Merge lp:~fluidity-core/fluidity/intel-testfix into lp:fluidity

[Tim Greaves]

A series of updates to short and medium test are implemented to enable them to run successfully on clusters, specifically the CX1 cluster at Imperial College where the Fluidity buildbot runs. This is a first pass at fixing, and there remain around twenty tests that need attention. The vast majority pass following the changes in this merge, though, which should leave minimal trunk noise for the remaining fixes -- some of which will involve changes outside the test infrastructure.

[lp:~fluidity-core/fluidity/intel-testfix]

4284. By Tim Greaves on 2013-10-10

Merging from trunk to bring the branch up to date.

4285. By Tim Greaves on 2013-10-10

Merging from trunk to keep the branch up to date.

[Jon Hill (jon-hill)]

Looks good to me.

review: Approve

[lp:~fluidity-core/fluidity/intel-testfix]

4286. By Tim Greaves on 2013-10-16

Update to merge trunk into the branch.

=== modified file 'python/fluidity/regressiontest.py'
--- python/fluidity/regressiontest.py	2013-01-21 13:01:43 +0000
+++ python/fluidity/regressiontest.py	2013-10-16 12:23:45 +0000
@@ -12,7 +12,7 @@
 
 class TestProblem:
     """A test records input information as well as tests for the output."""
-    def __init__(self, filename, verbose=False, replace=None, no_pbs=False):
+    def __init__(self, filename, verbose=False, replace=None, genpbs=False):
         """Read a regression test from filename and record its details."""
         self.name = ""
         self.command = replace
@@ -26,7 +26,7 @@
         self.pass_status = []
         self.warn_status = []
         self.filename = filename.split('/')[-1]
-        self.no_pbs = no_pbs
+        self.genpbs = genpbs
         # add dir to import path
         sys.path.insert(0, os.path.dirname(filename))
 
@@ -96,7 +96,7 @@
             raise Exception
 
     def is_finished(self):
-        if self.nprocs > 1 or self.length == "long":
+        if self.genpbs:
             file = os.environ["HOME"] + "/lock/" + self.random
             try:
                 os.remove(file)
@@ -131,7 +131,7 @@
         except OSError:
           self.log("No Makefile, not calling make")
 
-        if (not self.no_pbs) and (self.nprocs > 1 or self.length == "long"):
+        if self.genpbs:
             ret = self.call_genpbs(dir)
             self.log("cd "+dir+"; qsub " + self.filename[:-4] + ".pbs: " + self.command_line)
             os.system("cd "+dir+"; qsub " + self.filename[:-4] + ".pbs")

=== modified file 'tests/5material-droplet-parallel/5material-droplet-parallel.xml'
--- tests/5material-droplet-parallel/5material-droplet-parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/5material-droplet-parallel/5material-droplet-parallel.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,9 @@
   <name>Control volume, multi-material flow test</name>
   <owner userid="cwilson"/>
   <tags>flml solidity parallel</tags>
-    <problem_definition length="medium" nprocs="1">
-    <command_line>mpiexec -np 2 ../../bin/fluidity -v2 -l 5material-droplet_flredecomp.flml</command_line>
+    <problem_definition length="medium" nprocs="2">
+      <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l 5material-droplet 5material-droplet_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v2 -l 5material-droplet_flredecomp.flml</command_line>
   </problem_definition>  
   <variables>  
     <variable name="solvers_converged" language="python">

=== modified file 'tests/5material-droplet-parallel/Makefile'
--- tests/5material-droplet-parallel/Makefile	2012-08-13 11:42:30 +0000
+++ tests/5material-droplet-parallel/Makefile	2013-10-16 12:23:45 +0000
@@ -1,6 +1,5 @@
 input: clean
 	../../bin/gmsh2triangle --2d src/square.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l 5material-droplet 5material-droplet_flredecomp
 
 clean:
 	rm -rf *.halo *.stat *.vtu *.pvtu *.node *.ele *.edge *.log-0 *.err-0 *checkpoint *.convergence

=== modified file 'tests/Helmholtz-anisotropic-vector-mms-p1p1cg-structured/Makefile'
--- tests/Helmholtz-anisotropic-vector-mms-p1p1cg-structured/Makefile	2013-03-06 13:20:27 +0000
+++ tests/Helmholtz-anisotropic-vector-mms-p1p1cg-structured/Makefile	2013-10-16 12:23:45 +0000
@@ -1,8 +1,8 @@
 input:	clean
-	gmsh -2 -o MMS_A_structured.msh src/MMS_A_structured.geo
-	gmsh -2 -o MMS_B_structured.msh src/MMS_B_structured.geo
-	gmsh -2 -o MMS_C_structured.msh src/MMS_C_structured.geo
-	gmsh -2 -o MMS_D_structured.msh src/MMS_D_structured.geo
+	gmsh -2 -bin -o MMS_A_structured.msh src/MMS_A_structured.geo
+	gmsh -2 -bin -o MMS_B_structured.msh src/MMS_B_structured.geo
+	gmsh -2 -bin -o MMS_C_structured.msh src/MMS_C_structured.geo
+	gmsh -2 -bin -o MMS_D_structured.msh src/MMS_D_structured.geo
 
