Merge lp:~jon-hill/fluidity/diagnostic_check into lp:fluidity

[Jon Hill]

Fix the lookup paths for diagnostics check_options to search for hidden paths. Test for this too. Made a new module that contains all these weird and wonderful paths for both Populate_state and diagnostics. And anything else that needs them too!

[Jon Hill (jon-hill)]

Waiting on a green buildbot.

[Stephan Kramer (s-kramer)]

A few points:
* you have a few ALL CAPS words in there that shouldn't be: .OR. and DEP_LOOP
* in case(2) split_dependency(1) is the phase_name and split_dependency(2) is the field name, so the checks for additional fields after that as they currently are, don't make any sense.
* where is additional_diagnostic_fields defined? I can't find it anywhere...

review: Needs Fixing

[Jon Hill (jon-hill)]

1) The ALL CAPS are my code styling. I'll change the .OR. to .or., but the DEP_LOOP stays (I find it easier to spot in amongst the lower case code)

2) Not sure I entirely follow - if you have multiple phase support in your diagnostic, then it will appear in case(2) and you may still want to use, say, DistanceToBottom, which is one of the extra fields that can be checked for. The relative_path fields are checked within the correct material phase, but the others are absolute paths. Unless I got all this wrong! :)

3) Forgot to add the new module that contains the variables...fixed.

[lp:~jon-hill/fluidity/diagnostic_check]

4307. By Jon Hill on 2014-01-24

Helps if you add your new files

[Stephan Kramer (s-kramer)]

Ad 1) Fine, but in all other Fluidity code ALLCAPS is only used for parameters. If do loop labels are hard to find, it means that the loop is too long (as in this case: the code under both cases are a copy and paste, so that should really just be separated out in a subroutine)

Ad 2) For the relative paths you have "scalar_field::" // trim(split_dependency(1)) everywhere, where split_dependency(1) is a phase name. For the absolute paths, I'm not really sure it makes sense for the user to specify PhaseName::DistanceToTop as the user has no clue that these fields are actually put in one of the (or in this case all) states, so they should just refer to it as DistanceToTop. If you want to allow it however I have no objections to that.

[sam (samuel-d-parkinson)]

Hi Jon. I'll check this on Monday. Have a good weekend
On 24 Jan 2014 11:36, "Jon Hill" <email address hidden> wrote:

> Waiting on a green buildbot.
> --
>
> https://code.launchpad.net/~jon-hill/fluidity/diagnostic_check/+merge/203042
> You are requested to review the proposed merge of
> lp:~jon-hill/fluidity/diagnostic_check into lp:fluidity.
>

Unmerged revisions

4307. By Jon Hill on 2014-01-24

Helps if you add your new files

4306. By Jon Hill on 2014-01-24

Merge from trunk

4305. By Jon Hill on 2014-01-23

Fix dependency search paths to look in hidden places

=== modified file 'diagnostics/Diagnostic_Fields_New.F90.in'
--- diagnostics/Diagnostic_Fields_New.F90.in	2013-01-24 05:46:32 +0000
+++ diagnostics/Diagnostic_Fields_New.F90.in	2014-01-24 12:43:19 +0000
@@ -36,6 +36,7 @@
   use global_parameters, only : FIELD_NAME_LEN, OPTION_PATH_LEN
   use spud
   use state_module
+  use additional_field_locations
 
