Add missing files to SparseGrid examples (Heat conduct, Porous Diff)

example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/Makefile

+include ../../example.mk
+
+### This is a trick to avoid "Command not found if you no not have NVCC compiler". In practice the normal C++ compiler is used
+### internally the example disable with the preprocessor its code if not compiled with nvcc 
+CUDA_CC=
+CUDA_CC_LINK=
+ifdef CUDA_ON_CPU
+	CUDA_CC=mpic++ -x c++ $(INCLUDE_PATH)
+        INCLUDE_PATH_NVCC=
+        CUDA_CC_LINK=mpic++
+        CUDA_OPTIONS=
+		LIBS_SELECT=$(LIBS)
+else
+	ifeq (, $(shell which nvcc))
+        	CUDA_CC=mpic++ -x c++ $(INCLUDE_PATH)
+        	INCLUDE_PATH_NVCC=
+        	CUDA_CC_LINK=mpic++
+		CUDA_OPTIONS=
+		LIBS_SELECT=$(LIBS)
+	else
+        	CUDA_CC=nvcc -ccbin=mpic++
+        	CUDA_CC_LINK=nvcc -ccbin=mpic++
+		CUDA_OPTIONS=-use_fast_math  -arch=sm_61 -lineinfo
+		LIBS_SELECT=$(LIBS_NVCC)
+	endif
+endif
+
+ifeq ($(PROFILE),ON)
+        CUDA_CC=scorep --nocompiler  --cuda --mpp=mpi nvcc -ccbin=mpic++
+        CUDA_CC_LINK=scorep --nocompiler  --cuda --mpp=mpi nvcc -ccbin=mpic++
+else
+	CUDA_CC:=$(CUDA_CC)
+	CUDA_CC_LINK:=$(CUDA_CC_LINK)
+endif
+
+LDIR =
+OPT=
+
+INCLUDE_PATH_NVCC:=$(INCLUDE_PATH_NVCC) -I./include 
+
+OBJ = main.o
+
+heat_ceram:
+heat_ceram_test: OPT += -DTEST_RUN
+heat_ceram_test: heat_ceram
+
+%.o: %.cu
+	$(CUDA_CC) -O3 $(OPT) $(CUDA_OPTIONS) --extended-lambda --expt-relaxed-constexpr -g -c --std=c++14 -o $@ $< $(INCLUDE_PATH_NVCC)
+
+%.o: %.cpp
+	$(CC) -O3 $(OPT) -g -c --std=c++14 -o $@ $< $(INCLUDE_PATH)
+
+heat_ceram: $(OBJ)
+	$(CUDA_CC_LINK) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS_SELECT)
+
+heat_ceram2: $(OBJ)
+	$(CUDA_CC_LINK) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS_SELECT)
+
+all: heat_ceram
+
+run: heat_ceram_test
+	mpirun --oversubscribe -np 1 ./heat_ceram
+
+.PHONY: clean all run
+
+clean:
+	rm -f *.o *~ core heat_ceram
+

example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/include/RemoveLines.hpp

