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	tRenamed darcy flow main file to porousflow. Darcy calls now in darcy.cpp - sph…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 7b2baa5c83dfd64089f142f3e4f93eb7f6e91bbe
	parent ca8bad69c8b6200751129a40c8526c87405688b5
	Author: Anders Damsgaard <[email protected]>
	Date: Tue, 28 May 2013 10:22:09 +0200

	Renamed darcy flow main file to porousflow. Darcy calls now in darcy.cpp

	Diffstat:
	M src/CMakeLists.txt \| 2 +-
	M src/darcy.cpp \| 102 +++++++++--------------------…
	C src/darcy.cpp -> src/porousflow.cpp \| 0

	3 files changed, 29 insertions(+), 75 deletions(-)
	---
	diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
	t@@ -18,7 +18,7 @@ SET(CUDA_NVCC_FLAGS "--use_fast_math;-O3;-gencode=arch=compu…
	CUDA_ADD_EXECUTABLE(../sphere main.cpp file_io.cpp sphere.cpp device.cu utilit…
	CUDA_ADD_EXECUTABLE(../porosity porosity.cpp file_io.cpp sphere.cpp device.cu …
	CUDA_ADD_EXECUTABLE(../forcechains forcechains.cpp file_io.cpp sphere.cpp devi…
	-CUDA_ADD_EXECUTABLE(../darcy darcy.cpp file_io.cpp sphere.cpp device.cu utilit…
	+CUDA_ADD_EXECUTABLE(../porousflow porousflow.cpp darcy.cpp file_io.cpp sphere.…

	#ADD_EXECUTABLE(unittests boost-unit-tests.cpp sphere.cpp)
	#TARGET_LINK_LIBRARIES(unittests
	diff --git a/src/darcy.cpp b/src/darcy.cpp
	t@@ -1,85 +1,39 @@
	-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
	-/* SPHERE source code by Anders Damsgaard Christensen, 2010-12, */
	-/* a 3D Discrete Element Method algorithm with CUDA GPU acceleration. */
	-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
	-
	-// Licence: GNU Public License (GPL) v. 3. See license.txt.
	-// See doc/sphere-doc.pdf for full documentation.
	-// Compile with GNU make by typing 'make' in the src/ directory.
	-// SPHERE is called from the command line with './sphere_<architecture> projec…
	-
	-
	-// Including library files
	#include <iostream>
	#include <string>
	+#include <cstdio>
	#include <cstdlib>
	+#include <cmath>
	+#include <vector>
	+#include <algorithm>

	-// Including user files
	-#include "constants.h"
	+#include "typedefs.h"
	#include "datatypes.h"
	+#include "constants.h"
	#include "sphere.h"

	-//////////////////
	-// MAIN ROUTINE //
	-//////////////////
	-// The main loop returns the value 0 to the shell, if the program terminated
	-// successfully, and 1 if an error occured which caused the program to crash.
	-int main(const int argc, const char *argv[])
	-{
	- // Default values
	- int verbose = 1;
	- int dry = 0;
	- int nfiles = 0;
	-
	-
	- // Process input parameters
	- int i;
	- for (i=1; i<argc; ++i) { // skip argv[0]
	-
	- std::string argvi = std::string(argv[i]);
	-
	- // Display help if requested
	- if (argvi == "-h" \|\| argvi == "--help") {
	- std::cout << argv[0] << ": particle dynamics simulator\n"
	- << "Usage: " << argv[0] << " [OPTION[S]]... [FILE1 ...]\nOptio…
	- << "-h, --help\t\tprint help\n"
	- << "-n, --dry\t\tshow key experiment parameters and quit\n"
	- << std::endl;
	- return 0; // Exit with success
	- }
	+// Find hydraulic conductivities for each cell

	- else if (argvi == "-n" \|\| argvi == "--dry")
	- dry = 1;
	-
	- // The rest of the values must be input binary files
	- else {
	- nfiles++;
	-
	- if (verbose == 1)
	- std::cout << argv[0] << ": processing input file: " << argvi <<
	- std::endl;
	-
	- // Create DEM class, read data from input binary,
	- // do not check values, do not init cuda, do not transfer const
	- // mem
	- DEM dem(argvi, verbose, 0, dry, 0, 0);
	-
	- // Otherwise, start iterating through time
	- dem.startDarcy();
	-
	-
	- }
	+// Solve Darcy flow through particles
	+void DEM::startDarcy(
	+ const Float cellsizemultiplier)
	+{
	+ // Number of cells
	+ int nx = grid.L[0]/grid.num[0];
	+ int ny = grid.L[1]/grid.num[1];
	+ int nz = grid.L[2]/grid.num[2];
	+
	+ // Cell size
	+ Float dx = grid.L[0]/nx;
	+ Float dy = grid.L[1]/nx;
	+ Float dz = grid.L[2]/nx;
	+
	+ if (verbose == 1) {
	+ std::cout << "Fluid grid dimensions: "
	+ << nx << " * "
	+ << ny << " * "
	+ << nz << std::endl;
	}

	- // Check whether there are input files specified
	- if (!argv[0] \|\| argc == 1 \|\| nfiles == 0) {
	- std::cerr << argv[0] << ": missing input binary file\n"
	- << "See `" << argv[0] << " --help` for more information"
	- << std::endl;
	- return 1; // Return unsuccessful exit status
	- }

	- return 0; // Return successfull exit status
	-}
	-// END OF FILE
	-// vim: tabstop=8 expandtab shiftwidth=4 softtabstop=4
	+}
	+
	diff --git a/src/darcy.cpp b/src/porousflow.cpp