 clean:
 	rm -f *.vtu *.msh *.stat *.log fluidity.err-0 fluidity.log-0

=== modified file 'tests/Stokes_mms_cg_p2p1_tdepvisc/Stokes_mms_cg_p2p1_tdepvisc.xml'
--- tests/Stokes_mms_cg_p2p1_tdepvisc/Stokes_mms_cg_p2p1_tdepvisc.xml	2012-06-28 08:23:27 +0000
+++ tests/Stokes_mms_cg_p2p1_tdepvisc/Stokes_mms_cg_p2p1_tdepvisc.xml	2013-10-16 12:23:45 +0000
@@ -8,10 +8,10 @@
 <!--
 <command_line>
 make parallel-input &amp;&amp; 
-mpirun -np 4 fluidity -v2 -l MMS_A.flml &amp;&amp; mkdir -p MMS_A_logs &amp;&amp; mv fluidity.* MMS_A_logs/ &amp;&amp; 
-mpirun -np 4 fluidity -v2 -l MMS_B.flml &amp;&amp; mkdir -p MMS_B_logs &amp;&amp;  mv fluidity.* MMS_B_logs/ &amp;&amp; 
-mpirun -np 4 fluidity -v2 -l MMS_C.flml &amp;&amp; mkdir -p MMS_C_logs &amp;&amp;  mv fluidity.* MMS_C_logs/ &amp;&amp; 
-mpirun -np 4 fluidity -v2 -l MMS_D.flml &amp;&amp; mkdir -p MMS_D_logs &amp;&amp;  mv fluidity.* MMS_D_logs/
+mpiexec fluidity -v2 -l MMS_A.flml &amp;&amp; mkdir -p MMS_A_logs &amp;&amp; mv fluidity.* MMS_A_logs/ &amp;&amp; 
+mpiexec fluidity -v2 -l MMS_B.flml &amp;&amp; mkdir -p MMS_B_logs &amp;&amp;  mv fluidity.* MMS_B_logs/ &amp;&amp; 
+mpiexec fluidity -v2 -l MMS_C.flml &amp;&amp; mkdir -p MMS_C_logs &amp;&amp;  mv fluidity.* MMS_C_logs/ &amp;&amp; 
+mpiexec fluidity -v2 -l MMS_D.flml &amp;&amp; mkdir -p MMS_D_logs &amp;&amp;  mv fluidity.* MMS_D_logs/
 </command_line>-->
   </problem_definition>
   <variables>

=== modified file 'tests/Stokes_square_convection_1e4_p1p1_parallel/Stokes_square_convection_1e4_p1p1_parallel.xml'
--- tests/Stokes_square_convection_1e4_p1p1_parallel/Stokes_square_convection_1e4_p1p1_parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/Stokes_square_convection_1e4_p1p1_parallel/Stokes_square_convection_1e4_p1p1_parallel.xml	2013-10-16 12:23:45 +0000
@@ -5,9 +5,9 @@
 
   <tags>flml parallel</tags>
 
-  <problem_definition length="medium" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l Stokes-square-convection-1e4-p1p1-parallel Stokes-square-convection-1e4-p1p1-parallel_flredecomp &amp;&amp;
-mpiexec -np 2 ../../bin/fluidity -v2 -l Stokes-square-convection-1e4-p1p1-parallel_flredecomp.flml</command_line>
+  <problem_definition length="medium" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l Stokes-square-convection-1e4-p1p1-parallel Stokes-square-convection-1e4-p1p1-parallel_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v2 -l Stokes-square-convection-1e4-p1p1-parallel_flredecomp.flml</command_line>
   </problem_definition>
 
 <variables>  

=== modified file 'tests/Stokes_square_convection_1e4_p2p1_parallel/Stokes_square_convection_1e4_p2p1_parallel.xml'
--- tests/Stokes_square_convection_1e4_p2p1_parallel/Stokes_square_convection_1e4_p2p1_parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/Stokes_square_convection_1e4_p2p1_parallel/Stokes_square_convection_1e4_p2p1_parallel.xml	2013-10-16 12:23:45 +0000
@@ -5,9 +5,9 @@
 
   <tags>flml parallel</tags>
 
-  <problem_definition length="medium" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l Stokes-square-convection-1e4-p2p1-parallel Stokes-square-convection-1e4-p2p1-parallel_flredecomp &amp;&amp;
-mpiexec -np 2 ../../bin/fluidity -v2 -l Stokes-square-convection-1e4-p2p1-parallel_flredecomp.flml</command_line>
+  <problem_definition length="medium" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l Stokes-square-convection-1e4-p2p1-parallel Stokes-square-convection-1e4-p2p1-parallel_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v2 -l Stokes-square-convection-1e4-p2p1-parallel_flredecomp.flml</command_line>
   </problem_definition>
 
 <variables>  

=== modified file 'tests/backward_facing_step_2d_zoltan_sam/Makefile'
--- tests/backward_facing_step_2d_zoltan_sam/Makefile	2012-08-13 11:42:30 +0000
+++ tests/backward_facing_step_2d_zoltan_sam/Makefile	2013-10-16 12:23:45 +0000
@@ -1,6 +1,5 @@
 input:
 	gmsh -2 -o unstructured.msh src/unstructured.geo && ../../bin/gmsh2triangle --2d unstructured.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l backward_facing_step_2d backward_facing_step_2d_flredecomp
 	cp -r sam_output/* .
 
 clean:

=== modified file 'tests/backward_facing_step_2d_zoltan_sam/backward_facing_step_2d_zoltan_sam.xml'
--- tests/backward_facing_step_2d_zoltan_sam/backward_facing_step_2d_zoltan_sam.xml	2012-08-13 11:42:30 +0000
+++ tests/backward_facing_step_2d_zoltan_sam/backward_facing_step_2d_zoltan_sam.xml	2013-10-16 12:23:45 +0000
@@ -5,8 +5,8 @@
   <name>Two-dimensional backward facing step.</name>
   <owner userid="jhill1"/>
   <tags>flml zoltan parallel 2dadapt</tags>
-  <problem_definition length="medium" nprocs="1">
-      <command_line>mpiexec -n 2 ../../bin/fluidity backward_facing_step_2d_flredecomp.flml</command_line>
+  <problem_definition length="medium" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l backward_facing_step_2d backward_facing_step_2d_flredecomp ;  mpiexec ../../bin/fluidity backward_facing_step_2d_flredecomp.flml </command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/biology_6_component_parallel/Makefile'
--- tests/biology_6_component_parallel/Makefile	2012-08-13 11:42:30 +0000
+++ tests/biology_6_component_parallel/Makefile	2013-10-16 12:23:45 +0000
@@ -1,6 +1,5 @@
 input: clean
 	../../bin/create_aligned_mesh box 50 50 -- -50 10 10 10
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l biology_conservation_parallel biology_conservation_parallel_flredecomp
 
