From d2cd87005cfbfc8bf7c01ee3fd395903d235d5eb Mon Sep 17 00:00:00 2001
From: Peter Gottschling <peter.gottschling@simunova.com>
Date: Tue, 28 Apr 2009 13:25:06 +0000
Subject: [PATCH] =?UTF-8?q?Gr=C3=B6=C3=9Fter=20Merge=20in=20der=20Geschich?=
=?UTF-8?q?te=20von=20AMDiS.=20Mit=20Thomas'=20Beteiligung.?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
AMDiS/Makefile.in | 1 +
AMDiS/aclocal.m4 | 34 +-
AMDiS/autogen.sh | 47 ++
AMDiS/bin/Makefile.am | 52 +-
AMDiS/bin/Makefile.in | 204 +-----
AMDiS/configure | 208 ++++--
AMDiS/libtool | 47 +-
AMDiS/src/AMDiS.h | 10 +-
AMDiS/src/AMDiS_fwd.h | 82 +++
AMDiS/src/AdaptStationary.h | 5 +-
AMDiS/src/BFGS_Precond.cc | 68 --
AMDiS/src/BFGS_Precond.h | 168 -----
AMDiS/src/BasisFunction.h | 7 +-
AMDiS/src/BiCGSolver.h | 101 ---
AMDiS/src/BiCGSolver.hh | 193 ------
AMDiS/src/BiCGStab.h | 104 ---
AMDiS/src/BiCGStab.hh | 239 -------
AMDiS/src/BiCGStab2.h | 103 ---
AMDiS/src/BiCGStab2.hh | 228 -------
AMDiS/src/BiCGStab_M.hh | 191 ------
AMDiS/src/Boundary.h | 110 ++++
AMDiS/src/BoundaryCondition.h | 27 +-
AMDiS/src/BoundaryManager.h | 2 +-
AMDiS/src/BoxSmoother.h | 3 +
AMDiS/src/CGSolver.h | 114 ----
AMDiS/src/CGSolver.hh | 132 ----
AMDiS/src/CreatorInterface.h | 4 +
AMDiS/src/CreatorMap.cc | 178 +-----
AMDiS/src/CreatorMap.h | 25 +-
AMDiS/src/DOFIndexed.cc | 93 ++-
AMDiS/src/DOFIndexed.h | 12 +-
AMDiS/src/DOFMatrix.cc | 700 ++++-----------------
AMDiS/src/DOFMatrix.h | 308 ++++-----
AMDiS/src/DOFVector.cc | 2 +-
AMDiS/src/DOFVector.h | 34 +-
AMDiS/src/DOFVector.hh | 454 +++++++------
AMDiS/src/DataCollector.cc | 3 +-
AMDiS/src/DiagonalPreconditioner.cc | 59 --
AMDiS/src/DiagonalPreconditioner.h | 133 ----
AMDiS/src/DirichletBC.cc | 2 +-
AMDiS/src/DirichletBC.h | 8 +-
AMDiS/src/DualTraverse.h | 2 +-
AMDiS/src/Estimator.h | 11 +-
AMDiS/src/GMResSolver.h | 164 -----
AMDiS/src/GMResSolver.hh | 189 ------
AMDiS/src/GMResSolver2.h | 163 -----
AMDiS/src/GMResSolver2.hh | 191 ------
AMDiS/src/GSSmoother.cc | 9 +-
AMDiS/src/ILUPreconditioner.cc | 314 ---------
AMDiS/src/ILUPreconditioner.h | 181 ------
AMDiS/src/ILUTPreconditioner.cc | 247 --------
AMDiS/src/ILUTPreconditioner.h | 137 ----
AMDiS/src/ITL_OEMSolver.h | 141 +++++
AMDiS/src/ITL_Preconditioner.h | 177 ++++++
AMDiS/src/ITL_Solver.h | 180 ++++++
AMDiS/src/InterpolRestrictMatrix.cc | 23 +-
AMDiS/src/InterpolRestrictMatrix.h | 6 +-
AMDiS/src/JacobiSmoother.cc | 6 +
AMDiS/src/LeafData.cc | 5 +-
AMDiS/src/MatVecMultiplier.cc | 11 +-
AMDiS/src/MultiGridPreconWrapper.cc | 4 +
AMDiS/src/MultiGridPreconWrapper.h | 4 +
AMDiS/src/MultiGridSolver.cc | 184 +++---
AMDiS/src/MultiGridSolver.h | 14 +-
AMDiS/src/MultiGridSolverBase.h | 24 +-
AMDiS/src/MultiGridSolverBase.hh | 4 +
AMDiS/src/MultiGridWrapper.h | 5 +
AMDiS/src/Newton.h | 5 +-
AMDiS/src/NewtonS.h | 2 +-
AMDiS/src/NonLinSolver.h | 22 +-
AMDiS/src/NonLinSolver.hh | 2 +-
AMDiS/src/NonLinUpdater.h | 4 +-
AMDiS/src/ODirSolver.h | 101 ---
AMDiS/src/ODirSolver.hh | 167 -----
AMDiS/src/OEMSolver.h | 236 ++++---
AMDiS/src/OEMSolver.hh | 109 ----
AMDiS/src/OResSolver.h | 101 ---
AMDiS/src/OResSolver.hh | 160 -----
AMDiS/src/PeriodicBC.cc | 258 ++++++--
AMDiS/src/PeriodicBC.h | 7 +-
AMDiS/src/Preconditioner.h | 299 ---------
AMDiS/src/ProblemNonLin.cc | 8 +
AMDiS/src/ProblemNonLin.h | 4 +
AMDiS/src/ProblemScal.cc | 106 ++--
AMDiS/src/ProblemScal.h | 53 +-
AMDiS/src/ProblemStatBase.h | 5 +-
AMDiS/src/ProblemVec.cc | 127 ++--
AMDiS/src/ProblemVec.h | 61 +-
AMDiS/src/QN_Precond.h | 26 -
AMDiS/src/QN_Precond.hh | 141 -----
AMDiS/src/{BiCGStab_M.h => SolverMatrix.h} | 120 ++--
AMDiS/src/SparseVector.cc | 25 +
AMDiS/src/StlVector.cc | 81 ---
AMDiS/src/StlVector.h | 60 --
AMDiS/src/TFQMR.h | 115 ----
AMDiS/src/TFQMR.hh | 184 ------
AMDiS/src/UmfPackSolver.h | 103 ++-
AMDiS/src/UmfPackSolver.hh | 222 -------
AMDiS/src/Utilities.h | 44 ++
AMDiS/src/V3Vector.cc | 173 -----
AMDiS/src/V3Vector.h | 117 ----
AMDiS/src/VecSymSolver.h | 103 ---
AMDiS/src/VecSymSolver.hh | 443 -------------
103 files changed, 2494 insertions(+), 8191 deletions(-)
create mode 100755 AMDiS/autogen.sh
create mode 100644 AMDiS/src/AMDiS_fwd.h
delete mode 100755 AMDiS/src/BFGS_Precond.cc
delete mode 100755 AMDiS/src/BFGS_Precond.h
delete mode 100644 AMDiS/src/BiCGSolver.h
delete mode 100644 AMDiS/src/BiCGSolver.hh
delete mode 100644 AMDiS/src/BiCGStab.h
delete mode 100644 AMDiS/src/BiCGStab.hh
delete mode 100644 AMDiS/src/BiCGStab2.h
delete mode 100644 AMDiS/src/BiCGStab2.hh
delete mode 100644 AMDiS/src/BiCGStab_M.hh
delete mode 100644 AMDiS/src/CGSolver.h
delete mode 100644 AMDiS/src/CGSolver.hh
delete mode 100644 AMDiS/src/DiagonalPreconditioner.cc
delete mode 100644 AMDiS/src/DiagonalPreconditioner.h
delete mode 100644 AMDiS/src/GMResSolver.h
delete mode 100644 AMDiS/src/GMResSolver.hh
delete mode 100644 AMDiS/src/GMResSolver2.h
delete mode 100644 AMDiS/src/GMResSolver2.hh
delete mode 100644 AMDiS/src/ILUPreconditioner.cc
delete mode 100644 AMDiS/src/ILUPreconditioner.h
delete mode 100644 AMDiS/src/ILUTPreconditioner.cc
delete mode 100644 AMDiS/src/ILUTPreconditioner.h
create mode 100644 AMDiS/src/ITL_OEMSolver.h
create mode 100644 AMDiS/src/ITL_Preconditioner.h
create mode 100644 AMDiS/src/ITL_Solver.h
delete mode 100644 AMDiS/src/ODirSolver.h
delete mode 100644 AMDiS/src/ODirSolver.hh
delete mode 100644 AMDiS/src/OEMSolver.hh
delete mode 100644 AMDiS/src/OResSolver.h
delete mode 100644 AMDiS/src/OResSolver.hh
delete mode 100644 AMDiS/src/Preconditioner.h
delete mode 100755 AMDiS/src/QN_Precond.h
delete mode 100755 AMDiS/src/QN_Precond.hh
rename AMDiS/src/{BiCGStab_M.h => SolverMatrix.h} (53%)
delete mode 100644 AMDiS/src/StlVector.cc
delete mode 100644 AMDiS/src/StlVector.h
delete mode 100644 AMDiS/src/TFQMR.h
delete mode 100644 AMDiS/src/TFQMR.hh
delete mode 100644 AMDiS/src/UmfPackSolver.hh
create mode 100644 AMDiS/src/Utilities.h
delete mode 100644 AMDiS/src/V3Vector.cc
delete mode 100644 AMDiS/src/V3Vector.h
delete mode 100644 AMDiS/src/VecSymSolver.h
delete mode 100644 AMDiS/src/VecSymSolver.hh
diff --git a/AMDiS/Makefile.in b/AMDiS/Makefile.in
index a3d52949..2b28bece 100644
--- a/AMDiS/Makefile.in
+++ b/AMDiS/Makefile.in
@@ -139,6 +139,7 @@ PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
RANLIB = @RANLIB@
+SED = @SED@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
STRIP = @STRIP@
diff --git a/AMDiS/aclocal.m4 b/AMDiS/aclocal.m4
index c6b83dae..6cec4be8 100644
--- a/AMDiS/aclocal.m4
+++ b/AMDiS/aclocal.m4
@@ -1578,10 +1578,27 @@ linux*)
# before this can be enabled.
hardcode_into_libs=yes
+ # find out which ABI we are using
+ libsuff=
+ case "$host_cpu" in
+ x86_64*|s390x*|powerpc64*)
+ echo '[#]line __oline__ "configure"' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *64-bit*)
+ libsuff=64
+ sys_lib_search_path_spec="/lib${libsuff} /usr/lib${libsuff} /usr/local/lib${libsuff}"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+ esac
+
# Append ld.so.conf contents to the search path
if test -f /etc/ld.so.conf; then
- lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
- sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib${libsuff} /usr/lib${libsuff} $lt_ld_extra"
fi
# We used to test for /lib/ld.so.1 and disable shared libraries on
@@ -4288,6 +4305,9 @@ CC=$lt_[]_LT_AC_TAGVAR(compiler, $1)
# Is the compiler the GNU C compiler?
with_gcc=$_LT_AC_TAGVAR(GCC, $1)
+gcc_dir=\`gcc -print-file-name=. | $SED 's,/\.$,,'\`
+gcc_ver=\`gcc -dumpversion\`
+
# An ERE matcher.
EGREP=$lt_EGREP
@@ -4421,11 +4441,11 @@ striplib=$lt_striplib
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects=$lt_[]_LT_AC_TAGVAR(predep_objects, $1)
+predep_objects=\`echo $lt_[]_LT_AC_TAGVAR(predep_objects, $1) | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects=$lt_[]_LT_AC_TAGVAR(postdep_objects, $1)
+postdep_objects=\`echo $lt_[]_LT_AC_TAGVAR(postdep_objects, $1) | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -4437,7 +4457,7 @@ postdeps=$lt_[]_LT_AC_TAGVAR(postdeps, $1)
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path=$lt_[]_LT_AC_TAGVAR(compiler_lib_search_path, $1)
+compiler_lib_search_path=\`echo $lt_[]_LT_AC_TAGVAR(compiler_lib_search_path, $1) | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method=$lt_deplibs_check_method
@@ -4517,7 +4537,7 @@ variables_saved_for_relink="$variables_saved_for_relink"
link_all_deplibs=$_LT_AC_TAGVAR(link_all_deplibs, $1)
# Compile-time system search path for libraries
-sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+sys_lib_search_path_spec=\`echo $lt_sys_lib_search_path_spec | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Run-time system search path for libraries
sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
@@ -6353,6 +6373,7 @@ do
done
done
done
+IFS=$as_save_IFS
lt_ac_max=0
lt_ac_count=0
# Add /usr/xpg4/bin/sed as it is typically found on Solaris
@@ -6385,6 +6406,7 @@ for lt_ac_sed in $lt_ac_sed_list /usr/xpg4/bin/sed; do
done
])
SED=$lt_cv_path_SED
+AC_SUBST([SED])
AC_MSG_RESULT([$SED])
])
diff --git a/AMDiS/autogen.sh b/AMDiS/autogen.sh
new file mode 100755
index 00000000..701cc614
--- /dev/null
+++ b/AMDiS/autogen.sh
@@ -0,0 +1,47 @@
+#!/bin/sh
+
+echo "--> Running aclocal"
+aclocal
+if test "$?" != "0" ; then
+ echo "*** aclocal failed"
+ exit 1
+fi
+
+if test "`grep AC_CONFIG_HEADER configure.ac`" != "" -o \
+ "`grep AM_CONFIG_HEADER configure.ac`" != "" ; then
+ # if we use CONFIG_HEADER, then make sure to run autoheader
+ echo "--> Running autoheader"
+ autoheader
+ if test "$?" != "0" ; then
+ echo "*** autoheader failed"
+ exit 1
+ fi
+else
+ echo "--> autoheader not needed"
+fi
+
+echo "--> Running autoconf"
+autoconf
+if test "$?" != "0" ; then
+ echo "*** autoconf failed"
+ exit 1
+fi
+
+echo "--> Running libtoolize"
+libtoolize --automake --copy
+if test "$?" != "0" ; then
+ echo "*** libtoolize failed"
+ exit 1
+fi
+
+echo "--> Running automake"
+automake -a --copy --include-deps
+if test "$?" != "0" ; then
+ echo "*** automake failed"
+ exit 1
+fi
+
+echo;
+echo "Running ./configure $@"
+echo;
+./configure $@
diff --git a/AMDiS/bin/Makefile.am b/AMDiS/bin/Makefile.am
index d996bb32..5f73591b 100644
--- a/AMDiS/bin/Makefile.am
+++ b/AMDiS/bin/Makefile.am
@@ -33,7 +33,7 @@ if USE_PARALLEL_AMDIS
endif
if ENABLE_UMFPACK
- libamdis_la_CXXFLAGS += -DHAVE_UMFPACK=1
+ libamdis_la_CXXFLAGS += -DHAVE_UMFPACK=1 -DMTL_HAS_UMFPACK
AMDIS_INCLUDES += -I$(LIB_DIR)/UFconfig \
-I$(LIB_DIR)/AMD/Include \
-I$(LIB_DIR)/UMFPACK/Include
@@ -52,12 +52,14 @@ if ENABLE_BOOST
libamdis_la_CXXFLAGS += -DHAVE_BOOST=1
endif
-INCLUDES = $(AMDIS_INCLUDES) $(PARALLEL_INCLUDES)
+TEMPLATE_INCLUDES = -I../lib/mtl4 -I../lib/boost_1_34_1
+
+INCLUDES = $(AMDIS_INCLUDES) $(PARALLEL_INCLUDES) $(TEMPLATE_INCLUDES)
if AMDIS_DEBUG
- libamdis_la_CXXFLAGS += -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) -ftemplate-depth-30 $(INCLUDES) #-pedantic
+ libamdis_la_CXXFLAGS += -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) $(INCLUDES) #-pedantic
else
- libamdis_la_CXXFLAGS += -O2 -Wall -DDEBUG=0 $(OPENMP_FLAG) -ftemplate-depth-30 $(INCLUDES) #-pedantic
+ libamdis_la_CXXFLAGS += -O2 -Wall -DDEBUG=0 -DNDEBUG $(OPENMP_FLAG) -ftemplate-depth-100 $(INCLUDES) #-pedantic
endif
@@ -65,14 +67,10 @@ libamdis_la_SOURCES = \
$(PARALLEL_AMDIS_SOURCES) \
$(SOURCE_DIR)/MultiGridPreconWrapper.h $(SOURCE_DIR)/MultiGridPreconWrapper.cc \
$(SOURCE_DIR)/LagrangeInterpolRestrict.h \
-$(SOURCE_DIR)/BiCGStab.h $(SOURCE_DIR)/BiCGStab.hh \
-$(SOURCE_DIR)/BiCGStab2.h $(SOURCE_DIR)/BiCGStab2.hh \
$(SOURCE_DIR)/InterpolRestrictMatrix.h $(SOURCE_DIR)/InterpolRestrictMatrix.cc \
$(SOURCE_DIR)/DOFIndexed.h $(SOURCE_DIR)/DOFIndexed.cc \
$(SOURCE_DIR)/GNUPlotWriter.h $(SOURCE_DIR)/GNUPlotWriter.cc \
$(SOURCE_DIR)/SmootherBase.h \
-$(SOURCE_DIR)/StlVector.h $(SOURCE_DIR)/StlVector.cc \
-$(SOURCE_DIR)/V3Vector.h $(SOURCE_DIR)/V3Vector.cc \
$(SOURCE_DIR)/GSSMoother.h $(SOURCE_DIR)/GSSmoother.cc \
$(SOURCE_DIR)/JacobiSMoother.h $(SOURCE_DIR)/JacobiSmoother.cc \
$(SOURCE_DIR)/SparseVector.h $(SOURCE_DIR)/SparseVector.hh $(SOURCE_DIR)/SparseVector.cc \
@@ -130,50 +128,22 @@ $(SOURCE_DIR)/AdaptStationary.h $(SOURCE_DIR)/AdaptStationary.cc \
$(SOURCE_DIR)/AdaptInstationary.h $(SOURCE_DIR)/AdaptInstationary.cc \
$(SOURCE_DIR)/QPsiPhi.h \
$(SOURCE_DIR)/BasisFunction.h \
-$(SOURCE_DIR)/BiCGSolver.h $(SOURCE_DIR)/BiCGSolver.hh \
$(SOURCE_DIR)/Boundary.h \
-$(SOURCE_DIR)/CGSolver.h $(SOURCE_DIR)/CGSolver.hh \
+$(SOURCE_DIR)/ITL_Solver.h \
$(SOURCE_DIR)/CoarseningManager.h \
$(SOURCE_DIR)/CoarseningManager1d.h $(SOURCE_DIR)/CoarseningManager2d.h $(SOURCE_DIR)/CoarseningManager3d.h \
$(SOURCE_DIR)/demangle.h \
-$(SOURCE_DIR)/DiagonalPreconditioner.h $(SOURCE_DIR)/DiagonalPreconditioner.cc \
-$(SOURCE_DIR)/ILUPreconditioner.h $(SOURCE_DIR)/ILUPreconditioner.cc \
-$(SOURCE_DIR)/ILUTPreconditioner.h $(SOURCE_DIR)/ILUTPreconditioner.cc \
-$(SOURCE_DIR)/QN_Precond.h $(SOURCE_DIR)/QN_Precond.hh \
-$(SOURCE_DIR)/BFGS_Precond.h $(SOURCE_DIR)/BFGS_Precond.cc \
-$(SOURCE_DIR)/DOFAdmin.h \
-$(SOURCE_DIR)/DOFIterator.h \
-$(SOURCE_DIR)/DOFMatrix.h \
-$(SOURCE_DIR)/DOFVector.h $(SOURCE_DIR)/DOFVector.hh $(SOURCE_DIR)/DOFVector.cc \
-$(SOURCE_DIR)/Element.h $(SOURCE_DIR)/ElementConnection.h \
-$(SOURCE_DIR)/ElInfo.h $(SOURCE_DIR)/ElInfo1d.h $(SOURCE_DIR)/ElInfo2d.h $(SOURCE_DIR)/ElInfo3d.h \
-$(SOURCE_DIR)/Error.h $(SOURCE_DIR)/Error.hh \
-$(SOURCE_DIR)/Estimator.h $(SOURCE_DIR)/Estimator.cc \
-$(SOURCE_DIR)/ResidualEstimator.h $(SOURCE_DIR)/ResidualEstimator.cc \
-$(SOURCE_DIR)/ResidualParallelEstimator.h $(SOURCE_DIR)/ResidualParallelEstimator.cc \
-$(SOURCE_DIR)/FiniteElemSpace.h \
-$(SOURCE_DIR)/FixVec.h $(SOURCE_DIR)/FixVec.hh \
-$(SOURCE_DIR)/FixVecConvert.h \
-$(SOURCE_DIR)/Flag.h \
-$(SOURCE_DIR)/Global.h \
-$(SOURCE_DIR)/GMResSolver.h $(SOURCE_DIR)/GMResSolver.hh \
-$(SOURCE_DIR)/GMResSolver2.h $(SOURCE_DIR)/GMResSolver2.hh \
-$(SOURCE_DIR)/TFQMR.h $(SOURCE_DIR)/TFQMR.hh \
-$(SOURCE_DIR)/VecSymSolver.h $(SOURCE_DIR)/VecSymSolver.hh \
-$(SOURCE_DIR)/UmfPackSolver.h $(SOURCE_DIR)/UmfPackSolver.hh \
-$(SOURCE_DIR)/PardisoSolver.h $(SOURCE_DIR)/PardisoSolver.hh $(SOURCE_DIR)/PardisoSolver.cc \
-$(SOURCE_DIR)/DuneSolver.h $(SOURCE_DIR)/DuneSolver.hh $(SOURCE_DIR)/DuneSolver.cc \
+$(SOURCE_DIR)/DOFAdmin.h $(SOURCE_DIR)/DOFIterator.h $(SOURCE_DIR)/DOFMatrix.h $(SOURCE_DIR)/DOFVector.h $(SOURCE_DIR)/DOFVector.hh $(SOURCE_DIR)/DOFVector.cc $(SOURCE_DIR)/Element.h $(SOURCE_DIR)/ElementConnection.h \
+$(SOURCE_DIR)/ElInfo.h $(SOURCE_DIR)/ElInfo1d.h $(SOURCE_DIR)/ElInfo2d.h $(SOURCE_DIR)/ElInfo3d.h $(SOURCE_DIR)/Error.h \
+$(SOURCE_DIR)/Error.hh $(SOURCE_DIR)/Estimator.h $(SOURCE_DIR)/Estimator.cc $(SOURCE_DIR)/FiniteElemSpace.h $(SOURCE_DIR)/FixVec.h $(SOURCE_DIR)/FixVec.hh $(SOURCE_DIR)/FixVecConvert.h $(SOURCE_DIR)/Flag.h $(SOURCE_DIR)/Global.h \
+$(SOURCE_DIR)/UmfPackSolver.h \ $(SOURCE_DIR)/UmfPackSolver.hh \
$(SOURCE_DIR)/Lagrange.h $(SOURCE_DIR)/Line.h \
$(SOURCE_DIR)/MacroElement.h $(SOURCE_DIR)/MacroWriter.h \
$(SOURCE_DIR)/Markings.h $(SOURCE_DIR)/Markings.hh \
$(SOURCE_DIR)/MemoryManager.h \
$(SOURCE_DIR)/Mesh.h \
-$(SOURCE_DIR)/ODirSolver.h $(SOURCE_DIR)/ODirSolver.hh \
-$(SOURCE_DIR)/OEMSolver.h $(SOURCE_DIR)/OEMSolver.hh \
-$(SOURCE_DIR)/OResSolver.h $(SOURCE_DIR)/OResSolver.hh \
$(SOURCE_DIR)/Parameters.h \
$(SOURCE_DIR)/Parametric.h \
-$(SOURCE_DIR)/Preconditioner.h \
$(SOURCE_DIR)/Quadrature.h \
$(SOURCE_DIR)/RCNeighbourList.h \
$(SOURCE_DIRe)/RefinementManager.h \
diff --git a/AMDiS/bin/Makefile.in b/AMDiS/bin/Makefile.in
index 8eb9f3a3..9eef154d 100644
--- a/AMDiS/bin/Makefile.in
+++ b/AMDiS/bin/Makefile.in
@@ -37,7 +37,7 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
@USE_PARALLEL_AMDIS_TRUE@am__append_1 = -DHAVE_PARALLEL_AMDIS=1
-@ENABLE_UMFPACK_TRUE@am__append_2 = -DHAVE_UMFPACK=1
+@ENABLE_UMFPACK_TRUE@am__append_2 = -DHAVE_UMFPACK=1 -DMTL_HAS_UMFPACK
@ENABLE_UMFPACK_TRUE@am__append_3 = -I$(LIB_DIR)/UFconfig \
@ENABLE_UMFPACK_TRUE@ -I$(LIB_DIR)/AMD/Include \
@ENABLE_UMFPACK_TRUE@ -I$(LIB_DIR)/UMFPACK/Include
@@ -46,8 +46,8 @@ host_triplet = @host@
@ENABLE_DUNE_TRUE@am__append_5 = -DHAVE_DUNE=1
@ENABLE_DUNE_TRUE@am__append_6 = -I$(DUNE_DIR)
@ENABLE_BOOST_TRUE@am__append_7 = -DHAVE_BOOST=1
-@AMDIS_DEBUG_TRUE@am__append_8 = -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) -ftemplate-depth-30 $(INCLUDES) #-pedantic
-@AMDIS_DEBUG_FALSE@am__append_9 = -O2 -Wall -DDEBUG=0 $(OPENMP_FLAG) -ftemplate-depth-30 $(INCLUDES) #-pedantic
+@AMDIS_DEBUG_TRUE@am__append_8 = -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) $(INCLUDES) #-pedantic
+@AMDIS_DEBUG_FALSE@am__append_9 = -O2 -Wall -DDEBUG=0 -DNDEBUG $(OPENMP_FLAG) -ftemplate-depth-100 $(INCLUDES) #-pedantic
subdir = bin
DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -84,15 +84,11 @@ am__libamdis_la_SOURCES_DIST = $(PARALLEL_DIR)/ConditionalEstimator.h \
$(SOURCE_DIR)/MultiGridPreconWrapper.h \
$(SOURCE_DIR)/MultiGridPreconWrapper.cc \
$(SOURCE_DIR)/LagrangeInterpolRestrict.h \
- $(SOURCE_DIR)/BiCGStab.h $(SOURCE_DIR)/BiCGStab.hh \
- $(SOURCE_DIR)/BiCGStab2.h $(SOURCE_DIR)/BiCGStab2.hh \
$(SOURCE_DIR)/InterpolRestrictMatrix.h \
$(SOURCE_DIR)/InterpolRestrictMatrix.cc \
$(SOURCE_DIR)/DOFIndexed.h $(SOURCE_DIR)/DOFIndexed.cc \
$(SOURCE_DIR)/GNUPlotWriter.h $(SOURCE_DIR)/GNUPlotWriter.cc \
- $(SOURCE_DIR)/SmootherBase.h $(SOURCE_DIR)/StlVector.h \
- $(SOURCE_DIR)/StlVector.cc $(SOURCE_DIR)/V3Vector.h \
- $(SOURCE_DIR)/V3Vector.cc $(SOURCE_DIR)/GSSMoother.h \
+ $(SOURCE_DIR)/SmootherBase.h $(SOURCE_DIR)/GSSMoother.h \
$(SOURCE_DIR)/GSSmoother.cc $(SOURCE_DIR)/JacobiSMoother.h \
$(SOURCE_DIR)/JacobiSmoother.cc $(SOURCE_DIR)/SparseVector.h \
$(SOURCE_DIR)/SparseVector.hh $(SOURCE_DIR)/SparseVector.cc \
@@ -160,53 +156,29 @@ am__libamdis_la_SOURCES_DIST = $(PARALLEL_DIR)/ConditionalEstimator.h \
$(SOURCE_DIR)/AdaptStationary.cc \
$(SOURCE_DIR)/AdaptInstationary.h \
$(SOURCE_DIR)/AdaptInstationary.cc $(SOURCE_DIR)/QPsiPhi.h \
- $(SOURCE_DIR)/BasisFunction.h $(SOURCE_DIR)/BiCGSolver.h \
- $(SOURCE_DIR)/BiCGSolver.hh $(SOURCE_DIR)/Boundary.h \
- $(SOURCE_DIR)/CGSolver.h $(SOURCE_DIR)/CGSolver.hh \
- $(SOURCE_DIR)/CoarseningManager.h \
+ $(SOURCE_DIR)/BasisFunction.h $(SOURCE_DIR)/Boundary.h \
+ $(SOURCE_DIR)/ITL_Solver.h $(SOURCE_DIR)/CoarseningManager.h \
$(SOURCE_DIR)/CoarseningManager1d.h \
$(SOURCE_DIR)/CoarseningManager2d.h \
$(SOURCE_DIR)/CoarseningManager3d.h $(SOURCE_DIR)/demangle.h \
- $(SOURCE_DIR)/DiagonalPreconditioner.h \
- $(SOURCE_DIR)/DiagonalPreconditioner.cc \
- $(SOURCE_DIR)/ILUPreconditioner.h \
- $(SOURCE_DIR)/ILUPreconditioner.cc \
- $(SOURCE_DIR)/ILUTPreconditioner.h \
- $(SOURCE_DIR)/ILUTPreconditioner.cc $(SOURCE_DIR)/QN_Precond.h \
- $(SOURCE_DIR)/QN_Precond.hh $(SOURCE_DIR)/BFGS_Precond.h \
- $(SOURCE_DIR)/BFGS_Precond.cc $(SOURCE_DIR)/DOFAdmin.h \
- $(SOURCE_DIR)/DOFIterator.h $(SOURCE_DIR)/DOFMatrix.h \
- $(SOURCE_DIR)/DOFVector.h $(SOURCE_DIR)/DOFVector.hh \
- $(SOURCE_DIR)/DOFVector.cc $(SOURCE_DIR)/Element.h \
- $(SOURCE_DIR)/ElementConnection.h $(SOURCE_DIR)/ElInfo.h \
- $(SOURCE_DIR)/ElInfo1d.h $(SOURCE_DIR)/ElInfo2d.h \
- $(SOURCE_DIR)/ElInfo3d.h $(SOURCE_DIR)/Error.h \
- $(SOURCE_DIR)/Error.hh $(SOURCE_DIR)/Estimator.h \
- $(SOURCE_DIR)/Estimator.cc $(SOURCE_DIR)/ResidualEstimator.h \
- $(SOURCE_DIR)/ResidualEstimator.cc \
- $(SOURCE_DIR)/ResidualParallelEstimator.h \
- $(SOURCE_DIR)/ResidualParallelEstimator.cc \
+ $(SOURCE_DIR)/DOFAdmin.h $(SOURCE_DIR)/DOFIterator.h \
+ $(SOURCE_DIR)/DOFMatrix.h $(SOURCE_DIR)/DOFVector.h \
+ $(SOURCE_DIR)/DOFVector.hh $(SOURCE_DIR)/DOFVector.cc \
+ $(SOURCE_DIR)/Element.h $(SOURCE_DIR)/ElementConnection.h \
+ $(SOURCE_DIR)/ElInfo.h $(SOURCE_DIR)/ElInfo1d.h \
+ $(SOURCE_DIR)/ElInfo2d.h $(SOURCE_DIR)/ElInfo3d.h \
+ $(SOURCE_DIR)/Error.h $(SOURCE_DIR)/Error.hh \
+ $(SOURCE_DIR)/Estimator.h $(SOURCE_DIR)/Estimator.cc \
$(SOURCE_DIR)/FiniteElemSpace.h $(SOURCE_DIR)/FixVec.h \
$(SOURCE_DIR)/FixVec.hh $(SOURCE_DIR)/FixVecConvert.h \
$(SOURCE_DIR)/Flag.h $(SOURCE_DIR)/Global.h \
- $(SOURCE_DIR)/GMResSolver.h $(SOURCE_DIR)/GMResSolver.hh \
- $(SOURCE_DIR)/GMResSolver2.h $(SOURCE_DIR)/GMResSolver2.hh \
- $(SOURCE_DIR)/TFQMR.h $(SOURCE_DIR)/TFQMR.hh \
- $(SOURCE_DIR)/VecSymSolver.h $(SOURCE_DIR)/VecSymSolver.hh \
- $(SOURCE_DIR)/UmfPackSolver.h $(SOURCE_DIR)/UmfPackSolver.hh \
- $(SOURCE_DIR)/PardisoSolver.h $(SOURCE_DIR)/PardisoSolver.hh \
- $(SOURCE_DIR)/PardisoSolver.cc $(SOURCE_DIR)/DuneSolver.h \
- $(SOURCE_DIR)/DuneSolver.hh $(SOURCE_DIR)/DuneSolver.cc \
+ $(SOURCE_DIR)/UmfPackSolver.h \ $(SOURCE_DIR)/UmfPackSolver.hh \
$(SOURCE_DIR)/Lagrange.h $(SOURCE_DIR)/Line.h \
$(SOURCE_DIR)/MacroElement.h $(SOURCE_DIR)/MacroWriter.h \
$(SOURCE_DIR)/Markings.h $(SOURCE_DIR)/Markings.hh \
$(SOURCE_DIR)/MemoryManager.h $(SOURCE_DIR)/Mesh.h \
- $(SOURCE_DIR)/ODirSolver.h $(SOURCE_DIR)/ODirSolver.hh \
- $(SOURCE_DIR)/OEMSolver.h $(SOURCE_DIR)/OEMSolver.hh \
- $(SOURCE_DIR)/OResSolver.h $(SOURCE_DIR)/OResSolver.hh \
$(SOURCE_DIR)/Parameters.h $(SOURCE_DIR)/Parametric.h \
- $(SOURCE_DIR)/Preconditioner.h $(SOURCE_DIR)/Quadrature.h \
- $(SOURCE_DIR)/RCNeighbourList.h \
+ $(SOURCE_DIR)/Quadrature.h $(SOURCE_DIR)/RCNeighbourList.h \
$(SOURCE_DIRe)/RefinementManager.h \
$(SOURCE_DIR)/RefinementManager1d.h \
$(SOURCE_DIR)/RefinementManager2d.h \
@@ -270,7 +242,6 @@ am_libamdis_la_OBJECTS = $(am__objects_1) \
libamdis_la-MultiGridPreconWrapper.lo \
libamdis_la-InterpolRestrictMatrix.lo \
libamdis_la-DOFIndexed.lo libamdis_la-GNUPlotWriter.lo \
- libamdis_la-StlVector.lo libamdis_la-V3Vector.lo \
libamdis_la-GSSmoother.lo libamdis_la-JacobiSmoother.lo \
libamdis_la-SparseVector.lo libamdis_la-VertexVector.lo \
libamdis_la-PeriodicBC.lo libamdis_la-MultiGridSolver.lo \
@@ -294,18 +265,11 @@ am_libamdis_la_OBJECTS = $(am__objects_1) \
libamdis_la-ElementFileWriter.lo libamdis_la-ElInfo.lo \
libamdis_la-ElInfoStack.lo libamdis_la-Operator.lo \
libamdis_la-Mesh.lo libamdis_la-AdaptStationary.lo \
- libamdis_la-AdaptInstationary.lo \
- libamdis_la-DiagonalPreconditioner.lo \
- libamdis_la-ILUPreconditioner.lo \
- libamdis_la-ILUTPreconditioner.lo libamdis_la-BFGS_Precond.lo \
- libamdis_la-DOFVector.lo libamdis_la-Estimator.lo \
- libamdis_la-ResidualEstimator.lo \
- libamdis_la-ResidualParallelEstimator.lo \
- libamdis_la-PardisoSolver.lo libamdis_la-DuneSolver.lo \
- libamdis_la-ProblemInstat.lo libamdis_la-ProblemNonLin.lo \
- libamdis_la-NonLinUpdater.lo libamdis_la-QPsiPhi.lo \
- libamdis_la-BasisFunction.lo libamdis_la-Boundary.lo \
- libamdis_la-CoarseningManager.lo \
+ libamdis_la-AdaptInstationary.lo libamdis_la-DOFVector.lo \
+ libamdis_la-Estimator.lo libamdis_la-ProblemInstat.lo \
+ libamdis_la-ProblemNonLin.lo libamdis_la-NonLinUpdater.lo \
+ libamdis_la-QPsiPhi.lo libamdis_la-BasisFunction.lo \
+ libamdis_la-Boundary.lo libamdis_la-CoarseningManager.lo \
libamdis_la-CoarseningManager1d.lo \
libamdis_la-CoarseningManager2d.lo \
libamdis_la-CoarseningManager3d.lo libamdis_la-demangle.lo \
@@ -435,6 +399,7 @@ PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
RANLIB = @RANLIB@
+SED = @SED@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
STRIP = @STRIP@
@@ -509,19 +474,16 @@ AMDIS_INCLUDES = -I$(SOURCE_DIR) $(am__append_3) $(am__append_6)
libamdis_la_CXXFLAGS = $(am__append_1) $(am__append_2) $(am__append_4) \
$(am__append_5) $(am__append_7) $(am__append_8) \
$(am__append_9)
-INCLUDES = $(AMDIS_INCLUDES) $(PARALLEL_INCLUDES)
+TEMPLATE_INCLUDES = -I../lib/mtl4 -I../lib/boost_1_34_1
+INCLUDES = $(AMDIS_INCLUDES) $(PARALLEL_INCLUDES) $(TEMPLATE_INCLUDES)
libamdis_la_SOURCES = \
$(PARALLEL_AMDIS_SOURCES) \
$(SOURCE_DIR)/MultiGridPreconWrapper.h $(SOURCE_DIR)/MultiGridPreconWrapper.cc \
$(SOURCE_DIR)/LagrangeInterpolRestrict.h \
-$(SOURCE_DIR)/BiCGStab.h $(SOURCE_DIR)/BiCGStab.hh \
-$(SOURCE_DIR)/BiCGStab2.h $(SOURCE_DIR)/BiCGStab2.hh \
$(SOURCE_DIR)/InterpolRestrictMatrix.h $(SOURCE_DIR)/InterpolRestrictMatrix.cc \
$(SOURCE_DIR)/DOFIndexed.h $(SOURCE_DIR)/DOFIndexed.cc \
$(SOURCE_DIR)/GNUPlotWriter.h $(SOURCE_DIR)/GNUPlotWriter.cc \
$(SOURCE_DIR)/SmootherBase.h \
-$(SOURCE_DIR)/StlVector.h $(SOURCE_DIR)/StlVector.cc \
-$(SOURCE_DIR)/V3Vector.h $(SOURCE_DIR)/V3Vector.cc \
$(SOURCE_DIR)/GSSMoother.h $(SOURCE_DIR)/GSSmoother.cc \
$(SOURCE_DIR)/JacobiSMoother.h $(SOURCE_DIR)/JacobiSmoother.cc \
$(SOURCE_DIR)/SparseVector.h $(SOURCE_DIR)/SparseVector.hh $(SOURCE_DIR)/SparseVector.cc \
@@ -579,50 +541,22 @@ $(SOURCE_DIR)/AdaptStationary.h $(SOURCE_DIR)/AdaptStationary.cc \
$(SOURCE_DIR)/AdaptInstationary.h $(SOURCE_DIR)/AdaptInstationary.cc \
$(SOURCE_DIR)/QPsiPhi.h \
$(SOURCE_DIR)/BasisFunction.h \
-$(SOURCE_DIR)/BiCGSolver.h $(SOURCE_DIR)/BiCGSolver.hh \
$(SOURCE_DIR)/Boundary.h \
-$(SOURCE_DIR)/CGSolver.h $(SOURCE_DIR)/CGSolver.hh \
+$(SOURCE_DIR)/ITL_Solver.h \
$(SOURCE_DIR)/CoarseningManager.h \
$(SOURCE_DIR)/CoarseningManager1d.h $(SOURCE_DIR)/CoarseningManager2d.h $(SOURCE_DIR)/CoarseningManager3d.h \
$(SOURCE_DIR)/demangle.h \
-$(SOURCE_DIR)/DiagonalPreconditioner.h $(SOURCE_DIR)/DiagonalPreconditioner.cc \
-$(SOURCE_DIR)/ILUPreconditioner.h $(SOURCE_DIR)/ILUPreconditioner.cc \
-$(SOURCE_DIR)/ILUTPreconditioner.h $(SOURCE_DIR)/ILUTPreconditioner.cc \
-$(SOURCE_DIR)/QN_Precond.h $(SOURCE_DIR)/QN_Precond.hh \
-$(SOURCE_DIR)/BFGS_Precond.h $(SOURCE_DIR)/BFGS_Precond.cc \
-$(SOURCE_DIR)/DOFAdmin.h \
-$(SOURCE_DIR)/DOFIterator.h \
-$(SOURCE_DIR)/DOFMatrix.h \
-$(SOURCE_DIR)/DOFVector.h $(SOURCE_DIR)/DOFVector.hh $(SOURCE_DIR)/DOFVector.cc \
-$(SOURCE_DIR)/Element.h $(SOURCE_DIR)/ElementConnection.h \
-$(SOURCE_DIR)/ElInfo.h $(SOURCE_DIR)/ElInfo1d.h $(SOURCE_DIR)/ElInfo2d.h $(SOURCE_DIR)/ElInfo3d.h \
-$(SOURCE_DIR)/Error.h $(SOURCE_DIR)/Error.hh \
-$(SOURCE_DIR)/Estimator.h $(SOURCE_DIR)/Estimator.cc \
-$(SOURCE_DIR)/ResidualEstimator.h $(SOURCE_DIR)/ResidualEstimator.cc \
-$(SOURCE_DIR)/ResidualParallelEstimator.h $(SOURCE_DIR)/ResidualParallelEstimator.cc \
-$(SOURCE_DIR)/FiniteElemSpace.h \
-$(SOURCE_DIR)/FixVec.h $(SOURCE_DIR)/FixVec.hh \
-$(SOURCE_DIR)/FixVecConvert.h \
-$(SOURCE_DIR)/Flag.h \
-$(SOURCE_DIR)/Global.h \
-$(SOURCE_DIR)/GMResSolver.h $(SOURCE_DIR)/GMResSolver.hh \
-$(SOURCE_DIR)/GMResSolver2.h $(SOURCE_DIR)/GMResSolver2.hh \
-$(SOURCE_DIR)/TFQMR.h $(SOURCE_DIR)/TFQMR.hh \
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-$(SOURCE_DIR)/DuneSolver.h $(SOURCE_DIR)/DuneSolver.hh $(SOURCE_DIR)/DuneSolver.cc \
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+$(SOURCE_DIR)/Error.hh $(SOURCE_DIR)/Estimator.h $(SOURCE_DIR)/Estimator.cc $(SOURCE_DIR)/FiniteElemSpace.h $(SOURCE_DIR)/FixVec.h $(SOURCE_DIR)/FixVec.hh $(SOURCE_DIR)/FixVecConvert.h $(SOURCE_DIR)/Flag.h $(SOURCE_DIR)/Global.h \
+$(SOURCE_DIR)/UmfPackSolver.h \ $(SOURCE_DIR)/UmfPackSolver.hh \
$(SOURCE_DIR)/Lagrange.h $(SOURCE_DIR)/Line.h \
$(SOURCE_DIR)/MacroElement.h $(SOURCE_DIR)/MacroWriter.h \
$(SOURCE_DIR)/Markings.h $(SOURCE_DIR)/Markings.hh \
$(SOURCE_DIR)/MemoryManager.h \
$(SOURCE_DIR)/Mesh.h \
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-$(SOURCE_DIR)/OResSolver.h $(SOURCE_DIR)/OResSolver.hh \
$(SOURCE_DIR)/Parameters.h \
$(SOURCE_DIR)/Parametric.h \
-$(SOURCE_DIR)/Preconditioner.h \
$(SOURCE_DIR)/Quadrature.h \
$(SOURCE_DIR)/RCNeighbourList.h \
$(SOURCE_DIRe)/RefinementManager.h \
@@ -791,7 +725,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-AdaptParaReal.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-AdaptStationary.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Assembler.Plo@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-BasisFunction.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Boundary.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-BoundaryManager.Plo@am__quote@
@@ -808,10 +741,8 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-DOFMatrix.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-DOFVector.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-DataCollector.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-DiagonalPreconditioner.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-DirichletBC.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-DualTraverse.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-DuneSolver.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ElInfo.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ElInfo1d.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ElInfo2d.Plo@am__quote@
@@ -828,8 +759,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-GNUPlotWriter.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-GSSmoother.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Global.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ILUPreconditioner.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ILUTPreconditioner.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-InteriorBoundary.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-InterpolRestrictMatrix.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-JacobiSmoother.Plo@am__quote@
@@ -855,7 +784,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ParallelProblem.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Parameters.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Parametric.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-PardisoSolver.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-PeriodicBC.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-PngWriter.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ProblemInstat.Plo@am__quote@
@@ -874,14 +802,11 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-RefinementManager1d.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-RefinementManager2d.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-RefinementManager3d.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ResidualEstimator.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ResidualParallelEstimator.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-RobinBC.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ScalableQuadrature.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-SecondOrderAssembler.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-SparseVector.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-StandardProblemIteration.Plo@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-SubAssembler.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-SubElInfo.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-SurfaceQuadrature.Plo@am__quote@
@@ -890,7 +815,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Traverse.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-TraverseParallel.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Triangle.Plo@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-V3Vector.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ValueReader.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ValueWriter.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-VertexVector.Plo@am__quote@
@@ -991,20 +915,6 @@ libamdis_la-GNUPlotWriter.lo: $(SOURCE_DIR)/GNUPlotWriter.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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-libamdis_la-StlVector.lo: $(SOURCE_DIR)/StlVector.cc
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-
libamdis_la-GSSmoother.lo: $(SOURCE_DIR)/GSSmoother.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-GSSmoother.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-GSSmoother.Tpo" -c -o libamdis_la-GSSmoother.lo `test -f '$(SOURCE_DIR)/GSSmoother.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/GSSmoother.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-GSSmoother.Tpo" "$(DEPDIR)/libamdis_la-GSSmoother.Plo"; else rm -f "$(DEPDIR)/libamdis_la-GSSmoother.Tpo"; exit 1; fi
@@ -1313,34 +1223,6 @@ libamdis_la-AdaptInstationary.lo: $(SOURCE_DIR)/AdaptInstationary.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-AdaptInstationary.lo `test -f '$(SOURCE_DIR)/AdaptInstationary.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/AdaptInstationary.cc
-libamdis_la-DiagonalPreconditioner.lo: $(SOURCE_DIR)/DiagonalPreconditioner.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-DiagonalPreconditioner.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-DiagonalPreconditioner.Tpo" -c -o libamdis_la-DiagonalPreconditioner.lo `test -f '$(SOURCE_DIR)/DiagonalPreconditioner.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/DiagonalPreconditioner.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-DiagonalPreconditioner.Tpo" "$(DEPDIR)/libamdis_la-DiagonalPreconditioner.Plo"; else rm -f "$(DEPDIR)/libamdis_la-DiagonalPreconditioner.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/DiagonalPreconditioner.cc' object='libamdis_la-DiagonalPreconditioner.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-DiagonalPreconditioner.lo `test -f '$(SOURCE_DIR)/DiagonalPreconditioner.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/DiagonalPreconditioner.cc
-
-libamdis_la-ILUPreconditioner.lo: $(SOURCE_DIR)/ILUPreconditioner.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ILUPreconditioner.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ILUPreconditioner.Tpo" -c -o libamdis_la-ILUPreconditioner.lo `test -f '$(SOURCE_DIR)/ILUPreconditioner.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ILUPreconditioner.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ILUPreconditioner.Tpo" "$(DEPDIR)/libamdis_la-ILUPreconditioner.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ILUPreconditioner.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/ILUPreconditioner.cc' object='libamdis_la-ILUPreconditioner.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ILUPreconditioner.lo `test -f '$(SOURCE_DIR)/ILUPreconditioner.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ILUPreconditioner.cc
-
-libamdis_la-ILUTPreconditioner.lo: $(SOURCE_DIR)/ILUTPreconditioner.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ILUTPreconditioner.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ILUTPreconditioner.Tpo" -c -o libamdis_la-ILUTPreconditioner.lo `test -f '$(SOURCE_DIR)/ILUTPreconditioner.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ILUTPreconditioner.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ILUTPreconditioner.Tpo" "$(DEPDIR)/libamdis_la-ILUTPreconditioner.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ILUTPreconditioner.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/ILUTPreconditioner.cc' object='libamdis_la-ILUTPreconditioner.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ILUTPreconditioner.lo `test -f '$(SOURCE_DIR)/ILUTPreconditioner.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ILUTPreconditioner.cc
-
-libamdis_la-BFGS_Precond.lo: $(SOURCE_DIR)/BFGS_Precond.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-BFGS_Precond.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-BFGS_Precond.Tpo" -c -o libamdis_la-BFGS_Precond.lo `test -f '$(SOURCE_DIR)/BFGS_Precond.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/BFGS_Precond.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-BFGS_Precond.Tpo" "$(DEPDIR)/libamdis_la-BFGS_Precond.Plo"; else rm -f "$(DEPDIR)/libamdis_la-BFGS_Precond.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/BFGS_Precond.cc' object='libamdis_la-BFGS_Precond.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-BFGS_Precond.lo `test -f '$(SOURCE_DIR)/BFGS_Precond.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/BFGS_Precond.cc
-
libamdis_la-DOFVector.lo: $(SOURCE_DIR)/DOFVector.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-DOFVector.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-DOFVector.Tpo" -c -o libamdis_la-DOFVector.lo `test -f '$(SOURCE_DIR)/DOFVector.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/DOFVector.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-DOFVector.Tpo" "$(DEPDIR)/libamdis_la-DOFVector.Plo"; else rm -f "$(DEPDIR)/libamdis_la-DOFVector.Tpo"; exit 1; fi
@@ -1355,34 +1237,6 @@ libamdis_la-Estimator.lo: $(SOURCE_DIR)/Estimator.cc
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-Estimator.lo `test -f '$(SOURCE_DIR)/Estimator.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/Estimator.cc
-libamdis_la-ResidualEstimator.lo: $(SOURCE_DIR)/ResidualEstimator.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ResidualEstimator.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ResidualEstimator.Tpo" -c -o libamdis_la-ResidualEstimator.lo `test -f '$(SOURCE_DIR)/ResidualEstimator.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ResidualEstimator.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ResidualEstimator.Tpo" "$(DEPDIR)/libamdis_la-ResidualEstimator.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ResidualEstimator.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/ResidualEstimator.cc' object='libamdis_la-ResidualEstimator.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ResidualEstimator.lo `test -f '$(SOURCE_DIR)/ResidualEstimator.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ResidualEstimator.cc
-
-libamdis_la-ResidualParallelEstimator.lo: $(SOURCE_DIR)/ResidualParallelEstimator.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ResidualParallelEstimator.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ResidualParallelEstimator.Tpo" -c -o libamdis_la-ResidualParallelEstimator.lo `test -f '$(SOURCE_DIR)/ResidualParallelEstimator.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ResidualParallelEstimator.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ResidualParallelEstimator.Tpo" "$(DEPDIR)/libamdis_la-ResidualParallelEstimator.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ResidualParallelEstimator.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/ResidualParallelEstimator.cc' object='libamdis_la-ResidualParallelEstimator.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ResidualParallelEstimator.lo `test -f '$(SOURCE_DIR)/ResidualParallelEstimator.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ResidualParallelEstimator.cc
-
-libamdis_la-PardisoSolver.lo: $(SOURCE_DIR)/PardisoSolver.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-PardisoSolver.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-PardisoSolver.Tpo" -c -o libamdis_la-PardisoSolver.lo `test -f '$(SOURCE_DIR)/PardisoSolver.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/PardisoSolver.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-PardisoSolver.Tpo" "$(DEPDIR)/libamdis_la-PardisoSolver.Plo"; else rm -f "$(DEPDIR)/libamdis_la-PardisoSolver.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/PardisoSolver.cc' object='libamdis_la-PardisoSolver.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-PardisoSolver.lo `test -f '$(SOURCE_DIR)/PardisoSolver.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/PardisoSolver.cc
-
-libamdis_la-DuneSolver.lo: $(SOURCE_DIR)/DuneSolver.cc
-@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-DuneSolver.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-DuneSolver.Tpo" -c -o libamdis_la-DuneSolver.lo `test -f '$(SOURCE_DIR)/DuneSolver.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/DuneSolver.cc; \
-@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-DuneSolver.Tpo" "$(DEPDIR)/libamdis_la-DuneSolver.Plo"; else rm -f "$(DEPDIR)/libamdis_la-DuneSolver.Tpo"; exit 1; fi
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(SOURCE_DIR)/DuneSolver.cc' object='libamdis_la-DuneSolver.lo' libtool=yes @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@ $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-DuneSolver.lo `test -f '$(SOURCE_DIR)/DuneSolver.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/DuneSolver.cc
-
libamdis_la-ProblemInstat.lo: $(SOURCE_DIR)/ProblemInstat.cc
@am__fastdepCXX_TRUE@ if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ProblemInstat.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ProblemInstat.Tpo" -c -o libamdis_la-ProblemInstat.lo `test -f '$(SOURCE_DIR)/ProblemInstat.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ProblemInstat.cc; \
@am__fastdepCXX_TRUE@ then mv -f "$(DEPDIR)/libamdis_la-ProblemInstat.Tpo" "$(DEPDIR)/libamdis_la-ProblemInstat.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ProblemInstat.Tpo"; exit 1; fi
diff --git a/AMDiS/configure b/AMDiS/configure
index 3ac06158..4ad0e601 100755
--- a/AMDiS/configure
+++ b/AMDiS/configure
@@ -462,7 +462,7 @@ ac_includes_default="\
# include <unistd.h>
#endif"
-ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM mkdir_p AWK SET_MAKE am__leading_dot AMTAR am__tar am__untar MAINTAINER_MODE_TRUE MAINTAINER_MODE_FALSE MAINT AMDIS_DEBUG_TRUE AMDIS_DEBUG_FALSE CXX CC AMDIS_INTEL_TRUE AMDIS_INTEL_FALSE AMDIS_OPENMP_TRUE AMDIS_OPENMP_FALSE OPENMP_FLAG MPI_DIR USE_PARALLEL_AMDIS_TRUE USE_PARALLEL_AMDIS_FALSE ENABLE_UMFPACK_TRUE ENABLE_UMFPACK_FALSE ENABLE_MKL_TRUE ENABLE_MKL_FALSE DUNE_DIR ENABLE_DUNE_TRUE ENABLE_DUNE_FALSE ENABLE_BOOST_TRUE ENABLE_BOOST_FALSE CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE CXXFLAGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE build build_cpu build_vendor build_os host host_cpu host_vendor host_os EGREP LN_S ECHO AR ac_ct_AR RANLIB ac_ct_RANLIB CPP CXXCPP F77 FFLAGS ac_ct_F77 LIBTOOL LIBOBJS LTLIBOBJS'
+ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM mkdir_p AWK SET_MAKE am__leading_dot AMTAR am__tar am__untar MAINTAINER_MODE_TRUE MAINTAINER_MODE_FALSE MAINT AMDIS_DEBUG_TRUE AMDIS_DEBUG_FALSE CXX CC AMDIS_INTEL_TRUE AMDIS_INTEL_FALSE AMDIS_OPENMP_TRUE AMDIS_OPENMP_FALSE OPENMP_FLAG MPI_DIR USE_PARALLEL_AMDIS_TRUE USE_PARALLEL_AMDIS_FALSE ENABLE_UMFPACK_TRUE ENABLE_UMFPACK_FALSE ENABLE_MKL_TRUE ENABLE_MKL_FALSE DUNE_DIR ENABLE_DUNE_TRUE ENABLE_DUNE_FALSE ENABLE_BOOST_TRUE ENABLE_BOOST_FALSE CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE CXXFLAGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE build build_cpu build_vendor build_os host host_cpu host_vendor host_os SED EGREP LN_S ECHO AR ac_ct_AR RANLIB ac_ct_RANLIB CPP CXXCPP F77 FFLAGS ac_ct_F77 LIBTOOL LIBOBJS LTLIBOBJS'
ac_subst_files=''
# Initialize some variables set by options.
@@ -3909,6 +3909,7 @@ do
done
done
done
+IFS=$as_save_IFS
lt_ac_max=0
lt_ac_count=0
# Add /usr/xpg4/bin/sed as it is typically found on Solaris
@@ -3943,6 +3944,7 @@ done
fi
SED=$lt_cv_path_SED
+
echo "$as_me:$LINENO: result: $SED" >&5
echo "${ECHO_T}$SED" >&6
@@ -4383,7 +4385,7 @@ ia64-*-hpux*)
;;
*-*-irix6*)
# Find out which ABI we are using.
- echo '#line 4386 "configure"' > conftest.$ac_ext
+ echo '#line 4388 "configure"' > conftest.$ac_ext
if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
(eval $ac_compile) 2>&5
ac_status=$?