 USE_MODULES
   
@@ -973,9 +974,9 @@
      
     character(len = OPTION_PATH_LEN) :: dependency, field_name, field_path, field_type_path, state_name, state_path
     character(len = OPTION_PATH_LEN), dimension(:), allocatable :: dependencies, split_dependency
-    integer :: i, j, k, l, m, stat
-     
-    if(option_count("/material_phase/scalar_field/diagnostic") + &
+    integer :: i, j, k, l, m, af, stat
+    
+   if(option_count("/material_phase/scalar_field/diagnostic") + &
       & option_count("/material_phase/vector_field/diagnostic") + &
       & option_count("/material_phase/tensor_field/diagnostic") == 0) then
       ! Nothing to check
@@ -1017,28 +1018,92 @@
             if(stat /= SPUD_NO_ERROR) cycle
                   
             call tokenize(trim(dependency), dependencies, ",")
-            do m = 1, size(dependencies)
+            DEP_LOOP: do m = 1, size(dependencies)
               call tokenize(trim(dependencies(m)), split_dependency, "::")
               select case(size(split_dependency))
                 case(1)
                   if(option_count(trim(state_path) // "/scalar_field::" // trim(split_dependency(1))) + &
                     & option_count(trim(state_path) // "/vector_field::" // trim(split_dependency(1))) + &
-                    & option_count(trim(state_path) // "/tensor_field::" // trim(split_dependency(1))) == 0) then
-                    call field_error(state_name, field_name, "Field depends on " // split_dependency(1))
+                    & option_count(trim(state_path) // "/tensor_field::" // trim(split_dependency(1))) > 0) then
+                        cycle DEP_LOOP
                   end if
+                  ! We now need to check additional paths as the field may
+                  ! be hidden.
+                  ! check absolute fields
+                  do af=1, size(additional_fields_absolute)
+                      if (have_option(trim(additional_fields_absolute(af)) // "/scalar_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option(trim(additional_fields_absolute(af)) // "/vector_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option(trim(additional_fields_absolute(af)) // "/tensor_field::" // trim(split_dependency(1)))) then
+                              cycle DEP_LOOP
+                      end if
+                  end do
+
+                  ! check relative paths
+                  do af=1, size(additional_fields_relative)
+                      if (have_option(trim(state_path) // trim(additional_fields_relative(af)) // "/scalar_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option(trim(state_path) // trim(additional_fields_relative(af)) // "/vector_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option(trim(state_path) // trim(additional_fields_relative(af)) // "/tensor_field::" // trim(split_dependency(1)))) then
+                              cycle DEP_LOOP
+                      end if
+                  end do
+                  
+                  ! check other paths
+                  do af=1, size(additional_diagnostic_paths)
+                      if (have_option(trim(additional_diagnostic_paths(af)) // "/scalar_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option(trim(additional_diagnostic_paths(af)) // "/vector_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option(trim(additional_diagnostic_paths(af)) // "/tensor_field::" // trim(split_dependency(1)))) then
+                              cycle DEP_LOOP
+                      end if
+                  end do
+
+                  ! Still not found it...then error
+                  call field_error(state_name, field_name, "Field depends on " // split_dependency(1))
+                
                 case(2)
                   if(option_count("/material_phase::" // trim(split_dependency(1)) // "/scalar_field::" // trim(split_dependency(2))) + &
                     & option_count("/material_phase::" // trim(split_dependency(1)) // "/vector_field::" // trim(split_dependency(2))) + &
-                    & option_count("/material_phase::" // trim(split_dependency(1)) // "/tensor_field::" // trim(split_dependency(2))) == 0) then
-                    call field_error(state_name, field_name, "Field depends on " // trim(split_dependency(2)) // " in state " // split_dependency(1))
+                    & option_count("/material_phase::" // trim(split_dependency(1)) // "/tensor_field::" // trim(split_dependency(2))) > 0) then
+                        cycle DEP_LOOP
                   end if
+                  ! We now need to check additional paths as the field may
+                  ! be hidden.
+
+                  ! check absolute fields
+                  do af=1, size(additional_fields_absolute)
+                      if (have_option(trim(additional_fields_absolute(af)) // "/scalar_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option(trim(additional_fields_absolute(af)) // "/vector_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option(trim(additional_fields_absolute(af)) // "/tensor_field::" // trim(split_dependency(1)))) then
+                              cycle DEP_LOOP 
+                      end if
+                  end do
+
+                  ! check relative paths
+                  do af=1, size(additional_fields_relative)
+                      if (have_option("/material_phase::" // trim(split_dependency(1)) // trim(additional_fields_relative(af)) // "/scalar_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option("/material_phase::" // trim(split_dependency(1)) // trim(additional_fields_relative(af)) // "/vector_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option("/material_phase::" // trim(split_dependency(1)) // trim(additional_fields_relative(af)) // "/tensor_field::" // trim(split_dependency(1)))) then
+                              cycle DEP_LOOP
+                      end if
+                  end do
+                  
+                  ! check other paths - err, these are 
+                  do af=1, size(additional_diagnostic_paths)
+                      if (have_option(trim(additional_diagnostic_paths(af)) // "/scalar_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option(trim(additional_diagnostic_paths(af)) // "/vector_field::" // trim(split_dependency(1))) .OR. &
+                        & have_option(trim(additional_diagnostic_paths(af)) // "/tensor_field::" // trim(split_dependency(1)))) then
+                              cycle DEP_LOOP
+                      end if
+                  end do
+                
+                  call field_error(state_name, field_name, "Field depends on " // trim(split_dependency(2)) // " in state " // split_dependency(1))
+                
                 case default
                   ewrite(-1, *) "For dependency " // trim(dependencies(m))
                   call field_error(state_name, field_name, "Invalid dependency")
               end select
                
