpha(double alpha) const
+	{
+		if( colors.empty() )
+		{
+			double cc[4] = {c[0],c[1],c[2],alpha};
+			glColor4dv(c); 
+			for(unsigned k = 0; k < verts.size(); k+=3) 
+			{
+				glVertex3dv(cnt);
+				glVertex3dv(&verts[k]);
+				glVertex3dv(&verts[(k+3)%verts.size()]);
+			}
+		}
+		else
+		{
+			for(unsigned k = 0; k < verts.size(); k+=3) 
+			{
+				color_t t = cntcolor;
+				t.a() = alpha;
+				t.set_color();
+				glVertex3dv(cnt);
+				t = colors[k/3];
+				t.a() = alpha;
+				t.set_color();
+				glVertex3dv(&verts[k]);
+				t = colors[(k/3+1)%colors.size()];
+				t.a() = alpha;
+				t.set_color();
+				glVertex3dv(&verts[(k+3)%verts.size()]);
+			}
+		}
+	}
 	void draw() const
 	{
 		for(unsigned k = 0; k < verts.size(); k+=3) 
@@ -129,13 +396,15 @@ public:
 	void set_color(double r, double g, double b, double a) {c[0] = r; c[1] = g; c[2] = b; c[3] = a;}
 	void add_vert(double x, double y, double z) {unsigned s = (unsigned)verts.size(); verts.resize(s+3); verts[s] = x; verts[s+1] = y; verts[s+2] = z;}
 	void add_vert(double v[3]) {verts.insert(verts.end(),v,v+3);}