@@ -5518,7 +5520,7 @@ fi
# Provide some information about the compiler.
-echo "$as_me:5521:" \
+echo "$as_me:5523:" \
"checking for Fortran 77 compiler version" >&5
ac_compiler=`set X $ac_compile; echo $2`
{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5
@@ -6581,11 +6583,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:6584: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:6586: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:6588: \$? = $ac_status" >&5
+ echo "$as_me:6590: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -6849,11 +6851,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:6852: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:6854: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:6856: \$? = $ac_status" >&5
+ echo "$as_me:6858: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -6953,11 +6955,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:6956: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:6958: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:6960: \$? = $ac_status" >&5
+ echo "$as_me:6962: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -8418,10 +8420,31 @@ linux*)
# before this can be enabled.
hardcode_into_libs=yes
+ # find out which ABI we are using
+ libsuff=
+ case "$host_cpu" in
+ x86_64*|s390x*|powerpc64*)
+ echo '#line 8427 "configure"' > conftest.$ac_ext
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *64-bit*)
+ libsuff=64
+ sys_lib_search_path_spec="/lib${libsuff} /usr/lib${libsuff} /usr/local/lib${libsuff}"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+ esac
+
# Append ld.so.conf contents to the search path
if test -f /etc/ld.so.conf; then
- lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
- sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib${libsuff} /usr/lib${libsuff} $lt_ld_extra"
fi
# We used to test for /lib/ld.so.1 and disable shared libraries on
@@ -9298,7 +9321,7 @@ else
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<EOF
-#line 9301 "configure"
+#line 9324 "configure"
#include "confdefs.h"
#if HAVE_DLFCN_H
@@ -9398,7 +9421,7 @@ else
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<EOF
-#line 9401 "configure"
+#line 9424 "configure"
#include "confdefs.h"
#if HAVE_DLFCN_H
@@ -9729,6 +9752,9 @@ CC=$lt_compiler
# Is the compiler the GNU C compiler?
with_gcc=$GCC
+gcc_dir=\`gcc -print-file-name=. | $SED 's,/\.$,,'\`
+gcc_ver=\`gcc -dumpversion\`
+
# An ERE matcher.
EGREP=$lt_EGREP
@@ -9862,11 +9888,11 @@ striplib=$lt_striplib
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects=$lt_predep_objects
+predep_objects=\`echo $lt_predep_objects | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects=$lt_postdep_objects
+postdep_objects=\`echo $lt_postdep_objects | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -9878,7 +9904,7 @@ postdeps=$lt_postdeps
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path=$lt_compiler_lib_search_path
+compiler_lib_search_path=\`echo $lt_compiler_lib_search_path | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method=$lt_deplibs_check_method
@@ -9958,7 +9984,7 @@ variables_saved_for_relink="$variables_saved_for_relink"
link_all_deplibs=$link_all_deplibs
# Compile-time system search path for libraries
-sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+sys_lib_search_path_spec=\`echo $lt_sys_lib_search_path_spec | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Run-time system search path for libraries
sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
@@ -11738,11 +11764,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:11741: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:11767: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:11745: \$? = $ac_status" >&5
+ echo "$as_me:11771: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -11842,11 +11868,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:11845: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:11871: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:11849: \$? = $ac_status" >&5
+ echo "$as_me:11875: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -12374,10 +12400,31 @@ linux*)
# before this can be enabled.
hardcode_into_libs=yes
+ # find out which ABI we are using
+ libsuff=
+ case "$host_cpu" in
+ x86_64*|s390x*|powerpc64*)
+ echo '#line 12407 "configure"' > conftest.$ac_ext
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *64-bit*)
+ libsuff=64
+ sys_lib_search_path_spec="/lib${libsuff} /usr/lib${libsuff} /usr/local/lib${libsuff}"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+ esac
+
# Append ld.so.conf contents to the search path
if test -f /etc/ld.so.conf; then
- lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
- sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib${libsuff} /usr/lib${libsuff} $lt_ld_extra"
fi
# We used to test for /lib/ld.so.1 and disable shared libraries on
@@ -12761,6 +12808,9 @@ CC=$lt_compiler_CXX
# Is the compiler the GNU C compiler?
with_gcc=$GCC_CXX
+gcc_dir=\`gcc -print-file-name=. | $SED 's,/\.$,,'\`
+gcc_ver=\`gcc -dumpversion\`
+
# An ERE matcher.
EGREP=$lt_EGREP
@@ -12894,11 +12944,11 @@ striplib=$lt_striplib
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects=$lt_predep_objects_CXX
+predep_objects=\`echo $lt_predep_objects_CXX | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects=$lt_postdep_objects_CXX
+postdep_objects=\`echo $lt_postdep_objects_CXX | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -12910,7 +12960,7 @@ postdeps=$lt_postdeps_CXX
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path=$lt_compiler_lib_search_path_CXX
+compiler_lib_search_path=\`echo $lt_compiler_lib_search_path_CXX | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method=$lt_deplibs_check_method
@@ -12990,7 +13040,7 @@ variables_saved_for_relink="$variables_saved_for_relink"
link_all_deplibs=$link_all_deplibs_CXX
# Compile-time system search path for libraries
-sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+sys_lib_search_path_spec=\`echo $lt_sys_lib_search_path_spec | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Run-time system search path for libraries
sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
@@ -13412,11 +13462,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:13415: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:13465: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:13419: \$? = $ac_status" >&5
+ echo "$as_me:13469: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -13516,11 +13566,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:13519: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:13569: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:13523: \$? = $ac_status" >&5
+ echo "$as_me:13573: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -14961,10 +15011,31 @@ linux*)
# before this can be enabled.
hardcode_into_libs=yes
+ # find out which ABI we are using
+ libsuff=
+ case "$host_cpu" in
+ x86_64*|s390x*|powerpc64*)
+ echo '#line 15018 "configure"' > conftest.$ac_ext
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *64-bit*)
+ libsuff=64
+ sys_lib_search_path_spec="/lib${libsuff} /usr/lib${libsuff} /usr/local/lib${libsuff}"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+ esac
+
# Append ld.so.conf contents to the search path
if test -f /etc/ld.so.conf; then
- lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
- sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib${libsuff} /usr/lib${libsuff} $lt_ld_extra"
fi
# We used to test for /lib/ld.so.1 and disable shared libraries on
@@ -15348,6 +15419,9 @@ CC=$lt_compiler_F77
# Is the compiler the GNU C compiler?
with_gcc=$GCC_F77
+gcc_dir=\`gcc -print-file-name=. | $SED 's,/\.$,,'\`
+gcc_ver=\`gcc -dumpversion\`
+
# An ERE matcher.
EGREP=$lt_EGREP
@@ -15481,11 +15555,11 @@ striplib=$lt_striplib
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects=$lt_predep_objects_F77
+predep_objects=\`echo $lt_predep_objects_F77 | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects=$lt_postdep_objects_F77
+postdep_objects=\`echo $lt_postdep_objects_F77 | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -15497,7 +15571,7 @@ postdeps=$lt_postdeps_F77
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path=$lt_compiler_lib_search_path_F77
+compiler_lib_search_path=\`echo $lt_compiler_lib_search_path_F77 | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method=$lt_deplibs_check_method
@@ -15577,7 +15651,7 @@ variables_saved_for_relink="$variables_saved_for_relink"
link_all_deplibs=$link_all_deplibs_F77
# Compile-time system search path for libraries
-sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+sys_lib_search_path_spec=\`echo $lt_sys_lib_search_path_spec | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Run-time system search path for libraries
sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
@@ -15719,11 +15793,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:15722: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:15796: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:15726: \$? = $ac_status" >&5
+ echo "$as_me:15800: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -15987,11 +16061,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:15990: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:16064: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:15994: \$? = $ac_status" >&5
+ echo "$as_me:16068: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -16091,11 +16165,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:16094: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:16168: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:16098: \$? = $ac_status" >&5
+ echo "$as_me:16172: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -17556,10 +17630,31 @@ linux*)
# before this can be enabled.
hardcode_into_libs=yes
+ # find out which ABI we are using
+ libsuff=
+ case "$host_cpu" in
+ x86_64*|s390x*|powerpc64*)
+ echo '#line 17637 "configure"' > conftest.$ac_ext
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *64-bit*)
+ libsuff=64
+ sys_lib_search_path_spec="/lib${libsuff} /usr/lib${libsuff} /usr/local/lib${libsuff}"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+ esac
+
# Append ld.so.conf contents to the search path
if test -f /etc/ld.so.conf; then
- lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
- sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib${libsuff} /usr/lib${libsuff} $lt_ld_extra"
fi
# We used to test for /lib/ld.so.1 and disable shared libraries on
@@ -17943,6 +18038,9 @@ CC=$lt_compiler_GCJ
# Is the compiler the GNU C compiler?
with_gcc=$GCC_GCJ
+gcc_dir=\`gcc -print-file-name=. | $SED 's,/\.$,,'\`
+gcc_ver=\`gcc -dumpversion\`
+
# An ERE matcher.
EGREP=$lt_EGREP
@@ -18076,11 +18174,11 @@ striplib=$lt_striplib
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects=$lt_predep_objects_GCJ
+predep_objects=\`echo $lt_predep_objects_GCJ | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects=$lt_postdep_objects_GCJ
+postdep_objects=\`echo $lt_postdep_objects_GCJ | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -18092,7 +18190,7 @@ postdeps=$lt_postdeps_GCJ
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path=$lt_compiler_lib_search_path_GCJ
+compiler_lib_search_path=\`echo $lt_compiler_lib_search_path_GCJ | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method=$lt_deplibs_check_method
@@ -18172,7 +18270,7 @@ variables_saved_for_relink="$variables_saved_for_relink"
link_all_deplibs=$link_all_deplibs_GCJ
# Compile-time system search path for libraries
-sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+sys_lib_search_path_spec=\`echo $lt_sys_lib_search_path_spec | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Run-time system search path for libraries
sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
@@ -18424,6 +18522,9 @@ CC=$lt_compiler_RC
# Is the compiler the GNU C compiler?
with_gcc=$GCC_RC
+gcc_dir=\`gcc -print-file-name=. | $SED 's,/\.$,,'\`
+gcc_ver=\`gcc -dumpversion\`
+
# An ERE matcher.
EGREP=$lt_EGREP
@@ -18557,11 +18658,11 @@ striplib=$lt_striplib
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects=$lt_predep_objects_RC
+predep_objects=\`echo $lt_predep_objects_RC | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects=$lt_postdep_objects_RC
+postdep_objects=\`echo $lt_postdep_objects_RC | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -18573,7 +18674,7 @@ postdeps=$lt_postdeps_RC
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path=$lt_compiler_lib_search_path_RC
+compiler_lib_search_path=\`echo $lt_compiler_lib_search_path_RC | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method=$lt_deplibs_check_method
@@ -18653,7 +18754,7 @@ variables_saved_for_relink="$variables_saved_for_relink"
link_all_deplibs=$link_all_deplibs_RC
# Compile-time system search path for libraries
-sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+sys_lib_search_path_spec=\`echo $lt_sys_lib_search_path_spec | \$SED -e "s@\${gcc_dir}@\\\${gcc_dir}@g;s@\${gcc_ver}@\\\${gcc_ver}@g"\`
# Run-time system search path for libraries
sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
@@ -19567,6 +19668,7 @@ s,@host@,$host,;t t
s,@host_cpu@,$host_cpu,;t t
s,@host_vendor@,$host_vendor,;t t
s,@host_os@,$host_os,;t t
+s,@SED@,$SED,;t t
s,@EGREP@,$EGREP,;t t
s,@LN_S@,$LN_S,;t t
s,@ECHO@,$ECHO,;t t
diff --git a/AMDiS/libtool b/AMDiS/libtool
index 41ace2e6..e7cf2e55 100755
--- a/AMDiS/libtool
+++ b/AMDiS/libtool
@@ -44,7 +44,7 @@ available_tags=" CXX F77"
# ### BEGIN LIBTOOL CONFIG
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host NWRW03:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -93,6 +93,9 @@ CC="gcc"
# Is the compiler the GNU C compiler?
with_gcc=yes
+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+gcc_ver=`gcc -dumpversion`
+
# An ERE matcher.
EGREP="grep -E"
@@ -229,11 +232,11 @@ striplib="strip --strip-unneeded"
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects=""
+predep_objects=`echo "" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects=""
+postdep_objects=`echo "" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -245,7 +248,7 @@ postdeps=""
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path=""
+compiler_lib_search_path=`echo "" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method="pass_all"
@@ -325,10 +328,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=" /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/"
+sys_lib_search_path_spec=`echo " /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-3.0.1 /usr/lib/qt-3.3/lib "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
@@ -6760,7 +6763,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host NWRW03:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -6809,6 +6812,9 @@ CC="g++"
# Is the compiler the GNU C compiler?
with_gcc=yes
+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+gcc_ver=`gcc -dumpversion`
+
# An ERE matcher.
EGREP="grep -E"
@@ -6942,11 +6948,11 @@ striplib="strip --strip-unneeded"
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o"
+predep_objects=`echo "/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o"
+postdep_objects=`echo "/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -6958,7 +6964,7 @@ postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path="-L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../.."
+compiler_lib_search_path=`echo "-L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../.." | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method="pass_all"
@@ -7038,10 +7044,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=" /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/"
+sys_lib_search_path_spec=`echo " /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-3.0.1 /usr/lib/qt-3.3/lib "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
@@ -7065,7 +7071,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host NWRW03:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -7109,11 +7115,14 @@ LTCC="gcc"
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="g77"
+CC="f95"
# Is the compiler the GNU C compiler?
with_gcc=yes
+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+gcc_ver=`gcc -dumpversion`
+
# An ERE matcher.
EGREP="grep -E"
@@ -7250,11 +7259,11 @@ striplib="strip --strip-unneeded"
# Dependencies to place before the objects being linked to create a
# shared library.
-predep_objects=""
+predep_objects=`echo "" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Dependencies to place after the objects being linked to create a
# shared library.
-postdep_objects=""
+postdep_objects=`echo "" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Dependencies to place before the objects being linked to create a
# shared library.
@@ -7266,7 +7275,7 @@ postdeps=""
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path=""
+compiler_lib_search_path=`echo "" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method="pass_all"
@@ -7346,10 +7355,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
link_all_deplibs=unknown
# Compile-time system search path for libraries
-sys_lib_search_path_spec=" /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../ /lib/i386-redhat-linux/3.4.6/ /lib/ /usr/lib/i386-redhat-linux/3.4.6/ /usr/lib/"
+sys_lib_search_path_spec=`echo " /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-3.0.1 /usr/lib/qt-3.3/lib "
# Fix the shell variable $srcfile for the compiler.
fix_srcfile_path=""
diff --git a/AMDiS/src/AMDiS.h b/AMDiS/src/AMDiS.h
index 07ef0daf..d64d0761 100644
--- a/AMDiS/src/AMDiS.h
+++ b/AMDiS/src/AMDiS.h
@@ -6,13 +6,10 @@
#include "AdaptStationary.h"
#include "Assembler.h"
#include "BasisFunction.h"
-#include "BiCGSolver.h"
#include "Boundary.h"
-#include "BiCGStab_M.h"
#include "Boundary.h"
#include "BoundaryCondition.h"
#include "BoundaryManager.h"
-#include "CGSolver.h"
#include "CoarseningManager.h"
#include "CoarseningManager1d.h"
#include "CoarseningManager2d.h"
@@ -25,7 +22,6 @@
#include "DOFIterator.h"
#include "DOFMatrix.h"
#include "DOFVector.h"
-#include "DiagonalPreconditioner.h"
#include "DirichletBC.h"
#include "DualTraverse.h"
#include "ElInfo.h"
@@ -41,10 +37,11 @@
#include "FiniteElemSpace.h"
#include "FixVec.h"
#include "Flag.h"
-#include "GMResSolver.h"
#include "Global.h"
#include "GridWriter.h"
#include "InteriorBoundary.h"
+#include "ITL_Preconditioner.h"
+#include "ITL_Solver.h"
#include "Lagrange.h"
#include "LeafData.h"
#include "Line.h"
@@ -61,9 +58,7 @@
#include "NewtonS.h"
#include "NonLinSolver.h"
#include "NonLinUpdater.h"
-#include "ODirSolver.h"
#include "OEMSolver.h"
-#include "OResSolver.h"
#include "Operator.h"
#include "Parameters.h"
#include "Parametric.h"
@@ -71,7 +66,6 @@
#include "PeriodicMap.h"
#include "PeriodicBC.h"
#include "PngWriter.h"
-#include "Preconditioner.h"
#include "ProblemScal.h"
#include "ProblemVec.h"
#include "ProblemInstat.h"
diff --git a/AMDiS/src/AMDiS_fwd.h b/AMDiS/src/AMDiS_fwd.h
new file mode 100644
index 00000000..f51a3fd8
--- /dev/null
+++ b/AMDiS/src/AMDiS_fwd.h
@@ -0,0 +1,82 @@
+// ============================================================================
+// == ==
+// == AMDiS - Adaptive multidimensional simulations ==
+// == ==
+// ============================================================================
+// == ==
+// == crystal growth group ==
+// == ==
+// == Stiftung caesar ==
+// == Ludwig-Erhard-Allee 2 ==
+// == 53175 Bonn ==
+// == germany ==
+// == ==
+// ============================================================================
+// == ==
+// == http://www.caesar.de/cg/AMDiS ==
+// == ==
+// ============================================================================
+
+/** \file AMDiS_fwd.h */
+
+
+#ifndef AMDIS_AMDIS_FWD_INCLUDE
+#define AMDIS_AMDIS_FWD_INCLUDE
+
+namespace AMDiS {
+
+ class AdaptInfo;
+ class AdaptStationary;
+ class BasisFunction;
+ class BoundaryManager;
+ class CGSolver;
+ class CoarseningManager;
+ class DiagonalPreconditioner;
+ class DOFAdmin;
+ class DOFMatrix;
+ class Element;
+ class ElementMatrix;
+ class ElementVector;
+ class ElInfo;
+ class Estimator;
+ class FastQuadrature;
+ class FillInfo;
+ class FileWriterInterface;
+ class FiniteElemSpace;
+ class IdentityPreconditioner;
+ class InterpolRestrictMatrix;
+ class ITL_BasePreconditioner;
+ class LeafDataPeriodic;
+ class LevelAdmin;
+ class Marker;
+ class Mesh;
+ class MultiGridSortSolver;
+ class OEMSolver;
+ class Operator;
+ class ProblemInstat;
+ class ProblemIterationInterface;
+ class ProblemVec;
+ class PreconditionerScal;
+ class Quadrature;
+ class RCNeighbourList;
+ class RefinementManager;
+ class RobinBC;
+ class SystemVector;
+ class VertexVector;
+
+ template<typename ReturnType, typename ArgumentType> class AbstractFunction;
+ template<typename VectorType> class MatVecMultiplier;
+ template<typename T> class DOFVectorBase;
+ template<typename T> class DOFVector;
+ template<typename T> class ITL_Preconditioner;
+ template<typename T> class Matrix;
+ template<typename T> class MatVecMultiplier;
+ template<typename T> class SolverMatrix;
+ template<typename T> class SparseVector;
+ template<typename T> class Vector;
+
+ template <typename ITLSolver> class ITL_OEMSolver;
+
+} // namespace AMDiS
+
+#endif // AMDIS_AMDIS_FWD_INCLUDE
diff --git a/AMDiS/src/AdaptStationary.h b/AMDiS/src/AdaptStationary.h
index 8bf24778..c96204ee 100644
--- a/AMDiS/src/AdaptStationary.h
+++ b/AMDiS/src/AdaptStationary.h
@@ -34,13 +34,10 @@
#include "MemoryManager.h"
#include "AdaptInfo.h"
#include "AdaptBase.h"
+#include "AMDiS_fwd.h"
namespace AMDiS {
- class Element;
- template <typename T> class OEMSolver;
- class ProblemIterationInterface;
-
// ============================================================================
// ===== class AdaptStationary ================================================
// ============================================================================
diff --git a/AMDiS/src/BFGS_Precond.cc b/AMDiS/src/BFGS_Precond.cc
deleted file mode 100755
index 9ed4b20d..00000000
--- a/AMDiS/src/BFGS_Precond.cc
+++ /dev/null
@@ -1,68 +0,0 @@
-#include "BFGS_Precond.h"
-#include "QN_Precond.h"
-#include "FiniteElemSpace.h"
-#include "DOFAdmin.h"
-#include "DOFVector.h"
-#include "DOFMatrix.h"
-#include "DOFIterator.h"
-
-namespace AMDiS
-{
-
- void BFGS_Precond::addPair(DOFVector<double> *s, DOFVector<double> *y,
- double sy)
- {
- FUNCNAME("BFGS_Preconditioner::addPair()");
-
- if (!sy)
- sy = *s * *y;
- TEST_EXIT(sy > 0)("Vectors do not satisfy the curvature condition!\n");
-
- BFGS_Vectors newPair(s->getFESpace());
- newPair.setVectors(s, y, sy);
-
- if (k < m) {
- k++;
- } else {
- pairsVec.pop_back();
- }
-
- pairsVec.push_front(newPair);
-
- return;
- }
-
- void BFGS_Precond::precon(DOFVector<double> *vec)
- {
- FUNCNAME("BFGS_Preconditioner::precon()");
-
- int i = 0;
- double beta;
- double *alpha = GET_MEMORY(double, k);
-
- std::deque<BFGS_Vectors>::iterator pairsIterator(pairsVec.begin());
-
- while (pairsIterator != pairsVec.end()) {
- alpha[i] = pairsIterator->s * *vec;
- alpha[i] /= pairsIterator->sy;
- aXpY(-alpha[i], pairsIterator->y, *vec, bound);
- ++i;
- ++pairsIterator;
- }
-
- diagPrecond(*matrix[row], vec, bound);
-
- while (pairsIterator != pairsVec.begin()) {
- --pairsIterator;
- --i;
- beta = pairsIterator->y * *vec;
- beta /= pairsIterator->sy;
- aXpY(alpha[i]-beta, pairsIterator->s, *vec, bound);
- }
-
- FREE_MEMORY(alpha, double, k);
-
- return;
- }
-
-}
diff --git a/AMDiS/src/BFGS_Precond.h b/AMDiS/src/BFGS_Precond.h
deleted file mode 100755
index 56293303..00000000
--- a/AMDiS/src/BFGS_Precond.h
+++ /dev/null
@@ -1,168 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file BFGS_Precond.h */
-
-#ifndef AMDIS_BFGS_PRECONDITIONER_H
-#define AMDIS_BFGS_PRECONDITIONER_H
-
-#include "Parameters.h"
-#include "Preconditioner.h"
-#include "QN_Precond.h"
-
-namespace AMDiS
-{
-
- template<typename T> class DOFVector;
- template<typename T> class OEMSolver;
-
- // ============================================================================
- // ===== class BFGS_Vectors ===================================================
- // ============================================================================
-
- // Auxiliar class por storing pairs of DOFVectors and their scalar products.
- class BFGS_Vectors
- {
- public:
- MEMORY_MANAGED(BFGS_Vectors);
-
- /** \brief
- * Constructor.
- */
- BFGS_Vectors(const FiniteElemSpace *fe_space)
- : s(fe_space, "BFGS->s"), y(fe_space, "BFGS->y")
- {};
-
- inline void setVectors(DOFVector<double> *s_, DOFVector<double> *y_,
- double sy_=0.0)
- {
- s = *s_;
- y = *y_;
-
- if (!sy_)
- sy = s * y;
- else
- sy = sy_;
-
- return;
- };
-
- private:
- DOFVector<double> s, y;
- double sy;
-
- friend class BFGS_Precond;
- };
-
- // ============================================================================
- // ===== class BFGS_Precond ===================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * BFGS preconditioner.
- */
- class BFGS_Precond : public PreconditionerScal
- {
- public:
- MEMORY_MANAGED(BFGS_Precond);
-
- /** \brief
- * Creator class used in the PreconditionerMap.
- */
- class Creator : public PreconditionerScalCreator
- {
- public:
- MEMORY_MANAGED(Creator);
-
- /** \brief
- * Creates a new BFGS Preconditioner.
- */
- PreconditionerScal *create()
- {
- return NEW BFGS_Precond(size, row);
- };
- };
-
- /** \brief
- * Constructor.
- */
- BFGS_Precond(int size_ = 1, int row_ = 0) : PreconditionerScal(size_, row_) {
- k = 0;
-
- m = 2 * Global::getGeo(WORLD);
- GET_PARAMETER(1, "preconditioner->max. number of pairs", "%d", &m);
- m = std::max(0, std::min(m, 32));
- };
-
- /** \brief
- * Destructor.
- */
- virtual ~BFGS_Precond() {};
-
- /** \brief
- * realisation of Preconditioner::init
- */
- inline void init()
- {
- FUNCNAME("BFGS_Precond::init()");
- TEST_EXIT(matrix[row])("no matrix\n");
- };
-
- /** \brief
- * realisation of Preconditioner::precon
- */
- void precon(DOFVector<double> *vec);
-
- /** \brief
- * realisation of Preconditioner::exit
- */
- inline void exit() {};
-
-
- /* ----- Specific functions ----- */
-
- /** \brief
- * add pair of vectors
- */
- void addPair(DOFVector<double> *s, DOFVector<double> *y, double sy = 0.0);
-
- protected:
-
- /** \brief
- * list of pairs
- */
- std::deque<BFGS_Vectors> pairsVec;
-
- /** \brief
- * maximal number of pairs
- */
- int m;
-
- /** \brief
- * actual number of pairs
- */
- int k;
- };
-
-}
-
-#endif // AMDIS_BFGS_PRECONDITIONER_H
diff --git a/AMDiS/src/BasisFunction.h b/AMDiS/src/BasisFunction.h
index 62283a6a..24206efe 100644
--- a/AMDiS/src/BasisFunction.h
+++ b/AMDiS/src/BasisFunction.h
@@ -23,6 +23,7 @@
#define AMDIS_BASISFUNCTION_H
#include <string>
+#include "AMDiS_fwd.h"
#include "Global.h"
#include "Boundary.h"
#include "MatrixVector.h"
@@ -38,7 +39,7 @@ namespace AMDiS {
class Quadrature;
template <typename ReturnType, typename ArgumentType> class AbstractFunction;
- template <typename T> class DOFVector;
+ // template <typename T> class DOFVector;
template <typename T> class DOFIndexed;
template <typename T> class DimVec;
template <typename T> class DimMat;
@@ -345,7 +346,7 @@ namespace AMDiS {
* coefficient vector uh.
*/
double evalUh(const DimVec<double>& lambda, const double* uh) const;
-
+
/** \brief
* Evaluates elements value at barycentric coordinates lambda with local
* coefficient vector uh. If val is not NULL the result will be stored
@@ -354,7 +355,7 @@ namespace AMDiS {
*/
const WorldVector<double>& evalUh(const DimVec<double>& lambda,
const WorldVector<double>* uh, WorldVector<double>* val) const;
-
+
/** \brief
* Evaluates the gradient at barycentric coordinates lambda. Lambda is the
* Jacobian of the barycentric coordinates. uh is the local coefficient
diff --git a/AMDiS/src/BiCGSolver.h b/AMDiS/src/BiCGSolver.h
deleted file mode 100644
index e428ad4a..00000000
--- a/AMDiS/src/BiCGSolver.h
+++ /dev/null
@@ -1,101 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file BiCGSolver.h */
-
-#ifndef AMDIS_BICGSOLVER_H
-#define AMDIS_BICGSOLVER_H
-
-#include "OEMSolver.h"
-#include "MemoryManager.h"
-#include "CreatorInterface.h"
-
-namespace AMDiS {
-
- // ============================================================================
- // ===== class BiCGSolver =====================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Solves a linear system by a stabilized BiCG method and can be used for
- * symmetric system matrices.
- */
- template<typename VectorType>
- class BiCGSolver : public OEMSolver<VectorType>
- {
- public:
- MEMORY_MANAGED(BiCGSolver<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new BiCGSolver object.
- */
- OEMSolver<VectorType>* create() {
- return NEW BiCGSolver<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- BiCGSolver(std::string name);
-
- /** \brief
- * destructor
- */
- ~BiCGSolver();
-
- protected:
- /** \brief
- * realisation of OEMSolver::solveSystem
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv, VectorType *x, VectorType *b, bool reuseMatrix);
-
- /** \brief
- * realisation of OEMSolver::init
- */
- void init();
-
- /** \brief
- * realisation of OEMSolver::exit
- */
- void exit();
-
- private:
- // pointer to memory needed for solveSystem
- VectorType *rstar, *d, *s, *CAd, *h;
- };
-
-}
-
-#include "BiCGSolver.hh"
-
-#endif // AMDIS_BICGSOLVER_H
diff --git a/AMDiS/src/BiCGSolver.hh b/AMDiS/src/BiCGSolver.hh
deleted file mode 100644
index 14965297..00000000
--- a/AMDiS/src/BiCGSolver.hh
+++ /dev/null
@@ -1,193 +0,0 @@
-#include "Preconditioner.h"
-
-namespace AMDiS {
-
- template<typename VectorType>
- BiCGSolver<VectorType>::BiCGSolver(std::string name)
- : OEMSolver<VectorType>(name),
- rstar(NULL), d(NULL), s(NULL), CAd(NULL), h(NULL)
- {
- }
-
- template<typename VectorType>
- BiCGSolver<VectorType>::~BiCGSolver()
- {}
-
- template<typename VectorType>
- void BiCGSolver<VectorType>::init()
- {
- rstar = this->vectorCreator->create();
- d = this->vectorCreator->create();
- s = this->vectorCreator->create();
- CAd = this->vectorCreator->create();
- h = this->vectorCreator->create();
- }
-
- template<typename VectorType>
- void BiCGSolver<VectorType>::exit()
- {
- this->vectorCreator->free(rstar);
- this->vectorCreator->free(d);
- this->vectorCreator->free(s);
- this->vectorCreator->free(CAd);
- this->vectorCreator->free(h);
- }
-
- template<typename VectorType>
- int BiCGSolver<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x, VectorType *b, bool reuseMatrix)
- {
- FUNCNAME("BiCGSolver::solveSystem");
- VectorType *t = h;
-
- double res, old_res = -1.0;
- double rh1, rh2, dad, alpha, ast, att, omega, beta;
- int iter;
-
- const double TOL = 1.e-30;
-
- /*--------------------------------------------------------------------------*/
- /*--- Initalization ------------------------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- if (norm(b) < TOL)
- {
- INFO(this->info,2)("b == 0, x = 0 is the solution of the linear system\n");
- set(*x, 0.0);
- this->residual = 0.0;
- return(0);
- }
-
- // h = Ax
- matVec->matVec(NoTranspose, *x, *h);
-
- // h -= b
- *h -= *b;
-
- // rstar = h;
- *rstar = *h;
-
- // preconditioning
- if(this->leftPrecon) this->leftPrecon->precon(h);
- if(this->rightPrecon) this->rightPrecon->precon(b);
-
- /*--------------------------------------------------------------------------*/
- /*--- check initial residual ---------------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- res = norm(h);
-
- START_INFO();
- if (SOLVE_INFO(0, res, &old_res))
- return(0);
-
- // d = h
- *d = *h;
-
- // rh1 = h*rstar
- rh1 = *h * *rstar;
-
- /*--------------------------------------------------------------------------*/
- /*--- Iteration ----------------------------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- for (iter = 1; iter <= this->max_iter; iter++)
- {
- /*--------------------------------------------------------------------------*/
- /*--- calculate CA.d and CA.d*rstar --------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- // CAd = Ad
- matVec->matVec(NoTranspose, *d, *CAd);
-
- if(this->leftPrecon) this->leftPrecon->precon(CAd);
-
- // dad = CAd * rstar;
- dad = *CAd * *rstar;
-
- if (abs(rh1) < TOL) {
- BREAK_INFO("(h,r^*)_2 = 0", iter, res, &old_res);
- return(iter);
- }
- if (abs(dad) < TOL) {
- BREAK_INFO("(Ad,d^*)_2 = 0", iter, res, &old_res);
- return(iter);
- }
-
- /*-------------------------------------------------------------------------*/
- /*--- update s and t ----------------------------------------------------*/
- /*-------------------------------------------------------------------------*/
-
- alpha = rh1/dad;
-
- // s = h
- *s = *h;
-
- // s = -alpha CAd + s
- axpy(-alpha, *CAd, *s);
-
- // t = As
- matVec->matVec(NoTranspose, *s, *t);
-
- /*--------------------------------------------------------------------------*/
- /*--- calculate omega ----------------------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- // ast = s*t
- ast = *s * *t;
-
- // att = t*t
- att = *t * *t;
-
- if (abs(ast) < TOL) {
- INFO(this->info,2)("omega = 0");
- ast = ast > 0 ? TOL : -TOL;
- }
-
- if (att < TOL)
- {
- INFO(this->info,2)("t = 0");
- att = TOL;
- }
-
- omega= ast/att;
-
- /*--------------------------------------------------------------------------*/
- /*--- update x and calculate new h --------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- // x = -alpha d + x
- axpy(-alpha, *d, *x);
-
- // x = -omega s + x
- axpy(-omega, *s, *x);
-
- // h = s - omega * h
- *h *= -omega;
- *h += *s;
-
- res = norm(h);
- if (SOLVE_INFO(iter, res, &old_res))
- return(iter);
-
- if (this->leftPrecon) this->leftPrecon->precon(t);
-
- // rh2 = h * rstar
- rh2 = *h * *rstar;
-
- beta= (rh2/rh1)* (alpha/omega);
-
- // d = -omega CAd + d
- axpy(-omega, *CAd, *d);
-
- // d = h + beta d
- *d *= beta;
- *d += *h;
-
- rh1 = rh2;
- }
-
- return 0; // never reached !
- }
-
-}
diff --git a/AMDiS/src/BiCGStab.h b/AMDiS/src/BiCGStab.h
deleted file mode 100644
index e965c80d..00000000
--- a/AMDiS/src/BiCGStab.h
+++ /dev/null
@@ -1,104 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file BiCGStab.h */
-
-#ifndef AMDIS_BiCGStab_H
-#define AMDIS_BiCGStab_H
-
-#include "OEMSolver.h"
-#include "MemoryManager.h"
-#include "CreatorInterface.h"
-
-namespace AMDiS
-{
-
- // ============================================================================
- // ===== class BiCGStab =======================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Solves a linear system by the stabilized BiCG method.
- * Can be used for general system matrices.
- */
- template<typename VectorType>
- class BiCGStab : public OEMSolver<VectorType>
- {
- public:
- MEMORY_MANAGED(BiCGStab<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new BiCGStab object.
- */
- OEMSolver<VectorType>* create()
- {
- return NEW BiCGStab<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- BiCGStab(std::string name);
-
- /** \brief
- * destructor
- */
- ~BiCGStab();
-
- protected:
- /** \brief
- * realisation of OEMSolver::solveSystem
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b, bool reuseMatrix);
-
- /** \brief
- * realisation of OEMSolver::init
- */
- void init();
-
- /** \brief
- * realisation of OEMSolver::exit
- */
- void exit();
-
- private:
- // pointer to memory needed for solveSystem
- VectorType *r, *rstar, *p, *v, *t, *xmin;
- };
-
-}
-
-#include "BiCGStab.hh"
-
-#endif // AMDIS_BiCGStab_H
diff --git a/AMDiS/src/BiCGStab.hh b/AMDiS/src/BiCGStab.hh
deleted file mode 100644
index 7479cfdf..00000000
--- a/AMDiS/src/BiCGStab.hh
+++ /dev/null
@@ -1,239 +0,0 @@
-#include "Preconditioner.h"
-
-namespace AMDiS
-{
-
- template<typename VectorType>
- BiCGStab<VectorType>::BiCGStab(std::string name)
- : OEMSolver<VectorType>(name),
- r(NULL),
- rstar(NULL),
- p(NULL),
- v(NULL),
- t(NULL),
- xmin(NULL)
- {}
-
- template<typename VectorType>
- BiCGStab<VectorType>::~BiCGStab()
- {}
-
- template<typename VectorType>
- void BiCGStab<VectorType>::init()
- {
- r = this->vectorCreator->create();
- rstar = this->vectorCreator->create();
- p = this->vectorCreator->create();
- v = this->vectorCreator->create();
- t = this->vectorCreator->create();
- xmin = this->vectorCreator->create();
- }
-
- template<typename VectorType>
- void BiCGStab<VectorType>::exit()
- {
- this->vectorCreator->free(r);
- this->vectorCreator->free(rstar);
- this->vectorCreator->free(p);
- this->vectorCreator->free(v);
- this->vectorCreator->free(t);
- this->vectorCreator->free(xmin);
- }
-
- template<typename VectorType>
- int BiCGStab<VectorType>::solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b, bool reuseMatrix)
- {
- FUNCNAME("BiCGStab::solveSystem");
-
- double res, old_res = -1.0;
- double rh1, rh2, dad, alpha, ast, att, omega, beta;
- int iter;
-
- const double TOL = 1e-30;
-
- /*------------------------------------------------------------------------*/
- /*--- Initalization ----------------------------------------------------*/
- /*------------------------------------------------------------------------*/
-
- *p = *b;
- if (this->leftPrecon)
- this->leftPrecon->precon(p);
- double normB = norm(p);
-
- if (normB < TOL) {
- INFO(this->info,2)("b == 0; x = 0 is the solution of the linear system\n");
- setValue(*x, 0.0);
- this->residual = 0.0;
- return(0);
- }
-
- double save_tolerance = this->tolerance;
- if (this->relative)
- this->tolerance *= normB;
-
- *xmin = *x;
- int imin = 0;
-
- // h = Ax
- mv->matVec(NoTranspose, *x, *r);
-
- // h -= b
- *r *= -1.0;
- *r += *b;
-
- // preconditioning
- if (this->leftPrecon) this->leftPrecon->precon(r);
-
- // rstar = h;
- *rstar = *r;
-
- /*--- check initial residual -------------------------------------------*/
-
- res = norm(r);
-
- START_INFO();
- if (SOLVE_INFO(0, res, &old_res)) {
- if (this->relative)
- this->tolerance = save_tolerance;
- return(0);
- }
-
- double normrmin = res;
-
- // d = h
- *p = *r;
-
- // rh1 = h*rstar
- rh1 = *r * *rstar;
-
- /*------------------------------------------------------------------------*/
- /*--- Iteration --------------------------------------------------------*/
- /*------------------------------------------------------------------------*/
-
- for (iter = 1; iter <= this->max_iter; iter++) {
- /*--- calculate CA.d and CA.d*rstar ----------------------------------*/
-
- // CAd = Ad
- mv->matVec(NoTranspose, *p, *v);
-
- if (this->leftPrecon) this->leftPrecon->precon(v);
-
- // dad = CAd * rstar;
- dad = *v * *rstar;
-
- alpha = rh1/dad;
-
- if (abs(alpha) > 1e+6 * (res/norm(v))) {
- BREAK_INFO("(Ad,d^*)_2 = 0", iter, res, &old_res);
- break;
- }
-
- /*--- update s and t ------------------------------------------------*/
-
- // s = h
-
- // s = -alpha CAd + s
- axpy(-alpha, *v, *r);
-
- // x = -alpha d + x
- axpy(alpha, *p, *x);
-
- res = norm(r);
- if (res <= this->tolerance) {
- double red = res/old_res;
- INFO(this->info,2)("%5d | %12.5e | %8.2e\n", iter, res, red);
- INFO(this->info,6)("finished successfully with %d iterations\n", iter);
- if (this->relative)
- this->tolerance = save_tolerance;
- return(iter);
- }
-
- if (res < normrmin) { // update minimal norm quantities
- normrmin = res;
- *xmin = *x;
- imin = iter;
- } else if (res > normrmin * 1e+6) {
- INFO(this->info,2)("Linear solver diverges.\n");
- INFO(this->info,2)("Current iteration: %d.\n", iter);
- INFO(this->info,2)("Current residual: %e.\n", res);
- break;
- }
-
- // t = As
- mv->matVec(NoTranspose, *r, *t);
-
- if (this->leftPrecon)
- this->leftPrecon->precon(t);
-
- /*--- calculate omega ------------------------------------------------*/
-
- // ast = s*t
- ast = *r * *t;
-
- // att = t*t
- att = *t * *t;
-
- omega = ast/att;
-
- if (abs(omega) <= 1e-6 * (res/norm(t))) {
- BREAK_INFO("omega = 0", iter, res, &old_res);
- break;
- }
-
- /*--- update x and calculate new h ----------------------------------*/
-
- // x = -omega s + x
- axpy(omega, *r, *x);
-
- // h = s - omega * h
- axpy(-omega, *t, *r);
-
- res = norm(r);
- if (SOLVE_INFO(iter, res, &old_res) == 1) {
- if (this->relative)
- this->tolerance = save_tolerance;
- return(iter);
- }
-
- if (res < normrmin) { // update minimal norm quantities
- normrmin = res;
- *xmin = *x;
- imin = iter;
- } else if (res > normrmin * 1e+6) {
- INFO(this->info,2)("Linear solver diverges.\n");
- INFO(this->info,2)("Current iteration: %d.\n", iter);
- INFO(this->info,2)("Current residual: %e.\n", res);
- break;
- }
-
- // rh2 = h * rstar
- rh2 = *r * *rstar;
-
- beta = (rh2/rh1) * (alpha/omega);
-
- // d = -omega CAd + d
- axpy(-omega, *v, *p);
-
- // d = h + beta d
- *p *= beta;
- *p += *r;
-
- rh1 = rh2;
- }
-
- // returned solution is first with minimal residual
- *x = *xmin;
- iter = imin;
- this->residual = normrmin;
-
- if (this->relative)
- this->tolerance = save_tolerance;
-
- INFO(this->info,2)("The minimal norm was %e; it was achieved in iteration %d.\n",
- this->residual, iter);
-
- return(iter);
- }
-
-}
diff --git a/AMDiS/src/BiCGStab2.h b/AMDiS/src/BiCGStab2.h
deleted file mode 100644
index 054a5bfc..00000000
--- a/AMDiS/src/BiCGStab2.h
+++ /dev/null
@@ -1,103 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file BiCGStab2.h */
-
-#ifndef AMDIS_BiCGStab2_H
-#define AMDIS_BiCGStab2_H
-
-#include "OEMSolver.h"
-#include "MemoryManager.h"
-
-namespace AMDiS
-{
-
- // ============================================================================
- // ===== class BiCGStab2 ======================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Solves a linear system by the stabilized BiCG method.
- * Can be used for general non-singular system matrices.
- */
- template<typename VectorType>
- class BiCGStab2 : public OEMSolver<VectorType>
- {
- public:
- MEMORY_MANAGED(BiCGStab2<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new BiCGStab2 object.
- */
- OEMSolver<VectorType>* create()
- {
- return NEW BiCGStab2<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- BiCGStab2(std::string name);
-
- /** \brief
- * destructor
- */
- ~BiCGStab2();
-
- protected:
- /** \brief
- * realisation of OEMSolver::solveSystem
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b, bool reuseMatrix);
-
- /** \brief
- * realisation of OEMSolver::init
- */
- void init();
-
- /** \brief
- * realisation of OEMSolver::exit
- */
- void exit();
-
- private:
- // pointer to memory needed for solveSystem
- VectorType *r, *rstar, *u, *v, *s, *w, *t, *xmin;
- };
-
-}
-
-#include "BiCGStab2.hh"
-
-#endif // AMDIS_BiCGStab2_H
diff --git a/AMDiS/src/BiCGStab2.hh b/AMDiS/src/BiCGStab2.hh
deleted file mode 100644
index e0bdedbc..00000000
--- a/AMDiS/src/BiCGStab2.hh
+++ /dev/null
@@ -1,228 +0,0 @@
-#include "Preconditioner.h"
-
-namespace AMDiS
-{
-
- template<typename VectorType>
- BiCGStab2<VectorType>::BiCGStab2(std::string name)
- : OEMSolver<VectorType>(name),
- r(NULL), rstar(NULL), u(NULL), v(NULL), s(NULL), w(NULL), t(NULL),
- xmin(NULL)
- {}
-
- template<typename VectorType>
- BiCGStab2<VectorType>::~BiCGStab2()
- {}
-
- template<typename VectorType>
- void BiCGStab2<VectorType>::init()
- {
- r = this->vectorCreator->create();
- rstar = this->vectorCreator->create();
- u = this->vectorCreator->create();
- v = this->vectorCreator->create();
- s = this->vectorCreator->create();
- w = this->vectorCreator->create();
- t = this->vectorCreator->create();
- xmin = this->vectorCreator->create();
- }
-
- template<typename VectorType>
- void BiCGStab2<VectorType>::exit()
- {
- this->vectorCreator->free(r);
- this->vectorCreator->free(rstar);
- this->vectorCreator->free(u);
- this->vectorCreator->free(v);
- this->vectorCreator->free(s);
- this->vectorCreator->free(w);
- this->vectorCreator->free(t);
- this->vectorCreator->free(xmin);
- }
-
- template<typename VectorType>
- int BiCGStab2<VectorType>::solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b, bool reuseMatrix)
- {
- FUNCNAME("BiCGStab2::solveSystem()");
-
- double res, old_res = -1.0;
- double rho0, alpha, omega1, omega2, rho1, beta, gamma, mu, nu, tau;
- int iter;
-
- const double TOL = 1e-30;
-
- /*------------------------------------------------------------------------*/
- /*--- Initalization ----------------------------------------------------*/
- /*------------------------------------------------------------------------*/
-
- *u = *b;
- if (this->leftPrecon)
- this->leftPrecon->precon(u);
- double normB = norm(u);
-
- if (normB < TOL) {
- INFO(this->info, 2)("b == 0; x = 0 is the solution of the linear system\n");
- setValue(*x, 0.0);
- this->residual = 0.0;
- return(0);
- }
-
- double save_tolerance = this->tolerance;
- if (this->relative)
- this->tolerance *= normB;
-
- *xmin = *x;
- int imin = 0;
-
- // r = b - Ax
- mv->matVec(NoTranspose, *x, *r);
- *r *= -1.0;
- *r += *b;
-
- if (this->leftPrecon)
- this->leftPrecon->precon(r);
-
- /*--- check initial residual -------------------------------------------*/
-
- res = norm(r);
-
- START_INFO();
- if (SOLVE_INFO(0, res, &old_res)) {
- if (this->relative)
- this->tolerance = save_tolerance;
- return(0);
- }
-
- double normrmin = res;
-
- // setting for the method
- *rstar = *r;
- *rstar *= 1.0 / res;
-
- rho0 = 1.0;
- alpha = 0.0;
- omega2 = 1.0;
- setValue(*u, 0.0);
-
- /*------------------------------------------------------------------------*/
- /*--- Iteration --------------------------------------------------------*/
- /*------------------------------------------------------------------------*/
-
- for (iter = 1; iter <= this->max_iter; iter++) {
- rho0 *= -omega2;
-
- /*--- even BiCG step -------------------------------------------------*/
-
- // updating u
- rho1 = *r * *rstar;
- beta = alpha * rho1 / rho0;
- rho0 = rho1;
- *u *= -beta;
- *u += *r;
-
- // computing v
- mv->matVec(NoTranspose, *u, *v);
- if (this->leftPrecon)
- this->leftPrecon->precon(v);
-
- // Updating x and r
- gamma = *v * *rstar;
- alpha = rho0 / gamma;
- axpy(alpha, *u, *x);
- axpy(-alpha, *v, *r);
-
- // computing s
- mv->matVec(NoTranspose, *r, *s);
- if (this->leftPrecon)
- this->leftPrecon->precon(s);
-
- /*--- odd BiCG step --------------------------------------------------*/
-
- // updating v
- rho1 = *s * *rstar;
- beta = alpha * rho1 / rho0;
- rho0 = rho1;
- *v *= -beta;
- *v += *s;
-
- // computing w
- mv->matVec(NoTranspose, *v, *w);
- if (this->leftPrecon)
- this->leftPrecon->precon(w);
-
- // updating u, r and s
- gamma = *w * *rstar;
- alpha = rho0 / gamma;
- *u *= -beta;
- *u += *r;
- axpy(-alpha, *v, *r);
- axpy(-alpha, *w, *s);
-
- // computing t
- mv->matVec(NoTranspose, *s, *t);
- if (this->leftPrecon)
- this->leftPrecon->precon(t);
-
- /*--- CGR(2) part ----------------------------------------------------*/
-
- // computing constants
- omega1 = *r * *s;
- mu = *s * *s;
- nu = *s * *t;
- tau = *t * *t;
- omega2 = *r * *t;
- tau -= nu * nu / mu;
- omega2 -= nu * omega1 / mu;
- omega2 /= tau;
- omega1 -= nu * omega2;
- omega1 /= mu;
-
- // updating x
- axpy(omega1, *r, *x);
- axpy(omega2, *s, *x);
- axpy(alpha, *u, *x);
-
- // updating r
- axpy(-omega1, *s, *r);
- axpy(-omega2, *t, *r);
- /*--- checking accuracy ----------------------------------------------*/
-
- res = norm(r);
- if (SOLVE_INFO(iter, res, &old_res) == 1) {
- if (this->relative)
- this->tolerance = save_tolerance;
- return(iter);
- }
-
- // update minimal norm quantities
- if (res < normrmin) {
- normrmin = res;
- *xmin = *x;
- imin = iter;
- } else if (res > normrmin * 1e+6) {
- INFO(this->info,2)("Linear solver diverges.\n");
- INFO(this->info,2)("Current iteration: %d.\n", iter);
- INFO(this->info,2)("Current residual: %e.\n", res);
- break;
- }
-
- // updating u
- axpy(-omega1, *v, *u);
- axpy(-omega2, *w, *u);
- }
-
- // returned solution is first with minimal residual
- *x = *xmin;
- iter = imin;
- this->residual = normrmin;
-
- if (this->relative)
- this->tolerance = save_tolerance;
-
- INFO(this->info,2)("The minimal norm was %e; it was achieved in iteration %d.\n",
- this->residual, iter);
-
- return(iter);
- }
-}
diff --git a/AMDiS/src/BiCGStab_M.hh b/AMDiS/src/BiCGStab_M.hh
deleted file mode 100644
index 57789557..00000000
--- a/AMDiS/src/BiCGStab_M.hh
+++ /dev/null
@@ -1,191 +0,0 @@
-namespace AMDiS {
-
- template<typename VectorType>
- BiCGStab_M<VectorType>::BiCGStab_M(std::string name) : OEMSolver<VectorType>(name) {}
-
- template<typename VectorType>
- BiCGStab_M<VectorType>::~BiCGStab_M() {}
-
- template<typename VectorType>
- void BiCGStab_M<VectorType>::init()
- {
- r = this->vectorCreator->create();
- rt = this->vectorCreator->create();
- p = this->vectorCreator->create();
- v = this->vectorCreator->create();
- t = this->vectorCreator->create();
- ph = this->vectorCreator->create();
- sh = this->vectorCreator->create();
- xmin = this->vectorCreator->create();
- }
-
- template<typename VectorType>
- void BiCGStab_M<VectorType>::exit()
- {
- this->vectorCreator->free(r);
- this->vectorCreator->free(rt);
- this->vectorCreator->free(p);
- this->vectorCreator->free(v);
- this->vectorCreator->free(t);
- this->vectorCreator->free(ph);
- this->vectorCreator->free(sh);
- this->vectorCreator->free(xmin);
- }
-
- template<typename VectorType>
- int BiCGStab_M<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x, VectorType *b, bool reuseMatrix)
- {
- FUNCNAME("BiCGStab_M::solveSystem");
- double old_res = -1.0;
- int iter, imin;
- double n2b, normrmin, rho, rho1, omega, alpha = 0.0, beta, rtv;
-
- const double TOL_0 = 1e-30, TOL_INF = 1e+30;
-
- double save_tolerance = this->tolerance;
-
- // Check for all zero right hand side vector => all zero solution
- n2b = norm(b); // norm of rhs vector b
- if (n2b < TOL_0)
- {
- INFO(this->info,2)("b == 0, x = 0 is the solution of the linear system\n");
- set(*x, 0.0); // solution is all zeros
- this->residual = 0.0; // residual is zero
- return(0); // no iterations need to be performed
- }
-
- if (this->relative) this->tolerance *= n2b;
-
- // Set up for the method
- *xmin = *x; // iterate which has minimal residual so far
- imin = 0; // iteration at which xmin was computed
- matVec->matVec(NoTranspose, *x, *r);
- *r *= -1.0;
- *r += *b; // zero-th order residual
- this->residual = norm(r); // norm of the residual
-
- START_INFO();
- if (SOLVE_INFO(0, this->residual, &old_res) == 1)
- {
- if (this->relative) this->tolerance = save_tolerance;
- return(0); // initial guess is a good enough solution
- }
-
- *rt = *r; // shadow residual
- normrmin = this->residual; // norm of residual from xmin
- rho = 1.0;
- omega = 1.0;
-
- // Loop over maxit iterations (unless convergence or failure)
- for (iter = 1; iter <= this->max_iter; iter++)
- {
- rho1 = rho;
- rho = *r * *rt;
- if (abs(rho) < TOL_0 || abs(rho) > TOL_INF)
- {
- BREAK_INFO("R and RT have become orthogonal", iter, this->residual, &old_res);
- break;
- }
-
- if (iter == 1)
- *p = *r;
- else
- {
- beta = (rho/rho1) * (alpha/omega);
- if (abs(beta) < TOL_0 || abs(beta) > TOL_INF)
- {
- BREAK_INFO("beta has become too small or too large to continue "
- "computing", iter, this->residual, &old_res);
- break;
- }
- axpy(-omega, *v, *p);
- *p *= beta;
- *p += *r;
- }
-
- *ph = *p;
- if (this->leftPrecon)
- this->leftPrecon->precon(ph);
-
- matVec->matVec(NoTranspose, *ph, *v);
-
- rtv = *v * *rt;
- if (abs(rtv) < TOL_0 || abs(rtv) > TOL_INF)
- {
- BREAK_INFO("V and RT have become orthogonal", iter, this->residual, &old_res);
- break;
- }
-
- alpha = rho / rtv;
- if (abs(alpha) > TOL_INF)
- {
- BREAK_INFO("alpha has become too large to continue computing",
- iter, this->residual, &old_res);
- break;
- }
-
- axpy(alpha, *ph, *x); // form the "half" iterate
- axpy(-alpha, *v, *r); // and its residual
- this->residual = norm(r);
-
- if (this->residual < normrmin) // update minimal norm quantities
- {
- normrmin = this->residual;
- *xmin = *x;
- imin = iter;
- }
-
- if (abs(alpha) < TOL_0)
- {
- BREAK_INFO("Stagnation of the method", iter, this->residual, &old_res);
- break; // stagnation of the method
- }
-
- *sh = *r; // residual associated with xhalf
- if (this->leftPrecon)
- this->leftPrecon->precon(sh);
- matVec->matVec(NoTranspose, *sh, *t);
-
- omega = (*t * *r) / (*t * *t);
- if (abs(omega) > TOL_INF)
- {
- BREAK_INFO("omega has become too large to continue computing",
- iter, this->residual, &old_res);
- break;
- }
-
- axpy(omega, *sh, *x); // update x
- axpy(-omega, *t, *r);
- this->residual = norm(r);
- if (SOLVE_INFO(iter, this->residual, &old_res) == 1)
- {
- if (this->relative) this->tolerance = save_tolerance;
- return(iter); // check for convergence
- }
-
- if (this->residual < normrmin) // update minimal norm quantities
- {
- normrmin = this->residual;
- *xmin = *x;
- imin = iter;
- }
-
- if (abs(omega) < TOL_0)
- {
- BREAK_INFO("T and S have become orthogonal", iter, this->residual, &old_res);
- break; // stagnation of the method
- }
- } // end for (iter = 1; iter <= this->max_iter; iter++)
-
- // returned solution is first with minimal residual
- *x = *xmin;
- iter = imin;
- this->residual = normrmin;
-
- if (this->relative) this->tolerance = save_tolerance;
-
- return(iter);
- }
-
-}
diff --git a/AMDiS/src/Boundary.h b/AMDiS/src/Boundary.h
index 9769aa1a..c5ef7f33 100644
--- a/AMDiS/src/Boundary.h
+++ b/AMDiS/src/Boundary.h
@@ -41,6 +41,116 @@ namespace AMDiS {
/// Type specifier for the different boundary types
typedef signed int BoundaryType;
+ // /** \ingroup Triangulation
+ // * \brief
+ // * Holds information about the type of boundary associated to an edge/face,
+ // * and how new vertices are projected to the boundary in the case of curved
+ // * boundaries.
+ //
+ // class Boundary
+ // {
+ // public:
+ // MEMORY_MANAGED(Boundary);
+
+ // /** \brief
+ // * constructor
+ //
+ // Boundary(BoundaryType type=0) {
+ // bound = type;
+ // };
+
+ // /** \brief
+ // * copy constructor
+ //
+ // Boundary(const Boundary& old) { bound = old.getBound(); };
+
+ // /** \brief
+ // * destructor
+ //
+ // virtual ~Boundary() {};
+
+ // /** \brief
+ // * assignment operator
+ //
+ // Boundary& operator=(const Boundary& old) {
+ // if (this!=&old) bound = old.getBound();
+ // return *this;
+ // };
+
+ // /** \brief
+ // * Returns
+ // * -true: if a new vertex should be projected to a curved boundary
+ // * -false: otherwise
+ //
+ // virtual bool interpolateBoundary() { return false; };
+
+ // /** \brief
+ // * Projection to the curved boundary
+ //
+ // virtual void interpolateBoundary(WorldVector<double>& ) {};
+
+ // /** \brief
+ // * Returns \ref bound
+ //
+ // inline const BoundaryType getBound() const { return bound; };
+
+ // /** \brief
+ // * Returns
+ // * -true: is \ref bound is INTERIOR
+ // * -false: otherwise
+ //
+ // inline const bool isInterior() const {return (bound == INTERIOR);};
+
+ // /** \brief
+ // * Returns
+ // * -true: is \ref bound is DIRICHLET
+ // * -false: otherwise
+ //
+ // inline const bool isDirichlet() const {return (bound == DIRICHLET);};
+
+ // /** \brief
+ // * Returns
+ // * -true: is \ref bound is NEUMANN
+ // * -false: otherwise
+ //
+ // inline const bool isNeumann() const {return (bound == NEUMANN);};
+
+ // /** \brief
+ // * Returns
+ // * -true: is \ref bound is ROBIN
+ // * -false: otherwise
+ //
+ // inline const bool isRobin() const {return (bound == ROBIN);};
+
+ // /** \brief
+ // * Returns the new value of \ref bound with respect to its old value and
+ // * the value of bound_.
+ //
+ // BoundaryType newVal(const BoundaryType bound_);
+
+ // /** \brief
+ // * Returns the Boundary with given type from \ref boundaryMap.
+ //
+ // static Boundary* getBoundary(BoundaryType type);
+
+ // /** \brief
+ // * Adds Boundary b to \ref boundaryMap.
+ //
+ // //static void addBoundary(Boundary *b);
+
+ // protected:
+ // /** \brief
+ // * type of this boundary
+ //
+ // BoundaryType bound;
+
+ // protected:
+ // /** \brief
+ // * stl map of all existing boundaries.
+ //
+ // static ::std::map<BoundaryType, Boundary*> boundaryMap;
+ // };
+
BoundaryType newBound(BoundaryType oldBound, BoundaryType newBound);
}
diff --git a/AMDiS/src/BoundaryCondition.h b/AMDiS/src/BoundaryCondition.h
index 3f9d85df..7f403143 100644
--- a/AMDiS/src/BoundaryCondition.h
+++ b/AMDiS/src/BoundaryCondition.h
@@ -24,10 +24,10 @@
#include "Boundary.h"
#include "FiniteElemSpace.h"
+#include "AMDiS_fwd.h"
namespace AMDiS {
- class DOFMatrix;
template<typename T> class DOFVectorBase;
class Estimator;
class ElInfo;
@@ -43,7 +43,7 @@ namespace AMDiS {
* Sub class of BoundaryCondition. Local boundary conditions are filled
* while mesh traversal.
*/
- class BoundaryCondition
+ class BoundaryCondition //: public BoundaryCondition
{
public:
/** \brief
@@ -56,30 +56,23 @@ namespace AMDiS {
rowFESpace(rowFESpace_),
colFESpace(colFESpace_)
{
- if (!colFESpace)
- colFESpace = rowFESpace;
+ if(!colFESpace) colFESpace = rowFESpace;
};
/** \brief
* Returns \ref boundaryType.