+//
+// Created by jstark on 07.10.21.
+//
+
+#ifndef SUSSMAN_REDISTANCING_REMOVELINES_HPP
+#define SUSSMAN_REDISTANCING_REMOVELINES_HPP
+
+/**@brief Checks for thin lines and removes them by setting the value of the indicator function accordingly.
+ *
+ * @tparam grid_type Template type of OpenFPM grid.
+ * @tparam Phi_0_grid Property that contains the indicator or level-set function.
+ * @tparam sign_inside Sign that indicates that a node lies inside the object. Set to +1 or -1 depending on the
+ * convention you use.
+ * @param grid Grid that stores the indicator or level-set function.
+ */
+template <size_t Phi_0_grid, int sign_inside, typename grid_type>
+void removeLines(grid_type & grid)
+{
+	if(sign_inside == 0)
+	{
+		std::cout << "sign_inside was set to 0. However, it must be set to +1 or -1 depending on the level-set "
+					 "convention used. Aborting..." << std::endl;
+		abort();
+	}
+	for(int repeat = 0; repeat < 2; ++repeat)
+	{
+		grid.template ghost_get<Phi_0_grid>(KEEP_PROPERTIES);
+		if (sign_inside > 0)
+		{
+			auto dom = grid.getDomainIterator();
+			while(dom.isNext())
+			{
+				auto key = dom.get();
+				if (grid.template getProp<Phi_0_grid>(key) > 0)
+				{
+					for (int d = 0; d < grid_type::dims; ++d)
+					{
+						if (grid.template getProp<Phi_0_grid>(key.move(d, -1)) < 0
+								&& grid.template getProp<Phi_0_grid>(key.move(d, +1)) < 0)
+						{
+							grid.template getProp<Phi_0_grid>(key) = grid.template getProp<Phi_0_grid>(key.move(d, +1));
+							break;
+						}
+					}
+				}
+				++dom;
+			}
+		}
+		if (sign_inside < 0)
+		{
+			auto dom = grid.getDomainIterator();
+			while(dom.isNext())
+			{
+				auto key = dom.get();
+				if (grid.template getProp<Phi_0_grid>(key) < 0)
+				{
+					for (int d = 0; d < grid_type::dims; ++d)
+					{
+						if (grid.template getProp<Phi_0_grid>(key.move(d, -1)) > 0
+								&& grid.template getProp<Phi_0_grid>(key.move(d, +1)) > 0)
+						{
+							grid.template getProp<Phi_0_grid>(key) = grid.template getProp<Phi_0_grid>(key.move(d, +1));
+							break;
+						}
+					}
+				}
+				++dom;
+			}
+		}
+		
+	}
+}
+
+template <typename T>
+bool is_inside(T phi)
+{
+	return phi >= 0 - std::numeric_limits<T>::epsilon();
+}
+
+template <typename T>
+bool is_outside(T phi)
+{
+	return phi < 0 + std::numeric_limits<T>::epsilon();
+}
+
+/**@brief Checks for thin lines and thin spaces in between surfaces of 1dx thickness and removes them by setting the
+ * value of the indicator function equal accordingly.
+ *
+ * @tparam grid_type Template type of OpenFPM grid.
+ * @tparam Phi_0_grid Property that contains the indicator or level-set function.
+ * @param grid Grid that stores the indicator or level-set function.
+ */
+template <size_t Phi_0_grid, typename grid_type>
+void removeLinesAndThinSpaces(grid_type & grid, int repeat=3)
+{
+	for(int k = 0; k < repeat; ++k)
+	{
+		grid.template ghost_get<Phi_0_grid>(KEEP_PROPERTIES);
+		auto dom = grid.getDomainIterator();
+		while(dom.isNext())
+		{
+			auto key = dom.get();
+			for (int d = 0; d < grid_type::dims; ++d)
+			{
+				if (is_inside(grid.template getProp<Phi_0_grid>(key))) // If inside but neighbors are outside
+				{
+					if (is_outside(grid.template getProp<Phi_0_grid>(key.move(d, -1)))
+						&& is_outside(grid.template getProp<Phi_0_grid>(key.move(d, +1))))
+					{
+						grid.template getProp<Phi_0_grid>(key) = grid.template getProp<Phi_0_grid>(key.move(d, +1));
+						break;
+					}
+				}
+				else if (is_outside(grid.template getProp<Phi_0_grid>(key))) // If outside but neighbors are inside
+				{
+					if (is_inside(grid.template getProp<Phi_0_grid>(key.move(d, -1)))
+						&& is_inside(grid.template getProp<Phi_0_grid>(key.move(d, +1))))
+					{
+						grid.template getProp<Phi_0_grid>(key) = grid.template getProp<Phi_0_grid>(key.move(d, +1));
+						break;
+					}
+				}
+			}
+			++dom;
+		}
+	}
+}
+#endif //SUSSMAN_REDISTANCING_REMOVELINES_HPP