 clean:
 	# serial

=== modified file 'tests/biology_6_component_parallel/biology_6_component_parallel.xml'
--- tests/biology_6_component_parallel/biology_6_component_parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/biology_6_component_parallel/biology_6_component_parallel.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,9 @@
   <name>biology_6_component_parallel</name>
   <owner userid="jhill1"/>
   <tags>flml biology parallel</tags>
-  <problem_definition length="short" nprocs="1">
-      <command_line>mpiexec -n 2 ../../bin/fluidity biology_conservation_parallel_flredecomp.flml; fluidity biology_conservation.flml; </command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l biology_conservation_parallel biology_conservation_parallel_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity biology_conservation_parallel_flredecomp.flml; fluidity biology_conservation.flml</command_line>
     <!-- PZNDAC model running in a water column not solving for any physics. No sinking of detritus, so everything conserved -->
   </problem_definition>
   <variables>

=== modified file 'tests/channel-flow-dg/channel-flow-dg.xml'
--- tests/channel-flow-dg/channel-flow-dg.xml	2012-06-28 08:23:27 +0000
+++ tests/channel-flow-dg/channel-flow-dg.xml	2013-10-16 12:23:45 +0000
@@ -3,8 +3,7 @@
   <name>channel-flow-dg</name>
   <owner userid="dham"/>
   <problem_definition length="medium" nprocs="1">
-    <command_line>for layers in 4 8 16; do cp ./src/chan$layers.msh ./channel.msh; fluidity -v3 -l channel_viscous.flml; cp fluidity.log-0 channel-flow-dg-$layers.log-0; cp fluidity.err-0 channel-flow-dg-$layers.err-0; cp channel-flow-dg.stat channel-flow-dg-$layers.stat; done</command_line>
-<!--     <command_line>for layers in 16 32 64; do ./generate_mesh $layers; fluidity channel_viscous.flml; cp channel-flow-dg.stat channel-flow-dg-$layers.stat; done</command_line> -->
+    <command_line>cp ./src/chan4.msh ./channel.msh; fluidity -v3 -l channel_viscous.flml; cp fluidity.log-0 channel-flow-dg-4.log-0; cp fluidity.err-0 channel-flow-dg-4.err-0; cp channel-flow-dg.stat channel-flow-dg-4.stat; cp ./src/chan8.msh ./channel.msh; fluidity -v3 -l channel_viscous.flml; cp fluidity.log-0 channel-flow-dg-8.log-0; cp fluidity.err-0 channel-flow-dg-8.err-0; cp channel-flow-dg.stat channel-flow-dg-8.stat; cp ./src/chan16.msh ./channel.msh; fluidity -v3 -l channel_viscous.flml; cp fluidity.log-0 channel-flow-dg-16.log-0; cp fluidity.err-0 channel-flow-dg-16.err-0; cp channel-flow-dg.stat channel-flow-dg-16.stat</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/channel_wind_drag_parallel/Makefile'
--- tests/channel_wind_drag_parallel/Makefile	2012-06-28 08:23:27 +0000
+++ tests/channel_wind_drag_parallel/Makefile	2013-10-16 12:23:45 +0000
@@ -4,7 +4,6 @@
 	gmsh -3 -o channel.msh src/channel.geo
 	../../bin/gmsh2triangle channel.msh
 	../../bin/periodise channel_parallel.flml
-	mpiexec -np 4 ../../bin/flredecomp -i 1 -o 4 channel_parallel_periodised channel_parallel_periodised_flredecomp
 
 clean:
 	rm -f $(PROJECT).stat

=== modified file 'tests/channel_wind_drag_parallel/channel_wind_drag_parallel.xml'
--- tests/channel_wind_drag_parallel/channel_wind_drag_parallel.xml	2012-06-28 08:23:27 +0000
+++ tests/channel_wind_drag_parallel/channel_wind_drag_parallel.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,9 @@
   <name>Parallel periodic channel with wind-forcing and quadratic bottom drag.</name>
   <owner userid="amcvicar"/>
   <tags>flml zoltan parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -np 4 ../../bin/fluidity -v3 -l  channel_parallel_periodised_flredecomp.flml </command_line>
+  <problem_definition length="short" nprocs="4">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 4 channel_parallel_periodised channel_parallel_periodised_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v3 -l  channel_parallel_periodised_flredecomp.flml </command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/circle-2d-drag-zoltan/Makefile'
--- tests/circle-2d-drag-zoltan/Makefile	2012-08-13 11:42:30 +0000
+++ tests/circle-2d-drag-zoltan/Makefile	2013-10-16 12:23:45 +0000
@@ -1,8 +1,6 @@
 input: clean
 	../../bin/gmsh2triangle -2 src/circle-serial.msh
 	../../bin/gmsh2triangle -2 src/circle-parallel.msh
-	mpiexec -n 3 ../../bin/flredecomp -i 1 -o 3 -v -l circle-2d-drag-parallel circle-2d-drag-parallel_flredecomp
-	mpiexec -n 3 ../../bin/flredecomp -i 1 -o 3 -v -l circle-2d-drag-parallel-adaptive circle-2d-drag-parallel-adaptive_flredecomp
 
 clean:
 	rm -f *.halo *.ele *.edge *.face *.node *.poly *.vtu *.pvtu *.s *.d.* *.stat *.s *.log-0 *.err-0