*/
- inline BoundaryType getBoundaryType() {
- return boundaryType;
- };
+ inline BoundaryType getBoundaryType() { return boundaryType; };
/** \brief
* Returns \ref rowFESpace.
*/
- inline const FiniteElemSpace *getRowFESpace() {
- return rowFESpace;
- };
+ inline const FiniteElemSpace *getRowFESpace() { return rowFESpace; };
/** \brief
* Returns \ref rowFESpace.
*/
- inline const FiniteElemSpace *getColFESpace() {
- return colFESpace;
- };
+ inline const FiniteElemSpace *getColFESpace() { return colFESpace; };
virtual void initMatrix(DOFMatrix*) {};
@@ -121,17 +114,13 @@ namespace AMDiS {
*/
virtual double boundResidual(ElInfo *elInfo,
DOFMatrix *matrix,
- const DOFVectorBase<double> *dv) {
- return 0.0;
- };
+ const DOFVectorBase<double> *dv) { return 0.0; };
/** \brief
* Returns whether the condition must be treated as dirichlet condition
* while assemblage.
*/
- virtual bool isDirichlet() {
- return false;
- };
+ virtual bool isDirichlet() { return false; };
protected:
/** \brief
diff --git a/AMDiS/src/BoundaryManager.h b/AMDiS/src/BoundaryManager.h
index 78ab7c22..07e61713 100644
--- a/AMDiS/src/BoundaryManager.h
+++ b/AMDiS/src/BoundaryManager.h
@@ -24,12 +24,12 @@
#include <map>
+#include "AMDiS_fwd.h"
#include "Boundary.h"
#include "BoundaryCondition.h"
namespace AMDiS {
- class DOFMatrix;
class FiniteElemSpace;
template<typename T> class Vector;
template<typename T> class DOFVectorBase;
diff --git a/AMDiS/src/BoxSmoother.h b/AMDiS/src/BoxSmoother.h
index 19a6f500..52deed36 100644
--- a/AMDiS/src/BoxSmoother.h
+++ b/AMDiS/src/BoxSmoother.h
@@ -67,7 +67,9 @@ namespace AMDiS {
const Vector< std::set<DegreeOfFreedom>*> &dofSet)
{
FUNCNAME("BoxSmoother::smooth()");
+ ERROR_EXIT("Will be rewritten - Peter\n");
+#if 0
int i, j, k;
// allocate memory
@@ -211,6 +213,7 @@ namespace AMDiS {
++pos;
}
}
+#endif
};
protected:
diff --git a/AMDiS/src/CGSolver.h b/AMDiS/src/CGSolver.h
deleted file mode 100644
index f39a9690..00000000
--- a/AMDiS/src/CGSolver.h
+++ /dev/null
@@ -1,114 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file CGSolver.h */
-
-#ifndef AMDIS_CGSOLVER_H
-#define AMDIS_CGSOLVER_H
-
-namespace AMDiS {
-
- #include "OEMSolver.h"
- #include "MemoryManager.h"
-
- // ============================================================================
- // ===== class CGSolver =======================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Solves a linear system by the conjugate gradient method and can be used for
- * symmetric positive definite system matrices.
- *
- * The implementation is based on the following book: "Numerik linearer
- * Gleichungssystene", 2. Auflage, Andreas Meister. The algorithm is described
- * on page 124. The extension to the preconditioned cg method (pcg) is described
- * on page 207 in the same book. We here use the same variable names, but without
- * subscription.
- */
- template<typename VectorType>
- class CGSolver : public OEMSolver<VectorType>
- {
- public:
- MEMORY_MANAGED(CGSolver<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new CGSolver object.
- */
- OEMSolver<VectorType>* create() {
- return NEW CGSolver<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- CGSolver(std::string name);
-
- /** \brief
- * destructor
- */
- ~CGSolver();
-
- protected:
- /** \brief
- * Implements OEMSolver<VectorType>::init().
- */
- void init() {
- p = this->vectorCreator->create();
- r = this->vectorCreator->create();
- v = this->vectorCreator->create();
- z = this->vectorCreator->create();
- };
-
- /** \brief
- * Implements OEMSolver<VectorType>::exit().
- */
- void exit() {
- this->vectorCreator->free(p);
- this->vectorCreator->free(r);
- this->vectorCreator->free(v);
- this->vectorCreator->free(z);
- };
-
- /** \brief
- * Implements OEMSolver<VectorType>::solve().
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv, VectorType *x, VectorType *b, bool reuseMatrix);
-
- private:
- VectorType *p, *r, *v, *z;
- };
-}
-
-#include "CGSolver.hh"
-
-#endif // AMDIS_CGSOLVER_H
diff --git a/AMDiS/src/CGSolver.hh b/AMDiS/src/CGSolver.hh
deleted file mode 100644
index 7b1fa1e7..00000000
--- a/AMDiS/src/CGSolver.hh
+++ /dev/null
@@ -1,132 +0,0 @@
-#include "DOFVector.h"
-#include "DOFMatrix.h"
-#include "MatVecMultiplier.h"
-#include "StlVector.h"
-#include "V3Vector.h"
-
-namespace AMDiS {
-
- template<typename VectorType>
- CGSolver<VectorType>::CGSolver(std::string name)
- : OEMSolver<VectorType>(name)
- {}
-
- template<typename VectorType>
- CGSolver<VectorType>::~CGSolver() {}
-
- template<typename VectorType>
- int CGSolver<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x, VectorType *b, bool reuseMatrix)
- {
- FUNCNAME("CGSolver::solve()");
-
- const double TOL = 1.e-30;
-
-// std::cout << "b: " << std::endl;
-// print(b);
-
- // If norm of b is smaller than the tolarance, we can assume b to be zero.
- // Hence, x = 0 is the solution of the linear system.
- if (norm(b) < TOL) {
- INFO(this->info,2)("b == 0, x = 0 is the solution of the linear system\n");
- setValue(*x, 0.0);
- this->residual = 0.0;
-
- return(0);
- }
-
-// std::cout << "x: " << std::endl;
-// print(x);
-
- // p is temporaly used to calculate -x.
- *p = *x;
- *p *= -1.0;
-
- // r = b - Ax
- matVec->matVec(NoTranspose, *p, *r);
-// std::cout << "-Ax: " << std::endl;
-// print(r);
- *r += *b;
-
-// std::cout << "r: " << std::endl;
-// print(r);
-
- *p = *r;
- if (this->leftPrecon) {
- this->leftPrecon->precon(p);
- }
-
- // \alpha = (r,p)_2
- // without precondition, \alpha = (r,p)_2 = (r,r)_2 = \|r\|_2^2
-// std::cout << "Berechne Alpha: " << std::endl;
-// std::cout << "r: " << std::endl;
-// print(r);
-// std::cout << "p: " << std::endl;
-// print(p);
- double alpha = *r * *p;
-// std::cout << "alpha=" << alpha << std::endl;
-
- double alpha1, lambda, old_res = -1.0;
-
- START_INFO();
- // Test if x is already a solution of the lineas system.
- if (SOLVE_INFO(0, sqrt(alpha), &old_res)) {
- return(0);
- }
-
- for (int iter = 1; iter <= this->max_iter; iter++) {
- // std::cout << "---------------------------Ein Schritt---------------------------" << std::endl;
- // v = Ap
- matVec->matVec(NoTranspose, *p, *v);
-// std::cout << "p: " << std::endl;
-// print(p);
-// std::cout << "Ap: " << std::endl;
-// print(v);
-
- // \lambda = alpha / (v,p)_2
- lambda = *v * *p;
- if (abs(lambda) < TOL) {
- BREAK_INFO("(v,p)_2 = 0", iter, sqrt(alpha), &old_res);
- return(iter);
- }
- lambda = alpha / lambda;
-
- // x = x + \lambda * p
- axpy(lambda, *p, *x);
-
- // r = r - \lambda * v
- axpy(-lambda, *v, *r);
-
- *z = *r;
- if (this->leftPrecon) {
- this->leftPrecon->precon(z);
- }
-
- // \alpha_{m + 1} = (r,z)_2
- // without precondition, \alpha_{m + 1} = (r,z)_2 = (r,r)_2 = \|r\|_2^2
- alpha1 = *r * *z;
-
- // Check if x is a solution of the linear system.
- if (SOLVE_INFO(iter, sqrt(alpha1), &old_res)) {
- *p = *x;
- *p *= -1.0;
-
- // r = b - Ax
- matVec->matVec(NoTranspose, *p, *r);
- *r += *b;
-
- return(iter);
- }
-
- // p = z + (alpha_{m + 1} / alpha_{m}) * p
- xpay(alpha1 / alpha, *z, *p);
-
- // Put the value of the alpha_{m + 1} variable to alpha_{m} variable
- // for the next iteration.
- alpha = alpha1;
- }
-
- ERROR_EXIT("Should not be reached\n");
- return(0);
- }
-}
diff --git a/AMDiS/src/CreatorInterface.h b/AMDiS/src/CreatorInterface.h
index ea5e3a46..84cc948e 100644
--- a/AMDiS/src/CreatorInterface.h
+++ b/AMDiS/src/CreatorInterface.h
@@ -22,6 +22,8 @@
#ifndef AMDIS_CREATORINTERFACE_H
#define AMDIS_CREATORINTERFACE_H
+#include "DOFMatrix.h"
+
namespace AMDiS {
/** \ingroup Common
@@ -48,6 +50,8 @@ namespace AMDiS {
*/
virtual BaseClass* create() = 0;
+ virtual BaseClass* create(const DOFMatrix::base_matrix_type& A) { return 0; }
+
/** \brief
* Can be implemented by sub classes.
*/
diff --git a/AMDiS/src/CreatorMap.cc b/AMDiS/src/CreatorMap.cc
index d945a5dd..31c4206c 100644
--- a/AMDiS/src/CreatorMap.cc
+++ b/AMDiS/src/CreatorMap.cc
@@ -1,16 +1,13 @@
#include "CreatorMap.h"
#include "OEMSolver.h"
-#include "Preconditioner.h"
-#include "DiagonalPreconditioner.h"
-#include "ILUPreconditioner.h"
-#include "ILUTPreconditioner.h"
+#include "ITL_Solver.h"
+#include "ITL_Preconditioner.h"
#include "NonLinSolver.h"
#include "MatrixVector.h"
#include "SystemVector.h"
#include "Estimator.h"
-#include "ResidualEstimator.h"
-#include "ResidualParallelEstimator.h"
#include "RecoveryEstimator.h"
+#include "ResidualEstimator.h"
#include "LeafData.h"
#include "SurfaceRegion_ED.h"
#include "MultiGridWrapper.h"
@@ -19,99 +16,66 @@
#include "GSSmoother.h"
#include "JacobiSmoother.h"
#include "ElementRegion_ED.h"
-#include "BiCGStab.h"
-#include "BiCGStab2.h"
-#include "BFGS_Precond.h"
#include "BoxSmoother.h"
#include "MultiGridPreconWrapper.h"
-#include "GMResSolver2.h"
-#include "TFQMR.h"
-#include "VecSymSolver.h"
#include "UmfPackSolver.h"
-#include "PardisoSolver.h"
-#include "DuneSolver.h"
namespace AMDiS {
template<>
- void CreatorMap<OEMSolver<DOFVector<double> > >::addDefaultCreators()
+ void CreatorMap<OEMSolver>::addDefaultCreators()
{
- OEMSolverCreator<DOFVector<double> > *creator;
+ OEMSolverCreator *creator;
- creator = NEW BiCGSolver<DOFVector<double> >::Creator;
- addCreator("bicgstab_albert", creator);
-
- creator = NEW CGSolver<DOFVector<double> >::Creator;
+ creator = NEW CGSolver::Creator;
addCreator("cg", creator);
- creator = NEW GMResSolver<DOFVector<double> >::Creator;
- addCreator("gmres", creator);
-
- creator = NEW ODirSolver<DOFVector<double> >::Creator;
- addCreator("odir", creator);
+ creator = NEW BiCGSolver::Creator;
+ addCreator("bicg", creator);
- creator = NEW OResSolver<DOFVector<double> >::Creator;
- addCreator("ores", creator);
-
- creator = NEW BiCGStab<DOFVector<double> >::Creator;
+ creator = NEW BiCGStab::Creator;
addCreator("bicgstab", creator);
- creator = NEW MultiGridWrapperScal::Creator;
- addCreator("mg", creator);
-
- creator = NEW BiCGStab2<DOFVector<double> >::Creator;
+ creator = NEW BiCGStab2::Creator;
addCreator("bicgstab2", creator);
- // creator = NEW GMResSolver2<DOFVector<double> >::Creator;
- // addCreator("gmres2", creator);
-
- creator = NEW TFQMR<DOFVector<double> >::Creator;
- addCreator("tfqmr", creator);
+ creator = NEW BiCGStabEll::Creator;
+ addCreator("bicgstab_ell", creator);
-#ifdef HAVE_DUNE
- creator = NEW DuneSolver< DOFVector<double> >::Creator;
- addCreator("dune", creator);
+#ifdef HAVE_UMFPACK
+ creator = NEW UmfPackSolver::Creator;
+ addCreator("umfpack", creator);
#endif
}
-
- template<>
- void CreatorMap<SmootherBase<DOFMatrix,
- SparseVector<double>,
- std::set<DegreeOfFreedom> > >::addDefaultCreators()
- {
- SmootherCreator<DOFMatrix, SparseVector<double>, std::set<DegreeOfFreedom> > *creator;
-
- creator = NEW GSSmoother<DOFMatrix, SparseVector<double>, std::set<DegreeOfFreedom> >::Creator;
- addCreator("gs", creator);
-
- creator = NEW JacobiSmoother<DOFMatrix, SparseVector<double>, std::set<DegreeOfFreedom> >::Creator;
- addCreator("j", creator);
- }
-
-
template<>
- void CreatorMap<PreconditionerScal>::addDefaultCreators()
+ void CreatorMap<ITL_BasePreconditioner>::addDefaultCreators()
{
- CreatorInterface<PreconditionerScal> *creator;
+ CreatorInterface<ITL_BasePreconditioner> *creator;
creator = NEW DiagonalPreconditioner::Creator;
addCreator("diag", creator);
+ creator = NEW IdentityPreconditioner::Creator;
+ addCreator("no", creator);
+
creator = NEW ILUPreconditioner::Creator;
addCreator("ilu", creator);
- creator = NEW ILUTPreconditioner::Creator;
- addCreator("ilut", creator);
+ creator = NEW ICPreconditioner::Creator;
+ addCreator("ic", creator);
- creator = NEW BFGS_Precond::Creator;
- addCreator("bfgs", creator);
+#if 0
creator = NEW MGPreconWrapperScal::Creator;
addCreator("mg", creator);
+#endif
}
+
+
+#if 0
template<>
void CreatorMap<NonLinSolver<DOFVector<double> > >::addDefaultCreators()
{
@@ -123,87 +87,10 @@ namespace AMDiS {
creator = NEW NewtonS<DOFVector<double> >::Creator;
addCreator("newton_fs", creator);
}
-
-
- template<>
- void CreatorMap<OEMSolver<SystemVector> >::addDefaultCreators()
- {
- OEMSolverCreator<SystemVector> *creator;
-
- creator = NEW BiCGSolver<SystemVector>::Creator;
- addCreator("bicgstab_albert", creator);
-
- creator = NEW CGSolver<SystemVector>::Creator;
- addCreator("cg", creator);
-
- creator = NEW GMResSolver<SystemVector>::Creator;
- addCreator("gmres", creator);
-
- creator = NEW ODirSolver<SystemVector>::Creator;
- addCreator("odir", creator);
-
- creator = NEW OResSolver<SystemVector>::Creator;
- addCreator("ores", creator);
-
- creator = NEW BiCGStab<SystemVector>::Creator;
- addCreator("bicgstab", creator);
-
- creator = NEW BiCGStab2<SystemVector>::Creator;
- addCreator("bicgstab2", creator);
-
- creator = NEW MultiGridWrapperVec::Creator;
- addCreator("mg", creator);
-
- creator = NEW GMResSolver2<SystemVector>::Creator;
- addCreator("gmres2", creator);
-
- creator = NEW TFQMR<SystemVector>::Creator;
- addCreator("tfqmr", creator);
-
- creator = NEW VecSymSolver<SystemVector>::Creator;
- addCreator("vecsym", creator);
-
-#ifdef HAVE_UMFPACK
- creator = NEW UmfPackSolver<SystemVector>::Creator;
- addCreator("umfpack", creator);
-#endif
-
-#ifdef HAVE_MKL
- creator = NEW PardisoSolver<SystemVector>::Creator;
- addCreator("pardiso", creator);
-#endif
-
-#ifdef HAVE_DUNE
- creator = NEW DuneSolver<SystemVector>::Creator;
- addCreator("dune", creator);
#endif
- }
-
-
- template<>
- void CreatorMap<SmootherBase<Matrix<DOFMatrix*>,
- Vector<SparseVector<double>*>,
- Vector< std::set<DegreeOfFreedom>*> > >::addDefaultCreators()
- {
- SmootherCreator<Matrix<DOFMatrix*>,
- Vector<SparseVector<double>*>,
- Vector< std::set<DegreeOfFreedom>*> > *creator;
-
- creator = NEW GSSmoother<Matrix<DOFMatrix*>,
- Vector<SparseVector<double>*>,
- Vector< std::set<DegreeOfFreedom>*> >::Creator;
- addCreator("gs", creator);
-
- creator = NEW JacobiSmoother<Matrix<DOFMatrix*>,
- Vector<SparseVector<double>*>,
- Vector< std::set<DegreeOfFreedom>*> >::Creator;
- addCreator("j", creator);
-
- creator = NEW BoxSmoother::Creator;
- addCreator("box", creator);
- }
+#if 0
template<>
void CreatorMap<NonLinSolver<SystemVector> >::addDefaultCreators()
{
@@ -215,7 +102,7 @@ namespace AMDiS {
creator = NEW NewtonS<SystemVector>::Creator;
addCreator("newton_fs", creator);
}
-
+#endif
template<>
void CreatorMap<Estimator>::addDefaultCreators()
@@ -225,16 +112,10 @@ namespace AMDiS {
creator = NEW ResidualEstimator::Creator;
addCreator("residual", creator);
-#ifdef _OPENMP
- creator = NEW ResidualParallelEstimator::Creator;
- addCreator("residualparallel", creator);
-#endif
-
creator = NEW RecoveryEstimator::Creator;
addCreator("recovery", creator);
}
-
template<>
void CreatorMap<ElementData>::addDefaultCreators()
{
@@ -261,4 +142,5 @@ namespace AMDiS {
creator = NEW ElementRegion_ED::Creator;
addCreator("ElementRegion_ED", creator);
}
+
}
diff --git a/AMDiS/src/CreatorMap.h b/AMDiS/src/CreatorMap.h
index 7807ddc8..d56e7da5 100644
--- a/AMDiS/src/CreatorMap.h
+++ b/AMDiS/src/CreatorMap.h
@@ -69,18 +69,19 @@ namespace AMDiS {
static void addDefaultCreators();
- protected:
- /** \brief
- * Constructor is protected because derived maps should be singleton.
- */
- static void init() {
- if (!initialized) {
- initialized = true;
- NullCreator<BaseClass> *nullCreator = new NullCreator<BaseClass>;
- addCreator("no", nullCreator);
- addDefaultCreators();
- }
- }
+ protected:
+ /** \brief
+ * Constructor is protected because derived maps should be singleton.
+ */
+ static void init() {
+ if(!initialized) {
+ initialized = true;
+ NullCreator<BaseClass> *nullCreator = new NullCreator<BaseClass>;
+ // addCreator("no", nullCreator);
+ addCreator("0", nullCreator);
+ addDefaultCreators();
+ }
+ };
protected:
/** \brief
diff --git a/AMDiS/src/DOFIndexed.cc b/AMDiS/src/DOFIndexed.cc
index 07b8469e..1ebda059 100644
--- a/AMDiS/src/DOFIndexed.cc
+++ b/AMDiS/src/DOFIndexed.cc
@@ -1,15 +1,103 @@
#include "DOFIndexed.h"
#include "DOFMatrix.h"
+#include <boost/numeric/mtl/mtl.hpp>
+#include <boost/numeric/mtl/utility/tag.hpp>
+#include <boost/numeric/mtl/utility/category.hpp>
+#include <boost/numeric/linear_algebra/identity.hpp>
+
+
+// Defining the interface for MTL4
+namespace mtl {
+
+ // Let MTL4 know that DOFIndexed it is a column vector
+ namespace traits {
+ template <typename T>
+ struct category< AMDiS::DOFIndexed<T> >
+ {
+ typedef tag::dense_col_vector type;
+ };
+ }
+
+ namespace ashape {
+ template <typename T>
+ struct ashape< AMDiS::DOFIndexed<T> >
+ {
+ typedef cvec<typename ashape<T>::type> type;
+ };
+ }
+
+ // Modelling Collection and MutableCollection
+ template <typename T>
+ struct Collection< AMDiS::DOFIndexed<T> >
+ {
+ typedef T value_type;
+ typedef const T& const_reference;
+ typedef std::size_t size_type;
+ };
+
+ template <typename T>
+ struct MutableCollection< AMDiS::DOFIndexed<T> >
+ : public Collection< AMDiS::DOFIndexed<T> >
+ {
+ typedef T& reference;
+ };
+
+
+} // namespace mtl
+
+
+
namespace AMDiS {
+ // Some free functions used in MTL4
+
+ template <typename T>
+ inline std::size_t size(const AMDiS::DOFIndexed<T>& v)
+ {
+ return v.getSize();
+ }
+
+ template <typename T>
+ inline std::size_t num_rows(const AMDiS::DOFIndexed<T>& v)
+ {
+ return v.getSize();
+ }
+
+ template <typename T>
+ inline std::size_t num_cols(const AMDiS::DOFIndexed<T>& v)
+ {
+ return 1;
+ }
+
+
+ template <typename T>
+ inline void set_to_zero(AMDiS::DOFIndexed<T>& v)
+ {
+ using math::zero;
+ T ref, my_zero(zero(ref));
+
+ std::fill(v.begin(), v.end(), my_zero);
+ }
+
+
+
void mv(MatrixTranspose transpose,
const DOFMatrix &a,
- DOFIndexed<double> &x,
+ const DOFIndexed<double> &x,
DOFIndexed<double> &result,
bool add)
{
- FUNCNAME("DOFVector<T>::mv");
+ FUNCNAME("DOFIndexed<T>::mv");
+
+ if (transpose == NoTranspose)
+ mult(a.getBaseMatrix(), x, result);
+ else if (transpose == Transpose)
+ mult(trans(const_cast<DOFMatrix::base_matrix_type&>(a.getBaseMatrix())), x, result);
+ else
+ ERROR_EXIT("transpose = %d\n", transpose);
+
+#if 0
int irow, jcol;
double sum;
@@ -36,6 +124,7 @@ namespace AMDiS {
} else {
ERROR_EXIT("transpose=%d\n", transpose);
}
+#endif
}
}
diff --git a/AMDiS/src/DOFIndexed.h b/AMDiS/src/DOFIndexed.h
index 6f62ded8..743e3e2f 100644
--- a/AMDiS/src/DOFIndexed.h
+++ b/AMDiS/src/DOFIndexed.h
@@ -25,15 +25,10 @@
#include <vector>
#include "Global.h"
#include "DOFIterator.h"
+#include "AMDiS_fwd.h"
namespace AMDiS {
- class RCNeighbourList;
- class FiniteElemSpace;
- class DOFMatrix;
- class ElInfo;
- class Quadrature;
- class FastQuadrature;
// ============================================================================
// ===== class DOFIndexedBase =================================================
@@ -112,12 +107,13 @@ namespace AMDiS {
virtual const T& operator[](DegreeOfFreedom i) const = 0;
};
+
void mv(MatrixTranspose transpose,
const DOFMatrix &a,
- DOFIndexed<double> &x,
+ const DOFIndexed<double> &x,
DOFIndexed<double> &result,
bool add = false);
-}
+} // namespace AMDiS
#endif // AMDIS_DOFINDEXED_H
diff --git a/AMDiS/src/DOFMatrix.cc b/AMDiS/src/DOFMatrix.cc
index 4b44d3c5..843e42e5 100644
--- a/AMDiS/src/DOFMatrix.cc
+++ b/AMDiS/src/DOFMatrix.cc
@@ -15,16 +15,22 @@
#include "BoundaryManager.h"
#include "ElementMatrix.h"
#include "Assembler.h"
+#include "Utilities.h"
+
+#include <boost/numeric/mtl/mtl.hpp>
namespace AMDiS {
+ using namespace mtl;
+
DOFMatrix *DOFMatrix::traversePtr = NULL;
DOFMatrix::DOFMatrix()
- {
- rowFESpace = NULL;
- colFESpace = NULL;
- }
+ : rowFESpace(NULL),
+ colFESpace(NULL),
+ elementMatrix(NULL),
+ inserter(NULL)
+ {}
DOFMatrix::DOFMatrix(const FiniteElemSpace* rowFESpace_,
const FiniteElemSpace* colFESpace_,
@@ -32,7 +38,8 @@ namespace AMDiS {
: rowFESpace(rowFESpace_),
colFESpace(colFESpace_),
name(name_),
- coupleMatrix(false)
+ coupleMatrix(false),
+ inserter(NULL)
{
TEST_EXIT(rowFESpace)("no rowFESpace\n");
@@ -60,14 +67,14 @@ namespace AMDiS {
*this = rhs;
if (rowFESpace && rowFESpace->getAdmin())
(const_cast<DOFAdmin*>( rowFESpace->getAdmin()))->addDOFIndexed(this);
+
+ TEST_EXIT(rhs.inserter == 0)("Cannot copy during insertion");
+ inserter= 0;
}
DOFMatrix::~DOFMatrix()
{
FUNCNAME("DOFMatrix::~DOFMatrix()");
-
- matrix.clear();
-
if (rowFESpace && rowFESpace->getAdmin()) {
(const_cast<DOFAdmin*>(rowFESpace->getAdmin()))->removeDOFIndexed(this);
}
@@ -77,65 +84,28 @@ namespace AMDiS {
if (elementMatrix)
DELETE elementMatrix;
+ if (inserter) delete inserter;
}
void DOFMatrix::print() const
{
FUNCNAME("DOFMatrix::print()");
- int sizeUsed = rowFESpace->getAdmin()->getUsedSize();
-
- if (static_cast<int>(matrix.size()) < sizeUsed) {
- WARNING("DOFMatrix not yet initialized\n");
- return;
- }
-
- for (int i = 0; i < sizeUsed; i++) {
- DOFMatrix::MatrixRow row = matrix[i];
- MSG("row %3d:",i);
- int rowSize = static_cast<int>( row.size());
- for (int j = 0; j < rowSize; j++) {
- int jcol = row[j].col;
- if (entryUsed(i, j)) {
- Msg::print(" (%3d,%20.17lf)", jcol, row[j].entry);
- }
- }
- Msg::print("\n");
- }
- }
-
- void DOFMatrix::printRow(int i) const
- {
- FUNCNAME("DOFMatrix::printRow()");
-
- int sizeUsed = rowFESpace->getAdmin()->getUsedSize();
-
- if (static_cast<int>(matrix.size()) < sizeUsed) {
- WARNING("DOFMatrix not yet initialized\n");
- return;
- }
-
- DOFMatrix::MatrixRow row = matrix[i];
- MSG("row %3d:",i);
- int rowSize = static_cast<int>( row.size());
- for (int j = 0; j < rowSize; j++) {
- int jcol = row[j].col;
- if (entryUsed(i,j)) {
- Msg::print(" (%3d,%20.17lf)", jcol, row[j].entry);
- }
- }
- Msg::print("\n");
- }
+ using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
+ namespace traits= mtl::traits;
+ typedef base_matrix_type Matrix;
- /****************************************************************************/
- /* clear: remove all entries from dof_matrix */
- /****************************************************************************/
+ traits::row<Matrix>::type row(matrix);
+ traits::col<Matrix>::type col(matrix);
+ traits::const_value<Matrix>::type value(matrix);
- void DOFMatrix::clear()
- {
- int mSize = static_cast<int>(matrix.size());
- for (int i = 0; i < mSize; i++) {
- matrix[i].resize(0);
+ typedef traits::range_generator<major, Matrix>::type cursor_type;
+ typedef traits::range_generator<nz, cursor_type>::type icursor_type;
+
+ for (cursor_type cursor = begin<major>(matrix), cend = end<major>(matrix); cursor != cend; ++cursor) {
+ for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); icursor != icend; ++icursor)
+ Msg::print(" (%3d,%3d,%20.17lf)", row(*icursor), col(*icursor), value(*icursor));
+ Msg::print("\n");
}
}
@@ -143,26 +113,24 @@ namespace AMDiS {
{
FUNCNAME("DOFMatrix::symmetric()");
- DegreeOfFreedom row, col;
- double entry, tol = 1e-5;
+ double tol = 1e-5;
- DOFMatrix::Iterator matrixRow(this, USED_DOFS);
+ using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
+ namespace traits= mtl::traits;
+ typedef base_matrix_type Matrix;
- for (matrixRow.reset(); !matrixRow.end(); ++matrixRow) {
- row = matrixRow.getDOFIndex();
- int rowSize = matrixRow->size();
- for (int i = 0; i < rowSize; i++) {
- col = (*matrixRow)[i].col;
- entry = (*matrixRow)[i].entry;
- if (abs(entry - logAcc(col, row)) > tol) {
- MSG("matrix[%d][%d] = %e, matrix[%d][%d] = %e\n",
- row, col, entry, col, row, logAcc(col, row));
+ traits::row<Matrix>::type row(matrix);
+ traits::col<Matrix>::type col(matrix);
+ traits::const_value<Matrix>::type value(matrix);
+ typedef traits::range_generator<major, Matrix>::type cursor_type;
+ typedef traits::range_generator<nz, cursor_type>::type icursor_type;
+
+ for (cursor_type cursor = begin<major>(matrix), cend = end<major>(matrix); cursor != cend; ++cursor)
+ for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); icursor != icend; ++icursor)
+ // Compare each non-zero entry with its transposed
+ if (abs(value(*icursor) - matrix[col(*icursor)][row(*icursor)]) > tol)
return false;
- }
- }
- }
-
return true;
}
@@ -170,46 +138,7 @@ namespace AMDiS {
{
FUNCNAME("DOFMatrix::test()");
- int non_symmetric = 0, found = 0;
-
- /* test symmetry */
- for (int i = 0; i < static_cast<int>(matrix.size()); i++) {
- double sum = 0.0;
- DOFMatrix::MatrixRow *row = &matrix[i];
- for (int j = 0; j < static_cast<int>(row->size()); j++) {
- int jcol = (*row)[j].col;
- if (entryUsed(i, j)) {
- found = 0;
- if ((*row)[j].entry != (*row)[j].entry) {
- MSG("mat[%d,%d]=%10.5e ???\n", i, jcol, (*row)[j].entry);
- WAIT;
- }
- DOFMatrix::MatrixRow *row2 = &matrix[jcol];
- for (int k = 0; k < static_cast<int>(row->size()); k++) {
- int kcol = (*row)[k].col;
- if (entryUsed(jcol, k)) {
- if (kcol == i) {
- found = 1;
- if (abs((*row2)[k].entry - (*row)[j].entry) > 1.E-5) {
- non_symmetric = 1;
- MSG("mat[%d,%d]=%10.5e != mat[%d,%d]=%10.5e\n",
- i, jcol, (*row)[j].entry, jcol, i, (*row2)[k].entry);
- }
- row2 = NULL;
- break;
- }
- }
- }
- if (!found) {
- non_symmetric = 1;
- MSG("mat[%d,%d] not found\n", jcol, i);
- }
- }
- }
- if (abs(sum) > 1.E-5) {
- MSG("Zeilensumme[%d] = %10.5e\n", i, sum);
- }
- }
+ int non_symmetric = !symmetric();
if (non_symmetric) {
MSG("matrix `%s' not symmetric.\n", name.data());
@@ -219,8 +148,11 @@ namespace AMDiS {
}
+ // ok
DOFMatrix& DOFMatrix::operator=(const DOFMatrix& rhs)
{
+ TEST_EXIT(rhs.inserter == 0 && inserter == 0)("Cannot copy during insertion");
+
rowFESpace = rhs.rowFESpace;
colFESpace = rhs.colFESpace;
operators = rhs.operators;
@@ -249,198 +181,71 @@ namespace AMDiS {
{
FUNCNAME("DOFMatrix::addElementMatrix");
- DegreeOfFreedom row;
+ TEST_EXIT(inserter)("DOFMatrix is not in insertion mode");
+ inserter_type &ins= *inserter;
+
+ DegreeOfFreedom row, col;
+ double entry;
- int nRow = elMat.rowIndices.getSize();
- int nCol = elMat.colIndices.getSize();
+ int n_row = elMat.rowIndices.getSize();
+ int n_col = elMat.colIndices.getSize();
- for (int i = 0; i < nRow; i++) { // for all rows of element matrix
+ for (int i = 0; i < n_row; i++) { // for all rows of element matrix
row = elMat.rowIndices[i];
+
BoundaryCondition *condition =
bound ? boundaryManager->getBoundaryCondition(bound[i]) : NULL;
if (condition && condition->isDirichlet()) {
- applyDBCs.insert(static_cast<int>(row));
- } else {
- for (int j = 0; j < nCol; j++) { // for all columns
- addSparseDOFEntry(sign, row, elMat.colIndices[j],
- elMat[i][j], add);
- }
- }
+ if (!coupleMatrix)
+ ins[row][row]= 1.0;
+ } else
+ for (int j = 0; j < n_col; j++) { // for all columns
+ col = elMat.colIndices[j];
+ entry = elMat[i][j];
+ if (add)
+ ins[row][col]+= sign * entry;
+ else
+ ins[row][col]= sign * entry;
+ }
}
}
double DOFMatrix::logAcc(DegreeOfFreedom a,DegreeOfFreedom b) const
{
- int j;
-
- for (j = 0; j < static_cast<int>(matrix[a].size()); j++)
- if (b == matrix[a][j].col)
- break;
-
- return (j == static_cast<int>(matrix[a].size())) ? 0.0 : matrix[a][j].entry;
- }
-
- void DOFMatrix::changeColOfEntry(DegreeOfFreedom a,
- DegreeOfFreedom b,
- DegreeOfFreedom c)
- {
- int j;
-
- for (j = 0; j<static_cast<int>(matrix[a].size());j++)
- if (b == matrix[a][j].col)
- break;
-
- if (j != static_cast<int>(matrix[a].size()))
- matrix[a][j].col = c;
+ return matrix[a][b];
}
- void DOFMatrix::addSparseDOFEntry(double sign, int irow,
- int jcol, double entry,
- bool add)
- {
- FUNCNAME("DOFMatrix::addSparseDOFEntry()");
-
- MatrixRow *row = &(matrix[irow]);
-
- if (add && !entry)
- return;
-
- int freeCol = -1;
- int rowSize = static_cast<int>(row->size());
-
- TEST_EXIT_DBG(jcol >= 0 &&
- jcol < colFESpace->getAdmin()->getUsedSize())
- ("Column index %d out of range 0-%d\n", jcol, colFESpace->getAdmin()->getUsedSize() - 1);
-
- // first entry is diagonal entry
- if ((rowSize == 0) && (colFESpace == rowFESpace)) {
- MatEntry newEntry = {irow, 0.0};
- row->push_back(newEntry);
- rowSize = 1;
- }
-
- int i;
- // search jcol
- for (i = 0; i < rowSize; i++) {
- // jcol found ?
- if ((*row)[i].col == jcol) {
- break;
- }
- // remember free entry
- if ((*row)[i].col == UNUSED_ENTRY) {
- freeCol = i;
- }
- // no more entries
- if ((*row)[i].col == NO_MORE_ENTRIES) {
- freeCol = i;
- if (rowSize > i+1) {
- (*row)[i + 1].entry = NO_MORE_ENTRIES;
- }
- break;
- }
- }
-
- // jcol found?
- if (i < rowSize) {
- if (!add) {
- (*row)[i].entry = 0.0;
- }
-
- (*row)[i].entry += sign * entry;
- } else {
- if (freeCol == -1) {
- MatEntry newEntry = {jcol, sign * entry};
- row->push_back(newEntry);
- } else {
- (*row)[freeCol].col = jcol;
- if (!add)
- (*row)[freeCol].entry = 0.0;
- (*row)[freeCol].entry += sign * entry;
- }
- }
- }
-
- void DOFMatrix::addMatEntry(int row, MatEntry entry)
+ void DOFMatrix::freeDOFContent(int index)
{
- matrix[row].push_back(entry);
- }
+ using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
+ namespace traits= mtl::traits;
+ typedef base_matrix_type Matrix;
- void DOFMatrix::addMatEntry(int row, DegreeOfFreedom col, double value)
- {
- MatEntry entry;
- entry.col = col;
- entry.entry = value;
- matrix[row].push_back(entry);
- }
+ traits::row<Matrix>::type row(matrix);
+ traits::col<Matrix>::type col(matrix);
- void DOFMatrix::addRow(std::vector<MatEntry> row)
- {
- matrix.push_back(row);
- }
-
- void DOFMatrix::compressDOFIndexed(int first, int last,
- std::vector<DegreeOfFreedom> &newDOF)
- {
- for (int i = first; i <= last; i++) {
- if (newDOF[i] >= 0) {
- matrix[newDOF[i]].swap(matrix[i]);
- matrix[i].resize(0);
- }
- }
- int usedSize = rowFESpace->getAdmin()->getUsedSize();
- for (int i = 0; i < usedSize; i++) {
- std::vector<MatEntry> *row = reinterpret_cast<std::vector<MatEntry>*>(&(matrix[i]));
- int rowSize = static_cast<int>(row->size());
- for (int j = 0; j < rowSize; j++) {
- int col = (*row)[j].col;
- if (entryUsed(i, j))
- (*row)[j].col = newDOF[col];
- }
- }
- }
+ typedef traits::range_generator<major, Matrix>::type cursor_type;
+ typedef traits::range_generator<nz, cursor_type>::type icursor_type;
+
+ cursor_type cursor = begin<major>(matrix);
+ // Jump directly to corresponding row or column
+ cursor+= index;
- void DOFMatrix::freeDOFContent(int index)
- {
- int col = 0;
-
- if (0 < matrix[index].size()) {
- int nRows = matrix.size();
-
- // for all columns in this row
- int size = static_cast<int>(matrix[index].size());
- for (int i = 0; i < size; i++) {
- // if entry is used
- if (entryUsed(index, i)) {
- // get column of this entry
- col = matrix[index][i].col;
- if ((col != index) && (col < nRows)) { // remove symmetric entry if exists
- int colsize = static_cast<int>(matrix[col].size());
- for (int j = 0; j < colsize; j++) {
- int col2 = matrix[col][j].col;
- if (col2 == index) {
- matrix[col][j].col = DOFMatrix::UNUSED_ENTRY;
- } else if (col2 == DOFMatrix::NO_MORE_ENTRIES) {
- break;
- }
- }
- }
- } else if (col == DOFMatrix::NO_MORE_ENTRIES) {
- break;
- }
- }
- matrix[index].resize(0);
+ // Requires structural symmetry !!!
+ for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); icursor != icend; ++icursor) {
+ int my_row= row(*icursor), my_col= col(*icursor);
+ // Not very efficient (but general)
+ matrix.lvalue(my_row, my_col) = 0.0; // Need to call crop somewhere !!!! Peter
+ matrix.lvalue(my_col, my_row) = 0.0;
}
}
-
+ // Should work as before
void DOFMatrix::assemble(double factor, ElInfo *elInfo, const BoundaryType *bound)
{
FUNCNAME("DOFMatrix::assemble()");
- if (operators.size() == 0)
- return;
-
operators[0]->getAssembler(omp_get_thread_num())->
initElementMatrix(elementMatrix, elInfo);
@@ -476,7 +281,7 @@ namespace AMDiS {
{
FUNCNAME("DOFMatrix::assemble()");
- if (!op && operators.size() == 0) {
+ if(!op && operators.size() == 0) {
return;
}
@@ -516,7 +321,7 @@ namespace AMDiS {
operat->getAssembler(omp_get_thread_num())->
initElementMatrix(elementMatrix, mainElInfo);
- if (op) {
+ if(op) {
ERROR_EXIT("TODO");
// op->getElementMatrix(rowElInfo, colElInfo,
// smallElInfo, largeElInfo,
@@ -524,7 +329,7 @@ namespace AMDiS {
} else {
std::vector<Operator*>::iterator it;
std::vector<double*>::iterator factorIt;
- for (it = operators.begin(), factorIt = operatorFactor.begin();
+ for(it = operators.begin(), factorIt = operatorFactor.begin();
it != operators.end();
++it, ++factorIt) {
if ((*it)->getNeedDualTraverse()) {
@@ -549,6 +354,7 @@ namespace AMDiS {
}
}
+ // Should work as before
Flag DOFMatrix::getAssembleFlag()
{
Flag fillFlag(0);
@@ -560,133 +366,26 @@ namespace AMDiS {
return fillFlag;
}
- void DOFMatrix::mm(MatrixTranspose aTranspose,
- DOFMatrix& a,
- MatrixTranspose bTranspose,
- DOFMatrix& b)
- {
- FUNCNAME("DOFMatrix::mm()");
-
- WARNING("implementation not finished!!!\n");
-
- TEST_EXIT_DBG(a.getColFESpace() == b.getRowFESpace())
- ("a.colFESpace != b.rowFESpace\n");
- TEST_EXIT_DBG(rowFESpace == a.getRowFESpace())
- ("rowFESpace != a.rowFESpace\n");
- TEST_EXIT_DBG(colFESpace == b.getColFESpace())
- ("colFESpace != b.colFESpace\n");
-
- clear();
-
- int i, j;
-
- if (aTranspose == NoTranspose && bTranspose == NoTranspose) {
- int cols = b.getColFESpace()->getAdmin()->getUsedSize();
- DOFMatrix::Iterator rowIterator(this, USED_DOFS);
-
- // for every row ...
- for(rowIterator.reset(); !rowIterator.end(); ++rowIterator) {
- int rowIndex = rowIterator.getDOFIndex();
- // and every column of result
- for(i=0; i < cols; i++) {
- double entry = 0.0;
- // for every entry in a[i] ...
- for(j=0; j < static_cast<int>( a[rowIndex].size()); j++) {
- int logIndex = a[rowIndex][j].col;
- int physIndex = b.logToPhysIndex(logIndex, i);
- if(physIndex != -1) {
- entry += a[rowIndex][j].entry * b[logIndex][physIndex].entry;
- }
- }
- if (entry != 0.0) {
- addSparseDOFEntry(1.0, rowIndex, i, entry);
- }
- }
- }
- } else if(aTranspose == Transpose && bTranspose == NoTranspose) {
- DOFMatrix::Iterator aIterator(&a, USED_DOFS);
- DOFMatrix::Iterator bIterator(&b, USED_DOFS);
- for(aIterator.reset(), bIterator.reset();
- !aIterator.end();
- ++aIterator, ++bIterator)
- {
- std::vector<MatEntry>::const_iterator aRowIt;
- std::vector<MatEntry>::const_iterator bRowIt;
- for(aRowIt = aIterator->begin(); aRowIt != aIterator->end(); ++aRowIt) {
- int aCol = aRowIt->col;
- if(aCol == UNUSED_ENTRY) continue;
- if(aCol == NO_MORE_ENTRIES) break;
- for(bRowIt = bIterator->begin(); bRowIt !=bIterator->end(); ++bRowIt) {
- int bCol = bRowIt->col;
- if(bCol == UNUSED_ENTRY) continue;
- if(bCol == NO_MORE_ENTRIES) break;
-
- double entry = aRowIt->entry * bRowIt->entry;
-
- if (entry != 0.0) {
- addSparseDOFEntry(1.0, aCol, bCol, entry);
- }
- }
- }
- }
- } else if(aTranspose == NoTranspose && bTranspose == Transpose) {
- ERROR_EXIT("not yet\n");
- } else if(aTranspose == Transpose && bTranspose == Transpose) {
- ERROR_EXIT("not yet\n");
- }
- }
-
void DOFMatrix::axpy(double a,
const DOFMatrix& x,
const DOFMatrix& y)
{
- FUNCNAME("DOFMatrix::axpy()");
-
- TEST_EXIT_DBG(x.getRowFESpace() == y.getRowFESpace() &&
- rowFESpace == x.getRowFESpace())
+ FUNCNAME("DOFMatrix::axpy");
+ TEST_EXIT(x.getRowFESpace() == y.getRowFESpace() &&
+ rowFESpace == x.getRowFESpace())
("row fe-spaces not equal\n");
- TEST_EXIT_DBG(x.getColFESpace() == y.getColFESpace() &&
- colFESpace == x.getColFESpace())
+ TEST_EXIT(x.getColFESpace() == y.getColFESpace() &&
+ colFESpace == x.getColFESpace())
("col fe-spaces not equal\n");
-
- DOFMatrix::Iterator rowIterator(this, USED_DOFS);
- DOFMatrix::Iterator xIterator(const_cast<DOFMatrix*>(&x), USED_DOFS);
- DOFMatrix::Iterator yIterator(const_cast<DOFMatrix*>(&y), USED_DOFS);
-
- int i, rowIndex, colIndex;
-
- for(rowIterator.reset(), xIterator.reset(), yIterator.reset();
- !rowIterator.end();
- ++rowIterator, ++xIterator, ++yIterator)
- {
- rowIndex = rowIterator.getDOFIndex();
- // add x contributions to this row
- for(i=0; i < static_cast<int>((*xIterator).size()); i++) {
- colIndex = (*xIterator)[i].col;
- if (colIndex >= 0) {
- addSparseDOFEntry(a, rowIndex, colIndex, (*xIterator)[i].entry);
- }
- }
- // add y contributions to this row
- for(i=0; i < static_cast<int>((*yIterator).size()); i++) {
- colIndex = (*yIterator)[i].col;
- if (colIndex >= 0) {
- addSparseDOFEntry(1.0, rowIndex, colIndex, (*yIterator)[i].entry);
- }
- }
- }
+
+ matrix+= a * x.matrix + y.matrix;
+
}
+
void DOFMatrix::scal(double b)
{
- DOFMatrix::Iterator rowIterator(this, USED_DOFS);
- for (rowIterator.reset(); !rowIterator.end(); ++rowIterator) {
- for (int i = 0; i < static_cast<int>((*rowIterator).size()); i++) {
- if ((*rowIterator)[i].col >= 0) {
- (*rowIterator)[i].entry *= b;
- }
- }
- }
+ matrix*= b;
}
void DOFMatrix::addOperator(Operator *op, double* factor, double* estFactor)
@@ -698,63 +397,33 @@ namespace AMDiS {
void DOFMatrix::copy(const DOFMatrix& rhs)
{
- clear();
- DOFMatrix::Iterator rhsIterator(const_cast<DOFMatrix*>(&rhs), USED_DOFS);
- DOFMatrix::Iterator thisIterator(this, USED_DOFS);
- std::vector<MatEntry>::const_iterator colIt;
- std::vector<MatEntry>::const_iterator colBegin;
- std::vector<MatEntry>::const_iterator colEnd;
- for(rhsIterator.reset(), thisIterator.reset();
- !rhsIterator.end();
- ++rhsIterator, ++thisIterator)
- {
- colBegin = rhsIterator->begin();
- colEnd = rhsIterator->end();
- for(colIt = colBegin; colIt != colEnd; ++colIt) {
- MatEntry matEntry;
- matEntry.col = colIt->col;
- matEntry.entry = colIt->entry;
- thisIterator->push_back(matEntry);
- }
- }
+ matrix= rhs.matrix;
}
void DOFMatrix::removeRowsWithDBC(std::set<int> *rows)
- {
- for (std::set<int>::iterator it = rows->begin();
- it != rows->end();
- ++it) {
- if (coupleMatrix) {
- matrix[*it].resize(0);
- } else {
- matrix[*it].resize(1);
- matrix[*it][0].col = *it;
- matrix[*it][0].entry = 1.0;
- }
- }
+ {
+ ERROR_EXIT("TODO: removeRowsWithDBC");
- rows->clear();
- }
+// for (std::set<int>::iterator it = rows->begin();
+// it != rows->end();
+// ++it) {
+// if (coupleMatrix) {
+// matrix[*it].resize(0);
+// } else {
+// matrix[*it].resize(1);
+// matrix[*it][0].col = *it;
+// matrix[*it][0].entry = 1.0;
+// }
+// }
- int DOFMatrix::getNumCols() const {
- int max = 0;
- int rowSize = static_cast<int>(matrix.size());
- for (int i = 0; i < rowSize; i++) {
- int colSize = static_cast<int>(matrix[i].size());
- for (int j = 0; j < colSize; j++) {
- if (matrix[i][j].col > max) {
- max = matrix[i][j].col;
- }
- }
- }
-
- // Add one to the maximum value, because the indeces start with 0.
- return max + 1;
+// rows->clear();
}
-
void DOFMatrix::createPictureFile(const char* filename, int dim)
{
+ TEST_EXIT(0)("Not yet re-implemented.");
+
+#if 0
png_structp png_ptr = png_create_write_struct(PNG_LIBPNG_VER_STRING,
NULL, NULL, NULL);
@@ -811,139 +480,14 @@ namespace AMDiS {
png_destroy_write_struct(&png_ptr, &info_ptr);
fclose(fp);
+#endif
}
int DOFMatrix::memsize()
{
- int sizeDOFMatrix = sizeof(DOFMatrix);
- int sizeMatrix = sizeof(std::vector<MatrixRow>);
- for (int i = 0; i < static_cast<int>(matrix.size()); i++) {
- sizeMatrix += sizeof(MatrixRow) + matrix[i].size() * sizeof(MatEntry);
- }
-
- return sizeDOFMatrix + sizeMatrix;
- }
-
-
- double norm(std::vector<MatEntry> *row)
- {
- double result = 0.0;
- std::vector<MatEntry>::iterator it;
- for (it = row->begin(); it < row->end(); ++it) {
- result += (*it).entry * (*it).entry;
- }
-
- return(sqrt(result));
- }
-
- double min(std::vector<MatEntry> *row)
- {
- double result = 0.0;
- if (row->size() > 0) {
- result = (*row)[0].entry;
- }
-
- std::vector<MatEntry>::iterator it;
- for (it = row->begin(); it < row->end(); ++it) {
- if ((*it).entry < result) {
- result = (*it).entry;
- }
- }
-
- return(result);
+ return (num_rows(matrix) + matrix.nnz()) * sizeof(base_matrix_type::size_type)
+ + matrix.nnz() * sizeof(base_matrix_type::value_type);
}
- double max(std::vector<MatEntry> *row)
- {
- double result = 0.0;
- if (row->size() > 0) {
- result = (*row)[0].entry;
- }
-
- std::vector<MatEntry>::iterator it;
- for (it = row->begin(); it < row->end(); ++it) {
- if ((*it).entry > result) {
- result = (*it).entry;
- }
- }
-
- return(result);
- }
-
- void addDOFMatrix(DOFMatrix *result, const DOFMatrix *a, const DOFMatrix *b)
- {
- result->clear();
-
- DOFMatrix::Iterator resultIterator(result, USED_DOFS);
- DOFMatrix::Iterator aIterator(const_cast<DOFMatrix*>(a), USED_DOFS);
- DOFMatrix::Iterator bIterator(const_cast<DOFMatrix*>(b), USED_DOFS);
-
- for (resultIterator.reset(), aIterator.reset();
- !aIterator.end();
- ++resultIterator, ++aIterator) {
-
- *resultIterator = *aIterator;
- }
-
- for (resultIterator.reset(), bIterator.reset();
- !bIterator.end();
- ++resultIterator, ++bIterator) {
- std::vector<MatEntry>::iterator resultRowIt;
- std::vector<MatEntry>::const_iterator bRowIt;
-
- for (bRowIt = bIterator->begin();
- bRowIt != bIterator->end();
- ++bRowIt) {
- bool added = false;
- for (resultRowIt = resultIterator->begin();
- resultRowIt != resultIterator->end();
- ++resultRowIt) {
- if (bRowIt->col == resultRowIt->col) {
- resultRowIt->entry += bRowIt->entry;
-
- added = true;
- break;
- }
- }
-
- if (!added) {
- resultIterator->push_back(*bRowIt);
- }
- }
- }
- }
-
- void addDOFMatrix(DOFMatrix *result, const DOFMatrix *a)
- {
- DOFMatrix::Iterator resultIterator(result, USED_DOFS);
- DOFMatrix::Iterator aIterator(const_cast<DOFMatrix*>(a), USED_DOFS);
-
- for (resultIterator.reset(), aIterator.reset();
- !aIterator.end();
- ++resultIterator, ++aIterator) {
- std::vector<MatEntry>::iterator resultRowIt;
- std::vector<MatEntry>::const_iterator aRowIt;
-
- for (aRowIt = aIterator->begin();
- aRowIt != aIterator->end();
- ++aRowIt) {
- bool added = false;
- for (resultRowIt = resultIterator->begin();
- resultRowIt != resultIterator->end();
- ++resultRowIt) {
- if (aRowIt->col == resultRowIt->col) {
- resultRowIt->entry += aRowIt->entry;
-
- added = true;
- break;
- }
- }
-
- if (!added) {
- resultIterator->push_back(*aRowIt);
- }
- }
- }
- }
}
diff --git a/AMDiS/src/DOFMatrix.h b/AMDiS/src/DOFMatrix.h
index 49d5ea3c..5321efc2 100644
--- a/AMDiS/src/DOFMatrix.h
+++ b/AMDiS/src/DOFMatrix.h
@@ -30,7 +30,9 @@
#include <set>
#include <memory>
#include <list>
+#include <boost/numeric/mtl/mtl.hpp>
+#include "AMDiS_fwd.h"
#include "Global.h"
#include "Flag.h"
#include "RCNeighbourList.h"
@@ -47,20 +49,6 @@
namespace AMDiS {
- // ============================================================================
- // ===== forward declarations =================================================
- // ============================================================================
-
- class Mesh;
- class FiniteElemSpace;
- class ElInfo;
- class BasisFunction;
- class FillInfo;
- class Operator;
- class ElementMatrix;
- class BoundaryManager;
-
- template<typename T> class DOFVector;
// ===========================================================================
// ===== struct MatEntry =====================================================
@@ -168,16 +156,25 @@ namespace AMDiS {
/** \ingroup DOFAdministration
* \brief
* A DOFMatrix is a sparse matrix representation for matrices that work
- * on DOFVectors. Every row of a matrix is realized as a vector of MatEntry
- * objects. Each entry consists of a column DOF index and the corresponding
- * double matrix entry. Unused entries are marked with a negative column index.
+ * on DOFVectors. The underlying matrix type
+ * is a CRS matrix of double.
*/
- class DOFMatrix : public DOFIndexed< std::vector<MatEntry> >,
+ class DOFMatrix : public DOFIndexed<bool>,
public Serializable
{
public:
MEMORY_MANAGED(DOFMatrix);
+ /// Type of scalars in the underlying matrix
+ typedef double value_type;
+
+ /// Type of underlying matrix
+ typedef mtl::compressed2D<value_type> base_matrix_type;
+
+ /// Type of inserter for the base matrix;
+ typedef mtl::matrix::inserter<base_matrix_type> inserter_type;
+
+ private:
/** \ingroup DOFAdministration
* \brief
* Alias for DOFIterator< std::vector<MatEntry<T> > >. So one can access an
@@ -237,45 +234,38 @@ namespace AMDiS {
void copy(const DOFMatrix& rhs);
- /** \brief
- * Returns an iterator to the begin of matrix rows (\ref matrix.begin())
- */
- std::vector< std::vector<MatEntry> >::iterator begin() {
- return matrix.begin();
+ /// Access underlying matrix directly
+ base_matrix_type& getBaseMatrix()
+ {
+ return matrix;
}
- /** \brief
- * Returns an iterator to the end of matrix rows (\ref matrix.end())
- */
- std::vector< std::vector<MatEntry> >::iterator end() {
- return matrix.end();
+ /// Access underlying matrix directly (const)
+ const base_matrix_type& getBaseMatrix() const
+ {
+ return matrix;
}
+
+ // Only to get rid of the abstract functions, I hope they are not used
+ std::vector<bool>::iterator begin() {ERROR_EXIT("Shouldn't be used, only fake."); std::vector<bool> v; return v.begin();}
+ std::vector<bool>::iterator end() {ERROR_EXIT("Shouldn't be used, only fake."); std::vector<bool> v; return v.end();}
+#if 1
+
+ bool dummy; // Must be deleted later
+ bool& operator[](int i) {ERROR_EXIT("Shouldn't be used, only fake."); return dummy;}
+ const bool& operator[](int i) const {ERROR_EXIT("Shouldn't be used, only fake."); return dummy;}
+#endif
/** \brief
- * Used by DOFAdmin to compress the DOFMatrix
+ * DOFMatrix does not need to be compressed before assembling, when using MTL4.
*/
- virtual void compressDOFIndexed(int first, int last,
- std::vector<DegreeOfFreedom> &newDOF);
+ void compressDOFIndexed(int first, int last, std::vector<DegreeOfFreedom> &newDOF) {}
/** \brief
* Implements DOFIndexedBase::freeDOFContent()
*/
virtual void freeDOFContent(int index);
- /** \brief
- * Returns whether entry matrix[a][b] is used
- */
- inline bool entryUsed(DegreeOfFreedom a, int b) const {
- return (((matrix[a])[b]).col >= 0);
- }
-
- /** \brief
- * Returns true if matrix[a][b] has entry \ref NO_MORE_ENTRIES
- */
- inline bool noMoreEntries(DegreeOfFreedom a, int b) const {
- return (NO_MORE_ENTRIES == ((matrix[a])[b]).col);
- }
-
/** \brief
* Returns \ref coupleMatrix.
*/
@@ -290,13 +280,7 @@ namespace AMDiS {
coupleMatrix = c;
}
- /** \brief
- * Matrix-matrix multiplication.
- */
- void mm(MatrixTranspose aTranspose, DOFMatrix& a,
- MatrixTranspose bTranspose, DOFMatrix& b);
-
- /** \brief
+ /** \brief
* a*x + y
*/
void axpy(double a, const DOFMatrix& x, const DOFMatrix& y);
@@ -392,24 +376,30 @@ namespace AMDiS {
*/
void finishAssembling();
- /// Returns \ref matrix
- std::vector< std::vector<MatEntry> >& getMatrix() {
- return matrix;
- }
-
- ///
- void setMatrix(std::vector< std::vector<MatEntry> > m) {
- matrix = m;
- }
+ /** \brief
+ * Enable insertion for assembly. You can optionally give an upper limit for
+ * entries per row (per column for CCS matrices). Choosing this parameter
+ * too small can induce perceivable overhead for compressed matrices. Thus,
+ * it's better to choose a bit too large than too small.