example/SparseGrid/9_inhomogeneous_diffusion_porous_catalyst_CaCO3/Makefile

+include ../../example.mk
+
+### This is a trick to avoid "Command not found if you no not have NVCC compiler". In practice the normal C++ compiler is used
+### internally the example disable with the preprocessor its code if not compiled with nvcc 
+CUDA_CC=
+CUDA_CC_LINK=
+ifdef CUDA_ON_CPU
+	CUDA_CC=mpic++ -x c++ $(INCLUDE_PATH)
+        INCLUDE_PATH_NVCC=
+        CUDA_CC_LINK=mpic++
+        CUDA_OPTIONS=
+		LIBS_SELECT=$(LIBS)
+else
+	ifeq (, $(shell which nvcc))
+        	CUDA_CC=mpic++ -x c++ $(INCLUDE_PATH)
+        	INCLUDE_PATH_NVCC=
+        	CUDA_CC_LINK=mpic++
+		CUDA_OPTIONS=
+		LIBS_SELECT=$(LIBS)
+	else
+        	CUDA_CC=nvcc -ccbin=mpic++
+        	CUDA_CC_LINK=nvcc -ccbin=mpic++
+		CUDA_OPTIONS=-use_fast_math  -arch=sm_61 -lineinfo
+		LIBS_SELECT=$(LIBS_NVCC)
+	endif
+endif
+
+ifeq ($(PROFILE),ON)
+        CUDA_CC=scorep --nocompiler  --cuda --mpp=mpi nvcc -ccbin=mpic++
+        CUDA_CC_LINK=scorep --nocompiler  --cuda --mpp=mpi nvcc -ccbin=mpic++
+else
+	CUDA_CC:=$(CUDA_CC)
+	CUDA_CC_LINK:=$(CUDA_CC_LINK)
+endif
+
+LDIR =
+OPT=
+
+INCLUDE_PATH_NVCC:=$(INCLUDE_PATH_NVCC) -I./include 
+
+OBJ = main.o
+
+diff_CaCO3:
+diff_CaCO3_test: OPT += -DTEST_RUN
+diff_CaCO3_test: diff_CaCO3
+
+%.o: %.cu
+	$(CUDA_CC) -O3 $(OPT) $(CUDA_OPTIONS) --extended-lambda --expt-relaxed-constexpr -g -c --std=c++14 -o $@ $< $(INCLUDE_PATH_NVCC)
+
+%.o: %.cpp
+	$(CC) -O3 $(OPT) -g -c --std=c++14 -o $@ $< $(INCLUDE_PATH)
+
+diff_CaCO3: $(OBJ)
+	$(CUDA_CC_LINK) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS_SELECT)
+
+diff_CaCO32: $(OBJ)
+	$(CUDA_CC_LINK) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS_SELECT)
+
+all: diff_CaCO3
+
+run: diff_CaCO3_test
+	mpirun --oversubscribe -np 1 ./diff_CaCO3
+
+.PHONY: clean all run
+
+clean:
+	rm -f *.o *~ core diff_CaCO3
+

example/SparseGrid/9_inhomogeneous_diffusion_porous_catalyst_CaCO3/include/RemoveLines.hpp

