Implement element dof iterator class. May be used to iterate over all dofs of...

Implement element dof iterator class. May be used to iterate over all dofs of one element independent of dimension and degree of basis functions.

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@

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])
 ])
 

AMDiS/bin/Makefile.am

@@ -201,6 +201,7 @@ $(SOURCE_DIR)/ScalableQuadrature.h $(SOURCE_DIR)/ScalableQuadrature.cc \
 $(SOURCE_DIR)/SubElInfo.h $(SOURCE_DIR)/SubElInfo.cc \
 $(SOURCE_DIR)/SolutionDataStorage.h $(SOURCE_DIR)/SolutionDataStorage.hh \
 $(SOURCE_DIR)/InteriorBoundary.h $(SOURCE_DIR)/InteriorBoundary.cc \
+$(SOURCE_DIR)/ElementDofIteartor.h $(SOURCE_DIR)/ElementDofIterator.cc \
 $(SOURCE_DIR)/parareal/ProblemBase.h \
 $(SOURCE_DIR)/parareal/AdaptParaReal.h $(SOURCE_DIR)/parareal/AdaptParaReal.cc
 

AMDiS/bin/Makefile.in

@@ -219,6 +219,8 @@ am__libamdis_la_SOURCES_DIST =  \
 	$(SOURCE_DIR)/SolutionDataStorage.hh \
 	$(SOURCE_DIR)/InteriorBoundary.h \
 	$(SOURCE_DIR)/InteriorBoundary.cc \
+	$(SOURCE_DIR)/ElementDofIteartor.h \
+	$(SOURCE_DIR)/ElementDofIterator.cc \
 	$(SOURCE_DIR)/parareal/ProblemBase.h \
 	$(SOURCE_DIR)/parareal/AdaptParaReal.h \
 	$(SOURCE_DIR)/parareal/AdaptParaReal.cc
@@ -278,7 +280,8 @@ am_libamdis_la_OBJECTS = $(am__objects_2) libamdis_la-DOFIndexed.lo \
 	libamdis_la-ValueWriter.lo libamdis_la-VtkWriter.lo \
 	libamdis_la-PngWriter.lo libamdis_la-DataCollector.lo \
 	libamdis_la-ScalableQuadrature.lo libamdis_la-SubElInfo.lo \
-	libamdis_la-InteriorBoundary.lo libamdis_la-AdaptParaReal.lo
+	libamdis_la-InteriorBoundary.lo \
+	libamdis_la-ElementDofIterator.lo libamdis_la-AdaptParaReal.lo
 libamdis_la_OBJECTS = $(am_libamdis_la_OBJECTS)
 libcompositeFEM_la_LIBADD =
 am_libcompositeFEM_la_OBJECTS = libcompositeFEM_la-CFE_Integration.lo \
@@ -385,6 +388,7 @@ PACKAGE_TARNAME = @PACKAGE_TARNAME@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 RANLIB = @RANLIB@
+SED = @SED@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@
@@ -601,6 +605,7 @@ $(SOURCE_DIR)/ScalableQuadrature.h $(SOURCE_DIR)/ScalableQuadrature.cc \
 $(SOURCE_DIR)/SubElInfo.h $(SOURCE_DIR)/SubElInfo.cc \
 $(SOURCE_DIR)/SolutionDataStorage.h $(SOURCE_DIR)/SolutionDataStorage.hh \
 $(SOURCE_DIR)/InteriorBoundary.h $(SOURCE_DIR)/InteriorBoundary.cc \
+$(SOURCE_DIR)/ElementDofIteartor.h $(SOURCE_DIR)/ElementDofIterator.cc \
 $(SOURCE_DIR)/parareal/ProblemBase.h \
 $(SOURCE_DIR)/parareal/AdaptParaReal.h $(SOURCE_DIR)/parareal/AdaptParaReal.cc
 
@@ -727,6 +732,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ElInfoStack.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Element.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ElementData.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ElementDofIterator.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-ElementFileWriter.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-Estimator.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libamdis_la-FileWriter.Plo@am__quote@
@@ -1456,6 +1462,13 @@ libamdis_la-InteriorBoundary.lo: $(SOURCE_DIR)/InteriorBoundary.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-InteriorBoundary.lo `test -f '$(SOURCE_DIR)/InteriorBoundary.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/InteriorBoundary.cc
 
