Merge lp:~fluidity-core/fluidity/sediment_restructure into lp:~fluidity-core/fluidity/sediment

[Samuel Parkinson]

Restructure to match blueprint. Also added some additional error checks and edited the manual a little to reflect these changes.

[lp:~fluidity-core/fluidity/sediment_restructure]

3421. By Samuel Parkinson on 2011-10-28

added some deallocate commands

3422. By Samuel Parkinson on 2011-11-02

Changed definition of sediment to include submerged specific gravity instead of density. This allows for any reference and ambient density of sediment and removes 1000's in sediment code.

Also started adapting erosion subroutine to allow for several erosion algorithms

3423. By Samuel Parkinson on 2011-11-03

partly added Garcia_1991 entrainment algorithm

3424. By Samuel Parkinson on 2011-11-03

fixed bugs in reentrainment and also some bugs in k-epsilon scalar field diffusivity paths - still doesn't work

3425. By Samuel Parkinson on 2011-11-03

merge with trunk

3426. By Samuel Parkinson on 2011-11-07

Changed k-epsilon so that it initialises eddy_viscosity properly from kk and keps at start of simulation

Changed main/Fluids.F90 so that this is done before the initial dump to vtu files

Removed references to Prandtl number in Populate_State as they are not needed here

3427. By Samuel Parkinson on 2011-11-07

Added k-epsilon scalar field diffusivity diagnostic algorithm

3428. By Samuel Parkinson on 2011-11-07

moved k_epsilon init so that the initial diffusivities are calculated correctly

removed some print statements

3429. By Samuel Parkinson on 2011-11-17

First attempt at getting Garcia_1991 entrainmnet working
Added two diagnostic fields for d50 and standard deviation of bed sediment
Added interface for retrieving items from sediment fields
Added face_val_at_quad_tensor_dim_dim to face_val_at_quad interface
Removed unused k_epsilon code in populate state

3430. By Samuel Parkinson on 2011-11-17

merge with trunk

3431. By Samuel Parkinson on 2011-11-21

- changes to sediment interface in code to allow name and field of sediment field to be extracted using same interface as other items
- added ability to be able to provide an overriding viscosity to be used when calculating reentrainment
- revision of garcia entrainment fixing some bugs and including d50 value in algorithm (sitll need to include sd)
- added tests for garcia entrainment and also bedload calculation with diffusivity

3432. By Samuel Parkinson on 2011-11-23

rearranged and fixed bug in SedimentDiagnostics
fixed various bugs in reentrainment and reworked JHill reentrainment

3433. By Samuel Parkinson on 2011-11-29

Reentrainment now works for single sediment classes. Garcia still needs some work to have it working for multiple sediments. A working test has been created for reentrainment and a more challenging test for settling rate.

3434. By Samuel Parkinson on 2011-11-29

created diagnostic to calculate standard deviation of bed sediment diameters

3435. By Samuel Parkinson on 2011-11-29

merge with branch including remap_surface_to_field but then removed this change and approached it a different way which seems to work

3436. By Samuel Parkinson on 2011-11-29

calculation of standard deviation of bed sediment complete

3437. By Samuel Parkinson on 2011-11-30

now with reentrainment scaled by volume fraction

3438. By Samuel Parkinson on 2011-11-30

changed SedimentBedload to Bedload

3439. By Samuel Parkinson on 2011-11-30

removed k-epsilon changes

3440. By Samuel Parkinson on 2011-11-30

merge with k_epsilon_scalar_diffusivity branch

3441. By Samuel Parkinson on 2011-11-30

merge with revised k-epsilon scalar diffusivity branch

3442. By Samuel Parkinson on 2011-11-30

fixed two bugs, SedimentBedload split across two lines and viscosity field deallocation

3443. By Samuel Parkinson on 2011-11-30

removed vtu file from repository

[Jon Hill (jon-hill)]

Latest results look very encouraging and the coding standard is good, so merging this into the main sediment branch.

review: Approve

=== modified file '.bzrignore'
--- .bzrignore	2011-04-15 16:18:30 +0000
+++ .bzrignore	2011-11-30 17:31:28 +0000
@@ -2,3 +2,4 @@
 backward_facing_step_2d-high.flml
 examples/backward_facing_step_2d/coarse
 coarse
+matrixdump
 
=== modified file 'Makefile.in'
--- Makefile.in	2011-10-21 13:38:04 +0000
+++ Makefile.in	2011-11-30 17:31:28 +0000
@@ -27,7 +27,16 @@
 SHELL = @SHELL@
 
 PACKAGE_NAME = @PACKAGE_NAME@
-PACKAGE_VERSION = @PACKAGE_VERSION@
+
+# Ignore package version from autoconf. Instead, for packages
+# FLUIDITY_VERSION is passed into ./configure and used here. If it is not
+# set we obtain version information from bzr. Again, this is not done in
+# configure to ensure the info is up-to-date after a "bzr up" without reconfiguring
+ifeq ("@FLUIDITY_VERSION@","")
+PACKAGE_VERSION = `bzr version-info --custom --template='{branch_nick}.{revno}'`
+else
+PACKAGE_VERSION = "@FLUIDITY_VERSION@"
+endif
 
 FLUIDITY = $(PACKAGE_NAME)
 
@@ -40,6 +49,7 @@
 # Follow: www.gnu.org/prep/standards/html_node/Directory-Variables.html
 PACKAGE_NAME = @PACKAGE_NAME@
 prefix  = @prefix@
+exec_prefix  = @exec_prefix@
 bindir = @bindir@
 libdir = @libdir@
 datadir = @datadir@
@@ -62,6 +72,8 @@
 
 LINKER  = @LINKER@ @LDFLAGS@
 
+FLLINKER = @FLLINKER@ @LDFLAGS@ $(FCFLAGS)
+
 LIBS    = -L./lib -l$(FLUIDITY) @BLAS_LIBS@ @LIB_FEMDEM@ ./lib/libadaptivity.a \
            ./lib/libvtkfortran.a ./lib/libspatialindex.a ./lib/libspud.a ./lib/libjudy.a \
            @LIBS@
@@ -75,8 +87,6 @@
 
 EVAL = tools/silenteval.sh
 
-VERSION = $(shell bzr revision-info)
-
 ifeq (@MBA2D@,yes)
 LIBMBA2D = lib/libmba2d.a
 endif
@@ -109,7 +119,7 @@
 sub_system: $(LIBMBA2D) $(LIBMBA3D) $(LIBALGENCAN)  @LIB_FEMDEM@ \
 	lib/libadaptivity.a lib/libvtkfortran.a lib/libspatialindex.a \
 	lib/libspud.a lib/libjudy.a include/version.h
- 
+
 lib/libjudy.a:
 	@echo '    MKDIR lib'; mkdir -p lib
 	@cd libjudy; echo '    MAKE libjudy'; $(MAKE) > make.log ; $(MAKE) install >> make.log ; cd ..
@@ -143,7 +153,7 @@
 ifeq (@SPUD_ONLY@,yes)
 	@cd libspud;  echo '    MAKE libspud'; $(MAKE) ; $(MAKE) install-libspud
 else
-	@cd libspud;  echo '    MAKE libspud'; $(MAKE) ; $(MAKE) install; cd ..; cp lib*/python*/site-packages/libspud.so python/
+	@cd libspud;  echo '    MAKE libspud'; $(MAKE) ; $(MAKE) install-libspud; cd python; python setup.py build; cd ../..; cp libspud/python/build/lib*/libspud.so python/
 endif
 
 libfemtools: sub_system
@@ -190,8 +200,8 @@
 	@echo "    MKDIR bin"
 	@mkdir -p bin
 	@echo "    LD shallow_water"
-	@$(EVAL) $(LINKER) -o bin/hybridized_helmholtz_solver main/Hybridized_Helmholtz_Solver.o $(LIBS)
-	@$(EVAL) $(LINKER) -o bin/shallow_water main/Shallow_Water.o $(LIBS)
+	@$(EVAL) $(FLLINKER) -o bin/hybridized_helmholtz_solver main/Hybridized_Helmholtz_Solver.o $(LIBS)
+	@$(EVAL) $(FLLINKER) -o bin/shallow_water main/Shallow_Water.o $(LIBS)
 
 bin/hybridized_helmholtz_solver: fluidity_library main/Hybridized_Helmholtz_Solver.F90
 	@cd main; $(MAKE) Hybridized_Helmholtz_Solver.o
@@ -199,7 +209,7 @@
 	@echo "    MKDIR bin"
 	@mkdir -p bin
 	@echo "    LD hybridized_helmholtz_solver"
-	@$(EVAL) $(LINKER) -o bin/hybridized_helmholtz_solver main/Hybridized_Helmholtz_Solver.o $(LIBS)
+	@$(EVAL) $(FLLINKER) -o bin/hybridized_helmholtz_solver main/Hybridized_Helmholtz_Solver.o $(LIBS)
 
 bin/burgers_equation: fluidity_library main/Burgers_Equation.F90
 	@cd main; $(MAKE) Burgers_Equation.o
@@ -395,6 +405,9 @@
 	@cd horizontal_adaptivity/tests;   $(MAKE) clean
 	@echo "    CLEAN tools"
 	@cd tools;    $(MAKE) clean
+	@echo "    CLEAN adjoint"
+	@cd adjoint;    $(MAKE) clean
+	@cd adjoint/tests;    $(MAKE) clean
 	@echo "    CLEAN bathymetry"
 	@cd bathymetry;  $(MAKE) clean
 	@echo "    CLEAN ocean_forcing"
@@ -416,7 +429,7 @@
 	@cd main; $(MAKE) clean
 	@rm -fr bin/* lib
 
-clean: clean-light clean-test python_clean
+clean: clean-light clean-test python_clean clean-debian
 	@echo "    CLEAN libvtkfortran"
 	@cd libvtkfortran; $(MAKE) clean
 	@echo "    CLEAN libjudy"
@@ -433,17 +446,24 @@
 	@cd libalgencan; $(MAKE) clean
 	@echo "    CLEAN libwm"
 	@cd libwm; $(MAKE) clean
+	@echo "    CLEAN manual"
+	@cd manual; $(MAKE) clean
 	@CLEAN_LIBADAPT@
 	@rm -fr include/*.mod *.cache core *.o config.status
 	@find ./ \( -name work.pc \) -exec rm {} \;
 	@find ./ \( -name work.pcl \) -exec rm {} \;
 
+clean-debian:
+	@echo "    CLEAN debian"
+	@cd debian; rm -rf files tmp fluidity python-fluidity *.substvars *.debhelper* 
+
 clean-test:      
 	@echo "    CLEAN tests"
-	@cd tests; ../tools/testharness.py --clean >/dev/null
+	@cd tests; PYTHONPATH=../python ../tools/testharness.py --clean >/dev/null
+	@cd tests/data; $(MAKE) clean
 
 distclean: clean
-	@echo "   DISTCLEAN"
+	@echo "    DISTCLEAN"
 	@cd spatialindex-1.5 ; make distclean > /dev/null ; rm -rf	\
 	 make.log regressiontest/mvrtree/.deps				\
 	 regressiontest/rtree/.deps regressiontest/tprtree/.deps >	\
@@ -473,7 +493,7 @@
 	 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					\
+	 preprocessor/check_options.F90 schemas/flml			\
 	 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
@@ -482,7 +502,7 @@
 
 test: fltools bin/$(FLUIDITY) bin/shallow_water serialtest bin/burgers_equation
 
-serialtest:
+serialtest: fltools bin/$(FLUIDITY) bin/shallow_water
 ifeq (@MBA2D@,yes)
         ifeq (@ZOLTAN@,yes)
 	        @cd tests; ../bin/testharness -l short -p serial -e nozoltan -n $(THREADS)
@@ -497,7 +517,7 @@
         endif
 endif
 
-mediumtest: bin/burgers_equation
+mediumtest: fltools bin/$(FLUIDITY) manual bin/burgers_equation
 	@cd tests; ../bin/testharness -l medium $(EXCLUDE_TAGS) -n $(THREADS)
 
 mediumzoltantest:
@@ -599,7 +619,18 @@
 	$(MAKE) clean-light
 	@echo "    Congratulations, make makefiles succeeded!"
 
-install:
-	@mkdir -p $(DESTDIR)$(bindir)
+install: default fltools bin/shallow_water bin/burgers_equation
+	@mkdir -p $(DESTDIR)$(bindir) $(DESTDIR)$(docdir)/fluidity
 	cp bin/* $(DESTDIR)$(bindir)
-	cd python ; python setup.py install --root="${DESTDIR}" --prefix="$(prefix)"
+	rm -f $(DESTDIR)$(bindir)/spud-* $(DESTDIR)$(bindir)/diamond $(DESTDIR)$(bindir)/silenteval $(DESTDIR)$(bindir)/runut
+	[ -f manual/fluidity_manual.pdf ] && cp manual/fluidity_manual.pdf $(DESTDIR)$(docdir)/fluidity || true
+	mkdir -p $(DESTDIR)$(datadir)/fluidity
+	cp -r schemas/ $(DESTDIR)$(datadir)/fluidity/
+	mkdir -p $(DESTDIR)$(datadir)/diamond/schemata
+	cp schemas/flml $(DESTDIR)$(datadir)/diamond/schemata
+	cd python ; python setup.py install --root="${DESTDIR}" --prefix="$(prefix)" $$FLUIDITY_PYTHON_INSTALL_ARGS
+	cp -r examples/ $(DESTDIR)$(docdir)/fluidity
+	find $(DESTDIR)$(docdir)/fluidity/examples -type f -exec sed -i "s/\.\.\/\.\.\/\.\.\/bin\///" '{}' \;
+	find $(DESTDIR)$(docdir)/fluidity/examples -type f -exec sed -i "s/\.\.\/\.\.\/bin\///" '{}' \;
+	tar -czvf $(DESTDIR)$(docdir)/fluidity/examples.tar.gz $(DESTDIR)$(docdir)/fluidity/examples/
+	rm -rf $(DESTDIR)$(docdir)/fluidity/examples/
 
=== modified file 'aclocal.m4'
--- aclocal.m4	2011-10-03 17:24:46 +0000
+++ aclocal.m4	2011-11-30 17:31:28 +0000
@@ -500,7 +500,11 @@
       PetscInt  i,j,II,JJ,m,n,its
       PetscInt  Istart,Iend,ione
       PetscErrorCode ierr
+#if PETSC_VERSION_MINOR==2
+      PetscBool flg
+#else
       PetscTruth  flg
+#endif
       PetscScalar v,one,neg_one
       Vec         x,b,u
       Mat         A 
 
=== modified file 'assemble/Biology.F90'
--- assemble/Biology.F90	2011-10-19 17:55:20 +0000
+++ assemble/Biology.F90	2011-11-30 17:31:28 +0000
@@ -39,6 +39,9 @@
   use solvers
   use python_state
   use sparsity_patterns_meshes
+  use fefields
+  use field_options
+
   implicit none
 
   private
@@ -66,6 +69,14 @@
     type(state_type), intent(inout) :: state
 
     character(len=OPTION_PATH_LEN) :: prefix, algorithm
+    ! This is the photosynthetic radiation projected onto the 
+    ! same mesh as the biology fields
+    ! It also takes into account the "active" part of the solar radiation
+    type(scalar_field) :: par_bio
+    ! we use the phytoplankton as the "bio" mesh
+    type(scalar_field), pointer :: phytoplankton, PhotosyntheticRadiation
+    type(vector_field) :: coords
+    integer :: stat
 
     call backup_source_terms(state)
 
@@ -91,6 +102,24 @@
     ! Calculate the light field at every point.
     call solve_light_equation(state, prefix)
 
+    par_bio = extract_scalar_field(state, "_PAR", stat)
+    phytoplankton => extract_scalar_field(state, "Phytoplankton")
+    if (stat /= 0) then
+        ! field does not yet exist: create it
+        call allocate(par_bio,phytoplankton%mesh, name="_PAR")
+        call zero(par_bio)
+        call insert(state, par_bio, par_bio%name)
+        call deallocate(par_bio)
+        par_bio = extract_scalar_field(state, "_PAR", stat)
+    end if
+    PhotosyntheticRadiation => extract_scalar_field(state, "PhotosyntheticRadiation")
+    coords = get_coordinate_field(state, par_bio%mesh)
+    ! project the Photosynthetic radaition field onto the _PAR field
+    call project_field(PhotosyntheticRadiation, par_bio, coords)
+    ! scale it to get the active part
+    call scale(par_bio, 0.43)
+    call deallocate(coords)
+
     ! Calculate the sources and sinks at every point.
     call calculate_biology_from_python(state, prefix, algorithm)
 
@@ -210,13 +239,9 @@
     g=extract_vector_field(state, "GravityDirection")
     light=extract_scalar_field(state, "PhotosyntheticRadiation")
     P=extract_scalar_field(state, "Phytoplankton")
-    
-    if(continuity(light)<0) then
-      ! could be cleverer with this and check if diffusion is assembled
-      sparsity=>get_csr_sparsity_secondorder(state, light%mesh, light%mesh)
-    else
-      sparsity=>get_csr_sparsity_firstorder(state, light%mesh, light%mesh)
-    end if
+
+    ! Only need first order sparsity as we have no diffusion
+    sparsity=>get_csr_sparsity_firstorder(state, light%mesh, light%mesh)
 
     call get_option(trim(light%option_path)//&
          "/prognostic/absorption_coefficients/water", k_w)
@@ -369,23 +394,22 @@
           ! External face.
           face_2=face
        end if
-
-       call construct_light_interface(ele, ele_2, face, face_2, ni,&
+       
+       call construct_light_interface(face, face_2,&
             & light_mat, rhs, X, g, light, &
             & bc_value, bc_type)  
-            
     end do neighbourloop
 
   end subroutine construct_light_element
 
-  subroutine construct_light_interface(ele, ele_2, face, face_2, ni,&
+  subroutine construct_light_interface(face, face_2,&
             & light_mat, rhs, X, g, light, bc_value, bc_type)
     !!< Construct the element boundary integrals on the ni-th face of
     !!< element ele. For continuous discretisation, this is only boundary
     !!< faces. For DG it's all of them.
     implicit none
 
-    integer, intent(in) :: ele, ele_2, face, face_2, ni
+    integer, intent(in) :: face, face_2
     type(csr_matrix), intent(inout) :: light_mat
     type(scalar_field), intent(inout) :: rhs
     ! We pass these additional fields to save on state lookups.
@@ -399,7 +423,7 @@
 
     ! Face objects and numberings.
     type(element_type), pointer ::l_shape, l_shape_2
-    integer, dimension(face_loc(light,face)) :: l_face, l_face_l
+    integer, dimension(face_loc(light,face)) :: l_face
     integer, dimension(face_loc(light,face_2)) :: l_face_2
 
     ! Note that both sides of the face can be assumed to have the same
@@ -428,7 +452,7 @@
     ! Boundary nodes have both faces the same.
     boundary=(face==face_2)
     dirichlet=.false.
-    if (boundary) then
+    if (boundary .and. face < size(bc_type)) then
        if (bc_type(face)==BCTYPE_WEAKDIRICHLET) then
           dirichlet=.true.
        end if
 
=== modified file 'assemble/Diagnostic_fields_wrapper.F90'
--- assemble/Diagnostic_fields_wrapper.F90	2011-09-20 12:26:59 +0000
+++ assemble/Diagnostic_fields_wrapper.F90	2011-11-30 17:31:28 +0000
@@ -544,8 +544,11 @@
 
        ! Start of sediment diagnostics.
        if (have_option("/material_phase[0]/sediment")) then
-          call calculate_sinking_velocity(state(i))
+          call calculate_sediment_sinking_velocity(state(i))
           call calculate_sediment_flux(state(i))
+          call calculate_sediment_active_layer_d50(state(i))
+          call calculate_sediment_active_layer_sigma(state(i))
+          call calculate_sediment_active_layer_volume_fractions(state(i))
        end if
        ! End of sediment diagnostics.
 
 
=== modified file 'assemble/Divergence_Matrix_CV.F90'
--- assemble/Divergence_Matrix_CV.F90	2011-09-16 21:18:56 +0000
+++ assemble/Divergence_Matrix_CV.F90	2011-11-30 17:31:28 +0000
@@ -107,7 +107,7 @@
       type(vector_field) :: field_bc
 
       real, dimension(:,:,:), allocatable :: ct_mat_local, ct_mat_local_bdy
-      real, dimension(:), allocatable :: ct_rhs_local
+      real, dimension(:,:), allocatable :: ct_rhs_local
 
       logical :: l_get_ct
 
@@ -316,7 +316,7 @@
         allocate(field_nodes_bdy(field%mesh%faces%shape%loc))
         allocate(test_nodes_bdy(test_mesh%faces%shape%loc))
         allocate(ct_mat_local_bdy(x%dim, test_mesh%faces%shape%loc, field%mesh%faces%shape%loc), &
-                ct_rhs_local(test_mesh%faces%shape%loc))
+                 ct_rhs_local(x%dim, test_mesh%faces%shape%loc))
   
         surface_element_loop: do sele = 1, surface_element_count(test_mesh)
   
@@ -366,11 +366,11 @@
                       if((present(ct_rhs)).and.(field_bc_type(dim, sele)==BC_TYPE_WEAKDIRICHLET)) then
   
                         if(multiphase) then
-                           ct_rhs_local(iloc) = ct_rhs_local(iloc) + &
+                           ct_rhs_local(dim, iloc) = ct_rhs_local(dim, iloc) - &
                                  field_cvbdyshape%n(jloc,ggi)*detwei_bdy(ggi)*nvfrac_gi_f(ggi)*&
                                  normal_bdy(dim,ggi)*field_bc_val(dim, jloc)
                         else
-                           ct_rhs_local(iloc) = ct_rhs_local(iloc) + &
+                           ct_rhs_local(dim, iloc) = ct_rhs_local(dim, iloc) - &
                                  field_cvbdyshape%n(jloc,ggi)*detwei_bdy(ggi)*normal_bdy(dim,ggi)*&
                                  field_bc_val(dim, jloc)
                         end if
@@ -403,7 +403,7 @@
   
             if((present(ct_rhs)).and.(field_bc_type(dim, sele)==BC_TYPE_WEAKDIRICHLET)) then
   
-              call addto(ct_rhs, test_nodes_bdy, ct_rhs_local)
+              call addto(ct_rhs, test_nodes_bdy, ct_rhs_local(dim,:))
   
             elseif(l_get_ct) then
   
 
=== modified file 'assemble/Full_Projection.F90'
--- assemble/Full_Projection.F90	2011-04-06 15:37:23 +0000
+++ assemble/Full_Projection.F90	2011-11-30 17:31:28 +0000
@@ -44,8 +44,8 @@
     use petsc_solve_state_module
     use boundary_conditions_from_options
 
-#ifdef HAVE_PETSC_MODULES
 #include "petscversion.h"
+#ifdef HAVE_PETSC_MODULES
     use petsc
 #if PETSC_VERSION_MINOR==0
     use petscvec
 
=== modified file 'assemble/LES_viscosity.F90'
--- assemble/LES_viscosity.F90	2011-05-10 10:39:15 +0000
+++ assemble/LES_viscosity.F90	2011-11-30 17:31:28 +0000
@@ -54,17 +54,17 @@
     ewrite(2,*) "Initialising optional dynamic LES diagnostic fields"
     ! Filter width
     if(have_filter_width) then
-      tensorfield => extract_tensor_field(state, "DynamicFilterWidth")
+      tensorfield => extract_tensor_field(state, "FilterWidth")
       call zero(tensorfield)
     end if
     ! Strain rate field S1
     if(have_strain) then
-      tensorfield => extract_tensor_field(state, "DynamicStrainRate")
+      tensorfield => extract_tensor_field(state, "StrainRate")
       call zero(tensorfield)
     end if
     ! Filtered strain rate field S2
     if(have_filtered_strain) then
-      tensorfield => extract_tensor_field(state, "DynamicFilteredStrainRate")
+      tensorfield => extract_tensor_field(state, "FilteredStrainRate")
       call zero(tensorfield)
     end if
     ! Eddy viscosity field m_ij
@@ -98,31 +98,31 @@
 