=== modified file 'tests/circle-2d-drag-zoltan/circle-2d-drag-zoltan.xml'
--- tests/circle-2d-drag-zoltan/circle-2d-drag-zoltan.xml	2012-11-28 22:04:57 +0000
+++ tests/circle-2d-drag-zoltan/circle-2d-drag-zoltan.xml	2013-10-16 12:23:45 +0000
@@ -6,10 +6,12 @@
   <name>circle-2d-drag-zoltan</name>
   <owner userid="jhill1"/>
   <tags>flml zoltan parallel 2dadapt</tags>
-  <problem_definition length="medium" nprocs="1">
+  <problem_definition length="medium" nprocs="3">
       <command_line>fluidity circle-2d-drag-serial.flml;
-          mpiexec -n 3 ../../bin/fluidity circle-2d-drag-parallel_flredecomp.flml;
-          mpiexec -n 3 ../../bin/fluidity circle-2d-drag-parallel-adaptive_flredecomp.flml;
+mpiexec ../../bin/flredecomp -i 1 -o 3 -v -l circle-2d-drag-parallel circle-2d-drag-parallel_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity circle-2d-drag-parallel_flredecomp.flml;
+mpiexec ../../bin/flredecomp -i 1 -o 3 -v -l circle-2d-drag-parallel-adaptive circle-2d-drag-parallel-adaptive_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity circle-2d-drag-parallel-adaptive_flredecomp.flml
       </command_line>
   </problem_definition>
   <variables>

=== modified file 'tests/column-parallel/Makefile'
--- tests/column-parallel/Makefile	2012-11-08 17:26:18 +0000
+++ tests/column-parallel/Makefile	2013-10-16 12:23:45 +0000
@@ -1,7 +1,6 @@
 input: clean
 	gmsh -3 -o column.msh src/column.geo
 	../../bin/gmsh2triangle column.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l column-parallel column-parallel_flredecomp
 
 clean: 
 	rm -f  *.ele *.edge *.msh *.node *.face *.poly *.pvtu *.vtu *.s  *.stat *.log-* *.err-* matrixdump* *log *err

=== modified file 'tests/column-parallel/column-parallel.xml'
--- tests/column-parallel/column-parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/column-parallel/column-parallel.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,9 @@
   <name>column-parallel</name>
   <owner userid="jhill1"/>
   <tags>flml</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/fluidity -v1 -l column-parallel_flredecomp.flml </command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l column-parallel column-parallel_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v1 -l column-parallel_flredecomp.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/detectors_mesh_movement_parallel/Makefile'
--- tests/detectors_mesh_movement_parallel/Makefile	2012-07-24 16:34:10 +0000
+++ tests/detectors_mesh_movement_parallel/Makefile	2013-10-16 12:23:45 +0000
@@ -2,7 +2,6 @@
 
 input: clean
 	../../bin/gmsh2triangle --2d src/square.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l detectors detectors_flredecomp
 
 clean: clean-mesh clean-run
 clean-mesh:

=== modified file 'tests/detectors_mesh_movement_parallel/detectors_mesh_movement_parallel.xml'
--- tests/detectors_mesh_movement_parallel/detectors_mesh_movement_parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/detectors_mesh_movement_parallel/detectors_mesh_movement_parallel.xml	2013-10-16 12:23:45 +0000
@@ -3,8 +3,9 @@
   <name>Static detectors in a moving mesh in parallel</name>
   <owner userid="mlange"/>
   <tags>flml parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/fluidity -v2 -l detectors_flredecomp.flml</command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l detectors detectors_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v2 -l detectors_flredecomp.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/detectors_parallel_adaptivity/Makefile'
--- tests/detectors_parallel_adaptivity/Makefile	2012-07-24 16:34:10 +0000
+++ tests/detectors_parallel_adaptivity/Makefile	2013-10-16 12:23:45 +0000
@@ -2,7 +2,6 @@
 
 input: clean
 	../../bin/gmsh2triangle --2d src/square.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l detectors detectors_flredecomp
 
 clean: clean-mesh clean-run
 clean-mesh:

=== modified file 'tests/detectors_parallel_adaptivity/detectors_parallel_adaptivity.xml'
--- tests/detectors_parallel_adaptivity/detectors_parallel_adaptivity.xml	2012-08-13 11:42:30 +0000
+++ tests/detectors_parallel_adaptivity/detectors_parallel_adaptivity.xml	2013-10-16 12:23:45 +0000
@@ -3,8 +3,9 @@
   <name>Detectors with adaptivity in parallel</name>
   <owner userid="jhill1"/>
   <tags>flml parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/fluidity -v2 -l detectors_flredecomp.flml</command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l detectors detectors_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v2 -l detectors_flredecomp.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/detectors_parallel_init/Makefile'
--- tests/detectors_parallel_init/Makefile	2012-10-26 08:49:00 +0000
+++ tests/detectors_parallel_init/Makefile	2013-10-16 12:23:45 +0000
@@ -3,7 +3,6 @@
 input: clean
 	gmsh -2 -o src/square.msh src/square.geo
 	../../bin/gmsh2triangle --2d src/square.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 detectors detectors_flredecomp
 
 clean: clean-mesh clean-run
 clean-mesh:

=== modified file 'tests/detectors_parallel_init/detectors_parallel_init.xml'
--- tests/detectors_parallel_init/detectors_parallel_init.xml	2012-10-26 08:49:00 +0000
+++ tests/detectors_parallel_init/detectors_parallel_init.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,9 @@
   <name>detectors_parallel_init</name>
   <owner userid="mlange"/>
   <tags>flml</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/fluidity detectors_flredecomp.flml </command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 detectors detectors_flredecomp &amp;&amp;
+      mpiexec ../../bin/fluidity detectors_flredecomp.flml </command_line>
     <!-- Test that detectors are initialised correctly in parallel. -->
   </problem_definition>
   <variables>