+ */
+ void startInsertion(int nnz_per_row= 10)
+ {
+ if (inserter)
+ delete inserter, inserter= 0;
- /// Returns \ref matrix[n]
- const std::vector<MatEntry>& getRow(int n) const {
- return matrix[n];
+ inserter= new inserter_type(matrix, nnz_per_row);
}
- /// Returns \ref matrix[n]
- std::vector<MatEntry>& getRow(int n) {
- return matrix[n];
+ /** \brief
+ * Finishes insertion. For compressed matrix types, this is where the
+ * compression happens.
+ */
+ void finishInsertion()
+ {
+ TEST_EXIT(inserter)("Inserter wasn't used or is already finished.");
+
+ delete inserter;
+ inserter= 0;
}
/** \brief
@@ -437,7 +427,7 @@ namespace AMDiS {
/// Returns number of rows (\ref matrix.size())
inline int getSize() const {
- return matrix.size();
+ return num_rows(matrix);
}
/** \brief
@@ -448,6 +438,8 @@ namespace AMDiS {
return rowFESpace->getAdmin()->getUsedSize();
}
+
+ // Only fake, shouldn't be called
/** \brief
* Returns number of cols. For that, the function iteratos over all
* rows and searchs for the entry with the highest col number.
@@ -461,45 +453,9 @@ namespace AMDiS {
/// Resizes \ref matrix to n rows
inline void resize(int n) {
- TEST_EXIT_DBG(n >= 0)("Can't resize DOFMatrix to negative size\n");
- matrix.resize(n);
- }
-
- /// Returns \ref matrix[i] which is the i-th row
- inline const std::vector<MatEntry>& operator[](int i) const {
- TEST_EXIT_DBG((i >= 0) && (i < (static_cast<int>(matrix.size()))))
- ("Illegal matrix index %d.\n",i);
- return matrix[i];
- }
-
- /// Returns \ref matrix[i] which is the i-th row
- inline std::vector<MatEntry>& operator[](int i) {
- TEST_EXIT_DBG((i >= 0) && (i < (static_cast<int>(matrix.size()))))
- ("Illegal vector index %d.\n", i);
- return matrix[i];
- }
-
- /// Access to \ref matrix[a][b].entry
- inline double physAcc(DegreeOfFreedom a, DegreeOfFreedom b) const {
- return matrix[a][b].entry;
- }
-
- /// Access to \ref matrix[a][b].col
- inline DegreeOfFreedom physToLogIndex(DegreeOfFreedom a,
- DegreeOfFreedom b) const
- {
- return matrix[a][b].col;
- }
-
- /// Returns physical column index of logical index b in row a
- inline DegreeOfFreedom logToPhysIndex(DegreeOfFreedom a, DegreeOfFreedom b) const
- {
- int size = static_cast<int>(matrix[a].size());
- for (int j = 0; j < size; j++)
- if (b == matrix[a][j].col)
- return j;
-
- return -1;
+ TEST_EXIT_DBG(n >= 0)("Can't resize DOFMatrix to negative size\n");
+ // matrix.change_dim(n, n);
+ //WARNING("Obsolete function without effect -- Peter\n");
}
/// Returns value at logical indices a,b
@@ -508,14 +464,6 @@ namespace AMDiS {
/// Changes col at logical indices a,b to c
void changeColOfEntry(DegreeOfFreedom a, DegreeOfFreedom b, DegreeOfFreedom c);
- /// Changes col of \ref matrix[a][b] to c
- inline void changePhysColOfEntry(DegreeOfFreedom a,
- DegreeOfFreedom b,
- DegreeOfFreedom c)
- {
- matrix[a][b].col = c;
- }
-
/** \brief
* Creates an entry with logical indices irow, icol if there is no entry
* yet. Than sign * entry is added to the value at this logical indices
@@ -524,18 +472,6 @@ namespace AMDiS {
int irow, int jcol, double entry,
bool add = true);
- inline double *hasSparseDOFEntry(int irow, int jcol) {
- std::vector<MatEntry>::iterator it;
- std::vector<MatEntry>::iterator end = matrix[irow].end();
- for (it = matrix[irow].begin(); it != end; ++it) {
- if (it->col == NO_MORE_ENTRIES)
- return NULL;
- if (it->col == jcol)
- return &(it->entry);
- }
- return NULL;
- }
-
void addMatEntry(int row, MatEntry entry);
void addMatEntry(int row, int DegreeOfFreedom, double value);
@@ -547,11 +483,11 @@ namespace AMDiS {
/// Prints \ref matrix to stdout
void print() const;
- /// Prints a row of \ref matrix to stdout
- void printRow(int i) const;
-
/// Removes all matrix entries
- void clear();
+ void clear()
+ {
+ set_to_zero(matrix);
+ }
/// Test whether \ref matrix is symmetric. Exits if not.
void test();
@@ -584,28 +520,77 @@ namespace AMDiS {
void createPictureFile(const char* filename, int dim);
- void serialize(std::ostream &out)
+ private:
+ template <typename T>
+ void s_write(::std::ostream &out, const T& value)
{
- unsigned int matrixSize = matrix.size();
- unsigned int vecSize = 0;
-
- out.write(reinterpret_cast<const char*>(&matrixSize), sizeof(unsigned int));
- for(unsigned int i = 0; i < matrixSize; i++) {
- vecSize = matrix[i].size();
- out.write(reinterpret_cast<const char*>(&vecSize), sizeof(unsigned int));
- out.write(reinterpret_cast<const char*>(&(matrix[i][0])), vecSize * sizeof(MatEntry));
- }
+ out.write(reinterpret_cast<const char*>(&value), sizeof value);
+ }
+
+ public:
+ void serialize(::std::ostream &out)
+ {
+ using namespace mtl;
+
+ typedef traits::range_generator<tag::major, base_matrix_type>::type c_type;
+ typedef traits::range_generator<tag::nz, c_type>::type ic_type;
+
+ typedef Collection<base_matrix_type>::size_type size_type;
+ typedef Collection<base_matrix_type>::value_type value_type;
+
+ traits::row<base_matrix_type>::type row(matrix);
+ traits::col<base_matrix_type>::type col(matrix);
+ traits::const_value<base_matrix_type>::type value(matrix);
+
+ size_type rows= num_rows(matrix), cols= num_cols(matrix), total= matrix.nnz();
+ s_write(out, rows);
+ s_write(out, cols);
+ s_write(out, total);
+
+ for (c_type cursor(mtl::begin<tag::major>(matrix)), cend(mtl::end<tag::major>(matrix));
+ cursor != cend; ++cursor)
+ for (ic_type icursor(mtl::begin<tag::nz>(cursor)), icend(mtl::end<tag::nz>(cursor));
+ icursor != icend; ++icursor) {
+ size_type my_row= row(*icursor), my_col= col(*icursor);
+ value_type my_value= value(*icursor);
+ s_write(out, my_row);
+ s_write(out, my_col);
+ s_write(out, my_value);
+ }
}
- void deserialize(std::istream &in) {
- unsigned int matrixSize, vecSize;
+ private:
+ template <typename T>
+ void s_read(::std::istream &in, T& value)
+ {
+ in.read(reinterpret_cast<char*>(&value), sizeof value);
+ }
- in.read(reinterpret_cast<char*>(&matrixSize), sizeof(unsigned int));
- matrix.resize(matrixSize);
- for(unsigned int i = 0; i < matrixSize; i++) {
- in.read(reinterpret_cast<char*>(&vecSize), sizeof(unsigned int));
- matrix[i].resize(vecSize);
- in.read(reinterpret_cast<char*>(&(matrix[i][0])), vecSize * sizeof(MatEntry));
+ public:
+ void deserialize(::std::istream &in)
+ {
+ using namespace mtl;
+
+ typedef Collection<base_matrix_type>::size_type size_type;
+ typedef Collection<base_matrix_type>::value_type value_type;
+
+ size_type rows, cols, total;
+ s_read(in, rows);
+ s_read(in, cols);
+ s_read(in, total);
+
+ // Prepare matrix insertion
+ clear();
+ // matrix.change_dim(rows, cols) // do we want this?
+ inserter_type ins(matrix);
+
+ for (size_type i= 0; i < total; ++i) {
+ size_type my_row, my_col;
+ value_type my_value;
+ s_read(in, my_row);
+ s_read(in, my_col);
+ s_read(in, my_value);
+ ins(my_row, my_col) << my_value;
}
}
@@ -635,8 +620,8 @@ namespace AMDiS {
/// Name of the DOFMatrix
std::string name;
- /// Sparse matrix stored in an STL vector of MatrixRow objects
- std::vector<MatrixRow> matrix;
+ /// Sparse matrix, type is a template parameter by default compressed2D<double>
+ base_matrix_type matrix;
/// Used while mesh traversal
static DOFMatrix *traversePtr;
@@ -673,6 +658,9 @@ namespace AMDiS {
AO *applicationOrdering;
#endif
+ /// Inserter object: implemented as pointer, allocated and deallocated as needed
+ inserter_type *inserter;
+
friend class DOFAdmin;
friend class DOFVector<double>;
friend class DOFVector<unsigned char>;
@@ -680,24 +668,6 @@ namespace AMDiS {
friend class DOFVector<WorldVector<double> >;
};
-
- inline DegreeOfFreedom logToPhysIndex(DOFMatrix *m,
- DegreeOfFreedom a, DegreeOfFreedom b)
- {
- return m->logToPhysIndex(a, b);
- }
-
- double norm(std::vector<MatEntry> *row);
-
- double min(std::vector<MatEntry> *row);
-
- double max(std::vector<MatEntry> *row);
-
- /// Addes two matrices. The result matrix is overwritten.
- void addDOFMatrix(DOFMatrix *result, const DOFMatrix *a, const DOFMatrix *b);
-
- /// Addes matrix a to matrix result.
- void addDOFMatrix(DOFMatrix *result, const DOFMatrix *a);
}
#endif // AMDIS_DOFMATRIX_H
diff --git a/AMDiS/src/DOFVector.cc b/AMDiS/src/DOFVector.cc
index d6742ffe..51be6625 100644
--- a/AMDiS/src/DOFVector.cc
+++ b/AMDiS/src/DOFVector.cc
@@ -605,7 +605,7 @@ namespace AMDiS {
for (int i = 0; i < numBasFcts; i++) {
if (vec[myLocalIndices[i]] == nul) {
coords = basFcts->getCoords(i);
- vec[myLocalIndices[i]] += vBasFcts->evalUh(*coords, vLocalCoeffs,NULL) * factor;
+ vec[myLocalIndices[i]] += vBasFcts->evalUh(*coords, vLocalCoeffs, NULL) * factor;
}
}
elInfo = stack.traverseNext(elInfo);
diff --git a/AMDiS/src/DOFVector.h b/AMDiS/src/DOFVector.h
index ebd581b0..f56e7889 100644
--- a/AMDiS/src/DOFVector.h
+++ b/AMDiS/src/DOFVector.h
@@ -30,6 +30,7 @@
#include <memory>
#include <list>
+#include "AMDiS_fwd.h"
#include "FixVec.h"
#include "Global.h"
#include "Flag.h"
@@ -54,23 +55,6 @@ namespace AMDiS {
// ===== forward declarations ================================================
// ===========================================================================
- class Mesh;
- class FiniteElemSpace;
- class ElInfo;
- class DOFAdmin;
- class BasisFunction;
- class FillInfo;
- class Quadrature;
- class FastQuadrature;
- class DOFMatrix;
- class MultiGridSortSolver;
- class Operator;
- class ElementVector;
- class BoundaryManager;
-
- template<typename ResultType, typename ArgumentType> class AbstractFunction;
-
-
template<typename T>
class DOFVectorBase : public DOFIndexed<T>
{
@@ -345,6 +329,7 @@ namespace AMDiS {
*/
DOFVector()
: DOFVectorBase<T>(),
+ //elementVector(NULL),
feSpace(NULL),
coarsenOperation(NO_OPERATION)
{}
@@ -395,7 +380,6 @@ namespace AMDiS {
*/
virtual void compressDOFIndexed(int first, int last,
std::vector<DegreeOfFreedom> &newDof);
-
/** \brief
* Sets \ref coarsenOperation to op
*/
@@ -469,10 +453,6 @@ namespace AMDiS {
return vec[i];
}
- inline int getSize() {
- return vec.size();
- }
-
/** \brief
* Returns \ref vec[i]
*/
@@ -594,7 +574,7 @@ namespace AMDiS {
/// Used by interpol while mesh traversal
static int interpolFct(ElInfo* elinfo);
-
+
/// Prints \ref vec to stdout
void print() const;
@@ -626,9 +606,7 @@ namespace AMDiS {
WorldVector<DOFVector<T>*> *getGradient(WorldVector<DOFVector<T>*> *grad) const;
- DOFVector<WorldVector<T> >*
-
- getRecoveryGradient(DOFVector<WorldVector<T> >*) const;
+ DOFVector<WorldVector<T> >* getRecoveryGradient(DOFVector<WorldVector<T> >*) const;
#ifdef HAVE_PARALLEL_AMDIS
/// Sets the petsc application ordering object to map dof indices.
@@ -748,6 +726,10 @@ namespace AMDiS {
return DOFVector<DegreeOfFreedom>::operator[](i);
}
+ const DegreeOfFreedom& operator[](DegreeOfFreedom i) const {
+ return DOFVector<DegreeOfFreedom>::operator[](i);
+ }
+
/// Implements DOFIndexedBase::getSize()
int getSize() const {
return DOFVector<DegreeOfFreedom>::getSize();
diff --git a/AMDiS/src/DOFVector.hh b/AMDiS/src/DOFVector.hh
index d476dd76..233c6769 100644
--- a/AMDiS/src/DOFVector.hh
+++ b/AMDiS/src/DOFVector.hh
@@ -20,12 +20,60 @@
#include "Parameters.h"
#include "Traverse.h"
+#include <boost/numeric/mtl/mtl.hpp>
+#include <boost/numeric/mtl/utility/tag.hpp>
+#include <boost/numeric/mtl/utility/category.hpp>
+#include <boost/numeric/linear_algebra/identity.hpp>
+
+
+// Defining the interface for MTL4
+namespace mtl {
+
+ // Let MTL4 know that DOFVector it is a column vector
+ namespace traits {
+ template <typename T>
+ struct category< AMDiS::DOFVector<T> >
+ {
+ typedef tag::dense_col_vector type;
+ };
+ }
+
+ namespace ashape {
+ template <typename T>
+ struct ashape< AMDiS::DOFVector<T> >
+ {
+ typedef cvec<typename ashape<T>::type> type;
+ };
+ }
+
+ // Modelling Collection and MutableCollection
+ template <typename T>
+ struct Collection< AMDiS::DOFVector<T> >
+ {
+ typedef T value_type;
+ typedef const T& const_reference;
+ typedef std::size_t size_type;
+ };
+
+ template <typename T>
+ struct MutableCollection< AMDiS::DOFVector<T> >
+ : public Collection< AMDiS::DOFVector<T> >
+ {
+ typedef T& reference;
+ };
+
+
+} // namespace mtl
+
+
+
namespace AMDiS {
template<typename T>
DOFVectorBase<T>::DOFVectorBase(const FiniteElemSpace *f, std::string n)
: feSpace(f),
name(n),
+ elementVector(NULL),
boundaryManager(NULL)
{
nBasFcts = feSpace->getBasisFcts()->getNumber();
@@ -63,6 +111,7 @@ namespace AMDiS {
template<typename T>
DOFVector<T>::DOFVector(const FiniteElemSpace* f, std::string n)
: DOFVectorBase<T>(f, n),
+ //elementVector(NULL),
coarsenOperation(NO_OPERATION)
{
init(f, n);
@@ -77,7 +126,7 @@ namespace AMDiS {
{
name = n;
feSpace = f;
- if (feSpace && feSpace->getAdmin()) {
+ if(feSpace && feSpace->getAdmin()) {
(feSpace->getAdmin())->addDOFIndexed(this);
}
this->boundaryManager = NEW BoundaryManager(f);
@@ -86,7 +135,7 @@ namespace AMDiS {
template<typename T>
DOFVector<T>::~DOFVector()
{
- if (feSpace && feSpace->getAdmin()) {
+ if(feSpace && feSpace->getAdmin()) {
(feSpace->getAdmin())->removeDOFIndexed(this);
}
@@ -348,7 +397,21 @@ namespace AMDiS {
a.getSize(), a.getRowFESpace()->getAdmin()->getUsedSize());
}
- ysize = y.getSize();
+ // Create MTL vector as wrapper of y
+ mtl::vector::dense_vector<double> yy(y.getSize(), &y[0]);
+ DOFMatrix::base_matrix_type& A= a.getBaseMatrix();
+
+ if (transpose == NoTranspose)
+ yy= alpha*A*x + beta*yy;
+ else if (transpose == Transpose)
+ yy= alpha*trans(A)*x + beta*yy;
+ else
+ ERROR_EXIT("transpose=%d\n", transpose);
+
+
+#if 0
+
+ //ysize = y.getSize();
typename DOFVector<T>::Iterator vecIterator(dynamic_cast<DOFIndexed<T>*>(&y), FREE_DOFS);
for (vecIterator.reset(); !vecIterator.end(); ++vecIterator) {
@@ -402,6 +465,8 @@ namespace AMDiS {
else {
ERROR_EXIT("transpose=%d\n", transpose);
}
+#endif
+
}
template<typename T>
@@ -481,7 +546,7 @@ namespace AMDiS {
template<typename T>
void DOFVector<T>::interpol(AbstractFunction<T, WorldVector<double> > *fct)
{
- FUNCNAME("DOFVector<T>::interpol()");
+ FUNCNAME("interpol");
TEST_EXIT_DBG(fct)("no function to interpolate\n");
@@ -871,22 +936,26 @@ namespace AMDiS {
T operator*(DOFVector<T>& x, DOFVector<T>& y)
{
FUNCNAME("DOFVector<T>::operator*(DOFVector<T>& x, DOFVector<T>& y)");
+ T dot;
+ const DOFAdmin *admin = NULL;
- TEST_EXIT_DBG(x.getFESpace() && y.getFESpace())
+ TEST_EXIT(x.getFESpace() && y.getFESpace())
("feSpace is NULL: %8X, %8X\n", x.getFESpace(), y.getFESpace());
- TEST_EXIT_DBG(x.getFESpace()->getAdmin() &&
- (x.getFESpace()->getAdmin() == y.getFESpace()->getAdmin()))
+ TEST_EXIT((admin = x.getFESpace()->getAdmin()) && (admin == y.getFESpace()->getAdmin()))
("no admin or different admins: %8X, %8X\n",
x.getFESpace()->getAdmin(), y.getFESpace()->getAdmin());
- TEST_EXIT_DBG(x.getSize() == y.getSize())("different sizes\n");
+ TEST_EXIT(x.getSize() == y.getSize())("different sizes\n");
+
+ dot = 0;
- T dot = 0;
typename DOFVector<T>::Iterator xIterator(dynamic_cast<DOFIndexed<T>*>(&x), USED_DOFS);
typename DOFVector<T>::Iterator yIterator(dynamic_cast<DOFIndexed<T>*>(&y), USED_DOFS);
- for (xIterator.reset(), yIterator.reset(); !xIterator.end();
- ++xIterator, ++yIterator) {
- dot += (*xIterator) * (*yIterator);
- }
+ for (xIterator.reset(), yIterator.reset();
+ !xIterator.end();
+ ++xIterator, ++yIterator)
+ {
+ dot += (*xIterator) * (*yIterator);
+ };
return(dot);
}
@@ -898,94 +967,34 @@ namespace AMDiS {
DOFVector<T> &result,
bool add)
{
+ // Unfortunately needed
+ using namespace mtl;
+
FUNCNAME("DOFVector<T>::mv()");
- TEST_EXIT_DBG(a.getRowFESpace() && a.getColFESpace() && x.getFESpace() && result.getFESpace())
+ TEST_EXIT(a.getRowFESpace() && a.getColFESpace() && x.getFESpace() && result.getFESpace())
("getFESpace() is NULL: %8X, %8X, %8X, %8X\n",
a.getRowFESpace(), a.getColFESpace(), x.getFESpace(), result.getFESpace());
-
- TEST_EXIT_DBG((a.getRowFESpace()->getAdmin() && a.getColFESpace()->getAdmin()) &&
- (((transpose == NoTranspose) &&
- (a.getColFESpace()->getAdmin() == x.getFESpace()->getAdmin()) &&
- (a.getRowFESpace()->getAdmin() == result.getFESpace()->getAdmin())) ||
- ((transpose == Transpose) &&
- (a.getRowFESpace()->getAdmin() == x.getFESpace()->getAdmin()) &&
- (a.getColFESpace()->getAdmin() == result.getFESpace()->getAdmin()))))
+
+ const DOFAdmin *rowAdmin = a.getRowFESpace()->getAdmin();
+ const DOFAdmin *colAdmin = a.getColFESpace()->getAdmin();
+
+ TEST_EXIT((rowAdmin && colAdmin) &&
+ (((transpose == NoTranspose) && (colAdmin == x.getFESpace()->getAdmin()) &&
+ (rowAdmin == result.getFESpace()->getAdmin()))||
+ ((transpose == Transpose) && (rowAdmin == x.getFESpace()->getAdmin()) &&
+ (colAdmin == result.getFESpace()->getAdmin()))))
("no admin or different admins: %8X, %8X, %8X, %8X\n",
a.getRowFESpace()->getAdmin(), a.getColFESpace()->getAdmin(),
x.getFESpace()->getAdmin(), result.getFESpace()->getAdmin());
-
- if (transpose == NoTranspose) {
- TEST_EXIT_DBG(static_cast<int>(x.getSize()) >= a.getColFESpace()->getAdmin()->getUsedSize())
- ("x.size = %d too small: admin->sizeUsed = %d\n",
- x.getSize(), a.getColFESpace()->getAdmin()->getUsedSize());
- TEST_EXIT_DBG(static_cast<int>( result.getSize()) >= a.getRowFESpace()->getAdmin()->getUsedSize())
- ("size = %d too small: admin->sizeUsed = %d\n",
- result.getSize(), a.getRowFESpace()->getAdmin()->getUsedSize());
- TEST_EXIT_DBG(static_cast<int>( a.getSize()) >= a.getRowFESpace()->getAdmin()->getUsedSize())
- ("a.size = %d too small: admin->sizeUsed = %d\n",
- a.getSize(), a.getRowFESpace()->getAdmin()->getUsedSize());
-
-
- typename DOFVector<T>::Iterator vecIterator(dynamic_cast<DOFIndexed<T>*>(&result), USED_DOFS);
- DOFMatrix::Iterator rowIterator(const_cast<DOFMatrix*>(&a), USED_DOFS);
- for (vecIterator.reset(), rowIterator.reset(); !rowIterator.end();
- ++rowIterator, ++vecIterator) {
-
- double sum = 0;
- if (!add)
- *vecIterator = 0.0;
- for (std::vector<MatEntry>::iterator colIterator = rowIterator->begin();
- colIterator != rowIterator->end();
- colIterator++) {
-
- int jcol = colIterator->col;
- if (jcol >= 0) { // entry used?
- sum += (static_cast<double>(colIterator->entry)) * x[jcol];
- } else {
- if (jcol == DOFMatrix::NO_MORE_ENTRIES)
- break;
- }
- }
- *vecIterator += sum;
- }
- } else if (transpose == Transpose) {
- TEST_EXIT_DBG(static_cast<int>(x.getSize()) >= a.getRowFESpace()->getAdmin()->getUsedSize())
- ("x.size = %d too small: admin->sizeUsed = %d\n",
- x.getSize(), a.getRowFESpace()->getAdmin()->getUsedSize());
- TEST_EXIT_DBG(static_cast<int>( result.getSize()) >= a.getColFESpace()->getAdmin()->getUsedSize())
- ("size = %d too small: admin->sizeUsed = %d\n",
- result.getSize(), a.getColFESpace()->getAdmin()->getUsedSize());
- TEST_EXIT_DBG(static_cast<int>( a.getSize()) >= a.getRowFESpace()->getAdmin()->getUsedSize())
- ("a.size = %d too small: admin->sizeUsed = %d\n",
- a.getSize(), a.getRowFESpace()->getAdmin()->getUsedSize());
-
- if (!add) {
- typename DOFVector<T>::Iterator vecIterator(dynamic_cast<DOFIndexed<T>*>(&result), USED_DOFS);
- for (vecIterator.reset(); !vecIterator.end(); ++vecIterator) {
- *vecIterator = 0;
- }
- }
- typename DOFVector<T>::Iterator xIterator(const_cast<DOFIndexed<T>*>(dynamic_cast<const DOFIndexed<T>*>(&x)), USED_DOFS);
- DOFMatrix::Iterator rowIterator(const_cast<DOFMatrix*>(&a), USED_DOFS);
- for (xIterator.reset(), rowIterator.reset(); !rowIterator.end();
- ++rowIterator, ++xIterator) {
- T ax = (*xIterator);
- for (std::vector<MatEntry>::iterator colIterator = rowIterator->begin();
- colIterator != rowIterator->end();
- colIterator++) {
- int jcol = colIterator->col;
- if (jcol >= 0) // entry used?
- result[jcol] += (static_cast<double>(colIterator->entry)) * ax;
- else
- if (jcol == DOFMatrix::NO_MORE_ENTRIES) break;
- }
- }
- } else {
+ if (transpose == NoTranspose)
+ mult(a.getBaseMatrix(), x, result);
+ else if (transpose == Transpose)
+ mult(trans(const_cast<DOFMatrix::base_matrix_type&>(a.getBaseMatrix())), x, result);
+ else
ERROR_EXIT("transpose = %d\n", transpose);
- }
}
template<typename T>
@@ -995,26 +1004,43 @@ namespace AMDiS {
{
FUNCNAME("DOFVector<T>::axpy()");
- TEST_EXIT_DBG(x.getFESpace() && y.getFESpace())
+ TEST_EXIT(x.getFESpace() && y.getFESpace())
("feSpace is NULL: %8X, %8X\n", x.getFESpace(), y.getFESpace());
- TEST_EXIT_DBG(x.getFESpace()->getAdmin() &&
- (x.getFESpace()->getAdmin() == y.getFESpace()->getAdmin()))
+ const DOFAdmin *admin = x.getFESpace()->getAdmin();
+
+ TEST_EXIT((admin) && (admin == y.getFESpace()->getAdmin()))
("no admin or different admins: %8X, %8X\n",
x.getFESpace()->getAdmin(), y.getFESpace()->getAdmin());
- TEST_EXIT_DBG(static_cast<int>(x.getSize()) >= x.getFESpace()->getAdmin()->getUsedSize())
+ TEST_EXIT(static_cast<int>(x.getSize()) >= admin->getUsedSize())
("size = %d too small: admin->size = %d\n", x.getSize(),
- x.getFESpace()->getAdmin()->getUsedSize());
- TEST_EXIT_DBG(static_cast<int>(y.getSize()) >= x.getFESpace()->getAdmin()->getUsedSize())
+ admin->getUsedSize());
+ TEST_EXIT(static_cast<int>(y.getSize()) >= admin->getUsedSize())
("y.size = %d too small: admin->size = %d\n", y.getSize(),
- x.getFESpace()->getAdmin()->getUsedSize());
-
- typename DOFVector<T>::Iterator xIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&x)), USED_DOFS);
- typename DOFVector<T>::Iterator yIterator(dynamic_cast<DOFIndexed<T>*>(&y), USED_DOFS);
- for (xIterator.reset(), yIterator.reset(); !xIterator.end();
- ++xIterator, ++yIterator) {
- *yIterator += alpha * (*xIterator);
- }
+ admin->getUsedSize());
+
+ // This is the old implementation of the mv-multiplication. It have been changed
+ // because of the OpenMP-parallelization:
+// typename DOFVector<T>::Iterator xIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&x)), USED_DOFS);
+// typename DOFVector<T>::Iterator yIterator(dynamic_cast<DOFIndexed<T>*>(&y), USED_DOFS);
+// for(xIterator.reset(), yIterator.reset();
+// !xIterator.end();
+// ++xIterator, ++yIterator)
+// {
+// *yIterator += alpha * (*xIterator);
+// };
+
+ int i;
+ int maxI = y.getSize();
+
+#ifdef _OPENMP
+#pragma omp parallel for schedule(dynamic, 25000) default(shared) private(i)
+#endif
+ for (i = 0; i < maxI; i++) {
+ if (!admin->isDOFFree(i)) {
+ y[i] += alpha * x[i];
+ }
+ }
}
template<typename T>
@@ -1046,26 +1072,43 @@ namespace AMDiS {
{
FUNCNAME("DOFVector<T>::xpay()");
- TEST_EXIT_DBG(x.getFESpace() && y.getFESpace())
+ TEST_EXIT(x.getFESpace() && y.getFESpace())
("feSpace is NULL: %8X, %8X\n", x.getFESpace(), y.getFESpace());
- TEST_EXIT_DBG(x.getFESpace()->getAdmin() &&
- (x.getFESpace()->getAdmin() == y.getFESpace()->getAdmin()))
+ const DOFAdmin *admin = x.getFESpace()->getAdmin();
+
+ TEST_EXIT(admin && (admin == y.getFESpace()->getAdmin()))
("no admin or different admins: %8X, %8X\n",
x.getFESpace()->getAdmin(), y.getFESpace()->getAdmin());
- TEST_EXIT_DBG(static_cast<int>(x.getSize()) >= x.getFESpace()->getAdmin()->getUsedSize())
+ TEST_EXIT(static_cast<int>(x.getSize()) >= admin->getUsedSize())
("size = %d too small: admin->size = %d\n", x.getSize(),
- x.getFESpace()->getAdmin()->getUsedSize());
- TEST_EXIT_DBG(static_cast<int>(y.getSize()) >= x.getFESpace()->getAdmin()->getUsedSize())
+ admin->getUsedSize());
+ TEST_EXIT(static_cast<int>(y.getSize()) >= admin->getUsedSize())
("y.size = %d too small: admin->size = %d\n", y.getSize(),
- x.getFESpace()->getAdmin()->getUsedSize());
-
- typename DOFVector<T>::Iterator xIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&x)), USED_DOFS);
- typename DOFVector<T>::Iterator yIterator(dynamic_cast<DOFIndexed<T>*>(&y), USED_DOFS);
- for (xIterator.reset(), yIterator.reset(); !xIterator.end();
- ++xIterator, ++yIterator) {
- *yIterator = alpha *(*yIterator)+ (*xIterator);
- }
+ admin->getUsedSize());
+
+ // This is the old implementation of the mv-multiplication. It have been changed
+ // because of the OpenMP-parallelization:
+ // typename DOFVector<T>::Iterator xIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&x)), USED_DOFS);
+ // typename DOFVector<T>::Iterator yIterator(dynamic_cast<DOFIndexed<T>*>(&y), USED_DOFS);
+ // for(xIterator.reset(), yIterator.reset();
+ // !xIterator.end();
+ // ++xIterator, ++yIterator)
+ // {
+ // *yIterator = alpha *(*yIterator)+ (*xIterator);
+ // };
+
+ int i;
+ int maxI = y.getSize();
+
+#ifdef _OPENMP
+#pragma omp parallel for schedule(dynamic, 25000) default(shared) private(i)
+#endif
+ for (i = 0; i < maxI; i++) {
+ if (!admin->isDOFFree(i)) {
+ y[i] = alpha * y[i] + x[i];
+ }
+ }
}
template<typename T>
@@ -1075,10 +1118,12 @@ namespace AMDiS {
{
typename DOFVector<T>::Iterator vIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&v)), USED_DOFS);
typename DOFVector<T>::Iterator rIterator(dynamic_cast<DOFIndexed<T>*>(&result), USED_DOFS);
- for (vIterator.reset(), rIterator.reset(); !vIterator.end();
- ++vIterator, ++rIterator) {
- *rIterator = scal * (*vIterator);
- }
+ for(vIterator.reset(), rIterator.reset();
+ !vIterator.end();
+ ++vIterator, ++rIterator)
+ {
+ *rIterator = scal * (*vIterator);
+ };
return result;
}
@@ -1090,10 +1135,12 @@ namespace AMDiS {
{
typename DOFVector<T>::Iterator vIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&v)), USED_DOFS);
typename DOFVector<T>::Iterator rIterator(dynamic_cast<DOFIndexed<T>*>(&result), USED_DOFS);
- for (vIterator.reset(), rIterator.reset(); !vIterator.end();
- ++vIterator, ++rIterator) {
- *rIterator = (*vIterator) + scal;
- }
+ for(vIterator.reset(), rIterator.reset();
+ !vIterator.end();
+ ++vIterator, ++rIterator)
+ {
+ *rIterator = (*vIterator) + scal;
+ };
return result;
}
@@ -1105,124 +1152,135 @@ namespace AMDiS {
typename DOFVector<T>::Iterator v1Iterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&v1)), USED_DOFS);
typename DOFVector<T>::Iterator v2Iterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&v2)), USED_DOFS);
typename DOFVector<T>::Iterator rIterator(dynamic_cast<DOFIndexed<T>*>(&result), USED_DOFS);
- for (v1Iterator.reset(), v2Iterator.reset(), rIterator.reset(); !v1Iterator.end();
- ++v1Iterator, ++v2Iterator, ++rIterator) {
- *rIterator = (*v1Iterator) + (*v2Iterator);
- }
+ for(v1Iterator.reset(), v2Iterator.reset(), rIterator.reset();
+ !v1Iterator.end();
+ ++v1Iterator, ++v2Iterator, ++rIterator)
+ {
+ *rIterator = (*v1Iterator) + (*v2Iterator);
+ };
return result;
+
}
template<typename T>
- inline const DOFVector<T>& mod(const DOFVector<T>& v,
- DOFVector<T>& result)
+ const T *DOFVectorBase<T>::getLocalVector(const Element *el, T *d) const
{
- typename DOFVector<T>::Iterator vIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&v)), USED_DOFS);
- typename DOFVector<T>::Iterator rIterator(dynamic_cast<DOFIndexed<T>*>(&result), USED_DOFS);
+ static T* localVec = NULL;
+ const DOFAdmin* admin = feSpace->getAdmin();
- for (vIterator.reset(), rIterator.reset(); !vIterator.end();
- ++vIterator, ++rIterator) {
- *rIterator = fmod((*vIterator), 1.0);
- }
+ int i;
+ int nBasFcts = feSpace->getBasisFcts()->getNumber();
- return result;
- }
+ T *result;
+
+ if(d) {
+ result = d;
+ } else {
+ if(localVec) delete [] localVec;
+ localVec = new T[nBasFcts];
+ result = localVec;
+ }
- template<typename T>
- inline const DOFVector<T>& Tanh(const DOFVector<T>& v,
- DOFVector<T>& result)
- {
- typename DOFVector<T>::Iterator vIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&v)), USED_DOFS);
- typename DOFVector<T>::Iterator rIterator(dynamic_cast<DOFIndexed<T>*>(&result), USED_DOFS);
+ const DegreeOfFreedom *localIndices =
+ feSpace->getBasisFcts()->getLocalIndices(el, admin, NULL);
- double eps;
- GET_PARAMETER(1, "vecphase->epsilon", "%f", &eps);
- for (vIterator.reset(), rIterator.reset();
- !vIterator.end();
- ++vIterator, ++rIterator) {
- *rIterator = 0.5 * (1.0 - tanh(3.0 * (*vIterator) / eps));
+ for(i = 0; i < nBasFcts; i++) {
+ result[i] = (*this)[localIndices[i]];
}
return result;
}
-
template<typename T>
- const T *DOFVectorBase<T>::getVecAtQPs(const ElInfo *elInfo,
- const Quadrature *quad,
+ const T *DOFVectorBase<T>::getVecAtQPs(const ElInfo *elInfo,
+ const Quadrature *quad,
const FastQuadrature *quadFast,
- T *vecAtQPs) const
+ T *vecAtQPs) const
{
FUNCNAME("DOFVector<T>::getVecAtQPs()");
- TEST_EXIT_DBG(quad || quadFast)("neither quad nor quadFast defined\n");
+ TEST_EXIT(quad || quadFast)("neither quad nor quadFast defined\n");
- if (quad && quadFast) {
- TEST_EXIT_DBG(quad == quadFast->getQuadrature())
- ("quad != quadFast->quadrature\n");
+ if(quad && quadFast) {
+ TEST_EXIT(quad == quadFast->getQuadrature())
+ ("quad != quadFast->quadrature\n");
}
- TEST_EXIT_DBG(!quadFast || quadFast->getBasisFunctions() == feSpace->getBasisFcts())
+ TEST_EXIT(!quadFast || quadFast->getBasisFunctions() == feSpace->getBasisFcts())
("invalid basis functions");
+ Element *el = elInfo->getElement();
+
+ const Quadrature *quadrature = quadFast ? quadFast->getQuadrature() : quad;
+
const BasisFunction *basFcts = feSpace->getBasisFcts();
- int nPoints = quadFast ? quadFast->getQuadrature()->getNumPoints() : quad->getNumPoints();
+
+ int numPoints = quadrature->getNumPoints();
+ int nBasFcts = basFcts->getNumber();
+ int i, j;
+
static T *localvec = NULL;
+
T *result;
if (vecAtQPs) {
result = vecAtQPs;
} else {
- if (localvec)
- delete [] localvec;
- localvec = new T[nPoints];
- for (int i = 0; i < nPoints; i++) {
+ if(localvec) delete [] localvec;
+ localvec = new T[numPoints];
+ for(i = 0; i < numPoints; i++) {
localvec[i] = 0.0;
}
result = localvec;
}
-
- T *localVec = localVectors[omp_get_thread_num()];
- getLocalVector(elInfo->getElement(), localVec);
-
- for (int i = 0; i < nPoints; i++) {
- result[i] = 0.0;
- for (int j = 0; j < nBasFcts; j++) {
- result[i] += localVec[j] *
+
+ const T *localVec = getLocalVector(el, NULL);
+
+ for(i = 0; i < numPoints; i++) {
+ for(result[i] = j = 0; j < nBasFcts; j++) {
+ result[i] += localVec[j] *
(quadFast ?
(quadFast->getPhi(i, j)) :
((*(basFcts->getPhi(j)))(quad->getLambda(i))));
}
}
-
+
return const_cast<const T*>(result);
}
- template<typename T>
- const T *DOFVectorBase<T>::getLocalVector(const Element *el, T *d) const
+
+
+
+ // Some free functions used in MTL4
+
+ template <typename T>
+ inline std::size_t size(const AMDiS::DOFVector<T>& v)
{
- static T* localVec = NULL;
- T *result;
- if (d) {
- result = d;
- } else {
- if (localVec)
- delete [] localVec;
- localVec = new T[nBasFcts];
- result = localVec;
- }
-
- DegreeOfFreedom *myLocalIndices = localIndices[omp_get_thread_num()];
- feSpace->getBasisFcts()->getLocalIndices(el, feSpace->getAdmin(),
- myLocalIndices);
+ return v.getSize();
+ }
- for (int i = 0; i < nBasFcts; i++) {
- result[i] = (*this)[myLocalIndices[i]];
- }
-
- return result;
+ template <typename T>
+ inline std::size_t num_rows(const AMDiS::DOFVector<T>& v)
+ {
+ return v.getSize();
+ }
+
+ template <typename T>
+ inline std::size_t num_cols(const AMDiS::DOFVector<T>& v)
+ {
+ return 1;
+ }
+
+
+ template <typename T>
+ inline void set_to_zero(AMDiS::DOFVector<T>& v)
+ {
+ using math::zero;
+ T ref, my_zero(zero(ref));
+
+ std::fill(v.begin(), v.end(), my_zero);
}
- // integral u^2(1-u)^2
template<typename T>
double DOFVector<T>::DoubleWell(Quadrature* q) const
{
diff --git a/AMDiS/src/DataCollector.cc b/AMDiS/src/DataCollector.cc
index b5bb4c6e..c711e9d8 100644
--- a/AMDiS/src/DataCollector.cc
+++ b/AMDiS/src/DataCollector.cc
@@ -17,7 +17,7 @@ namespace AMDiS {
TEST_EXIT(feSpace)("no feSpace\n");
TEST_EXIT(values)("no value Vector\n");
-
+
// === get mesh ===
mesh_ = feSpace->getMesh();
@@ -25,6 +25,7 @@ namespace AMDiS {
localAdmin_ = const_cast<DOFAdmin*>(feSpace->getAdmin());
// === create vertex info vector ===
vertexInfos_ = NEW DOFVector< std::list<VertexInfo> >(feSpace, "vertex infos");
+
interpPointInd_ = NEW DOFVector<int>(feSpace, "interpolation point indices");
interpPointCoords_ = NEW DOFVector< std::list<WorldVector<double> > >(feSpace, "interpolation point coordinates");
dofCoords_ = NEW DOFVector< std::list<WorldVector<double> > >(feSpace, "dof coords");
diff --git a/AMDiS/src/DiagonalPreconditioner.cc b/AMDiS/src/DiagonalPreconditioner.cc
deleted file mode 100644
index 7a260aae..00000000
--- a/AMDiS/src/DiagonalPreconditioner.cc
+++ /dev/null
@@ -1,59 +0,0 @@
-#include "DiagonalPreconditioner.h"
-#include "FiniteElemSpace.h"
-#include "DOFAdmin.h"
-#include "DOFVector.h"
-#include "DOFMatrix.h"
-#include "DOFIterator.h"
-
-namespace AMDiS {
-
- void DiagonalPreconditioner::precon(DOFVector<double>* x)
- {
- FUNCNAME("DiagonalPreconditioner::precon()");
-
- TEST_EXIT_DBG(matrix[row])("no matrix\n");
- TEST_EXIT_DBG(x)("no solution vector\n");
-
- DOFMatrix::Iterator rowIterator((*matrix[row]), USED_DOFS);
- DOFVector<double>::Iterator vecIterator(x, USED_DOFS);
-
- if (bound) {
- ERROR_EXIT("not up to date\n");
- DOFVector<BoundaryType>::Iterator bIterator(const_cast<DOFVector<BoundaryType>*>(bound), USED_DOFS);
- for (vecIterator.reset(), rowIterator.reset(), bIterator.reset();
- !vecIterator.end(); ++vecIterator, ++bIterator, ++rowIterator) {
- // only non-dirichlet nodes will be preconditioned
- if ((*bIterator) <= 0 && rowIterator->size() != 0) {
- (*vecIterator) /= (*rowIterator)[0].entry;
- }
- }
- } else {
- for (vecIterator.reset(), rowIterator.reset();
- !vecIterator.end();
- ++vecIterator, ++rowIterator) {
- if (rowIterator->size() != 0) {
- (*vecIterator) /= (*rowIterator)[0].entry;
- }
- }
- }
- }
-
- void DiagonalPreconditionerStd::precon(std::vector<double>* x)
- {
- FUNCNAME("DiagonalPreconditionerStd::precon()");
-
- TEST_EXIT_DBG(x)("no solution vector\n");
- TEST_EXIT_DBG(x->size() == matrix->size())("solution vector and matrix have different size\n");
-
- std::vector<double>::iterator vecIt;
- std::vector< std::vector<MatEntry> >::iterator matrixIt;
-
- for (vecIt = x->begin(), matrixIt = matrix->begin();
- vecIt < x->end();
- ++vecIt, ++matrixIt) {
- if (matrixIt->size() != 0) {
- (*vecIt) /= (*matrixIt)[0].entry;
- }
- }
- }
-}
diff --git a/AMDiS/src/DiagonalPreconditioner.h b/AMDiS/src/DiagonalPreconditioner.h
deleted file mode 100644
index 77819b73..00000000
--- a/AMDiS/src/DiagonalPreconditioner.h
+++ /dev/null
@@ -1,133 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file DiagonalPreconditioner.h */
-
-#ifndef AMDIS_DIAGONAL_PRECONDITIONER_H
-#define AMDIS_DIAGONAL_PRECONDITIONER_H
-
-#include <vector>
-#include "Preconditioner.h"
-#include "MemoryManager.h"
-#include "CreatorInterface.h"
-
-namespace AMDiS {
-
- template<typename T> class DOFVector;
- template<typename T> class OEMSolver;
-
- // ============================================================================
- // ===== class DiagonalPreconditioner =========================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * diagonal preconditioner. Implements the singleton design pattern to allow
- * only one instance of this class.
- */
- class DiagonalPreconditioner : public PreconditionerScal
- {
- public:
- MEMORY_MANAGED(DiagonalPreconditioner);
-
- /** \brief
- * Creator class used in the PreconditionerMap.
- */
- class Creator : public PreconditionerScalCreator
- {
- public:
- MEMORY_MANAGED(Creator);
-
- /** \brief
- * Creates a DiagonalPreconditioner.
- */
- PreconditionerScal *create() {
- return NEW DiagonalPreconditioner(size, row);
- };
- };
-
- /** \brief
- * Constructor.
- */
- DiagonalPreconditioner(int size = 1, int row = 0)
- : PreconditionerScal(size, row)
- {};
-
- /** \brief
- * Destructor.
- */
- virtual ~DiagonalPreconditioner() {};
-
- /** \brief
- * realisation of Preconditioner::init
- */
- inline void init() {
- FUNCNAME("DiagonalPreconditioner::init");
- TEST_EXIT(matrix[row])("no matrix\n");
- };
-
- /** \brief
- * realisation of Preconditioner::precon
- */
- void precon(DOFVector<double> *x);
-
- /** \brief
- * realisation of Preconditioner::exit
- */
- inline void exit() {};
- };
-
-
- class DiagonalPreconditionerStd : public PreconditionerScalStd
- {
- public:
- MEMORY_MANAGED(DiagonalPreconditionerStd);
-
- /** \brief
- * Constructor.
- */
- DiagonalPreconditionerStd()
- {};
-
- /** \brief
- * Destructor.
- */
- virtual ~DiagonalPreconditionerStd() {};
-
- /** \brief
- * realisation of Preconditioner::init
- */
- inline void init() {};
-
- /** \brief
- * Realisation of Preconditioner::precon
- */
- void precon(std::vector<double>* x);
-
- /** \brief
- * realisation of Preconditioner::exit
- */
- inline void exit() {};
- };
-
-}
-
-#endif // AMDIS_DIAGONAL_PRECONDITIONER_H
diff --git a/AMDiS/src/DirichletBC.cc b/AMDiS/src/DirichletBC.cc
index 705a8829..15652327 100644
--- a/AMDiS/src/DirichletBC.cc
+++ b/AMDiS/src/DirichletBC.cc
@@ -15,7 +15,7 @@ namespace AMDiS {
dofVec(NULL)
{
worldCoords.resize(omp_get_overall_max_threads());
- };
+ }
DirichletBC::DirichletBC(BoundaryType type,
DOFVectorBase<double> *vec)
diff --git a/AMDiS/src/DirichletBC.h b/AMDiS/src/DirichletBC.h
index 5dfee096..d02d07fb 100644
--- a/AMDiS/src/DirichletBC.h
+++ b/AMDiS/src/DirichletBC.h
@@ -84,13 +84,9 @@ namespace AMDiS {
*/
double boundResidual(ElInfo*,
DOFMatrix *,
- const DOFVectorBase<double>*) {
- return 0.0;
- };
+ const DOFVectorBase<double>*) { return 0.0; };
- bool isDirichlet() {
- return true;
- };
+ bool isDirichlet() { return true; };
inline AbstractFunction<double, WorldVector<double> > *getF() {
return f;
diff --git a/AMDiS/src/DualTraverse.h b/AMDiS/src/DualTraverse.h
index 05d7e78d..91a93e55 100644
--- a/AMDiS/src/DualTraverse.h
+++ b/AMDiS/src/DualTraverse.h
@@ -42,7 +42,7 @@ namespace AMDiS {
basisFcts(NULL)
{}
- ~DualTraverse() {}
+ virtual ~DualTraverse() {}
/// Start dual traversal
bool traverseFirst(Mesh *mesh1,
diff --git a/AMDiS/src/Estimator.h b/AMDiS/src/Estimator.h
index 883eb5c9..de271ea1 100755
--- a/AMDiS/src/Estimator.h
+++ b/AMDiS/src/Estimator.h
@@ -26,6 +26,7 @@
#ifndef AMDIS_ESTIMATOR_H
#define AMDIS_ESTIMATOR_H
+#include "AMDiS_fwd.h"
#include "Flag.h"
#include "Global.h"
#include "FixVec.h"
@@ -34,16 +35,6 @@
namespace AMDiS {
- class ElInfo;
- class Quadrature;
- class FastQuadrature;
- class BasisFunction;
-
- class ProblemInstat;
- template<typename T> class DOFVector;
- class RobinBC;
- class DOFMatrix;
-
// ============================================================================
// ===== class Estimator ======================================================
// ============================================================================
diff --git a/AMDiS/src/GMResSolver.h b/AMDiS/src/GMResSolver.h
deleted file mode 100644
index 9a03ed34..00000000
--- a/AMDiS/src/GMResSolver.h
+++ /dev/null
@@ -1,164 +0,0 @@
-// ============================================================================
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file GMResSolver.h */
-
-#ifndef AMDIS_GMRESSOLVER_H
-#define AMDIS_GMRESSOLVER_H
-
-#include <vector>
-#include "OEMSolver.h"
-#include "MemoryManager.h"
-
-namespace AMDiS {
-
- // ============================================================================
- // ===== class GMResSolver ===================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Solves a linear system by the restarted GMRES(m) method (Generalized Minimal
- * Residual) for general nonsymmetric system matrices.
- *
- * The implementation is based on the following book: "Numerik linearer
- * Gleichungssystene", 2. Auflage, Andreas Meister. The algorithm is described
- * on pages 150 and 154 (for the restarted version). The extension to the
- * preconditioned GMRES(m) is based on the description in the book "Iterative
- * Methods for Sparse Linear Systems", second edition, Yousef Saad, on page 268.
- *
- * The orthogonal system is build using the modified Gram Schmidt (MGS) method.
- * The least square problem is solved using Givens transformations.
- *
- */
- template<typename VectorType>
- class GMResSolver : public OEMSolver<VectorType>
- {
- public:
- MEMORY_MANAGED(GMResSolver<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new GMResSolver object.
- */
- OEMSolver<VectorType>* create() {
- return NEW GMResSolver<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- GMResSolver(std::string name);
-
- /** \brief
- * destructor
- */
- ~GMResSolver();
-
- protected:
- /** \brief
- * realisation of OEMSolver::solveSystem
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b, bool reuseMatrix);
-
- /** \brief
- * realisation of OEMSolver::init
- */
- void init();
-
- /** \brief
- * realisation of OEMSolver::exit
- */
- void exit();
-
- /** \brief
- * One run of the GMRES(m) method. Is called from solveSystem().
- */
- int gmres(MatVecMultiplier<VectorType> *mv,
- VectorType *x,
- VectorType *b);
-
- private:
- /** \brief
- * Stores the tolerance boundary for numerical computations.
- */
- double TOL_;
-
- /** \brief
- * The parameter m of GMRES(m), i.e. the number of iterations before a restart of
- * the algorithm is forced.
- */
- int restart_;
-
- /** \brief
- * Stores intermediate results in the orthogonalization step.
- */
- VectorType *w_;
-
-
- VectorType *z_;
-
- VectorType *r_;
-
- /** \brief
- * Pointers to the vectors of the orthogonal system.
- */
- VectorType **v;
-
- /** \brief
- * Stores the gamma values for Givens transformations.
- */
- std::vector<double> gamma;
-
- /** \brief
- * Stores the c values for Givens transformations.
- */
- std::vector<double> c;
-
- /** \brief
- * Stores the s values for Givens transformations.
- */
- std::vector<double> s;
-
- std::vector<double> y_;
-
- /** \brief
- * H-Matrix computed in the GMRES algorithm.
- */
- std::vector< std::vector<double> > h;
- };
-
-
-}
-
-#include "GMResSolver.hh"
-
-#endif // AMDIS_GMRESSOLVER_H
diff --git a/AMDiS/src/GMResSolver.hh b/AMDiS/src/GMResSolver.hh
deleted file mode 100644
index cf442a3e..00000000
--- a/AMDiS/src/GMResSolver.hh
+++ /dev/null
@@ -1,189 +0,0 @@
-#include "GMResSolver.h"
-#include "Preconditioner.h"
-
-namespace AMDiS {
-
- template<typename VectorType>
- GMResSolver<VectorType>::GMResSolver(std::string name)
- : OEMSolver<VectorType>(name),
- TOL_(1.e-25),
- restart_(0),
- w_(NULL)
- {
- FUNCNAME("GMResSolver::GMResSolver()");
- GET_PARAMETER(0, name + "->restart", "%d", &restart_);
- TEST_EXIT(restart_)("restart not set\n");
- }
-
- template<typename VectorType>
- GMResSolver<VectorType>::~GMResSolver()
- {}
-
- template<typename VectorType>
- void GMResSolver<VectorType>::init()
- {
- // Create a new vector w.
- w_ = this->vectorCreator->create();
- z_ = this->vectorCreator->create();
- r_ = this->vectorCreator->create();
-
- // Get memory for the vector pointers and create the pointers afterwards.
- v = GET_MEMORY(VectorType*, restart_ + 1);
- for (int i = 0; i <= restart_; i++) {
- v[i] = this->vectorCreator->create();
- }
-
- // Resize all fields to the corresponding size.
- gamma.resize(restart_ + 1);
- c.resize(restart_);
- s.resize(restart_);
-
- y_.resize(restart_);
-
- h.resize(restart_ + 1);
- for (int i = 0; i <= restart_; i++) {
- h[i].resize(restart_);
- }
- }
-
- template<typename VectorType>
- void GMResSolver<VectorType>::exit()
- {
- // Empty used memory.
- if (w_) {
- this->vectorCreator->free(w_);
- this->vectorCreator->free(z_);
- this->vectorCreator->free(r_);
-
- for (int i = 0; i <= restart_; i++) {
- this->vectorCreator->free(v[i]);
- }
- }
- }
-
-
- template<typename VectorType>
- int GMResSolver<VectorType>::gmres(MatVecMultiplier<VectorType> *matVec,
- VectorType *x,
- VectorType *b)
- {
- FUNCNAME("GMResSolver::gmres()");
-
- // r_0 = b - Ax, where r_0 is already stored as the first vector in the
- // matrix V.
- matVec->matVec(NoTranspose, *x, *v[0]);
- xpay(-1.0, *b, *v[0]);
-
- // Left preconditioning, if required.
- if (this->leftPrecon) {
- this->leftPrecon->precon(v[0]);
- }
-
- // Compute the norm of r_0 = v_0.
- gamma[0] = norm(v[0]);
-
- // Normalize v_0.
- *v[0] *= (1 / gamma[0]);
-
- // If the norm of gamma_0 is less than the tolerance bounday, x is already
- // a good solution for Ax = b.
- if (gamma[0] < this->tolerance) {
- this->residual = gamma[0];
- return(0);
- }
-
- // Main loop of the GMRES algorithm.
- for (int j = 0; j < restart_; j++) {
- // w_j = A * v_j;
- matVec->matVec(NoTranspose, *v[j], *w_);
-
- // Preconditioning of w_j
- if (this->leftPrecon) {
- this->leftPrecon->precon(w_);
- }
-
- // w_j = A * v_j - \sum(h_ij * v_i)
- for (int i = 0; i <= j; i++) {
- // h_ij = (v_i, A * v_j)_2
- h[i][j] = *w_ * (*v[i]);
-
- // Update w_j
- axpy(-h[i][j], *v[i], *w_);
- }
-
- // h_{j + 1}{j} = \| w_j \|_2
- h[j + 1][j] = norm(w_);
-
- // Compute h_ij and h_{i + 1}{j} using parameters of the Givens rotation.
- for (int i = 0; i < j; i++) {
- double t1 = c[i] * h[i][j] + s[i] * h[i + 1][j];
- double t2 = -s[i] * h[i][j] + c[i] * h[i + 1][j];
- h[i][j] = t1;
- h[i + 1][j] = t2;
- }
-
- // Compute new beta
- double beta = sqrt(h[j][j] * h[j][j] + h[j + 1][j] * h[j + 1][j]);
- // Update s_j and c_j
- s[j] = h[j + 1][j] / beta;
- c[j] = h[j][j] / beta;
- // h_jj = beta
- h[j][j] = beta;
-
- // Update gammas
- gamma[j + 1] = -s[j] * gamma[j];
- gamma[j] *= c[j];
-
- // Set v_{j + 1} to w_j and normalize it.
- *v[j + 1] = *w_;
- *v[j + 1] *= 1 / h[j + 1][j];
- }
-
- // Compute the solution.
- for (int i = restart_ - 1; i >= 0; i--) {
- for (int k = i + 1; k < restart_; k++) {
- gamma[i] -= h[i][k] * gamma[k];
- }
- gamma[i] /= h[i][i];
- axpy(gamma[i], *v[i], *x);
- }
-
- // Update the new residual.
- this->residual = abs(gamma[restart_]);
-
- return restart_;
- }
-
-
- template<typename VectorType>
- int GMResSolver<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x, VectorType *b, bool reuseMatrix)
- {
- FUNCNAME("GMResSolver::solveSystem()");
-
- double old_res = -1.0;
-
- // If norm of b is smaller than the tolarance, we can assume b to be zero.
- // Hence, x = 0 is the solution of the linear system.
- if (norm(b) < TOL_) {
- INFO(this->info, 2)("b == 0, x = 0 is the solution of the linear system\n");
- setValue(*x, 0.0);
- this->residual = 0.0;
- return(0);
- }
-
- START_INFO();
- for (int iter = 0; iter <= this->max_iter; iter++) {
- // Solve Ax=b using GMRES(m).
- int k = gmres(matVec, x, b);
- // Check the new residual.
- if (SOLVE_INFO(iter, this->residual, &old_res))
- return(iter);
- TEST_EXIT(k != 0)("this must not happen\n");
- }
-
- ERROR_EXIT("Should not be reached\n");
- return(0);
- }
-
-}
diff --git a/AMDiS/src/GMResSolver2.h b/AMDiS/src/GMResSolver2.h
deleted file mode 100644
index 6e820643..00000000
--- a/AMDiS/src/GMResSolver2.h
+++ /dev/null
@@ -1,163 +0,0 @@
-// ============================================================================
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file GMResSolver2.h */
-
-#ifndef AMDIS_GMRESSOLVER2_H
-#define AMDIS_GMRESSOLVER2_H
-
-#include "OEMSolver.h"
-#include "MemoryManager.h"
-
-namespace AMDiS {
-
- // ============================================================================
- // ===== class GMResSolver2 ===================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Solves a linear system by the restarted GMRES(m) method (Generalized Minimal
- * Residual) for general nonsymmetric system matrices.