     ! Strain rate field S1
     if(have_strain) then
-      tensorfield => extract_tensor_field(state, "DynamicStrainRate")
+      tensorfield => extract_tensor_field(state, "StrainRate")
       tensor_loc=shape_tensor_rhs(ele_shape(nu, ele), strain_gi, detwei)
       call addto(tensorfield, ele_nodes(nu, ele), tensor_loc)
     end if
 
     ! Filtered strain rate field S2
     if(have_filtered_strain) then
-      tensorfield => extract_tensor_field(state, "DynamicFilteredStrainRate")
+      tensorfield => extract_tensor_field(state, "FilteredStrainRate")
       tensor_loc=shape_tensor_rhs(ele_shape(nu, ele), t_strain_gi, detwei)
       call addto(tensorfield, ele_nodes(nu, ele), tensor_loc)
     end if
 
     ! Filter width
     if(have_filter_width) then
-      tensorfield => extract_tensor_field(state, "DynamicFilterWidth")
+      tensorfield => extract_tensor_field(state, "FilterWidth")
       tensor_loc=shape_tensor_rhs(ele_shape(nu, ele), mesh_size_gi, detwei)
       call addto(tensorfield, ele_nodes(nu, ele), tensor_loc)
     end if
 
   end subroutine les_set_diagnostic_tensor_fields
 
-  subroutine leonard_tensor(mnu, positions, tnu, leonard, alpha, path)
+  subroutine leonard_tensor(nu, positions, tnu, leonard, alpha, path)
 
     ! Unfiltered velocity
-    type(vector_field), pointer               :: mnu
+    type(vector_field), pointer               :: nu
     type(vector_field), intent(in)            :: positions
     ! Filtered velocity
     type(vector_field), pointer               :: tnu
@@ -140,31 +140,30 @@
 
     ! Path is to level above solver options
     lpath = (trim(path)//"/dynamic_les")
-    ewrite(2,*) "path: ", trim(lpath)
-    ewrite(2,*) "alpha: ", alpha
+    ewrite(2,*) "filter factor alpha: ", alpha
 
-    ewrite_minmax(mnu)
+    ewrite_minmax(nu)
     ewrite_minmax(tnu)
 
-    call anisotropic_smooth_vector(mnu, positions, tnu, alpha, lpath)
+    call anisotropic_smooth_vector(nu, positions, tnu, alpha, lpath)
 
-    ewrite_minmax(mnu)
+    ewrite_minmax(nu)
     ewrite_minmax(tnu)
 
     ! Velocity products (ui*uj)
     allocate(ui_uj); allocate(tui_tuj)
-    call allocate(ui_uj, mnu%mesh, "NonlinearVelocityProduct")
-    call allocate(tui_tuj, mnu%mesh, "TestNonlinearVelocityProduct")
+    call allocate(ui_uj, nu%mesh, "NonlinearVelocityProduct")
+    call allocate(tui_tuj, nu%mesh, "TestNonlinearVelocityProduct")
     call zero(ui_uj); call zero(tui_tuj)
 
     ! Other local variables
-    allocate(u_loc(mnu%dim)); allocate(t_loc(mnu%dim, mnu%dim))
+    allocate(u_loc(nu%dim)); allocate(t_loc(nu%dim, nu%dim))
     u_loc=0.0; t_loc=0.0
 
     ! Get cross products of velocities
-    do i=1, node_count(mnu)
+    do i=1, node_count(nu)
       ! Mesh filter ^r
-      u_loc = node_val(mnu,i)
+      u_loc = node_val(nu,i)
       t_loc = outer_product(u_loc, u_loc)
       call set( ui_uj, i, t_loc )
       ! Test filter ^t
 
=== modified file 'assemble/Makefile.dependencies'
--- assemble/Makefile.dependencies	2011-10-19 13:24:47 +0000
+++ assemble/Makefile.dependencies	2011-11-30 17:31:28 +0000
@@ -131,11 +131,11 @@
 
 Biology.o ../include/biology.mod: Biology.F90 \
    ../include/boundary_conditions.mod ../include/fdebug.h \
-   ../include/fetools.mod ../include/fields.mod \
-   ../include/global_parameters.mod ../include/python_state.mod \
-   ../include/solvers.mod ../include/sparse_tools.mod \
-   ../include/sparsity_patterns_meshes.mod ../include/spud.mod \
-   ../include/state_module.mod
+   ../include/fefields.mod ../include/fetools.mod ../include/field_options.mod \
+   ../include/fields.mod ../include/global_parameters.mod \
+   ../include/python_state.mod ../include/solvers.mod \
+   ../include/sparse_tools.mod ../include/sparsity_patterns_meshes.mod \
+   ../include/spud.mod ../include/state_module.mod
 
 ../include/burgers_assembly.mod: Burgers_Assembly.o
 	@true
 
=== modified file 'assemble/Momentum_CG.F90'
--- assemble/Momentum_CG.F90	2011-10-19 13:53:05 +0000
+++ assemble/Momentum_CG.F90	2011-11-30 17:31:28 +0000
@@ -133,7 +133,7 @@
     
     ! LES coefficients and options
     real :: smagorinsky_coefficient
-    logical :: have_averaging, have_lilly, have_eddy_visc
+    logical :: have_lilly, have_eddy_visc, backscatter
     logical :: have_strain, have_filtered_strain, have_filter_width
 
     ! Temperature dependent viscosity coefficients:
@@ -235,9 +235,9 @@
       ! For 4th order:
       type(tensor_field):: grad_u
       ! For Germano Dynamic LES:
-      type(vector_field), pointer :: nu_av, mnu, mnu_av, tnu, tnu_av
-      type(tensor_field), pointer :: leonard, leonard_av
-      real                        :: alpha, alpha2
+      type(vector_field), pointer :: tnu
+      type(tensor_field), pointer :: leonard
+      real                        :: alpha
 
       ! for temperature dependent viscosity :
       type(scalar_field), pointer :: temperature
@@ -387,90 +387,47 @@
                  smagorinsky_coefficient)
          end if
          if(dynamic_les) then
-           ! Are we using averaged velocity to stabilise the model? NOT WORKING
-           have_averaging = have_option(trim(les_option_path)//"/dynamic_les/enable_averaging")
            ! Are we using the Lilly (1991) modification?
            have_lilly = have_option(trim(les_option_path)//"/dynamic_les/enable_lilly")
-           ! Get optional diagnostic fields
+
+           ! Whether or not to allow backscatter (negative eddy viscosity)
+           backscatter = have_option(trim(les_option_path)//"/dynamic_les/enable_backscatter")
+
+           ! Initialise optional diagnostic fields
            have_eddy_visc = have_option(trim(les_option_path)//"/dynamic_les/tensor_field::EddyViscosity")
-           have_strain = have_option(trim(les_option_path)//"/dynamic_les/tensor_field::DynamicStrainRate")
-           have_filtered_strain = have_option(trim(les_option_path)//"/dynamic_les/tensor_field::DynamicFilteredStrainRate")
-           have_filter_width = have_option(trim(les_option_path)//"/dynamic_les/tensor_field::DynamicFilterWidth")
+           have_strain = have_option(trim(les_option_path)//"/dynamic_les/tensor_field::StrainRate")
+           have_filtered_strain = have_option(trim(les_option_path)//"/dynamic_les/tensor_field::FilteredStrainRate")
+           have_filter_width = have_option(trim(les_option_path)//"/dynamic_les/tensor_field::FilterWidth")
+           call les_init_diagnostic_tensor_fields(state, have_eddy_visc, have_strain, have_filtered_strain, have_filter_width)
 
            ! Initialise necessary local fields.
            ewrite(2,*) "Initialising compulsory dynamic LES fields"
-           allocate(mnu); allocate(tnu); allocate(leonard)
-           call allocate(mnu, u%dim, u%mesh, "DynamicVelocity")
-           call allocate(tnu, u%dim, u%mesh, "DynamicFilteredVelocity")
-           call allocate(leonard, u%mesh, "DynamicLeonardTensor")
-           call zero(mnu); call zero(tnu); call zero(leonard)
-
-           ! Initialise optional diagnostic fields.
-           call les_init_diagnostic_tensor_fields(state, have_eddy_visc, have_strain, have_filtered_strain, have_filter_width)
-
-           ! Use time-averaged quantities. EXPERIMENTAL - DOES NOT WORK.
-           if(have_averaging) then
-             ewrite(2,*) "Initialising dynamic LES averaged fields"
-             ! Test-filtered velocity field
-             allocate(mnu_av); allocate(tnu_av); allocate(leonard_av)
-             call allocate(mnu_av, u%dim, u%mesh, "DynamicAverageVelocity")
-             call allocate(tnu_av, u%dim, u%mesh, "DynamicFilteredAverageVelocity")
-             call allocate(leonard_av, u%mesh, "DynamicAverageLeonardTensor")
-             call zero(mnu_av); call zero(tnu_av); call zero(leonard_av)
-
-             ! Averaged velocity field
-             ewrite(2,*) "Calculating averaged velocity"
-             !nu_av => vector_source_field(state, u)
-             !call calculate_time_averaged_vector(state, nu_av)
-           else
-             nu_av => dummyvector
-           end if
-
-           ! Are we filtering the velocity field to stabilise the model?
-           call get_option(trim(les_option_path)//"/dynamic_les/stabilisation_parameter", alpha2, default=0.0)
-           if(alpha2 > 0.0) then
-             ! Calculate mesh-filtered velocity
-             ewrite(2,*) "Calculating mesh-filtered velocity from Velocity (not NonlinearVelocity)"
-             call anisotropic_smooth_vector(u, x, mnu, alpha2, trim(les_option_path)//"/dynamic_les")
-             ! If averaging, we need to smooth the averaged velocity too!
-             if(have_averaging) then
-               call anisotropic_smooth_vector(nu_av, x, mnu_av, alpha2, trim(les_option_path)//"/dynamic_les")
-             else
-               mnu_av => dummyvector
-             end if
-           else if(alpha2==0.0) then
-             ! Point the dynamic velocity field at the Velocity field because we're not filtering it.
-             call set(mnu, u)
-             if(have_averaging) then
-               call set(mnu_av, nu_av)
-             else
-               mnu_av => dummyvector
-             end if
-           else
-             FLAbort("Incorrect value for dynamic LES stabilisation parameter.")
-           end if
-
-           ! Get (test filter)/(mesh filter) size ratio alpha
+           if(have_option(trim(les_option_path)//"/dynamic_les/vector_field::FilteredVelocity")) then
+             tnu => extract_vector_field(state, "FilteredVelocity")
+           else
+             allocate(tnu)
+             call allocate(tnu, u%dim, u%mesh, "FilteredVelocity")
+           end if
+           call zero(tnu)
+           allocate(leonard)
+           call allocate(leonard, u%mesh, "LeonardTensor")
+           call zero(leonard)
+
+           ! Get (test filter)/(mesh filter) size ratio alpha. Default value is 2.
            call get_option(trim(les_option_path)//"/dynamic_les/alpha", alpha, default=2.0)
 
            ! Calculate test-filtered velocity field and Leonard tensor field.
            ewrite(2,*) "Calculating test-filtered velocity and Leonard tensor"
-           call leonard_tensor(mnu, x, tnu, leonard, alpha, les_option_path)
-           if(have_averaging) then
-             call leonard_tensor(mnu_av, x, tnu_av, leonard_av, alpha, les_option_path)
-           else
-             tnu_av => dummyvector; leonard_av => dummytensor
-           end if
+           call leonard_tensor(nu, x, tnu, leonard, alpha, les_option_path)
 
            ewrite_minmax(leonard)
          else
-           have_averaging=.false.; have_lilly=.false.; have_eddy_visc=.false.
+           have_lilly=.false.; have_eddy_visc=.false.; backscatter=.false.
            have_strain=.false.; have_filtered_strain=.false.; have_filter_width=.false.
          end if
       else
          les_second_order=.false.; les_fourth_order=.false.; wale=.false.; dynamic_les=.false.
-         tnu => dummyvector; mnu => dummyvector; nu_av => dummyvector; tnu_av => dummyvector; mnu_av => dummyvector
-         leonard => dummytensor; leonard_av => dummytensor
+         tnu => dummyvector; leonard => dummytensor
       end if
       
 
@@ -670,7 +627,7 @@
               density, p, &
               source, absorption, buoyancy, gravity, &
               viscosity, grad_u, &
-              mnu, tnu, leonard, alpha, &
+              tnu, leonard, alpha, &
               gp, surfacetension, &
               assemble_ct_matrix_here, on_sphere, depth, &
               alpha_u_field, abs_wd, temperature, nvfrac)
@@ -835,14 +792,10 @@
       end if
 
       if (dynamic_les) then
-        call deallocate(mnu); deallocate(mnu)
-        call deallocate(tnu); deallocate(tnu)
+        if(.not. have_option(trim(les_option_path)//"/dynamic_les/vector_field::FilteredVelocity")) then
+          call deallocate(tnu); deallocate(tnu)
+        end if
         call deallocate(leonard); deallocate(leonard)
-        if (have_averaging) then
-          call deallocate(mnu_av); deallocate(mnu_av)
-          call deallocate(tnu_av); deallocate(tnu_av)
-          call deallocate(leonard_av); deallocate(leonard_av)
-        end if
       end if
 
       call deallocate(dummytensor)
@@ -1113,7 +1066,7 @@
                                             density, p, &
                                             source, absorption, buoyancy, gravity, &
                                             viscosity, grad_u, &
-                                            mnu, tnu, leonard, alpha, &
+                                            tnu, leonard, alpha, &
                                             gp, surfacetension, &
                                             assemble_ct_matrix_here, on_sphere, depth, &
                                             alpha_u_field, abs_wd, temperature, nvfrac)
@@ -1143,7 +1096,7 @@
       type(tensor_field), intent(in) :: viscosity, grad_u
 
       ! Fields for Germano Dynamic LES Model
-      type(vector_field), intent(in)    :: mnu, tnu
+      type(vector_field), intent(in)    :: tnu
       type(tensor_field), intent(in)    :: leonard
       real, intent(in)                  :: alpha
 
@@ -1341,7 +1294,7 @@
       ! Viscous terms
       if(have_viscosity .or. have_les) then
         call add_viscosity_element_cg(state, ele, test_function, u, oldu_val, nu, x, viscosity, grad_u, &
-           mnu, tnu, leonard, alpha, &
+           tnu, leonard, alpha, &
            du_t, detwei, big_m_tensor_addto, rhs_addto, temperature, nvfrac)
       end if
       
@@ -1956,7 +1909,7 @@
     end subroutine add_absorption_element_cg
       
     subroutine add_viscosity_element_cg(state, ele, test_function, u, oldu_val, nu, x, viscosity, grad_u, &
-         mnu, tnu, leonard, alpha, &
+        tnu, leonard, alpha, &
          du_t, detwei, big_m_tensor_addto, rhs_addto, temperature, nvfrac)
       type(state_type), intent(inout) :: state
       integer, intent(in) :: ele
@@ -1968,7 +1921,7 @@
       type(tensor_field), intent(in) :: grad_u
 
       ! Fields for Germano Dynamic LES Model
-      type(vector_field), intent(in)    :: mnu, tnu
+      type(vector_field), intent(in)    :: tnu
       type(tensor_field), intent(in)    :: leonard
       real, intent(in)                  :: alpha
 
@@ -1977,8 +1930,8 @@
       real, dimension(x%dim, x%dim, ele_ngi(u,ele))  :: strain_gi, t_strain_gi
       real, dimension(x%dim, x%dim, ele_ngi(u,ele))  :: mesh_size_gi, leonard_gi
       real, dimension(ele_ngi(u, ele))               :: strain_mod, t_strain_mod
-      type(element_type)                             :: shape_mnu
-      integer, dimension(:), pointer                 :: nodes_mnu
+      type(element_type)                             :: shape_nu
+      integer, dimension(:), pointer                 :: nodes_nu
 
       ! Temperature dependent viscosity:
       type(scalar_field), intent(in) :: temperature
@@ -2064,21 +2017,20 @@
             end do
          ! Germano dynamic model
          else if (dynamic_les) then
-            shape_mnu = ele_shape(mnu, ele)
-            nodes_mnu => ele_nodes(mnu, ele)
+            shape_nu = ele_shape(nu, ele)
+            nodes_nu => ele_nodes(nu, ele)
             les_tensor_gi=0.0
 
             ! Get strain S1 for unfiltered velocity (dim,dim,ngi)
-            strain_gi = les_strain_rate(du_t, ele_val(mnu, ele))
+            strain_gi = les_strain_rate(du_t, ele_val(nu, ele))
             ! Get strain S2 for test-filtered velocity (dim,dim,ngi)
             t_strain_gi = les_strain_rate(du_t, ele_val(tnu, ele))
-
             ! Filter width G1 associated with mesh size (units length^2)
-            mesh_size_gi = length_scale_tensor(du_t, shape_mnu)
+            mesh_size_gi = length_scale_tensor(du_t, ele_shape(u, ele))
             ! Leonard tensor L at gi
             leonard_gi =ele_val_at_quad(leonard, ele)
 
-            do gi=1, ele_ngi(mnu, ele)
+            do gi=1, ele_ngi(nu, ele)
               ! Get strain modulus |S1| for unfiltered velocity (ngi)
               strain_mod(gi) = sqrt( 2*sum(strain_gi(:,:,gi)*strain_gi(:,:,gi) ) )
               ! Get strain modulus |S2| for test-filtered velocity (ngi)
@@ -2092,42 +2044,52 @@
             else
               ! Choose original Germano model or Lilly's (1991) modification from options
               if(.not. have_lilly) then
-                do gi=1, ele_ngi(mnu, ele)
-                  ! L.S1
-                  numerator = sum( leonard_gi(:,:,gi)*strain_gi(:,:,gi) )
+                do gi=1, ele_ngi(nu, ele)
+                  ! |S1|*L.S1
+                  numerator = sum( leonard_gi(:,:,gi)*strain_gi(:,:,gi) )*strain_mod(gi)
+
                   ! alpha^2*|S2|*S2.S1
-                  ! This term is WRONG until I find a way of filtering the strain rate product.
-                  denominator = -2*alpha**2*t_strain_mod(gi)*sum(t_strain_gi(:,:,gi)*strain_gi(:,:,gi))
-                  ! Dynamic eddy viscosity m_ij
-                  ! N.B. If averaging, beware of operator not applying to every term.
-                  les_tensor_gi(:,:,gi) = numerator/denominator*strain_mod(gi)
-
-                  ! Artificial but it works!
+                  ! This term is WRONG until I find a way of filtering the strain rate product. The difference may be quite small though.
+                  denominator = -alpha**2*t_strain_mod(gi)*sum(t_strain_gi(:,:,gi)*strain_gi(:,:,gi))
+
+                  ! Dynamic eddy viscosity m_ij = C*S1
+                  les_tensor_gi(:,:,gi) = numerator/denominator
+
+                  ! Whether or not to allow negative eddy viscosity (backscattering)
+                  ! but do not allow (viscosity+eddy_viscosity) < 0.
                   if(any(les_tensor_gi(:,:,gi) < 0.0)) then
-                    les_tensor_gi(:,:,gi) = max(les_tensor_gi(:,:,gi),0.0)
+                    if(backscatter) then
+                      les_tensor_gi(:,:,gi) = max(les_tensor_gi(:,:,gi), epsilon(0.0) - viscosity_gi(:,:,gi))
+                    else
+                      les_tensor_gi(:,:,gi) = max(les_tensor_gi(:,:,gi),0.0)
+                    end if
                   end if
                 end do
               else if(have_lilly) then
-                do gi=1, ele_ngi(mnu, ele)
+                do gi=1, ele_ngi(nu, ele)
                   ! |S1|*L.S1
-                  numerator = t_strain_mod(gi)*sum(leonard_gi(:,:,gi)*t_strain_gi(:,:,gi))
+                  numerator = sum(leonard_gi(:,:,gi)*t_strain_gi(:,:,gi))*strain_mod(gi)
                   ! alpha^2*|S2|^2*S2.S2
-                  ! This term is WRONG until I find a way of filtering the strain rate product.
-                  denominator = -2*alpha**2*(t_strain_mod(gi))**2*sum(t_strain_gi(:,:,gi)*t_strain_gi(:,:,gi))
+                  ! This term is WRONG until I find a way of filtering the strain rate product. The difference may be quite small though.
+                  denominator = -alpha**2*(t_strain_mod(gi))**2*sum(t_strain_gi(:,:,gi)*t_strain_gi(:,:,gi))
                   ! Dynamic eddy viscosity m_ij
-                  ! N.B. If averaging, beware of operator not applying to every term.
-                  les_tensor_gi(:,:,gi) = numerator/denominator*strain_mod(gi)
+                  les_tensor_gi(:,:,gi) = numerator/denominator
 
-                  ! Artificial but it works!
+                  ! Whether or not to allow negative eddy viscosity (backscattering)
+                  ! but do not allow (viscosity+eddy_viscosity) < 0.
                   if(any(les_tensor_gi(:,:,gi) < 0.0)) then
-                    les_tensor_gi(:,:,gi) = max(les_tensor_gi(:,:,gi),0.0)
+                    if(backscatter) then
+                      les_tensor_gi(:,:,gi) = max(les_tensor_gi(:,:,gi), epsilon(0.0) - viscosity_gi(:,:,gi))
+                    else
+                      les_tensor_gi(:,:,gi) = max(les_tensor_gi(:,:,gi),0.0)
+                    end if
                   end if
                 end do
               end if
             end if
 
             ! Set diagnostic fields
-            call les_set_diagnostic_tensor_fields(state, mnu, ele, detwei, &
+            call les_set_diagnostic_tensor_fields(state, nu, ele, detwei, &
                  mesh_size_gi, strain_gi, t_strain_gi, les_tensor_gi, &
                  have_eddy_visc, have_strain, have_filtered_strain, have_filter_width)
 
 
=== modified file 'assemble/Momentum_Equation.F90'
--- assemble/Momentum_Equation.F90	2011-10-19 17:35:23 +0000
+++ assemble/Momentum_Equation.F90	2011-11-30 17:31:28 +0000
@@ -98,6 +98,8 @@
       logical, dimension(:), allocatable :: lump_mass
       ! are we using a cv pressure 
       logical :: cv_pressure 
+      ! for a CG pressure are we testing the continuity with cv
+      logical :: cg_pressure_cv_test_continuity
 
       ! Do we need to reassemble the C^T or CMC matrices?
       logical :: reassemble_all_ct_m, reassemble_all_cmc_m
@@ -179,7 +181,10 @@
          ! Scaled pressure mass matrix - used for preconditioning full projection solve:
          type(csr_matrix), target :: scaled_pressure_mass_matrix
          type(csr_sparsity), pointer :: scaled_pressure_mass_matrix_sparsity
-         ! Compressible pressure gradient operator/left hand matrix of CMC
+         ! Left hand matrix of CMC. For incompressibe flow this points to ct_m as they are identical, 
+         ! unless for CG pressure with CV tested continuity case when this matrix will be the 
+         ! CV divergence tested matrix and ct_m the CG divergence tested matrix (right hand matrix of CMC).
+         ! For compressible flow this differs to ct_m in that it will contain the variable density.
          type(block_csr_matrix_pointer), dimension(:), allocatable :: ctp_m
          ! The lumped mass matrix (may vary per component as absorption could be included)
          type(vector_field), dimension(1:size(state)) :: inverse_masslump, visc_inverse_masslump
@@ -377,6 +382,14 @@
                ! Get the pressure gradient matrix (i.e. the divergence matrix)
                ct_m(istate)%ptr => get_velocity_divergence_matrix(state(istate), get_ct=reassemble_ct_m) ! Sets reassemble_ct_m to true if it does not already exist in state(i) 
                reassemble_ct_m = reassemble_ct_m .or. reassemble_all_ct_m
+               
+               ! For the CG pressure with CV tested continuity case 
+               ! get the CV tested pressure gradient matrix (i.e. the divergence matrix)
+               ! if required with a different unique name. Note there is no need
+               ! to again decide reassemble_ct_m as ctp_m for this case is assembled when ct_m is.
+               if ((.not. use_compressible_projection) .and. cg_pressure_cv_test_continuity) then
+                  ctp_m(istate)%ptr => get_velocity_divergence_matrix(state(istate), ct_m_name = "CVTestedVelocityDivergenceMatrix")
+               end if
 