=== modified file 'tests/diffusion-dg-stretched/diffusion-dg-stretched.xml'
--- tests/diffusion-dg-stretched/diffusion-dg-stretched.xml	2012-06-28 08:23:27 +0000
+++ tests/diffusion-dg-stretched/diffusion-dg-stretched.xml	2013-10-16 12:23:45 +0000
@@ -3,7 +3,7 @@
   <name>diffusion-dg-stretched</name>
   <owner userid="colin"/>
   <problem_definition length="medium" nprocs="1">
-    <command_line>for layer in 5 10 20 30; do ./generate_mesh $layer 1000; fluidity diffusion-dg-stretched.flml; cp diffusion-dg-stretched.stat stretched-$layer.stat; cp diffusion-dg-stretched_1.vtu stretched-$layer.vtu; done</command_line>
+    <command_line>./generate_mesh 5 1000; fluidity diffusion-dg-stretched.flml; cp diffusion-dg-stretched.stat stretched-5.stat; cp diffusion-dg-stretched_1.vtu stretched-5.vtu; ./generate_mesh 10 1000; fluidity diffusion-dg-stretched.flml; cp diffusion-dg-stretched.stat stretched-10.stat; cp diffusion-dg-stretched_1.vtu stretched-10.vtu; ./generate_mesh 20 1000; fluidity diffusion-dg-stretched.flml; cp diffusion-dg-stretched.stat stretched-20.stat; cp diffusion-dg-stretched_1.vtu stretched-20.vtu; ./generate_mesh 30 1000; fluidity diffusion-dg-stretched.flml; cp diffusion-dg-stretched.stat stretched-30.stat; cp diffusion-dg-stretched_1.vtu stretched-30.vtu</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/diffusion_2d_p0_adaptive_parallel/Makefile'
--- tests/diffusion_2d_p0_adaptive_parallel/Makefile	2012-08-13 11:42:30 +0000
+++ tests/diffusion_2d_p0_adaptive_parallel/Makefile	2013-10-16 12:23:45 +0000
@@ -1,6 +1,5 @@
 input: clean
 	../../bin/gmsh2triangle --2d src/square.msh
-	mpiexec -n 3 ../../bin/flredecomp -i 1 -o 3 -v -l heat heat_flredecomp
 
 clean:
 	rm -f  *.ele *.edge *.node *.poly *.halo *.vtu *.pvtu fluidity.* *.s *.d.1 *.stat *detectors*

=== modified file 'tests/diffusion_2d_p0_adaptive_parallel/diffusion_2d_p0_adaptive_parallel.xml'
--- tests/diffusion_2d_p0_adaptive_parallel/diffusion_2d_p0_adaptive_parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/diffusion_2d_p0_adaptive_parallel/diffusion_2d_p0_adaptive_parallel.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,9 @@
   <name>heat_2d_dg</name>
   <owner userid="cwilson"/>
   <tags>flml zoltan parallel 2dadapt</tags>
-  <problem_definition length="medium" nprocs="1">
-    <command_line>mpiexec -np 3 fluidity -v2 -l heat_flredecomp.flml </command_line>
+  <problem_definition length="medium" nprocs="3">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 3 -v -l heat heat_flredecomp &amp;&amp;
+      mpiexec fluidity -v2 -l heat_flredecomp.flml </command_line>
     <!-- Two dimensional diffusion only problem. -->
   </problem_definition>
   <variables>

=== modified file 'tests/diffusion_2d_p0_parallel/Makefile'
--- tests/diffusion_2d_p0_parallel/Makefile	2012-08-13 11:42:30 +0000
+++ tests/diffusion_2d_p0_parallel/Makefile	2013-10-16 12:23:45 +0000
@@ -1,6 +1,5 @@
 input: clean
 	../../bin/gmsh2triangle --2d src/square.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp
 
 clean:
 	rm -fr  *.ele *.edge *.node *.poly *.halo *.vtu *.pvtu fluidity.* *.s *.d.1 *.stat heat_[0-9]* \

=== modified file 'tests/diffusion_2d_p0_parallel/diffusion_2d_p0_parallel.xml'
--- tests/diffusion_2d_p0_parallel/diffusion_2d_p0_parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/diffusion_2d_p0_parallel/diffusion_2d_p0_parallel.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,9 @@
   <name>heat_2d_dg</name>
   <owner userid="cwilson"/>
   <tags>flml parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -np 2 ../../bin/fluidity -v2 -l heat_flredecomp.flml </command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp &amp;&amp;
+      mpiexec ../../bin/fluidity -v2 -l heat_flredecomp.flml </command_line>
     <!-- Two dimensional diffusion only problem. -->
   </problem_definition>
   <variables>

=== modified file 'tests/flredecomp/flredecomp.xml'
--- tests/flredecomp/flredecomp.xml	2012-07-24 16:34:10 +0000
+++ tests/flredecomp/flredecomp.xml	2013-10-16 12:23:45 +0000
@@ -2,8 +2,8 @@
 <testproblem>
   <name>flredecomp</name>
   <owner userid="ggorman"/>
-  <problem_definition length = "short" nprocs = "1">
-    <command_line>make clean-run; mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l test test_flredecomp</command_line>
+  <problem_definition length = "short" nprocs = "4">
+    <command_line>make clean-run; mpiexec ../../bin/flredecomp -i 1 -o 4 -v -l test test_flredecomp</command_line>
   </problem_definition>
   <variables>
     <variable name = "partitions" language = "python">

=== modified file 'tests/flredecomp_1d/flredecomp_1d.xml'
--- tests/flredecomp_1d/flredecomp_1d.xml	2012-07-24 16:34:10 +0000
+++ tests/flredecomp_1d/flredecomp_1d.xml	2013-10-16 12:23:45 +0000
@@ -2,8 +2,8 @@
 <testproblem>
   <name>flredecomp</name>
   <owner userid="ggorman"/>
-  <problem_definition length = "short" nprocs = "1">
-    <command_line>make clean-run; mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l test test_flredecomp</command_line>
+  <problem_definition length = "short" nprocs = "4">
+    <command_line>make clean-run; mpiexec ../../bin/flredecomp -i 1 -o 4 -v -l test test_flredecomp</command_line>
   </problem_definition>
   <variables>
     <variable name = "partitions" language = "python">