+libamdis_la-ElementDofIterator.lo: $(SOURCE_DIR)/ElementDofIterator.cc
+@am__fastdepCXX_TRUE@	if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-ElementDofIterator.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-ElementDofIterator.Tpo" -c -o libamdis_la-ElementDofIterator.lo `test -f '$(SOURCE_DIR)/ElementDofIterator.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ElementDofIterator.cc; \
+@am__fastdepCXX_TRUE@	then mv -f "$(DEPDIR)/libamdis_la-ElementDofIterator.Tpo" "$(DEPDIR)/libamdis_la-ElementDofIterator.Plo"; else rm -f "$(DEPDIR)/libamdis_la-ElementDofIterator.Tpo"; exit 1; fi
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$(SOURCE_DIR)/ElementDofIterator.cc' object='libamdis_la-ElementDofIterator.lo' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCXX_FALSE@	$(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -c -o libamdis_la-ElementDofIterator.lo `test -f '$(SOURCE_DIR)/ElementDofIterator.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/ElementDofIterator.cc
+
 libamdis_la-AdaptParaReal.lo: $(SOURCE_DIR)/parareal/AdaptParaReal.cc
 @am__fastdepCXX_TRUE@	if $(LIBTOOL) --tag=CXX --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(libamdis_la_CXXFLAGS) $(CXXFLAGS) -MT libamdis_la-AdaptParaReal.lo -MD -MP -MF "$(DEPDIR)/libamdis_la-AdaptParaReal.Tpo" -c -o libamdis_la-AdaptParaReal.lo `test -f '$(SOURCE_DIR)/parareal/AdaptParaReal.cc' || echo '$(srcdir)/'`$(SOURCE_DIR)/parareal/AdaptParaReal.cc; \
 @am__fastdepCXX_TRUE@	then mv -f "$(DEPDIR)/libamdis_la-AdaptParaReal.Tpo" "$(DEPDIR)/libamdis_la-AdaptParaReal.Plo"; else rm -f "$(DEPDIR)/libamdis_la-AdaptParaReal.Tpo"; exit 1; fi

AMDiS/libtool

@@ -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"
@@ -325,7 +328,7 @@ 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 "
@@ -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"
@@ -7038,7 +7044,7 @@ 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 "
@@ -7114,6 +7120,9 @@ CC="g77"
 # 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"
@@ -7346,7 +7355,7 @@ 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/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/" | $SED -e "s@${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 "

AMDiS/src/AMDiS.h

@@ -29,6 +29,7 @@
 #include "ElInfo2d.h"
 #include "ElInfo3d.h"
 #include "Element.h"
+#include "ElementDofIterator.h"
 #include "Error.h"
 #include "Estimator.h"
 #include "FileWriter.h"

AMDiS/src/AMDiS_fwd.h

@@ -41,6 +41,7 @@ namespace AMDiS {
   class DOFMatrix;
   class DOFVectorDOF;
   class Element;
+  class ElementDofIterator;
   class ElInfo; 
   class ElMatrixInfo;
   class Estimator;

AMDiS/src/DOFIterator.h

@@ -235,9 +235,7 @@ namespace AMDiS {
   class DOFIterator : public DOFIteratorBase
   {
   public:
-    /** \brief
-     * Constructs a DOFIterator for cont of type t
-     */
+    /// Constructs a DOFIterator for cont of type t
     DOFIterator(DOFIndexed<T> *obj, DOFIteratorType t) 
       : DOFIteratorBase(dynamic_cast<DOFAdmin*>(obj->getFESpace()->getAdmin()), t),
 	iteratedObject(obj)

