merged windows port into trunk

AMDiS/AMDiSConfig.cmake.in

@@ -2,11 +2,11 @@ set(MTL_DIR ${AMDiS_DIR}/mtl4 CACHE PATH "the mtl directory")
 set(AMDiS_INCLUDE_DIR ${AMDiS_DIR}/include ${MTL_DIR})
 set(AMDiS_LIBRARIES amdis compositeFEM)
 set(AMDiS_LIBRARY_DIRS ${AMDiS_DIR}/lib)
-
-find_package(Boost 1.42 REQUIRED)
+find_package(Boost 1.42 REQUIRED system iostreams)
 if(Boost_FOUND)
-	set(AMDiS_LIBRARIES ${AMDiS_LIBRARIES} boost_system boost_iostreams)
-	set(AMDiS_LIBRARY_DIRS ${AMDiS_LIBRARY_DIRS} ${Boost_INCLUDE_DIR})
+	set(AMDiS_LIBRARIES ${AMDiS_LIBRARIES} ${Boost_LIBRARIES})
+	set(AMDiS_LIBRARY_DIRS ${AMDiS_LIBRARY_DIRS} ${Boost_LIBRARY_DIRS})
+	list(APPEND AMDiS_INCLUDE_DIR ${Boost_INCLUDE_DIR})
 endif(Boost_FOUND)
 
 set(AMDiS_NEED_PARMETIS @ENABLE_PARMETIS@)
@@ -31,7 +31,7 @@ if(AMDiS_NEED_UMFPACK)
 	)
 endif(AMDiS_NEED_UMFPACK)
 if(${AMDiS_FIND_COMPONENTS} MATCHES umfpack )
-	if( AMDiS_NEED_UMFPACK )
+	if( ${AMDiS_NEED_UMFPACK} )
 	  set(AMDiS_LIBRARIES ${AMDiS_LIBRARIES} umfpack blas)
 	else()
 	  set( AMDiS_umfpack_FOUND FALSE)

AMDiS/CMakeLists.txt

@@ -6,19 +6,24 @@ set(AMDiS_SOURCE_DIR "${AMDiS_SOURCE_DIR}/src")
 
 #needs: --enable-debug, enable-intel --enable-openmp --enable-parmetis --enable-parallel-domain --enable-umfpack --enable-mkl --enable-boost --enable-marmot
 
+SET(LIB_DIR ./lib)
+SET(SOURCE_DIR ${AMDiS_SOURCE_DIR})
+
 #TODO: use the cmake build type
+SET(MTL_DIR ${LIB_DIR}/mtl4/ CACHE PATH "mtl4 directory")
+
 option(ENABLE_DEBUG "debug" false)
 #option(ENABLE_INTEL "use intel compiler" false)
 option(ENABLE_OPENMP "use openmp" false)
 option(ENABLE_PARMETIS "use partion of unity and enable parmetis" false)
 option(ENABLE_PARALLEL_DOMAIN "use parallel domain decomposition" false)
-SET(PETSC_DIR "" CACHE STRING "Petsc directory for parallel domain decomposition" )
+SET(PETSC_DIR "" CACHE PATH "Petsc directory for parallel domain decomposition" )
 SET(PETSC_ARCH "" CACHE STRING "Petsc architecture")
 option(ENABLE_UMFPACK "use umfpack solver" false)
 option(ENABLE_MKL "use the mkl" false)
-SET(MKL_DIR "" CACHE STRING "MKL directory")
+SET(MKL_DIR "" CACHE PATH "MKL directory")
 option(ENABLE_DUNE "use dune" false)
-SET(DUNE_DIR "" CACHE STRING "Dune directory")
+SET(DUNE_DIR "" CACHE PATH "Dune directory")
 #option(ENABLE_BOOST "use the boost library" false)
 option(ENABLE_MARMOT "use marmot" false)
 option(ENABLE_GUI "compile the gui" false)
@@ -36,6 +41,16 @@ endif(ENABLE_INTEL)
 #if(ENABLE_BOOST)
 	SET(COMPILEFLAGS "${COMPILEFLAGS} -DHAVE_BOOST=1")
 	find_package(Boost 1.42 REQUIRED)
+        if(Boost_FOUND)
+		include_directories(${Boost_INCLUDE_DIR})
+		message("boost lib-dirs: ${Boost_LIBRARY_DIRS}")
+		message("use the boost dir: ${Boost_INCLUDE_DIR}")
+		if(WIN32)
+			message("the windows find_boost does not set the boost library paths, please set it")
+			SET(Boost_LIBRARY_DIRS CACHE PATH "The directory containing the boost libraries")
+		endif(WIN32)		
+		link_directories(${Boost_LIBRARY_DIRS})
+	endif(Boost_FOUND)
 #endif(ENABLE_BOOST)
 