- *
- * The implementation is based on the following book: "Numerik linearer
- * Gleichungssystene", 2. Auflage, Andreas Meister. The algorithm is described
- * on pages 150 and 154 (for the restarted version). The extension to the
- * preconditioned GMRES(m) is based on the description in the book "Iterative
- * Methods for Sparse Linear Systems", second edition, Yousef Saad, on page 268.
- *
- * The orthogonal system is build using the modified Gram Schmidt (MGS) method.
- * The least square problem is solved using Givens transformations.
- *
- */
- template<typename VectorType>
- class GMResSolver2 : public OEMSolver<VectorType>
- {
- public:
- MEMORY_MANAGED(GMResSolver2<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new GMResSolver object.
- */
- OEMSolver<VectorType>* create() {
- return NEW GMResSolver2<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- GMResSolver2(std::string name);
-
- /** \brief
- * destructor
- */
- ~GMResSolver2();
-
- protected:
- /** \brief
- * realisation of OEMSolver::solveSystem
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b, bool reuseMatrix);
-
- /** \brief
- * realisation of OEMSolver::init
- */
- void init();
-
- /** \brief
- * realisation of OEMSolver::exit
- */
- void exit();
-
- /** \brief
- * One run of the GMRES(m) method. Is called from solveSystem().
- */
- int gmres(MatVecMultiplier<VectorType> *mv,
- VectorType *x,
- VectorType *b);
-
- private:
- /** \brief
- * Stores the tolerance boundary for numerical computations.
- */
- double TOL_;
-
- /** \brief
- * The parameter m of GMRES(m), i.e. the number of iterations before a restart of
- * the algorithm is forced.
- */
- int restart_;
-
- /** \brief
- * Stores intermediate results in the orthogonalization step.
- */
- VectorType *w_;
-
-
- VectorType *z_;
-
- VectorType *r_;
-
- /** \brief
- * Pointers to the vectors of the orthogonal system.
- */
- VectorType **v;
-
- /** \brief
- * Stores the gamma values for Givens transformations.
- */
- vector<double> gamma;
-
- /** \brief
- * Stores the c values for Givens transformations.
- */
- vector<double> c;
-
- /** \brief
- * Stores the s values for Givens transformations.
- */
- vector<double> s;
-
- vector<double> y_;
-
- /** \brief
- * H-Matrix computed in the GMRES algorithm.
- */
- vector< vector<double> > h;
- };
-
-
-}
-
-#include "GMResSolver2.hh"
-
-#endif // AMDIS_GMRESSOLVER2_H
diff --git a/AMDiS/src/GMResSolver2.hh b/AMDiS/src/GMResSolver2.hh
deleted file mode 100644
index 63fb90c2..00000000
--- a/AMDiS/src/GMResSolver2.hh
+++ /dev/null
@@ -1,191 +0,0 @@
-#include "GMResSolver2.h"
-#include "Preconditioner.h"
-
-namespace AMDiS {
-
- template<typename VectorType>
- GMResSolver2<VectorType>::GMResSolver2(std::string name)
- : OEMSolver<VectorType>(name),
- TOL_(1.e-25),
- restart_(0),
- w_(NULL)
- {
- FUNCNAME("GMResSolver2::GMResSolver2()");
- GET_PARAMETER(0, name + "->restart", "%d", &restart_);
- TEST_EXIT(restart_)("restart not set\n");
- }
-
- template<typename VectorType>
- GMResSolver2<VectorType>::~GMResSolver2()
- {}
-
- template<typename VectorType>
- void GMResSolver2<VectorType>::init()
- {
- // Create a new vector w.
- w_ = this->vectorCreator->create();
- z_ = this->vectorCreator->create();
- r_ = this->vectorCreator->create();
-
- // Get memory for the vector pointers and create the pointers afterwards.
- v = GET_MEMORY(VectorType*, restart_ + 1);
- for (int i = 0; i <= restart_; i++) {
- v[i] = this->vectorCreator->create();
- }
-
- // Resize all fields to the corresponding size.
- gamma.resize(restart_ + 1);
- c.resize(restart_);
- s.resize(restart_);
-
- y_.resize(restart_);
-
- h.resize(restart_ + 1);
- for (int i = 0; i <= restart_; i++) {
- h[i].resize(restart_);
- }
- }
-
- template<typename VectorType>
- void GMResSolver2<VectorType>::exit()
- {
- // Empty used memory.
- if (w_) {
- this->vectorCreator->free(w_);
- this->vectorCreator->free(z_);
- this->vectorCreator->free(r_);
-
- for (int i = 0; i <= restart_; i++) {
- this->vectorCreator->free(v[i]);
- }
- }
- }
-
-
- template<typename VectorType>
- int GMResSolver2<VectorType>::gmres(MatVecMultiplier<VectorType> *matVec,
- VectorType *x,
- VectorType *b)
- {
- FUNCNAME("GMResSolver2::gmres()");
-
- // r_0 = b - Ax, where r_0 is already stored as the first vector in the
- // matrix V.
- matVec->matVec(NoTranspose, *x, *v[0]);
- xpay(-1.0, *b, *v[0]);
-
- // Left preconditioning, if required.
- if (this->leftPrecon) {
- this->leftPrecon->precon(v[0]);
- }
-
- // Compute the norm of r_0 = v_0.
- gamma[0] = norm(v[0]);
-
- // Normalize v_0.
- *v[0] *= (1 / gamma[0]);
-
- // If the norm of gamma_0 is less than the tolerance bounday, x is already
- // a good solution for Ax = b.
- if (gamma[0] < this->tolerance) {
- this->residual = gamma[0];
- return(0);
- }
-
- // Main loop of the GMRES algorithm.
- for (int j = 0; j < restart_; j++) {
- // w_j = A * v_j;
- matVec->matVec(NoTranspose, *v[j], *w_);
-
- // Preconditioning of w_j
- if (this->leftPrecon) {
- this->leftPrecon->precon(w_);
- }
-
- // w_j = A * v_j - \sum(h_ij * v_i)
- for (int i = 0; i <= j; i++) {
- // h_ij = (v_i, A * v_j)_2
- h[i][j] = *w_ * (*v[i]);
-
- // Update w_j
- axpy(-h[i][j], *v[i], *w_);
- }
-
- // h_{j + 1}{j} = \| w_j \|_2
- h[j + 1][j] = norm(w_);
-
- // Compute h_ij and h_{i + 1}{j} using parameters of the Givens rotation.
- for (int i = 0; i < j; i++) {
- double t1 = c[i] * h[i][j] + s[i] * h[i + 1][j];
- double t2 = -s[i] * h[i][j] + c[i] * h[i + 1][j];
- h[i][j] = t1;
- h[i + 1][j] = t2;
- }
-
- // Compute new beta
- double beta = sqrt(h[j][j] * h[j][j] + h[j + 1][j] * h[j + 1][j]);
- // Update s_j and c_j
- s[j] = h[j + 1][j] / beta;
- c[j] = h[j][j] / beta;
- // h_jj = beta
- h[j][j] = beta;
-
- // Update gammas
- gamma[j + 1] = -s[j] * gamma[j];
- gamma[j] *= c[j];
-
- // Set v_{j + 1} to w_j and normalize it.
- *v[j + 1] = *w_;
- *v[j + 1] *= 1 / h[j + 1][j];
- }
-
- // Compute the solution.
- for (int i = restart_ - 1; i >= 0; i--) {
- for (int k = i + 1; k < restart_; k++) {
- gamma[i] -= h[i][k] * gamma[k];
- }
- gamma[i] /= h[i][i];
- axpy(gamma[i], *v[i], *x);
- }
-
- // Update the new residual.
- this->residual = abs(gamma[restart_]);
-
- return restart_;
- }
-
-
- template<typename VectorType>
- int GMResSolver2<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x, VectorType *b,
- bool reuseMatrix)
- {
- FUNCNAME("GMResSolver2::solveSystem()");
-
- double old_res = -1.0;
-
- // If norm of b is smaller than the tolarance, we can assume b to be zero.
- // Hence, x = 0 is the solution of the linear system.
- if (norm(b) < TOL_) {
- INFO(this->info, 2)("b == 0, x = 0 is the solution of the linear system\n");
- setValue(*x, 0.0);
- this->residual = 0.0;
- return(0);
- }
-
- START_INFO();
- for (int iter = 0; iter <= this->max_iter; iter++) {
- // Solve Ax=b using GMRES(m).
- int k = gmres(matVec, x, b);
- // Check the new residual.
- if (SOLVE_INFO(iter, this->residual, &old_res))
- return(iter);
- TEST_EXIT(k != 0)("this must not happen\n");
- }
-
- ERROR_EXIT("Should not be reached\n");
- return(0);
- }
-
-}
-
diff --git a/AMDiS/src/GSSmoother.cc b/AMDiS/src/GSSmoother.cc
index b87d7198..2f26b126 100755
--- a/AMDiS/src/GSSmoother.cc
+++ b/AMDiS/src/GSSmoother.cc
@@ -16,6 +16,9 @@ namespace AMDiS {
int iterations,
const std::set<DegreeOfFreedom> &dofSet)
{
+ ERROR_EXIT("Will be rewritten - Peter\n");
+
+#if 0
int i, j, rowNumber, colNumber, numCols;
double entry, diagEntry = 0.0;
@@ -83,6 +86,7 @@ namespace AMDiS {
// (*solution)[rowNumber] += (1.0 - omega_) * oldSolution;
// }
// }
+#endif
}
template<>
@@ -95,6 +99,9 @@ namespace AMDiS {
int iterations,
const Vector< std::set<DegreeOfFreedom>*> &dofSet)
{
+ ERROR_EXIT("Will be rewritten - Peter\n");
+
+#if 0
int numComponents = s->getSize();
int i, j, k, l;
int rowNumber, colNumber, numCols;
@@ -143,6 +150,6 @@ namespace AMDiS {
}
}
}
+#endif
}
-
}
diff --git a/AMDiS/src/ILUPreconditioner.cc b/AMDiS/src/ILUPreconditioner.cc
deleted file mode 100644
index 34c7a12a..00000000
--- a/AMDiS/src/ILUPreconditioner.cc
+++ /dev/null
@@ -1,314 +0,0 @@
-#include <iostream>
-#include <sstream>
-#include <vector>
-
-#include "ILUPreconditioner.h"
-#include "DOFVector.h"
-#include "DOFMatrix.h"
-#include "DOFIterator.h"
-#include "MatVecMultiplier.h"
-#include "StlVector.h"
-
-namespace AMDiS {
-
- void ILUPreconditioner::init()
- {
- FUNCNAME("ILUPreconditioner::init()");
-
- clock_t first = clock();
-
- ilu_.resize(matrix.getSize());
-
- for (int i = 0; i < matrix.getSize(); i++) {
- if ((*matrix[i])) {
- ilu_[i] = NEW DOFMatrix((*(*matrix[i])));
- }
- }
-
-
- DOFMatrix *ilu = ilu_[row];
-
- int matrixSize = ilu->getRowFESpace()->getAdmin()->getUsedSize();
-
- // Sort all rows corresponding to their position in the matrix.
- diag_.resize(matrixSize);
- for (int i = 0; i < matrixSize; i++) {
- diag_[i] = (*ilu)[i][0].entry;
- sort((*ilu)[i].begin(), (*ilu)[i].end(), CmpMatEntryCol());
- }
-
- // For i = 1, ..., n - 1, Do
- for (int i = 1; i < matrixSize; i++) {
-
- // For k = 0, ..., i - 1 and for (i,k) \in NZ(ilu), Do
- for (int col1 = 0; col1 < static_cast<int>((*ilu)[i].size()); col1++) {
- // k is the logical index of the col1-th column in the i-th row.
- int k = (*ilu)[i][col1].col;
- if ((k < i) && // due to the condition that k goes up to i - 1
- (k >= 0) && // the entry is valid
- ((*ilu)[i][col1].entry != 0.0)) { // the entry is non-zero, hence in NZ(ilu)
- // Compute a_ik = a_ik / a_kk
- (*ilu)[i][col1].entry = (*ilu)[i][col1].entry / diag_[k];
-
- // For j = k + 1, ..., n - 1 and for (i,j) \in NZ(ilu), Do
- for (int col2 = col1 + 1; col2 < static_cast<int>((*ilu)[i].size()); col2++) {
- // j is the logical index of the col2-th column in the i-th row.
- int j = (*ilu)[i][col2].col;
-
- // Because the rows are sorted, we start at position col1 + 1, and all non-valid
- // entries have col < 0, we do not need to check for non-valid entries.
- if ((*ilu)[i][col2].entry != 0.0) {
- int physKJ = (*ilu).logToPhysIndex(k, j);
- // If physKJ is negativ, the corresponding entry is zero and we do not need
- // to compute the new element.
- if (physKJ >= 0) {
- // Compute a_ij = a_ij - a_ik * a_kj
- (*ilu)[i][col2].entry = (*ilu)[i][col2].entry - ((*ilu)[i][col1].entry * (*ilu)[k][physKJ].entry);
- // Do not forgett to update the diagonal entries, if we have computed on
- // a diagonal element.
- if (i == j) {
- diag_[i] = (*ilu)[i][col2].entry;
- }
- }
- }
- }
- }
- }
- }
-
- MSG("preconditioning of the coefficient matrix needed %.5f seconds\n",
- TIME_USED(first,clock()));
- }
-
- void ILUPreconditioner::exit()
- {
- for (int i = 0; i < ilu_.getSize(); i++) {
- if ((*matrix[i])) {
- DELETE ilu_[i];
- }
- }
- }
-
- void ILUPreconditioner::precon(DOFVector<double>* x)
- {
- DOFMatrix *ilu = ilu_[row];
-
- // The solution of P * x = b must be calculated in the
- // following. Note that the vector b is stored in x to
- // saving space.
- // We solve the equation with forward and backward substitution
- // of the factorization P = L * U.
-
- DOFVector<double>::Iterator itx(x, USED_DOFS);
-
- // Forward substitution: L * y = b
- // We use x to save the new results of y. Note that all diagonal
- // elements of L are 1, hence we do not need to devide the term
- // by the diagonal elements.
- int i = 0;
- for (itx.reset(); !itx.end(); ++itx, ++i) {
- // y_i = b_i
- // Must not be assigned directly, since x = b and y will take
- // the results of y.
-
- std::vector<MatEntry> *m = &(*ilu)[i];
-
- // y_i = b_i - \sum_{1}^{i-1} ( l_{i,k} * y_k )
- for (int col = 0; col < static_cast<int>((*m).size()); col++) {
- int k = (*m)[col].col;
- if (k >= 0) {
- if (k < i) {
- (*itx) -= (*m)[col].entry * (*x)[k];
- } else {
- // If for an entry k < i does not hold, it will be also false
- // for all other elements in th column, because the columns
- // are sorted.
- break;
- }
- }
- }
- }
-
-
- // Backward substitution: R * x = y
- do {
- itx--;
- i--;
-
- std::vector<MatEntry> *m = &(*ilu)[i];
-
- // x_i = y_i - \sum_{i + 1}^(n} ( r_{i,k} * x_k )
- // The sum is build backwards, since the directon of calculation does not
- // matter for the result, but we can break the search if k > i does not
- // hold (the cols of ilu_ are sorted!) and so make the calculation faster.
- for (int col = static_cast<int>((*m).size()) - 1; col >= 0; col--) {
- int k = (*m)[col].col;
- if (k > i) {
- (*itx) -= (*m)[col].entry * (*x)[k];
- } else {
- break;
- }
- }
-
- // x_i = x_i / r_{i,i}
- (*itx) /= diag_[i];
-
- } while (!itx.begin());
- }
-
-
-
-
-
-
-
-
-
- /////////////////////////////
-
- void ILUPreconditionerStd::init()
- {
- FUNCNAME("ILUPreconditionerStd::init()");
-
- clock_t first = clock();
-
- ilu_ = *matrix;
-
- int matrixSize = ilu_.size();
-
-// ilu_.resize(matrixSize);
-
-// for (int i = 0; i < matrixSize; i++) {
-// ilu_[i] = (*matrix
-// }
-
- std::vector< std::vector<MatEntry> > *ilu = &ilu_;
-
-
-
- // Sort all rows corresponding to their position in the matrix.
- diag_.resize(matrixSize);
- for (int i = 0; i < matrixSize; i++) {
- diag_[i] = (*ilu)[i][0].entry;
- sort((*ilu)[i].begin(), (*ilu)[i].end(), CmpMatEntryCol());
- }
-
- // For i = 1, ..., n - 1, Do
- for (int i = 1; i < matrixSize; i++) {
-
- // For k = 0, ..., i - 1 and for (i,k) \in NZ(ilu), Do
- for (int col1 = 0; col1 < static_cast<int>((*ilu)[i].size()); col1++) {
- // k is the logical index of the col1-th column in the i-th row.
- int k = (*ilu)[i][col1].col;
- if ((k < i) && // due to the condition that k goes up to i - 1
- (k >= 0) && // the entry is valid
- ((*ilu)[i][col1].entry != 0.0)) { // the entry is non-zero, hence in NZ(ilu)
- // Compute a_ik = a_ik / a_kk
- (*ilu)[i][col1].entry = (*ilu)[i][col1].entry / diag_[k];
-
- // For j = k + 1, ..., n - 1 and for (i,j) \in NZ(ilu), Do
- for (int col2 = col1 + 1; col2 < static_cast<int>((*ilu)[i].size()); col2++) {
- // j is the logical index of the col2-th column in the i-th row.
- int j = (*ilu)[i][col2].col;
-
- // Because the rows are sorted, we start at position col1 + 1, and all non-valid
- // entries have col < 0, we do not need to check for non-valid entries.
- if ((*ilu)[i][col2].entry != 0.0) {
- // int physKJ = (*ilu).logToPhysIndex(k, j);
- int physKJ = logToPhysIndex(ilu, k, j);
-
- // If physKJ is negativ, the corresponding entry is zero and we do not need
- // to compute the new element.
- if (physKJ >= 0) {
- // Compute a_ij = a_ij - a_ik * a_kj
- (*ilu)[i][col2].entry = (*ilu)[i][col2].entry - ((*ilu)[i][col1].entry * (*ilu)[k][physKJ].entry);
- // Do not forgett to update the diagonal entries, if we have computed on
- // a diagonal element.
- if (i == j) {
- diag_[i] = (*ilu)[i][col2].entry;
- }
- }
- }
- }
- }
- }
- }
-
- MSG("preconditioning of the coefficient matrix needed %.5f seconds\n",
- TIME_USED(first,clock()));
- }
-
- void ILUPreconditionerStd::exit()
- {
- }
-
- void ILUPreconditionerStd::precon(std::vector<double> *x)
- {
- std::vector< std::vector<MatEntry> > *ilu = &ilu_;
-
- // The solution of P * x = b must be calculated in the
- // following. Note that the vector b is stored in x to
- // saving space.
- // We solve the equation with forward and backward substitution
- // of the factorization P = L * U.
-
- // DOFVector<double>::Iterator itx(x, USED_DOFS);
-
- std::vector<double>::iterator itx;
-
- // Forward substitution: L * y = b
- // We use x to save the new results of y. Note that all diagonal
- // elements of L are 1, hence we do not need to devide the term
- // by the diagonal elements.
- int i = 0;
- for (itx = x->begin(); itx != x->end(); ++itx, ++i) {
- // y_i = b_i
- // Must not be assigned directly, since x = b and y will take
- // the results of y.
-
- std::vector<MatEntry> *m = &(*ilu)[i];
-
- // y_i = b_i - \sum_{1}^{i-1} ( l_{i,k} * y_k )
- for (int col = 0; col < static_cast<int>((*m).size()); col++) {
- int k = (*m)[col].col;
- if (k >= 0) {
- if (k < i) {
- (*itx) -= (*m)[col].entry * (*x)[k];
- } else {
- // If for an entry k < i does not hold, it will be also false
- // for all other elements in th column, because the columns
- // are sorted.
- break;
- }
- }
- }
- }
-
-
- // Backward substitution: R * x = y
- do {
- itx--;
- i--;
-
- std::vector<MatEntry> *m = &(*ilu)[i];
-
- // x_i = y_i - \sum_{i + 1}^(n} ( r_{i,k} * x_k )
- // The sum is build backwards, since the directon of calculation does not
- // matter for the result, but we can break the search if k > i does not
- // hold (the cols of ilu_ are sorted!) and so make the calculation faster.
- for (int col = static_cast<int>((*m).size()) - 1; col >= 0; col--) {
- int k = (*m)[col].col;
- if (k > i) {
- (*itx) -= (*m)[col].entry * (*x)[k];
- } else {
- break;
- }
- }
-
- // x_i = x_i / r_{i,i}
- (*itx) /= diag_[i];
-
- } while (itx != x->begin());
- }
-
-}
diff --git a/AMDiS/src/ILUPreconditioner.h b/AMDiS/src/ILUPreconditioner.h
deleted file mode 100644
index 104001aa..00000000
--- a/AMDiS/src/ILUPreconditioner.h
+++ /dev/null
@@ -1,181 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file ILUPreconditioner.h */
-
-#ifndef AMDIS_ILU_PRECONDITIONER_H
-#define AMDIS_ILU_PRECONDITIONER_H
-
-#include <vector>
-#include "Preconditioner.h"
-#include "MemoryManager.h"
-#include "CreatorInterface.h"
-#include "DOFMatrix.h"
-
-namespace AMDiS {
-
- template<typename T> class DOFVector;
- template<typename T> class OEMSolver;
-
- // ============================================================================
- // ===== class ILUPreconditioner ==============================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * ILU (Incomplete LU factorization) preconditioner.
- *
- * The preconditioner is implemented following the book "Iterative Methods for
- * Sparce Linear Systems", second edition, Yousef Saad. The preconditioner is
- * described in chapter 10.3 (algorithm 10.4).
- */
- class ILUPreconditioner : public PreconditionerScal
- {
- public:
- MEMORY_MANAGED(ILUPreconditioner);
-
- /** \brief
- * Creater class used in PreconditionerMap.
- */
- class Creator : public PreconditionerScalCreator
- {
- public:
- MEMORY_MANAGED(Creator);
-
- /** \brief
- * Creates an ILUPreconditioner.
- */
- PreconditionerScal *create() {
- return NEW ILUPreconditioner(size, row);
- };
- };
-
- /** \brief
- * Constructor.
- */
- ILUPreconditioner(int size = 1, int row = 0)
- : PreconditionerScal(size, row)
- {};
-
- /** \brief
- * Destructor.
- */
- virtual ~ILUPreconditioner() {};
-
- /** \brief
- * Realisation of Preconditioner::init
- *
- * In the initalization phase the incomplete LU factorization
- * of the coefficent matrix is calculated.
- */
- void init();
-
- /** \brief
- * Realisation of Preconditioner::exit
- */
- void exit();
-
- /** \brief
- * Realisation of Preconditioner::precon
- */
- void precon(DOFVector<double>* x);
-
- private:
- /** \brief
- * This matrix stores the incomplete LU factorization
- * of the coefficient matrix.
- */
- // DOFMatrix *ilu_;
- Vector<DOFMatrix*> ilu_;
-
- /** \brief
- * Here we store the diagonal elements of ilu_ matrix. This
- * allows faster computations.
- */
- std::vector<double> diag_;
- };
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- class ILUPreconditionerStd : public PreconditionerScalStd
- {
- public:
- MEMORY_MANAGED(ILUPreconditionerStd);
-
-
- /** \brief
- * Constructor.
- */
- ILUPreconditionerStd() {};
-
- /** \brief
- * Destructor.
- */
- virtual ~ILUPreconditionerStd() {};
-
- /** \brief
- * Realisation of Preconditioner::init
- *
- * In the initalization phase the incomplete LU factorization
- * of the coefficent matrix is calculated.
- */
- void init();
-
- /** \brief
- * Realisation of Preconditioner::exit
- */
- void exit();
-
- /** \brief
- * Realisation of Preconditioner::precon
- */
- void precon(std::vector<double>* x);
-
- private:
- /** \brief
- * This matrix stores the incomplete LU factorization
- * of the coefficient matrix.
- */
- std::vector< std::vector<MatEntry> > ilu_;
-
- /** \brief
- * Here we store the diagonal elements of ilu_ matrix. This
- * allows faster computations.
- */
- std::vector<double> diag_;
- };
-
-}
-
-#endif // AMDIS_ILU_PRECONDITIONER_H
diff --git a/AMDiS/src/ILUTPreconditioner.cc b/AMDiS/src/ILUTPreconditioner.cc
deleted file mode 100644
index 04f966b1..00000000
--- a/AMDiS/src/ILUTPreconditioner.cc
+++ /dev/null
@@ -1,247 +0,0 @@
-#include <vector>
-#include "ILUTPreconditioner.h"
-#include "DOFVector.h"
-#include "DOFMatrix.h"
-#include "DOFIterator.h"
-#include "MatVecMultiplier.h"
-
-namespace AMDiS {
-
- void ILUTPreconditioner::init()
- {
- FUNCNAME("ILUTPreconditioner::init()");
-
- TEST_EXIT(matrix[row])("no matrix\n");
-
- clock_t first = clock();
-
- // Make a copy of the system matrix.
- ilu_ = (*(*matrix[row]));
-
- int matrixSize = ilu_.getRowFESpace()->getAdmin()->getUsedSize();
-
- diag_.resize(matrixSize);
-
- // For i = 1, ..., n, Do
- for (int i = 0; i < matrixSize; i++) {
- // We do not make a real copy of the row, but instead w is a pointer to
- // the current row.
- std::vector<MatEntry> *w = &(ilu_[i]);
-
-
- // Calculate tau_i by calculating the 2-norm of the current row and
- // multiplying the result with the parameter tau.
- double taui = 0.0;
- for (int col1 = 0; col1 < static_cast<int>((*w).size()); col1++) {
- taui += (*w)[col1].entry * (*w)[col1].entry;
- }
- taui = sqrt(taui) * tau_;
-
-
- // For k = 1, ..., i - 1 and when w_k not= 0, Do
- for (int col1 = 0; col1 < static_cast<int>((*w).size()); col1++) {
- // Pointer to the w_ik element
- MatEntry *w_k = &((*w)[col1]);
-
- // Get the logical index k of the current element of row w.
- int k = (*w_k).col;
-
- if ((k < i) && // must be smaller than i due to the loop condition
- (k >= 0) && // must be a valid entry
- ((*w_k).entry != 0.0)) { // must be non zero due to the loop condition
-
- // w_k := w_k / a_kk (note that the diagonal elements are always stored in the first entry of a row)
- (*w_k).entry /= (*(*matrix[row]))[k][0].entry;
-
- // Dropping rule to w_k
- // It is checked if the absolute value of w_k is smaller than tau_i
- if (fabs((*w_k).entry) < taui) {
- // Do not delete the element yet but set it to zero, so it will be deleted
- // when the second dropping rule will be applied.
- (*w_k).entry = 0.0;
- } else {
- // w := w - w_k * u_k*
- // To compute the result, all elements of u_k are multiplied with w_k. Then
- // we check if there is an element in w with the same column index. If yes,
- // the result of the multiplication is substracted from the corresponding
- // element in w. Otherwise, a new element in w with the negative value of
- // the multiplication is created.
- for (int col2 = 0; col2 < static_cast<int>(ilu_[k].size()); col2++) {
-
- // Pointer to the current element of row u_k*
- MatEntry *u_kj = &ilu_[k][col2];
-
- // We are in the k-th row of matrix ilu_. The row is devided into L and
- // U factorization. Hence, all elements of U in ilu_ must have a column
- // index that is greater than k.
- if (((*u_kj).col > k) && // must be a U element
- ((*u_kj).entry != 0.0)) { // must be non zero
-
- // w_k * u_kj
- double v = (*w_k).entry * (*u_kj).entry;
-
- // search for the physical index of the j-th column in row w.
- int index = -1;
- for (int z = 0; z < static_cast<int>((*w).size()); z++) {
- if ((*w)[z].col == (*u_kj).col) {
- index = z;
- break;
- }
- }
-
- if (index >= 0) {
- // If there is a j-th column in row w, make the substraction.
- (*w)[index].entry -= v;
- } else {
- // Otherwise, if the absolut value of the result of the multiplication
- // is greater than the relative tolerance, create a new element in w.
- if (fabs(v) > taui) {
- MatEntry newEntry = {(*u_kj).col, -v};
- (*w).push_back(newEntry);
- }
- }
- }
-
- }
- }
- }
- }
-
- // Apply second dropping rule.
- // First, remove all elements which absolut value is smaller than tau_i.
- (*w).erase(remove_if((*w).begin(), (*w).end(), MatEntryValueLess(taui)),
- (*w).end());
-
- // Calculate the number of elements in the L-part of the current row.
- int nL = 0;
- for (int k = 1; k < static_cast<int>((*w).size()); k++) {
- if ((*w)[k].col < i) {
- nL++;
- }
- }
- // Calculate the number of elements in the U-part of the current row.
- int nU = (*w).size() - nL - 1;
-
- // Now we check, if there are more elements in L- and U-parts of the row
- // than we should store. If it is so, the final number of elements is
- // reduced to p.
- if (nL > p_) {
- nL = p_;
- }
- if (nU > p_) {
- nU = p_;
- }
-
- // First, we sort the row in such a way that the first element will stay to be
- // the diagonal element, then all the elements of the L-part follows and after
- // them all the elements of the U-part. Because we are in the i-th row, elements
- // of L must have a column index smaller than i.
- // itMiddle is then an iterator to the first element of the U-part.
- std::vector<MatEntry>::iterator itMiddle =
- partition((*w).begin() + 1, (*w).end(), MatEntryColLess(i));
-
- // If there are elements in the L-part:
- if (nL > 0) {
- // Search for the nL largest elements in the L-part of the row.
- nth_element((*w).begin() + 1,
- (*w).begin() + 1 + nL,
- itMiddle - 1,
- CmpMatEntryAbsValueGreater());
-
- // Delete all the elements that do not belong to the nL largest elements
- // in the L-part.
- itMiddle = (*w).erase((*w).begin() + nL + 1, itMiddle);
- }
-
- // If there are elements in the U-part:
- if (nU > 0) {
- // Search for the nU largest elements in the U-part of the row.
- nth_element(itMiddle,
- itMiddle + nU,
- (*w).end(),
- CmpMatEntryAbsValueGreater());
-
- // Delete all the elements that do not belong to the nU largest elements
- // in the L-part.
- (*w).erase(itMiddle + nU, (*w).end());
- }
-
- // Store the diagonal element and sort the line.
- diag_[i] = (*w)[0].entry;
- sort((*w).begin(), (*w).end(), CmpMatEntryCol());
- }
-
-
- MSG("preconditioning of the coefficient matrix needed %.5f seconds\n",
- TIME_USED(first,clock()));
- }
-
-
- void ILUTPreconditioner::exit()
- {
- ilu_.clear();
- }
-
- void ILUTPreconditioner::precon(DOFVector<double>* x)
- {
- // The solution of P * x = b must be calculated in the
- // following. Note that the vector b is stored in x to
- // saving space.
- // We solve the equation with forward and backward substitution
- // of the factorization P = L * U.
-
- DOFVector<double>::Iterator itx(x, USED_DOFS);
-
- // Forward substitution: L * y = b
- // We use x to save the new results of y. Note that all diagonal
- // elements of L are 1, hence we do not need to devide the term
- // by the diagonal elements.
- int i = 0;
- for (itx.reset(); !itx.end(); ++itx, ++i)
- {
- // y_i = b_i
- // Must not be assigned directly, since x = b and y will take
- // the results of y.
-
- // y_i = b_i - \sum_{1}^{i-1} ( l_{i,k} * y_k )
- for (int col = 0; col < static_cast<int>(ilu_[i].size()); col++) {
- int k = ilu_[i][col].col;
- if (k >= 0) {
- if (k < i) {
- (*itx) -= ilu_[i][col].entry * (*x)[k];
- } else {
- // If for an entry k < i does not hold, it will be also false
- // for all other elements in th column, because the columns
- // are sorted.
- break;
- }
- }
- }
- }
-
-
- // Backward substitution: R * x = y
- do {
- itx--;
- i--;
-
- // x_i = y_i - \sum_{i + 1}^(n} ( r_{i,k} * x_k )
- // The sum is build backwards, since the directon of calculation does not
- // matter for the result, but we can break the search if k > i does not
- // hold (the cols of ilu_ are sorted!) and so make the calculation faster.
- for (int col = static_cast<int>(ilu_[i].size()) - 1; col >= 0; col--) {
- int k = ilu_[i][col].col;
- if (k > i) {
- (*itx) -= ilu_[i][col].entry * (*x)[k];
- } else {
- break;
- }
- }
-
- // x_i = x_i / r_{i,i}
- (*itx) /= diag_[i];
-
- } while (!itx.begin());
- }
-
-}
diff --git a/AMDiS/src/ILUTPreconditioner.h b/AMDiS/src/ILUTPreconditioner.h
deleted file mode 100644
index 32916824..00000000
--- a/AMDiS/src/ILUTPreconditioner.h
+++ /dev/null
@@ -1,137 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file ILUTPreconditioner.h */
-
-#ifndef AMDIS_ILUT_PRECONDITIONER_H
-#define AMDIS_ILUT_PRECONDITIONER_H
-
-#include <vector>
-#include "Preconditioner.h"
-#include "MemoryManager.h"
-#include "CreatorInterface.h"
-#include "DOFMatrix.h"
-#include "Parameters.h"
-
-namespace AMDiS {
-
- template<typename T> class DOFVector;
- template<typename T> class OEMSolver;
-
- // ============================================================================
- // ===== class ILUTPreconditioner ==============================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * ILUT (Incomplete LU factorization with Threshold) preconditioner.
- *
- * The preconditioner is implemented following the book "Iterative Methods for
- * Sparce Linear Systems", second edition, Yousef Saad. The preconditioner is
- * described in chapter 10.4 (algorithm 10.6).
- * We have changed the dropping rules of the original algorithm to that the
- * absolut values of w_k are checked.
- */
- class ILUTPreconditioner : public PreconditionerScal
- {
- public:
- MEMORY_MANAGED(ILUTPreconditioner);
-
- /** \brief
- * Creater class used in PreconditionerMap.
- */
- class Creator : public PreconditionerScalCreator
- {
- public:
- MEMORY_MANAGED(Creator);
-
- /** \brief
- * Creates an ILUPreconditioner.
- */
- PreconditionerScal *create() {
- return NEW ILUTPreconditioner(this->name_, size, row);
- };
- };
-
- /** \brief
- * Constructor.
- */
- ILUTPreconditioner(std::string name, int size = 1, int row = 0)
- : PreconditionerScal(size, row),
- name_(name),
- tau_(0.0001),
- p_(8)
- {
- GET_PARAMETER(0, name + "->tau", "%f", &tau_);
- GET_PARAMETER(0, name + "->p", "%d", &p_);
- };
-
- /** \brief
- * Destructor.
- */
- virtual ~ILUTPreconditioner() {};
-
- /** \brief
- * Realisation of Preconditioner::init
- *
- */
- void init();
-
- /** \brief
- * Realisation of Preconditioner::exit
- */
- void exit();
-
- /** \brief
- * Realisation of Preconditioner::precon
- */
- void precon(DOFVector<double>* x);
-
- private:
- std::string name_;
-
- /** \brief
- * This matrix stores the incomplete LU factorization
- * of the coefficient matrix.
- */
- DOFMatrix ilu_;
-
- /** \brief
- * Here we store the diagonal elements of ilu_ matrix. This
- * allows faster computations.
- */
- std::vector<double> diag_;
-
- /** \brief
- * Stores the threshold factor for the preconditioning process.
- */
- double tau_;
-
- /** \brief
- * Stores the number of entries that are finally stored in each row
- * of L and U. Hence, the total number of elements in each row of ilu_
- * is 2p + 1 (the diagonal element is always stored).
- */
- int p_;
- };
-}
-
-#endif // AMDIS_ILUT_PRECONDITIONER_H
diff --git a/AMDiS/src/ITL_OEMSolver.h b/AMDiS/src/ITL_OEMSolver.h
new file mode 100644
index 00000000..3dc952eb
--- /dev/null
+++ b/AMDiS/src/ITL_OEMSolver.h
@@ -0,0 +1,141 @@
+// ============================================================================
+// == ==
+// == AMDiS - Adaptive multidimensional simulations ==
+// == ==
+// ============================================================================
+// == ==
+// == crystal growth group ==
+// == ==
+// == Stiftung caesar ==
+// == Ludwig-Erhard-Allee 2 ==
+// == 53175 Bonn ==
+// == germany ==
+// == ==
+// ============================================================================
+// == ==
+// == http://www.caesar.de/cg/AMDiS ==
+// == ==
+// ============================================================================
+
+/** \file ITL_OEMSolver.h */
+
+
+#ifndef AMDIS_ITL_OEM_SOLVER_H
+#define AMDIS_ITL_OEM_SOLVER_H
+
+#include "OEMSolver.h"
+#include "ITL_Preconditioner.h"
+#include "SolverMatrix.h"
+#include "DOFVector.h"
+#include "SystemVector.h"
+#include "DOFMatrix.h"
+#include "Parameters.h"
+
+#include <boost/numeric/itl/itl.hpp>
+#include <boost/numeric/mtl/mtl.hpp>
+
+namespace AMDiS {
+
+
+ /**
+ * \ingroup Solver
+ *
+ *\brief
+ * Template for using solvers from ITL in AMDiS.
+ */
+ template <typename ITLSolver>
+ class ITL_OEMSolver : public OEMSolver
+ {
+ typedef ITL_Preconditioner<itl::pc::identity<DOFMatrix> > id_t;
+
+ public:
+ /// The constructor reads needed parameters and sets solvers \ref name.
+ ITL_OEMSolver(::std::string name) : OEMSolver(name) {}
+
+ ~ITL_OEMSolver() {}
+
+
+ /// Solves the system iteratively
+ // This function is virtual because derived class calls solver with parameter
+ virtual int solveSystem(const DOFMatrix::base_matrix_type& A,
+ mtl::dense_vector<value_type>& x,
+ const mtl::dense_vector<value_type>& b)
+ {
+ itl::cyclic_iteration<value_type> iter(b, this->max_iter, this->relative,
+ this->tolerance, this->print_cycle);
+ return ITLSolver()(A, x, b, *this->leftPrecon, *this->rightPrecon, iter);
+ }
+
+
+ /// Creator class used in the OEMSolverMap.
+ class Creator : public OEMSolverCreator
+ {
+ public:
+ MEMORY_MANAGED(Creator);
+
+ virtual ~Creator() {}
+
+ /// Returns a new CGSolver object.
+ OEMSolver* create() {
+ return NEW ITL_OEMSolver<ITLSolver>(this->name);
+ }
+ };
+
+ };
+
+
+ /**
+ * \ingroup Solver
+ *
+ *\brief
+ * Template for using solvers from ITL that have one run-time parameter in AMDiS.
+ */
+ template <typename ITLSolver>
+ class ITL_OEMSolver_para
+ : public OEMSolver // ITL_OEMSolver<ITLSolver>
+ {
+ typedef DOFMatrix::value_type value_type;
+ public:
+ /// The constructor reads needed parameters and sets solvers \ref name.
+ ITL_OEMSolver_para(::std::string name)
+ : OEMSolver(name), para(1)
+ {
+ GET_PARAMETER(0, name + "->para", "%d", ¶);
+ }
+
+ ~ITL_OEMSolver_para() {}
+
+ /// Set parameter of iterative solver
+ void setPara(int p) { para= p; }
+
+ /// Solves the system iteratively
+ int solveSystem(const DOFMatrix::base_matrix_type& A,
+ mtl::dense_vector<value_type>& x,
+ const mtl::dense_vector<value_type>& b)
+ {
+ itl::cyclic_iteration<value_type> iter(b, this->max_iter, this->relative,
+ this->tolerance, this->print_cycle);
+ return ITLSolver()(A, x, b, *this->leftPrecon, *this->rightPrecon, iter, para);
+ }
+
+ class Creator : public OEMSolverCreator
+ {
+ public:
+ MEMORY_MANAGED(Creator);
+
+ virtual ~Creator() {}
+
+ /// Returns a new CGSolver object.
+ OEMSolver* create() {
+ return NEW ITL_OEMSolver_para<ITLSolver>(this->name);
+ }
+ };
+
+ private:
+ int para;
+ };
+
+
+} // namespace AMDiS
+
+#endif // AMDIS_ITL_OEM_SOLVER_H
diff --git a/AMDiS/src/ITL_Preconditioner.h b/AMDiS/src/ITL_Preconditioner.h
new file mode 100644
index 00000000..0352c0e2
--- /dev/null
+++ b/AMDiS/src/ITL_Preconditioner.h
@@ -0,0 +1,177 @@
+// ============================================================================
+// == ==
+// == AMDiS - Adaptive multidimensional simulations ==
+// == ==
+// ============================================================================
+// == ==
+// == crystal growth group ==
+// == ==
+// == Stiftung caesar ==
+// == Ludwig-Erhard-Allee 2 ==
+// == 53175 Bonn ==
+// == germany ==
+// == ==
+// ============================================================================
+// == ==
+// == http://www.caesar.de/cg/AMDiS ==
+// == ==
+// ============================================================================
+
+/** \file ITL_Preconditioner.h */
+
+#ifndef AMDIS_ITL_PRECONDITIONER_H
+#define AMDIS_ITL_PRECONDITIONER_H
+
+#include "DOFMatrix.h"
+#include "CreatorInterface.h"
+
+#include <boost/numeric/itl/itl.hpp>
+#include <boost/numeric/itl/pc/ilu_0.hpp>
+#include <boost/numeric/itl/pc/ic_0.hpp>
+
+namespace AMDiS {
+
+ // ============================================================================
+ // ===== class ITL_Preconditioner ==============================================
+ // ============================================================================
+
+
+ /**
+ * \ingroup Solver
+ *
+ * \brief Common base class for wrappers to use ITL preconditioners in AMDiS.
+ */
+ class ITL_BasePreconditioner
+ {
+ public:
+ typedef DOFMatrix::value_type value_type;
+
+ virtual ~ITL_BasePreconditioner() {}
+
+ virtual mtl::dense_vector<value_type>
+ member_solve(const mtl::dense_vector<value_type>& vin) const = 0;
+
+ virtual mtl::dense_vector<value_type>
+ member_adjoint_solve(const mtl::dense_vector<value_type>& vin) const = 0;
+ };
+
+ inline mtl::dense_vector<DOFMatrix::value_type>
+ solve(const ITL_BasePreconditioner& P, const mtl::dense_vector<DOFMatrix::value_type>& vin)
+ {
+ return P.member_solve(vin);
+ }
+
+ inline mtl::dense_vector<DOFMatrix::value_type>
+ adjoint_solve(const ITL_BasePreconditioner& P, const mtl::dense_vector<DOFMatrix::value_type>& vin)
+ {
+ return P.member_adjoint_solve(vin);
+ }
+
+ /**
+ * \ingroup Solver
+ *
+ * \brief Wrapper for using ITL preconditioners in AMDiS.
+ */
+ template <typename Preconditioner>
+ class ITL_Preconditioner : public ITL_BasePreconditioner
+ {
+ typedef DOFMatrix::value_type value_type;
+ public:
+ ITL_Preconditioner(const DOFMatrix::base_matrix_type& A) : precon(A) {}
+
+ mtl::dense_vector<value_type>
+ member_solve(const mtl::dense_vector<value_type>& vin) const
+ {
+ return solve(precon, vin);
+ }
+
+ mtl::dense_vector<value_type>
+ member_adjoint_solve(const mtl::dense_vector<value_type>& vin) const
+ {
+ return adjoint_solve(precon, vin);
+ }
+
+ /// Creator class used in the OEMSolverMap.
+ class Creator : public CreatorInterface<ITL_BasePreconditioner>
+ {
+ public:
+ MEMORY_MANAGED(Creator);
+
+ virtual ~Creator() {};
+
+ /** \brief
+ * Creates an ITL preconditioner
+ */
+ ITL_BasePreconditioner *create(const DOFMatrix::base_matrix_type& A) {
+ return NEW ITL_Preconditioner<Preconditioner>(A);
+ }
+
+ ITL_BasePreconditioner *create() {
+ ERROR_EXIT("Must not be called! Only defined to avoid abstract function."); return 0;
+ }
+ };
+
+ private:
+ Preconditioner precon;
+ };
+
+
+ // ============================================================================
+ // ===== class DiagonalPreconditioner =========================================
+ // ============================================================================
+
+ /**
+ * \ingroup Solver
+ *
+ * \brief
+ * Diagonal preconditioner.
+ */
+ class DiagonalPreconditioner
+ : public ITL_Preconditioner<itl::pc::diagonal<DOFMatrix::base_matrix_type> >
+ {
+ typedef ITL_Preconditioner<itl::pc::diagonal<DOFMatrix::base_matrix_type> > base;
+
+ DiagonalPreconditioner(const DOFMatrix::base_matrix_type& A) : base(A) {}
+ };
+
+ /**
+ * \ingroup Solver
+ *
+ * \brief
+ * Identity preconditioner. Behaves like no preconditioning.
+ */
+ class IdentityPreconditioner
+ : public ITL_Preconditioner<itl::pc::identity<DOFMatrix::base_matrix_type> >
+ {
+ typedef ITL_Preconditioner<itl::pc::identity<DOFMatrix::base_matrix_type> > base;
+
+ IdentityPreconditioner(const DOFMatrix::base_matrix_type& A) : base(A) {}
+ };
+
+
+ // ============================================================================
+ // ===== class ILUPreconditioner ==============================================
+ // ============================================================================
+
+ /**
+ * \ingroup Solver
+ *
+ * \brief
+ * ILU (Incomplete LU factorization) preconditioner.
+ *
+ * The preconditioner is used from ITL. It corresponds for instance to "Iterative Methods for
+ * Sparce Linear Systems", second edition, Yousef Saad. The preconditioner is
+ * described in chapter 10.3 (algorithm 10.4).
+ */
+ class ILUPreconditioner
+ : public ITL_Preconditioner< itl::pc::ilu_0<DOFMatrix::base_matrix_type> >
+ {};
+
+ class ICPreconditioner
+ : public ITL_Preconditioner< itl::pc::ic_0<DOFMatrix::base_matrix_type> >
+ {};
+
+
+} // namespace AMDiS
+
+#endif // AMDIS_ITL_PRECONDITIONER_H
diff --git a/AMDiS/src/ITL_Solver.h b/AMDiS/src/ITL_Solver.h
new file mode 100644
index 00000000..3043d36b
--- /dev/null
+++ b/AMDiS/src/ITL_Solver.h
@@ -0,0 +1,180 @@
+// ============================================================================
+// == ==
+// == AMDiS - Adaptive multidimensional simulations ==
+// == ==
+// ============================================================================
+// == ==
+// == crystal growth group ==
+// == ==
+// == Stiftung caesar ==
+// == Ludwig-Erhard-Allee 2 ==
+// == 53175 Bonn ==
+// == germany ==
+// == ==
+// ============================================================================
+// == ==
+// == http://www.caesar.de/cg/AMDiS ==
+// == ==
+// ============================================================================
+
+/** \file ITL_Preconditioner.h */
+
+#ifndef AMDIS_ITL_SOLVER_H
+#define AMDIS_ITL_SOLVER_H
+
+#include "ITL_OEMSolver.h"
+#include <boost/numeric/itl/krylov/cg.hpp>
+#include <boost/numeric/itl/krylov/bicg.hpp>
+#include <boost/numeric/itl/krylov/bicgstab.hpp>
+#include <boost/numeric/itl/krylov/bicgstab_2.hpp>
+#include <boost/numeric/itl/krylov/bicgstab_ell.hpp>
+
+namespace AMDiS {
+
+ // ============================================================================
+ // ===== class CGSolver =======================================================
+ // ============================================================================
+
+ /// Helper class to establish a type from a function
+ class cg_solver_type
+ {
+ public:
+ template < class LO, class X, class B, class L, class R, class I >
+ int operator()(const LO& A, X& x, const B& b, const L& l, const R& r, I& iter)
+ { return itl::cg(A, x, b, l, r, iter); }
+ };
+
+
+ /**
+ * \ingroup Solver
+ *
+ * \brief
+ * Solves a linear system by the conjugate gradient method and can be used for
+ * symmetric positive definite system matrices.
+ */
+ class CGSolver : public ITL_OEMSolver<cg_solver_type>
+ {
+ public:
+ /// The constructor reads required parameters and sets solvers \ref name.
+ CGSolver(std::string name) : ITL_OEMSolver<cg_solver_type>(name) {}
+ };
+
+
+ // ============================================================================
+ // ===== class BiCGSolver =====================================================
+ // ============================================================================
+
+ /// Helper class to establish a type from a function
+ class bicg_solver_type
+ {
+ public:
+ template < class LO, class X, class B, class L, class R, class I >
+ int operator()(const LO& A, X& x, const B& b, const L& l, const R&, I& iter)
+ { return itl::bicg(A, x, b, l, iter); }
+ };
+
+ /**
+ * \ingroup Solver
+ *
+ * \brief
+ * Solves a linear system by a stabilized BiCG method and can be used for
+ * system matrices.
+ */
+ class BiCGSolver : public ITL_OEMSolver<bicg_solver_type>
+ {
+ public:
+ /// The constructor reads required parameters and sets solvers \ref name.
+ BiCGSolver(::std::string name) : ITL_OEMSolver<bicg_solver_type>(name) {}
+ };
+
+
+ // ============================================================================
+ // ===== class BiCGStab =======================================================
+ // ============================================================================
+
+ /// Helper class to establish a type from a function
+ class bicgstab_type
+ {
+ public:
+ template < class LinOp, class X, class B, class L, class R, class I >
+ int operator()(const LinOp& A, X& x, const B& b, const L& l, const R&, I& iter)
+ { return itl::bicgstab(A, x, b, l, iter); }
+ };
+
+
+ /**
+ * \ingroup Solver
+ *
+ * \brief
+ * Solves a linear system by a stabilized BiCG method and can be used for
+ * system matrices.
+ */
+ class BiCGStab : public ITL_OEMSolver<bicgstab_type>
+ {
+ public:
+ /// The constructor reads required parameters and sets solvers \ref name.
+ BiCGStab(::std::string name) : ITL_OEMSolver<bicgstab_type>(name) {}
+ };
+
+
+ // ============================================================================
+ // ===== class BiCGStab2 ======================================================
+ // ============================================================================
+
+ /// Helper class to establish a type from a function
+ class bicgstab2_type
+ {
+ public:
+ template < class LinOp, class X, class B, class L, class R, class I >
+ int operator()(const LinOp& A, X& x, const B& b, const L& l, const R&, I& iter)
+ { return itl::bicgstab_2(A, x, b, l, iter); }
+ };
+
+
+ /**
+ * \ingroup Solver
+ *
+ * \brief
+ * Solves a linear system by a stabilized BiCG method and can be used for
+ * system matrices.
+ */
+ class BiCGStab2 : public ITL_OEMSolver<bicgstab2_type>
+ {
+ public:
+ /// The constructor reads required parameters and sets solvers \ref name.
+ BiCGStab2(::std::string name) : ITL_OEMSolver<bicgstab2_type>(name) {}
+ };
+
+
+ // ============================================================================
+ // ===== class BiCGStabEll ======================================================
+ // ============================================================================
+
+ /// Helper class to establish a type from a function
+ class bicgstab_ell_type
+ {
+ public:
+ template < class LinOp, class X, class B, class L, class R, class I >
+ int operator()(const LinOp& A, X& x, const B& b, const L& l, const R& r, I& iter, int ell)
+ { return itl::bicgstab_ell(A, x, b, l, r, iter, ell); }
+ };
+
+ /**
+ * \ingroup Solver
+ *
+ * \brief
+ * Solves a linear system by a stabilized BiCG method and can be used for
+ * system matrices.
+ */
+ class BiCGStabEll : public ITL_OEMSolver_para<bicgstab_ell_type>
+ {
+ public:
+ /// The constructor reads required parameters and sets solvers \ref name.
+ BiCGStabEll(::std::string name) : ITL_OEMSolver_para<bicgstab_ell_type>(name) {}
+ };
+
+
+} // namespace AMDiS
+
+#endif // AMDIS_ITL_SOLVER
+
diff --git a/AMDiS/src/InterpolRestrictMatrix.cc b/AMDiS/src/InterpolRestrictMatrix.cc
index ce924771..e1f2de8a 100644
--- a/AMDiS/src/InterpolRestrictMatrix.cc
+++ b/AMDiS/src/InterpolRestrictMatrix.cc
@@ -142,12 +142,30 @@ namespace AMDiS {
}
}
+ // Disabled for the moment
+
+ void InterpolRestrictMatrix::mv(DOFVectorBase<double> *src,
+ DOFVectorBase<double> *dest,
+ int coarseLevel)
+ {ERROR_EXIT("Will be rewritten - Peter\n");}
+
+ void InterpolRestrictMatrix::assembleDOFMatrix(DOFMatrix *dest,
+ int coarseLevel)
+ {ERROR_EXIT("Will be rewritten - Peter\n");}
+
+ void InterpolRestrictMatrix::print()
+ {ERROR_EXIT("Will be rewritten - Peter\n");}
+
+
+#if 0
+
+
void InterpolRestrictMatrix::mv(DOFVectorBase<double> *src,
DOFVectorBase<double> *dest,
int coarseLevel)
{
FUNCNAME("InterpolRestrictMatrix::mv()");
-
+
if(!initialized_) {
initialized_ = true;
fillMemory();
@@ -544,4 +562,5 @@ namespace AMDiS {
}
}
}
-}
+#endif
+} // namespace AMDiS
diff --git a/AMDiS/src/InterpolRestrictMatrix.h b/AMDiS/src/InterpolRestrictMatrix.h
index d45ec5ee..3e7c84b2 100644
--- a/AMDiS/src/InterpolRestrictMatrix.h
+++ b/AMDiS/src/InterpolRestrictMatrix.h
@@ -4,15 +4,13 @@
#include <map>
#include <vector>
#include <string>
+
+#include "AMDiS_fwd.h"
#include "Global.h"
#include "MemoryManager.h"
namespace AMDiS {
- class DOFMatrix;
- class Element;
- template<typename T> class DOFVectorBase;
-
/** \brief
* Defines the data structure for a general interpolation or restriction matrix.