AMDiS/src/DOFVector.hh

@@ -459,6 +459,8 @@ namespace AMDiS {
   template<typename T>
   int DOFVector<T>::interpolFct(ElInfo* elinfo)
   {
+    std::cout << "Interpol = " << elinfo->getElement()->getIndex() << std::endl;
+
     const BasisFunction *basFct = traverseVector->getFESpace()->getBasisFcts();
     const DOFAdmin* admin = traverseVector->getFESpace()->getAdmin();
     const DegreeOfFreedom *dof =  basFct->getLocalIndices(const_cast<Element *>(elinfo->getElement()),
@@ -469,9 +471,16 @@ namespace AMDiS {
 								      traverseVector->interFct, 
 								      NULL);
 
+    //    std::cout << "ptr = " << dof << std::endl;
+
     int number = basFct->getNumber();
-    for (int i = 0; i < number; i++)
+    for (int i = 0; i < number; i++) {
+//       std::cout << "i = " << i << std::endl;
+//       std::cout << "DOF = " << dof[i] << std::endl;
+//       std::cout << "new val = " << inter_val[i] << std::endl;
+//       std::cout << "old val = " <<       (*traverseVector)[dof[i]] << std::endl;
       (*traverseVector)[dof[i]] = inter_val[i];
+    }
 
     return 0;
   }

AMDiS/src/Element.cc

@@ -383,9 +383,8 @@ namespace AMDiS {
       GeoIndex position = INDEX_OF_DIM(pos, dim);
       int ndof = 0;
 
-      for (int i = 0; i < mesh->getNumberOfDOFAdmin(); i++) {
-	ndof += mesh->getDOFAdmin(i).getNumberOfDOFs(position);	
-      }
+      for (int i = 0; i < mesh->getNumberOfDOFAdmin(); i++)
+	ndof += mesh->getDOFAdmin(i).getNumberOfDOFs(position);	      
 
       if (ndof > 0) {
 	for (int i = 0; i < mesh->getGeo(position); i++) {
@@ -433,6 +432,8 @@ namespace AMDiS {
 
   void Element::deserialize(std::istream &in)
   {
+    FUNCNAME("Element::deserialize()");
+
     std::string typeName;
 
     // read children
@@ -443,15 +444,16 @@ namespace AMDiS {
       if (typeName == "Line") {
 	child[0] = new Line(NULL);
 	child[1] = new Line(NULL);      
-      }
-      if (typeName == "Triangle") {
+      }else  if (typeName == "Triangle") {
 	child[0] = new Triangle(NULL);
 	child[1] = new Triangle(NULL);      
-      }
-      if (typeName == "Tetrahedron") {
+      } else  if (typeName == "Tetrahedron") {
 	child[0] = new Tetrahedron(NULL);
 	child[1] = new Tetrahedron(NULL);      
+      } else {
+	ERROR_EXIT("Wrong element type!\n");
       }
+
       child[0]->deserialize(in);
       child[1]->deserialize(in);
     } else {
@@ -464,14 +466,18 @@ namespace AMDiS {
 
     dof = new DegreeOfFreedom*[nodes]; 
 
+    //    std::cout << "-- n = " << nodes << std::endl;
+
     for (int i = 0; i < nodes; i++) {
-      int dofs;
-      in.read(reinterpret_cast<char*>(&dofs), sizeof(int));
+      int nDofs;
+      in.read(reinterpret_cast<char*>(&nDofs), sizeof(int));
+
+      //      std::cout << "d = " << nDofs << std::endl;
 
-      if (dofs) {
-	if (dofs != -1) {
-	  dof[i] = new DegreeOfFreedom[dofs];
-	  in.read(reinterpret_cast<char*>(dof[i]), dofs * sizeof(DegreeOfFreedom));
+      if (nDofs) {
+	if (nDofs != -1) {
+	  dof[i] = new DegreeOfFreedom[nDofs];
+	  in.read(reinterpret_cast<char*>(dof[i]), nDofs * sizeof(DegreeOfFreedom));
 	  if (Mesh::serializedDOFs[dof[i][0]] != NULL) {
 	    DegreeOfFreedom *dofPtr = Mesh::serializedDOFs[dof[i][0]];
 	    delete [] dof[i];
@@ -482,16 +488,21 @@ namespace AMDiS {
 	} else {
 	  DegreeOfFreedom index;
 	  in.read(reinterpret_cast<char*>(&index), sizeof(DegreeOfFreedom));
+	  TEST_EXIT(Mesh::serializedDOFs.find(index) != Mesh::serializedDOFs.end())
+	    ("This should never happen!\n");
 	  dof[i] = Mesh::serializedDOFs[index];
+	  //	  std::cout << "i = " << index << " " << Mesh::serializedDOFs[index] << " " << Mesh::serializedDOFs[index][0] << std::endl;
 	}
       } else {
 	dof[i] = NULL;
       }
     }
-    
+   
     // read index
     in.read(reinterpret_cast<char*>(&index), sizeof(int));
 
