diff --git a/AMDiS/AMDiSConfig.cmake.in b/AMDiS/AMDiSConfig.cmake.in
index 1344f66f908e16663ed4cc19141ff8452929545e..fc2212be2eb14aca9e33b41b86be7d0e7b868bbd 100644
--- a/AMDiS/AMDiSConfig.cmake.in
+++ b/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 ${AMDiS_LIBRARIES} umfpack blas)
else()
set( AMDiS_umfpack_FOUND FALSE)
diff --git a/AMDiS/CMakeLists.txt b/AMDiS/CMakeLists.txt
index c35d706333437571243e2ad8dbfc64190fffe07a..e0adb1e74dfce4974ac029bc94ab98f643b92960 100644
--- a/AMDiS/CMakeLists.txt
+++ b/AMDiS/CMakeLists.txt
@@ -6,19 +6,24 @@ set(AMDiS_SOURCE_DIR "${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
diff --git a/AMDiS/src/Debug.cc b/AMDiS/src/Debug.cc
index 619289eeeec1bb8a6f7f7b21461330187014d8fd..627ee2449a0fdd0be92e8523b06b00b721470fbe 100644
--- a/AMDiS/src/Debug.cc
+++ b/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
}
diff --git a/AMDiS/src/ITL_Solver.h b/AMDiS/src/ITL_Solver.h
index 7c57d2ab0639637432ad20bb1f48988641e84ee8..fb1774ddb71fdae4aadc8156ef82330d4efaef15 100644
--- a/AMDiS/src/ITL_Solver.h
+++ b/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 {
diff --git a/AMDiS/src/MathFunctions.h b/AMDiS/src/MathFunctions.h
index 335d144c3e8784efb8a356e6b72c7f468e16bff3..31edf00f39583cc758ef80b8a953de084fd2fff7 100644
--- a/AMDiS/src/MathFunctions.h
+++ b/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
diff --git a/AMDiS/src/Parameters.cc b/AMDiS/src/Parameters.cc
index 6d30383675df895d7275f05980a82d7a80638e84..c64527fdec0df9e9146026e48c9e24f1b72687d6 100644
--- a/AMDiS/src/Parameters.cc
+++ b/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();
diff --git a/AMDiS/src/PeriodicBC.h b/AMDiS/src/PeriodicBC.h
index 9a8795f37954fef4ceaa6bfdcbce2f3b6b4e6012..05015d842da3d13e36aef400ad4d90f7ca088d69 100644
--- a/AMDiS/src/PeriodicBC.h
+++ b/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++) {
diff --git a/AMDiS/src/itl/minres.hpp b/AMDiS/src/itl/minres.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..2c6fa729e58959a9fa0db4fd32122b06a9d2b9f1
--- /dev/null
+++ b/AMDiS/src/itl/minres.hpp
@@ -0,0 +1,87 @@
+// 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
+