               deallocate(split_dependency)
-            end do
+            end do DEP_LOOP
             deallocate(dependencies)
           end do
         end do

=== added file 'preprocessor/Additional_Field_Locations.F90'
--- preprocessor/Additional_Field_Locations.F90	1970-01-01 00:00:00 +0000
+++ preprocessor/Additional_Field_Locations.F90	2014-01-24 12:43:19 +0000
@@ -0,0 +1,88 @@
+!    Copyright (C) 2006 Imperial College London and others.
+!    
+!    Please see the AUTHORS file in the main source directory for a full list
+!    of copyright holders.
+!
+!    Prof. C Pain
+!    Applied Modelling and Computation Group
+!    Department of Earth Science and Engineering
+!    Imperial College London
+!
+!    [e-mail]
+!    
+!    This library is free software; you can redistribute it and/or
+!    modify it under the terms of the GNU Lesser General Public
+!    License as published by the Free Software Foundation,
+!    version 2.1 of the License.
+!
+!    This library is distributed in the hope that it will be useful,
+!    but WITHOUT ANY WARRANTY; without even the implied warranty of
+!    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+!    Lesser General Public License for more details.
+!
+!    You should have received a copy of the GNU Lesser General Public
+!    License along with this library; if not, write to the Free Software
+!    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307
+!    USA
+
+#include "fdebug.h"
+
+module additional_field_locations
+
+    use global_parameters, only: OPTION_PATH_LEN
+    
+    implicit none
+      
+
+    public :: additional_fields_absolute, additional_fields_relative, grandchild_paths 
+    public :: additional_diagnostic_paths
+    
+    !! A list of locations in which additional scalar/vector/tensor fields
+    !! are to be found. These are absolute paths in the schema.
+    character(len=OPTION_PATH_LEN), dimension(8) :: additional_fields_absolute=&
+       (/ &
+       "/ocean_biology/pznd                                                                                                   ", &
+       "/ocean_biology/six_component                                                                                          ", &
+       "/ocean_forcing/iceshelf_meltrate/Holland08                                                                            ", &
+       "/ocean_forcing/bulk_formulae/output_fluxes_diagnostics                                                                ", &
+       "/porous_media                                                                                                         ", &
+       "/material_phase[0]/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/dynamic_les ", &
+       "/material_phase[0]/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/second_order", &
+       "/material_phase[0]/sediment/                                                                                          " &
+       /)
+       
+    !! A list of relative paths under /material_phase[i]
+    !! that are searched for additional fields to be added.
+    character(len=OPTION_PATH_LEN), dimension(13) :: additional_fields_relative=&
+       (/ &
+       "/subgridscale_parameterisations/Mellor_Yamada                                                       ", &
+       "/subgridscale_parameterisations/prescribed_diffusivity                                              ", &
+       "/subgridscale_parameterisations/GLS                                                                 ", &
+       "/subgridscale_parameterisations/k-epsilon                                                           ", &
+       "/subgridscale_parameterisations/k-epsilon/debugging_options/source_term_output_fields               ", &
+       "/subgridscale_parameterisations/k-epsilon/debugging_options/prescribed_source_terms                 ", &
+       "/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/second_order", &
+       "/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/fourth_order", &
+       "/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/wale        ", &
+       "/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/dynamic_les ", &
+       "/vector_field::Velocity/prognostic/equation::ShallowWater                                           ", &
+       "/vector_field::Velocity/prognostic/equation::ShallowWater/bottom_drag                               ", &
+       "/vector_field::BedShearStress/diagnostic/calculation_method/velocity_gradient                       " &
+       /)
+
+    !! Relative paths under a field that are searched for grandchildren
+    !! (moved here because of extremely obscure intel ICE -Stephan)
+    character(len=OPTION_PATH_LEN), dimension(1):: &
+         grandchild_paths = (/&
+         &    "/spatial_discretisation/inner_element" &
+         /)
+
+    !! List of other fields that Populate_State handles under the hood, but are
+    !! needed for diagnostic dependencies.
+    character(len=OPTION_PATH_LEN), dimension(1):: additional_diagnostic_paths = &
+        (/ &
+         &    "/geometry/ocean_boundaries" &
+        /)
+
+
+end module additional_field_locations