+    //    std::cout << "index = " << index << std::endl;
+
     // read mark
     in.read(reinterpret_cast<char*>(&mark), sizeof(signed char));
 

AMDiS/src/ElementDofIterator.cc

+#include "ElementDofIterator.h"
+#include "Mesh.h"
+#include "DOFAdmin.h"
+#include "Element.h"
+
+namespace AMDiS {
+
+  void ElementDofIterator::reset(Element* element)
+  {
+    FUNCNAME("ElementDofIterator::reset()");
+
+    dofs = element->getDOF();
+    mesh = element->getMesh();
+    dim = mesh->getDim();
+
+    // Start with vertices.
+    pos = 0;
+    elementPos = 0;
+    dofPos = 0;
+
+    // Get geo index of vertices in the given dimension.
+    posIndex = INDEX_OF_DIM(pos, dim);
+    // Get number of dofs per vertex (should be one in all cases).
+    nDofs = admin->getNumberOfDOFs(posIndex);
+
+    TEST_EXIT_DBG(nDofs != 0)("Mh, I've to think about this situation!\n");
+
+    // Calculate displacement. Is used if there is more than one dof admin on the mesh.
+    n0 = admin->getNumberOfPreDOFs(posIndex);
+    // Get first dof index position for vertices.
+    node0 = mesh->getNode(posIndex);
+    // Get number of vertices in this dimension.
+    nElements = Global::getGeo(posIndex, mesh->getDim());
+  }
+
+  bool ElementDofIterator::next()
+  {
+    // First iteratore over the dofs of one element (vertex, edge, face).
+    dofPos++;
+
+    if (dofPos >= nDofs) {
+      // We are finished with all dofs of on element. Go to the next one.
+      dofPos = 0;
+      elementPos++;
+
+      if (elementPos >= nElements) {
+	// We are finished with all element.
+	elementPos = 0;
+
+	// Increase position, i.e., go from vertices to edges to faces and search
+	// for the next position with dofs.
+	do {
+	  pos++;
+	  // Get geo index posistion.
+	  posIndex = INDEX_OF_DIM(pos, dim);
+	  // Get number of dofs in this position.
+	  nDofs = admin->getNumberOfDOFs(posIndex);
+	} while (nDofs == 0 && pos <= dim);
+	
+	if (pos <= dim) {
+	  // We have found on more position with dofs.
+
+	  // Get number of elements in this position, i.e, the number of vertices,.
+	  // edges and faces in the given dimension.
+	  nElements = Global::getGeo(posIndex, dim);
+	  // Calculate displacement. Is used if there is more than one dof admin on the mesh.
+	  n0 = admin->getNumberOfPreDOFs(posIndex);
+	  // Get first dof index position for the geo index position.
+	  node0 = mesh->getNode(posIndex);
+	} else {
+	  // That's all, we jave traversed all dofs of the mesh element.
+	  return false;
+	}
+
+      }
+    }
+
+    return true;
+  } 
+}

