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	tadded ghost nodes to vidx - sphere - GPU-based 3D discrete element method algo…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 9110244001e9a56f0e98907b59b5c870a8ae8951
	parent a9f8a2dd9e09d2d28668068702d302ed7f6fbe46
	Author: Anders Damsgaard <[email protected]>
	Date: Tue, 3 Jun 2014 16:52:27 +0200

	added ghost nodes to vidx

	Diffstat:
	M CMakeLists.txt \| 10 +++++-----
	M src/navierstokes.cuh \| 10 ++++++++--
	M tests/io_tests_fluid.py \| 4 ++--

	3 files changed, 15 insertions(+), 9 deletions(-)
	---
	diff --git a/CMakeLists.txt b/CMakeLists.txt
	t@@ -29,13 +29,13 @@ find_package(OpenMP)
	enable_testing()

	# Set build type = Debug
	-#set(CMAKE_BUILD_TYPE Debug)
	-#if (CUDA_FOUND)
	-# set(CUDA_NVCC_FLAGS -g;-G)
	-#endif()
	+set(CMAKE_BUILD_TYPE Debug)
	+if (CUDA_FOUND)
	+ set(CUDA_NVCC_FLAGS -g;-G)
	+endif()

	# Set build type = Release
	-set(CMAKE_BUILD_TYPE Release)
	+#set(CMAKE_BUILD_TYPE Release)

	# Add source directory to project.
	add_subdirectory(src)
	diff --git a/src/navierstokes.cuh b/src/navierstokes.cuh
	t@@ -222,8 +222,14 @@ __inline__ __device__ unsigned int idx(
	__inline__ __device__ unsigned int vidx(
	const int x, const int y, const int z)
	{
	- return x + (devC_grid.num[0]+1)*y
	- + (devC_grid.num[0]+1)(devC_grid.num[1]+1)z;
	+ // without ghost nodes
	+ //return x + (devC_grid.num[0]+1)*y
	+ //+ (devC_grid.num[0]+1)(devC_grid.num[1]+1)z;
	+
	+ // with ghost nodes
	+ // the ghost nodes are placed at x,y,z = -1 and WIDTH+1
	+ return (x+1) + (devC_grid.num[0]+3)*(y+1)
	+ + (devC_grid.num[0]+3)(devC_grid.num[1]+3)(z+1);
	}

	// Find averaged cell velocities from cell-face velocities. This function works
	diff --git a/tests/io_tests_fluid.py b/tests/io_tests_fluid.py
	t@@ -22,8 +22,8 @@ py.readbin("../input/" + orig.sid + ".bin", verbose=False)
	compare(orig, py, "Python IO:")

	# Test C++ IO routines
	-orig.run(verbose=True, hideinputfile=True)
	-#orig.run(verbose=True, hideinputfile=False)
	+#orig.run(verbose=True, hideinputfile=True)
	+orig.run(verbose=True, hideinputfile=False, cudamemcheck=True)
	cpp = sphere.sim(fluid=True)
	cpp.readbin("../output/" + orig.sid + ".output00000.bin", verbose=False)
	compare(orig, cpp, "C++ IO: ")