                ! Get the pressure poisson matrix (i.e. the CMC/projection matrix)
                cmc_m => get_pressure_poisson_matrix(state(istate), get_cmc=reassemble_cmc_m) ! ...and similarly for reassemble_cmc_m
@@ -514,10 +527,13 @@
                                        diagonal=diagonal_big_m, name="BIG_m")
             end if
 
-            ! Initialise the big_m and ct_m matrices
+            ! Initialise the big_m, ct_m and ctp_m matrices
             call zero(big_m(istate))
             if(reassemble_ct_m) then
-               call zero(ct_m(istate)%ptr)
+               call zero(ct_m(istate)%ptr)               
+               if ((.not. use_compressible_projection) .and. cg_pressure_cv_test_continuity) then
+                  call zero(ctp_m(istate)%ptr)
+               end if
             end if
 
             ! Allocate the momentum RHS
@@ -563,6 +579,8 @@
                   call subtract_geostrophic_pressure_gradient(mom_rhs(istate), state(istate))
                end if
             else
+               ! This call will form the ct_rhs, which for use_compressible_projection
+               ! or cg_pressure_cv_test_continuity is formed for a second time later below.
                call construct_momentum_cg(u, p, density, x, &
                      big_m(istate), mom_rhs(istate), ct_m(istate)%ptr, &
                      ct_rhs(istate), mass(istate), inverse_masslump(istate), visc_inverse_masslump(istate), &
@@ -607,22 +625,20 @@
                call wall_functions(big_m(istate), mom_rhs(istate), state(istate))
             end if
 
-            ! Add mass source-absorption for implicit solids
-            if (have_option("/implicit_solids/two_way_coupling")) then
-               call add_mass_source_absorption(ct_rhs(istate), state(istate))
-            end if
-
             call profiler_toc(u, "assembly")
 
             call profiler_tic(p, "assembly")
             if(cv_pressure) then
+               ! This call will form the ct_rhs, which for use_compressible_projection
+               ! is formed for a second time later below.
                call assemble_divergence_matrix_cv(ct_m(istate)%ptr, state(istate), ct_rhs=ct_rhs(istate), &
                                              test_mesh=p%mesh, field=u, get_ct=reassemble_ct_m)
             end if
 
-            !! Assemble divergence matrix C^T
-            ! At the moment cg does its own ct assembly. We might change this in
-            ! the future.
+            ! Assemble divergence matrix C^T.
+            ! At the moment cg does its own ct assembly. We might change this in the future.
+            ! This call will form the ct_rhs, which for use_compressible_projection
+            ! or cg_pressure_cv_test_continuity is formed for a second time later below.
             if(dg(istate) .and. .not. cv_pressure) then
                call assemble_divergence_matrix_cg(ct_m(istate)%ptr, state(istate), ct_rhs=ct_rhs(istate), &
                  test_mesh=p%mesh, field=u, get_ct=reassemble_ct_m)
@@ -658,15 +674,35 @@
             call profiler_tic(p, "assembly")
             
             if (prognostic_p .and. .not.reduced_model) then
-
+               
+               ! Set up the left C matrix in CMC
+               
                if(use_compressible_projection) then
                   allocate(ctp_m(istate)%ptr)
                   call allocate(ctp_m(istate)%ptr, ct_m(istate)%ptr%sparsity, (/1, u%dim/), name="CTP_m")
+                  ! NOTE that this is not optimal in that the ct_rhs
+                  ! was formed already above. The call here will overwrite those values.
                   if(cv_pressure) then
                      call assemble_compressible_divergence_matrix_cv(ctp_m(istate)%ptr, state, ct_rhs(istate))
                   else
                      call assemble_compressible_divergence_matrix_cg(ctp_m(istate)%ptr, state, ct_rhs(istate))
+                  end if               
+               else                  
+                  ! Incompressible scenario
+                  if (cg_pressure_cv_test_continuity) then
+                     ! Form the CV tested divergence matrix and ct_rhs.
+                     ! This will only reassemble ctp_m when ct_m 
+                     ! also requires reassemble. NOTE that this is not optimal in that the ct_rhs
+                     ! was formed already above. The call here will overwrite those values.
+                     call assemble_divergence_matrix_cv(ctp_m(istate)%ptr, state(istate), ct_rhs=ct_rhs(istate), &
+                                                        test_mesh=p%mesh, field=u, get_ct=reassemble_ct_m)
+                  else                  
+                     ! ctp_m is identical to ct_m
+                     ctp_m(istate)%ptr => ct_m(istate)%ptr
                   end if
+               end if
+               
+               if (use_compressible_projection .or. cg_pressure_cv_test_continuity) then
                   if (have_rotated_bcs(u)) then
                      if (dg(istate)) then
                        call zero_non_owned(u)
@@ -679,9 +715,18 @@
                      end if
                      call rotate_ct_m_sphere(state(istate), ctp_m(istate)%ptr, u)
                   end if
-               else
-                  ctp_m(istate)%ptr => ct_m(istate)%ptr  ! Incompressible scenario
-               end if
+               end if
+
+               ! Add mass source-absorption for implicit solids.
+               ! This needs to be done after ct_rhs has been formed
+               ! in the divergence routines as they zero the field.
+               ! This routine assumes the continuity is tested with 
+               ! FE basis functions, so is not correct for cv_pressure
+               ! or cg_pressure_cv_test_continuity.
+               if (have_option("/implicit_solids/two_way_coupling")) then
+                  call add_mass_source_absorption(ct_rhs(istate), state(istate))
+               end if
+
                ewrite_minmax(ctp_m(istate)%ptr)
                ewrite_minmax(ct_rhs(istate))
 
@@ -1242,6 +1287,11 @@
          cv_pressure = have_option(trim(p%option_path)//&
                            "/prognostic/spatial_discretisation/control_volumes")
 
+         ! For CG pressure are we testing the continuity with the CV dual 
+         cg_pressure_cv_test_continuity = have_option(trim(p%option_path)//&
+                   &"/prognostic/spatial_discretisation/continuous_galerkin&
+                   &/test_continuity_with_cv_dual")
+
       end subroutine get_pressure_options
 
 
@@ -1750,9 +1800,11 @@
 
       subroutine momentum_equation_check_options
 
-         integer :: i, nmat
+         integer :: i, nmat, bc, nbc
          character(len=FIELD_NAME_LEN) :: schur_scheme
          character(len=FIELD_NAME_LEN) :: schur_preconditioner
+         character(len=FIELD_NAME_LEN) :: pressure_mesh
+         character(len=FIELD_NAME_LEN) :: pressure_mesh_element_type
 
          ewrite(1,*) 'Checking momentum discretisation options'
 
@@ -2004,6 +2056,91 @@
                   FLExit("Lump the mass matrix (of the velocity) if you want to make use of the low Reynolds number fix")
                end if
             end if
+
+            ! Check options for case with CG pressure and
+            ! testing continuity with CV dual mesh. 
+            ! Will not work with compressible, free surface or 
+            ! wetting and drying and implicit solids two way coupling. 
+            ! Also will not work if the pressure is on a mesh that has 
+            ! bubble or trace shape functions.
+            if (have_option("/material_phase["//int2str(i)//&
+                                 &"]/scalar_field::Pressure/prognostic&
+                                 &/spatial_discretisation/continuous_galerkin&
+                                 &/test_continuity_with_cv_dual")) then
+               
+               ! Check that the incompressible projection is being used
+               if(.not.have_option("/material_phase["//int2str(i)//&
+                                 &"]/scalar_field::Pressure/prognostic&
+                                 &/scheme/use_projection_method")) then
+
+                  ewrite(-1,*) "Error: For a CG Pressure the continuity"
+                  ewrite(-1,*) "can only be tested with the cv dual mesh"
+                  ewrite(-1,*) "if the pressure scheme is the incompressible"
+                  ewrite(-1,*) "projection method, which is given by the option"
+                  ewrite(-1,*) "path material_phase/Pressure/spatial_discretisation/"
+                  ewrite(-1,*) "continuous_galerkin/scheme/use_projection_method"
+                  FLExit("Use incompressible projection method if wanting to test continuity with cv dual with CG pressure")                  
+               end if
+               
+               ! Check that there are no free_surface boundary conditions for Velocity
+               nbc = option_count("/material_phase["//int2str(i)//"]/vector_field::Velocity&
+                                  &/prognostic/boundary_conditions")
+               
+               bc_loop: do bc = 0, nbc - 1               
+
+                  if(have_option("/material_phase["//int2str(i)//"]/vector_field::Velocity/prognostic&
+                                 &/boundary_conditions["//int2str(bc)//"]/type::free_surface")) then
+                     ewrite(-1,*) "Cannot have free_surface BC for Velocity of phase ",i+1
+                     ewrite(-1,*) "when using a CG pressure with a CV tested continuity equation"
+                     FLExit("For CG Pressure cannot test the continuity equation with CV when Velocity has a free_surface BC")
+                  end if               
+
+               end do bc_loop
+               
+               ! Check that the wetting_and_drying model is not being used
+               if(have_option("/mesh_adaptivity/mesh_movement/free_surface/wetting_and_drying")) then
+                  FLExit("For CG Pressure cannot test the continuity equation with CV when using the wetting and drying model")
+               end if
+               
+               ! Check that implicit solids two way coupling is not being used
+               if (have_option("/implicit_solids/two_way_coupling")) then
+                  FLExit("For CG Pressure cannot test the continuity equation with CV when using implicit solids two way coupling model")
+               end if
+               
+               ! get the pressure mesh name
+               call get_option("/material_phase["//int2str(i)//"]/scalar_field::Pressure/prognostic/mesh/name", &
+                                pressure_mesh)
+               
+               ! check that the pressure mesh options 
+               ! do NOT say bubble or trace
+               call get_option("/geometry/mesh::"//trim(pressure_mesh)//"/from_mesh/mesh_shape/element_type", &
+                                pressure_mesh_element_type, &
+                                default = "lagranian")
+               
+               if (trim(pressure_mesh_element_type) == "bubble") then
+                  FLExit("For CG Pressure cannot test the continuity equation with CV if the pressure mesh has element type bubble")
+               end if
+               
+               if (trim(pressure_mesh_element_type) == "trace") then
+                  FLExit("For CG Pressure cannot test the continuity equation with CV if the pressure mesh has element type trace")
+               end if
+               
+            end if
+            
+            ! Check that is using implicit solids two way coupling that 
+            ! the pressure is NOT CV. CV pressure implies CV tested continuity
+            ! which is not possible yet for the two way coupling terms.
+            ! Note the check of CG pressure with CV tested continuity 
+            ! and implicit solids two way coupling has been done above.
+            if (have_option("/implicit_solids/two_way_coupling")) then
+               
+               if (have_option("/material_phase["//int2str(i)//&
+                                 &"]/scalar_field::Pressure/prognostic&
+                                 &/spatial_discretisation/control_volumes")) then
+                  FLExit("Cannot use implicit solids two way coupling if the pressure is control volume discretised")
+               end if
+               
+            end if
             
          end do
 
 
=== modified file 'assemble/State_Matrices.F90'
--- assemble/State_Matrices.F90	2011-07-18 16:53:16 +0000
+++ assemble/State_Matrices.F90	2011-11-30 17:31:28 +0000
@@ -248,17 +248,19 @@
   
   end function get_pressure_stabilisation_matrix_multiple_states
   
-  function get_velocity_divergence_matrix_single_state(state, get_ct) result(ct_m)
+  function get_velocity_divergence_matrix_single_state(state, get_ct, ct_m_name) result(ct_m)
     !!< extracts the ct matrix from state, 
     !!< if it fails to find it it returns get_ct=.true. to indicate that it needs assembling
+    !!< if ct_m_name is present then that name is used else a default is used.
     type(block_csr_matrix), pointer :: ct_m
     type(state_type), intent(inout) :: state
     logical, intent(inout), optional :: get_ct
-  
+    character(len=*), intent(in), optional :: ct_m_name
+
     type(state_type), dimension(1) :: states
     
     states = (/state/)
-    ct_m => get_velocity_divergence_matrix(states, get_ct=get_ct)
+    ct_m => get_velocity_divergence_matrix(states, get_ct=get_ct, ct_m_name = ct_m_name)
     state = states(1)
 
     ! In multi-phase simulations, C^T depends on the phase volume fraction,
@@ -269,24 +271,33 @@
 
   end function get_velocity_divergence_matrix_single_state
 
-  function get_velocity_divergence_matrix_multiple_states(states, get_ct) result(ct_m)
+  function get_velocity_divergence_matrix_multiple_states(states, get_ct, ct_m_name) result(ct_m)
     !!< extracts the ct matrix from states, 
     !!< if it fails to find it it returns get_ct=.true. to indicate that it needs assembling
+    !!< if ct_m_name is present then that name is used else a default is used.
     type(block_csr_matrix), pointer :: ct_m
     type(state_type), dimension(:), intent(inout) :: states
     logical, intent(inout), optional :: get_ct
-    
+    character(len=*), intent(in), optional :: ct_m_name
+
     integer :: stat, i
     type(mesh_type), pointer :: p_mesh, u_mesh
     type(vector_field), pointer :: velocity
     type(csr_sparsity), pointer :: ct_sparsity
     type(block_csr_matrix) :: temp_ct_m
-    
+    character(len=FIELD_NAME_LEN) :: l_ct_m_name
+
     integer, save :: last_mesh_movement = -1
     
+    ! Form the ct_m_name dependent on interface argument
+    if (present(ct_m_name)) then
+       l_ct_m_name = trim(ct_m_name)
+    else
+       l_ct_m_name = "VelocityDivergenceMatrix"
+    end if
     
     if(present(get_ct)) get_ct = .false.
-    ct_m => extract_block_csr_matrix(states, "VelocityDivergenceMatrix", stat)
+    ct_m => extract_block_csr_matrix(states, trim(l_ct_m_name), stat)
     
     if(stat/=0) then
       if(present(get_ct)) get_ct = .true.
@@ -300,11 +311,11 @@
       
       ct_sparsity => get_csr_sparsity_firstorder(states, p_mesh, u_mesh)
       
-      call allocate(temp_ct_m, ct_sparsity, blocks=(/1,velocity%dim/), name="VelocityDivergenceMatrix")
-      call insert(states, temp_ct_m, name="VelocityDivergenceMatrix")
+      call allocate(temp_ct_m, ct_sparsity, blocks=(/1,velocity%dim/), name=trim(l_ct_m_name))
+      call insert(states, temp_ct_m, name=trim(l_ct_m_name))
       call deallocate(temp_ct_m)
       
-      ct_m => extract_block_csr_matrix(states, "VelocityDivergenceMatrix")
+      ct_m => extract_block_csr_matrix(states, trim(l_ct_m_name))
     else
       ! just check if we need to reassemble the matrix anyway
       if(present(get_ct)) get_ct = (eventcount(EVENT_MESH_MOVEMENT)/=last_mesh_movement)
 
=== modified file 'assemble/Zoltan_callbacks.F90'
--- assemble/Zoltan_callbacks.F90	2011-09-26 17:04:31 +0000
+++ assemble/Zoltan_callbacks.F90	2011-11-30 17:31:28 +0000
@@ -173,7 +173,7 @@
     real :: quality, min_quality, my_min_quality
     
     ! variables for recording the local maximum/minimum edge weights and local 90th percentile edge weight
-    real(zoltan_float) :: min_weight, max_weight, ninety_weight, my_max_weight
+    real(zoltan_float) :: min_weight, max_weight, ninety_weight, my_max_weight, my_min_weight
     
     integer, dimension(:), pointer :: my_nelist, nbor_nelist
     
@@ -295,7 +295,6 @@
           end if
        end do
        
-       value = maxval(ewgts(head:head+size(neighbours)-1))
        head = head + size(neighbours)
     end do
     
@@ -307,8 +306,14 @@
     my_max_weight = maxval(ewgts(1:head-1))
     
     ! calculate the local minimum edge weight
-    min_weight = minval(ewgts(1:head-1))
-    call MPI_ALLREDUCE(my_max_weight,max_weight,1,MPI_INTEGER,MPI_MAX, MPI_COMM_FEMTOOLS,err)
+    my_min_weight = minval(ewgts(1:head-1))
+
+    ! calculate global maximum edge weight
+    call MPI_ALLREDUCE(my_max_weight,max_weight,1,MPI_REAL,MPI_MAX, MPI_COMM_FEMTOOLS,err)
+
+    ! calculate global minimum edge weight
+    call MPI_ALLREDUCE(my_min_weight,min_weight,1,MPI_REAL,MPI_MIN, MPI_COMM_FEMTOOLS,err)
+
     ! calculate the local 90th percentile edge weight   
     ninety_weight = max_weight * 0.90
     
 
=== modified file 'configure'
--- configure	2011-10-21 10:05:25 +0000
+++ configure	2011-11-30 17:31:28 +0000
@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68 for fluidity trunk.3665.
+# Generated by GNU Autoconf 2.67 for fluidity None.
 #
 #
 # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
@@ -89,7 +89,6 @@
 IFS=" ""	$as_nl"
 
 # Find who we are.  Look in the path if we contain no directory separator.
-as_myself=
 case $0 in #((
   *[\\/]* ) as_myself=$0 ;;
   *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
@@ -215,18 +214,11 @@
   # We cannot yet assume a decent shell, so we have to provide a
 	# neutralization value for shells without unset; and this also
 	# works around shells that cannot unset nonexistent variables.
-	# Preserve -v and -x to the replacement shell.
 	BASH_ENV=/dev/null
 	ENV=/dev/null
 	(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
 	export CONFIG_SHELL
-	case $- in # ((((
-	  *v*x* | *x*v* ) as_opts=-vx ;;
-	  *v* ) as_opts=-v ;;
-	  *x* ) as_opts=-x ;;
-	  * ) as_opts= ;;
-	esac
-	exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
+	exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
 fi
 
     if test x$as_have_required = xno; then :
@@ -557,8 +549,8 @@
 # Identity of this package.
 PACKAGE_NAME='fluidity'
 PACKAGE_TARNAME='fluidity'
-PACKAGE_VERSION='trunk.3665'
-PACKAGE_STRING='fluidity trunk.3665'
+PACKAGE_VERSION='None'
+PACKAGE_STRING='fluidity None'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -615,6 +607,7 @@
 BUILD_LIBADAPT
 DEFINE_MPI
 USE_CPP
+FLLINKER
 LINKER
 OPTIMIZATION_FFLAGS
 FORTRAN_REAL_8
@@ -686,6 +679,7 @@
 build_vendor
 build_cpu
 build
+FLUIDITY_VERSION
 target_alias
 host_alias
 build_alias
@@ -1185,7 +1179,7 @@
     $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2
     expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
       $as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2
-    : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}"
+    : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}
     ;;
 
   esac
@@ -1323,7 +1317,7 @@
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures fluidity trunk.3665 to adapt to many kinds of systems.
+\`configure' configures fluidity None to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1392,7 +1386,7 @@
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of fluidity trunk.3665:";;
+     short | recursive ) echo "Configuration of fluidity None:";;
    esac
   cat <<\_ACEOF
 
@@ -1540,8 +1534,8 @@
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-fluidity configure trunk.3665
-generated by GNU Autoconf 2.68
+fluidity configure None
+generated by GNU Autoconf 2.67
 
 Copyright (C) 2010 Free Software Foundation, Inc.
 This configure script is free software; the Free Software Foundation
@@ -1587,7 +1581,7 @@
 
 	ac_retval=1
 fi
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_f77_try_compile
@@ -1625,7 +1619,7 @@
 
 	ac_retval=1
 fi
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_fc_try_compile
@@ -1663,7 +1657,7 @@
 
 	ac_retval=1
 fi
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_c_try_compile
@@ -1701,7 +1695,7 @@
 
 	ac_retval=1
 fi
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_cxx_try_compile
@@ -1738,7 +1732,7 @@
 
     ac_retval=1
 fi
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_c_try_cpp
@@ -1780,7 +1774,7 @@
        ac_retval=$ac_status
 fi
   rm -rf conftest.dSYM conftest_ipa8_conftest.oo
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_c_try_run
@@ -1958,7 +1952,7 @@
 rm -f conftest.val
 
   fi
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_c_compute_int
@@ -1972,7 +1966,7 @@
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if eval \${$3+:} false; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -1990,7 +1984,7 @@
 eval ac_res=\$$3
 	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
 $as_echo "$ac_res" >&6; }
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
 
 } # ac_fn_c_check_header_compile
 
@@ -2035,7 +2029,7 @@
   # interfere with the next link command; also delete a directory that is
   # left behind by Apple's compiler.  We do this before executing the actions.
   rm -rf conftest.dSYM conftest_ipa8_conftest.oo
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_c_try_link
@@ -2081,7 +2075,7 @@
   # interfere with the next link command; also delete a directory that is
   # left behind by Apple's compiler.  We do this before executing the actions.
   rm -rf conftest.dSYM conftest_ipa8_conftest.oo
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_cxx_try_link
@@ -2127,7 +2121,7 @@
   # interfere with the next link command; also delete a directory that is
   # left behind by Apple's compiler.  We do this before executing the actions.
   rm -rf conftest.dSYM conftest_ipa8_conftest.oo
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_f77_try_link
@@ -2140,7 +2134,7 @@
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if eval \${$3+:} false; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -2211,7 +2205,7 @@
 eval ac_res=\$$3
 	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
 $as_echo "$ac_res" >&6; }
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
 
 } # ac_fn_c_check_func
 
@@ -2256,7 +2250,7 @@
   # interfere with the next link command; also delete a directory that is
   # left behind by Apple's compiler.  We do this before executing the actions.
   rm -rf conftest.dSYM conftest_ipa8_conftest.oo
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_fc_try_link
@@ -2298,7 +2292,7 @@
        ac_retval=$ac_status
 fi
   rm -rf conftest.dSYM conftest_ipa8_conftest.oo
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_fc_try_run
@@ -2335,7 +2329,7 @@
 
     ac_retval=1
 fi
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
   as_fn_set_status $ac_retval
 
 } # ac_fn_cxx_try_cpp
@@ -2348,10 +2342,10 @@
 ac_fn_cxx_check_header_mongrel ()
 {
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  if eval \${$3+:} false; then :
+  if eval "test \"\${$3+set}\"" = set; then :
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if eval \${$3+:} false; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 fi
 eval ac_res=\$$3
@@ -2414,7 +2408,7 @@
 esac
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if eval \${$3+:} false; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   eval "$3=\$ac_header_compiler"
@@ -2423,15 +2417,15 @@
 	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
 $as_echo "$ac_res" >&6; }
 fi
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
 
 } # ac_fn_cxx_check_header_mongrel
 cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by fluidity $as_me trunk.3665, which was
-generated by GNU Autoconf 2.68.  Invocation command line was
+It was created by fluidity $as_me None, which was
+generated by GNU Autoconf 2.67.  Invocation command line was
 
   $ $0 $@
 
@@ -2689,7 +2683,7 @@
       || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "failed to load site script $ac_site_file
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
   fi
 done
 
@@ -2782,6 +2776,10 @@
 ac_config_headers="$ac_config_headers include/config.h"
 
 
+# we ignore PACKAGE_VERSION as it is useless
+# instead we pass on FLUIDITY_VERSION from the env. if it is set
+
+
 echo "Hostname: `hostname`"
 