=== modified file 'preprocessor/Makefile.dependencies'
--- preprocessor/Makefile.dependencies	2012-11-19 20:46:44 +0000
+++ preprocessor/Makefile.dependencies	2014-01-24 12:43:19 +0000
@@ -1,4 +1,11 @@
 # Dependencies generated by create_makefile.py. DO NOT EDIT
+../include/additional_field_locations.mod: Additional_Field_Locations.o
+	@true
+
+Additional_Field_Locations.o ../include/additional_field_locations.mod: \
+   Additional_Field_Locations.F90 ../include/fdebug.h \
+   ../include/global_parameters.mod
+
 ../include/boundary_conditions_from_options.mod: \
    Boundary_Conditions_From_Options.o
 	@true
@@ -50,6 +57,7 @@
 	@true
 
 Populate_State.o ../include/populate_state_module.mod: Populate_State.F90 \
+   ../include/additional_field_locations.mod \
    ../include/boundary_conditions_from_options.mod ../include/climatology.mod \
    ../include/coordinates.mod ../include/data_structures.mod \
    ../include/diagnostic_variables.mod ../include/elements.mod \

=== modified file 'preprocessor/Makefile.in'
--- preprocessor/Makefile.in	2011-10-21 10:05:25 +0000
+++ preprocessor/Makefile.in	2014-01-24 12:43:19 +0000
@@ -54,8 +54,8 @@
 TESTLIBS = $(shell echo @LIBS@ | sed 's@./lib/lib\([a-z]*\)\.a@-l\1@g')
 
 OBJS = Populate_State.o Populate_Sub_State.o Reserve_State.o Field_Priority_Lists.o\
-       Physics_From_Options.o VTK_Cache.o Initialise_Fields.o \
-			 Boundary_Conditions_From_Options.o synthetic_bc.o Tidal_Modelling.o
+       Physics_From_Options.o VTK_Cache.o Initialise_Fields.o Additional_Field_Locations.o \
+	   Boundary_Conditions_From_Options.o synthetic_bc.o Tidal_Modelling.o
 
