merge trunk

Author: slmouradian

Makefile.in

@@ -435,7 +435,7 @@ distclean: clean
 	 include/spatialindex include/spud include/spud.h		\
 	 include/spud_enums.h include/tinystr.h include/tinyxml.h	\
 	 include/version.h include/vtk.h				\
-	 preprocessor/check_options.F90 schemas/flml			\
+	 preprocessor/check_options.F90 \
 	 preprocessor/register_diagnostics.F90 python/setup.py >	\
 	 /dev/null
 	@for i in `find ./*/ -name Makefile.in`; do rm -f `echo $$i | sed 's/.in$$//'`; done > /dev/null
@@ -551,7 +551,7 @@ install: default fltools
 	mkdir -p $(DESTDIR)$(datadir)/fluidity
 	cp -r schemas/ $(DESTDIR)$(datadir)/fluidity/
 	mkdir -p $(DESTDIR)$(datadir)/diamond/schemata
-	cp schemas/flml $(DESTDIR)$(datadir)/diamond/schemata
+	sed 's/$${datadir}/$(subst /,\/,$(datadir))/g' schemas/flml.in > $(DESTDIR)$(datadir)/diamond/schemata/flml
 	cd python ; python setup.py install --root=$(shell echo ${DESTDIR} | sed 's/^$$/\//') --prefix="$(prefix)" $$FLUIDITY_PYTHON_INSTALL_ARGS
 	cp -r examples/ $(DESTDIR)$(docdir)/fluidity
 	find $(DESTDIR)$(docdir)/fluidity/examples -type f -exec sed -i "s/\.\.\/\.\.\/\.\.\/bin\///" '{}' \;

aclocal.m4

@@ -945,76 +945,6 @@ EOD`
 	#
 ])
 
-AC_DEFUN([ACX_zoltan], [
-# Set variables...
-AC_ARG_WITH(
-	[zoltan],
-	[  --with-zoltan=prefix        Prefix where zoltan is installed],
-	[zoltan="$withval"],
-    [])
-
-tmpLIBS=$LIBS
-tmpCPPFLAGS=$CPPFLAGS
-if test $zoltan != no; then
-  if test $zoltan != yes; then
-    zoltan_LIBS_PATH="$zoltan/lib"
-    zoltan_INCLUDES_PATH="$zoltan/include"
-    # Ensure the comiler finds the library...
-    tmpLIBS="$tmpLIBS -L$zoltan_LIBS_PATH"
-    tmpCPPFLAGS="$tmpCPPFLAGS  -I/$zoltan_INCLUDES_PATH"
-  fi
-  tmpLIBS="$tmpLIBS -L/usr/lib -L/usr/local/lib/ -lzoltan -lparmetis -lmetis $ZOLTAN_DEPS"
-  tmpCPPFLAGS="$tmpCPPFLAGS -I/usr/include/ -I/usr/local/include/"
-fi
-LIBS=$tmpLIBS
-CPPFLAGS=$tmpCPPFLAGS
-# Check that the compiler uses the library we specified...
-if test -e $zoltan_LIBS_PATH/libzoltan.a; then
-  echo "note: using $zoltan_LIBS_PATH/libzoltan.a"
-fi 
-
-# Check that the compiler uses the include path we specified...
-if test -e $zoltan_INCLUDES_PATH/zoltan.mod; then
-	echo "note: using $zoltan_INCLUDES_PATH/zoltan.mod"
-fi 
-
-AC_LANG_SAVE
-AC_LANG_C
-AC_CHECK_LIB(
-	[zoltan],
-	[Zoltan_Initialize],
-	[AC_DEFINE(HAVE_ZOLTAN,1,[Define if you have zoltan library.])],
-	[AC_MSG_ERROR( [Could not link in the zoltan library... exiting] )] )
-
-# Small test for zoltan .mod files:
-AC_LANG(Fortran)
-ac_ext=F90
-# In fluidity's makefile we explicitly add CPPFLAGS, temporarily add it to
-# FCFLAGS here for this zoltan test:
-tmpFCFLAGS="$FCFLAGS"
-FCFLAGS="$FCFLAGS $CPPFLAGS"
-AC_LINK_IFELSE(
-[AC_LANG_SOURCE([
-program test_zoltan
- use zoltan
-end program test_zoltan
-])],
-[
-AC_MSG_NOTICE([Great success! Zoltan .mod files exist and are usable])
-],
-[
-cp conftest.F90 test_zoltan.F90
-AC_MSG_FAILURE([Failed to find zoltan.mod files])])
-# And now revert FCFLAGS
-FCFLAGS="$tmpFCFLAGS"
-AC_LANG_RESTORE
-
-ZOLTAN="yes"
-AC_SUBST(ZOLTAN)
-
-echo $LIBS
-])dnl ACX_zoltan
-
 AC_DEFUN([ACX_adjoint], [
 # Set variables...
 AC_ARG_WITH(