=== modified file 'tests/flredecomp_2d/flredecomp_2d.xml'
--- tests/flredecomp_2d/flredecomp_2d.xml	2012-07-24 16:34:10 +0000
+++ tests/flredecomp_2d/flredecomp_2d.xml	2013-10-16 12:23:45 +0000
@@ -2,8 +2,8 @@
 <testproblem>
   <name>flredecomp</name>
   <owner userid="ggorman"/>
-  <problem_definition length = "short" nprocs = "1">
-    <command_line>make clean-run; mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l test test_flredecomp</command_line>
+  <problem_definition length = "short" nprocs = "4">
+    <command_line>make clean-run; mpiexec ../../bin/flredecomp -i 1 -o 4 -v -l test test_flredecomp</command_line>
   </problem_definition>
   <variables>
     <variable name = "partitions" language = "python">

=== modified file 'tests/flredecomp_2d_fieldweighted/flredecomp_2d_fieldweighted.xml'
--- tests/flredecomp_2d_fieldweighted/flredecomp_2d_fieldweighted.xml	2012-09-11 09:11:56 +0000
+++ tests/flredecomp_2d_fieldweighted/flredecomp_2d_fieldweighted.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,8 @@
   <owner userid="rhodrid"/>
   <tags>flml</tags>
 
-  <problem_definition length="medium" nprocs="1">
-    <command_line>mpiexec -n 16 flredecomp -i 1 -o 16 flredecomp-2d-fieldweighted Parallel-NP16-flredecomp-2d-fieldweighted</command_line>
+  <problem_definition length="medium" nprocs="16">
+    <command_line>mpiexec flredecomp -i 1 -o 16 flredecomp-2d-fieldweighted Parallel-NP16-flredecomp-2d-fieldweighted</command_line>
   </problem_definition>
 
   <variables>

=== modified file 'tests/geopressure_convergence/Makefile'
--- tests/geopressure_convergence/Makefile	2012-07-24 16:34:10 +0000
+++ tests/geopressure_convergence/Makefile	2013-10-16 12:23:45 +0000
@@ -1,49 +1,40 @@
-FLMLMODEL1 = geopressure_8
-FLMLMODEL2 = geopressure_16
-FLMLMODEL3 = geopressure_32
-FLMLMODEL4 = geopressure_64
-
 default: input
 
 input:
 	tar -xvjf src/meshes.tar.bz2
-	cp $(FLMLMODEL1).flml $(FLMLMODEL2).flml 
-	sed -i "s/"$(FLMLMODEL1)"/"$(FLMLMODEL2)"/g" $(FLMLMODEL2).flml 
-	sed -i "s/square-8/square-16/g" $(FLMLMODEL2).flml 
-	cp $(FLMLMODEL1).flml $(FLMLMODEL3).flml 
-	sed -i "s/"$(FLMLMODEL1)"/"$(FLMLMODEL3)"/g" $(FLMLMODEL3).flml 
-	sed -i "s/square-8/square-32/g" $(FLMLMODEL3).flml 
-	cp $(FLMLMODEL1).flml $(FLMLMODEL4).flml 
-	sed -i "s/"$(FLMLMODEL1)"/"$(FLMLMODEL4)"/g" $(FLMLMODEL4).flml 
-	sed -i "s/square-8/square-64/g" $(FLMLMODEL4).flml
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l $(FLMLMODEL1) $(FLMLMODEL1)_flredecomp
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l $(FLMLMODEL2) $(FLMLMODEL2)_flredecomp
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l $(FLMLMODEL3) $(FLMLMODEL3)_flredecomp
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l $(FLMLMODEL4) $(FLMLMODEL4)_flredecomp
+	cp geopressure_8.flml geopressure_16.flml 
+	sed -i "s/"geopressure_8"/"geopressure_16"/g" geopressure_16.flml 
+	sed -i "s/square-8/square-16/g" geopressure_16.flml 
+	cp geopressure_8.flml geopressure_32.flml 
+	sed -i "s/"geopressure_8"/"geopressure_32"/g" geopressure_32.flml 
+	sed -i "s/square-8/square-32/g" geopressure_32.flml 
+	cp geopressure_8.flml geopressure_64.flml 
+	sed -i "s/"geopressure_8"/"geopressure_64"/g" geopressure_64.flml 
+	sed -i "s/square-8/square-64/g" geopressure_64.flml
 
 
 clean: clean-mesh clean-run-debug
-	rm -f $(FLMLMODEL2).flml
-	rm -f $(FLMLMODEL3).flml
-	rm -f $(FLMLMODEL4).flml
+	rm -f geopressure_16.flml
+	rm -f geopressure_32.flml
+	rm -f geopressure_64.flml
 	rm -rf *flredecomp*
 clean-mesh:
 	rm -f square-?*.edge square-?*.ele square-?*.node
 	rm -f square-?*_?*.edge square-?*_*.ele square-?*_?*.node square-?*_?*.halo
 clean-run:
-	rm -f $(FLMLMODEL1)_?*_?*.vtu rm -f $(FLMLMODEL1)_?*.pvtu
-	rm -f $(FLMLMODEL1).detectors $(FLMLMODEL1).stat tmpf*
-	rm -f $(FLMLMODEL2)_?*_?*.vtu rm -f $(FLMLMODEL2)_?*.pvtu
-	rm -f $(FLMLMODEL2).detectors $(FLMLMODEL2).stat tmpf*
-	rm -f $(FLMLMODEL3)_?*_?*.vtu rm -f $(FLMLMODEL3)_?*.pvtu
-	rm -f $(FLMLMODEL3).detectors $(FLMLMODEL3).stat tmpf*
-	rm -f $(FLMLMODEL4)_?*_?*.vtu rm -f $(FLMLMODEL4)_?*.pvtu
-	rm -f $(FLMLMODEL4).detectors $(FLMLMODEL4).stat tmpf*
+	rm -f geopressure_8_?*_?*.vtu rm -f geopressure_8_?*.pvtu
+	rm -f geopressure_8.detectors geopressure_8.stat tmpf*
+	rm -f geopressure_16_?*_?*.vtu rm -f geopressure_16_?*.pvtu
+	rm -f geopressure_16.detectors geopressure_16.stat tmpf*
+	rm -f geopressure_32_?*_?*.vtu rm -f geopressure_32_?*.pvtu
+	rm -f geopressure_32.detectors geopressure_32.stat tmpf*
+	rm -f geopressure_64_?*_?*.vtu rm -f geopressure_64_?*.pvtu
+	rm -f geopressure_64.detectors geopressure_64.stat tmpf*
 	rm -f fluidity.err-?* fluidity.log-?*
 	rm -f matrixdump matrixdump.info
 	rm -f *.log
-	rm -rf $(FLMLMODEL1)_?
-	rm -rf $(FLMLMODEL2)_?
-	rm -rf $(FLMLMODEL3)_?
-	rm -rf $(FLMLMODEL4)_?
+	rm -rf geopressure_8_?
+	rm -rf geopressure_16_?
+	rm -rf geopressure_32_?
+	rm -rf geopressure_64_?
 clean-run-debug: clean-run