 # Store enviroment variables
@@ -2876,7 +2874,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
 $as_echo_n "checking build system type... " >&6; }
-if ${ac_cv_build+:} false; then :
+if test "${ac_cv_build+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_build_alias=$build_alias
@@ -2892,7 +2890,7 @@
 $as_echo "$ac_cv_build" >&6; }
 case $ac_cv_build in
 *-*-*) ;;
-*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5;;
+*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;;
 esac
 build=$ac_cv_build
 ac_save_IFS=$IFS; IFS='-'
@@ -2910,7 +2908,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5
 $as_echo_n "checking host system type... " >&6; }
-if ${ac_cv_host+:} false; then :
+if test "${ac_cv_host+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test "x$host_alias" = x; then
@@ -2925,7 +2923,7 @@
 $as_echo "$ac_cv_host" >&6; }
 case $ac_cv_host in
 *-*-*) ;;
-*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5;;
+*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;;
 esac
 host=$ac_cv_host
 ac_save_IFS=$IFS; IFS='-'
@@ -2956,7 +2954,7 @@
 set dummy $ac_tool_prefix$ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_F77+:} false; then :
+if test "${ac_cv_prog_F77+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$F77"; then
@@ -3000,7 +2998,7 @@
 set dummy $ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_ac_ct_F77+:} false; then :
+if test "${ac_cv_prog_ac_ct_F77+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$ac_ct_F77"; then
@@ -3158,7 +3156,7 @@
 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error 77 "Fortran 77 compiler cannot create executables
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 else
   { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
 $as_echo "yes" >&6; }
@@ -3201,7 +3199,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "cannot compute suffix of executables: cannot compile and link
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 rm -f conftest conftest$ac_cv_exeext
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
@@ -3254,7 +3252,7 @@
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "cannot run Fortran 77 compiled programs.
 If you meant to cross compile, use \`--host'.
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
     fi
   fi
 fi
@@ -3265,7 +3263,7 @@
 ac_clean_files=$ac_clean_files_save
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
 $as_echo_n "checking for suffix of object files... " >&6; }
-if ${ac_cv_objext+:} false; then :
+if test "${ac_cv_objext+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat > conftest.$ac_ext <<_ACEOF
@@ -3300,7 +3298,7 @@
 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "cannot compute suffix of object files: cannot compile
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 rm -f conftest.$ac_cv_objext conftest.$ac_ext
 fi
@@ -3314,7 +3312,7 @@
 ac_ext=F
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU Fortran 77 compiler" >&5
 $as_echo_n "checking whether we are using the GNU Fortran 77 compiler... " >&6; }
-if ${ac_cv_f77_compiler_gnu+:} false; then :
+if test "${ac_cv_f77_compiler_gnu+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat > conftest.$ac_ext <<_ACEOF
@@ -3342,7 +3340,7 @@
 FFLAGS=
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $F77 accepts -g" >&5
 $as_echo_n "checking whether $F77 accepts -g... " >&6; }
-if ${ac_cv_prog_f77_g+:} false; then :
+if test "${ac_cv_prog_f77_g+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   FFLAGS=-g
@@ -3395,7 +3393,7 @@
 ac_compiler_gnu=$ac_cv_f77_compiler_gnu
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to get verbose linking output from $F77" >&5
 $as_echo_n "checking how to get verbose linking output from $F77... " >&6; }
-if ${ac_cv_prog_f77_v+:} false; then :
+if test "${ac_cv_prog_f77_v+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat > conftest.$ac_ext <<_ACEOF
@@ -3425,8 +3423,7 @@
 # gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH,
 # LIBRARY_PATH; skip all such settings.
 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 |
-  sed '/^Driving:/d; /^Configured with:/d;
-      '"/^[_$as_cr_Letters][_$as_cr_alnum]*=/d"`
+  grep -v 'Driving:' | grep -v "^[_$as_cr_Letters][_$as_cr_alnum]*="`
 $as_echo "$ac_f77_v_output" >&5
 FFLAGS=$ac_save_FFLAGS
 
@@ -3491,7 +3488,7 @@
 $as_echo "$ac_cv_prog_f77_v" >&6; }
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Fortran 77 libraries of $F77" >&5
 $as_echo_n "checking for Fortran 77 libraries of $F77... " >&6; }
-if ${ac_cv_f77_libs+:} false; then :
+if test "${ac_cv_f77_libs+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test "x$FLIBS" != "x"; then
@@ -3516,8 +3513,7 @@
 # gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH,
 # LIBRARY_PATH; skip all such settings.
 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 |
-  sed '/^Driving:/d; /^Configured with:/d;
-      '"/^[_$as_cr_Letters][_$as_cr_alnum]*=/d"`
+  grep -v 'Driving:' | grep -v "^[_$as_cr_Letters][_$as_cr_alnum]*="`
 $as_echo "$ac_f77_v_output" >&5
 FFLAGS=$ac_save_FFLAGS
 
@@ -3713,7 +3709,7 @@
 set dummy $ac_tool_prefix$ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_FC+:} false; then :
+if test "${ac_cv_prog_FC+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$FC"; then
@@ -3757,7 +3753,7 @@
 set dummy $ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_ac_ct_FC+:} false; then :
+if test "${ac_cv_prog_ac_ct_FC+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$ac_ct_FC"; then
@@ -3839,7 +3835,7 @@
 ac_ext=F
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU Fortran compiler" >&5
 $as_echo_n "checking whether we are using the GNU Fortran compiler... " >&6; }
-if ${ac_cv_fc_compiler_gnu+:} false; then :
+if test "${ac_cv_fc_compiler_gnu+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat > conftest.$ac_ext <<_ACEOF
@@ -3867,7 +3863,7 @@
 FCFLAGS=
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $FC accepts -g" >&5
 $as_echo_n "checking whether $FC accepts -g... " >&6; }
-if ${ac_cv_prog_fc_g+:} false; then :
+if test "${ac_cv_prog_fc_g+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   FCFLAGS=-g
@@ -3915,7 +3911,7 @@
 ac_compiler_gnu=$ac_cv_fc_compiler_gnu
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to get verbose linking output from $FC" >&5
 $as_echo_n "checking how to get verbose linking output from $FC... " >&6; }
-if ${ac_cv_prog_fc_v+:} false; then :
+if test "${ac_cv_prog_fc_v+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat > conftest.$ac_ext <<_ACEOF
@@ -3945,8 +3941,7 @@
 # gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH,
 # LIBRARY_PATH; skip all such settings.
 ac_fc_v_output=`eval $ac_link 5>&1 2>&1 |
-  sed '/^Driving:/d; /^Configured with:/d;
-      '"/^[_$as_cr_Letters][_$as_cr_alnum]*=/d"`
+  grep -v 'Driving:' | grep -v "^[_$as_cr_Letters][_$as_cr_alnum]*="`
 $as_echo "$ac_fc_v_output" >&5
 FCFLAGS=$ac_save_FCFLAGS
 
@@ -4011,7 +4006,7 @@
 $as_echo "$ac_cv_prog_fc_v" >&6; }
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Fortran libraries of $FC" >&5
 $as_echo_n "checking for Fortran libraries of $FC... " >&6; }
-if ${ac_cv_fc_libs+:} false; then :
+if test "${ac_cv_fc_libs+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test "x$FCLIBS" != "x"; then
@@ -4036,8 +4031,7 @@
 # gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH,
 # LIBRARY_PATH; skip all such settings.
 ac_fc_v_output=`eval $ac_link 5>&1 2>&1 |
-  sed '/^Driving:/d; /^Configured with:/d;
-      '"/^[_$as_cr_Letters][_$as_cr_alnum]*=/d"`
+  grep -v 'Driving:' | grep -v "^[_$as_cr_Letters][_$as_cr_alnum]*="`
 $as_echo "$ac_fc_v_output" >&5
 FCFLAGS=$ac_save_FCFLAGS
 
@@ -4289,7 +4283,7 @@
 set dummy $ac_tool_prefix$ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_CC+:} false; then :
+if test "${ac_cv_prog_CC+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$CC"; then
@@ -4333,7 +4327,7 @@
 set dummy $ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_ac_ct_CC+:} false; then :
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$ac_ct_CC"; then
@@ -4386,7 +4380,7 @@
 test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "no acceptable C compiler found in \$PATH
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 
 # Provide some information about the compiler.
 $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
@@ -4415,7 +4409,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
 $as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
-if ${ac_cv_c_compiler_gnu+:} false; then :
+if test "${ac_cv_c_compiler_gnu+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -4452,7 +4446,7 @@
 ac_save_CFLAGS=$CFLAGS
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
 $as_echo_n "checking whether $CC accepts -g... " >&6; }
-if ${ac_cv_prog_cc_g+:} false; then :
+if test "${ac_cv_prog_cc_g+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_save_c_werror_flag=$ac_c_werror_flag
@@ -4530,7 +4524,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
 $as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
-if ${ac_cv_prog_cc_c89+:} false; then :
+if test "${ac_cv_prog_cc_c89+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_cv_prog_cc_c89=no
@@ -4641,7 +4635,7 @@
 set dummy $ac_tool_prefix$ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_CXX+:} false; then :
+if test "${ac_cv_prog_CXX+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$CXX"; then
@@ -4685,7 +4679,7 @@
 set dummy $ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_ac_ct_CXX+:} false; then :
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$ac_ct_CXX"; then
@@ -4763,7 +4757,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
 $as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
-if ${ac_cv_cxx_compiler_gnu+:} false; then :
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -4800,7 +4794,7 @@
 ac_save_CXXFLAGS=$CXXFLAGS
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
 $as_echo_n "checking whether $CXX accepts -g... " >&6; }
-if ${ac_cv_prog_cxx_g+:} false; then :
+if test "${ac_cv_prog_cxx_g+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_save_cxx_werror_flag=$ac_cxx_werror_flag
@@ -4894,7 +4888,7 @@
   CPP=
 fi
 if test -z "$CPP"; then
-  if ${ac_cv_prog_CPP+:} false; then :
+  if test "${ac_cv_prog_CPP+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
       # Double quotes because CPP needs to be expanded
@@ -5010,7 +5004,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "C preprocessor \"$CPP\" fails sanity check
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 
 ac_ext=c
@@ -5025,7 +5019,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
 $as_echo_n "checking for grep that handles long lines and -e... " >&6; }
-if ${ac_cv_path_GREP+:} false; then :
+if test "${ac_cv_path_GREP+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -z "$GREP"; then
@@ -5088,7 +5082,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
 $as_echo_n "checking for egrep... " >&6; }
-if ${ac_cv_path_EGREP+:} false; then :
+if test "${ac_cv_path_EGREP+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
@@ -5155,7 +5149,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
 $as_echo_n "checking for ANSI C header files... " >&6; }
-if ${ac_cv_header_stdc+:} false; then :
+if test "${ac_cv_header_stdc+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -5288,7 +5282,7 @@
 # This bug is HP SR number 8606223364.
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking size of long int" >&5
 $as_echo_n "checking size of long int... " >&6; }
-if ${ac_cv_sizeof_long_int+:} false; then :
+if test "${ac_cv_sizeof_long_int+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if ac_fn_c_compute_int "$LINENO" "(long int) (sizeof (long int))" "ac_cv_sizeof_long_int"        "$ac_includes_default"; then :
@@ -5298,7 +5292,7 @@
      { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error 77 "cannot compute sizeof (long int)
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
    else
      ac_cv_sizeof_long_int=0
    fi
@@ -5329,7 +5323,7 @@
 ac_compiler_gnu=$ac_cv_f77_compiler_gnu
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to get verbose linking output from $F77" >&5
 $as_echo_n "checking how to get verbose linking output from $F77... " >&6; }
-if ${ac_cv_prog_f77_v+:} false; then :
+if test "${ac_cv_prog_f77_v+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat > conftest.$ac_ext <<_ACEOF
@@ -5359,8 +5353,7 @@
 # gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH,
 # LIBRARY_PATH; skip all such settings.
 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 |
-  sed '/^Driving:/d; /^Configured with:/d;
-      '"/^[_$as_cr_Letters][_$as_cr_alnum]*=/d"`
+  grep -v 'Driving:' | grep -v "^[_$as_cr_Letters][_$as_cr_alnum]*="`
 $as_echo "$ac_f77_v_output" >&5
 FFLAGS=$ac_save_FFLAGS
 
@@ -5425,7 +5418,7 @@
 $as_echo "$ac_cv_prog_f77_v" >&6; }
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Fortran 77 libraries of $F77" >&5
 $as_echo_n "checking for Fortran 77 libraries of $F77... " >&6; }
-if ${ac_cv_f77_libs+:} false; then :
+if test "${ac_cv_f77_libs+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test "x$FLIBS" != "x"; then
@@ -5450,8 +5443,7 @@
 # gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH,
 # LIBRARY_PATH; skip all such settings.
 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 |
-  sed '/^Driving:/d; /^Configured with:/d;
-      '"/^[_$as_cr_Letters][_$as_cr_alnum]*=/d"`
+  grep -v 'Driving:' | grep -v "^[_$as_cr_Letters][_$as_cr_alnum]*="`
 $as_echo "$ac_f77_v_output" >&5
 FFLAGS=$ac_save_FFLAGS
 
@@ -5638,7 +5630,7 @@
 ac_compiler_gnu=$ac_cv_fc_compiler_gnu
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to get verbose linking output from $FC" >&5
 $as_echo_n "checking how to get verbose linking output from $FC... " >&6; }
-if ${ac_cv_prog_fc_v+:} false; then :
+if test "${ac_cv_prog_fc_v+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat > conftest.$ac_ext <<_ACEOF
@@ -5668,8 +5660,7 @@
 # gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH,
 # LIBRARY_PATH; skip all such settings.
 ac_fc_v_output=`eval $ac_link 5>&1 2>&1 |
-  sed '/^Driving:/d; /^Configured with:/d;
-      '"/^[_$as_cr_Letters][_$as_cr_alnum]*=/d"`
+  grep -v 'Driving:' | grep -v "^[_$as_cr_Letters][_$as_cr_alnum]*="`
 $as_echo "$ac_fc_v_output" >&5
 FCFLAGS=$ac_save_FCFLAGS
 
@@ -5734,7 +5725,7 @@
 $as_echo "$ac_cv_prog_fc_v" >&6; }
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Fortran libraries of $FC" >&5
 $as_echo_n "checking for Fortran libraries of $FC... " >&6; }
-if ${ac_cv_fc_libs+:} false; then :
+if test "${ac_cv_fc_libs+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test "x$FCLIBS" != "x"; then
@@ -5759,8 +5750,7 @@
 # gfortran 4.3 outputs lines setting COLLECT_GCC_OPTIONS, COMPILER_PATH,
 # LIBRARY_PATH; skip all such settings.
 ac_fc_v_output=`eval $ac_link 5>&1 2>&1 |
-  sed '/^Driving:/d; /^Configured with:/d;
-      '"/^[_$as_cr_Letters][_$as_cr_alnum]*=/d"`
+  grep -v 'Driving:' | grep -v "^[_$as_cr_Letters][_$as_cr_alnum]*="`
 $as_echo "$ac_fc_v_output" >&5
 FCFLAGS=$ac_save_FCFLAGS
 
@@ -5949,7 +5939,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dummy main to link with Fortran 77 libraries" >&5
 $as_echo_n "checking for dummy main to link with Fortran 77 libraries... " >&6; }
-if ${ac_cv_f77_dummy_main+:} false; then :
+if test "${ac_cv_f77_dummy_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_f77_dm_save_LIBS=$LIBS
@@ -6046,7 +6036,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "linking to Fortran libraries from C fails
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 
 ac_ext=c
@@ -6061,7 +6051,7 @@
 ac_compiler_gnu=$ac_cv_f77_compiler_gnu
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Fortran 77 name-mangling scheme" >&5
 $as_echo_n "checking for Fortran 77 name-mangling scheme... " >&6; }
-if ${ac_cv_f77_mangling+:} false; then :
+if test "${ac_cv_f77_mangling+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat > conftest.$ac_ext <<_ACEOF
@@ -6208,7 +6198,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "cannot compile a simple Fortran program
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 
@@ -6357,7 +6347,7 @@
 set dummy python$PYTHON_VERSION; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_path_PYTHON+:} false; then :
+if test "${ac_cv_path_PYTHON+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   case $PYTHON in
@@ -6421,7 +6411,7 @@
 Moreover, to disable this check, set PYTHON_NOVERSIONCHECK
 to something else than an empty string.
 
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 		else
 			{ $as_echo "$as_me:${as_lineno-$LINENO}: result: skip at user request" >&5
 $as_echo "skip at user request" >&6; }
@@ -6692,7 +6682,7 @@
    for your distribution.  The exact name of this package varies among them.
   ============================================================================
 
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 	  PYTHON_VERSION=""
 	fi
 
@@ -6741,7 +6731,7 @@
 if test "$enable_cgal" = "yes" ; then
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lCGAL" >&5
 $as_echo_n "checking for cos in -lCGAL... " >&6; }
-if ${ac_cv_lib_CGAL_cos+:} false; then :
+if test "${ac_cv_lib_CGAL_cos+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -6783,7 +6773,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_CGAL_cos" >&5
 $as_echo "$ac_cv_lib_CGAL_cos" >&6; }
-if test "x$ac_cv_lib_CGAL_cos" = xyes; then :
+if test "x$ac_cv_lib_CGAL_cos" = x""yes; then :
   HAVE_CGAL=yes
 else
   HAVE_CGAL=no
@@ -6831,7 +6821,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dummy main to link with Fortran libraries" >&5
 $as_echo_n "checking for dummy main to link with Fortran libraries... " >&6; }
-if ${ac_cv_fc_dummy_main+:} false; then :
+if test "${ac_cv_fc_dummy_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_fc_dm_save_LIBS=$LIBS
@@ -6944,7 +6934,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "linking to Fortran libraries from C fails
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 
 ac_ext=c
@@ -6959,7 +6949,7 @@
 ac_compiler_gnu=$ac_cv_fc_compiler_gnu
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Fortran name-mangling scheme" >&5
 $as_echo_n "checking for Fortran name-mangling scheme... " >&6; }
-if ${ac_cv_fc_mangling+:} false; then :
+if test "${ac_cv_fc_mangling+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat > conftest.$ac_ext <<_ACEOF
@@ -7122,7 +7112,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "cannot compile a simple Fortran program
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 
@@ -7360,7 +7350,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_mkl_def_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lmkl_def" >&5
 $as_echo_n "checking for $sgemm in -lmkl_def... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -7420,7 +7410,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_mkl_ipf_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lmkl_ipf" >&5
 $as_echo_n "checking for $sgemm in -lmkl_ipf... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -7480,7 +7470,7 @@
         as_ac_Lib=`$as_echo "ac_cv_lib_mkl_em64t_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lmkl_em64t" >&5
 $as_echo_n "checking for $sgemm in -lmkl_em64t... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -7543,7 +7533,7 @@
 	unset ac_cv_lib_mkl_def_sgemm
 	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for lsame in -lmkl_lapack" >&5
 $as_echo_n "checking for lsame in -lmkl_lapack... " >&6; }
-if ${ac_cv_lib_mkl_lapack_lsame+:} false; then :
+if test "${ac_cv_lib_mkl_lapack_lsame+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -7593,13 +7583,13 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mkl_lapack_lsame" >&5
 $as_echo "$ac_cv_lib_mkl_lapack_lsame" >&6; }
-if test "x$ac_cv_lib_mkl_lapack_lsame" = xyes; then :
+if test "x$ac_cv_lib_mkl_lapack_lsame" = x""yes; then :
 
 	    acx_lapack_ok=yes;
 		as_ac_Lib=`$as_echo "ac_cv_lib_mkl_def_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lmkl_def" >&5
 $as_echo_n "checking for $sgemm in -lmkl_def... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -7668,7 +7658,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_acml_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lacml" >&5
 $as_echo_n "checking for $sgemm in -lacml... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -7730,7 +7720,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_f77blas_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lf77blas" >&5
 $as_echo_n "checking for $sgemm in -lf77blas... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -7792,7 +7782,7 @@
         as_ac_Lib=`$as_echo "ac_cv_lib_veclib_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lveclib" >&5
 $as_echo_n "checking for $sgemm in -lveclib... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -7856,7 +7846,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_blas_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lblas" >&5
 $as_echo_n "checking for $sgemm in -lblas... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -7910,7 +7900,7 @@
 if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dgemm in -ldgemm" >&5
 $as_echo_n "checking for dgemm in -ldgemm... " >&6; }
-if ${ac_cv_lib_dgemm_dgemm+:} false; then :
+if test "${ac_cv_lib_dgemm_dgemm+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -7960,11 +7950,11 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dgemm_dgemm" >&5
 $as_echo "$ac_cv_lib_dgemm_dgemm" >&6; }
-if test "x$ac_cv_lib_dgemm_dgemm" = xyes; then :
+if test "x$ac_cv_lib_dgemm_dgemm" = x""yes; then :
   as_ac_Lib=`$as_echo "ac_cv_lib_sgemm_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lsgemm" >&5
 $as_echo_n "checking for $sgemm in -lsgemm... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8033,7 +8023,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_cxml_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lcxml" >&5
 $as_echo_n "checking for $sgemm in -lcxml... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8095,7 +8085,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_dxml_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -ldxml" >&5
 $as_echo_n "checking for $sgemm in -ldxml... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8157,7 +8147,7 @@
 	if test "x$GCC" != xyes; then # only works with Sun CC
 		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for acosp in -lsunmath" >&5
 $as_echo_n "checking for acosp in -lsunmath... " >&6; }
-if ${ac_cv_lib_sunmath_acosp+:} false; then :
+if test "${ac_cv_lib_sunmath_acosp+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8207,11 +8197,11 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_sunmath_acosp" >&5
 $as_echo "$ac_cv_lib_sunmath_acosp" >&6; }
-if test "x$ac_cv_lib_sunmath_acosp" = xyes; then :
+if test "x$ac_cv_lib_sunmath_acosp" = x""yes; then :
   as_ac_Lib=`$as_echo "ac_cv_lib_sunperf_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lsunperf" >&5
 $as_echo_n "checking for $sgemm in -lsunperf... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8278,7 +8268,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_scs_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lscs" >&5
 $as_echo_n "checking for $sgemm in -lscs... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8340,7 +8330,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_complib.sgimath_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lcomplib.sgimath" >&5
 $as_echo_n "checking for $sgemm in -lcomplib.sgimath... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8405,7 +8395,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_blas_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lblas" >&5
 $as_echo_n "checking for $sgemm in -lblas... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8460,7 +8450,7 @@
   as_ac_Lib=`$as_echo "ac_cv_lib_essl_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lessl" >&5
 $as_echo_n "checking for $sgemm in -lessl... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8528,7 +8518,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_blas_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lblas" >&5
 $as_echo_n "checking for $sgemm in -lblas... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8591,7 +8581,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_blas_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lblas" >&5
 $as_echo_n "checking for $sgemm in -lblas... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8719,7 +8709,7 @@
 $as_echo "$as_me: Appear to be using Portland Group compiler suite. Check if ACML is also available." >&6;}
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dgesv in -lacml" >&5
 $as_echo_n "checking for dgesv in -lacml... " >&6; }
-if ${ac_cv_lib_acml_dgesv+:} false; then :
+if test "${ac_cv_lib_acml_dgesv+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8769,7 +8759,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_acml_dgesv" >&5
 $as_echo "$ac_cv_lib_acml_dgesv" >&6; }
-if test "x$ac_cv_lib_acml_dgesv" = xyes; then :
+if test "x$ac_cv_lib_acml_dgesv" = x""yes; then :
   found_blas=yes
 else
   found_blas=no
@@ -8783,7 +8773,7 @@
 $as_echo "$as_me: Appear to be using Sun Studio compiler suite. Check if Sun Performance Library is also available." >&6;}
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dgesv in -lsunperf" >&5
 $as_echo_n "checking for dgesv in -lsunperf... " >&6; }
-if ${ac_cv_lib_sunperf_dgesv+:} false; then :
+if test "${ac_cv_lib_sunperf_dgesv+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -8833,7 +8823,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_sunperf_dgesv" >&5
 $as_echo "$ac_cv_lib_sunperf_dgesv" >&6; }
-if test "x$ac_cv_lib_sunperf_dgesv" = xyes; then :
+if test "x$ac_cv_lib_sunperf_dgesv" = x""yes; then :
   found_blas=yes ; acx_blas_ok=yes
 else
   found_blas=no
@@ -8992,7 +8982,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_mkl_def_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lmkl_def" >&5
 $as_echo_n "checking for $sgemm in -lmkl_def... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9023,7 +9013,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_mkl_ipf_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lmkl_ipf" >&5
 $as_echo_n "checking for $sgemm in -lmkl_ipf... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9054,7 +9044,7 @@
         as_ac_Lib=`$as_echo "ac_cv_lib_mkl_em64t_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lmkl_em64t" >&5
 $as_echo_n "checking for $sgemm in -lmkl_em64t... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9088,7 +9078,7 @@
 	unset ac_cv_lib_mkl_def_sgemm
 	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for lsame in -lmkl_lapack" >&5
 $as_echo_n "checking for lsame in -lmkl_lapack... " >&6; }
-if ${ac_cv_lib_mkl_lapack_lsame+:} false; then :
+if test "${ac_cv_lib_mkl_lapack_lsame+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9109,13 +9099,13 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mkl_lapack_lsame" >&5
 $as_echo "$ac_cv_lib_mkl_lapack_lsame" >&6; }
-if test "x$ac_cv_lib_mkl_lapack_lsame" = xyes; then :
+if test "x$ac_cv_lib_mkl_lapack_lsame" = x""yes; then :
 