* Both can be used to map vectors from a fine mesh to a coarser mesh and vice
diff --git a/AMDiS/src/JacobiSmoother.cc b/AMDiS/src/JacobiSmoother.cc
index 8a4e5a64..0aeed6a4 100755
--- a/AMDiS/src/JacobiSmoother.cc
+++ b/AMDiS/src/JacobiSmoother.cc
@@ -16,6 +16,9 @@ namespace AMDiS {
int iterations,
const std::set<DegreeOfFreedom> &dofSet)
{
+ ERROR_EXIT("Will be rewritten - Peter\n");
+
+#if 0
int i, j, rowNumber, colNumber, numCols;
double entry, diagEntry = 0.0;
@@ -52,6 +55,7 @@ namespace AMDiS {
(*solution)[rowNumber] += (1.0 - omega_) * oldSolution[rowNumber];
}
}
+#endif
}
template<>
@@ -66,6 +70,7 @@ namespace AMDiS {
{
ERROR_EXIT("not yet (still gs)\n");
+#if 0
int numComponents = s->getSize();
int i, j, k, l;
int rowNumber, colNumber, numCols;
@@ -114,6 +119,7 @@ namespace AMDiS {
}
}
}
+#endif
}
}
diff --git a/AMDiS/src/LeafData.cc b/AMDiS/src/LeafData.cc
index 25d7e32b..4a78281e 100644
--- a/AMDiS/src/LeafData.cc
+++ b/AMDiS/src/LeafData.cc
@@ -32,7 +32,10 @@ namespace AMDiS {
int elTypeParent)
{
- bool test = otherChild->deleteElementData(ESTIMATABLE);
+#ifndef NDEBUG
+ bool test =
+#endif
+ otherChild->deleteElementData(ESTIMATABLE);
TEST_EXIT_DBG(test)("couldn't delete LeafDataEstimatable at otherChild");
parent->setElementData(NEW LeafDataEstimatable(parent->getElementData()));
diff --git a/AMDiS/src/MatVecMultiplier.cc b/AMDiS/src/MatVecMultiplier.cc
index d670b60b..741e8753 100644
--- a/AMDiS/src/MatVecMultiplier.cc
+++ b/AMDiS/src/MatVecMultiplier.cc
@@ -8,7 +8,8 @@
#include "DOFVector.h"
#include "MatrixVector.h"
#include "SystemVector.h"
-#include "V3Vector.h"
+
+// These sources are rather suspicious -- Peter
namespace AMDiS {
@@ -69,6 +70,9 @@ namespace AMDiS {
template<>
void MassLumpingMatVec<DOFMatrix, DOFVector<double> >::calcMassLumpingMatrix(DOFMatrix *m)
{
+ ERROR_EXIT("Will be rewritten (if any needs it) - Peter\n");
+
+#if 0
// create new or clear old matrix
if (!matrix) {
matrix = NEW DOFMatrix(m->getRowFESpace(),
@@ -110,11 +114,15 @@ namespace AMDiS {
(*rowIt2)[0].col = rowIt2.getDOFIndex();
(*rowIt2)[0].entry = 1.0 / rowSum;
}
+#endif
}
template<>
void MassLumpingMatVec<Matrix<DOFMatrix*>, SystemVector>::calcMassLumpingMatrix(Matrix<DOFMatrix*> *m)
{
+ ERROR_EXIT("Will be rewritten (if any needs it) - Peter\n");
+
+#if 0
int numComponents = m->getNumRows();
// create new or clear old matrix
if(!matrix) {
@@ -163,6 +171,7 @@ namespace AMDiS {
(*rowIt2)[0].entry = 1.0 / rowSum;
}
}
+#endif
}
diff --git a/AMDiS/src/MultiGridPreconWrapper.cc b/AMDiS/src/MultiGridPreconWrapper.cc
index bdddb726..42ef2f8e 100644
--- a/AMDiS/src/MultiGridPreconWrapper.cc
+++ b/AMDiS/src/MultiGridPreconWrapper.cc
@@ -1,3 +1,5 @@
+#if 0
+
#include "MultiGridPreconWrapper.h"
#include "MultiGridSolver.h"
#include "DOFVector.h"
@@ -43,3 +45,5 @@ namespace AMDiS {
}
}
+
+#endif
diff --git a/AMDiS/src/MultiGridPreconWrapper.h b/AMDiS/src/MultiGridPreconWrapper.h
index 3dfb38d0..961c75d0 100644
--- a/AMDiS/src/MultiGridPreconWrapper.h
+++ b/AMDiS/src/MultiGridPreconWrapper.h
@@ -22,6 +22,8 @@
#ifndef AMDIS_MULTIGRIDPRECONWRAPPER_H
#define AMDIS_MULTIGRIDPRECONWRAPPER_H
+#if 0
+
#include "Preconditioner.h"
#include "MemoryManager.h"
@@ -93,3 +95,5 @@ namespace AMDiS {
}
#endif
+
+#endif
diff --git a/AMDiS/src/MultiGridSolver.cc b/AMDiS/src/MultiGridSolver.cc
index a58e7d69..8a56fd7c 100644
--- a/AMDiS/src/MultiGridSolver.cc
+++ b/AMDiS/src/MultiGridSolver.cc
@@ -1,3 +1,5 @@
+#if 0
+
#include "MultiGridSolver.h"
#include "FiniteElemSpace.h"
#include "DOFVector.h"
@@ -14,11 +16,47 @@
#include "InterpolRestrictMatrix.h"
#include "LagrangeInterpolRestrict.h"
#include "DirichletBC.h"
-#include "OpenMP.h"
namespace AMDiS {
- MultiGridSolverScal::MultiGridSolverScal(const std::string &name)
+
+ MultiGridSolverScal::MultiGridSolverScal(const ::std::string &name)
+ : MultiGridSolverBase<DOFMatrix, DOFVector<double> >(name) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::initMaxLevel() {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::initMultiGrid(bool initMG) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::exitMultiGrid() {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::smooth(int level, int steps) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::prolongate(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::restrict(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::computeResidual(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::computeRHS(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::computeCorrection(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::fixSolution(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::exactSolve(int level) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ bool MultiGridSolverScal::toleranceReached(double tol) {ERROR_EXIT("Will be rewritten - Peter\n"); return true; }
+ void MultiGridSolverScal::initFullMultiGrid() {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverScal::fmgInterpol(int level) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ MultiGridSolverVec::MultiGridSolverVec(const ::std::string &name)
+ : MultiGridSolverBase<Matrix<DOFMatrix*>, SystemVector>(name) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::initMaxLevel() {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::initMultiGrid(bool initMG) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::exitMultiGrid() {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::smooth(int level, int steps) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::prolongate(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::restrict(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::computeResidual(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::computeRHS(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::computeCorrection(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::fixSolution(int level, int coarseLevel) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::exactSolve(int level) {ERROR_EXIT("Will be rewritten - Peter\n");}
+ bool MultiGridSolverVec::toleranceReached(double tol) {ERROR_EXIT("Will be rewritten - Peter\n"); return true; }
+ void MultiGridSolverVec::initFullMultiGrid() {ERROR_EXIT("Will be rewritten - Peter\n");}
+ void MultiGridSolverVec::fmgInterpol(int level) {ERROR_EXIT("Will be rewritten - Peter\n");}
+
+
+#if 0
+
+ MultiGridSolverScal::MultiGridSolverScal(const ::std::string &name)
: MultiGridSolverBase<DOFMatrix, DOFVector<double> >(name),
sparseResidual_(NULL),
denseResidual_(NULL),
@@ -39,11 +77,11 @@ namespace AMDiS {
GET_PARAMETER(0, name_ + "->use galerkin operator", "%d", &galerkin_);
// Create smoother
- std::string smootherType("gs");
+ ::std::string smootherType("gs");
GET_PARAMETER(0, name_ + "->smoother", &smootherType);
- SmootherCreator<DOFMatrix, SparseVector<double>, std::set<DegreeOfFreedom> > *smootherCreator =
- dynamic_cast<SmootherCreator<DOFMatrix, SparseVector<double>, std::set<DegreeOfFreedom> >*>(
- CreatorMap<SmootherBase<DOFMatrix, SparseVector<double>, std::set<DegreeOfFreedom> > >::getCreator(smootherType));
+ SmootherCreator<DOFMatrix, SparseVector<double>, ::std::set<DegreeOfFreedom> > *smootherCreator =
+ dynamic_cast<SmootherCreator<DOFMatrix, SparseVector<double>, ::std::set<DegreeOfFreedom> >*>(
+ CreatorMap<SmootherBase<DOFMatrix, SparseVector<double>, ::std::set<DegreeOfFreedom> > >::getCreator(smootherType));
if (smootherCreator && !smootherCreator->isNullCreator()) {
smootherCreator->setName(name_ + "->smoother");
@@ -120,8 +158,7 @@ namespace AMDiS {
}
}
- int error = mesh->queryCoarseDOFs();
- TEST_EXIT(error)("preserve coarse dofs not set in mesh\n");
+ TEST_EXIT(mesh->queryCoarseDOFs())("preserve coarse dofs not set in mesh\n");
const BasisFunction *basFcts = feSpace->getBasisFcts();
int numDOFs = basFcts->getNumber();
@@ -150,17 +187,14 @@ namespace AMDiS {
int level;
// Iterators for all operators of the system matrix.
- std::vector<Operator*>::iterator it;
- std::vector<Operator*>::iterator opBegin = systemMatrix_->getOperatorsBegin();
- std::vector<Operator*>::iterator opEnd = systemMatrix_->getOperatorsEnd();
-
- std::vector<double*>::iterator factorIt;
- std::vector<double*>::iterator factorBegin = systemMatrix_->getOperatorFactorBegin();
+ ::std::vector<Operator*>::iterator it;
+ ::std::vector<Operator*>::iterator opBegin = systemMatrix_->getOperatorsBegin();
+ ::std::vector<Operator*>::iterator opEnd = systemMatrix_->getOperatorsEnd();
+ ::std::vector<double*>::iterator factorIt;
+ ::std::vector<double*>::iterator factorBegin = systemMatrix_->getOperatorFactorBegin();
ElementMatrix *elementMatrix = NULL;
- ERROR_EXIT("Initialize elementMatrix with a non NULL value!\n");
-
- BoundaryType *bound = GET_MEMORY(BoundaryType, numDOFs);
+ const BoundaryType *bound;
TraverseStack stack;
@@ -193,8 +227,8 @@ namespace AMDiS {
element = elInfo->getElement();
level = elInfo->getLevel();
basFcts->getLocalIndices(element, admin, dofs);
- basFcts->getBound(elInfo, bound);
- (*opBegin)->getAssembler(omp_get_thread_num())->initElementMatrix(elementMatrix, elInfo);
+ bound = basFcts->getBound(elInfo, NULL);
+ elementMatrix = (*opBegin)->getAssembler()->initElementMatrix(elementMatrix, elInfo);
bool levelUsed = isMGLevel_[level];
@@ -277,8 +311,6 @@ namespace AMDiS {
} // if-else element is leaf
elInfo = stack.traverseNext(elInfo);
} // while elInfo
-
- FREE_MEMORY(bound, BoundaryType, numDOFs);
if (!galerkin_) {
// Fill boundary conditions
@@ -324,7 +356,7 @@ namespace AMDiS {
DOFMatrix *fineMatrix = levels_[maxLevel_].matrix_;
for (level = maxLevel_ - 1; level >= minLevel_; level--) {
- std::map< std::pair<int, int>, bool> visited;
+ ::std::map< ::std::pair<int, int>, bool> visited;
coarseMatrix =
isMGLevel_[level] ?
@@ -360,7 +392,7 @@ namespace AMDiS {
for (int i = 0; i < dim + 1; i++) {
for (int j = 0; j < dim + 1; j++) {
- if(visited[std::pair<int, int>(fineDOFs[i], fineDOFs[j])] == false)
+ if(visited[::std::pair<int, int>(fineDOFs[i], fineDOFs[j])] == false)
coarseMatrix->addSparseDOFEntry(1.0,
parentDOFs[i],
parentDOFs[j],
@@ -371,7 +403,7 @@ namespace AMDiS {
for (int i = 0; i < dim + 1; i++) {
for (int j = 0; j < dim + 1; j++) {
- if(visited[std::pair<int, int>(fineDOFs[i], fineDOFs[j])] == false)
+ if(visited[::std::pair<int, int>(fineDOFs[i], fineDOFs[j])] == false)
coarseMatrix->addSparseDOFEntry(1.0,
parentDOFs[i],
parentDOFs[j],
@@ -382,7 +414,7 @@ namespace AMDiS {
for (int i = 0; i < dim + 1; i++) {
for (int j = 0; j < 2; j++) {
- if(visited[std::pair<int, int>(fineDOFs[i], fineDOFs[dim + 1])] == false) {
+ if(visited[::std::pair<int, int>(fineDOFs[i], fineDOFs[dim + 1])] == false) {
coarseMatrix->addSparseDOFEntry(0.5,
parentDOFs[i],
parentDOFs[j],
@@ -398,7 +430,7 @@ namespace AMDiS {
}
}
- if (visited[std::pair<int, int>(fineDOFs[dim + 1], fineDOFs[dim + 1])] == false) {
+ if (visited[::std::pair<int, int>(fineDOFs[dim + 1], fineDOFs[dim + 1])] == false) {
for (int i = 0; i < 2; i++) {
for (int j = 0; j < 2; j++) {
coarseMatrix->addSparseDOFEntry(0.25,
@@ -412,8 +444,8 @@ namespace AMDiS {
for (int i = 0; i < dim + 2; i++) {
for (int j = 0; j < dim + 2; j++) {
- visited[std::pair<int, int>(fineDOFs[i], fineDOFs[j])] = true;
- visited[std::pair<int, int>(fineDOFs[j], fineDOFs[i])] = true;
+ visited[::std::pair<int, int>(fineDOFs[i], fineDOFs[j])] = true;
+ visited[::std::pair<int, int>(fineDOFs[j], fineDOFs[i])] = true;
}
}
}
@@ -429,7 +461,7 @@ namespace AMDiS {
for (int i = 0; i < dim + 1; i++) {
for (int j = 0; j < dim + 1; j++) {
- if (!visited[std::pair<int, int>(parentDOFs[i], parentDOFs[j])]) {
+ if (!visited[::std::pair<int, int>(parentDOFs[i], parentDOFs[j])]) {
coarseMatrix->addSparseDOFEntry(1.0,
parentDOFs[i],
parentDOFs[j],
@@ -550,8 +582,8 @@ namespace AMDiS {
levels_[coarseLevel].oldSolution_->copy(*(levels_[level].solution_),
levels_[level].nearestNeighbourDOFs_);
- std::vector<Element*>::iterator elIt, elBegin, elEnd;
- std::vector<int>::iterator typeIt;
+ ::std::vector<Element*>::iterator elIt, elBegin, elEnd;
+ ::std::vector<int>::iterator typeIt;
for (int i = level; i > coarseLevel; i--) {
elBegin = levels_[i-1].elements_.begin();
@@ -827,7 +859,7 @@ namespace AMDiS {
// ===============================================================================
// ===============================================================================
- MultiGridSolverVec::MultiGridSolverVec(const std::string &name)
+ MultiGridSolverVec::MultiGridSolverVec(const ::std::string &name)
: MultiGridSolverBase<Matrix<DOFMatrix*>, SystemVector>(name),
sparseResidual_(NULL),
denseResidual_(NULL),
@@ -850,14 +882,14 @@ namespace AMDiS {
GET_PARAMETER(0, name_ + "->use galerkin operator", "%d", &galerkin_);
// Create smoother
- std::string smootherType("gs");
+ ::std::string smootherType("gs");
GET_PARAMETER(0, name_ + "->smoother", &smootherType);
if(smootherType == "box") {
boxSmoothing_ = true;
}
- SmootherCreator<Matrix<DOFMatrix*>, Vector<SparseVector<double>*>, Vector< std::set<DegreeOfFreedom>*> > *smootherCreator =
- dynamic_cast<SmootherCreator<Matrix<DOFMatrix*>, Vector<SparseVector<double>*>, Vector< std::set<DegreeOfFreedom>*> >*>(
- CreatorMap<SmootherBase<Matrix<DOFMatrix*>, Vector<SparseVector<double>*>, Vector< std::set<DegreeOfFreedom>*> > >::getCreator(smootherType)
+ SmootherCreator<Matrix<DOFMatrix*>, Vector<SparseVector<double>*>, Vector< ::std::set<DegreeOfFreedom>*> > *smootherCreator =
+ dynamic_cast<SmootherCreator<Matrix<DOFMatrix*>, Vector<SparseVector<double>*>, Vector< ::std::set<DegreeOfFreedom>*> >*>(
+ CreatorMap<SmootherBase<Matrix<DOFMatrix*>, Vector<SparseVector<double>*>, Vector< ::std::set<DegreeOfFreedom>*> > >::getCreator(smootherType)
);
if(smootherCreator && !smootherCreator->isNullCreator()) {
smootherCreator->setName(name_ + "->smoother");
@@ -871,7 +903,7 @@ namespace AMDiS {
void MultiGridSolverVec::initMaxLevel()
{
int comp, numComps = solution_->getNumVectors();
- std::set<Mesh*> meshes;
+ ::std::set<Mesh*> meshes;
for(comp = 0; comp < numComps; comp++) {
Mesh *mesh = solution_->getDOFVector(comp)->getFESpace()->getMesh();
if(find(meshes.begin(), meshes.end(), mesh) == meshes.end()) {
@@ -904,7 +936,7 @@ namespace AMDiS {
// Get fe spaces and create residual vectors
sparseResidual_ = NEW Vector<SparseVector<double>*>(numComponents_);
- std::vector<FiniteElemSpace*> feSpaces(numComponents_);
+ ::std::vector<FiniteElemSpace*> feSpaces(numComponents_);
for (int i = 0; i < numComponents_; i++) {
feSpaces[i] = const_cast<FiniteElemSpace*>
(solution_->getDOFVector(i)->getFESpace());
@@ -924,8 +956,9 @@ namespace AMDiS {
Mesh *mesh = feSpaces[0]->getMesh();
int dim = mesh->getDim();
- int error = mesh->queryCoarseDOFs();
- TEST_EXIT(error)("preserve coarse dofs not set in mesh\n");
+ TEST_EXIT(mesh->queryCoarseDOFs())
+ ("preserve coarse dofs not set in mesh\n");
+
// Check which level is a multigrid level and set the corresponding field
// to true.
@@ -958,7 +991,7 @@ namespace AMDiS {
levels_[i].components_.resize(numComponents_);
levels_[i].levelDOFs_.resize(numComponents_);
- std::map<FiniteElemSpace*, FESpaceData*> feSpaceData;
+ ::std::map<FiniteElemSpace*, FESpaceData*> feSpaceData;
MeshData *meshData = NEW MeshData;
levels_[i].solution_ = NEW Vector<SparseVector<double>*>(numComponents_);
@@ -1053,17 +1086,16 @@ namespace AMDiS {
elInfo = stack.traverseNext(elInfo);
}
- BoundaryType *bound = GET_MEMORY(BoundaryType, numDOFs);
-
for (int col = 0; col < numComponents_; col++) {
DOFMatrix *dofMatrix = (*systemMatrix_)[row][col];
- if (dofMatrix) {
- std::vector<Operator*>::iterator it;
- std::vector<Operator*>::iterator opBegin = dofMatrix->getOperatorsBegin();
- std::vector<Operator*>::iterator opEnd = dofMatrix->getOperatorsEnd();
- std::vector<double*>::iterator factorIt;
- std::vector<double*>::iterator factorBegin = dofMatrix->getOperatorFactorBegin();
+ if(dofMatrix) {
+ ::std::vector<Operator*>::iterator it;
+ ::std::vector<Operator*>::iterator opBegin = dofMatrix->getOperatorsBegin();
+ ::std::vector<Operator*>::iterator opEnd = dofMatrix->getOperatorsEnd();
+ ::std::vector<double*>::iterator factorIt;
+ ::std::vector<double*>::iterator factorBegin = dofMatrix->getOperatorFactorBegin();
ElementMatrix *elementMatrix = NULL;
+ const BoundaryType *bound;
// assemble level matrices and create dof sets
elInfo = stack.traverseFirst(mesh, -1,
@@ -1077,8 +1109,8 @@ namespace AMDiS {
element = elInfo->getElement();
level = elInfo->getLevel();
basFcts->getLocalIndices(element, admin, dofs);
- basFcts->getBound(elInfo, bound);
- (*opBegin)->getAssembler(omp_get_thread_num())->initElementMatrix(elementMatrix, elInfo);
+ bound = basFcts->getBound(elInfo, NULL);
+ elementMatrix = (*opBegin)->getAssembler()->initElementMatrix(elementMatrix, elInfo);
bool levelUsed = isMGLevel_[level];
if (levelUsed) {
@@ -1169,7 +1201,6 @@ namespace AMDiS {
}
}
- FREE_MEMORY(bound, BoundaryType, numDOFs);
FREE_MEMORY(dofs, DegreeOfFreedom, numDOFs);
}
@@ -1210,7 +1241,7 @@ namespace AMDiS {
for (level = maxLevel_ - 1; level >= 0; level--) {
if (level >= minLevel_) {
- std::map< std::pair<int, int>, bool> visited;
+ ::std::map< ::std::pair<int, int>, bool> visited;
coarseMatrix =
isMGLevel_[level] ?
(*(levels_[level].matrix_))[row][col] :
@@ -1244,7 +1275,7 @@ namespace AMDiS {
for (int i = 0; i < dim + 1; i++) {
for(int j = 0; j < dim + 1; j++) {
- if (visited[std::pair<int, int>(fineDOFs[i], fineDOFs[j])] == false) {
+ if (visited[::std::pair<int, int>(fineDOFs[i], fineDOFs[j])] == false) {
coarseMatrix->addSparseDOFEntry(1.0,
parentDOFs[i],
parentDOFs[j],
@@ -1256,7 +1287,7 @@ namespace AMDiS {
for (int i = 0; i < dim + 1; i++) {
for (int j = 0; j < dim + 1; j++) {
- if (visited[std::pair<int, int>(fineDOFs[i], fineDOFs[j])] == false) {
+ if (visited[::std::pair<int, int>(fineDOFs[i], fineDOFs[j])] == false) {
coarseMatrix->addSparseDOFEntry(1.0,
parentDOFs[i],
parentDOFs[j],
@@ -1268,7 +1299,7 @@ namespace AMDiS {
for (int i = 0; i < dim + 1; i++) {
for (int j = 0; j < 2; j++) {
- if (visited[std::pair<int, int>(fineDOFs[i], fineDOFs[dim + 1])] == false) {
+ if (visited[::std::pair<int, int>(fineDOFs[i], fineDOFs[dim + 1])] == false) {
coarseMatrix->addSparseDOFEntry(0.5,
parentDOFs[i],
parentDOFs[j],
@@ -1284,7 +1315,7 @@ namespace AMDiS {
}
}
- if (visited[std::pair<int, int>(fineDOFs[dim + 1], fineDOFs[dim + 1])] == false) {
+ if (visited[::std::pair<int, int>(fineDOFs[dim + 1], fineDOFs[dim + 1])] == false) {
for (int i = 0; i < 2; i++) {
for (int j = 0; j < 2; j++) {
coarseMatrix->addSparseDOFEntry(0.25,
@@ -1298,8 +1329,8 @@ namespace AMDiS {
for (int i = 0; i < dim + 2; i++) {
for (int j = 0; j < dim + 2; j++) {
- visited[std::pair<int, int>(fineDOFs[i], fineDOFs[j])] = true;
- visited[std::pair<int, int>(fineDOFs[j], fineDOFs[i])] = true;
+ visited[::std::pair<int, int>(fineDOFs[i], fineDOFs[j])] = true;
+ visited[::std::pair<int, int>(fineDOFs[j], fineDOFs[i])] = true;
}
}
}
@@ -1316,7 +1347,7 @@ namespace AMDiS {
for (int i = 0; i < dim + 1; i++) {
for (int j = 0; j < dim + 1; j++) {
- if (!visited[std::pair<int, int>(parentDOFs[i], parentDOFs[j])]) {
+ if (!visited[::std::pair<int, int>(parentDOFs[i], parentDOFs[j])]) {
coarseMatrix->addSparseDOFEntry(1.0,
parentDOFs[i],
parentDOFs[j],
@@ -1342,7 +1373,7 @@ namespace AMDiS {
if (boxSmoothing_) {
boxDOFs_.resize(numComponents_);
for (int i = 0; i < numComponents_; i++) {
- boxDOFs_[i] = new std::set<DegreeOfFreedom>;
+ boxDOFs_[i] = new ::std::set<DegreeOfFreedom>;
}
}
@@ -1385,15 +1416,15 @@ namespace AMDiS {
{
int numLevels = maxLevel_ + 1;
- std::set<FESpaceData*> deletedFESpaceData;
- std::set<MeshData*> deletedMeshData;
+ ::std::set<FESpaceData*> deletedFESpaceData;
+ ::std::set<MeshData*> deletedMeshData;
for (int i = 0; i < numLevels; i++) {
if (isMGLevel_[i]) {
for (int j = 0; j < numComponents_; j++) {
if (levels_[i].components_[j].meshData_) {
- std::set<MeshData*>::iterator it;
- it = std::find(deletedMeshData.begin(),
+ ::std::set<MeshData*>::iterator it;
+ it = ::std::find(deletedMeshData.begin(),
deletedMeshData.end(),
levels_[i].components_[j].meshData_);
if (it == deletedMeshData.end()) {
@@ -1403,8 +1434,8 @@ namespace AMDiS {
}
}
if (levels_[i].components_[j].feSpaceData_) {
- std::set<FESpaceData*>::iterator it;
- it = std::find(deletedFESpaceData.begin(),
+ ::std::set<FESpaceData*>::iterator it;
+ it = ::std::find(deletedFESpaceData.begin(),
deletedFESpaceData.end(),
levels_[i].components_[j].feSpaceData_);
if (it == deletedFESpaceData.end()) {
@@ -1454,7 +1485,7 @@ namespace AMDiS {
{
if (boxSmoothing_) {
for (int iteration = 0; iteration < steps; iteration++) {
- std::vector<Element*>::iterator elIt, elBegin, elEnd;
+ ::std::vector<Element*>::iterator elIt, elBegin, elEnd;
elBegin = levels_[level].elements_.begin();
elEnd = levels_[level].elements_.end();
for (elIt = elBegin; elIt != elEnd; ++elIt) {
@@ -1518,8 +1549,8 @@ namespace AMDiS {
void MultiGridSolverVec::restrict(int level, int coarseLevel)
{
- std::vector<Element*>::iterator elIt, elBegin, elEnd;
- std::vector<int>::iterator typeIt;
+ ::std::vector<Element*>::iterator elIt, elBegin, elEnd;
+ ::std::vector<int>::iterator typeIt;
for (int comp = 0; comp < numComponents_; comp++) {
(*(levels_[coarseLevel].oldSolution_))[comp]->
@@ -1568,7 +1599,7 @@ namespace AMDiS {
{
DOFMatrix *matrix;
SparseVector<double> *res, *sol, *rhs;
- std::set<DegreeOfFreedom> *dofSet;
+ ::std::set<DegreeOfFreedom> *dofSet;
for (int i = 0; i < numComponents_; i++) {
res = (*sparseResidual_)[i];
res->clear();
@@ -1590,7 +1621,7 @@ namespace AMDiS {
{
DOFMatrix *matrix;
SparseVector<double> *oldSol, *rhs, *res;
- std::set<DegreeOfFreedom> *dofSet;
+ ::std::set<DegreeOfFreedom> *dofSet;
for (int i = 0; i < numComponents_; i++) {
rhs = (*(levels_[coarseLevel].rhs_))[i];
rhs->clear();
@@ -1613,7 +1644,7 @@ namespace AMDiS {
void MultiGridSolverVec::computeCorrection(int level, int coarseLevel)
{
SparseVector<double> *res, *sol, *oldSol;
- std::set<DegreeOfFreedom> *dofSet;
+ ::std::set<DegreeOfFreedom> *dofSet;
for (int comp = 0; comp < numComponents_; comp++) {
dofSet = &(levels_[coarseLevel].components_[comp].feSpaceData_->fineDOFs_);
sol = (*(levels_[coarseLevel].solution_))[comp];
@@ -1628,7 +1659,7 @@ namespace AMDiS {
void MultiGridSolverVec::fixSolution(int level, int coarseLevel)
{
SparseVector<double> *fineSol, *coarseSol, *res;
- std::set<DegreeOfFreedom> *dofSet;
+ ::std::set<DegreeOfFreedom> *dofSet;
for (int comp = 0; comp < numComponents_; comp++) {
fineSol = (*(levels_[level].solution_))[comp];
coarseSol = (*(levels_[coarseLevel].solution_))[comp];
@@ -1654,7 +1685,7 @@ namespace AMDiS {
FUNCNAME("MultiGridSolverVec::toleranceReached()");
SparseVector<double> *sol;
- std::set<DegreeOfFreedom> *dofSet;
+ ::std::set<DegreeOfFreedom> *dofSet;
for (int level = minLevel_; level < maxLevel_ + 1; level++) {
if (isMGLevel_[level]) {
for (int i = 0; i < numComponents_; i++) {
@@ -1693,5 +1724,8 @@ namespace AMDiS {
ERROR_EXIT("not yet\n");
}
+#endif
}
+
+#endif
diff --git a/AMDiS/src/MultiGridSolver.h b/AMDiS/src/MultiGridSolver.h
index 40f84def..2e2de061 100644
--- a/AMDiS/src/MultiGridSolver.h
+++ b/AMDiS/src/MultiGridSolver.h
@@ -22,6 +22,9 @@
#ifndef AMDIS_MULTIGRIDSOLVER_H
#define AMDIS_MULTIGRIDSOLVER_H
+#if 0
+
+#include "AMDiS_fwd.h"
#include "MultiGridSolverBase.h"
#include <vector>
#include "Global.h"
@@ -33,15 +36,6 @@
namespace AMDiS {
- class DOFMatrix;
- template<typename T> class DOFVector;
- template<typename T> class SparseVector;
- class LevelAdmin;
- class FiniteElemSpace;
- class DOFAdmin;
- class RCNeighbourList;
- class InterpolRestrictMatrix;
-
/** \brief
* Implementation of the multigrid solver base class for scalar problems.
*/
@@ -633,3 +627,5 @@ namespace AMDiS {
}
#endif
+
+#endif
diff --git a/AMDiS/src/MultiGridSolverBase.h b/AMDiS/src/MultiGridSolverBase.h
index 8480db2f..5294b3f4 100755
--- a/AMDiS/src/MultiGridSolverBase.h
+++ b/AMDiS/src/MultiGridSolverBase.h
@@ -22,8 +22,8 @@
#ifndef AMDIS_MULTIGRIDSOLVERBASE_H
#define AMDIS_MULTIGRIDSOLVERBASE_H
-#include "InterpolRestrictMatrix.h"
-#include "LagrangeInterpolRestrict.h"
+#if 0
+
#include <string>
namespace AMDiS {
@@ -35,12 +35,12 @@ namespace AMDiS {
/** \brief
* Constructor, reads all multigrid parameters from the init file.
*/
- MultiGridSolverBase(const std::string &name);
+ MultiGridSolverBase(const ::std::string &name) ;
/** \brief
* Destructor
*/
- virtual ~MultiGridSolverBase() {}
+ virtual ~MultiGridSolverBase() {};
/** \brief
* Abstract function for solving an equation using multigrid method.
@@ -107,7 +107,7 @@ namespace AMDiS {
/** \brief
* Name of the problem, corresponding to the name in the init file.
*/
- std::string name_;
+ ::std::string name_;
/** \brief
* Tolerance for the computation. The multigrid method finished, if the
@@ -147,21 +147,11 @@ namespace AMDiS {
* zero value.
*/
int fmg_;
-
- /** \brief
- * interpolMatrices[n][m] stores the interpolation matrix for
- * n-dimensional elements and m-dimensional basis functions.
- */
- InterpolRestrictMatrix *interpolMatrices[3][4];
-
- /** \brief
- * interpolMatrices[n][m] stores the restriction matrix for
- * n-dimensional elements and m-dimensional basis functions.
- */
- InterpolRestrictMatrix *restrictMatrices[3][4];
};
}
#include "MultiGridSolverBase.hh"
#endif
+
+#endif
diff --git a/AMDiS/src/MultiGridSolverBase.hh b/AMDiS/src/MultiGridSolverBase.hh
index c4ff0c2f..77b9d9aa 100644
--- a/AMDiS/src/MultiGridSolverBase.hh
+++ b/AMDiS/src/MultiGridSolverBase.hh
@@ -1,3 +1,5 @@
+#if 0
+
#include "Global.h"
#include "Parameters.h"
@@ -136,3 +138,5 @@ namespace AMDiS {
}
}
+
+#endif
diff --git a/AMDiS/src/MultiGridWrapper.h b/AMDiS/src/MultiGridWrapper.h
index a0f6dcf1..272cc2e1 100644
--- a/AMDiS/src/MultiGridWrapper.h
+++ b/AMDiS/src/MultiGridWrapper.h
@@ -22,6 +22,8 @@
#ifndef AMDIS_MULTIGRIDWRAPPER_H
#define AMDIS_MULTIGRIDWRAPPER_H
+#if 0
+
#include "MultiGridSolver.h"
#include "MatVecMultiplier.h"
#include "OEMSolver.h"
@@ -29,6 +31,7 @@
namespace AMDiS {
+
/** \brief
* Wrapper to make the multigrid solver accessible as a normal scal solver.
*/
@@ -144,3 +147,5 @@ namespace AMDiS {
}
#endif
+
+#endif
diff --git a/AMDiS/src/Newton.h b/AMDiS/src/Newton.h
index d1bcc75f..1b6b1e25 100644
--- a/AMDiS/src/Newton.h
+++ b/AMDiS/src/Newton.h
@@ -25,13 +25,12 @@
#include "MemoryManager.h"
#include "CreatorInterface.h"
#include "NonLinSolver.h"
+#include "AMDiS_fwd.h"
namespace AMDiS {
class FiniteElemSpace;
- template<typename VectorType> class OEMSolver;
-
// ============================================================================
// ===== class Newton =========================================================
// ============================================================================
@@ -71,7 +70,7 @@ namespace AMDiS {
* Calls constructor of base class NonLinSolver
*/
Newton(const std::string& name_,
- OEMSolver<VectorType> *linSolver_,
+ OEMSolver *linSolver_,
NonLinUpdater<VectorType> *updater)
: NonLinSolver<VectorType>(name_, linSolver_, updater)
{};
diff --git a/AMDiS/src/NewtonS.h b/AMDiS/src/NewtonS.h
index db7661f5..6f7a2019 100644
--- a/AMDiS/src/NewtonS.h
+++ b/AMDiS/src/NewtonS.h
@@ -66,7 +66,7 @@ namespace AMDiS {
* Calls constructor of base class NonLinSolver
*/
NewtonS(const std::string& name_,
- OEMSolver<VectorType> *linSolver_,
+ OEMSolver *linSolver_,
NonLinUpdater<VectorType> *updater)
: NonLinSolver<VectorType>(name_, linSolver_, updater),
b(NULL),
diff --git a/AMDiS/src/NonLinSolver.h b/AMDiS/src/NonLinSolver.h
index ca729bd2..9e87bd32 100644
--- a/AMDiS/src/NonLinSolver.h
+++ b/AMDiS/src/NonLinSolver.h
@@ -22,14 +22,17 @@
#ifndef AMDIS_NONLINSOLVER_H
#define AMDIS_NONLINSOLVER_H
+#if 0
+
#include <string>
#include "Global.h"
#include "CreatorInterface.h"
+#include "AMDiS_fwd.h"
+#include "OEMSolver.h"
namespace AMDiS {
- template<typename VectorType> class OEMSolver;
template<typename VectorType> class NonLinUpdater;
// ============================================================================
@@ -53,7 +56,7 @@ namespace AMDiS {
* \param name name of this solver
*/
NonLinSolver(const std::string &name_,
- OEMSolver<VectorType> *linSolver_,
+ OEMSolver *linSolver_,
NonLinUpdater<VectorType> *updater);
/** \brief
@@ -88,7 +91,7 @@ namespace AMDiS {
vectorCreator = creator;
};
- inline OEMSolver<VectorType> *getLinearSolver() { return linSolver; };
+ inline OEMSolver *getLinearSolver() { return linSolver; };
inline void setNonLinUpdater(NonLinUpdater<VectorType> *up) {
nonLinUpdater = up;
@@ -124,12 +127,14 @@ namespace AMDiS {
{
FUNCNAME("NonLinSolver::solveLinearSystem()");
TEST_EXIT(linSolver)("no solver\n");
- return linSolver->solve(matVec, x, fh, lPrecon, rPrecon);
+ ERROR_EXIT("Not yet re-implemented!\n");
+ return -1;
+ // return linSolver->solve(matVec, x, fh, lPrecon, rPrecon);
};
protected:
std::string name; /**< \brief name of the solver */
- OEMSolver<VectorType> *linSolver; /**< \brief linear solver*/
+ OEMSolver *linSolver; /**< \brief linear solver*/
NonLinUpdater<VectorType> *nonLinUpdater; /**< \brief non linear updater */
double tolerance; /**< \brief solver tolerance */
int maxIter; /**< \brief maximal # of iterations */
@@ -156,7 +161,7 @@ namespace AMDiS {
void setName(std::string name_) { name = name_; };
- void setLinearSolver(OEMSolver<VectorType> *solver) { linearSolver = solver; };
+ void setLinearSolver(OEMSolver *solver) { linearSolver = solver; };
void setNonLinUpdater(NonLinUpdater<VectorType> *updater) {
nonLinUpdater = updater;
@@ -164,7 +169,7 @@ namespace AMDiS {
protected:
std::string name;
- OEMSolver<VectorType> *linearSolver;
+ OEMSolver *linearSolver;
NonLinUpdater<VectorType> *nonLinUpdater;
};
@@ -174,5 +179,8 @@ namespace AMDiS {
#include "Newton.h"
#include "NewtonS.h"
+
+#endif
+
#endif // AMDIS_NONLINSOLVER_H
diff --git a/AMDiS/src/NonLinSolver.hh b/AMDiS/src/NonLinSolver.hh
index 6dfb84a9..7bfb4e34 100644
--- a/AMDiS/src/NonLinSolver.hh
+++ b/AMDiS/src/NonLinSolver.hh
@@ -5,7 +5,7 @@ namespace AMDiS {
template<typename VectorType>
NonLinSolver<VectorType>::NonLinSolver(const std::string& name_,
- OEMSolver<VectorType> *solver,
+ OEMSolver *solver,
NonLinUpdater<VectorType> *updater)
: name(name_),
linSolver(solver),
diff --git a/AMDiS/src/NonLinUpdater.h b/AMDiS/src/NonLinUpdater.h
index bffe7026..5ee90dbe 100644
--- a/AMDiS/src/NonLinUpdater.h
+++ b/AMDiS/src/NonLinUpdater.h
@@ -22,15 +22,13 @@
#ifndef AMDIS_NONLINAPDATOR_H
#define AMDIS_NONLINAPDATOR_H
+#include "AMDiS_fwd.h"
#include "MemoryManager.h"
#include "SystemVector.h"
#include "MatrixVector.h"
namespace AMDiS {
- class DOFMatrix;
- template<typename T> class DOFVector;
-
// =========================================================================
// ===== class NonLinUpdater ===============================================
// =========================================================================
diff --git a/AMDiS/src/ODirSolver.h b/AMDiS/src/ODirSolver.h
deleted file mode 100644
index 15ba9c97..00000000
--- a/AMDiS/src/ODirSolver.h
+++ /dev/null
@@ -1,101 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file ODirSolver.h */
-
-#ifndef AMDIS_ODIRSOLVER_H
-#define AMDIS_ODIRSOLVER_H
-
-#include "OEMSolver.h"
-#include "MemoryManager.h"
-
-namespace AMDiS {
-
- // ============================================================================
- // ===== class BiCGSolver =====================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Solves a linear system by the method of orthogonal directions and can be
- * used for symmetric positive system matrices.
- */
- template<typename VectorType>
- class ODirSolver : public OEMSolver<VectorType>
- {
- public:
- MEMORY_MANAGED(ODirSolver<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new ODirSolver object.
- */
- OEMSolver<VectorType>* create() {
- return NEW ODirSolver<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- ODirSolver(std::string name);
-
- /** \brief
- * destructor
- */
- ~ODirSolver();
-
- protected:
- /** \brief
- * realisation of OEMSolver::solveSystem
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b, bool reuseMatrix);
-
- /** \brief
- * realisation of OEMSolver::init
- */
- void init();
-
- /** \brief
- * realisation of OEMSolver::exit
- */
- void exit();
-
- private:
- // pointer to memory needed for solveSystem
- VectorType *Ad, *d, *d_old, *r, *h;
- };
-
-}
-
-#include "ODirSolver.hh"
-
-#endif // AMDIS_ODIR_SOLVER_H
diff --git a/AMDiS/src/ODirSolver.hh b/AMDiS/src/ODirSolver.hh
deleted file mode 100644
index 11fcdaa2..00000000
--- a/AMDiS/src/ODirSolver.hh
+++ /dev/null
@@ -1,167 +0,0 @@
-#include "Preconditioner.h"
-
-namespace AMDiS {
-
- template<typename VectorType>
- ODirSolver<VectorType>::ODirSolver(std::string name)
- : OEMSolver<VectorType>(name),
- Ad(NULL), d(NULL), d_old(NULL), r(NULL), h(NULL)
- {
- }
-
- template<typename VectorType>
- ODirSolver<VectorType>::~ODirSolver()
- {}
-
- template<typename VectorType>
- void ODirSolver<VectorType>::init()
- {
- Ad = this->vectorCreator->create();
- d = this->vectorCreator->create();
- d_old = this->vectorCreator->create();
- r = this->vectorCreator->create();
- h = this->vectorCreator->create();
- }
-
- template<typename VectorType>
- void ODirSolver<VectorType>::exit()
- {
- this->vectorCreator->free(Ad);
- this->vectorCreator->free(d);
- this->vectorCreator->free(d_old);
- this->vectorCreator->free(r);
- this->vectorCreator->free(h);
- }
-
- template<typename VectorType>
- int ODirSolver<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x, VectorType *b, bool reuseMatrix)
- {
- FUNCNAME("ODirSolver::solveSystem");
-
- double res, old_res = -1.0;
- double dad, dad_old, rd, alpha, gamma, sigma;
- int iter;
- VectorType *swap = NULL;
- const double TOL = 1.e-30;
-
- /*--------------------------------------------------------------------------*/
- /*--- Initalization ------------------------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- if (norm(b) < TOL)
- {
- INFO(this->info,2)("b == 0, x = 0 is the solution of the linear system\n");
- set(*x, 0.0);
- return(0);
- }
-
- // r = Ax
- matVec->matVec(NoTranspose, *x, *r);
-
- // r = -b + r
- *r -= *b;
-
- // h = r
- *h = *r;
-
- if (this->leftPrecon) {
- this->leftPrecon->precon(h);
- }
-
- // d = h
- *d = *h;
-
- // d_old = 0;
- set(*d_old, 0.0);
-
- dad_old = 1.0;
-
- /*--------------------------------------------------------------------------*/
- /*--- check initial residual ---------------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- res = norm(r);
-
- START_INFO();
- if (SOLVE_INFO(0, res, &old_res))
- return(0);
-
- /*--------------------------------------------------------------------------*/
- /*--- Iteration ----------------------------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- for (iter = 1; iter <= this->max_iter; iter++)
- {
- /*--------------------------------------------------------------------------*/
- /*--- calculate r.d, A.d and d.A.d ---------------------------------------*/
- /*--------------------------------------------------------------------------*/
- // rd = r*d
- rd = *r * *d;
-
- // Ad = A*d
- matVec->matVec(NoTranspose, *d, *Ad);
-
- // dad = d*Ad
- dad = *d * *Ad;
-
- if (abs(dad) < TOL)
- {
- BREAK_INFO("(Ad,d)_2 = 0", iter, res, &old_res);
- return(iter);
- }
-
- /*--------------------------------------------------------------------------*/
- /*--- update x and calculate new r --------------------------------------*/
- /*--------------------------------------------------------------------------*/
- alpha = rd/dad;
-
- // x = -alpha d + x
- axpy(-alpha, *d, *x);
-
- // r = -alpha Ad + r
- axpy(-alpha, *Ad, *r);
-
- res = norm(r);
- if (SOLVE_INFO(iter, res, &old_res))
- return(iter);
-
- // h = Ad
- *h = *Ad;
-
- if (this->leftPrecon) this->leftPrecon->precon(h);
-
- /*--------------------------------------------------------------------------*/
- /*--- calculate gamma and sigma ------------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- // gamma = h*Ad/dad
- gamma = (*h * *Ad)/dad;
- sigma = dad/dad_old;
-
- /*--------------------------------------------------------------------------*/
- /*--- compute new d and save old values ----------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- // swap d and d_old
- //swap(*d, *d_old);
- swap = d;
- d = d_old;
- d_old = swap;
-
- // d = -sigma * d
- *d *= -sigma;
-
- // d = -gamma d_old + d
- axpy(-gamma, *d_old, *d);
-
- // d = h + d
- *d += *h;
-
- dad_old= dad;
- }
-
- return 0; // never reached !
- }
-
-}
diff --git a/AMDiS/src/OEMSolver.h b/AMDiS/src/OEMSolver.h
index 3830691c..c338e76e 100644
--- a/AMDiS/src/OEMSolver.h
+++ b/AMDiS/src/OEMSolver.h
@@ -31,100 +31,128 @@
#ifndef AMDIS_OEM_SOLVER_H
#define AMDIS_OEM_SOLVER_H
-// ============================================================================
-// ===== includes =============================================================
-// ============================================================================
-
#include "Global.h"
+#include "AMDiS_fwd.h"
+#include "Parameters.h"
+#include "SolverMatrix.h"
+#include "DOFVector.h"
+#include "SystemVector.h"
+#include "DOFMatrix.h"
+#include "ITL_Preconditioner.h"
namespace AMDiS {
- // ============================================================================
- // ===== forward declarations =================================================
- // ============================================================================
-
- template<typename VectorType> class Preconditioner;
- template<typename VectorType> class CreatorInterface;
- template<typename VectorType> class MatVecMultiplier;
-
- // ============================================================================
- // ===== definitions ==========================================================
- // ============================================================================
-
- /** \brief prints information before solving the system */
-#define START_INFO() this->start_info(funcName)
-
- /** \brief prints information after solving the system */
-#define BREAK_INFO(st,it,res,ores) \
- this->break_info(funcName,st,it,res,ores)
-
- /** \brief prints information while solving the system */
-#define SOLVE_INFO(it,res,ores) \
- this->solve_info(funcName,it,res,ores)
-
-
- // ============================================================================
- // ===== class OEMSolver ======================================================
- // ============================================================================
-
/**
* \ingroup Solver
*
*\brief
* Solver for linear equation systems.
- * Virtual base class for OEM solvers.
*/
- template<typename VectorType>
class OEMSolver
{
public:
+
+ typedef DOFMatrix::base_matrix_type matrix_type;
+ typedef DOFMatrix::value_type value_type;
+
/** \brief
* The constructor reads needed parameters and sets solvers \ref name.
*/
- OEMSolver(std::string name);
-
- /** \brief
- * Virtual destructor because OEMSolver is pure virtual.
- */
- virtual ~OEMSolver();
-
- void initParameters();
+ OEMSolver(std::string str)
+ : name(str),
+ tolerance(0),
+ relative(0),
+ max_iter(1000),
+ info(0),
+ residual(0),
+ print_cycle(100),
+ leftPrecon(NULL),
+ rightPrecon(NULL)
+ {}
/** \brief
- * Solves the linear system.
+ *
*/
- int solve(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b,
- Preconditioner<VectorType> *lPrecon = NULL,
- Preconditioner<VectorType> *rPrecon = NULL,
- bool reuseMatrix = false)
+ virtual ~OEMSolver()
{
- FUNCNAME("OEMSolver::solve()");
- TEST_EXIT(mv)("no matVec\n");
- TEST_EXIT(vectorCreator)("no vectorCreator\n");
-
- leftPrecon = lPrecon;
- rightPrecon = rPrecon;
-
- init();
+ if (leftPrecon) delete leftPrecon;
+ if (rightPrecon) delete rightPrecon;
+ }
- if (leftPrecon)
- leftPrecon->init();
+ void initParameters()
+ {
+ FUNCNAME("OEMSolver::initParameters()");
- if (rightPrecon)
- rightPrecon->init();
+ GET_PARAMETER(0, name + "->tolerance", "%f", &tolerance);
+ GET_PARAMETER(0, name + "->relative tolerance", "%f", &relative);
+ GET_PARAMETER(0, name + "->max iteration", "%d", &max_iter);
+ GET_PARAMETER(0, name + "->print cycle", "%d", &print_cycle);
+ GET_PARAMETER(0, name + "->info", "%d", &info);
+ }
- int iter = solveSystem(mv, x, b, reuseMatrix);
+ /** Set left Preconditioner
+ *
+ * It is assumed that the solver owns the preconditioner from this call.
+ * That means that the preconditioner is deleted by the solver when not needed.
+ */
+ void setLeftPrecon(ITL_BasePreconditioner* p)
+ {
+ if (leftPrecon) delete leftPrecon;
+ leftPrecon= p;
+ }
- if (leftPrecon)
- leftPrecon->exit();
+ /** Set right Preconditioner
+ *
+ * It is assumed that the solver owns the preconditioner from this call.
+ * That means that the preconditioner is deleted by the solver when not needed.
+ */
+ void setRightPrecon(ITL_BasePreconditioner* p)
+ {
+ if (rightPrecon) delete rightPrecon;
+ rightPrecon= p;
+ }
- if (rightPrecon)
- rightPrecon->exit();
+ /// Linear System to be solved in the derived class
+ virtual int solveSystem(const DOFMatrix::base_matrix_type& A,
+ mtl::dense_vector<value_type>& x,
+ const mtl::dense_vector<value_type>& b) = 0;
+
- exit();
+ /// Solve a linear system for a scalar problem.
+ int solveSystem(const SolverMatrix<DOFMatrix>& A,
+ DOFVector<double>& x,
+ DOFVector<double>& b)
+ {
+ mtl::dense_vector<value_type> xx(x.getUsedSize(), &x[0]),
+ bb(b.getUsedSize(), &b[0]);
+ return solveSystem(A.getMatrix(), xx, bb);
+ }
- return iter;
+ /// Solve a linear system for a vectorial problem.
+ int solveSystem(const SolverMatrix<Matrix<DOFMatrix*> >& A,
+ SystemVector& x,
+ SystemVector& b)
+ {
+ int ns= x.getSize(), // Number of systems.
+ size= x.getUsedSize(); // Size of all DOFVectors
+
+ // Copy vectors
+ mtl::dense_vector<value_type> xx(size), bb(size);
+ for (int i = 0, counter = 0; i < ns; i++) {
+ DOFVector<double>::Iterator it(b.getDOFVector(i), USED_DOFS);
+ for (it.reset(); !it.end(); ++it)
+ bb[counter++] = *it;
+ }
+
+ // Solver on DOFVector for single system
+ int r= solveSystem(A.getMatrix(), xx, bb);
+
+ for (int i = 0, counter = 0; i < ns; i++) {
+ DOFVector<double>::Iterator it(x.getDOFVector(i), USED_DOFS);
+ for (it.reset(); !it.end(); ++it)
+ *it = xx[counter++];
+ }
+ return r;
}
// ===== getting-methods ======================================================
@@ -196,52 +224,9 @@ namespace AMDiS {
inline void setInfo(int i) {
info = i;
}
-
- inline void setVectorCreator(CreatorInterface<VectorType> *creator) {
- vectorCreator = creator;
- }
-
- inline CreatorInterface<VectorType>* getVectorCreator() {
- return vectorCreator;
- }
/** \} */
- protected:
- /** \brief
- * To be overloaded by concrete solvers.
- */
- virtual void init() = 0;
-
- /** \brief
- * To be overloaded by concrete solvers.
- */
- virtual void exit() = 0;
-
- /** \brief
- * To be overloaded by concrete solvers.
- */
- virtual int solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x,
- VectorType *b,
- bool reuseMatrix) = 0;
-
-
- /** \brief
- * Prints start information. Uses \ref START_INFO.
- */
- void start_info(const char *);
-
- /** \brief
- * Prints break information. Uses \ref BREAK_INFO.
- */
- void break_info(const char *, const char *, int, double, double *);
-
- /** \brief
- * Prints solve information. Uses \ref SOLVE_INFO.
- */
- int solve_info(const char *, int, double, double *);
-
protected:
/** \brief
* solvers name.
@@ -249,14 +234,14 @@ namespace AMDiS {
std::string name;
/** \brief
- * solver tolerance. Set in OEMSolver's constructor.
+ * Solver tolerance |r|. Set in OEMSolver's constructor.
*/
double tolerance;
/** \brief
- * solver relative. Set in OEMSolver's constructor.
+ * Relative solver tolerance |r|/|r0|. Set in OEMSolver's constructor.
*/
- bool relative;
+ double relative;
/** \brief
* maximal number of iterations. Set in OEMSolver's constructor.
@@ -273,12 +258,12 @@ namespace AMDiS {
*/
double residual;
- Preconditioner<VectorType> *leftPrecon;
-
- Preconditioner<VectorType> *rightPrecon;
+ /// Print cycle, after how many iterations the residuum norm is logged.
+ int print_cycle;
- CreatorInterface<VectorType> *vectorCreator;
+ ITL_BasePreconditioner *leftPrecon;
+ ITL_BasePreconditioner *rightPrecon;
};
// ============================================================================
@@ -291,8 +276,7 @@ namespace AMDiS {
* \brief
* Interface for creators of concrete OEMSolvers.
*/
- template<typename T>
- class OEMSolverCreator : public CreatorInterface<OEMSolver<T> >
+ class OEMSolverCreator : public CreatorInterface<OEMSolver>
{
public:
virtual ~OEMSolverCreator() {}
@@ -300,8 +284,8 @@ namespace AMDiS {
/** \brief
* Sets \ref problem
*/
- void setName(std::string name_) {
- name = name_;
+ void setName(std::string str) {
+ name = str;
}
protected:
@@ -313,14 +297,6 @@ namespace AMDiS {
};
}
-#include "OEMSolver.hh"
-
-#include "Preconditioner.h"
-#include "BiCGSolver.h"
-#include "BiCGStab_M.h"
-#include "CGSolver.h"
-#include "GMResSolver.h"
-#include "ODirSolver.h"
-#include "OResSolver.h"
+#include "ITL_Solver.h"
#endif // AMDIS_OEM_SOLVER_H
diff --git a/AMDiS/src/OEMSolver.hh b/AMDiS/src/OEMSolver.hh
deleted file mode 100644
index aa2d25f0..00000000
--- a/AMDiS/src/OEMSolver.hh
+++ /dev/null
@@ -1,109 +0,0 @@
-#include "CreatorInterface.h"
-#include "Parameters.h"
-#include "Preconditioner.h"
-#include "CreatorMap.h"
-#include "MatVecMultiplier.h"
-
-namespace AMDiS {
-
- template<typename VectorType>
- OEMSolver<VectorType>::OEMSolver(std::string name_)
- : name(name_),
- tolerance(1.e-8),
- relative(false),
- max_iter(1000),
- info(0),
- residual(0),
- leftPrecon(NULL),
- rightPrecon(NULL),
- vectorCreator(NULL)
- {
- FUNCNAME("OEMSolver::OEMSolver");
- }
-
-
- template<typename VectorType>
- void OEMSolver<VectorType>::initParameters()
- {
- FUNCNAME("OEMSolver::initParameters()");
-
- GET_PARAMETER(0, name + "->tolerance", "%f", &tolerance);
- GET_PARAMETER(0, name + "->relative", "%d", &relative);
- GET_PARAMETER(0, name + "->max iteration", "%d", &max_iter);
- GET_PARAMETER(0, name + "->info", "%d", &info);
- }
-
- template<typename VectorType>
- OEMSolver<VectorType>::~OEMSolver()
- {
- FUNCNAME("OEMSolver::~OEMSolver");
-
- if (vectorCreator)
- DELETE vectorCreator;
- }
-
-
- template<typename VectorType>
- void OEMSolver<VectorType>::start_info(const char *funcName)
- {
- info = info > 10 ? 10 : info;
-
- INFO(info,6)("with tolerance %e\n", tolerance);
- PRINT_INFO(info,6)("\n");
- INFO(info,2)("iter. | residual | red.\n");
- return;
- }
-
- template<typename VectorType>
- void OEMSolver<VectorType>::break_info(const char *funcName,
- const char *reason,
- int iter,
- double res,
- double *ores)
- {
- if (ores && *ores > 0) {
- INFO(info,2)("%5d | %12.5e | %8.2e\n", iter, res, res / (*ores));
- } else {
- INFO(info,2)("%5d | %12.5e |\n", iter, res);
- }
- INFO(info,2)("stop due to: %s\n", reason);
-
- residual = res;
- }
-
- template<typename VectorType>
- int OEMSolver<VectorType>::solve_info(const char * funcName, int iter,
- double res, double *ores)
- {
- static int step[11] = {0, 1000, 500, 200, 100, 50, 20, 10, 5, 2, 1};
-
- if (res <= tolerance || (info && (iter%step[info] == 0)) || iter == max_iter) {
- if (ores) {
- if (*ores > 0.0) {
- double red = res/(*ores);
- INFO(info,2)("%5d | %12.5e | %8.2e\n", iter, res, red);
- } else {
- INFO(info,2)("%5d | %12.5e | --------\n", iter, res);
- }
- *ores = res;
- } else {
- INFO(info,2)("%5d | %12.5e |\n", iter, res);
- }
- }
-
- residual = res;
-
- if (iter == max_iter && res > tolerance) {
- INFO(info,1)("tolerance %e not reached after %d iterations\n", tolerance, iter);
- return(2);
- }
-
- if (res <= tolerance) {
- INFO(info,6)("finished successfully with %d iterations\n");
- return(1);
- }
-
- return 0;
- }
-
-}
diff --git a/AMDiS/src/OResSolver.h b/AMDiS/src/OResSolver.h
deleted file mode 100644
index 8d731b37..00000000
--- a/AMDiS/src/OResSolver.h
+++ /dev/null
@@ -1,101 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file OResSolver.h */
-
-#ifndef AMDIS_ORESSOLVER_H
-#define AMDIS_ORESSOLVER_H
-
-#include "OEMSolver.h"
-#include "MemoryManager.h"
-
-namespace AMDiS {
-
- // ============================================================================
- // ===== class OResSolver =====================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Solves a linear system by the method of orthogonal residuals and can be used
- * for symmetric system matrices.
- */
- template<typename VectorType>
- class OResSolver : public OEMSolver<VectorType>
- {
- public:
- MEMORY_MANAGED(OResSolver<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new OResSolver object.
- */
- OEMSolver<VectorType>* create() {
- return NEW OResSolver<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- OResSolver(std::string name);
-
- /** \brief
- * destructor
- */
- ~OResSolver();
-
- protected:
- /** \brief
- * realisation of OEMSolver::solveSystem
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b, bool reuseMatrix);
-
- /** \brief
- * realisation of OEMSolver::init
- */
- void init();
-
- /** \brief
- * realisation of OEMSolver::exit
- */
- void exit();
-
- private:
- // pointer to memory needed for solveSystem
- VectorType *Ad, *d, *d_old, *r, *h, *Ad_old, *Ah;
- };
-
-}
-
-#include "OResSolver.hh"
-
-#endif // AMDIS_ORESSOLVER_H
diff --git a/AMDiS/src/OResSolver.hh b/AMDiS/src/OResSolver.hh
deleted file mode 100644
index 74e95865..00000000
--- a/AMDiS/src/OResSolver.hh
+++ /dev/null
@@ -1,160 +0,0 @@
-#include "Preconditioner.h"
-
-namespace AMDiS {
-
- template<typename VectorType>
- OResSolver<VectorType>::OResSolver(std::string name)
- : OEMSolver<VectorType>(name),
- Ad(NULL), d(NULL), d_old(NULL), r(NULL), h(NULL), Ad_old(NULL), Ah(NULL)
- {
- }
-
- template<typename VectorType>
- OResSolver<VectorType>::~OResSolver()
- {}
-
- template<typename VectorType>
- void OResSolver<VectorType>::init()
- {
- Ad = this->vectorCreator->create();
- d = this->vectorCreator->create();
- d_old = this->vectorCreator->create();
- r = this->vectorCreator->create();
- h = this->vectorCreator->create();
- Ad_old = this->vectorCreator->create();
- Ah = this->vectorCreator->create();
- }
-
- template<typename T>
- void OResSolver<T>::exit()
- {
- this->vectorCreator->free(Ad);
- this->vectorCreator->free(d);
- this->vectorCreator->free(d_old);
- this->vectorCreator->free(r);
- this->vectorCreator->free(h);
- this->vectorCreator->free(Ad_old);
- this->vectorCreator->free(Ah);
- }
-
- template<typename VectorType>
- int OResSolver<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x, VectorType *b,
- bool reuseMatrix)
- {
- FUNCNAME("OResSolver::solveSystem");
-
- double alpha, gamma, sigma;
- double daad, daad_old, rad, res, old_res = -1.0;
- int iter; //, dim2;
- VectorType *swap = NULL;
-
- /*--------------------------------------------------------------------------*/
- /*--- Initalization ------------------------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- // r = Ax
- matVec->matVec(NoTranspose, *x, *r);
-
- // r = - b + r
- *r -= *b;
-
- // h = r
- *h = *r;
-
- if (this->leftPrecon) this->leftPrecon->precon(h);
-
- // d = h
- *d = *h;
-
- /*--- d_old = 0 and Ad_old = 0 ---------------*/
- set(*d_old, 0.0);
- set(*Ad_old, 0.0);
-
- // Ad = A*d
- matVec->matVec(NoTranspose, *d, *Ad);
-
- daad_old = 1.0;
-
- /*--------------------------------------------------------------------------*/
- /*--- check initial residual ---------------------------------------------*/
- /*--------------------------------------------------------------------------*/
-
- res = norm(r);
-
- START_INFO();
- if (SOLVE_INFO(0, res, &old_res))
- return(0);
-
- for (iter = 1; iter <= this->max_iter; iter++) {
- /*--- compute r.Ad and d.A.A.d ---------------------------------------------*/
- // rad = r * Ad
- rad = *r * *Ad;
-
- // daad = Ad * Ad
- daad = *Ad * *Ad;
-
- if (daad <= 1.e-30) {
- BREAK_INFO("(Ad,d)_2 = 0", iter, res, &old_res);
- return(iter);
- }
-
- /*--- update u and r ------------------------------------------------------*/
-
- alpha= rad/daad;
-
- // x = -alpha d + x
- axpy(-alpha, *d, *x);
-
- // r = - alpha Ad + r
- axpy(-alpha, *Ad, *r);
-
- res = norm(r);
-
- if (SOLVE_INFO(iter, res, &old_res))
- return(iter);
-
- // h = Ad
- *h = *Ad;
-
- if (this->leftPrecon) this->leftPrecon->precon(h);
-
- // Ah = A * h
- matVec->matVec(NoTranspose, *h, *Ah);
-
- // gamma = Ah * Ad / daad
- gamma = (*Ah * *Ad)/daad;
- sigma = daad/daad_old;
-
- /*--- compute new d.Ad, save old values! ----------------------------------*/
- // swap d and d_old
- swap = d_old;
- d_old = d;
- d = swap;
-
- // swap Ad_old and Ad
- swap = Ad_old;
- Ad_old = Ad;
- Ad = swap;
-
- /*--- d,Ad *= -sigma --------------*/
- *d *= -sigma;
- *Ad *= -sigma;
-
- /*--- d,Ad -= gamma*d_old,Ad_old --*/
- axpy(-gamma, *d_old, *d);
- axpy(-gamma, *Ad_old, *Ad);
-
- // d = h + d
- *d += *h;
-
- // Ad = Ah + Ad
- *Ad += *Ah;
-
- daad_old = daad;
- }
-
- return 0; // never reached !