AMDiS/src/ElementDofIterator.h

+// ============================================================================
+// ==                                                                        ==
+// == AMDiS - Adaptive multidimensional simulations                          ==
+// ==                                                                        ==
+// ============================================================================
+// ==                                                                        ==
+// ==  crystal growth group                                                  ==
+// ==                                                                        ==
+// ==  Stiftung caesar                                                       ==
+// ==  Ludwig-Erhard-Allee 2                                                 ==
+// ==  53175 Bonn                                                            ==
+// ==  germany                                                               ==
+// ==                                                                        ==
+// ============================================================================
+// ==                                                                        ==
+// ==  http://www.caesar.de/cg/AMDiS                                         ==
+// ==                                                                        ==
+// ============================================================================
+
+/** \file ElementDofIterator.h */
+
+#ifndef AMDIS_ELEMENTDOFITERATOR_H
+#define AMDIS_ELEMENTDOFITERATOR_H
+
+#include "AMDiS_fwd.h"
+#include "Global.h"
+
+namespace AMDiS {
+
+  /** \brief
+   * This class implements an iterator to iterate over all dofs of one element
+   * independet of dimension and the degree of basis functions.
+   *
+   * Should be used in the following way:
+   *
+   *    ElementDofIterator elDofIter(admin);
+   *    elDofIter.reset(el);
+   *    do {
+   *       elDofIter.getDOF();
+   *    } while (elDofIter.next());
+   *
+   */
+  class ElementDofIterator
+  {
+  public:
+    /// Constructor.
+    ElementDofIterator(const DOFAdmin* dofAdmin)
+      : admin(dofAdmin)
+    {}
+
+    /// Start a new traverse with the given element.
+    void reset(Element* el);
+
+    /// Go to next dof. Returns false, if there is dof anymore.
+    bool next();
+
+    /// Returns the dof index of the current dof.
+    const DegreeOfFreedom getDof()
+    {
+      return dofs[node0 + elementPos][n0 + dofPos];
+    }
+    
+    /// Returns a pointer to the current dof.
+    const DegreeOfFreedom* getDofPtr()
+    {
+      return &dofs[node0 + elementPos][n0 + dofPos];
+    }
+
+  protected:
+    /// The dof admin for which dofs should be traversed.
+    const DOFAdmin* admin;
+
+    /// Pointer to the dofs that should be traversed.
+    const DegreeOfFreedom **dofs;
+
+    /// Mesh on which the element is defined.
+    Mesh* mesh;
+
+    /// Dimension of the mesh.
+    int dim;
+
+    /// Current position (i.e., vertex, edge, face) of the traverse.
+    int pos;
+
+    /// Dimension dependent geo index of the current position in traverse.
+    GeoIndex posIndex;
+
+    /** \brief
+     * Number of dofs at the current traverse position. Examples: independent of 
+     * dimension and  degree of basis functions there is only one dof per vertex. 
+     * But in 2d and with 3rd degree lagrange basis functions there are two 
+     * dofs per edge.
+     */
+    int nDofs;
+
+    /** \brief
+     * Displacement of dof indices. Used of more than one dof admin is defined 
+     * on the mesh.
+     */
+    int n0;
+
+    /// Dof index of the first dof at this geo index position.
+    int node0;
+    
+    /** \brief
+     * Number of elements in the current geo position. Examples: 3 vertices in 2d,
+     * 1 face in 2d, 4 faces in 3d, etc.
+     */
+    int nElements;
+
+    /// Current element (vertex, edge, face) that is traversed.
+    int elementPos;
+
+    /// Currrent dof that is traversed on the current element;
+    int dofPos;
+  };
+}
+
+#endif // AMDIS_ELEMENTDOFITERATOR_H

AMDiS/src/QPsiPhi.cc

@@ -42,14 +42,17 @@ namespace AMDiS {
       k(NULL),
       l(NULL)
   {
-    FUNCNAME("Q11PsiPhi::Q11PsiPhi");
-    const FastQuadrature      *q_phi, *q_psi;
-    int                       i, j, lk, ll, n, iq, all_entries, n_psi, n_phi;
-    double                      val, grdi, grdj;
-    int                       d=ps->getDim();
+    FUNCNAME("Q11PsiPhi::Q11PsiPhi()");
+
+    const FastQuadrature *q_phi, *q_psi;
+    int j, lk, ll, n, iq, all_entries, n_psi, n_phi;
+    double val, grdi, grdj;
+    int d = ps->getDim();
  
-    if (!psi)  psi = phi;
-    if (!phi)  phi = psi;
+    if (!psi)
+      psi = phi;
+    if (!phi)