assemble/Full_Projection.F90

@@ -336,6 +336,24 @@ subroutine petsc_solve_setup_full_projection(y,A,b,ksp,petsc_numbering_p,name,so
         state, inner_mesh, blocks(div_matrix_comp,2), inner_option_path, matrix_has_solver_cache=.false., &
         mesh_positions=mesh_positions)
       rotation_matrix => extract_petsc_csr_matrix(state, "RotationMatrix", stat=rotation_stat)
+
+      if (associated(mesh_positions)) then
+        if (rotation_stat==0) then
+          call attach_null_space_from_options(inner_M%M, inner_solver_option_path, &
+            positions=mesh_positions, rotation_matrix=rotation_matrix%M, &
+            petsc_numbering=petsc_numbering_u)
+        else
+          call attach_null_space_from_options(inner_M%M, inner_solver_option_path, &
+            positions=mesh_positions, petsc_numbering=petsc_numbering_u)
+        end if
+      elseif (rotation_stat==0) then
+        call attach_null_space_from_options(inner_M%M, inner_solver_option_path, &
+          rotation_matrix=rotation_matrix%M, petsc_numbering=petsc_numbering_u)
+      else
+        call attach_null_space_from_options(inner_M%M, inner_solver_option_path, &
+          petsc_numbering=petsc_numbering_u)
+      end if
+
       if (associated(prolongators)) then
         if (rotation_stat==0) then
           FLExit("Rotated boundary conditions do not work with mg prolongators")
@@ -344,31 +362,13 @@ subroutine petsc_solve_setup_full_projection(y,A,b,ksp,petsc_numbering_p,name,so
         if (associated(surface_nodes)) then
           FLExit("Internal smoothing not available for inner solve")
         end if
-        if (associated(mesh_positions)) then
-          call setup_ksp_from_options(ksp_schur, inner_M%M, inner_M%M, &
-            inner_solver_option_path, petsc_numbering=petsc_numbering_u, startfromzero_in=.true., &
-            prolongators=prolongators, positions=mesh_positions)
-        else
-          call setup_ksp_from_options(ksp_schur, inner_M%M, inner_M%M, &
-            inner_solver_option_path, petsc_numbering=petsc_numbering_u, startfromzero_in=.true., &
-            prolongators=prolongators)
-        end if
+        call setup_ksp_from_options(ksp_schur, inner_M%M, inner_M%M, &
+          inner_solver_option_path, petsc_numbering=petsc_numbering_u, startfromzero_in=.true., &
+          prolongators=prolongators)
         do i=1, size(prolongators)
           call deallocate(prolongators(i))
         end do
         deallocate(prolongators)
-      else if (associated(mesh_positions) .and. rotation_stat==0) then
-        call setup_ksp_from_options(ksp_schur, inner_M%M, inner_M%M, &
-          inner_solver_option_path, petsc_numbering=petsc_numbering_u, startfromzero_in=.true., &
-          positions=mesh_positions, rotation_matrix=rotation_matrix%M)
-      else if (associated(mesh_positions)) then
-        call setup_ksp_from_options(ksp_schur, inner_M%M, inner_M%M, &
-          inner_solver_option_path, petsc_numbering=petsc_numbering_u, startfromzero_in=.true., &
-          positions=mesh_positions)
-      else if (rotation_stat==0) then
-        call setup_ksp_from_options(ksp_schur, inner_M%M, inner_M%M, &
-          inner_solver_option_path, petsc_numbering=petsc_numbering_u, startfromzero_in=.true., &
-          rotation_matrix=rotation_matrix%M)
       else
         call setup_ksp_from_options(ksp_schur, inner_M%M, inner_M%M, &
           inner_solver_option_path, petsc_numbering=petsc_numbering_u, startfromzero_in=.true.)
@@ -388,6 +388,8 @@ subroutine petsc_solve_setup_full_projection(y,A,b,ksp,petsc_numbering_p,name,so
 
       if(have_preconditioner_matrix) then
          pmat=csr2petsc(preconditioner_matrix, petsc_numbering_p, petsc_numbering_p)
+      else
+         pmat=A
       end if
 
       ! Set up RHS and Solution vectors (note these are loaded later):
@@ -399,12 +401,8 @@ subroutine petsc_solve_setup_full_projection(y,A,b,ksp,petsc_numbering_p,name,so
 
       parallel=IsParallel()
 
-      if(have_preconditioner_matrix) then
-         call SetupKSP(ksp,A,pmat,solver_option_path,parallel,petsc_numbering_p, lstartfromzero)
-      else
-         ! If preconditioner matrix is not required, send in A instead:
-         call SetupKSP(ksp,A,A,solver_option_path,parallel,petsc_numbering_p, lstartfromzero)
-      end if
+      call attach_null_space_from_options(A, solver_option_path, pmat=pmat, petsc_numbering=petsc_numbering_p)
+      call SetupKSP(ksp,A,pmat,solver_option_path,parallel,petsc_numbering_p, lstartfromzero)
 
       ! Destroy the matrices setup for the schur complement computation. While
       ! these matrices are destroyed here, they are still required for the inner solve,