 	    acx_lapack_ok=yes;
 		as_ac_Lib=`$as_echo "ac_cv_lib_mkl_def_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lmkl_def" >&5
 $as_echo_n "checking for $sgemm in -lmkl_def... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9155,7 +9145,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_acml_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lacml" >&5
 $as_echo_n "checking for $sgemm in -lacml... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9188,7 +9178,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_f77blas_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lf77blas" >&5
 $as_echo_n "checking for $sgemm in -lf77blas... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9221,7 +9211,7 @@
         as_ac_Lib=`$as_echo "ac_cv_lib_veclib_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lveclib" >&5
 $as_echo_n "checking for $sgemm in -lveclib... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9256,7 +9246,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_blas_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lblas" >&5
 $as_echo_n "checking for $sgemm in -lblas... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9281,7 +9271,7 @@
 if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dgemm in -ldgemm" >&5
 $as_echo_n "checking for dgemm in -ldgemm... " >&6; }
-if ${ac_cv_lib_dgemm_dgemm+:} false; then :
+if test "${ac_cv_lib_dgemm_dgemm+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9302,11 +9292,11 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dgemm_dgemm" >&5
 $as_echo "$ac_cv_lib_dgemm_dgemm" >&6; }
-if test "x$ac_cv_lib_dgemm_dgemm" = xyes; then :
+if test "x$ac_cv_lib_dgemm_dgemm" = x""yes; then :
   as_ac_Lib=`$as_echo "ac_cv_lib_sgemm_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lsgemm" >&5
 $as_echo_n "checking for $sgemm in -lsgemm... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9346,7 +9336,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_cxml_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lcxml" >&5
 $as_echo_n "checking for $sgemm in -lcxml... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9379,7 +9369,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_dxml_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -ldxml" >&5
 $as_echo_n "checking for $sgemm in -ldxml... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9412,7 +9402,7 @@
 	if test "x$GCC" != xyes; then # only works with Sun CC
 		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for acosp in -lsunmath" >&5
 $as_echo_n "checking for acosp in -lsunmath... " >&6; }
-if ${ac_cv_lib_sunmath_acosp+:} false; then :
+if test "${ac_cv_lib_sunmath_acosp+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9433,11 +9423,11 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_sunmath_acosp" >&5
 $as_echo "$ac_cv_lib_sunmath_acosp" >&6; }
-if test "x$ac_cv_lib_sunmath_acosp" = xyes; then :
+if test "x$ac_cv_lib_sunmath_acosp" = x""yes; then :
   as_ac_Lib=`$as_echo "ac_cv_lib_sunperf_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lsunperf" >&5
 $as_echo_n "checking for $sgemm in -lsunperf... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9475,7 +9465,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_scs_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lscs" >&5
 $as_echo_n "checking for $sgemm in -lscs... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9508,7 +9498,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_complib.sgimath_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lcomplib.sgimath" >&5
 $as_echo_n "checking for $sgemm in -lcomplib.sgimath... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9544,7 +9534,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_blas_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lblas" >&5
 $as_echo_n "checking for $sgemm in -lblas... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9570,7 +9560,7 @@
   as_ac_Lib=`$as_echo "ac_cv_lib_essl_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lessl" >&5
 $as_echo_n "checking for $sgemm in -lessl... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9609,7 +9599,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_blas_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lblas" >&5
 $as_echo_n "checking for $sgemm in -lblas... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9643,7 +9633,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_blas_$sgemm" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $sgemm in -lblas" >&5
 $as_echo_n "checking for $sgemm in -lblas... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9835,7 +9825,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_mkl_lapack_$dsyev" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $dsyev in -lmkl_lapack" >&5
 $as_echo_n "checking for $dsyev in -lmkl_lapack... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9868,7 +9858,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_sunperf_$dsyev" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $dsyev in -lsunperf" >&5
 $as_echo_n "checking for $dsyev in -lsunperf... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9919,7 +9909,7 @@
 	as_ac_Lib=`$as_echo "ac_cv_lib_lapack_$dsyev" | $as_tr_sh`
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $dsyev in -llapack" >&5
 $as_echo_n "checking for $dsyev in -llapack... " >&6; }
-if eval \${$as_ac_Lib+:} false; then :
+if eval "test \"\${$as_ac_Lib+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -9980,7 +9970,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lstdc++" >&5
 $as_echo_n "checking for main in -lstdc++... " >&6; }
-if ${ac_cv_lib_stdcpp_main+:} false; then :
+if test "${ac_cv_lib_stdcpp_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -10024,7 +10014,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_stdcpp_main" >&5
 $as_echo "$ac_cv_lib_stdcpp_main" >&6; }
-if test "x$ac_cv_lib_stdcpp_main" = xyes; then :
+if test "x$ac_cv_lib_stdcpp_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBSTDC__ 1
 _ACEOF
@@ -10035,7 +10025,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lm" >&5
 $as_echo_n "checking for main in -lm... " >&6; }
-if ${ac_cv_lib_m_main+:} false; then :
+if test "${ac_cv_lib_m_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -10079,7 +10069,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_main" >&5
 $as_echo "$ac_cv_lib_m_main" >&6; }
-if test "x$ac_cv_lib_m_main" = xyes; then :
+if test "x$ac_cv_lib_m_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBM 1
 _ACEOF
@@ -10090,7 +10080,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lpthread" >&5
 $as_echo_n "checking for main in -lpthread... " >&6; }
-if ${ac_cv_lib_pthread_main+:} false; then :
+if test "${ac_cv_lib_pthread_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -10134,7 +10124,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_pthread_main" >&5
 $as_echo "$ac_cv_lib_pthread_main" >&6; }
-if test "x$ac_cv_lib_pthread_main" = xyes; then :
+if test "x$ac_cv_lib_pthread_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBPTHREAD 1
 _ACEOF
@@ -10145,7 +10135,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing utInit" >&5
 $as_echo_n "checking for library containing utInit... " >&6; }
-if ${ac_cv_search_utInit+:} false; then :
+if test "${ac_cv_search_utInit+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_func_search_save_LIBS=$LIBS
@@ -10195,11 +10185,11 @@
 fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext
-  if ${ac_cv_search_utInit+:} false; then :
+  if test "${ac_cv_search_utInit+set}" = set; then :
   break
 fi
 done
-if ${ac_cv_search_utInit+:} false; then :
+if test "${ac_cv_search_utInit+set}" = set; then :
 
 else
   ac_cv_search_utInit=no
@@ -10243,7 +10233,7 @@
   if test "$enable_openmp" != no; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CXX option to support OpenMP" >&5
 $as_echo_n "checking for $CXX option to support OpenMP... " >&6; }
-if ${ac_cv_prog_cxx_openmp+:} false; then :
+if test "${ac_cv_prog_cxx_openmp+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -10643,7 +10633,7 @@
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
 $as_echo_n "checking for a BSD-compatible install... " >&6; }
 if test -z "$INSTALL"; then
-if ${ac_cv_path_install+:} false; then :
+if test "${ac_cv_path_install+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
@@ -10723,7 +10713,7 @@
 set dummy gmake; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_MAKE+:} false; then :
+if test "${ac_cv_prog_MAKE+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$MAKE"; then
@@ -10765,7 +10755,7 @@
 set dummy ar; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_AR+:} false; then :
+if test "${ac_cv_prog_AR+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$AR"; then
@@ -10805,7 +10795,7 @@
 set dummy ${ac_tool_prefix}ranlib; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_RANLIB+:} false; then :
+if test "${ac_cv_prog_RANLIB+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$RANLIB"; then
@@ -10845,7 +10835,7 @@
 set dummy ranlib; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_ac_ct_RANLIB+:} false; then :
+if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$ac_ct_RANLIB"; then
@@ -11068,7 +11058,7 @@
 set dummy $ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_MPIF90+:} false; then :
+if test "${ac_cv_prog_MPIF90+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$MPIF90"; then
@@ -11114,7 +11104,7 @@
 set dummy $ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_MPIF77+:} false; then :
+if test "${ac_cv_prog_MPIF77+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$MPIF77"; then
@@ -11158,7 +11148,7 @@
 set dummy $ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_MPICC+:} false; then :
+if test "${ac_cv_prog_MPICC+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$MPICC"; then
@@ -11201,7 +11191,7 @@
 set dummy $ac_prog; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_MPICXX+:} false; then :
+if test "${ac_cv_prog_MPICXX+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if test -n "$MPICXX"; then
@@ -11467,7 +11457,7 @@
   fi
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for nc_create in -lnetcdf" >&5
 $as_echo_n "checking for nc_create in -lnetcdf... " >&6; }
-if ${ac_cv_lib_netcdf_nc_create+:} false; then :
+if test "${ac_cv_lib_netcdf_nc_create+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -11517,7 +11507,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_netcdf_nc_create" >&5
 $as_echo "$ac_cv_lib_netcdf_nc_create" >&6; }
-if test "x$ac_cv_lib_netcdf_nc_create" = xyes; then :
+if test "x$ac_cv_lib_netcdf_nc_create" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBNETCDF 1
 _ACEOF
@@ -11535,7 +11525,7 @@
   # Check for separate fortran lib.
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ncopn_ in -lnetcdff" >&5
 $as_echo_n "checking for ncopn_ in -lnetcdff... " >&6; }
-if ${ac_cv_lib_netcdff_ncopn_+:} false; then :
+if test "${ac_cv_lib_netcdff_ncopn_+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -11585,7 +11575,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_netcdff_ncopn_" >&5
 $as_echo "$ac_cv_lib_netcdff_ncopn_" >&6; }
-if test "x$ac_cv_lib_netcdff_ncopn_" = xyes; then :
+if test "x$ac_cv_lib_netcdff_ncopn_" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBNETCDFF 1
 _ACEOF
@@ -11628,7 +11618,7 @@
 LIBS="$tmpLIBS -L$ParMetis_LIBS_PATH -lparmetis -lmetis -lm"
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ParMETIS_V3_AdaptiveRepart in -lparmetis" >&5
 $as_echo_n "checking for ParMETIS_V3_AdaptiveRepart in -lparmetis... " >&6; }
-if ${ac_cv_lib_parmetis_ParMETIS_V3_AdaptiveRepart+:} false; then :
+if test "${ac_cv_lib_parmetis_ParMETIS_V3_AdaptiveRepart+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -11678,7 +11668,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_parmetis_ParMETIS_V3_AdaptiveRepart" >&5
 $as_echo "$ac_cv_lib_parmetis_ParMETIS_V3_AdaptiveRepart" >&6; }
-if test "x$ac_cv_lib_parmetis_ParMETIS_V3_AdaptiveRepart" = xyes; then :
+if test "x$ac_cv_lib_parmetis_ParMETIS_V3_AdaptiveRepart" = x""yes; then :
 
 $as_echo "#define HAVE_PARMETIS 1" >>confdefs.h
 
@@ -11756,7 +11746,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Zoltan_Initialize in -lzoltan" >&5
 $as_echo_n "checking for Zoltan_Initialize in -lzoltan... " >&6; }
-if ${ac_cv_lib_zoltan_Zoltan_Initialize+:} false; then :
+if test "${ac_cv_lib_zoltan_Zoltan_Initialize+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -11806,7 +11796,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_zoltan_Zoltan_Initialize" >&5
 $as_echo "$ac_cv_lib_zoltan_Zoltan_Initialize" >&6; }
-if test "x$ac_cv_lib_zoltan_Zoltan_Initialize" = xyes; then :
+if test "x$ac_cv_lib_zoltan_Zoltan_Initialize" = x""yes; then :
 
 $as_echo "#define HAVE_ZOLTAN 1" >>confdefs.h
 
@@ -11888,7 +11878,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for adj_register_equation in -ladjoint" >&5
 $as_echo_n "checking for adj_register_equation in -ladjoint... " >&6; }
-if ${ac_cv_lib_adjoint_adj_register_equation+:} false; then :
+if test "${ac_cv_lib_adjoint_adj_register_equation+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -11938,7 +11928,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_adjoint_adj_register_equation" >&5
 $as_echo "$ac_cv_lib_adjoint_adj_register_equation" >&6; }
-if test "x$ac_cv_lib_adjoint_adj_register_equation" = xyes; then :
+if test "x$ac_cv_lib_adjoint_adj_register_equation" = x""yes; then :
 
 $as_echo "#define HAVE_ADJOINT 1" >>confdefs.h
 HAVE_ADJOINT=yes
@@ -11984,8 +11974,8 @@
   have_x=disabled
 else
   case $x_includes,$x_libraries in #(
-    *\'*) as_fn_error $? "cannot use X directory names containing '" "$LINENO" 5;; #(
-    *,NONE | NONE,*) if ${ac_cv_have_x+:} false; then :
+    *\'*) as_fn_error $? "cannot use X directory names containing '" "$LINENO" 5 ;; #(
+    *,NONE | NONE,*) if test "${ac_cv_have_x+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   # One or both of the vars are not set, and there is no cached value.
@@ -12332,7 +12322,7 @@
 else
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dnet_ntoa in -ldnet" >&5
 $as_echo_n "checking for dnet_ntoa in -ldnet... " >&6; }
-if ${ac_cv_lib_dnet_dnet_ntoa+:} false; then :
+if test "${ac_cv_lib_dnet_dnet_ntoa+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -12382,14 +12372,14 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dnet_dnet_ntoa" >&5
 $as_echo "$ac_cv_lib_dnet_dnet_ntoa" >&6; }
-if test "x$ac_cv_lib_dnet_dnet_ntoa" = xyes; then :
+if test "x$ac_cv_lib_dnet_dnet_ntoa" = x""yes; then :
   X_EXTRA_LIBS="$X_EXTRA_LIBS -ldnet"
 fi
 
     if test $ac_cv_lib_dnet_dnet_ntoa = no; then
       { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dnet_ntoa in -ldnet_stub" >&5
 $as_echo_n "checking for dnet_ntoa in -ldnet_stub... " >&6; }
-if ${ac_cv_lib_dnet_stub_dnet_ntoa+:} false; then :
+if test "${ac_cv_lib_dnet_stub_dnet_ntoa+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -12439,7 +12429,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dnet_stub_dnet_ntoa" >&5
 $as_echo "$ac_cv_lib_dnet_stub_dnet_ntoa" >&6; }
-if test "x$ac_cv_lib_dnet_stub_dnet_ntoa" = xyes; then :
+if test "x$ac_cv_lib_dnet_stub_dnet_ntoa" = x""yes; then :
   X_EXTRA_LIBS="$X_EXTRA_LIBS -ldnet_stub"
 fi
 
@@ -12458,14 +12448,14 @@
     # The functions gethostbyname, getservbyname, and inet_addr are
     # in -lbsd on LynxOS 3.0.1/i386, according to Lars Hecking.
     ac_fn_c_check_func "$LINENO" "gethostbyname" "ac_cv_func_gethostbyname"
-if test "x$ac_cv_func_gethostbyname" = xyes; then :
+if test "x$ac_cv_func_gethostbyname" = x""yes; then :
 
 fi
 
     if test $ac_cv_func_gethostbyname = no; then
       { $as_echo "$as_me:${as_lineno-$LINENO}: checking for gethostbyname in -lnsl" >&5
 $as_echo_n "checking for gethostbyname in -lnsl... " >&6; }
-if ${ac_cv_lib_nsl_gethostbyname+:} false; then :
+if test "${ac_cv_lib_nsl_gethostbyname+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -12515,14 +12505,14 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_nsl_gethostbyname" >&5
 $as_echo "$ac_cv_lib_nsl_gethostbyname" >&6; }
-if test "x$ac_cv_lib_nsl_gethostbyname" = xyes; then :
+if test "x$ac_cv_lib_nsl_gethostbyname" = x""yes; then :
   X_EXTRA_LIBS="$X_EXTRA_LIBS -lnsl"
 fi
 
       if test $ac_cv_lib_nsl_gethostbyname = no; then
 	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for gethostbyname in -lbsd" >&5
 $as_echo_n "checking for gethostbyname in -lbsd... " >&6; }
-if ${ac_cv_lib_bsd_gethostbyname+:} false; then :
+if test "${ac_cv_lib_bsd_gethostbyname+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -12572,7 +12562,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_bsd_gethostbyname" >&5
 $as_echo "$ac_cv_lib_bsd_gethostbyname" >&6; }
-if test "x$ac_cv_lib_bsd_gethostbyname" = xyes; then :
+if test "x$ac_cv_lib_bsd_gethostbyname" = x""yes; then :
   X_EXTRA_LIBS="$X_EXTRA_LIBS -lbsd"
 fi
 
@@ -12587,14 +12577,14 @@
     # must be given before -lnsl if both are needed.  We assume that
     # if connect needs -lnsl, so does gethostbyname.
     ac_fn_c_check_func "$LINENO" "connect" "ac_cv_func_connect"
-if test "x$ac_cv_func_connect" = xyes; then :
+if test "x$ac_cv_func_connect" = x""yes; then :
 
 fi
 
     if test $ac_cv_func_connect = no; then
       { $as_echo "$as_me:${as_lineno-$LINENO}: checking for connect in -lsocket" >&5
 $as_echo_n "checking for connect in -lsocket... " >&6; }
-if ${ac_cv_lib_socket_connect+:} false; then :
+if test "${ac_cv_lib_socket_connect+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -12644,7 +12634,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_socket_connect" >&5
 $as_echo "$ac_cv_lib_socket_connect" >&6; }
-if test "x$ac_cv_lib_socket_connect" = xyes; then :
+if test "x$ac_cv_lib_socket_connect" = x""yes; then :
   X_EXTRA_LIBS="-lsocket $X_EXTRA_LIBS"
 fi
 
@@ -12652,14 +12642,14 @@
 
     # Guillermo Gomez says -lposix is necessary on A/UX.
     ac_fn_c_check_func "$LINENO" "remove" "ac_cv_func_remove"
-if test "x$ac_cv_func_remove" = xyes; then :
+if test "x$ac_cv_func_remove" = x""yes; then :
 
 fi
 
     if test $ac_cv_func_remove = no; then
       { $as_echo "$as_me:${as_lineno-$LINENO}: checking for remove in -lposix" >&5
 $as_echo_n "checking for remove in -lposix... " >&6; }
-if ${ac_cv_lib_posix_remove+:} false; then :
+if test "${ac_cv_lib_posix_remove+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -12709,7 +12699,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_posix_remove" >&5
 $as_echo "$ac_cv_lib_posix_remove" >&6; }
-if test "x$ac_cv_lib_posix_remove" = xyes; then :
+if test "x$ac_cv_lib_posix_remove" = x""yes; then :
   X_EXTRA_LIBS="$X_EXTRA_LIBS -lposix"
 fi
 
@@ -12717,14 +12707,14 @@
 
     # BSDI BSD/OS 2.1 needs -lipc for XOpenDisplay.
     ac_fn_c_check_func "$LINENO" "shmat" "ac_cv_func_shmat"
-if test "x$ac_cv_func_shmat" = xyes; then :
+if test "x$ac_cv_func_shmat" = x""yes; then :
 
 fi
 
     if test $ac_cv_func_shmat = no; then
       { $as_echo "$as_me:${as_lineno-$LINENO}: checking for shmat in -lipc" >&5
 $as_echo_n "checking for shmat in -lipc... " >&6; }
-if ${ac_cv_lib_ipc_shmat+:} false; then :
+if test "${ac_cv_lib_ipc_shmat+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -12774,7 +12764,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_ipc_shmat" >&5
 $as_echo "$ac_cv_lib_ipc_shmat" >&6; }
-if test "x$ac_cv_lib_ipc_shmat" = xyes; then :
+if test "x$ac_cv_lib_ipc_shmat" = x""yes; then :
   X_EXTRA_LIBS="$X_EXTRA_LIBS -lipc"
 fi
 
@@ -12792,7 +12782,7 @@
   # John Interrante, Karl Berry
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for IceConnectionNumber in -lICE" >&5
 $as_echo_n "checking for IceConnectionNumber in -lICE... " >&6; }
-if ${ac_cv_lib_ICE_IceConnectionNumber+:} false; then :
+if test "${ac_cv_lib_ICE_IceConnectionNumber+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -12842,7 +12832,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_ICE_IceConnectionNumber" >&5
 $as_echo "$ac_cv_lib_ICE_IceConnectionNumber" >&6; }
-if test "x$ac_cv_lib_ICE_IceConnectionNumber" = xyes; then :
+if test "x$ac_cv_lib_ICE_IceConnectionNumber" = x""yes; then :
   X_PRE_LIBS="$X_PRE_LIBS -lSM -lICE"
 fi
 
@@ -12958,7 +12948,11 @@
       PetscInt  i,j,II,JJ,m,n,its
       PetscInt  Istart,Iend,ione
       PetscErrorCode ierr
+#if PETSC_VERSION_MINOR==2
+      PetscBool flg
+#else
       PetscTruth  flg
+#endif
       PetscScalar v,one,neg_one
       Vec         x,b,u
       Mat         A
@@ -13045,7 +13039,7 @@
 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "Failed to compile and link PETSc program.
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext conftest.$ac_ext
@@ -13092,7 +13086,7 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing PCHYPRESetType" >&5
 $as_echo_n "checking for library containing PCHYPRESetType... " >&6; }
-if ${ac_cv_search_PCHYPRESetType+:} false; then :
+if test "${ac_cv_search_PCHYPRESetType+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_func_search_save_LIBS=$LIBS
@@ -13113,11 +13107,11 @@
 fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext
-  if ${ac_cv_search_PCHYPRESetType+:} false; then :
+  if test "${ac_cv_search_PCHYPRESetType+set}" = set; then :
   break
 fi
 done
-if ${ac_cv_search_PCHYPRESetType+:} false; then :
+if test "${ac_cv_search_PCHYPRESetType+set}" = set; then :
 
 else
   ac_cv_search_PCHYPRESetType=no
@@ -13171,7 +13165,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "cannot run test program while cross compiling
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 else
   cat > conftest.$ac_ext <<_ACEOF
       program main
@@ -13206,7 +13200,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "cannot run test program while cross compiling
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 else
   cat > conftest.$ac_ext <<_ACEOF
       program main
@@ -13241,7 +13235,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "cannot run test program while cross compiling
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 else
   cat > conftest.$ac_ext <<_ACEOF
       program main
@@ -13278,7 +13272,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "cannot run test program while cross compiling
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 else
   cat > conftest.$ac_ext <<_ACEOF
       program main
@@ -13545,6 +13539,7 @@
 
 
 