 SET(LIB_DIR ./lib)
@@ -152,7 +167,7 @@ if(ENABLE_PARMETIS)
 				${SOURCE_DIR}/ParallelProblem.cc ${SOURCE_DIR}/ParMetisPartitioner.cc 
 				${SOURCE_DIR}/PollutionError.cc)
 	SET(COMPILEFLAGS "${COMPILEFLAGS} -DHAVE_PARALLEL_AMDIS=1")
-	INSTALL(FILES ${LIB_DIR}/ParMetis-3.1/parmetis.h
+        INSTALL(FILES ${LIB_DIR}/ParMetis-3.1/parmetis.h
 			${LIB_DIR}/ParMetis-3.1/libparmetis.a
 			${LIB_DIR}/ParMetis-3.1/libmetis.a
 			DESTINATION amdis/parmetis
@@ -186,21 +201,20 @@ endif(ENABLE_OPENMP)
 if(ENABLE_UMFPACK)
 	include_directories(${LIB_DIR}/UFconfig ${LIB_DIR}/AMD/Include ${LIB_DIR}/UMFPACK/Include)
 	SET(COMPILEFLAGS "${COMPILEFLAGS} -DHAVE_UMFPACK=1 -DMTL_HAS_UMFPACK")
-	FILE(GLOB UMFPACK_HEADERS "${LIB_DIR}/UMFPACK/Include/*.h")
-	  INSTALL(FILES ${UMFPACK_HEADERS} DESTINATION amdis/umfpack/include)
-
-	  FILE(GLOB UMFPACK_HEADERS "${LIB_DIR}/AMD/Include/*.h")
-	    INSTALL(FILES ${UMFPACK_HEADERS} DESTINATION amdis/amd/include)
+        FILE(GLOB UMFPACK_HEADERS "${LIB_DIR}/UMFPACK/Include/*.h")
+	INSTALL(FILES ${UMFPACK_HEADERS} DESTINATION amdis/umfpack/include)
 
-	  FILE(GLOB HEADERS "${LIB_DIR}/UFconfig/*.h")
-	    INSTALL(FILES ${HEADERS} DESTINATION amdis/ufconfig/)
+	FILE(GLOB UMFPACK_HEADERS "${LIB_DIR}/AMD/Include/*.h")
+	INSTALL(FILES ${UMFPACK_HEADERS} DESTINATION amdis/amd/include)
 
-	  FILE(GLOB HEADERS "${LIB_DIR}/UFconfig/xerbla/*.h")
-	    INSTALL(FILES ${HEADERS} DESTINATION amdis/ufconfig/xerbla)
+	FILE(GLOB HEADERS "${LIB_DIR}/UFconfig/*.h")
+	INSTALL(FILES ${HEADERS} DESTINATION amdis/ufconfig/)
 
-	  INSTALL(FILES ${LIB_DIR}/UMFPACK/Lib/libumfpack.a DESTINATION amdis/umfpack/)
-	  INSTALL(FILES ${LIB_DIR}/AMD/Lib/libamd.a DESTINATION amdis/amd/)
+	FILE(GLOB HEADERS "${LIB_DIR}/UFconfig/xerbla/*.h")
+	INSTALL(FILES ${HEADERS} DESTINATION amdis/ufconfig/xerbla)
 
+	INSTALL(FILES ${LIB_DIR}/UMFPACK/Lib/libumfpack.a DESTINATION amdis/umfpack/)
+	INSTALL(FILES ${LIB_DIR}/AMD/Lib/libamd.a DESTINATION amdis/amd/)
 endif(ENABLE_UMFPACK)
 
 if(ENABLE_MKL)
@@ -221,12 +235,16 @@ SET(COMPOSITE_FEM_SRC ${COMPOSITE_SOURCE_DIR}/CFE_Integration.cc ${COMPOSITE_SOU
 		      ${COMPOSITE_SOURCE_DIR}/SubElementAssembler.cc )
 