=== modified file 'tests/geopressure_convergence/geopressure_convergence.xml'
--- tests/geopressure_convergence/geopressure_convergence.xml	2012-07-24 16:34:10 +0000
+++ tests/geopressure_convergence/geopressure_convergence.xml	2013-10-16 12:23:45 +0000
@@ -3,12 +3,16 @@
   <name>Geopressure convergence test</name>
   <owner userid="piggt01"/>
   <tags>flml parallel</tags>
-  <problem_definition length = "medium" nprocs = "1">
-    <command_line>make clean-run; rm -f 8.log 16.log 32.log 64.log;
-mpiexec -n 2 ../../bin/fluidity -v2 geopressure_8_flredecomp.flml > 8.log;
-mpiexec -n 2 ../../bin/fluidity -v2 geopressure_16_flredecomp.flml > 16.log;
-mpiexec -n 2 ../../bin/fluidity -v2 geopressure_32_flredecomp.flml > 32.log;
-mpiexec -n 2 ../../bin/fluidity -v2 geopressure_64_flredecomp.flml > 64.log;
+  <problem_definition length = "medium" nprocs = "2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l geopressure_8 geopressure_8_flredecomp &amp;&amp;
+	mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l geopressure_16 geopressure_16_flredecomp &amp;&amp;
+	mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l geopressure_32 geopressure_32_flredecomp &amp;&amp;
+	mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l geopressure_64 geopressure_64_flredecomp &amp;&amp;
+      make clean-run; rm -f 8.log 16.log 32.log 64.log;
+mpiexec ../../bin/fluidity -v2 geopressure_8_flredecomp.flml &gt; 8.log;
+mpiexec ../../bin/fluidity -v2 geopressure_16_flredecomp.flml &gt; 16.log;
+mpiexec ../../bin/fluidity -v2 geopressure_32_flredecomp.flml &gt; 32.log;
+mpiexec ../../bin/fluidity -v2 geopressure_64_flredecomp.flml &gt; 64.log;
     </command_line>
   </problem_definition>
   <variables>

=== modified file 'tests/geopressure_convergence_p1/Makefile'
--- tests/geopressure_convergence_p1/Makefile	2012-07-24 16:34:10 +0000
+++ tests/geopressure_convergence_p1/Makefile	2013-10-16 12:23:45 +0000
@@ -1,49 +1,40 @@
-FLMLMODEL1 = geopressure_8
-FLMLMODEL2 = geopressure_16
-FLMLMODEL3 = geopressure_32
-FLMLMODEL4 = geopressure_64
-
 default: input
 
 input:
 	tar -xvjf src/meshes.tar.bz2
-	cp $(FLMLMODEL1).flml $(FLMLMODEL2).flml 
-	sed -i "s/"$(FLMLMODEL1)"/"$(FLMLMODEL2)"/g" $(FLMLMODEL2).flml 
-	sed -i "s/square-8/square-16/g" $(FLMLMODEL2).flml 
-	cp $(FLMLMODEL1).flml $(FLMLMODEL3).flml 
-	sed -i "s/"$(FLMLMODEL1)"/"$(FLMLMODEL3)"/g" $(FLMLMODEL3).flml 
-	sed -i "s/square-8/square-32/g" $(FLMLMODEL3).flml 
-	cp $(FLMLMODEL1).flml $(FLMLMODEL4).flml 
-	sed -i "s/"$(FLMLMODEL1)"/"$(FLMLMODEL4)"/g" $(FLMLMODEL4).flml 
-	sed -i "s/square-8/square-64/g" $(FLMLMODEL4).flml
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l $(FLMLMODEL1) $(FLMLMODEL1)_flredecomp
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l $(FLMLMODEL2) $(FLMLMODEL2)_flredecomp
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l $(FLMLMODEL3) $(FLMLMODEL3)_flredecomp
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l $(FLMLMODEL4) $(FLMLMODEL4)_flredecomp
+	cp geopressure_8.flml geopressure_16.flml 
+	sed -i "s/"geopressure_8"/"geopressure_16"/g" geopressure_16.flml 
+	sed -i "s/square-8/square-16/g" geopressure_16.flml 
+	cp geopressure_8.flml geopressure_32.flml 
+	sed -i "s/"geopressure_8"/"geopressure_32"/g" geopressure_32.flml 
+	sed -i "s/square-8/square-32/g" geopressure_32.flml 
+	cp geopressure_8.flml geopressure_64.flml 
+	sed -i "s/"geopressure_8"/"geopressure_64"/g" geopressure_64.flml 
+	sed -i "s/square-8/square-64/g" geopressure_64.flml
 
