From ce5914c895c7e1fb741bc89cb88342d5d2d76a66 Mon Sep 17 00:00:00 2001
From: Serhii Yaskovets <yaskovet@mpi-cbg.de>
Date: Wed, 28 Jun 2023 18:30:01 +0200
Subject: [PATCH] Add missing files to SparseGrid examples (Heat conduct,
Porous Diff)
---
.../Makefile | 68 ++++++++++
.../include/RemoveLines.hpp | 128 ++++++++++++++++++
.../Makefile | 68 ++++++++++
.../include/RemoveLines.hpp | 128 ++++++++++++++++++
4 files changed, 392 insertions(+)
create mode 100644 example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/Makefile
create mode 100755 example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/include/RemoveLines.hpp
create mode 100644 example/SparseGrid/9_inhomogeneous_diffusion_porous_catalyst_CaCO3/Makefile
create mode 100755 example/SparseGrid/9_inhomogeneous_diffusion_porous_catalyst_CaCO3/include/RemoveLines.hpp
diff --git a/example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/Makefile b/example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/Makefile
new file mode 100644
index 000000000..f0dfe8b92
--- /dev/null
+++ b/example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/Makefile
@@ -0,0 +1,68 @@
+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
+
diff --git a/example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/include/RemoveLines.hpp b/example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/include/RemoveLines.hpp
new file mode 100755
index 000000000..520438b26
--- /dev/null
+++ b/example/SparseGrid/10_heat_conduction_reticulate_porous_ceramics/include/RemoveLines.hpp
@@ -0,0 +1,128 @@
+//
+// 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
diff --git a/example/SparseGrid/9_inhomogeneous_diffusion_porous_catalyst_CaCO3/Makefile b/example/SparseGrid/9_inhomogeneous_diffusion_porous_catalyst_CaCO3/Makefile
new file mode 100644
index 000000000..ec2f1f90d
--- /dev/null
+++ b/example/SparseGrid/9_inhomogeneous_diffusion_porous_catalyst_CaCO3/Makefile
@@ -0,0 +1,68 @@
+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
+
diff --git a/example/SparseGrid/9_inhomogeneous_diffusion_porous_catalyst_CaCO3/include/RemoveLines.hpp b/example/SparseGrid/9_inhomogeneous_diffusion_porous_catalyst_CaCO3/include/RemoveLines.hpp
new file mode 100755
index 000000000..520438b26
--- /dev/null
+++ b/example/SparseGrid/9_inhomogeneous_diffusion_porous_catalyst_CaCO3/include/RemoveLines.hpp
@@ -0,0 +1,128 @@
+//
+// 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
--
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