 #mtl4 includes
-include_directories(${LIB_DIR}/mtl4)
+include_directories(${MTL_DIR})
 include_directories(${SOURCE_DIR})
 
 add_library(amdis SHARED ${AMDIS_SRC} ${PARALLEL_AMDIS_SRC} ${PARALLEL_DOMAIN_AMDIS_SRC})
 add_library(compositeFEM SHARED ${COMPOSITE_FEM_SRC})
+target_link_libraries(compositeFEM amdis)
 
+if(WIN32)
+	SET(COMPILEFLAGS "${COMPILEFLAGS} -D_SCL_SECURE_NO_WARNINGS -D_CRT_SECURE_NO_WARNINGS")
+endif(WIN32)
 message("compileflags: ${COMPILEFLAGS}")
 SET_TARGET_PROPERTIES(amdis PROPERTIES COMPILE_FLAGS "${COMPILEFLAGS}")
 if(ENABLE_MARMOT)
@@ -244,6 +262,8 @@ FILE(GLOB HEADERS "${AMDiS_SOURCE_DIR}/parallel/*.h")
 INSTALL(FILES ${HEADERS} DESTINATION amdis/include/parallel/)
 FILE(GLOB HEADERS "${AMDiS_SOURCE_DIR}/time/*.h")
 INSTALL(FILES ${HEADERS} DESTINATION amdis/include/time/)
+FILE(GLOB HEADERS "${AMDiS_SOURCE_DIR}/itl/*.hpp")
+INSTALL(FILES ${HEADERS} DESTINATION amdis/include/itl)
 
 configure_file(${AMDiS_BINARY_DIR}/AMDiSConfig.cmake.in
 		${AMDiS_BINARY_DIR}/AMDiSConfig.cmake

AMDiS/src/Debug.cc

@@ -301,10 +301,17 @@ namespace AMDiS {
       }
 
       std::cout << "value = 0: " << counter0 << std::endl;
+#ifdef WIN32
       for (std::map<int, int>::iterator it = counter.begin(); it != counter.end(); ++it)
-	std::cout << pow(10, it->first) << " <= values <= " 
+	    std::cout << pow(double(10), it->first) << " <= values <= " 
+		  << pow(double(10), it->first + 1) << ": " 
+		  << it->second << std::endl;
+#else
+      for (std::map<int, int>::iterator it = counter.begin(); it != counter.end(); ++it)
+	    std::cout << pow(10, it->first) << " <= values <= " 
 		  << pow(10, it->first + 1) << ": " 
 		  << it->second << std::endl;
+#endif
     }
 
 

AMDiS/src/ITL_Solver.h

@@ -33,7 +33,7 @@
 #include <boost/numeric/itl/krylov/idr_s.hpp>
 #include <boost/numeric/itl/krylov/qmr.hpp>
 #include <boost/numeric/itl/krylov/tfqmr.hpp>
-#include <boost/numeric/itl/krylov/minres.hpp>
+#include "itl/minres.hpp"
 
 
 namespace AMDiS {

AMDiS/src/MathFunctions.h

@@ -2,7 +2,9 @@
 #define AMDIS_MATHFUNCTIONS_H
 
 #include "Global.h"
+#include <limits>
 
+using namespace std;
 namespace AMDiS {
   //converts signed distance to phasefield
   inline double Phi1(double r, double eps) { return 0.5 * (1 - tanh(3 * r / eps)); }
@@ -18,13 +20,17 @@ namespace AMDiS {
     return 0;
   }
 
-  //convert Phi1 to r
   inline double Phi1ToR(double p1, double eps) {
-	return eps / 3.0 * atanh( max(-1 + 1.0e-14, min(1 - 1.0e-14, 1 - 2 * p1)) );
+    double x = max(-1.0 + numeric_limits< double >::epsilon(), 
+		    min(1.0 - numeric_limits< double >::epsilon(), p1));
+    return eps / 3.0 * log((1 + x) / (1 - x)) * 0.5;
   }
-  //convert Phi2 to r
+
   inline double Phi2ToR(double p2, double eps) {
-	return eps / 3.0 * atanh( max(-1 + 1.0e-14, min(1 - 1.0e-14, 1 + 2 * p2)) );
+    double x = max(-1.0 + numeric_limits< double >::epsilon(), 
+		    min(1.0 - numeric_limits< double >::epsilon(), 1 + 2 * p2));
+    return eps / 3.0 * log( (1 + x) / (1 - x) );
   }
+
 }
 #endif

AMDiS/src/Parameters.cc

@@ -6,7 +6,11 @@
 #include <cstring>
 #include <sys/types.h>
 #include <sys/stat.h>
+
+#ifndef WIN32
 #include <unistd.h>
+#endif
+
 #include "Parameters.h"
 #include "Serializer.h"
 