 .SUFFIXES: .f90 .F90 .cpp .c .o .a
 

=== modified file 'preprocessor/Populate_State.F90'
--- preprocessor/Populate_State.F90	2013-10-28 06:46:48 +0000
+++ preprocessor/Populate_State.F90	2014-01-24 12:43:19 +0000
@@ -58,6 +58,7 @@
   use fields_halos
   use read_triangle
   use initialise_ocean_forcing_module
+  use additional_field_locations
 
   implicit none
 
@@ -81,46 +82,6 @@
 
   end interface allocate_field_as_constant
     
-  !! A list of locations in which additional scalar/vector/tensor fields
-  !! are to be found. These are absolute paths in the schema.
-  character(len=OPTION_PATH_LEN), dimension(8) :: additional_fields_absolute=&
-       (/ &
-       "/ocean_biology/pznd                                                                                                   ", &
-       "/ocean_biology/six_component                                                                                          ", &
-       "/ocean_forcing/iceshelf_meltrate/Holland08                                                                            ", &
-       "/ocean_forcing/bulk_formulae/output_fluxes_diagnostics                                                                ", &
-       "/porous_media                                                                                                         ", &
-       "/material_phase[0]/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/dynamic_les ", &
-       "/material_phase[0]/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/second_order", &
-       "/material_phase[0]/sediment/                                                                                          " &
-       /)
-       
-  !! A list of relative paths under /material_phase[i]
-  !! that are searched for additional fields to be added.
-  character(len=OPTION_PATH_LEN), dimension(13) :: additional_fields_relative=&
-       (/ &
-       "/subgridscale_parameterisations/Mellor_Yamada                                                       ", &
-       "/subgridscale_parameterisations/prescribed_diffusivity                                              ", &
-       "/subgridscale_parameterisations/GLS                                                                 ", &
-       "/subgridscale_parameterisations/k-epsilon                                                           ", &
-       "/subgridscale_parameterisations/k-epsilon/debugging_options/source_term_output_fields               ", &
-       "/subgridscale_parameterisations/k-epsilon/debugging_options/prescribed_source_terms                 ", &
-       "/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/second_order", &
-       "/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/fourth_order", &
-       "/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/wale        ", &
-       "/vector_field::Velocity/prognostic/spatial_discretisation/continuous_galerkin/les_model/dynamic_les ", &
-       "/vector_field::Velocity/prognostic/equation::ShallowWater                                           ", &
-       "/vector_field::Velocity/prognostic/equation::ShallowWater/bottom_drag                               ", &
-       "/vector_field::BedShearStress/diagnostic/calculation_method/velocity_gradient                       " &
-       /)
-
-  !! Relative paths under a field that are searched for grandchildren
-  !! (moved here because of extremely obscure intel ICE -Stephan)
-  character(len=OPTION_PATH_LEN), dimension(1):: &
-         grandchild_paths = (/&
-         &    "/spatial_discretisation/inner_element" &
-         /)
-
 contains
 
 