- }
-
-}
diff --git a/AMDiS/src/PeriodicBC.cc b/AMDiS/src/PeriodicBC.cc
index 1c70953d..17e0622e 100644
--- a/AMDiS/src/PeriodicBC.cc
+++ b/AMDiS/src/PeriodicBC.cc
@@ -9,15 +9,15 @@
namespace AMDiS {
- std::vector<PeriodicDOFMapping*> PeriodicDOFMapping::mappings_;
+ ::std::vector<PeriodicDOFMapping*> PeriodicDOFMapping::mappings_;
PeriodicDOFMapping*
PeriodicDOFMapping::providePeriodicDOFMapping(const BasisFunction *basFcts)
{
- std::vector<PeriodicDOFMapping*>::iterator it;
- std::vector<PeriodicDOFMapping*>::iterator end = mappings_.end();
- for (it = mappings_.begin(); it != end; ++it) {
- if ((*it)->basFcts_ == basFcts) {
+ ::std::vector<PeriodicDOFMapping*>::iterator it;
+ ::std::vector<PeriodicDOFMapping*>::iterator end = mappings_.end();
+ for(it = mappings_.begin(); it != end; ++it) {
+ if((*it)->basFcts_ == basFcts) {
return *it;
}
}
@@ -32,9 +32,9 @@ namespace AMDiS {
{
FUNCNAME("PeriodicDOFMapping::PeriodicDOFMapping()");
TEST_EXIT(basFcts_->getDim() > 1)("dim == 1\n");
- int num = basFcts_->getNumber();
+ int i, num = basFcts_->getNumber();
DimVec<double> *lambda;
- for (int i = 0; i < num; i++) {
+ for(i = 0; i < num; i++) {
lambda = basFcts_->getCoords(i);
indexOfCoords_[*lambda] = i;
}
@@ -42,9 +42,9 @@ namespace AMDiS {
PeriodicDOFMapping::~PeriodicDOFMapping()
{
- std::map<DimVec<int>, DegreeOfFreedom*, DimVecLess<int> >::iterator it;
- for (it = dofPermutation_.begin(); it != dofPermutation_.end(); ++it) {
- if (it->second) {
+ ::std::map<DimVec<int>, DegreeOfFreedom*, DimVecLess<int> >::iterator it;
+ for(it = dofPermutation_.begin(); it != dofPermutation_.end(); ++it) {
+ if(it->second) {
FREE_MEMORY(it->second, DegreeOfFreedom, basFcts_->getNumber());
}
}
@@ -55,17 +55,20 @@ namespace AMDiS {
{
FUNCNAME("PeriodicDOFMapping::getDOFPermutation()");
- if (dofPermutation_[vertexPermutation] == NULL) {
+ if(dofPermutation_[vertexPermutation] == NULL) {
+ //MSG("new dof permutation needed\n");
+
+ int i, j;
int dim = basFcts_->getDim();
int num = basFcts_->getNumber();
int sum = 0;
- for (int i = 0; i < dim + 1; i++) {
+ for(i = 0; i < dim + 1; i++) {
sum += i - vertexPermutation[i];
- TEST_EXIT_DBG(vertexPermutation[i] < dim + 1)
+ TEST_EXIT(vertexPermutation[i] < dim + 1)
("invalid vertexPermuation\n");
}
- TEST_EXIT_DBG(sum == 0)("invalid vertexPermutation\n");
+ TEST_EXIT(sum == 0)("invalid vertexPermutation\n");
// create dof permutation
DimVec<double> *lambda;
@@ -73,15 +76,28 @@ namespace AMDiS {
DegreeOfFreedom *mapping = GET_MEMORY(DegreeOfFreedom, num);
- for (int i = 0; i < num; i++) {
+ for(i = 0; i < num; i++) {
lambda = basFcts_->getCoords(i);
- for (int j = 0; j < dim + 1; j++) {
+ for(j = 0; j < dim + 1; j++) {
newLambda[vertexPermutation[j]] = (*lambda)[j];
}
mapping[i] = indexOfCoords_[newLambda];
}
dofPermutation_[vertexPermutation] = mapping;
+
+ // MSG("vertex permutation: ");
+ // for(i = 0; i < dim+1; i++) {
+ // MSG("%d ", vertexPermutation[i]);
+ // }
+ // MSG("\n");
+
+ // MSG("dof permutation: ");
+ // for(i = 0; i < num; i++) {
+ // MSG("%d ", dofPermutation_[vertexPermutation][i]);
+ // }
+ // MSG("\n");
+ // WAIT;
}
return dofPermutation_[vertexPermutation];
@@ -92,7 +108,7 @@ namespace AMDiS {
: BoundaryCondition(type, rowFESpace_, NULL),
masterMatrix_(NULL)
{
- if (rowFESpace->getMesh()->getDim() > 1) {
+ if(rowFESpace->getMesh()->getDim() > 1) {
periodicDOFMapping_ =
PeriodicDOFMapping::providePeriodicDOFMapping(rowFESpace_->getBasisFcts());
} else {
@@ -107,17 +123,25 @@ namespace AMDiS {
{
FUNCNAME("PeriodicBC::initMatrix()");
- if (!masterMatrix_) {
+ // MSG("begin initMatrix...\n");
+
+ if(!masterMatrix_) {
masterMatrix_ = matrix;
+
Mesh *mesh = matrix->getRowFESpace()->getMesh();
+
associated_ = mesh->getPeriodicAssociations()[boundaryType];
- TEST_EXIT(associated_)
- ("no associations for periodic boundary condition %d\n", boundaryType);
+ TEST_EXIT(associated_)("no associations for periodic boundary condition %d\n",
+ boundaryType);
+
+ const BasisFunction *basFcts = rowFESpace->getBasisFcts();
+ int num = basFcts->getNumber();
- neighIndices_ = GET_MEMORY(DegreeOfFreedom,
- rowFESpace->getBasisFcts()->getNumber());
+ neighIndices_ = GET_MEMORY(DegreeOfFreedom, num);
}
+
+ //MSG("end initMatrix...\n");
}
void PeriodicBC::fillBoundaryCondition(DOFMatrix *matrix,
@@ -126,24 +150,33 @@ namespace AMDiS {
const BoundaryType *localBound,
int nBasFcts)
{
- if (matrix == masterMatrix_) {
+ if(matrix == masterMatrix_) {
+
int dim = rowFESpace->getMesh()->getDim();
-
- if (dim > 1) {
+ if(dim > 1) {
+ int i, j;
DOFAdmin *admin = rowFESpace->getAdmin();
+
FixVec<int, WORLD> elFace(dim, NO_INIT);
FixVec<int, WORLD> neighFace(dim, NO_INIT);
DimVec<int> vertexPermutation(dim, NO_INIT);
+
const BasisFunction *basFcts = rowFESpace->getBasisFcts();
int num = basFcts->getNumber();
+
Element *element = elInfo->getElement();
+
DimVec<DegreeOfFreedom> periodicDOFs(dim-1, NO_INIT);
+
int vertex, index, side;
+
GeoIndex sideGeoIndex = INDEX_OF_DIM(dim-1, dim);
- for (side = 0; side < dim + 1; side++) {
- if (elInfo->getBoundary(sideGeoIndex, side) == boundaryType) {
- for (vertex = 0; vertex < dim; vertex++) {
+ for(side = 0; side < dim + 1; side++) {
+
+ if(elInfo->getBoundary(sideGeoIndex, side) == boundaryType) {
+
+ for(vertex = 0; vertex < dim; vertex++) {
index = element->getVertexOfPosition(sideGeoIndex,
side,
vertex);
@@ -151,36 +184,34 @@ namespace AMDiS {
}
Element *neigh = elInfo->getNeighbour(side);
+
basFcts->getLocalIndices(neigh, admin, neighIndices_);
- int oppVertex = 0;
- for (int i = 0; i < dim + 1; i++) {
+ int oppVertex = 0;
+ for(i = 0; i < dim + 1; i++) {
// get vertex permutation
- if (i == side) {
+ if(i == side) {
vertexPermutation[i] = 0;
} else {
DegreeOfFreedom periodicDOF =
periodicDOFs[element->getPositionOfVertex(side, i)];
- int j;
- for (j = 0; j < dim + 1; j++) {
- if (neigh->getDOF(j, 0) == periodicDOF)
- break;
+ for(j = 0; j < dim + 1; j++) {
+ if(neigh->getDOF(j, 0) == periodicDOF) break;
}
vertexPermutation[i] = j;
}
oppVertex += i - vertexPermutation[i];
}
-
vertexPermutation[side] = oppVertex;
// get DOF permutation
const DegreeOfFreedom *dofPermutation =
periodicDOFMapping_->getDOFPermutation(vertexPermutation);
-
+
// set associated dofs
- for (int i = 0; i < num; i++) {
- if ((*(basFcts->getCoords(i)))[side] == 0) {
+ for(i = 0; i < num; i++) {
+ if((*(basFcts->getCoords(i)))[side] == 0) {
(*associated_)[dofIndices[i]] = neighIndices_[dofPermutation[i]];
}
}
@@ -194,38 +225,134 @@ namespace AMDiS {
{
FUNCNAME("PeriodicBC::exitMatrix()");
- TEST_EXIT_DBG(matrix)("no matrix\n");
+ TEST_EXIT(matrix)("no matrix\n");
- if (matrix == masterMatrix_) {
- FREE_MEMORY(neighIndices_, DegreeOfFreedom,
- rowFESpace->getBasisFcts()->getNumber());
+ if(matrix == masterMatrix_) {
+ const BasisFunction *basFcts = rowFESpace->getBasisFcts();
+ int num = basFcts->getNumber();
+ FREE_MEMORY(neighIndices_, DegreeOfFreedom, num);
masterMatrix_ = NULL;
}
-
- std::vector< std::vector<MatEntry> >::iterator rowIt;
- std::vector< std::vector<MatEntry> >::iterator rowEnd = matrix->end();
+ // ---------- different assemblage style --------
+
+ // DOFMatrix::Iterator matrixRow(matrix, USED_DOFS);
+ // for(matrixRow.reset(); !matrixRow.end(); ++matrixRow) {
+ // row = matrixRow.getDOFIndex();
+
+ // rowSize = matrixRow->size();
+ // newRow = ((*associated_)[row] == -1) ? row : (*associated_)[row];
+
+ // if(row < newRow) {
+ // for(i = 0; i < rowSize; i++) {
+ // col = (*matrixRow)[i].col;
+ // if(col == DOFMatrix::NO_MORE_ENTRIES) break;
+ // if(col == DOFMatrix::UNUSED_ENTRY) continue;
+ // newCol = ((*associated_)[col] == -1) ? col : (*associated_)[col];
+ // if(col < newCol) {
+ // entry = (*matrixRow)[i].entry;
+ // (*matrixRow)[i].col = DOFMatrix::UNUSED_ENTRY;
+ // (*matrixRow)[i].entry = 0.0;
+ // matrix->addSparseDOFEntry(1.0, row, newCol, entry, true);
+ // }
+ // }
+ // rowSize = matrixRow->size();
+ // for(i = 0; i < rowSize; i++) {
+ // col = (*matrixRow)[i].col;
+ // if(col == DOFMatrix::NO_MORE_ENTRIES) break;
+ // if(col == DOFMatrix::UNUSED_ENTRY) continue;
+ // entry = (*matrixRow)[i].entry;
+ // matrix->addSparseDOFEntry(1.0, newRow, col, entry, true);
+ // }
+ // matrixRow->resize(2);
+ // (*matrixRow)[0].col = row;
+ // (*matrixRow)[0].entry = 100.0;1.0;
+ // (*matrixRow)[1].col = newRow;
+ // (*matrixRow)[1].entry = -100.0;-1.0;
+ // }
+ // }
+
+
+ // --- method 2 ---
+
+ // for(matrixRow.reset(); !matrixRow.end(); ++matrixRow) {
+ // row = matrixRow.getDOFIndex();
+ // newRow = ((*associated_)[row] == -1) ? row : (*associated_)[row];
+ // if(row < newRow) {
+ // // remember old row matrix[row]
+ // ::std::vector<MatEntry> oldMatrixRow = *matrixRow;
+ // // add new row to old row
+ // ::std::vector<MatEntry> &newMatrixRow = matrix->getRow(newRow);
+ // rowSize = newMatrixRow.size();
+ // for(i = 0; i < rowSize; i++) {
+ // col = newMatrixRow[i].col;
+ // if(col == DOFMatrix::NO_MORE_ENTRIES) break;
+ // if(col == DOFMatrix::UNUSED_ENTRY) continue;
+ // newCol = ((*associated_)[col] == -1) ? col : (*associated_)[col];
+ // entry = newMatrixRow[i].entry;
+ // matrix->addSparseDOFEntry(1.0, row, newCol, entry, true);
+ // }
+ // // add old row to new row
+ // rowSize = oldMatrixRow.size();
+ // for(i = 0; i < rowSize; i++) {
+ // col = oldMatrixRow[i].col;
+ // if(col == DOFMatrix::NO_MORE_ENTRIES) break;
+ // if(col == DOFMatrix::UNUSED_ENTRY) continue;
+ // newCol = ((*associated_)[col] == -1) ? col : (*associated_)[col];
+ // entry = oldMatrixRow[i].entry;
+ // matrix->addSparseDOFEntry(1.0, newRow, newCol, entry, true);
+ // }
+ // }
+ // }
+
+
+ // DOFVector<DegreeOfFreedom>::Iterator rowIt(associated_, USED_DOFS);
+ // DOFVector<DegreeOfFreedom>::Iterator colIt(associated_, USED_DOFS);
+
+
+ // Mesh *mesh = matrix->getRowFESpace()->getMesh();
+
+ using namespace mtl;
+
+ // Compute reorder matrix (newRow and newCol yields transposed!!!)
+ matrix::traits::reorder<>::type R= matrix::reorder(*associated_);
+ DOFMatrix::base_matrix_type &A= matrix->getBaseMatrix(), B, D, E, TR;
+
+ A*= 0.5;
+ // Half of entries with decreased row index + half of the strict lower origing
+ B= strict_upper(R) * A + strict_lower(A);
+ // Add half of entries with same row and decreased column index + half of increased columns
+ // Remark regarding column permutation: trans(strict_upper(trans(X))) == strict_lower(X)
+ // B+= bands(trans(R), 0, 1) * (A * strict_lower(R) + lower(A)); -> make this work one day!!!
+ TR= trans(R);
+ D= bands(TR, 0, 1);
+ E= A * strict_lower(R) + lower(A);
+ B+= D * E;
+ swap(A, B);
+
+#if 0 // The matrix operations above should be identical with the code below
+
+ ::std::vector< ::std::vector<MatEntry> >::iterator rowIt;
+ ::std::vector< ::std::vector<MatEntry> >::iterator rowEnd = matrix->end();
int colIndex, rowSize;
int row, col, newRow, newCol;
double entry, *newEntryPtr;
- for (rowIt = matrix->begin(), row = 0; rowIt != rowEnd; ++rowIt, ++row) {
+ for(rowIt = matrix->begin(), row = 0; rowIt != rowEnd; ++rowIt, ++row) {
rowSize = static_cast<int>(rowIt->size());
newRow = (*associated_)[row];
- for (colIndex = 0; colIndex < rowSize; colIndex++) {
+ for(colIndex = 0; colIndex < rowSize; colIndex++) {
col = (*rowIt)[colIndex].col;
- if (col == DOFMatrix::UNUSED_ENTRY)
- continue;
- if (col == DOFMatrix::NO_MORE_ENTRIES)
- break;
+ if(col == DOFMatrix::UNUSED_ENTRY) continue;
+ if(col == DOFMatrix::NO_MORE_ENTRIES) break;
newCol = (*associated_)[col];
newEntryPtr = matrix->hasSparseDOFEntry(newRow, newCol);
- if ((row < newRow) ||
- ((row == newRow) && (col < newCol)) ||
- !newEntryPtr)
+ if((row < newRow) ||
+ ((row == newRow) && (col < newCol)) ||
+ !newEntryPtr)
{
- if (!newEntryPtr) {
+ if(!newEntryPtr) {
entry = 0.5 * (*rowIt)[colIndex].entry;
(*rowIt)[colIndex].entry = entry;
matrix->addSparseDOFEntry(1.0, newRow, newCol, entry, false);
@@ -236,6 +363,9 @@ namespace AMDiS {
}
}
}
+#endif
+
+ //MSG("end exitMatrix...\n");
}
void PeriodicBC::exitVector(DOFVectorBase<double>* vector)
@@ -252,17 +382,29 @@ namespace AMDiS {
Mesh *mesh = vector->getFESpace()->getMesh();
VertexVector *associated_ = mesh->getPeriodicAssociations()[boundaryType];
- for (vecIt.reset(); !vecIt.end(); ++vecIt) {
+ for(vecIt.reset(); !vecIt.end(); ++vecIt) {
dof = vecIt.getDOFIndex();
newDOF = (*associated_)[dof];
- if (dof < newDOF) {
+ if(dof < newDOF) {
+ // ---------- different assemblage style --------
+ // (*vector)[newDOF] += (*vector)[dof];
+ // (*vector)[dof] = 0.0;
+
+
+ // --- method 2 ----
+ // //entry = (*vector)[dof];
+ // (*vector)[dof] += (*vector)[newDOF];
+ // (*vector)[newDOF] = (*vector)[dof];
+
entry = ((*vector)[dof] + (*vector)[newDOF]) * 0.5;
(*vector)[dof] = entry;
(*vector)[newDOF] = entry;
}
}
+
+ //MSG("end exitVector...\n");
}
}
diff --git a/AMDiS/src/PeriodicBC.h b/AMDiS/src/PeriodicBC.h
index bdbbe143..baa592d6 100644
--- a/AMDiS/src/PeriodicBC.h
+++ b/AMDiS/src/PeriodicBC.h
@@ -22,6 +22,7 @@
#ifndef AMDIS_PERIODICBC_H
#define AMDIS_PERIODICBC_H
+#include "AMDiS_fwd.h"
#include "BoundaryCondition.h"
#include "MemoryManager.h"
#include "FixVec.h"
@@ -30,12 +31,6 @@
namespace AMDiS {
- class ElInfo;
- class DOFMatrix;
- class BasisFunction;
- class VertexVector;
- class LeafDataPeriodic;
-
template<typename T>
class DimVecLess
{
diff --git a/AMDiS/src/Preconditioner.h b/AMDiS/src/Preconditioner.h
deleted file mode 100644
index 32fe39ee..00000000
--- a/AMDiS/src/Preconditioner.h
+++ /dev/null
@@ -1,299 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file Preconditioner.h */
-
-#ifndef AMDIS_PRECONDITIONER_H
-#define AMDIS_PRECONDITIONER_H
-
-#include <vector>
-
-#include "DOFVector.h"
-#include "MatrixVector.h"
-#include "SystemVector.h"
-#include <string>
-
-namespace AMDiS {
-
- // ============================================================================
- // ===== class Preconditioner =================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Pure virtual base class for all preconditioners.
- * A Preconditioner is used by an OEMSolver before solving the linear system to
- * reduce the number of needed iterations.
- */
- template<typename Vector>
- class Preconditioner
- {
- public:
- /** \brief
- * Destructor.
- */
- virtual ~Preconditioner() {};
-
- /** \brief
- * Initialisation of the preconditioner
- */
- virtual void init() = 0;
-
- /** \brief
- * Precondition function which should be implemented.
- */
- virtual void precon(Vector *x) = 0;
-
- /** \brief
- * Frees needed memory.
- */
- virtual void exit() = 0;
- };
-
- // ============================================================================
- // ===== class PreconditionerScal =============================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * Base class for DOFVector preconditioners.
- */
- class PreconditionerScal : public Preconditioner<DOFVector<double> >
- {
- public:
- /** \brife
- * Constructor.
- */
- PreconditionerScal(int numSystems = 1, int r = 0)
- : matrix(numSystems),
- bound(NULL),
- row(r)
- {
- TEST_EXIT(r < numSystems)("r must be smaller than numSystems\n");
- matrix.set(NULL);
- };
-
- /** \brief
- * Sets \ref matrix.
- */
- inline void setMatrix(DOFMatrix **m, int system = 0) {
- TEST_EXIT(system < matrix.getSize())("invalid system number\n");
- matrix[system] = m;
- };
-
- /** \brief
- * Sets \ref bound.
- */
- inline void setBound(DOFVector<BoundaryType> *b) {
- bound = b;
- };
-
- protected:
- /** \brief
- * Matrix used for preconditioning.
- */
- Vector<DOFMatrix**> matrix;
-
- /** \brief
- * Boundary vector
- */
- DOFVector<BoundaryType> *bound;
-
- /** \brief
- * Row of the component in vector valued problems.
- */
- int row;
- };
-
-
-
- // ============================================================================
- // ===== class PreconditionerScalStd ==========================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * Base class for DOFVector preconditioners.
- */
- class PreconditionerScalStd : public Preconditioner< std::vector<double> >
- {
- public:
- /** \brife
- * Constructor.
- */
- PreconditionerScalStd()
- {};
-
- /** \brief
- * Sets \ref matrix.
- */
- inline void setMatrix(std::vector< std::vector<MatEntry> > *m) {
- matrix = m;
- };
-
- protected:
- /** \brief
- * Matrix used for preconditioning.
- */
-
- std::vector< std::vector<MatEntry> > *matrix;
- };
-
-
- // ============================================================================
- // ===== PreconditionerScalCreator ============================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Interface for creators of concrete scalar preconditioners.
- */
- class PreconditionerScalCreator
- : public CreatorInterface<PreconditionerScal>
- {
- public:
- PreconditionerScalCreator()
- : size(1), row(0)
- {};
-
- virtual ~PreconditionerScalCreator() {};
-
- /** \brief
- * Sets \ref problem
- */
- void setSizeAndRow(int size_, int row_) {
- size = size_;
- row = row_;
- };
-
- /** \brief
- * Sets \ref problem
- */
- void setName(std::string name) {
- name_ = name;
- };
-
- protected:
- int size;
- int row;
-
- std::string name_;
- };
-
-
-
- // ============================================================================
- // ===== class PreconditionerVec ==============================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- * Base class for vector valued preconditioners.
- */
- class PreconditionerVec : public Preconditioner<SystemVector>
- {
- public:
- MEMORY_MANAGED(PreconditionerVec);
-
- /** \brief
- * Constructor.
- */
- PreconditionerVec(int numSystems)
- : scalPrecons(numSystems)
- {
- scalPrecons.set(NULL);
- };
-
- /** \brief
- * Destructor.
- */
- virtual ~PreconditionerVec() {};
-
- /** \brief
- * Initialisation of the preconditioner
- */
- virtual void init() {
- int i;
- int size = scalPrecons.getSize();
-
-#ifdef _OPENMP
-#pragma omp parallel for num_threads(min(size, omp_get_max_threads()))
-#endif
- for (i = 0; i < size; i++) {
- scalPrecons[i]->init();
- }
- };
-
- /** \brief
- * Preconditioning method
- */
- virtual void precon(SystemVector *x) {
- int i;
- int size = scalPrecons.getSize();
-#ifdef _OPENMP
-#pragma omp parallel for num_threads(min(size, omp_get_max_threads()))
-#endif
- for (i = 0; i < size; i++) {
- scalPrecons[i]->precon(x->getDOFVector(i));
- }
- };
-
- /** \brief
- * Frees needed memory.
- */
- virtual void exit() {
- int size = scalPrecons.getSize();
- for (int i = 0; i < size; i++) {
- scalPrecons[i]->exit();
- }
- };
-
- /** \brief
- * Sets scalar preconditioner for system i.
- */
- inline void setScalarPrecon(int i, PreconditionerScal *p) {
- scalPrecons[i] = p;
- };
-
- /** \brief
- * Gets i-th scalar preconditioner.
- */
- inline PreconditionerScal *getScalarPrecon(int i) {
- return scalPrecons[i];
- };
-
- protected:
- /** \brief
- * Scalar Preconditioners.
- */
- Vector<PreconditionerScal*> scalPrecons;
- };
-
-}
-
-#endif // AMDIS_PRECONDITIONER_H
-
diff --git a/AMDiS/src/ProblemNonLin.cc b/AMDiS/src/ProblemNonLin.cc
index 2c0e672a..6840800d 100644
--- a/AMDiS/src/ProblemNonLin.cc
+++ b/AMDiS/src/ProblemNonLin.cc
@@ -5,6 +5,7 @@
#include "Traverse.h"
#include "AdaptInfo.h"
+#if 0
namespace AMDiS {
void ProblemNonLinScal::initialize(Flag initFlag,
@@ -56,6 +57,7 @@ namespace AMDiS {
void ProblemNonLinScal::createNonLinSolver()
{
// create non-linear solver
+#if 0
std::string nonLinSolverType("no");
GET_PARAMETER(0, name + "->nonlin solver", &nonLinSolverType);
@@ -68,13 +70,16 @@ namespace AMDiS {
nonLinSolverCreator->setNonLinUpdater(updater_);
nonLinSolver_ = nonLinSolverCreator->create();
nonLinSolver_->setVectorCreator(NEW DOFVector<double>::Creator(feSpace));
+#endif
}
void ProblemNonLinScal::solve(AdaptInfo *adaptInfo)
{
+#if 0
TEST_EXIT(nonLinSolver_)("no non-linear solver!\n");
int iter = nonLinSolver_->solve(matVec, solution, rhs, leftPrecon, rightPrecon);
adaptInfo->setSolverIterations(iter);
+#endif
}
@@ -145,6 +150,7 @@ namespace AMDiS {
void ProblemNonLinVec::createNonLinSolver()
{
+#if 0
// create non-linear solver
std::string nonLinSolverType("no");
@@ -160,6 +166,7 @@ namespace AMDiS {
nonLinSolver_->setVectorCreator(NEW SystemVector::Creator("temp",
componentSpaces,
nComponents));
+#endif
}
@@ -206,3 +213,4 @@ namespace AMDiS {
}
}
+#endif
diff --git a/AMDiS/src/ProblemNonLin.h b/AMDiS/src/ProblemNonLin.h
index 2c2c8b49..14045706 100644
--- a/AMDiS/src/ProblemNonLin.h
+++ b/AMDiS/src/ProblemNonLin.h
@@ -30,6 +30,8 @@
#include "SystemVector.h"
#include "MatrixVector.h"
+#if 0
+
namespace AMDiS {
template<typename Vector> class NonLinSolver;
@@ -267,5 +269,7 @@ namespace AMDiS {
}
+#endif
+
#endif
diff --git a/AMDiS/src/ProblemScal.cc b/AMDiS/src/ProblemScal.cc
index 08603d8b..84fdbb30 100644
--- a/AMDiS/src/ProblemScal.cc
+++ b/AMDiS/src/ProblemScal.cc
@@ -11,7 +11,6 @@
#include "FiniteElemSpace.h"
#include "Estimator.h"
#include "OEMSolver.h"
-#include "Preconditioner.h"
#include "MatVecMultiplier.h"
#include "DOFVector.h"
#include "Marker.h"
@@ -24,6 +23,7 @@
#include "PeriodicBC.h"
#include "ValueReader.h"
#include "ElementFileWriter.h"
+#include "ProblemVec.h"
namespace AMDiS {
@@ -47,10 +47,6 @@ namespace AMDiS {
DELETE marker;
if (solver)
DELETE solver;
- if (leftPrecon)
- DELETE leftPrecon;
- if (rightPrecon)
- DELETE rightPrecon;
if (mesh)
DELETE mesh;
@@ -195,7 +191,6 @@ namespace AMDiS {
}
}
-
void ProblemScal::setMeshFromProblemVec(ProblemVec* pv, int i)
{
mesh = pv->getMesh(i);
@@ -203,7 +198,6 @@ namespace AMDiS {
refinementManager = pv->getRefinementManager(i);
}
-
Flag ProblemScal::markElements(AdaptInfo *adaptInfo)
{
if (marker)
@@ -214,13 +208,11 @@ namespace AMDiS {
return 0;
}
-
Flag ProblemScal::refineMesh(AdaptInfo *adaptInfo)
{
return refinementManager->refineMesh(mesh);
}
-
Flag ProblemScal::coarsenMesh(AdaptInfo *adaptInfo)
{
if (adaptInfo->isCoarseningAllowed(0)) {
@@ -244,7 +236,10 @@ namespace AMDiS {
#endif
clock_t first = clock();
- int iter = solver->solve(matVec, solution, rhs, leftPrecon, rightPrecon);
+
+ SolverMatrix<DOFMatrix> solverMatrix;
+ solverMatrix.setMatrix(*systemMatrix);
+ int iter = solver->solveSystem(solverMatrix, *solution, *rhs);
#ifdef _OPENMP
INFO(info, 8)("solution of discrete system needed %.5f seconds system time / %.5f seconds wallclock time\n",
@@ -271,13 +266,13 @@ namespace AMDiS {
if (mesh) {
WARNING("mesh already created\n");
} else {
- if (initFlag.isSet(CREATE_MESH) ||
+ if(initFlag.isSet(CREATE_MESH) ||
((!adoptFlag.isSet(INIT_MESH))&&
(initFlag.isSet(INIT_SYSTEM)||initFlag.isSet(INIT_FE_SPACE)))) {
createMesh();
}
- if (adoptProblem &&
+ if(adoptProblem &&
(adoptFlag.isSet(INIT_MESH) ||
adoptFlag.isSet(INIT_SYSTEM) ||
adoptFlag.isSet(INIT_FE_SPACE))) {
@@ -299,6 +294,7 @@ namespace AMDiS {
(initFlag.isSet(INIT_SYSTEM) && !adoptFlag.isSet(INIT_FE_SPACE))) {
createFESpace();
}
+
if (adoptProblem &&
(adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
TEST_EXIT(!feSpace)("feSpace already created");
@@ -358,10 +354,10 @@ namespace AMDiS {
if (marker) {
WARNING("marker already created\n");
} else {
- if (initFlag.isSet(INIT_MARKER)) {
+ if(initFlag.isSet(INIT_MARKER)) {
createMarker();
}
- if (adoptProblem && adoptFlag.isSet(INIT_MARKER)) {
+ if(adoptProblem && adoptFlag.isSet(INIT_MARKER)) {
TEST_EXIT(!marker)("marker already created\n");
marker = adoptProblem->getMarker();
}
@@ -371,7 +367,7 @@ namespace AMDiS {
WARNING("no marker created\n");
// === create file writer ===
- if (initFlag.isSet(INIT_FILEWRITER)) {
+ if(initFlag.isSet(INIT_FILEWRITER)) {
createFileWriter();
}
@@ -418,7 +414,7 @@ namespace AMDiS {
mesh->getMacroFileInfo());
mesh->clearMacroFileInfo();
}
-
+
// === do global refinements ===
if (initFlag.isSet(INIT_GLOBAL_REFINES)) {
int globalRefinements = 0;
@@ -466,50 +462,12 @@ namespace AMDiS {
// === create solver ===
std::string solverType("no");
GET_PARAMETER(0, name + "->solver", &solverType);
- OEMSolverCreator<DOFVector<double> > *solverCreator =
- dynamic_cast<OEMSolverCreator<DOFVector<double> >*>(CreatorMap<OEMSolver<DOFVector<double> > >::getCreator(solverType));
+ OEMSolverCreator *solverCreator =
+ dynamic_cast<OEMSolverCreator*>(CreatorMap<OEMSolver>::getCreator(solverType));
TEST_EXIT(solverCreator)("no solver type\n");
solverCreator->setName(name + "->solver");
solver = solverCreator->create();
solver->initParameters();
-
- // === create preconditioners ===
- std::string preconType("no");
- Preconditioner<DOFVector<double> > *precon;
- GET_PARAMETER(0, name + "->solver->left precon", &preconType);
- CreatorInterface<PreconditionerScal> *preconCreator =
- CreatorMap<PreconditionerScal>::getCreator(preconType);
-
- if (!preconCreator->isNullCreator()) {
- dynamic_cast<PreconditionerScalCreator*>(preconCreator)->setSizeAndRow(1, 0);
- dynamic_cast<PreconditionerScalCreator*>(preconCreator)->setName(name + "->solver->left precon");
- }
-
- precon = preconCreator->create();
-
- if (precon) {
- dynamic_cast<PreconditionerScal*>(precon)->setMatrix(&systemMatrix);
- leftPrecon = precon;
- }
-
- preconType.assign("no");
- GET_PARAMETER(0, name + "->solver->right precon", &preconType);
- preconCreator = CreatorMap<PreconditionerScal>::getCreator(preconType);
-
- if (!preconCreator->isNullCreator()) {
- dynamic_cast<PreconditionerScalCreator*>(preconCreator)->setSizeAndRow(1, 0);
- dynamic_cast<PreconditionerScalCreator*>(preconCreator)->setName(name + "->solver->left precon");
- }
-
- precon = preconCreator->create();
- if (precon) {
- dynamic_cast<PreconditionerScal*>(precon)->setMatrix(&systemMatrix);
- rightPrecon = precon;
- }
-
- // === create vector creator ===
- solver->setVectorCreator(new DOFVector<double>::Creator(feSpace));
-
}
void ProblemScal::createEstimator()
@@ -599,9 +557,24 @@ namespace AMDiS {
if (useGetBound)
assembleFlag |= Mesh::FILL_BOUND;
- systemMatrix->clear();
+ // systemMatrix->clear();
rhs->set(0.0);
+ DOFMatrix::base_matrix_type& base_matrix= systemMatrix->getBaseMatrix();
+
+ int nnz_per_row= 0;
+ if (num_rows(base_matrix) != 0)
+ nnz_per_row= int(double(base_matrix.nnz()) / num_rows(base_matrix) * 1.2);
+ if (nnz_per_row < 5)
+ nnz_per_row= 5;
+
+ // Correct dimensionality of matrix
+ base_matrix.change_dim(feSpace->getAdmin()->getUsedSize(),
+ feSpace->getAdmin()->getUsedSize());
+
+ // Reuse old sparsity information (if available) or default
+ systemMatrix->startInsertion(nnz_per_row);
+
// fill boundary conditions
if (systemMatrix->getBoundaryManager())
systemMatrix->getBoundaryManager()->initMatrix(systemMatrix);
@@ -648,6 +621,7 @@ namespace AMDiS {
solution->getBoundaryManager()->exitVector(solution);
INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n", TIME_USED(first,clock()));
+ systemMatrix->finishInsertion();
#ifdef HAVE_PARALLEL_AMDIS
// PetscErrorCode ierr;
@@ -656,6 +630,7 @@ namespace AMDiS {
// ierr = MatCreate(PETSC_COMM_WORLD, &A); CHKERRQ(ierr);
#endif
+ createPrecon();
}
void ProblemScal::writeResidualMesh(AdaptInfo *adaptInfo, const std::string name)
@@ -676,6 +651,23 @@ namespace AMDiS {
fw.writeFiles(adaptInfo, true);
}
+ void ProblemScal::createPrecon()
+ {
+ ::std::string preconType("no");
+ GET_PARAMETER(0, name + "->solver->left precon", &preconType);
+
+ CreatorInterface<ITL_BasePreconditioner> *preconCreator =
+ CreatorMap<ITL_BasePreconditioner>::getCreator(preconType);
+
+ solver->setLeftPrecon( preconCreator->create(systemMatrix->getBaseMatrix()) );
+
+ preconType= "no";
+ GET_PARAMETER(0, name + "->solver->right precon", &preconType);
+
+ preconCreator = CreatorMap<ITL_BasePreconditioner>::getCreator(preconType);
+ solver->setRightPrecon( preconCreator->create(systemMatrix->getBaseMatrix()) );
+ }
+
void ProblemScal::serialize(std::ostream &out)
{
FUNCNAME("ProblemScal::serialize()");
diff --git a/AMDiS/src/ProblemScal.h b/AMDiS/src/ProblemScal.h
index 3b6cd776..4efc76a2 100644
--- a/AMDiS/src/ProblemScal.h
+++ b/AMDiS/src/ProblemScal.h
@@ -24,6 +24,7 @@
#include <list>
+#include "AMDiS_fwd.h"
#include "Global.h"
#include "ProblemStatBase.h"
#include "MemoryManager.h"
@@ -31,7 +32,6 @@
#include "FixVec.h"
#include "Boundary.h"
#include "StandardProblemIteration.h"
-#include "ProblemVec.h"
#ifdef HAVE_PARALLEL_AMDIS
#include "petscao.h"
@@ -39,20 +39,7 @@
namespace AMDiS {
- class Operator;
- class DOFMatrix;
- class FiniteElemSpace;
- class Estimator;
- template<typename T> class OEMSolver;
- template<typename T> class Preconditioner;
- template<typename T> class MatVecMultiplier;
- template<typename T> class DOFVector;
- class Marker;
- class AdaptInfo;
- class ElInfo;
- class FileWriterInterface;
- class RefinementManager;
- class CoarseningManager;
+
class ProblemScal : public ProblemStatBase,
public StandardProblemIteration
@@ -73,8 +60,6 @@ namespace AMDiS {
rhs(NULL),
systemMatrix(NULL),
matVec(NULL),
- leftPrecon(NULL),
- rightPrecon(NULL),
useGetBound(true),
refinementManager(NULL),
coarseningManager(NULL),
@@ -155,6 +140,8 @@ namespace AMDiS {
*/
virtual void buildBeforeCoarsen(AdaptInfo *adaptInfo, Flag) {}
+ void createPrecon();
+
/** \brief
* Implementation of ProblemStatBase::buildAfterCoarsen().
* Assembles \ref A and \ref rhs.
@@ -268,7 +255,7 @@ namespace AMDiS {
}
/// Returns \ref solver.
- inline OEMSolver<DOFVector<double> >* getSolver() {
+ inline OEMSolver* getSolver() {
return solver;
}
@@ -287,16 +274,6 @@ namespace AMDiS {
return useGetBound;
}
- /// Returns \ref leftPrecon.
- inline Preconditioner<DOFVector<double> > *getLeftPrecon() {
- return leftPrecon;
- }
-
- /// Returns \ref rightPrecon.
- inline Preconditioner<DOFVector<double> > *getRightPrecon() {
- return rightPrecon;
- }
-
///
inline CoarseningManager *getCoarseningManager() {
return coarseningManager;
@@ -324,20 +301,10 @@ namespace AMDiS {
}
/// Sets \ref solver.
- inline void setSolver(OEMSolver<DOFVector<double> >* sol) {
+ inline void setSolver(OEMSolver* sol) {
solver = sol;
}
- /// Sets \ref leftPrecon.
- inline void setLeftPrecon(Preconditioner<DOFVector<double> > *p) {
- leftPrecon = p;
- }
-
- /// Sets \ref rightPrecon.
- inline void setRightPrecon(Preconditioner<DOFVector<double> > *p) {
- rightPrecon = p;
- }
-
/// Sets \ref marker.
inline void setMarker(Marker *m) {
marker = m;
@@ -374,7 +341,7 @@ namespace AMDiS {
Estimator *estimator;
/// Linear solver of this problem. Used in \ref solve().
- OEMSolver<DOFVector<double> > *solver;
+ OEMSolver *solver;
/// DOFVector storing the calculated solution of the problem.
DOFVector<double> *solution;
@@ -388,12 +355,6 @@ namespace AMDiS {
/// Matrix-vector multiplication
MatVecMultiplier<DOFVector<double> > *matVec;
- /// Left preconditioner. Used in \ref solver.
- Preconditioner<DOFVector<double> > *leftPrecon;
-
- /// Right preconditioner. Used in \ref solver.
- Preconditioner<DOFVector<double> > *rightPrecon;
-
/// Determines whether domain boundaries should be considered at assembling.
bool useGetBound;
diff --git a/AMDiS/src/ProblemStatBase.h b/AMDiS/src/ProblemStatBase.h
index 12d9633c..4d5f704e 100644
--- a/AMDiS/src/ProblemStatBase.h
+++ b/AMDiS/src/ProblemStatBase.h
@@ -44,7 +44,7 @@ namespace AMDiS {
const Flag INIT_ADAPT = 0X80L;
const Flag INIT_FILEWRITER = 0X100L;
const Flag INIT_GLOBAL_REFINES = 0X1000L;
-
+
// For time dependent problems
const Flag INIT_INITIAL_PROBLEM = 0X200L;
const Flag INIT_UH_OLD = 0X400L;
@@ -58,8 +58,7 @@ namespace AMDiS {
const Flag INIT_ALL = INIT_FE_SPACE | INIT_MESH | CREATE_MESH | INIT_SYSTEM |
INIT_SOLVER | INIT_ESTIMATOR | INIT_MARKER |
INIT_ADAPT | INIT_FILEWRITER | INIT_INITIAL_PROBLEM |
- INIT_UH_OLD | INIT_UPDATER | INIT_NONLIN_SOLVER |
- INIT_GLOBAL_REFINES ;
+ INIT_UH_OLD | INIT_UPDATER | INIT_NONLIN_SOLVER ;
const Flag MESH_REFINED = 1;
const Flag MESH_COARSENED = 2;
diff --git a/AMDiS/src/ProblemVec.cc b/AMDiS/src/ProblemVec.cc
index 51e6c431..0467afe8 100644
--- a/AMDiS/src/ProblemVec.cc
+++ b/AMDiS/src/ProblemVec.cc
@@ -17,7 +17,6 @@
#include "DualTraverse.h"
#include "Mesh.h"
#include "OEMSolver.h"
-#include "Preconditioner.h"
#include "MatVecMultiplier.h"
#include "DirichletBC.h"
#include "RobinBC.h"
@@ -353,73 +352,12 @@ namespace AMDiS {
// === create solver ===
std::string solverType("no");
GET_PARAMETER(0, name + "->solver", &solverType);
- OEMSolverCreator<SystemVector> *solverCreator =
- dynamic_cast<OEMSolverCreator<SystemVector>*>(
- CreatorMap<OEMSolver<SystemVector> >
- ::getCreator(solverType)
- );
+ OEMSolverCreator *solverCreator =
+ dynamic_cast<OEMSolverCreator*>(CreatorMap<OEMSolver>::getCreator(solverType));
TEST_EXIT(solverCreator)("no solver type\n");
solverCreator->setName(name + "->solver");
solver = solverCreator->create();
solver->initParameters();
-
- // === create preconditioners ===
- std::string preconType("no");
-
- PreconditionerScal *scalPrecon;
- PreconditionerVec *vecPrecon = NEW PreconditionerVec(nComponents);
-
- GET_PARAMETER(0, name + "->solver->left precon", &preconType);
- CreatorInterface<PreconditionerScal> *preconCreator =
- CreatorMap<PreconditionerScal>::getCreator(preconType);
-
- if (!preconCreator->isNullCreator()) {
- dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
- setName(name + "->solver->left precon");
-
- for (int i = 0; i < nComponents; i++) {
- dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
- setSizeAndRow(nComponents, i);
-
- scalPrecon = preconCreator->create();
- for (int j = 0; j < nComponents; j++) {
- scalPrecon->setMatrix(&(*systemMatrix)[i][j], j);
- }
- vecPrecon->setScalarPrecon(i, scalPrecon);
- }
- leftPrecon = vecPrecon;
- }
-
-
- vecPrecon = NEW PreconditionerVec(nComponents);
-
- GET_PARAMETER(0, name + "->solver->right precon", &preconType);
- preconCreator =
- CreatorMap<PreconditionerScal>::getCreator(preconType);
-
- if (!preconCreator->isNullCreator()) {
- dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
- setName(name + "->solver->left precon");
-
-
- for (int i = 0; i < nComponents; i++) {
- dynamic_cast<PreconditionerScalCreator*>(preconCreator)->
- setSizeAndRow(nComponents, i);
-
- scalPrecon = preconCreator->create();
- for (int j = 0; j < nComponents; j++) {
- scalPrecon->setMatrix(&(*systemMatrix)[i][j], j);
- }
- vecPrecon->setScalarPrecon(i, scalPrecon);
- }
- rightPrecon = vecPrecon;
- }
-
-
- // === create vector creator ===
- solver->setVectorCreator(NEW SystemVector::Creator("temp",
- componentSpaces,
- nComponents));
}
void ProblemVec::createEstimator()
@@ -565,8 +503,8 @@ namespace AMDiS {
#endif
clock_t first = clock();
- int iter = solver->solve(matVec, solution, rhs, leftPrecon, rightPrecon, fixedMatrix);
-
+ int iter = solver->solveSystem(solverMatrix, *solution, *rhs);
+
#ifdef _OPENMP
INFO(info, 8)("solution of discrete system needed %.5f seconds system time / %.5f seconds wallclock time\n",
TIME_USED(first, clock()), omp_get_wtime() - wtime);
@@ -731,11 +669,21 @@ namespace AMDiS {
rhs->getDOFVector(i)->set(0.0);
for (int j = 0; j < nComponents; j++) {
if ((*systemMatrix)[i][j]) {
- // The matrix should not be deleted, if it was assembled before
- // and it is marked to be assembled only once.
- if (!(assembleMatrixOnlyOnce[i][j] && assembledMatrix[i][j]) && asmMatrix) {
- (*systemMatrix)[i][j]->clear();
- }
+ DOFMatrix* dof_matrix= (*systemMatrix)[i][j];
+ DOFMatrix::base_matrix_type& base_matrix= dof_matrix->getBaseMatrix();
+
+ int nnz_per_row= 0;
+ if (num_rows(base_matrix) != 0)
+ nnz_per_row= int(double(base_matrix.nnz()) / num_rows(base_matrix) * 1.2);
+ if (nnz_per_row < 5)
+ nnz_per_row= 5;
+
+ // Correct dimensionality of matrix
+ base_matrix.change_dim(componentSpaces[i]->getAdmin()->getUsedSize(),
+ componentSpaces[j]->getAdmin()->getUsedSize());
+
+ // Reuse old sparsity information (if available) or default
+ dof_matrix->startInsertion(nnz_per_row);
}
}
}
@@ -854,6 +802,15 @@ namespace AMDiS {
assembleFlag);
}
+ // Finish insertion
+ for (int i = 0; i < nComponents; i++)
+ for (int j = 0; j < nComponents; j++)
+ if ((*systemMatrix)[i][j])
+ (*systemMatrix)[i][j]->finishInsertion();
+
+ solverMatrix.setMatrix(*systemMatrix);
+ createPrecon();
+
#ifdef _OPENMP
INFO(info, 8)("buildAfterCoarsen needed %.5f seconds system time / %.5f seconds wallclock time\n",
TIME_USED(first, clock()), omp_get_wtime() - wtime);
@@ -863,6 +820,24 @@ namespace AMDiS {
#endif
}
+ void ProblemVec::createPrecon()
+ {
+ ::std::string preconType("no");
+ GET_PARAMETER(0, name + "->solver->left precon", &preconType);
+
+ CreatorInterface<ITL_BasePreconditioner> *preconCreator =
+ CreatorMap<ITL_BasePreconditioner>::getCreator(preconType);
+
+ solver->setLeftPrecon( preconCreator->create(solverMatrix.getMatrix()) );
+
+ preconType= "no";
+ GET_PARAMETER(0, name + "->solver->right precon", &preconType);
+
+ preconCreator = CreatorMap<ITL_BasePreconditioner>::getCreator(preconType);
+ solver->setRightPrecon( preconCreator->create(solverMatrix.getMatrix()) );
+ }
+
+
void ProblemVec::writeFiles(AdaptInfo *adaptInfo, bool force)
{
FUNCNAME("ProblemVec::writeFiles()");
@@ -965,10 +940,8 @@ namespace AMDiS {
(*systemMatrix)[system][i]->getBoundaryManager()->addBoundaryCondition(dirichlet);
}
}
-
if (rhs)
rhs->getDOFVector(system)->getBoundaryManager()->addBoundaryCondition(dirichlet);
-
if (solution)
solution->getDOFVector(system)->getBoundaryManager()->addBoundaryCondition(dirichlet);
}
@@ -1052,6 +1025,10 @@ namespace AMDiS {
// values have to be set to zero.
*tmpMatrix = *matrix;
tmpMatrix->clear();
+
+ tmpMatrix->getBaseMatrix().change_dim(matrix->getRowFESpace()->getAdmin()->getUsedSize(),
+ matrix->getColFESpace()->getAdmin()->getUsedSize());
+ tmpMatrix->startInsertion();
}
if (vector) {
@@ -1097,6 +1074,8 @@ namespace AMDiS {
elInfo = stack.traverseNext(elInfo);
}
+ tmpMatrix->finishInsertion();
+
// After mesh traverse, all thread have to added their private matrices and
// vectors to the global public matrix and public vector. Therefore, this is
// a critical section, which is allowed to be executed by on thread only at
@@ -1107,7 +1086,7 @@ namespace AMDiS {
#pragma omp critical
#endif
{
- addDOFMatrix(matrix, tmpMatrix);
+ matrix->getBaseMatrix() += tmpMatrix->getBaseMatrix();
// Remove rows corresponding to DOFs on a Dirichlet boundary.
matrix->removeRowsWithDBC(tmpMatrix->getApplyDBCs());
diff --git a/AMDiS/src/ProblemVec.h b/AMDiS/src/ProblemVec.h
index de21bbd3..e1cae1eb 100644
--- a/AMDiS/src/ProblemVec.h
+++ b/AMDiS/src/ProblemVec.h
@@ -25,6 +25,7 @@
#include <vector>
#include <list>
+#include "AMDiS_fwd.h"
#include "ProblemStatBase.h"
#include "Parameters.h"
#include "Boundary.h"
@@ -32,26 +33,11 @@
#include "StandardProblemIteration.h"
#include "ElementFileWriter.h"
#include "ComponentTraverseInfo.h"
+#include "AbstractFunction.h"
+#include "SolverMatrix.h"
namespace AMDiS {
- template<typename t1, typename t2> class AbstractFunction;
- class Operator;
- class SystemVector;
- class DOFMatrix;
- class FiniteElemSpace;
- class Estimator;
- class Marker;
- class AdaptStationary;
- class AdaptInfo;
- class FileWriterInterface;
- class CoarseningManager;
- class RefinementManager;
- class Mesh;
- template<typename T> class OEMSolver;
- template<typename T> class Preconditioner;
- template<typename T> class MatVecMultiplier;
-
class ProblemVec : public ProblemStatBase,
public StandardProblemIteration
{
@@ -71,8 +57,6 @@ namespace AMDiS {
rhs(NULL),
systemMatrix(NULL),
matVec(NULL),
- leftPrecon(NULL),
- rightPrecon(NULL),
useGetBound(true),
info(10),
allowFirstRef(false),
@@ -80,7 +64,6 @@ namespace AMDiS {
{
GET_PARAMETER(0, name + "->components", "%d", &nComponents);
TEST_EXIT(nComponents > 0)("components not set!\n");
-
estimator.resize(nComponents, NULL);
marker.resize(nComponents, NULL);
@@ -182,6 +165,9 @@ namespace AMDiS {
bool assembleMatrix = true,
bool assembleVector = true);
+ void createPrecon();
+
+
/** \brief
* Determines the execution order of the single adaption steps. If adapt is
* true, mesh adaption will be performed. This allows to avoid mesh adaption,
@@ -352,7 +338,7 @@ namespace AMDiS {
}
/// Returns \ref solver.
- inline OEMSolver<SystemVector>* getSolver() {
+ inline OEMSolver* getSolver() {
return solver;
}
@@ -376,16 +362,6 @@ namespace AMDiS {
return useGetBound;
}
- /// Returns \ref leftPrecon.
- inline Preconditioner<SystemVector> *getLeftPrecon() {
- return leftPrecon;
- }
-
- /// Returns \ref rightPrecon.
- inline Preconditioner<SystemVector> *getRightPrecon() {
- return rightPrecon;
- }
-
/** \} */
// ===== setting-methods ======================================================
@@ -415,20 +391,10 @@ namespace AMDiS {
}
/// Sets \ref solver.
- inline void setSolver(OEMSolver<SystemVector>* sol) {
+ inline void setSolver(OEMSolver* sol) {
solver = sol;
}
- /// Sets \ref leftPrecon.
- inline void setLeftPrecon(Preconditioner<SystemVector> *p) {
- leftPrecon = p;
- }
-
- /// Sets \ref rightPrecon.
- inline void setRightPrecon(Preconditioner<SystemVector> *p) {
- rightPrecon = p;
- }
-
///
inline void setAssembleMatrixOnlyOnce(int i, int j, bool value = true) {
assembleMatrixOnlyOnce[i][j] = value;
@@ -520,7 +486,7 @@ namespace AMDiS {
std::vector<Estimator*> estimator;
/// Linear solver of this problem. Used in \ref solve().
- OEMSolver<SystemVector> *solver;
+ OEMSolver *solver;
/// System vector storing the calculated solution of the problem.
SystemVector *solution;
@@ -531,6 +497,9 @@ namespace AMDiS {
/// System matrix
Matrix<DOFMatrix*> *systemMatrix;
+ /// Composed system matrix
+ SolverMatrix<Matrix<DOFMatrix*> > solverMatrix;
+
/** \brief
* Some DOFMatrices of the systemMatrix may be assembled only once (for
* example if they are independent of the time or older solutions). If
@@ -551,12 +520,6 @@ namespace AMDiS {
/// Matrix-vector multiplication
MatVecMultiplier<SystemVector> *matVec;
- /// Left preconditioner. Used in \ref solver.
- Preconditioner<SystemVector> *leftPrecon;
-
- /// Right preconditioner. Used in \ref solver.
- Preconditioner<SystemVector> *rightPrecon;
-
/// Determines whether domain boundaries should be considered at assembling.
bool useGetBound;
diff --git a/AMDiS/src/QN_Precond.h b/AMDiS/src/QN_Precond.h
deleted file mode 100755
index edc038d0..00000000
--- a/AMDiS/src/QN_Precond.h
+++ /dev/null
@@ -1,26 +0,0 @@
-/** \file QN_Precond.h */
-
-#ifndef QN_PRECOND_H
-#define QN_PRECOND_H
-
-#include "DOFVector.h"
-
-namespace AMDiS
-{
-
- template<typename T>
- void diagPrecond(const DOFMatrix *A, DOFVector<T>* vec,
- DOFVector<BoundaryType> *bound = NULL);
-
- template<typename T>
- void aXpY(double a, const DOFVector<T>& x, DOFVector<T>& y,
- DOFVector<BoundaryType> *bound = NULL);
-
- template<typename T>
- void XpaY(double a, const DOFVector<T>& x, DOFVector<T>& y,
- DOFVector<BoundaryType> *bound = NULL);
-
-}
-
-#include "QN_Precond.hh"
-#endif // QN_PRECOND_H
diff --git a/AMDiS/src/QN_Precond.hh b/AMDiS/src/QN_Precond.hh
deleted file mode 100755
index 5bb4a35e..00000000
--- a/AMDiS/src/QN_Precond.hh
+++ /dev/null
@@ -1,141 +0,0 @@
-#include "DOFVector.h"
-
-namespace AMDiS
-{
-
- template<typename T>
- void diagPrecond(DOFMatrix *A, DOFVector<T> *vec,
- DOFVector<BoundaryType> *bound)
- {
- FUNCNAME("QN_Precond::diagPrecond()");
-
- TEST(A)("No matrix; doing nothing\n");
-
- DOFMatrix::Iterator rowIterator(A, USED_DOFS);
- typename DOFVector<T>::Iterator vecIterator(vec, USED_DOFS);
-
- if (bound) {
- DOFVector<BoundaryType>::Iterator
- bIterator(const_cast<DOFVector<BoundaryType>*>(bound), USED_DOFS);
-
- for (vecIterator.reset(), rowIterator.reset(), bIterator.reset();
- !vecIterator.end(); ++vecIterator, ++bIterator, ++rowIterator)
- {
- // only non-dirichlet nodes will be preconditioned
- if ((*bIterator) <= 0 && rowIterator->size() != 0)
- (*vecIterator) *= (1.0 / (*rowIterator)[0].entry);
- }
- } else {
- for (vecIterator.reset(), rowIterator.reset(); !vecIterator.end();
- ++vecIterator, ++rowIterator)
- {
- if (rowIterator->size() != 0)
- (*vecIterator) *= (1.0 / (*rowIterator)[0].entry);
- }
- }
-
- return;
- }
-
- template<typename T>
- void aXpY(double alpha, const DOFVector<T>& x, DOFVector<T>& y,
- DOFVector<BoundaryType> *bound)
- {
- FUNCNAME("QN_Precond::aXpY()");
- const DOFAdmin *admin;
-
- TEST_EXIT(x.getFESpace() && y.getFESpace())
- ("feSpace is NULL: %8X, %8X\n", x.getFESpace(), y.getFESpace());
- TEST_EXIT((admin = x.getFESpace()->getAdmin()) &&
- (admin == y.getFESpace()->getAdmin()))
- ("no admin or different admins: %8X, %8X\n",
- x.getFESpace()->getAdmin(), y.getFESpace()->getAdmin());
- TEST_EXIT(static_cast<int>(x.getSize()) >= admin->getUsedSize())
- ("size = %d too small: admin->size = %d\n", x.getSize(),
- admin->getUsedSize());
- TEST_EXIT(static_cast<int>(y.getSize()) >= admin->getUsedSize())
- ("y.size = %d too small: admin->size = %d\n", y.getSize(),
- admin->getUsedSize());
-
- typename DOFVector<T>::Iterator
- xIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&x)),
- USED_DOFS);
- typename DOFVector<T>::Iterator yIterator(dynamic_cast<DOFIndexed<T>*>(&y),
- USED_DOFS);
-
- if (bound) {
- DOFVector<BoundaryType>::Iterator
- bIterator(const_cast<DOFVector<BoundaryType>*>(bound), USED_DOFS);
-
- for (xIterator.reset(), yIterator.reset(), bIterator.reset();
- !xIterator.end();
- ++xIterator, ++yIterator, ++bIterator)
- {
- // only non-dirichlet nodes will be updated
- if ((*bIterator) <= 0 )
- *yIterator += alpha * (*xIterator);
- }
- } else {
- for (xIterator.reset(), yIterator.reset(); !xIterator.end();
- ++xIterator, ++yIterator)
- {
- *yIterator += alpha * (*xIterator);
- }
- }
-
- return;
- }
-
- template<typename T>
- void XpaY(double alpha, const DOFVector<T>& x, DOFVector<T>& y,
- DOFVector<BoundaryType> *bound)
- {
- FUNCNAME("QN_Precond::aXpY()");
- const DOFAdmin *admin;
-
- TEST_EXIT(x.getFESpace() && y.getFESpace())
- ("feSpace is NULL: %8X, %8X\n", x.getFESpace(), y.getFESpace());
- TEST_EXIT((admin = x.getFESpace()->getAdmin()) &&
- (admin == y.getFESpace()->getAdmin()))
- ("no admin or different admins: %8X, %8X\n",
- x.getFESpace()->getAdmin(), y.getFESpace()->getAdmin());
- TEST_EXIT(static_cast<int>(x.getSize()) >= admin->getUsedSize())
- ("size = %d too small: admin->size = %d\n", x.getSize(),
- admin->getUsedSize());
- TEST_EXIT(static_cast<int>(y.getSize()) >= admin->getUsedSize())
- ("y.size = %d too small: admin->size = %d\n", y.getSize(),
- admin->getUsedSize());
-
- typename DOFVector<T>::Iterator
- xIterator(dynamic_cast<DOFIndexed<T>*>(const_cast<DOFVector<T>*>(&x)),
- USED_DOFS);
- typename DOFVector<T>::Iterator yIterator(dynamic_cast<DOFIndexed<T>*>(&y),
- USED_DOFS);
-
- if (bound) {
- DOFVector<BoundaryType>::Iterator
- bIterator(const_cast<DOFVector<BoundaryType>*>(bound), USED_DOFS);
-
- for (xIterator.reset(), yIterator.reset(), bIterator.reset();
- !xIterator.end();
- ++xIterator, ++yIterator, ++bIterator)
- {
- // only non-dirichlet nodes will be updated
- if ((*bIterator) <= 0 ) {
- *yIterator *= alpha;
- *yIterator += *xIterator;
- }
- }
- } else {
- for (xIterator.reset(), yIterator.reset(); !xIterator.end();
- ++xIterator, ++yIterator)
- {
- *yIterator *= alpha;
- *yIterator += *xIterator;
- }
- }
-
- return;
- }
-
-}
diff --git a/AMDiS/src/BiCGStab_M.h b/AMDiS/src/SolverMatrix.h
similarity index 53%
rename from AMDiS/src/BiCGStab_M.h
rename to AMDiS/src/SolverMatrix.h
index c9f36d0f..0c4d23b8 100644
--- a/AMDiS/src/BiCGStab_M.h
+++ b/AMDiS/src/SolverMatrix.h
@@ -17,82 +17,74 @@
// == ==
// ============================================================================
-/** \file BiCGStab_M.h */
+/** \file SolverMatrix.h */
+
+#ifndef AMDIS_SOLVERMATRIX_H
+#define AMDIS_SOLVERMATRIX_H
+
+
+#include "DOFMatrix.h"
-#ifndef BICGStab_M_H
-#define BICGStab_M_H
namespace AMDiS {
// ============================================================================
- // ===== class BiCGStab_M =====================================================
+ // ===== class SolverMatrix ===================================================
// ============================================================================
/**
- * \ingroup Solver
- *
- * \brief
- * Solves a linear system by a stabilized BiCG method.