+
 if test "$smart_fortran" = "yes" ; then
   F77=$MPIF90
 else
@@ -13620,7 +13615,7 @@
 # This bug is HP SR number 8606223364.
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking size of void *" >&5
 $as_echo_n "checking size of void *... " >&6; }
-if ${ac_cv_sizeof_void_p+:} false; then :
+if test "${ac_cv_sizeof_void_p+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   if ac_fn_c_compute_int "$LINENO" "(long int) (sizeof (void *))" "ac_cv_sizeof_void_p"        "$ac_includes_default"; then :
@@ -13630,7 +13625,7 @@
      { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error 77 "cannot compute sizeof (void *)
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
    else
      ac_cv_sizeof_void_p=0
    fi
@@ -13677,7 +13672,9 @@
 $as_echo "$as_me: Building on hector xe6; disabling shared libraries" >&6;}
         SHFLAG=--disable-shared
         SPUD_ONLY="yes"
+        FLLINKER=$CXX
     else
+        FLLINKER=$FC
         SHFLAG=--enable-shared
     fi
 
@@ -13763,7 +13760,7 @@
 else
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dsaupd in -larpack" >&5
 $as_echo_n "checking for dsaupd in -larpack... " >&6; }
-if ${ac_cv_lib_arpack_dsaupd+:} false; then :
+if test "${ac_cv_lib_arpack_dsaupd+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -13784,7 +13781,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_arpack_dsaupd" >&5
 $as_echo "$ac_cv_lib_arpack_dsaupd" >&6; }
-if test "x$ac_cv_lib_arpack_dsaupd" = xyes; then :
+if test "x$ac_cv_lib_arpack_dsaupd" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBARPACK 1
 _ACEOF
@@ -13871,7 +13868,7 @@
         # header files are another matter.
         { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -ldl" >&5
 $as_echo_n "checking for main in -ldl... " >&6; }
-if ${ac_cv_lib_dl_main+:} false; then :
+if test "${ac_cv_lib_dl_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -13915,7 +13912,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_main" >&5
 $as_echo "$ac_cv_lib_dl_main" >&6; }
-if test "x$ac_cv_lib_dl_main" = xyes; then :
+if test "x$ac_cv_lib_dl_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBDL 1
 _ACEOF
@@ -13926,7 +13923,7 @@
 
         { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lvtksys" >&5
 $as_echo_n "checking for main in -lvtksys... " >&6; }
-if ${ac_cv_lib_vtksys_main+:} false; then :
+if test "${ac_cv_lib_vtksys_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -13970,7 +13967,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_vtksys_main" >&5
 $as_echo "$ac_cv_lib_vtksys_main" >&6; }
-if test "x$ac_cv_lib_vtksys_main" = xyes; then :
+if test "x$ac_cv_lib_vtksys_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBVTKSYS 1
 _ACEOF
@@ -13981,7 +13978,7 @@
 
         { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lvtkCommon" >&5
 $as_echo_n "checking for main in -lvtkCommon... " >&6; }
-if ${ac_cv_lib_vtkCommon_main+:} false; then :
+if test "${ac_cv_lib_vtkCommon_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -14025,7 +14022,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_vtkCommon_main" >&5
 $as_echo "$ac_cv_lib_vtkCommon_main" >&6; }
-if test "x$ac_cv_lib_vtkCommon_main" = xyes; then :
+if test "x$ac_cv_lib_vtkCommon_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBVTKCOMMON 1
 _ACEOF
@@ -14038,7 +14035,7 @@
                 unset ac_cv_lib_vtkCommon_main
                 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lvtkCommon" >&5
 $as_echo_n "checking for main in -lvtkCommon... " >&6; }
-if ${ac_cv_lib_vtkCommon_main+:} false; then :
+if test "${ac_cv_lib_vtkCommon_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -14082,7 +14079,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_vtkCommon_main" >&5
 $as_echo "$ac_cv_lib_vtkCommon_main" >&6; }
-if test "x$ac_cv_lib_vtkCommon_main" = xyes; then :
+if test "x$ac_cv_lib_vtkCommon_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBVTKCOMMON 1
 _ACEOF
@@ -14105,7 +14102,7 @@
 
         { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lvtkzlib" >&5
 $as_echo_n "checking for main in -lvtkzlib... " >&6; }
-if ${ac_cv_lib_vtkzlib_main+:} false; then :
+if test "${ac_cv_lib_vtkzlib_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -14149,7 +14146,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_vtkzlib_main" >&5
 $as_echo "$ac_cv_lib_vtkzlib_main" >&6; }
-if test "x$ac_cv_lib_vtkzlib_main" = xyes; then :
+if test "x$ac_cv_lib_vtkzlib_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBVTKZLIB 1
 _ACEOF
@@ -14160,7 +14157,7 @@
 
         { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lvtkexpat" >&5
 $as_echo_n "checking for main in -lvtkexpat... " >&6; }
-if ${ac_cv_lib_vtkexpat_main+:} false; then :
+if test "${ac_cv_lib_vtkexpat_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -14204,7 +14201,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_vtkexpat_main" >&5
 $as_echo "$ac_cv_lib_vtkexpat_main" >&6; }
-if test "x$ac_cv_lib_vtkexpat_main" = xyes; then :
+if test "x$ac_cv_lib_vtkexpat_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBVTKEXPAT 1
 _ACEOF
@@ -14215,7 +14212,7 @@
 
         { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lvtkFiltering" >&5
 $as_echo_n "checking for main in -lvtkFiltering... " >&6; }
-if ${ac_cv_lib_vtkFiltering_main+:} false; then :
+if test "${ac_cv_lib_vtkFiltering_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -14259,7 +14256,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_vtkFiltering_main" >&5
 $as_echo "$ac_cv_lib_vtkFiltering_main" >&6; }
-if test "x$ac_cv_lib_vtkFiltering_main" = xyes; then :
+if test "x$ac_cv_lib_vtkFiltering_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBVTKFILTERING 1
 _ACEOF
@@ -14270,7 +14267,7 @@
 
         { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lvtkGraphics" >&5
 $as_echo_n "checking for main in -lvtkGraphics... " >&6; }
-if ${ac_cv_lib_vtkGraphics_main+:} false; then :
+if test "${ac_cv_lib_vtkGraphics_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -14314,7 +14311,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_vtkGraphics_main" >&5
 $as_echo "$ac_cv_lib_vtkGraphics_main" >&6; }
-if test "x$ac_cv_lib_vtkGraphics_main" = xyes; then :
+if test "x$ac_cv_lib_vtkGraphics_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBVTKGRAPHICS 1
 _ACEOF
@@ -14325,7 +14322,7 @@
 
         { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lvtkIO" >&5
 $as_echo_n "checking for main in -lvtkIO... " >&6; }
-if ${ac_cv_lib_vtkIO_main+:} false; then :
+if test "${ac_cv_lib_vtkIO_main+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -14369,7 +14366,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_vtkIO_main" >&5
 $as_echo "$ac_cv_lib_vtkIO_main" >&6; }
-if test "x$ac_cv_lib_vtkIO_main" = xyes; then :
+if test "x$ac_cv_lib_vtkIO_main" = x""yes; then :
   cat >>confdefs.h <<_ACEOF
 #define HAVE_LIBVTKIO 1
 _ACEOF
@@ -14393,7 +14390,7 @@
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C++ preprocessor" >&5
 $as_echo_n "checking how to run the C++ preprocessor... " >&6; }
 if test -z "$CXXCPP"; then
-  if ${ac_cv_prog_CXXCPP+:} false; then :
+  if test "${ac_cv_prog_CXXCPP+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
       # Double quotes because CXXCPP needs to be expanded
@@ -14509,7 +14506,7 @@
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
 as_fn_error $? "C++ preprocessor \"$CXXCPP\" fails sanity check
-See \`config.log' for more details" "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 
 ac_ext=cpp
@@ -14520,13 +14517,13 @@
 
 
 ac_fn_cxx_check_header_mongrel "$LINENO" "vtkCellData.h" "ac_cv_header_vtkCellData_h" "$ac_includes_default"
-if test "x$ac_cv_header_vtkCellData_h" = xyes; then :
+if test "x$ac_cv_header_vtkCellData_h" = x""yes; then :
   CPPFLAGS="$CPPFLAGS -DHAVE_VTK=1"
                 VTK=yes
 
 else
   ac_fn_cxx_check_header_mongrel "$LINENO" "vtk-5.0/vtkCellData.h" "ac_cv_header_vtk_5_0_vtkCellData_h" "$ac_includes_default"
-if test "x$ac_cv_header_vtk_5_0_vtkCellData_h" = xyes; then :
+if test "x$ac_cv_header_vtk_5_0_vtkCellData_h" = x""yes; then :
   CPPFLAGS="$CPPFLAGS -DHAVE_VTK=1"
                         VTK=yes
                         vtk_header_relative_path="vtk-5.0/"
@@ -14683,7 +14680,7 @@
 if test "$enable_hyperlight" = "yes"; then
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for hyperlight/Hyperlight.h" >&5
 $as_echo_n "checking for hyperlight/Hyperlight.h... " >&6; }
-if ${ac_cv_file_hyperlight_Hyperlight_h+:} false; then :
+if test "${ac_cv_file_hyperlight_Hyperlight_h+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   test "$cross_compiling" = yes &&
@@ -14696,7 +14693,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_file_hyperlight_Hyperlight_h" >&5
 $as_echo "$ac_cv_file_hyperlight_Hyperlight_h" >&6; }
-if test "x$ac_cv_file_hyperlight_Hyperlight_h" = xyes; then :
+if test "x$ac_cv_file_hyperlight_Hyperlight_h" = x""yes; then :
 
 cat >>confdefs.h <<_ACEOF
 #define HAVE_HYPERLIGHT_HYPERLIGHT_H 1
@@ -14714,7 +14711,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for hyperlight/Hyperlight.cpp" >&5
 $as_echo_n "checking for hyperlight/Hyperlight.cpp... " >&6; }
-if ${ac_cv_file_hyperlight_Hyperlight_cpp+:} false; then :
+if test "${ac_cv_file_hyperlight_Hyperlight_cpp+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   test "$cross_compiling" = yes &&
@@ -14727,7 +14724,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_file_hyperlight_Hyperlight_cpp" >&5
 $as_echo "$ac_cv_file_hyperlight_Hyperlight_cpp" >&6; }
-if test "x$ac_cv_file_hyperlight_Hyperlight_cpp" = xyes; then :
+if test "x$ac_cv_file_hyperlight_Hyperlight_cpp" = x""yes; then :
 
 cat >>confdefs.h <<_ACEOF
 #define HAVE_HYPERLIGHT_HYPERLIGHT_CPP 1
@@ -14745,7 +14742,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for hyperlight/Sky.h" >&5
 $as_echo_n "checking for hyperlight/Sky.h... " >&6; }
-if ${ac_cv_file_hyperlight_Sky_h+:} false; then :
+if test "${ac_cv_file_hyperlight_Sky_h+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   test "$cross_compiling" = yes &&
@@ -14758,7 +14755,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_file_hyperlight_Sky_h" >&5
 $as_echo "$ac_cv_file_hyperlight_Sky_h" >&6; }
-if test "x$ac_cv_file_hyperlight_Sky_h" = xyes; then :
+if test "x$ac_cv_file_hyperlight_Sky_h" = x""yes; then :
 
 cat >>confdefs.h <<_ACEOF
 #define HAVE_HYPERLIGHT_SKY_H 1
@@ -14776,7 +14773,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for hyperlight/Sky.cpp" >&5
 $as_echo_n "checking for hyperlight/Sky.cpp... " >&6; }
-if ${ac_cv_file_hyperlight_Sky_cpp+:} false; then :
+if test "${ac_cv_file_hyperlight_Sky_cpp+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   test "$cross_compiling" = yes &&
@@ -14789,7 +14786,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_file_hyperlight_Sky_cpp" >&5
 $as_echo "$ac_cv_file_hyperlight_Sky_cpp" >&6; }
-if test "x$ac_cv_file_hyperlight_Sky_cpp" = xyes; then :
+if test "x$ac_cv_file_hyperlight_Sky_cpp" = x""yes; then :
 
 cat >>confdefs.h <<_ACEOF
 #define HAVE_HYPERLIGHT_SKY_CPP 1
@@ -14807,7 +14804,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for hyperlight/Iop.h" >&5
 $as_echo_n "checking for hyperlight/Iop.h... " >&6; }
-if ${ac_cv_file_hyperlight_Iop_h+:} false; then :
+if test "${ac_cv_file_hyperlight_Iop_h+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   test "$cross_compiling" = yes &&
@@ -14820,7 +14817,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_file_hyperlight_Iop_h" >&5
 $as_echo "$ac_cv_file_hyperlight_Iop_h" >&6; }
-if test "x$ac_cv_file_hyperlight_Iop_h" = xyes; then :
+if test "x$ac_cv_file_hyperlight_Iop_h" = x""yes; then :
 
 cat >>confdefs.h <<_ACEOF
 #define HAVE_HYPERLIGHT_IOP_H 1
@@ -14838,7 +14835,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for hyperlight/Iop.cpp" >&5
 $as_echo_n "checking for hyperlight/Iop.cpp... " >&6; }
-if ${ac_cv_file_hyperlight_Iop_cpp+:} false; then :
+if test "${ac_cv_file_hyperlight_Iop_cpp+set}" = set; then :
   $as_echo_n "(cached) " >&6
 else
   test "$cross_compiling" = yes &&
@@ -14851,7 +14848,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_file_hyperlight_Iop_cpp" >&5
 $as_echo "$ac_cv_file_hyperlight_Iop_cpp" >&6; }
-if test "x$ac_cv_file_hyperlight_Iop_cpp" = xyes; then :
+if test "x$ac_cv_file_hyperlight_Iop_cpp" = x""yes; then :
 
 cat >>confdefs.h <<_ACEOF
 #define HAVE_HYPERLIGHT_IOP_CPP 1
@@ -14870,7 +14867,7 @@
 
 fi
 
-ac_config_files="$ac_config_files Makefile debug/Makefile bathymetry/Makefile ocean_forcing/Makefile ocean_forcing/tests/Makefile sediments/Makefile hyperlight/Makefile femtools/Makefile femtools/tests/Makefile forward_interfaces/Makefile horizontal_adaptivity/Makefile horizontal_adaptivity/tests/Makefile preprocessor/Makefile error_measures/Makefile error_measures/tests/Makefile parameterisation/Makefile parameterisation/tests/Makefile fldecomp/Makefile assemble/Makefile assemble/tests/Makefile diagnostics/Makefile main/Makefile tools/Makefile python/setup.py adjoint/Makefile adjoint/tests/Makefile climatology/Makefile libmba2d/Makefile libmba3d/Makefile libjudy/Makefile libjudy/src/Makefile libjudy/src/JudyCommon/Makefile libjudy/src/Judy1/Makefile libjudy/src/JudyL/Makefile libjudy/src/JudySL/Makefile libjudy/src/JudyHS/Makefile libalgencan/Makefile libwm/Makefile libvtkfortran/Makefile reduced_modelling/Makefile"
+ac_config_files="$ac_config_files Makefile debug/Makefile bathymetry/Makefile ocean_forcing/Makefile ocean_forcing/tests/Makefile sediments/Makefile hyperlight/Makefile femtools/Makefile femtools/tests/Makefile forward_interfaces/Makefile horizontal_adaptivity/Makefile horizontal_adaptivity/tests/Makefile preprocessor/Makefile error_measures/Makefile error_measures/tests/Makefile parameterisation/Makefile parameterisation/tests/Makefile fldecomp/Makefile assemble/Makefile assemble/tests/Makefile diagnostics/Makefile main/Makefile tools/Makefile python/setup.py adjoint/Makefile adjoint/tests/Makefile climatology/Makefile libmba2d/Makefile libmba3d/Makefile libjudy/Makefile libjudy/src/Makefile libjudy/src/JudyCommon/Makefile libjudy/src/Judy1/Makefile libjudy/src/JudyL/Makefile libjudy/src/JudySL/Makefile libjudy/src/JudyHS/Makefile libalgencan/Makefile libwm/Makefile libvtkfortran/Makefile schemas/flml reduced_modelling/Makefile"
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -14936,21 +14933,10 @@
      :end' >>confcache
 if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
   if test -w "$cache_file"; then
-    if test "x$cache_file" != "x/dev/null"; then
+    test "x$cache_file" != "x/dev/null" &&
       { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
 $as_echo "$as_me: updating cache $cache_file" >&6;}
-      if test ! -f "$cache_file" || test -h "$cache_file"; then
-	cat confcache >"$cache_file"
-      else
-        case $cache_file in #(
-        */* | ?:*)
-	  mv -f confcache "$cache_file"$$ &&
-	  mv -f "$cache_file"$$ "$cache_file" ;; #(
-        *)
-	  mv -f confcache "$cache_file" ;;
-	esac
-      fi
-    fi
+    cat confcache >$cache_file
   else
     { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
 $as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
@@ -14982,7 +14968,7 @@
 
 
 
-: "${CONFIG_STATUS=./config.status}"
+: ${CONFIG_STATUS=./config.status}
 ac_write_fail=0
 ac_clean_files_save=$ac_clean_files
 ac_clean_files="$ac_clean_files $CONFIG_STATUS"
@@ -15083,7 +15069,6 @@
 IFS=" ""	$as_nl"
 
 # Find who we are.  Look in the path if we contain no directory separator.
-as_myself=
 case $0 in #((
   *[\\/]* ) as_myself=$0 ;;
   *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
@@ -15390,8 +15375,8 @@
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by fluidity $as_me trunk.3665, which was
-generated by GNU Autoconf 2.68.  Invocation command line was
+This file was extended by fluidity $as_me None, which was
+generated by GNU Autoconf 2.67.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
   CONFIG_HEADERS  = $CONFIG_HEADERS
@@ -15452,8 +15437,8 @@
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-fluidity config.status trunk.3665
-configured by $0, generated by GNU Autoconf 2.68,
+fluidity config.status None
+configured by $0, generated by GNU Autoconf 2.67,
   with options \\"\$ac_cs_config\\"
 
 Copyright (C) 2010 Free Software Foundation, Inc.
@@ -15614,9 +15599,10 @@
     "libalgencan/Makefile") CONFIG_FILES="$CONFIG_FILES libalgencan/Makefile" ;;
     "libwm/Makefile") CONFIG_FILES="$CONFIG_FILES libwm/Makefile" ;;
     "libvtkfortran/Makefile") CONFIG_FILES="$CONFIG_FILES libvtkfortran/Makefile" ;;
+    "schemas/flml") CONFIG_FILES="$CONFIG_FILES schemas/flml" ;;
     "reduced_modelling/Makefile") CONFIG_FILES="$CONFIG_FILES reduced_modelling/Makefile" ;;
 
-  *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
+  *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;;
   esac
 done
 
@@ -15638,10 +15624,9 @@
 # after its creation but before its name has been assigned to `$tmp'.
 $debug ||
 {
-  tmp= ac_tmp=
+  tmp=
   trap 'exit_status=$?
-  : "${ac_tmp:=$tmp}"
-  { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
+  { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
 ' 0
   trap 'as_fn_exit 1' 1 2 13 15
 }
@@ -15649,13 +15634,12 @@
 
 {
   tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
-  test -d "$tmp"
+  test -n "$tmp" && test -d "$tmp"
 }  ||
 {
   tmp=./conf$$-$RANDOM
   (umask 077 && mkdir "$tmp")
 } || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
-ac_tmp=$tmp
 
 # Set up the scripts for CONFIG_FILES section.
 # No need to generate them if there are no CONFIG_FILES.
@@ -15677,7 +15661,7 @@
   ac_cs_awk_cr=$ac_cr
 fi
 
-echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
+echo 'BEGIN {' >"$tmp/subs1.awk" &&
 _ACEOF
 
 
@@ -15705,7 +15689,7 @@
 rm -f conf$$subs.sh
 
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&
+cat >>"\$tmp/subs1.awk" <<\\_ACAWK &&
 _ACEOF
 sed -n '
 h
@@ -15753,7 +15737,7 @@
 rm -f conf$$subs.awk
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 _ACAWK
-cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
+cat >>"\$tmp/subs1.awk" <<_ACAWK &&
   for (key in S) S_is_set[key] = 1
   FS = ""
 
@@ -15785,7 +15769,7 @@
   sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
 else
   cat
-fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
+fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
   || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
 _ACEOF
 
@@ -15819,7 +15803,7 @@
 # No need to generate them if there are no CONFIG_HEADERS.
 # This happens for instance with `./config.status Makefile'.
 if test -n "$CONFIG_HEADERS"; then
-cat >"$ac_tmp/defines.awk" <<\_ACAWK ||
+cat >"$tmp/defines.awk" <<\_ACAWK ||
 BEGIN {
 _ACEOF
 
@@ -15831,8 +15815,8 @@
 # handling of long lines.
 ac_delim='%!_!# '
 for ac_last_try in false false :; do
-  ac_tt=`sed -n "/$ac_delim/p" confdefs.h`
-  if test -z "$ac_tt"; then
+  ac_t=`sed -n "/$ac_delim/p" confdefs.h`
+  if test -z "$ac_t"; then
     break
   elif $ac_last_try; then
     as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
@@ -15933,7 +15917,7 @@
   esac
   case $ac_mode$ac_tag in
   :[FHL]*:*);;
-  :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;;
+  :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;;
   :[FH]-) ac_tag=-:-;;
   :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
   esac
@@ -15952,7 +15936,7 @@
     for ac_f
     do
       case $ac_f in
-      -) ac_f="$ac_tmp/stdin";;
+      -) ac_f="$tmp/stdin";;
       *) # Look for the file first in the build tree, then in the source tree
 	 # (if the path is not absolute).  The absolute path cannot be DOS-style,
 	 # because $ac_f cannot contain `:'.
@@ -15961,7 +15945,7 @@
 	   [\\/$]*) false;;
 	   *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
 	   esac ||
-	   as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;;
+	   as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;;
       esac
       case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
       as_fn_append ac_file_inputs " '$ac_f'"
@@ -15987,8 +15971,8 @@
     esac
 
     case $ac_tag in
-    *:-:* | *:-) cat >"$ac_tmp/stdin" \
-      || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+    *:-:* | *:-) cat >"$tmp/stdin" \
+      || as_fn_error $? "could not create $ac_file" "$LINENO" 5  ;;
     esac
     ;;
   esac
@@ -16118,22 +16102,21 @@
 s&@INSTALL@&$ac_INSTALL&;t t
 $ac_datarootdir_hack
 "
-eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
-  >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \
+  || as_fn_error $? "could not create $ac_file" "$LINENO" 5
 
 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
-  { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
-  { ac_out=`sed -n '/^[	 ]*datarootdir[	 ]*:*=/p' \
-      "$ac_tmp/out"`; test -z "$ac_out"; } &&
+  { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
+  { ac_out=`sed -n '/^[	 ]*datarootdir[	 ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
 which seems to be undefined.  Please make sure it is defined" >&5
 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
 which seems to be undefined.  Please make sure it is defined" >&2;}
 
-  rm -f "$ac_tmp/stdin"
+  rm -f "$tmp/stdin"
   case $ac_file in
-  -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";;
-  *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";;
+  -) cat "$tmp/out" && rm -f "$tmp/out";;
+  *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
   esac \
   || as_fn_error $? "could not create $ac_file" "$LINENO" 5
  ;;
@@ -16144,20 +16127,20 @@
   if test x"$ac_file" != x-; then
     {
       $as_echo "/* $configure_input  */" \
-      && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs"
-    } >"$ac_tmp/config.h" \
+      && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs"
+    } >"$tmp/config.h" \
       || as_fn_error $? "could not create $ac_file" "$LINENO" 5
-    if diff "$ac_file" "$ac_tmp/config.h" >/dev/null 2>&1; then
+    if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then
       { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
 $as_echo "$as_me: $ac_file is unchanged" >&6;}
     else
       rm -f "$ac_file"
-      mv "$ac_tmp/config.h" "$ac_file" \
+      mv "$tmp/config.h" "$ac_file" \
 	|| as_fn_error $? "could not create $ac_file" "$LINENO" 5
     fi
   else
     $as_echo "/* $configure_input  */" \
-      && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs" \
+      && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \
       || as_fn_error $? "could not create -" "$LINENO" 5
   fi
  ;;
 