+//
+// Created by jstark on 07.10.21.
+//
+
+#ifndef SUSSMAN_REDISTANCING_REMOVELINES_HPP
+#define SUSSMAN_REDISTANCING_REMOVELINES_HPP
+
+/**@brief Checks for thin lines and removes them by setting the value of the indicator function accordingly.
+ *
+ * @tparam grid_type Template type of OpenFPM grid.
+ * @tparam Phi_0_grid Property that contains the indicator or level-set function.
+ * @tparam sign_inside Sign that indicates that a node lies inside the object. Set to +1 or -1 depending on the
+ * convention you use.
+ * @param grid Grid that stores the indicator or level-set function.
+ */
+template <size_t Phi_0_grid, int sign_inside, typename grid_type>
+void removeLines(grid_type & grid)
+{
+	if(sign_inside == 0)
+	{
+		std::cout << "sign_inside was set to 0. However, it must be set to +1 or -1 depending on the level-set "
+					 "convention used. Aborting..." << std::endl;
+		abort();
+	}
+	for(int repeat = 0; repeat < 2; ++repeat)
+	{
+		grid.template ghost_get<Phi_0_grid>(KEEP_PROPERTIES);
+		if (sign_inside > 0)
+		{
+			auto dom = grid.getDomainIterator();
+			while(dom.isNext())
+			{
+				auto key = dom.get();
+				if (grid.template getProp<Phi_0_grid>(key) > 0)
+				{
+					for (int d = 0; d < grid_type::dims; ++d)
+					{
+						if (grid.template getProp<Phi_0_grid>(key.move(d, -1)) < 0
+								&& grid.template getProp<Phi_0_grid>(key.move(d, +1)) < 0)
+						{
+							grid.template getProp<Phi_0_grid>(key) = grid.template getProp<Phi_0_grid>(key.move(d, +1));
+							break;
+						}
+					}
+				}
+				++dom;
+			}
+		}
+		if (sign_inside < 0)
+		{
+			auto dom = grid.getDomainIterator();
+			while(dom.isNext())
+			{
+				auto key = dom.get();
+				if (grid.template getProp<Phi_0_grid>(key) < 0)
+				{
+					for (int d = 0; d < grid_type::dims; ++d)
+					{
+						if (grid.template getProp<Phi_0_grid>(key.move(d, -1)) > 0
+								&& grid.template getProp<Phi_0_grid>(key.move(d, +1)) > 0)
+						{
+							grid.template getProp<Phi_0_grid>(key) = grid.template getProp<Phi_0_grid>(key.move(d, +1));
+							break;
+						}
+					}
+				}
+				++dom;
+			}
+		}
+		
+	}
+}
+
+template <typename T>
+bool is_inside(T phi)
+{
+	return phi >= 0 - std::numeric_limits<T>::epsilon();
+}
+
+template <typename T>
+bool is_outside(T phi)
+{
+	return phi < 0 + std::numeric_limits<T>::epsilon();
+}
+
+/**@brief Checks for thin lines and thin spaces in between surfaces of 1dx thickness and removes them by setting the
+ * value of the indicator function equal accordingly.
+ *
+ * @tparam grid_type Template type of OpenFPM grid.
+ * @tparam Phi_0_grid Property that contains the indicator or level-set function.
+ * @param grid Grid that stores the indicator or level-set function.
+ */
+template <size_t Phi_0_grid, typename grid_type>
+void removeLinesAndThinSpaces(grid_type & grid, int repeat=3)
+{
+	for(int k = 0; k < repeat; ++k)
+	{
+		grid.template ghost_get<Phi_0_grid>(KEEP_PROPERTIES);
+		auto dom = grid.getDomainIterator();
+		while(dom.isNext())
+		{
+			auto key = dom.get();
+			for (int d = 0; d < grid_type::dims; ++d)
+			{
+				if (is_inside(grid.template getProp<Phi_0_grid>(key))) // If inside but neighbors are outside
+				{
+					if (is_outside(grid.template getProp<Phi_0_grid>(key.move(d, -1)))
+						&& is_outside(grid.template getProp<Phi_0_grid>(key.move(d, +1))))
+					{
+						grid.template getProp<Phi_0_grid>(key) = grid.template getProp<Phi_0_grid>(key.move(d, +1));
+						break;
+					}
+				}
+				else if (is_outside(grid.template getProp<Phi_0_grid>(key))) // If outside but neighbors are inside
+				{
+					if (is_inside(grid.template getProp<Phi_0_grid>(key.move(d, -1)))
+						&& is_inside(grid.template getProp<Phi_0_grid>(key.move(d, +1))))
+					{
+						grid.template getProp<Phi_0_grid>(key) = grid.template getProp<Phi_0_grid>(key.move(d, +1));
+						break;
+					}
+				}
+			}
+			++dom;
+		}
+	}
+}
+#endif //SUSSMAN_REDISTANCING_REMOVELINES_HPP