- * Can be used for general matrices.
+ * \brief Helper class to provide complete matrix for ITL solvers and preconditioners
*/
- template<typename VectorType>
- class BiCGStab_M : public OEMSolver<VectorType>
+
+ // General case undefined !
+ template <typename Matrix>
+ class SolverMatrix { };
+
+
+ // DOFMatrix, i.e. ScalarProblem
+ template <>
+ class SolverMatrix<DOFMatrix>
{
- public:
- MEMORY_MANAGED(BiCGStab_M<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new BiCGStab_M object.
- */
- OEMSolver<VectorType>* create()
+ public :
+ SolverMatrix() : matrix(0) {}
+
+ void setMatrix(const DOFMatrix& A)
{
- return NEW BiCGStab_M<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- BiCGStab_M(std::string name);
-
- /** \brief
- * destructor
- */
- ~BiCGStab_M();
-
- protected:
- /** \brief
- * Implements OEMSolver<VectorType>::init().
- */
- void init();
-
- /** \brief
- * Implements OEMSolver<VectorType>::exit().
- */
- void exit();
-
- /** \brief
- * Implements OEMSolver<VectorType>::solve().
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv, VectorType *x, VectorType *b, bool reuseMatrix);
-
- private:
- // Pointers to memory needed for solveSystem
- VectorType *r, *rt, *p, *v, *t, *ph, *sh, *xmin;
+ matrix= &A.getBaseMatrix();
+ }
+
+ const DOFMatrix::base_matrix_type& getMatrix() const { return *matrix; }
+
+ private:
+ const DOFMatrix::base_matrix_type* matrix;
};
-}
-#include "BiCGStab_M.hh"
+ // VectorProblem
+ template <>
+ class SolverMatrix<Matrix<DOFMatrix*> >
+ {
+ public :
+ void setMatrix(const Matrix<DOFMatrix*>& A)
+ {
+ int ns = A.getSize(), size = A[0][0]->getFESpace()->getAdmin()->getUsedSize(),
+ new_size = ns * size;
+ matrix.change_dim(new_size, new_size);
+ DOFMatrix::inserter_type ins(matrix);
+ for (int rb= 0; rb < ns; ++rb)
+ for (int cb= 0; cb < ns; ++cb)
+ if (A[rb][cb])
+ ins[rb * size][cb * size] << A[rb][cb]->getBaseMatrix();
+ }
+
+ const DOFMatrix::base_matrix_type& getMatrix() const { return matrix; }
+
+ private:
+ DOFMatrix::base_matrix_type matrix;
+ };
+
+
+
+} // namespace AMDiS
-#endif // BICGStab_M_H
+#endif // AMDIS_SOLVERMATRIX_H
diff --git a/AMDiS/src/SparseVector.cc b/AMDiS/src/SparseVector.cc
index 0435130b..5e144280 100644
--- a/AMDiS/src/SparseVector.cc
+++ b/AMDiS/src/SparseVector.cc
@@ -2,6 +2,8 @@
#include "DOFVector.h"
#include "FiniteElemSpace.h"
+#include <boost/numeric/mtl/mtl.hpp>
+
namespace AMDiS {
template<>
@@ -43,6 +45,28 @@ namespace AMDiS {
std::set<DegreeOfFreedom> &dofSet,
bool add)
{
+ using namespace mtl;
+ using mtl::tag::nz; using mtl::begin; using mtl::end;
+ namespace traits= mtl::traits;
+ typedef DOFMatrix::base_matrix_type Matrix;
+ Matrix &matrix= a.getBaseMatrix();
+
+ traits::row<Matrix>::type row(matrix);
+ traits::col<Matrix>::type col(matrix);
+ traits::const_value<Matrix>::type value(matrix);
+
+ typedef traits::range_generator<tag::row, Matrix>::type cursor_type;
+ typedef traits::range_generator<nz, cursor_type>::type icursor_type;
+
+ for (cursor_type cursor = begin<tag::row>(matrix), cend = end<tag::row>(matrix); cursor != cend; ++cursor) {
+ icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor);
+ double sum= add ? result[row(*icursor)] : 0.0;
+ for (; icursor != icend; ++icursor)
+ sum+= value(*icursor) * const_cast<SparseVector<double>&>(x)[col(*icursor)];
+ result[row(*icursor)]= sum;
+ }
+
+#if 0
//DOFMatrix::Iterator matIt(const_cast<DOFMatrix*>(&a), USED_DOFS);
std::vector<MatEntry>::iterator rowIt, rowEnd;
@@ -62,6 +86,7 @@ namespace AMDiS {
result[row] += rowIt->entry * const_cast<SparseVector<double>&>(x)[col];
}
}
+#endif
}
template<>
diff --git a/AMDiS/src/StlVector.cc b/AMDiS/src/StlVector.cc
deleted file mode 100644
index f971f29f..00000000
--- a/AMDiS/src/StlVector.cc
+++ /dev/null
@@ -1,81 +0,0 @@
-#include <vector>
-#include <math.h>
-#include "StlVector.h"
-
-namespace AMDiS {
-
- double norm(std::vector<double> *vec) {
- double v = 0;
- for (int i = 0; i < static_cast<int>(vec->size()); i++) {
- v += (*vec)[i] * (*vec)[i];
- }
- return sqrt(v);
- }
-
- void setValue(std::vector<double>& x, double value) {
- for (int i = 0; i < static_cast<int>(x.size()); i++) {
- x[i] = value;
- }
- }
-
- const std::vector<double>& operator*=(std::vector<double>& x, double scal) {
- for (int i = 0; i < static_cast<int>(x.size()); i++) {
- x[i] *= scal;
- }
-
- return x;
- }
-
- const std::vector<double>& operator+=(std::vector<double>& x1,
- const std::vector<double>& x2) {
- for (int i = 0; i < static_cast<int>(x1.size()); i++) {
- x1[i] += x2[i];
- }
-
- return x1;
- }
-
- double operator*(std::vector<double>& x1, std::vector<double>& x2) {
- double result = 0.0;
-
- for (int i = 0; i < static_cast<int>(x1.size()); i++) {
- result += x1[i] * x2[i];
- }
-
- return result;
- }
-
- void axpy(double alpha, const std::vector<double>& x, std::vector<double>& y) {
- for (int i = 0; i < static_cast<int>(y.size()); i++) {
- y[i] += alpha * x[i];
- }
- }
-
- void xpay(double alpha, const std::vector<double>& x, std::vector<double>& y) {
- for (int i = 0; i < static_cast<int>(y.size()); i++) {
- y[i] = alpha * y[i] + x[i];
- }
- }
-
- int logToPhysIndex(std::vector< std::vector<MatEntry> > *matrix, int a, int b)
- {
- int j;
-
- for (j = 0; j < static_cast<int>((*matrix)[a].size()); j++)
- if (b == (*matrix)[a][j].col)
- break;
-
- return (j == static_cast<int>((*matrix)[a].size())) ? -1 : j;
- }
-
- void print(std::vector<double> *vec)
- {
- std::cout << "[";
-
- for (int i = 0; i < static_cast<int>(vec->size()); i++) {
- std::cout << (*vec)[i] << " , ";
- }
-
- std::cout << "]" << std::endl;
- }
-}
diff --git a/AMDiS/src/StlVector.h b/AMDiS/src/StlVector.h
deleted file mode 100644
index 7dde8302..00000000
--- a/AMDiS/src/StlVector.h
+++ /dev/null
@@ -1,60 +0,0 @@
-#ifndef AMDIS_STLVECTOR_H
-#define AMDIS_STLVECTOR_H
-
-#include <vector>
-#include "CreatorInterface.h"
-#include "MemoryManager.h"
-#include "DOFMatrix.h"
-
-namespace AMDiS {
-
- class StlVectorCreator : public CreatorInterface< std::vector<double> > {
- public:
- MEMORY_MANAGED(StlVectorCreator);
-
- StlVectorCreator(int size)
- : size_(size)
- {};
-
- virtual ~StlVectorCreator() {};
-
- std::vector<double> *create() {
- std::vector<double> *vec = new std::vector<double>(size_, 0.0);
-
- return vec;
- };
-
- void free(std::vector<double> *vec) {
- delete vec;
- };
-
- private:
- int size_;
- };
-
- double norm(std::vector<double> *vec);
-
- inline int size(std::vector<double> *vec)
- {
- return vec->size();
- }
-
- void setValue(std::vector<double>& x, double value);
-
- const std::vector<double>& operator*=(std::vector<double>& x, double scal);
-
- const std::vector<double>& operator+=(std::vector<double>& x1,
- const std::vector<double>& x2);
-
- double operator*(std::vector<double>& x1, std::vector<double>& x2);
-
- void axpy(double alpha, const std::vector<double>& x, std::vector<double>& y);
-
- void xpay(double alpha, const std::vector<double>& x, std::vector<double>& y);
-
- int logToPhysIndex(std::vector< std::vector<MatEntry> > *m, int a, int b);
-
- void print(std::vector<double> *vec);
-}
-
-#endif
diff --git a/AMDiS/src/TFQMR.h b/AMDiS/src/TFQMR.h
deleted file mode 100644
index e127e267..00000000
--- a/AMDiS/src/TFQMR.h
+++ /dev/null
@@ -1,115 +0,0 @@
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file TFQMR.h */
-
-#ifndef AMDIS_TFQMR_H
-#define AMDIS_TFQMR_H
-
-#include "OEMSolver.h"
-#include "MemoryManager.h"
-
-namespace AMDiS {
-
- // ============================================================================
- // ===== class TFQMR ==========================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- */
- template<typename VectorType>
- class TFQMR : public OEMSolver<VectorType>
- {
- public:
- MEMORY_MANAGED(GMResSolver2<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new TFQMR object.
- */
- OEMSolver<VectorType>* create() {
- return NEW TFQMR<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- TFQMR(std::string name);
-
- /** \brief
- * destructor
- */
- ~TFQMR();
-
- protected:
- /** \brief
- * realisation of OEMSolver::solveSystem
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b, bool reuseMatrix);
-
- /** \brief
- * realisation of OEMSolver::init
- */
- void init();
-
- /** \brief
- * realisation of OEMSolver::exit
- */
- void exit();
-
- private:
- /** \brief
- * Stores the tolerance boundary for numerical computations.
- */
- double TOL_;
-
- VectorType *r0_;
-
- /** \brief
- * Stores intermediate results in the orthogonalization step.
- */
- VectorType *w_;
-
- /** \brief
- * Pointers to the vectors of the orthogonal system.
- */
- VectorType *y1_, *y2_;
-
- VectorType *v_, *d_, *tmp_;
-
- };
-
-
-}
-
-#include "TFQMR.hh"
-
-#endif // AMDIS_TFQMR_H
diff --git a/AMDiS/src/TFQMR.hh b/AMDiS/src/TFQMR.hh
deleted file mode 100644
index d2ae5e92..00000000
--- a/AMDiS/src/TFQMR.hh
+++ /dev/null
@@ -1,184 +0,0 @@
-#include "TFQMR.h"
-#include "Preconditioner.h"
-
-namespace AMDiS {
-
- template<typename VectorType>
- TFQMR<VectorType>::TFQMR(std::string name)
- : OEMSolver<VectorType>(name),
- TOL_(1.e-25)
- {
- FUNCNAME("TFQMR::TFQMR()");
- }
-
- template<typename VectorType>
- TFQMR<VectorType>::~TFQMR()
- {}
-
- template<typename VectorType>
- void TFQMR<VectorType>::init()
- {
- r0_ = this->vectorCreator->create();
- w_ = this->vectorCreator->create();
- y1_ = this->vectorCreator->create();
- y2_ = this->vectorCreator->create();
- v_ = this->vectorCreator->create();
- d_ = this->vectorCreator->create();
- tmp_ = this->vectorCreator->create();
- }
-
- template<typename VectorType>
- void TFQMR<VectorType>::exit()
- {
- if (r0_) {
- this->vectorCreator->free(r0_);
- this->vectorCreator->free(w_);
- this->vectorCreator->free(y1_);
- this->vectorCreator->free(y2_);
- this->vectorCreator->free(v_);
- this->vectorCreator->free(d_);
- this->vectorCreator->free(tmp_);
- }
- }
-
- template<typename VectorType>
- int TFQMR<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x,
- VectorType *b,
- bool reuseMatrix)
- {
- DOFMatrix *m = (dynamic_cast<StandardMatVec<DOFMatrix, VectorType> *>(matVec))->getMatrix();
-
- matVec->matVec(NoTranspose, *x, *r0_);
- xpay(-1.0, *b, *r0_);
- double tau = norm(r0_);
- std::cout << "NORM: " << tau << std::endl;
-
- for (int iter = 0; iter < 1000; iter++) {
- for (int i = 0; i < x->getSize(); i++) {
- (*y1_)[i] = (*b)[i];
-
- for (int j = 0; j < static_cast<int>((*m)[i].size()); j++) {
- MatEntry a = (*m)[i][j];
-
- if (a.col != i) {
- (*y1_)[i] -= (*x)[i] * a.entry;
- }
- }
-
- (*y1_)[i] /= (*m)[i][0].entry;
- }
-
- *x = *y1_;
- }
-
- matVec->matVec(NoTranspose, *x, *r0_);
- xpay(-1.0, *b, *r0_);
- tau = norm(r0_);
- std::cout << "NORM: " << tau << std::endl;
-
- return 1000;
- }
-
- // template<typename VectorType>
-// int TFQMR<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
-// VectorType *x,
-// VectorType *b)
-// {
-// FUNCNAME("TFQMR::solveSystem()");
-
-// double old_res = -1.0;
-
-// // If norm of b is smaller than the tolarance, we can assume b to be zero.
-// // Hence, x = 0 is the solution of the linear system.
-// if (norm(b) < TOL_) {
-// INFO(this->info, 2)("b == 0, x = 0 is the solution of the linear system\n");
-// set(*x, 0.0);
-// this->residual = 0.0;
-// return(0);
-// }
-
-// // r_0 = b - Ax, where r_0 is already stored as the first vector in the
-// // matrix V.
-// matVec->matVec(NoTranspose, *x, *r0_);
-// xpay(-1.0, *b, *r0_);
-
-// if (this->leftPrecon)
-// this->leftPrecon->precon(r0_);
-
-// *y1_ = *r0_;
-// *w_ = *r0_;
-// double tau = norm(r0_);
-
-// if (tau < this->tolerance) {
-// this->residual = tau;
-// return(0);
-// }
-
-// matVec->matVec(NoTranspose, *y1_, *v_);
-// d_->set(0.0);
-// double eta = 0.0;
-// double theta = 0.0;
-// double rho1 = tau * tau;
-// double rho2 = 0.0;
-// double alpha = 0.0;
-// double beta = 0.0;
-// double c = 0.0;
-
-// START_INFO();
-// for (int j = 1; j <= this->max_iter; j++) {
-// rho2 = *v_ * *r0_;
-// alpha = rho1 / rho2;
-// *y2_ = *y1_;
-// axpy(-alpha, *v_, *y2_);
-
-// for (int m = 2 * j - 1; m <= 2 * j; m++) {
-// matVec->matVec(NoTranspose, *y1_, *tmp_);
-// axpy(-alpha, *tmp_, *w_);
-
-// if (this->leftPrecon)
-// this->leftPrecon->precon(w_);
-
-// xpay(theta * theta * eta / alpha, *y1_, *d_);
-
-
-// theta = norm(w_) / tau;
-// c = 1 / sqrt(theta * theta + 1);
-// eta = c * c * alpha;
-// axpy(eta, *d_, *x);
-// tau = tau * theta * c;
-// this->residual = sqrt(m + 1) * tau;
-// *y1_ = *y2_;
-// }
-
-// if (SOLVE_INFO(j - 1, this->residual, &old_res))
-// return(j - 1);
-
-// rho2 = *w_ * *r0_;
-// beta = rho2 / rho1;
-// *y1_ = *w_;
-// axpy(beta, *y2_, *y1_);
-
-
-// matVec->matVec(NoTranspose, *y2_, *tmp_);
-
-// if (this->leftPrecon)
-// this->leftPrecon->precon(tmp_);
-
-// xpay(beta, *tmp_, *v_);
-
-// matVec->matVec(NoTranspose, *y1_, *tmp_);
-
-// if (this->leftPrecon)
-// this->leftPrecon->precon(tmp_);
-
-
-// xpay(beta, *tmp_, *v_);
-
-// rho1 = rho2;
-// }
-
-// return 0;
-// }
-
-}
diff --git a/AMDiS/src/UmfPackSolver.h b/AMDiS/src/UmfPackSolver.h
index 6bc57c89..893ca76a 100644
--- a/AMDiS/src/UmfPackSolver.h
+++ b/AMDiS/src/UmfPackSolver.h
@@ -22,11 +22,13 @@
#ifndef AMDIS_UMFPACKSOLVER_H
#define AMDIS_UMFPACKSOLVER_H
-#ifdef HAVE_UMFPACK
+#if defined HAVE_UMFPACK && defined MTL_HAS_UMFPACK
#include "OEMSolver.h"
#include "MemoryManager.h"
+#include <boost/numeric/mtl/interface/umfpack_solve.hpp>
+
namespace AMDiS {
// ============================================================================
@@ -42,16 +44,14 @@ namespace AMDiS {
*
* This is a direct solver for large sparse matrices.
*/
- template<typename VectorType>
- class UmfPackSolver : public OEMSolver<VectorType>
+
+ class UmfPackSolver : public OEMSolver
{
public:
- MEMORY_MANAGED(UmfPackSolver<VectorType>);
+ MEMORY_MANAGED(UmfPackSolver);
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
+ /// Creator class used in the OEMSolverMap.
+ class Creator : public OEMSolverCreator
{
public:
MEMORY_MANAGED(Creator);
@@ -61,78 +61,45 @@ namespace AMDiS {
/** \brief
* Returns a new UmfPackSolver object.
*/
- OEMSolver<VectorType>* create() {
- return NEW UmfPackSolver<VectorType>(this->name);
+ OEMSolver* create() {
+ return NEW UmfPackSolver(this->name);
};
};
- /** \brief
- * constructor
- */
- UmfPackSolver(std::string name);
-
- /** \brief
- * destructor
- */
- ~UmfPackSolver();
- protected:
- /** \brief
- * Implements OEMSolver<VectorType>::init().
- */
- void init() {
- p = this->vectorCreator->create();
- r = this->vectorCreator->create();
+ /// Constructor
+ UmfPackSolver(::std::string name)
+ : OEMSolver(name),
+ solver(0)
+ {
+ GET_PARAMETER(0, name + "->store symbolic", "%d", &store_symbolic);
+ // GET_PARAMETER(0, name + "->multiple rhs", "%d", &multipleRhs);
}
- /** \brief
- * Implements OEMSolver<VectorType>::exit().
- */
- void exit() {
- this->vectorCreator->free(p);
- this->vectorCreator->free(r);
+ /// Destructor
+ ~UmfPackSolver() { if (solver) delete solver;}
+
+ /// Solves the system directly
+ int solveSystem(const DOFMatrix::base_matrix_type& A,
+ mtl::dense_vector<value_type>& x,
+ const mtl::dense_vector<value_type>& b)
+ {
+ if (!solver)
+ solver= new mtl::matrix::umfpack::solver<matrix_type>(A);
+ else if (store_symbolic)
+ solver->update_numeric();
+ else
+ solver->update();
+ return (*solver)(x, b);
}
-
- /** \brief
- * Implements OEMSolver<VectorType>::solve().
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv, VectorType *x, VectorType *b, bool reuseMatrix);
+
private:
- /** \brief
- * These vectors are justed to calculate the final residual of the solution.
- */
- VectorType *r, *p;
-
- /** \brief
- * Stores the result of umfpack_di_symbolic (the symbolic analysis which is needed
- * for the numeric factorization).
- */
- void *symbolic_;
-
- /** \brief
- * Stores the result of umfpack_di_numeric, if multiple right hand sides will occure.
- */
- void *numeric;
-
- /** \brief
- * If the symbolic analysis should be done only once (for example, if the matrices
- * to solve have all the same pattern because of no adaptivity), this variable
- * is one, otherwise 0 and the symbolic analysis will be performed at every call
- * of solveSystem().
- */
- int storeSymbolic_;
-
- /** \brief
- * If not zero, Umfpack is prepared to solve multiple following systems with equal
- * system matrix but different right hand side vectors.
- */
- int multipleRhs;
+ mtl::matrix::umfpack::solver<matrix_type> *solver;
+ int store_symbolic;
};
}
-#include "UmfPackSolver.hh"
-
#endif // HAVE_UMFPACK
#endif // AMDIS_UMFPACKSOLVER_H
diff --git a/AMDiS/src/UmfPackSolver.hh b/AMDiS/src/UmfPackSolver.hh
deleted file mode 100644
index 9762b0fa..00000000
--- a/AMDiS/src/UmfPackSolver.hh
+++ /dev/null
@@ -1,222 +0,0 @@
-#include <vector>
-
-#include "UmfPackSolver.h"
-#include "DOFMatrix.h"
-#include "MatVecMultiplier.h"
-
-#include "umfpack.h"
-
-
-namespace AMDiS {
-
- template<typename VectorType>
- UmfPackSolver<VectorType>::UmfPackSolver(std::string name)
- : OEMSolver<VectorType>(name),
- symbolic_(NULL),
- storeSymbolic_(0),
- multipleRhs(0)
- {
- GET_PARAMETER(0, name + "->store symbolic", "%d", &storeSymbolic_);
- GET_PARAMETER(0, name + "->multiple rhs", "%d", &multipleRhs);
- }
-
- template<typename VectorType>
- UmfPackSolver<VectorType>::~UmfPackSolver()
- {
- if (storeSymbolic_ && (symbolic_ != NULL)) {
- umfpack_di_free_symbolic(&symbolic_);
- }
- }
-
- template<typename VectorType>
- int UmfPackSolver<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x, VectorType *b,
- bool reuseMatrix)
- {
- FUNCNAME("UmfPackSolver::solveSystem()");
-
- TEST_EXIT(x->getSize() == b->getSize())("Vectors x and b must have the same size!");
-
- // Extract the matrix of DOF-matrices.
- StandardMatVec<Matrix<DOFMatrix*>, SystemVector> *stdMatVec =
- dynamic_cast<StandardMatVec<Matrix<DOFMatrix*>, SystemVector> *>(matVec);
- Matrix<DOFMatrix*> *m = stdMatVec->getMatrix();
-
- // Number of systems.
- int nComponents = m->getSize();
-
- // Calculate size of the new composed matrix.
- int newMatrixSize = 0;
- std::vector<int> matricesSize(nComponents);
-
- for (int i = 0; i < nComponents; i++) {
- for (int j = 0; j < nComponents; j++) {
- if ((*m)[i][j]) {
- matricesSize[i] = ((*m)[i][j])->getFESpace()->getAdmin()->getUsedSize();
- newMatrixSize += matricesSize[i];
- break;
- }
- }
- }
-
- // int newMatrixSize = ((*m)[0][0])->getFESpace()->getAdmin()->getUsedSize() * nComponents;
-
- // The new matrix has to be stored in compressed col format, therefore
- // the cols are collected.
- std::vector< std::vector< MatEntry > > cols(newMatrixSize, std::vector<MatEntry>(0));
-
- // Counter for the number of non-zero elements in the new matrix.
- int nElements = 0;
-
- for (int stencilRow = 0, shiftRow = 0; stencilRow < nComponents; stencilRow++) {
-
- int shiftCol = 0;
-
- for (int stencilCol = 0; stencilCol < nComponents; stencilCol++) {
-
- if (!(*m)[stencilRow][stencilCol]) {
- shiftCol += matricesSize[stencilCol];
- continue;
- }
-
- DOFMatrix::Iterator matrixRow((*m)[stencilRow][stencilCol], USED_DOFS);
- int rowIndex = 0;
- for (matrixRow.reset(); !matrixRow.end(); matrixRow++, rowIndex++) {
- for (int i = 0; i < static_cast<int>((*matrixRow).size()); i++) {
- if ((*matrixRow)[i].col >= 0) {
- MatEntry me;
- me.entry = (*matrixRow)[i].entry;
- // The col field is used to store the row number of the new element.
- me.col = rowIndex + shiftRow;
-
- // And save the new element in the corresponding column.
- cols[(*matrixRow)[i].col + shiftCol].push_back(me);
-
- nElements++;
- }
-
- }
- }
-
-
- shiftCol += matricesSize[stencilCol];
- }
-
- shiftRow += matricesSize[stencilRow];
- }
-
-
- // Data fields for UMFPack.
- int *Ap = (int*)malloc(sizeof(int) * (newMatrixSize + 1));
- int *Ai = (int*)malloc(sizeof(int) * nElements);
- double *Ax = (double*)malloc(sizeof(double) * nElements);
- double *bvec = (double*)malloc(sizeof(double) * newMatrixSize);
- double *xvec = (double*)malloc(sizeof(double) * newMatrixSize);
-
- // Resort the right hand side of the linear system.
- for (int i = 0, counter = 0; i < b->getSize(); i++) {
- DOFVector<double>::Iterator it(b->getDOFVector(i), USED_DOFS);
-
- for (it.reset(); !it.end(); ++it) {
- bvec[counter++] = *it;
- }
- }
-
-
- // Create fields Ap, Ai and Ax.
- int elCounter = 0;
- Ap[0] = 0;
- for (int i = 0; i < newMatrixSize; i++) {
- Ap[i + 1] = Ap[i] + cols[i].size();
-
- // The cols has to be sorted for using them in UMFPack.
- sort(cols[i].begin(), cols[i].end(), CmpMatEntryCol());
-
- for (int j = 0; j < static_cast<int>(cols[i].size()); j++) {
- Ai[elCounter] = cols[i][j].col;
- Ax[elCounter] = cols[i][j].entry;
-
- elCounter++;
- }
- }
-
-
- double Control[UMFPACK_CONTROL];
- double Info[UMFPACK_INFO];
- int status = 0;
-
- MSG("solving system with UMFPack ...\n");
-
- // Use default setings.
- umfpack_di_defaults(Control);
-
- // Run UMFPack.
- if (!(storeSymbolic_) ||
- (storeSymbolic_ && (symbolic_ == NULL))) {
-
- status = umfpack_di_symbolic(newMatrixSize, newMatrixSize, Ap, Ai, Ax,
- &symbolic_, Control, Info);
- if (!status == UMFPACK_OK) {
- ERROR_EXIT("UMFPACK Error in function umfpack_di_symbolic");
- }
- }
-
- if (!((multipleRhs != 0) && (reuseMatrix))) {
- // With multiple rhs are allowed, but not this time, free the matrix
- // factorization of last solution step,
- if ((multipleRhs != 0) && !reuseMatrix) {
- umfpack_di_free_numeric(&numeric);
- }
-
- status = umfpack_di_numeric(Ap, Ai, Ax, symbolic_, &numeric, Control, Info);
- if (!status == UMFPACK_OK) {
- ERROR_EXIT("UMFPACK Error in function umfpack_di_numeric");
- }
- }
-
- status = umfpack_di_solve(UMFPACK_A, Ap, Ai, Ax, xvec, bvec, numeric, Control, Info);
- if (!status == UMFPACK_OK) {
- ERROR_EXIT("UMFPACK Error in function umfpack_di_solve");
- }
-
- if (!storeSymbolic_) {
- umfpack_di_free_symbolic(&symbolic_);
- }
- if (multipleRhs == 0) {
- umfpack_di_free_numeric(&numeric);
- }
-
-
- // Copy and resort solution.
- for (int i = 0, counter = 0; i < x->getSize(); i++) {
- DOFVector<double>::Iterator it(x->getDOFVector(i), USED_DOFS);
-
- for (it.reset(); !it.end(); it++) {
- *it = xvec[counter++];
- }
- }
-
- free(Ap);
- free(Ai);
- free(Ax);
- free(bvec);
- free(xvec);
-
- // Calculate and print the residual.
- *p = *x;
- *p *= -1.0;
- matVec->matVec(NoTranspose, *p, *r);
- *r += *b;
-
- this->residual = norm(r);
-
- MSG("Residual: %e\n", this->residual);
-
- if (this->residual > this->tolerance) {
- ERROR_EXIT("UMFPACK could not solve the system!\n");
- }
-
- return(1);
- }
-}
-
diff --git a/AMDiS/src/Utilities.h b/AMDiS/src/Utilities.h
new file mode 100644
index 00000000..143704eb
--- /dev/null
+++ b/AMDiS/src/Utilities.h
@@ -0,0 +1,44 @@
+// ============================================================================
+// == ==
+// == AMDiS - Adaptive multidimensional simulations ==
+// == ==
+// ============================================================================
+// == ==
+// == crystal growth group ==
+// == ==
+// == Stiftung caesar ==
+// == Ludwig-Erhard-Allee 2 ==
+// == 53175 Bonn ==
+// == germany ==
+// == ==
+// ============================================================================
+// == ==
+// == http://www.caesar.de/cg/AMDiS ==
+// == ==
+// ============================================================================
+
+/** \file Utilities.h */
+
+#ifndef AMDIS_UTILITIES_H
+#define AMDIS_UTILITIES_H
+
+#include <vector>
+#include <algorithm>
+
+
+
+template <typename T>
+std::vector<T> inline invert_reorder(const std::vector<T>& v)
+{
+ T my_max= *std::max_element(v.begin(), v.end()) + 1;
+ std::vector<T> u(my_max, T(-1));
+ for (int i= 0; i < v.size(); i++)
+ if (v[i] >= 0) {
+ assert(u[v[i]] == -1); // check double insertion
+ u[v[i]]= T(i);
+ }
+ assert(find(u.begin(), u.end(), T(-1)) == u.end()); // check if all entries are set
+ return u;
+}
+
+#endif // AMDIS_UTILITIES_H
diff --git a/AMDiS/src/V3Vector.cc b/AMDiS/src/V3Vector.cc
deleted file mode 100644
index 5f67a62b..00000000
--- a/AMDiS/src/V3Vector.cc
+++ /dev/null
@@ -1,173 +0,0 @@
-#include "V3Vector.h"
-#include "StlVector.h"
-
-namespace AMDiS {
-
- M33::M33()
- {
- data.resize(9);
- for (int i = 0; i < 9; i++) {
- data[i] = 0.0;
- }
- };
-
- M33::~M33()
- {};
-
- void M33::set(int row, int col, double value)
- {
- data[row * 3 + col] = value;
- };
-
- void M33::print()
- {
- std::cout << "[";
-
- for (int i = 0; i < 9; i++) {
- std::cout << data[i] << ",";
- }
-
- std::cout << "]" << std::endl;
- };
-
-/* double norm(std::vector<V3> *v) {
- double result = 0.0;
-
- std::vector<V3>::iterator it;
-
- for (it = v->begin(); it < v->end(); ++it) {
- result += (*it)[0] * (*it)[0] + (*it)[1] * (*it)[1] + (*it)[2] * (*it)[2];
- }
-
- return(sqrt(result));
- };
-
- void setValue(std::vector<V3>& v, double value)
- {
- std::vector<V3>::iterator it;
-
- for (it = v.begin(); it < v.end(); ++it) {
- (*it)[0] = value;
- (*it)[1] = value;
- (*it)[2] = value;
- };
- };
-
- const V3& operator += (V3& x1, const V3 x2)
- {
- x1[0] += x2[0];
- x1[1] += x2[1];
- x1[2] += x2[2];
-
- return(x1);
- }
-
- const std::vector<V3>& operator*=(std::vector<V3>& x, double scal)
- {
- std::vector<V3>::iterator it;
-
- for (it = x.begin(); it < x.end(); ++it) {
- (*it)[0] *= scal;
- (*it)[1] *= scal;
- (*it)[2] *= scal;
- }
-
- return(x);
- };
-
- const std::vector<V3>& operator+=(std::vector<V3>& x1,
- const std::vector<V3>& x2)
- {
- std::vector<V3>::iterator it1;
- std::vector<V3>::const_iterator it2;
-
- for (it1 = x1.begin(), it2 = x2.begin();
- it1 < x1.end();
- ++it1, ++it2) {
- (*it1)[0] += (*it2)[0];
- (*it1)[1] += (*it2)[1];
- (*it1)[2] += (*it2)[2];
- };
-
- return(x1);
- };
-
- double operator*(std::vector<V3>& x1, std::vector<V3>& x2)
- {
- double result = 0.0;
-
- std::vector<V3>::iterator it1, it2;
-
- for (it1 = x1.begin(), it2 = x2.begin();
- it1 < x1.end();
- ++it1, ++it2) {
- result += (*it1)[0] * (*it2)[0] +
- (*it1)[1] * (*it2)[1] +
- (*it1)[2] * (*it2)[2];
- }
-
- return(result);
- };
-
-
- void axpy(double alpha, const std::vector<V3>& x, std::vector<V3>& y)
- {
- std::vector<V3>::const_iterator it1;
- std::vector<V3>::iterator it2;
-
- for (it1 = x.begin(), it2 = y.begin();
- it1 < x.end();
- ++it1, ++it2) {
- (*it2)[0] += alpha * (*it1)[0];
- (*it2)[1] += alpha * (*it1)[1];
- (*it2)[2] += alpha * (*it1)[2];
- }
- };
-
- void xpay(double alpha, const std::vector<V3>& x, std::vector<V3>& y)
- {
- std::vector<V3>::const_iterator it1;
- std::vector<V3>::iterator it2;
-
- for (it1 = x.begin(), it2 = y.begin();
- it1 < x.end();
- ++it1, ++it2) {
- (*it2)[0] = alpha * (*it2)[0] + (*it1)[0];
- (*it2)[1] = alpha * (*it2)[1] + (*it1)[1];
- (*it2)[2] = alpha * (*it2)[2] + (*it1)[2];
- }
- };
-
- V3 mult(M33 mat, V3 vec)
- {
- V3 result(3);
-
- result[0] = mat[0] * vec[0] + mat[1] * vec[1] + mat[2] * vec[2];
- result[1] = mat[3] * vec[0] + mat[4] * vec[1] + mat[5] * vec[2];
- result[2] = mat[6] * vec[0] + mat[7] * vec[1] + mat[8] * vec[2];
-
-// std::cout << "------------------------" << std::endl;
-// std::cout << "M = ";
-// mat.print();
-// std::cout << "v = ";
-// print(&vec);
-// std::cout << "r = ";
-// print(&result);
-
- return(result);
- };
-
- void print(std::vector<V3> *v)
- {
- std::vector<V3>::const_iterator it;
-
- std::cout << "[";
-
- for (it = v->begin(); it < v->end(); ++it) {
- std::cout << "(" << (*it)[0] << "," << (*it)[1] << "," << (*it)[2] << ") ";
- }
-
- std::cout << "]" << std::endl;
- };
-*/
-}
diff --git a/AMDiS/src/V3Vector.h b/AMDiS/src/V3Vector.h
deleted file mode 100644
index 601eab4a..00000000
--- a/AMDiS/src/V3Vector.h
+++ /dev/null
@@ -1,117 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file V3Vector.h */
-
-#ifndef AMDIS_V3VECTOR_H
-#define AMDIS_V3VECTOR_H
-
-#include <vector>
-#include "Global.h"
-#include "MemoryManager.h"
-#include "CreatorInterface.h"
-
-namespace AMDiS {
-
- class M33 {
- public:
- M33();
-
- ~M33();
-
- void set(int row, int col, double value);
-
- bool operator==(const M33 &a) const {
- return data == a.getData();
- };
-
- bool operator!=(const M33 &a) const {
- return data != a.getData();
- };
-
- std::vector<double> getData() const {
- return data;
- };
-
- inline double operator[](int i) const {
- return(data[i]);
- }
-
- void print();
-
- private:
- std::vector<double> data;
- };
-
- struct MatEntry33
- {
- DegreeOfFreedom col;
-
- M33 entry;
- };
-/*
- typedef std::vector<double> V3;
-
- class V3Creator : public CreatorInterface< std::vector<V3> > {
- public:
- MEMORY_MANAGED(V3Creator);
-
- V3Creator(int size)
- : size_(size)
- {};
-
- virtual ~V3Creator() {};
-
- std::vector<V3> *create() {
- std::vector<V3> *vec = new std::vector<V3>(size_, V3(3));
-
- return vec;
- };
-
- void free(std::vector<V3> *vec) {
- delete vec;
- };
-
- private:
- int size_;
- };
-
- double norm(std::vector<V3> *v);
-
- void setValue(std::vector<V3>& v, double value);
-
- const V3& operator += (V3& x1, const V3 x2);
-
- const std::vector<V3>& operator*=(std::vector<V3>& x, double scal);
-
- const std::vector<V3>& operator+=(std::vector<V3>& x1,
- const std::vector<V3>& x2);
-
- double operator*(std::vector<V3>& x1, std::vector<V3>& x2);
-
- void axpy(double alpha, const std::vector<V3>& x, std::vector<V3>& y);
-
- void xpay(double alpha, const std::vector<V3>& x, std::vector<V3>& y);
-
- V3 mult(M33 mat, V3 vec);
-
- void print(std::vector<V3> *v);*/
-}
-
-#endif
diff --git a/AMDiS/src/VecSymSolver.h b/AMDiS/src/VecSymSolver.h
deleted file mode 100644
index 130d50b3..00000000
--- a/AMDiS/src/VecSymSolver.h
+++ /dev/null
@@ -1,103 +0,0 @@
-// ============================================================================
-// == ==
-// == AMDiS - Adaptive multidimensional simulations ==
-// == ==
-// ============================================================================
-// == ==
-// == crystal growth group ==
-// == ==
-// == Stiftung caesar ==
-// == Ludwig-Erhard-Allee 2 ==
-// == 53175 Bonn ==
-// == germany ==
-// == ==
-// ============================================================================
-// == ==
-// == http://www.caesar.de/cg/AMDiS ==
-// == ==
-// ============================================================================
-
-/** \file VecSymSolver.h */
-
-#ifndef AMDIS_VECSYMSOLVER_H
-#define AMDIS_VECSYMSOLVER_H
-
-#include "OEMSolver.h"
-#include "MemoryManager.h"
-#include "V3Vector.h"
-
-namespace AMDiS {
-
- // ============================================================================
- // ===== class VecSymSolver ===================================================
- // ============================================================================
-
- /**
- * \ingroup Solver
- *
- * \brief
- */
- template<typename VectorType>
- class VecSymSolver : public OEMSolver<VectorType>
- {
- public:
- MEMORY_MANAGED(VecSymSolver<VectorType>);
-
- /** \brief
- * Creator class used in the OEMSolverMap.
- */
- class Creator : public OEMSolverCreator<VectorType>
- {
- public:
- MEMORY_MANAGED(Creator);
-
- virtual ~Creator() {};
-
- /** \brief
- * Returns a new CGSolver object.
- */
- OEMSolver<VectorType>* create() {
- return NEW VecSymSolver<VectorType>(this->name);
- };
- };
-
- /** \brief
- * constructor
- */
- VecSymSolver(std::string name);
-
- /** \brief
- * destructor
- */
- ~VecSymSolver();
- protected:
- /** \brief
- * Implements OEMSolver<VectorType>::init().
- */
- void init() {
- p = this->vectorCreator->create();
- r = this->vectorCreator->create();
- };
-
- /** \brief
- * Implements OEMSolver<VectorType>::exit().
- */
- void exit() {
- this->vectorCreator->free(p);
- };
-
- /** \brief
- * Implements OEMSolver<VectorType>::solve().
- */
- int solveSystem(MatVecMultiplier<VectorType> *mv,
- VectorType *x, VectorType *b, bool reuseMatrix);
-
- private:
- VectorType *r, *p;
- };
-}
-
-#include "VecSymSolver.hh"
-
-#endif // AMDIS_VECSYMSOLVER_H
-
diff --git a/AMDiS/src/VecSymSolver.hh b/AMDiS/src/VecSymSolver.hh
deleted file mode 100644
index 76a1cd6f..00000000
--- a/AMDiS/src/VecSymSolver.hh
+++ /dev/null
@@ -1,443 +0,0 @@
-//#include <fstream>
-
-#include <vector>
-
-#include "VecSymSolver.h"
-#include "DOFMatrix.h"
-#include "DiagonalPreconditioner.h"
-#include "ILUPreconditioner.h"
-#include "MatVecMultiplier.h"
-
-namespace AMDiS {
-
- template<typename VectorType>
- VecSymSolver<VectorType>::VecSymSolver(std::string name)
- : OEMSolver<VectorType>(name)
- {}
-
- template<typename VectorType>
- VecSymSolver<VectorType>::~VecSymSolver() {}
-
-/* template<typename VectorType>
- int VecSymSolver<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x, VectorType *b)
- {
- FUNCNAME("VecSymSolver::solveSystem()");
-
- StandardMatVec<Matrix<DOFMatrix*>, SystemVector> *stdMatVec =
- dynamic_cast<StandardMatVec<Matrix<DOFMatrix*>, SystemVector> *>(matVec);
-
- Matrix<DOFMatrix*> *m = stdMatVec->getMatrix();
-
- DOFMatrix* dofm = (*m)[0][0];
-
- int nComponents = m->getSize();
- int oneMatrixSize = dofm->getFESpace()->getAdmin()->getUsedSize();
- int bigMatrixSize = oneMatrixSize;
-
- std::vector< std::vector< MatEntry33 > > newm;
- newm.resize(bigMatrixSize);
-
- std::vector<V3> xvec(bigMatrixSize);
- std::vector<V3> bvec(bigMatrixSize);
- for (int i = 0; i < bigMatrixSize; i++) {
- xvec[i].resize(3);
- bvec[i].resize(3);
- }
-
- for (int stencilRow = 0; stencilRow < nComponents; stencilRow++) {
- for (int stencilCol = 0; stencilCol < nComponents; stencilCol++) {
-
- if (!(*m)[stencilRow][stencilCol]) {
-// std::cout << "Matrix " << stencilRow << "-" << stencilCol << " ist 0!" << std::endl;
- continue;
- } else {
- (*m)[stencilRow][stencilCol]->print();
-
- if ((*m)[stencilRow][stencilCol]->symmetric()) {
- std::cout << "Matrix " << stencilRow << "-" << stencilCol << " ist symmetrisch!" << std::endl;
- } else {
- std::cout << "Matrix " << stencilRow << "-" << stencilCol << " ist nicht symmetrisch!" << std::endl;
- }
- };
-
- DOFMatrix::Iterator matrixRow((*m)[stencilRow][stencilCol], USED_DOFS);
- int rowIndex = 0;
- for (matrixRow.reset(); !matrixRow.end(); ++matrixRow, rowIndex++) {
- for (int i = 0; i < static_cast<int>((*matrixRow).size()); i++) {
- if ((*matrixRow)[i].col >= 0) {
- MatEntry33 *newMe = NULL;
-
-// if ((stencilRow == 0) && (stencilCol == 0) &&
-// (rowIndex == 0) && ((*matrixRow)[i].col == 0)) {
-// std::cout << "Dich habe ich: " << (*matrixRow)[i].entry << std::endl;
-// }
-
- for (int j = 0; j < static_cast<int>(newm[rowIndex].size()); j++) {
- if (newm[rowIndex][j].col == (*matrixRow)[i].col) {
- newMe = &(newm[rowIndex][j]);
- }
- }
-
- if (newMe == NULL) {
-// if ((rowIndex == 0) && ((*matrixRow)[i].col == 0)) {
-// std::cout << "0-Matrix neu anlegen!" << std::endl;
-// };
-
- MatEntry33 newMe;
- newMe.col = (*matrixRow)[i].col;
- newMe.entry.set(stencilRow, stencilCol, (*matrixRow)[i].entry);
- newm[rowIndex].push_back(newMe);
-
-// if ((rowIndex == 0) && ((*matrixRow)[i].col == 0)) {
-// std::cout << "0-Matrix: " << std::endl;
-// newMe.entry.print();
-// }
-
- } else {
- newMe->entry.set(stencilRow, stencilCol, (*matrixRow)[i].entry);
-
-// if ((rowIndex == 0) && ((*matrixRow)[i].col == 0)) {
-// std::cout << "0-Matrix: " << std::endl;
-// newMe->entry.print();
-// }
- }
-
- }
- }
- }
-
- }
- }
-
-
- for (int i = 0; i < static_cast<int>(newm.size()); i++) {
-
- for (int j = 0; j < static_cast<int>(newm[j].size()); j++) {
- if (newm[i][j].col == i) {
- MatEntry33 tmp = newm[i][0];
- newm[i][0] = newm[i][j];
- newm[i][j] = tmp;
-
- break;
- }
- }
- }
-
-
- std::cout << "Gesuchter Vektor ist: " << std::endl;
-
- for (int i = 0; i < x->getSize(); i++) {
- DOFVector<double>::Iterator it(x->getDOFVector(i), USED_DOFS);
-
- int counter = 0;
- for (it.reset(); !it.end(); it++, counter++) {
- std::cout << (*it) << std::endl;
-
- xvec[counter][i] = *it;
- }
- }
-
- std::cout << "Rechte Seite ist: " << std::endl;
-
- for (int i = 0; i < b->getSize(); i++) {
- DOFVector<double>::Iterator it(b->getDOFVector(i), USED_DOFS);
-
- int counter = 0;
- for (it.reset(); !it.end(); it++, counter++) {
- std::cout << (*it) << std::endl;
-
- bvec[counter][i] = *it;
- }
- }
-
-
- bool isSym = true;
-
- for (int i = 0; i < static_cast<int>(newm.size()); i++) {
-
-// std::cout << "Zeile " << i << ": " << std::endl;
-
- for (int j = 0; j < static_cast<int>(newm[i].size()); j++) {
- int col = newm[i][j].col;
-
-// std::cout << col << ": [ ";
-// for (int k = 0; k < 9; k++) {
-// std::cout << newm[i][j].entry[k] << " ";
-// }
-// std::cout << "], ";
-
- if (col != i) {
- for (int k = 0; k < static_cast<int>(newm[col].size()); k++) {
- if (newm[col][k].col == i) {
- if (newm[i][j].entry != newm[col][k].entry) {
- isSym = false;
- }
- }
- }
- }
- }
-
-// std::cout << std::endl;
- }
-
- if (isSym) {
- std::cout << "Gesamtmatrix ist symmetrisch!" << std::endl;
- } else {
- std::cout << "Gesamtmatrix ist nicht symmetrisch!" << std::endl;
- }
-
- CGSolver< std::vector<V3> > solver2(this->name);
- solver2.initParameters();
- solver2.setVectorCreator(NEW V3Creator(bigMatrixSize));
-
- StandardMatVec< std::vector< std::vector<MatEntry33> >, std::vector<V3> > mv(&newm);
-
- *p = *x;
- *p *= -1.0;
- matVec->matVec(NoTranspose, *p, *r);
- *r += *b;
-
- std::cout << "Checking res 1: " << norm(r) << std::endl;
-
- solver2.solve(&mv, &xvec, &bvec);
-
- for (int i = 0; i < x->getSize(); i++) {
- DOFVector<double>::Iterator it(x->getDOFVector(i), USED_DOFS);
-
- int counter = 0;
- for (it.reset(); !it.end(); it++, counter++) {
- *it = xvec[counter][i];
- }
- }
-
- *p = *x;
- *p *= -1.0;
- matVec->matVec(NoTranspose, *p, *r);
- *r += *b;
-
- std::cout << "Checking res 2: " << norm(r) << std::endl;
-
- ERROR_EXIT("na, dass wars wohl!\n");
-
- return(0);
- }
-*/
-
-
- template<typename VectorType>
- int VecSymSolver<VectorType>::solveSystem(MatVecMultiplier<VectorType> *matVec,
- VectorType *x, VectorType *b, bool reuseMatrix)
- {
- FUNCNAME("VecSymSolver::solveSystem()");
-
- StandardMatVec<Matrix<DOFMatrix*>, SystemVector> *stdMatVec =
- dynamic_cast<StandardMatVec<Matrix<DOFMatrix*>, SystemVector> *>(matVec);
-
- Matrix<DOFMatrix*> *m = stdMatVec->getMatrix();
-
- DOFMatrix* dofm = (*m)[0][0];
-
- int nComponents = m->getSize();
- int oneMatrixSize = dofm->getFESpace()->getAdmin()->getUsedSize();
- int bigMatrixSize = oneMatrixSize * nComponents;
-
- std::vector< std::vector< MatEntry > > newm(bigMatrixSize, std::vector<MatEntry>(0));
- std::vector<double> xvec(bigMatrixSize);
- std::vector<double> bvec(bigMatrixSize);
-
- int nElements = 0;
-
- for (int stencilRow = 0; stencilRow < nComponents; stencilRow++) {
- for (int stencilCol = 0; stencilCol < nComponents; stencilCol++) {
-
- if (!(*m)[stencilRow][stencilCol]) {
- continue;
- }
-
- // std::cout << "------------------------------" << std::endl;
- // std::cout << "Matrix " << stencilRow << " - " << stencilCol << std::endl;
-
- // (*m)[stencilRow][stencilCol]->print();
-
- DOFMatrix::Iterator matrixRow((*m)[stencilRow][stencilCol], USED_DOFS);
- int rowIndex = 0;
- for (matrixRow.reset(); !matrixRow.end(); matrixRow++, rowIndex++) {
- for (int i = 0; i < static_cast<int>((*matrixRow).size()); i++) {
- if ((*matrixRow)[i].col >= 0) {
- MatEntry newMe;
- newMe.entry = (*matrixRow)[i].entry;
- newMe.col = ((*matrixRow)[i].col * nComponents) + stencilCol;
-
- newm[(rowIndex * nComponents) + stencilRow].push_back(newMe);
-
- nElements++;
- }
- }
- }
-
-// if ((*m)[stencilRow][stencilCol]->symmetric()) {
-// std::cout << "Matrix " << stencilRow << "-" << stencilCol << " ist symmetrisch!" << std::endl;
-// } else {
-// std::cout << "Matrix " << stencilRow << "-" << stencilCol << " ist nicht symmetrisch!" << std::endl;
-// }
-
-
- }
- }
-
-
- for (int i = 0; i < static_cast<int>(newm.size()); i++) {
- for (int j = 0; j < static_cast<int>(newm[i].size()); j++) {
- if (newm[i][j].col == i) {
- MatEntry tmp = newm[i][0];
- newm[i][0] = newm[i][j];
- newm[i][j] = tmp;
-
- break;
- }
- }
- }
-
-// std::cout << "-------------------------------" << std::endl;
-// for (int i = 0; i < static_cast<int>(newm.size()); i++) {
-// std::cout << "row : " << i << std::endl;
-// for (int j = 0; j < static_cast<int>(newm[i].size()); j++) {
-// std::cout << " ( " << newm[i][j].col << ", " << newm[i][j].entry << ")";
-// }
-// std::cout << std::endl;
-// }
-
- for (int i = 0; i < x->getSize(); i++) {
- DOFVector<double>::Iterator it(x->getDOFVector(i), USED_DOFS);
-
- int counter = 0;
- for (it.reset(); !it.end(); it++, counter++) {
- xvec[counter * nComponents + i] = *it;
- }
- }
-
- for (int i = 0; i < b->getSize(); i++) {
- DOFVector<double>::Iterator it(b->getDOFVector(i), USED_DOFS);
-
- int counter = 0;
- for (it.reset(); !it.end(); it++, counter++) {
- bvec[counter * nComponents + i] = *it;
- }
- }
-
- /* ======= CHOLMOD =========
- std::fstream file;
-
- file.open("matrix.m", fstream::out);
- file << newm.size() << " " << newm.size() << " " << nElements << std::endl;
- for (int i = 0; i < static_cast<int>(newm.size()); i++) {
- for (int j = 0; j < static_cast<int>(newm[i].size()); j++) {
- file << i + 1 << " " << newm[i][j].col + 1 << " " << newm[i][j].entry << std::endl;
- }
- }
- file.close();
-
- file.open("vector.m", fstream::out);
- file << bvec.size() << " 1" << std::endl;
- for (int i = 0; i < static_cast<int>(bvec.size()); i++) {
- file << bvec[i] << std::endl;
- }
- file.close();
- */
-
- bool isSym = true;
-
- for (int i = 0; i < static_cast<int>(newm.size()); i++) {
- for (int j = 0; j < static_cast<int>(newm[i].size()); j++) {
- int col = newm[i][j].col;
-
- if (col != i) {
- for (int k = 0; k < static_cast<int>(newm[col].size()); k++) {
- if (newm[col][k].col == i) {
- if (newm[i][j].entry != newm[col][k].entry) {
- isSym = false;
- }
- }
- }
- }
- }
- }
-
- if (isSym) {
- std::cout << "Matrix is symmetrisch!" << std::endl;
- } else {
- std::cout << "Matrix ist nicht symmetrisch!" << std::endl;
- }
-
-
-
- /* ======= CHOLMOD =========
-
- double one [2] = {1,0}, m1 [2] = {-1,0};
- cholmod_sparse *A;
- cholmod_dense *ch_b;
- cholmod_dense *ch_x;
- cholmod_dense *ch_r;
- cholmod_common c;
- cholmod_factor *L;
- cholmod_start(&c);
-
- FILE *f = fopen("matrix.m", "r");
- A = cholmod_read_sparse(f, &c);
- fclose(f);
-
- f = fopen("vector.m", "r");
- ch_b = cholmod_read_dense(f, &c);
- fclose(f);
-
- L = cholmod_analyze(A, &c);
- cholmod_factorize(A, L, &c);
-
- ch_x = cholmod_solve(CHOLMOD_A, L, ch_b, &c);
- ch_r = cholmod_copy_dense(ch_b, &c);
- cholmod_sdmult (A, 0, m1, one, ch_x, ch_r, &c) ;
- std::cout << "NORM: " << cholmod_norm_dense(ch_r, 2, &c) << std::endl;
-
- cholmod_finish(&c);
- */
-
- //GMResSolver2< std::vector<double> > solver2(this->name);
- //CGSolver< std::vector<double> > solver2(this->name);
- // BiCGStab< std::vector<double> > solver2(this->name);
-
- // solver2.initParameters();
- // solver2.setVectorCreator(NEW StlVectorCreator(bigMatrixSize));
-
- // StandardMatVec< std::vector< std::vector<MatEntry> >, std::vector<double> > mv(&newm);
-
- // ILUPreconditionerStd ilu;
- // ilu.setMatrix(&newm);
-
- // DiagonalPreconditionerStd diag;
- // diag.setMatrix(&newm);
-
- // solver2.solve(&mv, &xvec, &bvec, &diag);
-
- for (int i = 0; i < x->getSize(); i++) {
- DOFVector<double>::Iterator it(x->getDOFVector(i), USED_DOFS);
-
- int counter = 0;
- for (it.reset(); !it.end(); it++, counter++) {
- *it = xvec[counter * nComponents + i];
- }
- }
-
- *p = *x;
- *p *= -1.0;
- matVec->matVec(NoTranspose, *p, *r);
- *r += *b;
-
- std::cout << "NORM: " << norm(r) << std::endl;
-
- // ERROR_EXIT("DA\n");
-
- return(1);
- }
-
-}
--
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