=== modified file 'configure.in'
--- configure.in	2011-10-21 10:05:25 +0000
+++ configure.in	2011-11-30 17:31:28 +0000
@@ -26,11 +26,15 @@
 #    USA
 
 dnl Process this file with autoconf to produce a configure script.
-# Version is comprised of the branch name and the repository revision number.
-AC_INIT(fluidity, m4_esyscmd([echo -n `bzr info | egrep 'parent branch|checkout of' | awk -F/ '{print $(NF-1)}'`.`bzr revision-info | awk '{print $1}'`]))
+
+AC_INIT(fluidity, None)
 
 AC_CONFIG_HEADERS(include/config.h)
 
+# we ignore PACKAGE_VERSION as it is useless
+# instead we pass on FLUIDITY_VERSION from the env. if it is set
+AC_SUBST(FLUIDITY_VERSION)
+
 echo "Hostname: `hostname`"
 
 # Store enviroment variables
@@ -1114,6 +1118,7 @@
 AC_SUBST(FORTRAN_REAL_8)
 AC_SUBST(OPTIMIZATION_FFLAGS)
 AC_SUBST(LINKER)
+AC_SUBST(FLLINKER)
 
 dnl Specific f90 options
 AC_SUBST(USE_CPP)
@@ -1212,7 +1217,9 @@
         AC_MSG_NOTICE([Building on hector xe6; disabling shared libraries])
         SHFLAG=--disable-shared
         SPUD_ONLY="yes"
+        FLLINKER=$CXX
     else
+        FLLINKER=$FC
         SHFLAG=--enable-shared
     fi
     AC_SUBST(SPUD_ONLY)
@@ -1532,4 +1539,5 @@
       	  libalgencan/Makefile
           libwm/Makefile
           libvtkfortran/Makefile
+          schemas/flml
 	  reduced_modelling/Makefile)
 
=== removed file 'debian/README.Debian'
--- debian/README.Debian	2009-12-16 14:11:47 +0000
+++ debian/README.Debian	1970-01-01 00:00:00 +0000
@@ -1,6 +0,0 @@
-fluidity for Debian
--------------------
-
-<possible notes regarding this package - if none, delete this file>
-
- -- David Ham <[e-mail]>  Mon, 05 Nov 2007 15:35:54 +0000
 
=== modified file 'debian/changelog'
--- debian/changelog	2009-12-16 14:11:47 +0000
+++ debian/changelog	2011-11-30 17:31:28 +0000
@@ -1,3 +1,29 @@
+fluidity (4.1maverick1) maverick; urgency=low
+
+  * Fluidity release 4.1
+
+ -- Tim Bond <[e-mail]>  Mon, 07 Nov 2011 12:49:49 +0000
+
+fluidity (4.0.999prerelease1maverick5) maverick; urgency=low
+
+  * Additional trunk changes brought in prior to release
+  * Adding in an examples tarball to the package for release
+
+ -- Tim Bond <[e-mail]> Sun, 06 Nov 2011 20:49:11 +0000
+
+fluidity (4.0.999prerelease1maverick4) maverick; urgency=low
+
+  * Removing fluidity-dev dependency; replacing with best guess at what is
+    needed for everyday running and to run the examples.
+
+ -- Tim Bond <[e-mail]>  Thu, 03 Nov 2011 21:03:59 +0000
+
+fluidity (4.0.999prerelease1maverick1) maverick; urgency=low
+
+  * Fix the Debian packaging for release 4.1.
+
+ -- Patrick Farrell <[e-mail]>  Wed, 02 Nov 2011 14:19:12 +0000
+
 fluidity (3.4.svn6573) unstable; urgency=low
 
   * Another general update. In particular, several tools were out of date.
 
=== modified file 'debian/compat'
--- debian/compat	2009-12-16 14:11:47 +0000
+++ debian/compat	2011-11-30 17:31:28 +0000
@@ -1,1 +1,1 @@
-5
+7
 
=== modified file 'debian/control'
--- debian/control	2009-12-16 14:11:47 +0000
+++ debian/control	2011-11-30 17:31:28 +0000
@@ -1,14 +1,16 @@
 Source: fluidity
-Section: unknown
+Section: science
 Priority: extra
-Maintainer: David Ham <[e-mail]>
-Build-Depends: debhelper (>= 5), autotools-dev
-Standards-Version: 3.7.2
+Maintainer: Patrick Farrell <[e-mail]>
+Build-Depends: debhelper (>= 7.0.50~), fluidity-dev
+Standards-Version: 3.9.1
+XS-Python-Version: >= 2.5
+Homepage: http://amcg.ese.ic.ac.uk/fluidity
 
 Package: fluidity
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, fluidity-dev
-Description: 3D adaptive CFD from Imperial College London
+Depends: ${shlibs:Depends}, ${misc:Depends}, diamond, triangle | triangle-bin, python, gmsh, python-lxml, python-scipy, python-numpy, python-vtk, python-matplotlib, python-sympy, python-fluidity
+Description: 3D adaptive CFD model from Imperial College London
  Fluidity is a general purpose multi-phase CFD code capable of solving
  numerically the Navier-Stokes and accompanying field equations on
  arbitrary unstructured finite element meshes. It uses a moving finite
@@ -16,3 +18,18 @@
  the mesh with time dependent problems. It has a wide range of Finite
  element/spectral elements and full spectral methods which include
  many elements for mixed formulations.
+
+Package: python-fluidity
+Architecture: any
+Section: python
+XB-Python-Version: ${python:Versions}
+Depends: ${python:Depends}, ${misc:Depends}
+Description: 3D adaptive CFD model from Imperial College London
+ Fluidity is a general purpose multi-phase CFD code capable of solving
+ numerically the Navier-Stokes and accompanying field equations on
+ arbitrary unstructured finite element meshes. It uses a moving finite
+ element/spectral element method which allows arbitrary movement of
+ the mesh with time dependent problems. It has a wide range of Finite
+ element/spectral elements and full spectral methods which include
+ many elements for mixed formulations. This package contains the
+ Python scripts used by Fluidity.
 
=== modified file 'debian/copyright'
--- debian/copyright	2009-12-16 14:11:47 +0000
+++ debian/copyright	2011-11-30 17:31:28 +0000
@@ -1,24 +1,20 @@
 This package was debianized by David Ham <[e-mail]> on
 Mon, 05 Nov 2007 15:35:54 +0000.
 
-It was downloaded from <url://example.com>
+It was downloaded from http://amcg.ese.ic.ac.uk/fluidity
 
 Upstream Author(s): 
 
-    <put author's name and email here>
-    <likewise for another author>
+    See AUTHORS
 
 Copyright: 
 
-    <Copyright (C) YYYY Name OfAuthor>
-    <likewise for another author>
+    See AUTHORS
+    Copyright (C) 2002-2012 Imperial College London
 
 License:
 
-    <Put the license of the package here indented by 4 spaces>
+    LGPL v2.1
 
 The Debian packaging is (C) 2007, David Ham <[e-mail]> and
 is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
 
=== removed file 'debian/dirs'
--- debian/dirs	2009-12-16 14:11:47 +0000
+++ debian/dirs	1970-01-01 00:00:00 +0000
@@ -1,2 +0,0 @@
-usr/bin
-usr/sbin
 
=== modified file 'debian/docs'
--- debian/docs	2009-12-16 14:11:47 +0000
+++ debian/docs	2011-11-30 17:31:28 +0000
@@ -1,3 +1,2 @@
 AUTHORS
 README
-LICENSE
 
=== added file 'debian/fluidity.dirs'
--- debian/fluidity.dirs	1970-01-01 00:00:00 +0000
+++ debian/fluidity.dirs	2011-11-30 17:31:28 +0000
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/doc
 
=== added file 'debian/fluidity.install'
--- debian/fluidity.install	1970-01-01 00:00:00 +0000
+++ debian/fluidity.install	2011-11-30 17:31:28 +0000
@@ -0,0 +1,4 @@
+usr/bin/*
+usr/share/doc/*
+usr/share/diamond/schemata/*
+usr/share/fluidity/*
 
=== added file 'debian/python-fluidity.install'
--- debian/python-fluidity.install	1970-01-01 00:00:00 +0000
+++ debian/python-fluidity.install	2011-11-30 17:31:28 +0000
@@ -0,0 +1,2 @@
+usr/lib/python*/dist-packages/fluidity/*
+usr/lib/python*/dist-packages/*.py
 
=== modified file 'debian/rules'
--- debian/rules	2009-12-16 14:11:47 +0000
+++ debian/rules	2011-11-30 17:31:28 +0000
@@ -7,104 +7,25 @@
 # This special exception was added by Craig Small in version 0.37 of dh-make.
 
 # Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-
-# These are used for cross-compiling and for saving the configure script
-# from having to guess our platform (since we know it already)
-DEB_HOST_GNU_TYPE   ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
-DEB_BUILD_GNU_TYPE  ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
-
-
-export PATH:=/usr/lib/mpich-amcg-gcc4/bin:$(PATH)
-export FC=gfortran
-export F77=gfortran
-export F90=gfortran
-export CC=gcc
-export CXX=g++
-export PETSC_DIR=/usr/lib/petscdir/2.3.3-amcg
-export PETSC_ARCH=amcg-gcc4-opt
-export LIBS=-lX11
-
-
-config.status: configure
-	dh_testdir
-	# Add here commands to configure the package.
-
-ifneq "$(wildcard /usr/share/misc/config.sub)" ""
-	cp -f /usr/share/misc/config.sub config.sub
-endif
-ifneq "$(wildcard /usr/share/misc/config.guess)" ""
-	cp -f /usr/share/misc/config.guess config.guess
-endif
-	./configure --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs"
-
-
-build: build-stamp
-
-build-stamp:  config.status
-	dh_testdir
-
-	# Add here commands to compile the package.
-	$(MAKE)
-	#docbook-to-man debian/fluidity.sgml > fluidity.1
-
-	touch $@
-
-clean:
-	dh_testdir
-	dh_testroot
-	rm -f build-stamp 
-
-	# Add here commands to clean up after the build process.
-	$(MAKE) clean
-	rm -f config.sub config.guess
-
-	dh_clean 
-
-install: build
-	dh_testdir
-	dh_testroot
-	dh_clean -k 
-	dh_installdirs
-	# Add here commands to install the package into debian/fluidity.
-	$(MAKE) DESTDIR=$(CURDIR)/debian/fluidity install
-
-
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
-
-# Build architecture-dependent files here.
-binary-arch: build install
-	dh_testdir
-	dh_testroot
-	dh_installchangelogs 
-	dh_installdocs
-	dh_installexamples
-#	dh_install
-#	dh_installmenu
-#	dh_installdebconf	
-#	dh_installlogrotate
-#	dh_installemacsen
-#	dh_installpam
-#	dh_installmime
-#	dh_python
-#	dh_installinit
-#	dh_installcron
-#	dh_installinfo
-	dh_installman
-	dh_link
-	dh_strip
-	dh_compress
-	dh_fixperms
-#	dh_perl
-#	dh_makeshlibs
-	dh_installdeb
-	dh_shlibdeps
-	dh_gencontrol
-	dh_md5sums
-	dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install 
+export DH_VERBOSE=1
+export PETSC_DIR=/usr/lib/petscdir/3.1
+export PETSC_ARCH=linux-gnu-c-opt
+export prefix=/usr
+export DEB_BUILD_OPTIONS=nostrip
+export PYTHONPATH=
+export FLUIDITY_PYTHON_INSTALL_ARGS=--install-layout=deb
+# setting this sets the version number reported by ./fluidity --version
+# it also stops the build system trying to use bzr to get a version number
+export FLUIDITY_VERSION=fluidity/4.1
+
+%:
+	dh --with=python2 $@
+
+override_dh_auto_build:
+	make -j8
+	make manual
+
+override_dh_auto_configure:
+	./configure --prefix=/usr --enable-2d-adaptivity --datadir=/usr/share --datarootdir=/usr/share --docdir=/usr/share/doc
+
+override_dh_auto_test:
 
=== modified file 'diagnostics/Differential_Operators.F90'
--- diagnostics/Differential_Operators.F90	2011-04-22 17:28:48 +0000
+++ diagnostics/Differential_Operators.F90	2011-11-30 17:31:28 +0000
@@ -55,6 +55,7 @@
   private
   
   public :: calculate_grad, calculate_div, calculate_curl, calculate_perp, &
+    & calculate_hessian, calculate_grad_vector, &
     & calculate_curl_2d, calculate_finite_element_divergence, &
     & calculate_finite_element_divergence_transpose, &
     & calculate_scalar_advection, calculate_scalar_laplacian, &
@@ -79,6 +80,39 @@
     
   end subroutine calculate_grad
 
+  subroutine calculate_grad_vector(state, t_field)
+    type(state_type), intent(inout) :: state
+    type(tensor_field), intent(inout) :: t_field
+    
+    type(vector_field), pointer :: source_field
+    type(vector_field), pointer :: positions
+
+    positions => extract_vector_field(state, "Coordinate")
+    source_field => vector_source_field(state, t_field)
+
+    call check_source_mesh_derivative(source_field, "grad_vector")
+
+    call grad(source_field, positions, t_field)
+
+  end subroutine calculate_grad_vector
+
+  subroutine calculate_hessian(state, t_field)
+    ! Compute Hessian of a scalar field
+    type(state_type), intent(inout) :: state
+    type(tensor_field), intent(inout) :: t_field
+    
+    type(scalar_field), pointer :: source_field
+    type(vector_field), pointer :: positions
+
+    positions => extract_vector_field(state, "Coordinate")
+    source_field => scalar_source_field(state, t_field)
+
+    call check_source_mesh_derivative(source_field, "hessian")
+
+    call compute_hessian(source_field, positions, t_field)
+
+  end subroutine calculate_hessian
+
   subroutine calculate_div(state, s_field)
     type(state_type), intent(in) :: state
     type(scalar_field), intent(inout) :: s_field
 
=== modified file 'diagnostics/Field_Copies.F90'
--- diagnostics/Field_Copies.F90	2011-04-22 17:28:48 +0000
+++ diagnostics/Field_Copies.F90	2011-11-30 17:31:28 +0000
@@ -448,18 +448,19 @@
     ! NOT a tensor here. Alpha is a scaling constant for the mesh size tensor.
     real :: alpha
     type(scalar_field), pointer :: source_field
-    type(vector_field), pointer :: positions
+    type(vector_field), pointer :: positions, velocity
 
     ewrite(1, *) "In calculate_helmholtz_anisotropic_smoothed_scalar"
 
-    positions       => extract_vector_field(state, "Coordinate")
+    positions => extract_vector_field(state, "Coordinate")
+    velocity  => extract_vector_field(state, "Velocity")
     source_field => scalar_source_field(state, s_field, allocated = allocated)
 
     path = trim(complete_field_path(s_field%option_path)) // "/algorithm"
     call get_option(trim(path) // "/smoothing_length_scale", alpha)
-    call anisotropic_smooth_scalar(source_field, positions, s_field, alpha, path)
-
     ewrite(2, *) "alpha = ", alpha
+    call anisotropic_smooth_scalar(source_field, positions, velocity, s_field, alpha, path)
+
     ewrite_minmax(source_field)
     ewrite_minmax(s_field)
 
@@ -485,9 +486,9 @@
 
     path = trim(complete_field_path(v_field%option_path)) // "/algorithm"
     call get_option(trim(path) // "/smoothing_length_scale", alpha)
+    ewrite(2, *) "alpha = ", alpha
     call anisotropic_smooth_vector(source_field, positions, v_field, alpha, path)
 
-    ewrite(2, *) "alpha = ", alpha
     ewrite_minmax(source_field)
     ewrite_minmax(v_field)
     
@@ -512,9 +513,9 @@
 
     path = trim(complete_field_path(t_field%option_path)) // "/algorithm"
     call get_option(trim(path) // "/smoothing_length_scale", alpha)
+    ewrite(2, *) "alpha = ", alpha
     call anisotropic_smooth_tensor(source_field, positions, t_field, alpha, path)
 
-    ewrite(2, *) "alpha = ", alpha
     ewrite_minmax(source_field)
     ewrite_minmax(t_field)
     
 
=== modified file 'diagnostics/Momentum_Diagnostics.F90'
--- diagnostics/Momentum_Diagnostics.F90	2011-10-03 12:48:49 +0000
+++ diagnostics/Momentum_Diagnostics.F90	2011-11-30 17:31:28 +0000
@@ -44,7 +44,7 @@
   use spud
   use state_fields_module
   use state_module
-  use sediment
+  use sediment, only : get_n_sediment_fields, get_sediment_item
   
   implicit none
   
@@ -54,7 +54,7 @@
             calculate_buoyancy, calculate_coriolis, calculate_tensor_second_invariant, &
             calculate_imposed_material_velocity_source, calculate_imposed_material_velocity_absorption, &
             calculate_scalar_potential, calculate_projection_scalar_potential, &
-            calculate_geostrophic_velocity, calculate_hessian
+            calculate_geostrophic_velocity, calculate_k_epsilon_diffusivity
            
   
 contains
@@ -74,23 +74,78 @@
     call strain_rate(source_field, positions, t_field)
 
   end subroutine calculate_strain_rate
-
-  subroutine calculate_hessian(state, t_field)
-    ! Compute Hessian of a scalar field
-    type(state_type), intent(inout) :: state
+ 
+  subroutine calculate_k_epsilon_diffusivity(state, t_field)
+    ! calculates scalar field diffusivity based upon eddy viscosity and background
+    !  diffusivity
+    type(state_type), intent(inout)   :: state
     type(tensor_field), intent(inout) :: t_field
-    
-    type(scalar_field), pointer :: source_field
-    type(vector_field), pointer :: positions
-
-    positions => extract_vector_field(state, "Coordinate")
-    source_field => scalar_source_field(state, t_field)
-
-    call check_source_mesh_derivative(source_field, "hessian")
-
-    call compute_hessian(source_field, positions, t_field)
-
-  end subroutine calculate_hessian
+    character(len = OPTION_PATH_LEN)  :: parent_path
+    integer                           :: slash_location, i, stat
+    real                              :: prandtl_schmidt, local_background_diffusivity
+    type(scalar_field)                :: local_background_diffusivity_field
+    type(tensor_field), pointer       :: global_background_diffusivity, eddy_viscosity
+    type(tensor_field)                :: background_diffusivity
+
+    ewrite(1,*) 'In calculate_k_epsilon_diffusivity'
+
+    ! get parent scalar field path
+    slash_location = scan(t_field%option_path, '/', .true.)
+    parent_path = t_field%option_path(1:slash_location-1)
+
+    ! check options
+    if (.not.(have_option(trim(parent_path)//'/subgridscale_parameterisation::k-epsilon')))&
+         & then
+       FLExit('you must have /subgridscale_parameterisation(k-epsilon) to be able to calculate&
+            & diffusivity based upon the k-epsilon model')
+    end if
+
+    ! get prandtl_schmidt number
+    call get_option(trim(parent_path)//'/subgridscale_parameterisation::k-epsilon/Prandtl_&
+         &Schmidt_Number', prandtl_schmidt, stat=stat)
+    if (stat /= 0) then 
+       prandtl_schmidt = 1.0
+    end if
+
+    ! allocate and zero required fields
+    call allocate(background_diffusivity, t_field%mesh, name="background_diff&
+         &usivity")
+    call zero(background_diffusivity)
+    call allocate(local_background_diffusivity_field, t_field%mesh, name="local_backgro&
+         &und_diffusivity_field")
+    call zero(local_background_diffusivity_field)
+
+    ! set background_diffusivity (local takes precendence over global)
+    call get_option(trim(parent_path)//'/subgridscale_parameterisation::k-epsilon/Backg&
+            &roundDiffusivity', local_background_diffusivity, stat=stat)
+    if (stat == 0) then 
+       ! set local isotropic background diffusivity
+       call addto(local_background_diffusivity_field, local_background_diffusivity)
+       do i = 1, background_diffusivity%dim(1)
+          call set(background_diffusivity, i, i, local_background_diffusivity_field)
+       end do
+    else
+       global_background_diffusivity => extract_tensor_field(state, 'BackgroundDiffusivity', stat=stat)
+       if (stat == 0) then 
+          call set(background_diffusivity, global_background_diffusivity)
+       end if
+    end if
+
+    ! get eddy viscosity
+    eddy_viscosity => extract_tensor_field(state, 'EddyViscosity', stat)
+    if (stat /= 0) then 
+       FLExit("No EddyViscosity field was found. Check the k-epsilon model is turned on an&
+            &d you have a valid flml input file.")
+    end if
+
+    call zero(t_field)
+    call addto(t_field, background_diffusivity)
+    call addto(t_field, eddy_viscosity, 1.0/prandtl_schmidt) 
+
+    call deallocate(background_diffusivity)
+    call deallocate(local_background_diffusivity_field)
+
+  end subroutine calculate_k_epsilon_diffusivity
 
   subroutine calculate_sediment_concentration_dependent_viscosity(state, t_field)
     ! calculates viscosity based upon total sediment concentration
@@ -101,25 +156,23 @@
     type(tensor_field), pointer :: zero_conc_viscosity
     type(scalar_field) :: rhs
     integer :: sediment_classes, i
-    character(len = OPTION_PATH_LEN) :: class_name
+    character(len = FIELD_NAME_LEN) :: field_name
     
-    ewrite(1,*) 'In calculate sediment concentration dependent viscosity'
+    ewrite(1,*) 'In calculate_sediment_concentration_dependent_viscosity'
 
-    sediment_classes = get_nSediments()
+    sediment_classes = get_n_sediment_fields()
 
     if (sediment_classes > 0) then
         allocate(sediment_concs(sediment_classes))
         
-        class_name=get_sediment_name(1)
-        sediment_concs(1)%ptr => extract_scalar_field(state,trim(class_name))
+        call get_sediment_item(state, 1, sediment_concs(1)%ptr)
         
         call allocate(rhs, sediment_concs(1)%ptr%mesh, name="Rhs")
         call set(rhs, 1.0)
         
         ! get sediment concentrations and remove c/0.65 from rhs
         do i=1, sediment_classes
-           class_name=get_sediment_name(i)
-           sediment_concs(i)%ptr => extract_scalar_field(state,trim(class_name))
+           call get_sediment_item(state, i, sediment_concs(i)%ptr)
            call addto(rhs, sediment_concs(i)%ptr, scale=-(1.0/0.65))
         end do
         
@@ -128,17 +181,22 @@
            call set(rhs, i, node_val(rhs, i)**(-1.625))
         end do
         
+        ! check for presence of ZeroSedimentConcentrationViscosity field
+        if (.not. has_tensor_field(state, "ZeroSedimentConcentrationViscosity")) then
+           FLExit("You must specify an zero sediment concentration viscosity to be able &
+                &to calculate sediment concentration dependent viscosity field values")
+        endif
         zero_conc_viscosity => extract_tensor_field(state, 'ZeroSedimentConcentrationViscosity')
         
         call set(t_field, zero_conc_viscosity)
         call scale(t_field, rhs)
         ewrite_minmax(t_field) 
 
+        deallocate(sediment_concs)
         call deallocate(rhs)
     else
         ewrite(1,*) 'No sediment in problem definition'
     end if  
-
   end subroutine calculate_sediment_concentration_dependent_viscosity
   
   subroutine calculate_tensor_second_invariant(state, s_field)
 
=== modified file 'diagnostics/Simple_Diagnostics.F90'
--- diagnostics/Simple_Diagnostics.F90	2011-09-27 20:36:00 +0000
+++ diagnostics/Simple_Diagnostics.F90	2011-11-30 17:31:28 +0000
@@ -157,6 +157,7 @@
     type(scalar_field), pointer :: source_field
     real :: a, b, spin_up_time, current_time, dt, averaging_period
     integer :: stat
+    logical :: absolute_vals=.false.
 