@@ -581,7 +585,9 @@ namespace AMDiS {
     
     lfn.insert(fpos,".#");
 
-
+#ifdef WIN32
+    int val(0);
+#else
     struct stat buf;
 
     int val = lstat(lfn.c_str(), &buf);
@@ -589,6 +595,7 @@ namespace AMDiS {
       if (buf.st_mode&S_IFLNK && buf.st_size > 0)
 	ERROR_EXIT("Unsaved version of init file exists\n");
 
+#endif
     initIntern();
     if (0 == fn.size()) {
       Global::init();

AMDiS/src/PeriodicBC.h

@@ -34,7 +34,7 @@ namespace AMDiS {
   class DimVecLess 
   {
   public:
-    bool operator()(const DimVec<T> &v1, const DimVec<T> &v2) 
+    bool operator()(const DimVec<T> &v1, const DimVec<T> &v2) const
     {
       int  size = v1.getSize();
       for (int i = 0; i < size; i++) {

AMDiS/src/itl/minres.hpp

+// Software License for MTL
+//
+// Copyright (c) 2007 The Trustees of Indiana University.
+//               2008 Dresden University of Technology and the Trustees of Indiana University.
+// All rights reserved.
+// Authors: Peter Gottschling and Andrew Lumsdaine
+//
+// This file is part of the Matrix Template Library
+//
+// See also license.mtl.txt in the distribution.
+
+// Written by Thomas Witkowski
+
+#ifndef ITL_MINRES_INCLUDE
+#define ITL_MINRES_INCLUDE
+
+#include <boost/numeric/mtl/concept/collection.hpp>
+
+namespace itl {
+
+   template < typename Matrix, typename Vector,
+         typename LeftPreconditioner, typename RightPreconditioner, 
+typename Iteration >
+   int minres(const Matrix &A, Vector &x, const Vector &b, const 
+LeftPreconditioner &L, const RightPreconditioner &R, Iteration& iter)
+   {
+
+     using std::abs;
+     using mtl::irange; using mtl::imax; using math::reciprocal;
+     typedef typename mtl::Collection<Vector>::value_type Scalar;
+     typedef typename mtl::Collection<Vector>::size_type Size;
+
+     if (size(b) == 0)
+       throw mtl::logic_error("empty rhs vector");
+
+     Scalar                zero= math::zero(b[0]), one= math::one(b[0]);
+     Vector v0(size(x), zero), v1(b - A * x), v2(v1), z1(solve(L, v1)), z2(size(x), zero);
+     Vector w0(size(x), zero), w1(size(x), zero), w2(size(x), zero);
+
+     Scalar s0(zero), s1(zero), c0(one), c1(one), gamma0(one);
+     Scalar gamma1(sqrt(dot(z1, v1))), gamma2(zero), eta(gamma1);
+     Scalar sigma1(one), alpha0(zero), alpha1(zero), alpha2(zero), alpha3(zero);
+
+     while (!iter.finished(abs(eta))) {
+       z1 *= reciprocal(gamma1);
+       v2 = A * z1;
+       sigma1 = dot(v2, z1);
+       v2 += -(sigma1 / gamma1) * v1 - (gamma1 / gamma0) * v0;
+
+       z2 = solve(L, v2);
+
+       gamma2 = sqrt(dot(z2, v2));
+       alpha0 = c1 * sigma1 - c0 * s1 * gamma1;
+       alpha1 = sqrt(alpha0 * alpha0 + gamma2 * gamma2);
+       alpha2 = s1 * sigma1 + c0 * c1 * gamma1;
+       alpha3 = s0 * gamma1;
+
+       c0 = c1;
+       c1 = alpha0 / alpha1;
+       s0 = s1;
+       s1 = gamma2 / alpha1;
+
+       w2 = z1 - alpha3 * w0 - alpha2 * w1;
+       w2 *=  reciprocal(alpha1);
+
+       x += c1 * eta * w2;
+       eta *= -s1;
+
+       w0 = w1;
+       w1 = w2;
+       v0 = v1;
+       v1 = v2;
+       z1 = z2;
+
+       gamma0 = gamma1;
+       gamma1 = gamma2;
+
+       ++iter;
+     }
+
+     return iter;
+   }
+
+} // namespace itl;
+
+#endif // ITL_MINRES_INCLUDE
+