=== added directory 'tests/additional_fields_diagnostics_check'
=== added file 'tests/additional_fields_diagnostics_check/Makefile'
--- tests/additional_fields_diagnostics_check/Makefile	1970-01-01 00:00:00 +0000
+++ tests/additional_fields_diagnostics_check/Makefile	2014-01-24 12:43:19 +0000
@@ -0,0 +1,24 @@
+FLMLMODEL = diagnostics
+MODEL = diagnostics
+
+default: input
+
+input:
+
+clean: clean-mesh clean-run-debug
+clean-mesh:
+clean-run:
+	rm -f $(FLMLMODEL)_?*.pvtu $(FLMLMODEL)_?*.vtu
+	rm -f $(FLMLMODEL).detectors $(FLMLMODEL).stat tmpf*
+	rm -f fluidity.err-?* fluidity.log-?*
+	rm -f matrixdump matrixdump.info
+	rm -f $(FLMLMODEL)_?*_checkpoint.flml
+	rm -f $(FLMLMODEL)_?*_checkpoint_?*.ele $(FLMLMODEL)_?*_checkpoint_?*.face $(FLMLMODEL)_?*_checkpoint_?*.halo $(FLMLMODEL)_?*_checkpoint_?*.node
+	rm -f $(FLMLMODEL)_?*_?*_checkpoint.pvtu $(FLMLMODEL)_?*_?*_checkpoint.vtu
+	rm -f $(FLMLMODEL)_?*_checkpoint.ele $(FLMLMODEL)_?*_checkpoint.face $(FLMLMODEL)_?*_checkpoint.node
+	rm -f $(FLMLMODEL)_?*_checkpoint.vtu
+clean-run-debug: clean-run
+	rm -f adapted_mesh_?*.vtu bounding_box_?*_?*.vtu final_metric_?*.vtu gmon.out gradation_metric_?*.vtu interpolation_metric_final_?*.vtu interpolation_metric_hessian_?*_?*.vtu interpolation_metric_merge_?*_?*.vtu interpolation_metric_metric_?*_?*.vtu metric_input_?*_?*.vtu
+	rm -f adapted_mesh.face adapted_mesh.ele adapted_mesh.node
+	rm -f adapted_mesh_?*.face adapted_mesh_?*.ele adapted_mesh_?*.node
+	rm -f adapted_state_?*.pvtu adapted_state_?*.vtu

=== added file 'tests/additional_fields_diagnostics_check/additional_fields_diagnostics_check.xml'
--- tests/additional_fields_diagnostics_check/additional_fields_diagnostics_check.xml	1970-01-01 00:00:00 +0000
+++ tests/additional_fields_diagnostics_check/additional_fields_diagnostics_check.xml	2014-01-24 12:43:19 +0000
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<testproblem>
+  <name>additional_fields_diagnostic_check</name>
+  <owner userid="jhill1"/>
+  <tags>flml</tags>
+  <problem_definition length = "short" nprocs = "1">
+    <command_line>make clean-run-debug; fluidity -v2 -l diagnostics.flml</command_line>
+  </problem_definition>
+  <variables>
+    <variable name="solvers_converged" language="python">
+import os
+files = os.listdir("./")
+solvers_converged = not "matrixdump" in files and not "matrixdump.info" in files
+    </variable>
+    <variable name = "error_present" language = "python">
+error_present = False
+for line in file("fluidity.err-0", "r"):
+   if line.startswith("Error message: Field depends on"):
+      error_present = True
+      break
+    </variable>
+  </variables>
+  <pass_tests>
+    <test name="Solvers converged" language="python">
+      assert(solvers_converged)
+    </test>
+    <test name="Fluidity failed with the expected error" language = "python">
+assert(not error_present)
+    </test>
+  </pass_tests>
+  <warn_tests>
+  </warn_tests>
+</testproblem>