     if (timestep==0) then 
       last_output_time = 0.0
@@ -167,10 +168,12 @@
     call get_option("/timestepping/current_time", current_time)
     call get_option("/timestepping/timestep", dt)
 
+    absolute_vals=have_option(trim(s_field%option_path)//"/diagnostic/algorithm/absolute_values")
     call get_option(trim(s_field%option_path)//"/diagnostic/algorithm/spin_up_time", spin_up_time, stat)
     if (stat /=0) spin_up_time=0.
 
     source_field => scalar_source_field(state, s_field)
+    if(absolute_vals) source_field%val = abs(source_field%val)
 
     if (current_time>spin_up_time) then
         a = (current_time-spin_up_time-dt)/(current_time-spin_up_time)
@@ -230,6 +233,7 @@
     type(vector_field), pointer :: source_field
     real :: a, b, spin_up_time, current_time, dt
     integer :: stat
+    logical :: absolute_vals
 
     if (timestep==0) then 
       call initialise_diagnostic_from_checkpoint(v_field)
@@ -239,9 +243,11 @@
     call get_option("/timestepping/current_time", current_time)
     call get_option("/timestepping/timestep", dt)
 
+    absolute_vals=have_option(trim(v_field%option_path)//"/diagnostic/algorithm/absolute_values")
     call get_option(trim(v_field%option_path)//"/diagnostic/algorithm/spin_up_time", spin_up_time, stat)
     if (stat /=0) spin_up_time=0.
     source_field => vector_source_field(state, v_field)
+    if(absolute_vals) source_field%val = abs(source_field%val)
 
     if (current_time>spin_up_time) then
       a = (current_time-spin_up_time-dt)/(current_time-spin_up_time); b = dt/(current_time-spin_up_time)
@@ -374,33 +380,54 @@
     type(scalar_field), intent(inout) :: s_field
 
     type(scalar_field), pointer :: read_field
-    character(len = OPTION_PATH_LEN) :: path, filename
+    character(len = OPTION_PATH_LEN) :: filename
     logical :: checkpoint_exists
-    
-    path = "/geometry/mesh::CoordinateMesh/from_file/file_name"
-    call get_option(trim(path), filename)
+    integer :: i
+    integer :: stat
+
+    stat = 1
+
+    do i = 1, option_count("/geometry/mesh")
+      if(have_option("/geometry/mesh["//int2str(i)//"]/from_file/file_name")) then
+        call get_option("/geometry/mesh["//int2str(i)//"]/from_file/file_name", filename, stat)
+        ewrite(2,*) "mesh from file: ", filename
+      end if
+    end do
+    if (stat /= 0) return
+
     if(isparallel()) then
-      filename = parallel_filename(trim_file_extension(filename), ".vtu")
+        filename = parallel_filename(trim_file_extension(filename), ".vtu")
     else
-      filename = trim(filename) // ".vtu"
+        filename = trim(filename) // ".vtu"
     end if
     inquire(file=trim(filename), exist=checkpoint_exists)
     
     if (checkpoint_exists) then
-      read_field => vtk_cache_read_scalar_field(filename, trim(s_field%name))
-      call set(s_field, read_field)
+        read_field => vtk_cache_read_scalar_field(filename, trim(s_field%name))
+        call set(s_field, read_field)
     end if
+
   end subroutine initialise_diagnostic_scalar_from_checkpoint
 
   subroutine initialise_diagnostic_vector_from_checkpoint(v_field) 
     type(vector_field), intent(inout) :: v_field
 
     type(vector_field), pointer :: read_field
-    character(len = OPTION_PATH_LEN) :: path, filename
+    character(len = OPTION_PATH_LEN) :: filename
     logical :: checkpoint_exists
-    
-    path = "/geometry/mesh::CoordinateMesh/from_file/file_name"
-    call get_option(trim(path), filename)
+    integer :: i
+    integer :: stat
+
+    stat = 1
+
+    do i = 1, option_count("/geometry/mesh")
+      if(have_option("/geometry/mesh["//int2str(i)//"]/from_file/file_name")) then
+        call get_option("/geometry/mesh["//int2str(i)//"]/from_file/file_name", filename , stat)
+        ewrite(2,*) "mesh from file: ", filename
+      end if
+    end do
+    if (stat /= 0) return
+
     if(isparallel()) then
       filename = parallel_filename(trim_file_extension(filename), ".vtu")
     else
@@ -412,17 +439,28 @@
       read_field => vtk_cache_read_vector_field(filename, trim(v_field%name))
       call set(v_field, read_field)
     end if
+
   end subroutine initialise_diagnostic_vector_from_checkpoint
 
   subroutine initialise_diagnostic_tensor_from_checkpoint(t_field) 
     type(tensor_field), intent(inout) :: t_field
 
     type(tensor_field), pointer :: read_field
-    character(len = OPTION_PATH_LEN) :: path, filename
+    character(len = OPTION_PATH_LEN) :: filename
     logical :: checkpoint_exists
-    
-    path = "/geometry/mesh::CoordinateMesh/from_file/file_name"
-    call get_option(trim(path), filename)
+    integer :: i
+    integer :: stat
+
+    stat = 1
+
+    do i = 1, option_count("/geometry/mesh")
+      if(have_option("/geometry/mesh["//int2str(i)//"]/from_file/file_name")) then
+        call get_option("/geometry/mesh["//int2str(i)//"]/from_file/file_name", filename, stat)
+        ewrite(2,*) "mesh from file: ", filename
+      end if
+    end do
+    if (stat /= 0) return
+
     if(isparallel()) then
       filename = parallel_filename(trim_file_extension(filename), ".vtu")
     else
@@ -434,6 +472,7 @@
       read_field => vtk_cache_read_tensor_field(filename, trim(t_field%name))
       call set(t_field, read_field)
     end if
+
   end subroutine initialise_diagnostic_tensor_from_checkpoint
 
  end module simple_diagnostics
 
=== modified file 'error_measures/Geometric_constraints_metric.F90'
--- error_measures/Geometric_constraints_metric.F90	2011-02-28 16:03:39 +0000
+++ error_measures/Geometric_constraints_metric.F90	2011-11-30 17:31:28 +0000
@@ -37,7 +37,6 @@
 
     integer :: dim
     integer :: stat, stat2
-    real :: gradation_parameter
 
     real, dimension(error_metric%dim(1) * error_metric%dim(2) * node_count(error_metric)) :: geometric_edge_lengths_raw
     type(tensor_field) :: geometric_edge_lengths
@@ -73,8 +72,6 @@
     deallocate(lsenlist)
 
     geometric_edge_lengths = wrap_tensor_field(error_metric%mesh, geometric_edge_lengths_raw, "GeometricEdgeLengths")
-    call get_option("/mesh_adaptivity/hr_adaptivity/enable_gradation/gradation_parameter", gradation_parameter, stat=stat)
-    call set_option("/mesh_adaptivity/hr_adaptivity/enable_gradation/gradation_parameter", 1.1, stat=stat2)
 
     call bound_metric(geometric_edge_lengths, state)
     if (.not. isparallel()) then
@@ -93,12 +90,6 @@
       end do
     end if
 
-    if (stat == 0) then
-      call set_option("/mesh_adaptivity/hr_adaptivity/enable_gradation/gradation_parameter", gradation_parameter)
-    else
-      call delete_option("/mesh_adaptivity/hr_adaptivity/enable_gradation/gradation_parameter")
-    end if
-
     if (debug_metric) then
       call allocate(edgelen, error_metric%mesh, "Desired edge lengths")
       call allocate(geometric_edgelen, error_metric%mesh, "Geometric edge lengths")
 
=== added directory 'examples/backward_facing_step_2d/Ilinca-data'
=== added file 'examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-1.33.dat'
--- examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-1.33.dat	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-1.33.dat	2011-11-30 17:31:28 +0000
@@ -0,0 +1,17 @@
+-0.07421875  -0.00109682881773
+-0.07421875  0.102351447044
+-0.09765625  0.161118380542
+-0.11328125  0.367784020936
+-0.125  0.485837438424
+-0.10546875  0.619131003695
+0.125  0.829433497537
+0.2734375  0.905518780788
+0.47265625  0.967576200739
+0.59765625  1.01375846675
+0.7265625  1.04522013547
+0.828125  1.09105603448
+0.87890625  1.12136314655
+0.95703125  1.19640932882
+0.984375  1.27070504926
+0.99609375  1.37432650862
+0.99609375  1.52210975985
 
=== added file 'examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-16.0.dat'
--- examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-16.0.dat	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-16.0.dat	2011-11-30 17:31:28 +0000
@@ -0,0 +1,17 @@
+0.335234899329  0
+0.377516778523  0
+0.424496644295  0
+0.487919463087  0
+0.530201342282  0
+0.570145856868  0.0148514851485
+0.600706026979  0.0445544554455
+0.64538341418  0.10396039604
+0.680699714267  0.207920792079
+0.741982856004  0.475247524752
+0.800905375772  0.727722772277
+0.859839524221  0.99504950495
+0.899935211642  1.20297029703
+0.937681905774  1.41089108911
+0.958915874809  1.5297029703
+0.984905973819  1.72277227723
+1.00152335703  1.94554455446
 
=== added file 'examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-2.66.dat'
--- examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-2.66.dat	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-2.66.dat	2011-11-30 17:31:28 +0000
@@ -0,0 +1,16 @@
+-0.101288826687  -0.00150397927851
+-0.143442023688  0.0275729534393
+-0.172769619619  0.175652246569
+-0.155787186932  0.250161886658
+-0.134501702421  0.384141374052
+-0.10057861425  0.50345706348
+0.0683892799699  0.639629853989
+0.14444467654  0.715016815324
+0.24157667161  0.7758653103
+0.338729555282  0.851565600652
+0.511854281119  0.943245670837
+0.646982641572  1.01950995342
+0.803208489127  1.09608756502
+0.942577235603  1.18726630878
+0.993440979258  1.35138804754
+1.00210974871  1.51488312828
 
=== added file 'examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-5.33.dat'
--- examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-5.33.dat	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-5.33.dat	2011-11-30 17:31:28 +0000
@@ -0,0 +1,19 @@
+-0.208481081307  -0.00600725877101
+-0.251074214676  0.0221517667181
+-0.204392807976  0.111760043386
+-0.161924825831  0.171832631096
+-0.0939468524467  0.247361395019
+0.0590505193776  0.384214258896
+0.131304492929  0.445162905177
+0.207792749572  0.520941971549
+0.280046723124  0.58189061783
+0.365066121564  0.643214717784
+0.586041466772  0.855596345584
+0.734825414042  0.962913520504
+0.798569104334  1.02361186434
+0.875078219515  1.08468566184
+0.92180134329  1.14488340078
+0.964248466898  1.21966125735
+0.993909307079  1.30876892912
+1.01082558091  1.38279587835
+1.01024154186  1.79454340662
 
=== added file 'examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-8.0.dat'
--- examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-8.0.dat	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-expt-8.0.dat	2011-11-30 17:31:28 +0000
@@ -0,0 +1,16 @@
+0.144407894737  0.000732803543512
+0.168092105263  0.00112363210005
+0.191776315789  0.0163659458051
+0.206578947368  0.04631318395
+0.236184210526  0.150762115685
+0.304276315789  0.315252084419
+0.416776315789  0.435920401251
+0.514473684211  0.586047420532
+0.561842105263  0.646235018239
+0.6625  0.781559405941
+0.736513157895  0.842186685774
+0.825328947368  0.977315659197
+0.896381578947  1.1121515112
+0.949671052632  1.24669424179
+0.985197368421  1.44034979156
+0.997039473684  1.72272342366
 
=== added file 'examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-1.33.dat'
--- examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-1.33.dat	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-1.33.dat	2011-11-30 17:31:28 +0000
@@ -0,0 +1,18 @@
+-0.109375  0.0722752463054
+-0.09765625  0.249788331281
+-0.0703125  0.412754002463
+0.02734375  0.798433651478
+0.10546875  0.888258158867
+0.23046875  0.94921875
+0.3515625  0.995343288177
+0.44140625  1.01144935345
+0.5703125  1.05768934729
+0.7578125  1.10479525862
+0.87890625  1.1509197968
+0.9609375  1.24080203202
+0.99609375  1.43343980911
+0.9921875  2.17229833744
+0.984375  2.48252770936
+0.9765625  2.65975215517
+0.9140625  2.83616841133
+0.83984375  2.92374153325
 
=== added file 'examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-16.0.dat'
--- examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-16.0.dat	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-16.0.dat	2011-11-30 17:31:28 +0000
@@ -0,0 +1,15 @@
+0.516153897269  0.0594059405941
+0.542062595521  0.148514851485
+0.60097348661  0.386138613861
+0.650441889827  0.564356435644
+0.728156355904  0.816831683168
+0.791730347531  1.0099009901
+0.843536115357  1.17326732673
+0.930658183268  1.44059405941
+0.980173101203  1.67821782178
+1.00147684232  1.88613861386
+0.996918399894  2.06435643564
+0.959578709549  2.37623762376
+0.894004585022  2.62871287129
+0.795509668417  2.83663366337
+0.725109641837  2.92574257426
 
=== added file 'examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-2.66.dat'
--- examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-2.66.dat	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-2.66.dat	2011-11-30 17:31:28 +0000
@@ -0,0 +1,16 @@
+-0.223528920268  0.0857894846782
+-0.202285212959  0.190065381321
+-0.0583418628454  0.533787312264
+0.00929542748522  0.623900737368
+0.102270590939  0.729241952666
+0.233242119775  0.84999895557
+0.427506109916  0.971695945523
+0.659724688238  1.07910513233
+0.866605393437  1.17128652894
+0.968019551731  1.27675307585
+0.997764919683  1.42570969022
+0.986025525871  2.07900068932
+0.978254966265  2.55413280973
+0.948969147536  2.73191569361
+0.91531761118  2.80567334406
+0.814216781902  2.92298372778
 
=== added file 'examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-5.33.dat'
--- examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-5.33.dat	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-5.33.dat	2011-11-30 17:31:28 +0000
@@ -0,0 +1,16 @@
+-0.102206833257  0.0706478661716
+-0.0640982854282  0.20412164699
+0.0462433774144  0.413249342956
+0.237432731217  0.624754912186
+0.322452129657  0.68607901214
+0.44145008552  0.792520128489
+0.581702890993  0.914292269826
+0.794230528555  1.08230778858
+0.887739351717  1.15858745985
+0.981123023654  1.32309874432
+1.00212757081  1.5148929957
+1.00559008802  2.07381836386
+1.00519377581  2.35321847232
+0.9793083309  2.60245713571
+0.940845187935  2.71897292562
+0.881106336824  2.83486295941
 
=== added file 'examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-8.0.dat'
--- examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-8.0.dat	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Ilinca-data/Ilinca-U-num-8.0.dat	2011-11-30 17:31:28 +0000
@@ -0,0 +1,17 @@
+0.191776315789  0.0312174309536
+0.242105263158  0.254820218864
+0.336842105263  0.434601354872
+0.416776315789  0.569583767587
+0.502631578947  0.674960917144
+0.677302631579  0.915467040125
+0.846052631579  1.11132100052
+0.905263157895  1.2014069828
+0.958552631579  1.33594971339
+0.982236842105  1.45515242314
+0.994078947368  1.70782308494
+0.997039473684  1.87123827514
+0.988157894737  2.27208181344
+0.976315789474  2.4055497655
+0.925986842105  2.62749153205
+0.83125  2.81899752475
+0.748355263158  2.9067385357
 
=== added file 'examples/backward_facing_step_2d/Makefile'
--- examples/backward_facing_step_2d/Makefile	1970-01-01 00:00:00 +0000
+++ examples/backward_facing_step_2d/Makefile	2011-11-30 17:31:28 +0000
@@ -0,0 +1,31 @@
+BIN=../../../bin
+preprocess:
+	@if [ "x" == "x${TYPE}" ]; then echo "**********ERROR: Commandline should be make preprocess TYPE=type, where type is reference or kepsilon"; false; fi;
+	echo **********Installing directory for $(TYPE) run:
+	install -d $(TYPE); \
+	cd $(TYPE); \
+	ln -s ../backward_facing_step_2d_kim_$(TYPE).flml .; \
+	echo **********Generating mesh for $(TYPE) simulation.; \
+	gmsh -2 -o step2d-kim-med.msh ../src/step2d-kim-med.geo; \
+	$(BIN)/gmsh2triangle -2 step2d-kim-med.msh; \
+	cd ..
+
+run:
+	@if [ "x" == "x${TYPE}" ]; then echo "**********ERROR: Commandline should be make run TYPE=type, where type is reference or kepsilon"; false; fi;
+	@echo **********Running the $(TYPE) simulation:
+	cd $(TYPE) &&  $(BIN)/fluidity -v2 -l backward_facing_step_2d_kim_$(TYPE).flml &&  cd ..
+
+postprocess:
+	@if [ "x" == "x${TYPE}" ]; then echo "**********ERROR: Commandline should be make postprocess TYPE=type, where type is reference or kepsilon"; false; fi;
+	@echo **********Calling the velocity data extraction and reattachment length calculation python script:
+	cd $(TYPE); \
+	ln -s ../postprocessor_2d.py .; \
+	./postprocessor_2d.py $(TYPE); \
+	cd ..
+
+input: clean preprocess
+
+clean:
+	@echo **********Cleaning the output from previous fluidity runs
+	rm -r kepsilon reference *.pdf
+
 
=== removed file 'examples/backward_facing_step_2d/Makefile'
--- examples/backward_facing_step_2d/Makefile	2011-10-21 14:11:04 +0000
+++ examples/backward_facing_step_2d/Makefile	1970-01-01 00:00:00 +0000
@@ -1,51 +0,0 @@
-BIN=../../../bin
-RE=4700
-JOB=high
-ROOT=$(PWD)
-
-preprocess: 
-	@echo **********Generating a 2D mesh:
-	@$(foreach NN,coarse med fine, \
-		echo **********Installing directory for $(NN) simulation.; \
-		install -d $(RE)-$(JOB)-$(NN); \
-		if [ -d "$(RE)-$(JOB)-$(NN)" ]; then \
-			cd $(RE)-$(JOB)-$(NN); \
-			ln -sf ../backward_facing_step_2d-$(RE)-$(JOB)-$(NN).flml .; \
-			echo **********Generating mesh for $(NN) simulation.; \
-			gmsh -2 -optimize -o step2d-$(NN).msh ../src/step2d-$(NN).geo; \
-			$(BIN)/gmsh2triangle -2 step2d-$(NN).msh ; \
-			cd $(ROOT); \
-		fi; \
-	)
-
-run:
-	@echo **********Running the test on different meshes:
-	@$(foreach NN,coarse med fine, \
-		if [ -d "$(RE)-$(JOB)-$(NN)" ]; then \
-			cd $(RE)-$(JOB)-$(NN); \
-			echo **********Running simulation for $(NN) mesh.; \
-			$(BIN)/fluidity -v2 -l backward_facing_step_2d-$(RE)-$(JOB)-$(NN).flml; \
-			cd $(ROOT); \
-		fi; \
-	)
-
-postprocess:
-	@echo **********Calling the velocity data extraction and reattachment length calculation python script:
-	@$(foreach NN,coarse med fine, \
-		if [ -d "$(RE)-$(JOB)-$(NN)" ]; then \
-			cd $(RE)-$(JOB)-$(NN); \
-			ln -s ../postprocessor_2d.py .; \
-			./postprocessor_2d.py $(RE) $(JOB) $(NN); \
-			cd $(ROOT); \
-		fi; \
-	)
-
-input: clean preprocess
-
-clean:
-	@echo **********Cleaning the output from previous fluidity runs
-	@$(foreach NN,coarse med fine, \
-		if [ -d "$(RE)-$(JOB)-$(NN)" ]; then \
-			echo **********Cleaning folder $(RE)-$(JOB)-$(NN); \
-			rm -r $(RE)-$(JOB)-$(NN); fi; \
-	)
 
=== removed file 'examples/backward_facing_step_2d/backward_facing_step_2d-4700-high-coarse.flml'
--- examples/backward_facing_step_2d/backward_facing_step_2d-4700-high-coarse.flml	2011-04-26 15:43:25 +0000
+++ examples/backward_facing_step_2d/backward_facing_step_2d-4700-high-coarse.flml	1970-01-01 00:00:00 +0000
@@ -1,591 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<fluidity_options>
-  <simulation_name>
-    <string_value lines="1">backward_facing_step_2d-high-coarse</string_value>
-  </simulation_name>
-  <problem_type>
-    <string_value lines="1">fluids</string_value>
-  </problem_type>
-  <geometry>
-    <dimension>
-      <integer_value rank="0">2</integer_value>
-    </dimension>
-    <mesh name="CoordinateMesh">
-      <from_file file_name="step2d-coarse">
-        <format name="triangle"/>
-        <stat>
-          <include_in_stat/>
-        </stat>
-      </from_file>
-    </mesh>
-    <mesh name="VelocityMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <mesh name="PressureMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <quadrature>
-      <degree>
-        <integer_value rank="0">3</integer_value>
-      </degree>
-    </quadrature>
-  </geometry>
-  <io>
-    <dump_format>
-      <string_value>vtk</string_value>
-    </dump_format>
-    <dump_period_in_timesteps>
-      <constant>
-        <integer_value rank="0">10</integer_value>
-      </constant>
-    </dump_period_in_timesteps>
-    <output_mesh name="CoordinateMesh"/>
-    <stat/>
-  </io>
-  <timestepping>
-    <current_time>
-      <real_value rank="0">0.0</real_value>
-    </current_time>
-    <timestep>
-      <real_value rank="0">0.05</real_value>
-    </timestep>
-    <finish_time>
-      <real_value rank="0">300.0</real_value>
-    </finish_time>
-    <nonlinear_iterations>
-      <integer_value rank="0">2</integer_value>
-    </nonlinear_iterations>
-    <adaptive_timestep>
-      <requested_cfl>
-        <real_value rank="0">1.0</real_value>
-      </requested_cfl>
-      <courant_number name="CFLNumber">
-        <mesh name="VelocityMesh"/>
-      </courant_number>
-    </adaptive_timestep>
-    <steady_state>
-      <tolerance>
-        <real_value rank="0">1.e-5</real_value>
-        <infinity_norm/>
-      </tolerance>
-      <steady_state_file>
-        <plain_text_output/>
-      </steady_state_file>
-    </steady_state>
-  </timestepping>
-  <material_phase name="Fluid">
-    <subgridscale_parameterisations>
-      <k-epsilon>
-        <scalar_field name="TurbulentKineticEnergy" rank="0">
-          <prognostic>
-            <mesh name="VelocityMesh"/>
-            <equation name="AdvectionDiffusion"/>
-            <spatial_discretisation>
-              <control_volumes>
-                <face_value name="FiniteElement">
-                  <limit_face_value>
-                    <limiter name="Sweby">
-                      <project_upwind_value_from_point>
-                        <store_upwind_elements>
-                          <store_upwind_quadrature/>
-                        </store_upwind_elements>
-                      </project_upwind_value_from_point>
-                    </limiter>
-                  </limit_face_value>
-                </face_value>
-                <diffusion_scheme name="ElementGradient"/>
-              </control_volumes>
-              <conservative_advection>
-                <real_value rank="0">0</real_value>
-              </conservative_advection>
-            </spatial_discretisation>
-            <temporal_discretisation>
-              <theta>
-                <real_value rank="0">0.5</real_value>
-              </theta>
-              <control_volumes>
-                <number_advection_iterations>
-                  <integer_value rank="0">3</integer_value>
-                </number_advection_iterations>
-                <limit_theta/>
-              </control_volumes>
-            </temporal_discretisation>
-            <solver>
-              <iterative_method name="cg"/>
-              <preconditioner name="hypre">
-                <hypre_type name="boomeramg"/>
-              </preconditioner>
-              <relative_error>
-                <real_value rank="0">1.e-7</real_value>
-              </relative_error>
-              <max_iterations>
-                <integer_value rank="0">1000</integer_value>