=== added file 'tests/additional_fields_diagnostics_check/diagnostics.flml'
--- tests/additional_fields_diagnostics_check/diagnostics.flml	1970-01-01 00:00:00 +0000
+++ tests/additional_fields_diagnostics_check/diagnostics.flml	2014-01-24 12:43:19 +0000
@@ -0,0 +1,115 @@
+<?xml version='1.0' encoding='utf-8'?>
+<fluidity_options>
+  <simulation_name>
+    <string_value lines="1">diagnostics</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="square">
+        <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">4</integer_value>
+      </degree>
+    </quadrature>
+  </geometry>
+  <io>
+    <dump_format>
+      <string_value>vtk</string_value>
+    </dump_format>
+    <dump_period>
+      <constant>
+        <real_value rank="0">1</real_value>
+      </constant>
+    </dump_period>
+    <output_mesh name="VelocityMesh"/>
+    <stat/>
+  </io>
+  <timestepping>
+    <current_time>
+      <real_value rank="0">0.0</real_value>
+    </current_time>
+    <timestep>
+      <real_value rank="0">1.0</real_value>
+    </timestep>
+    <finish_time>
+      <real_value rank="0">1.0</real_value>
+    </finish_time>
+  </timestepping>
+  <physical_parameters/>
+  <material_phase name="Fluid">
+    <subgridscale_parameterisations>
+      <prescribed_diffusivity>
+        <tensor_field name="PrescribedDiffusivity" rank="2">
+          <prescribed>
+            <mesh name="VelocityMesh"/>
+            <value name="WholeMesh">
+              <isotropic>
+                <constant>
+                  <real_value rank="0">1</real_value>
+                </constant>
+              </isotropic>
+            </value>
+            <output/>
+          </prescribed>
+        </tensor_field>
+      </prescribed_diffusivity>
+    </subgridscale_parameterisations>
+    <vector_field name="Velocity" rank="1">
+      <prescribed>
+        <mesh name="VelocityMesh"/>
+        <value name="WholeMesh">
+          <constant>
+            <real_value shape="2" dim1="dim" rank="1">0.0 0.0</real_value>
+          </constant>
+        </value>
+        <output>
+          <exclude_from_vtu/>
+        </output>
+        <stat>
+          <exclude_from_stat/>
+        </stat>
+        <detectors>
+          <exclude_from_detectors/>
+        </detectors>
+      </prescribed>
+    </vector_field>
+    <tensor_field name="CopyOfHiddenField" rank="2">
+      <diagnostic>
+        <algorithm material_phase_support="single" source_field_type="tensor" source_field_name="PrescribedDiffusivity" name="tensor_copy"/>
+        <mesh name="VelocityMesh"/>
+        <output/>
+        <stat>
+          <include_in_stat/>
+        </stat>
+      </diagnostic>
+    </tensor_field>
+  </material_phase>
+</fluidity_options>

=== added file 'tests/additional_fields_diagnostics_check/square.edge'
--- tests/additional_fields_diagnostics_check/square.edge	1970-01-01 00:00:00 +0000
+++ tests/additional_fields_diagnostics_check/square.edge	2014-01-24 12:43:19 +0000
@@ -0,0 +1,12 @@
+8 1
+1 1 2 1
+2 2 3 1
+3 7 8 2
+4 8 9 2
+5 1 4 4
+6 4 7 4
+7 3 6 3
+8 6 9 3
+# Created by triangletools.WriteTriangle
+# Command: /usr/bin/ipython
+# Thu Apr  2 13:34:14 2009

=== added file 'tests/additional_fields_diagnostics_check/square.ele'
--- tests/additional_fields_diagnostics_check/square.ele	1970-01-01 00:00:00 +0000
+++ tests/additional_fields_diagnostics_check/square.ele	2014-01-24 12:43:19 +0000
@@ -0,0 +1,12 @@
+8 3 1
+1 1 4 5 0
+2 1 5 2 0
+3 2 5 6 0
+4 2 6 3 0
+5 4 7 8 0
+6 4 8 5 0
+7 5 8 9 0
+8 5 9 6 0
+# Created by triangletools.WriteTriangle
+# Command: /usr/bin/ipython
+# Thu Apr  2 13:34:14 2009

=== added file 'tests/additional_fields_diagnostics_check/square.node'
--- tests/additional_fields_diagnostics_check/square.node	1970-01-01 00:00:00 +0000
+++ tests/additional_fields_diagnostics_check/square.node	2014-01-24 12:43:19 +0000
@@ -0,0 +1,13 @@
+9 2 0 0
+1 0.0 0.0
+2 0.0 0.5
+3 0.0 1.0
+4 0.5 0.0
+5 0.5 0.5
+6 0.5 1.0
+7 1.0 0.0
+8 1.0 0.5
+9 1.0 1.0
+# Created by triangletools.WriteTriangle
+# Command: /usr/bin/ipython
+# Thu Apr  2 13:34:14 2009