 
 clean: clean-mesh clean-run-debug
-	rm -f $(FLMLMODEL2).flml
-	rm -f $(FLMLMODEL3).flml
-	rm -f $(FLMLMODEL4).flml
+	rm -f geopressure_16.flml
+	rm -f geopressure_32.flml
+	rm -f geopressure_64.flml
 	rm -rf *flredecomp*
 clean-mesh:
 	rm -f square-?*.edge square-?*.ele square-?*.node
 	rm -f square-?*_?*.edge square-?*_*.ele square-?*_?*.node square-?*_?*.halo
 clean-run:
-	rm -f $(FLMLMODEL1)_?*_?*.vtu rm -f $(FLMLMODEL1)_?*.pvtu
-	rm -f $(FLMLMODEL1).detectors $(FLMLMODEL1).stat tmpf*
-	rm -f $(FLMLMODEL2)_?*_?*.vtu rm -f $(FLMLMODEL2)_?*.pvtu
-	rm -f $(FLMLMODEL2).detectors $(FLMLMODEL2).stat tmpf*
-	rm -f $(FLMLMODEL3)_?*_?*.vtu rm -f $(FLMLMODEL3)_?*.pvtu
-	rm -f $(FLMLMODEL3).detectors $(FLMLMODEL3).stat tmpf*
-	rm -f $(FLMLMODEL4)_?*_?*.vtu rm -f $(FLMLMODEL4)_?*.pvtu
-	rm -f $(FLMLMODEL4).detectors $(FLMLMODEL4).stat tmpf*
+	rm -f geopressure_8_?*_?*.vtu rm -f geopressure_8_?*.pvtu
+	rm -f geopressure_8.detectors geopressure_8.stat tmpf*
+	rm -f geopressure_16_?*_?*.vtu rm -f geopressure_16_?*.pvtu
+	rm -f geopressure_16.detectors geopressure_16.stat tmpf*
+	rm -f geopressure_32_?*_?*.vtu rm -f geopressure_32_?*.pvtu
+	rm -f geopressure_32.detectors geopressure_32.stat tmpf*
+	rm -f geopressure_64_?*_?*.vtu rm -f geopressure_64_?*.pvtu
+	rm -f geopressure_64.detectors geopressure_64.stat tmpf*
 	rm -f fluidity.err-?* fluidity.log-?*
 	rm -f matrixdump matrixdump.info
 	rm -f *.log
-	rm -rf $(FLMLMODEL1)_?
-	rm -rf $(FLMLMODEL2)_?
-	rm -rf $(FLMLMODEL3)_?
-	rm -rf $(FLMLMODEL4)_?
+	rm -rf geopressure_8_?
+	rm -rf geopressure_16_?
+	rm -rf geopressure_32_?
+	rm -rf geopressure_64_?
 clean-run-debug: clean-run

=== modified file 'tests/geopressure_convergence_p1/geopressure_convergence_p1.xml'
--- tests/geopressure_convergence_p1/geopressure_convergence_p1.xml	2012-07-24 16:34:10 +0000
+++ tests/geopressure_convergence_p1/geopressure_convergence_p1.xml	2013-10-16 12:23:45 +0000
@@ -3,12 +3,17 @@
   <name>Geopressure convergence test (P1)</name>
   <owner userid="piggt01"/>
   <tags>flml parallel</tags>
-  <problem_definition length = "medium" nprocs = "1">
-    <command_line>make clean-run; rm -f 8.log 16.log 32.log 64.log;
-mpiexec -n 2 ../../bin/fluidity -v2 geopressure_8_flredecomp.flml > 8.log;
-mpiexec -n 2 ../../bin/fluidity -v2 geopressure_16_flredecomp.flml > 16.log;
-mpiexec -n 2 ../../bin/fluidity -v2 geopressure_32_flredecomp.flml > 32.log;
-mpiexec -n 2 ../../bin/fluidity -v2 geopressure_64_flredecomp.flml > 64.log;
+  <problem_definition length = "medium" nprocs = "2">
+    <command_line>
+      make clean-run; rm -f 8.log 16.log 32.log 64.log &amp;&amp;
+      mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l geopressure_8 geopressure_8_flredecomp &amp;&amp;
+      mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l geopressure_16 geopressure_16_flredecomp &amp;&amp;
+      mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l geopressure_32 geopressure_32_flredecomp &amp;&amp;
+      mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l geopressure_64 geopressure_64_flredecomp &amp;&amp;
+      mpiexec ../../bin/fluidity -v2 geopressure_8_flredecomp.flml &gt; 8.log;
+      mpiexec ../../bin/fluidity -v2 geopressure_16_flredecomp.flml &gt; 16.log;
+      mpiexec ../../bin/fluidity -v2 geopressure_32_flredecomp.flml &gt; 32.log;
+      mpiexec ../../bin/fluidity -v2 geopressure_64_flredecomp.flml &gt; 64.log;
     </command_line>
   </problem_definition>
   <variables>

=== modified file 'tests/heat_2d_dg/Makefile'
--- tests/heat_2d_dg/Makefile	2012-08-13 11:42:30 +0000
+++ tests/heat_2d_dg/Makefile	2013-10-16 12:23:45 +0000
@@ -1,6 +1,5 @@
 input: clean
 	../../bin/gmsh2triangle --2d src/square.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp
 
 clean:
 	rm -fr  *.ele *.edge *.node *.poly *.halo *.vtu *.pvtu fluidity.* *.s *.d.1 *.stat heat_[01] \

=== modified file 'tests/heat_2d_dg/heat_2d_dg.xml'
--- tests/heat_2d_dg/heat_2d_dg.xml	2012-08-13 11:42:30 +0000
+++ tests/heat_2d_dg/heat_2d_dg.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,9 @@
   <name>heat_2d_dg</name>
   <owner userid="dham"/>
   <tags>flml parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -np 2 ../../bin/fluidity -l heat_flredecomp.flml </command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp &amp;&amp;
+      mpiexec ../../bin/fluidity -l heat_flredecomp.flml </command_line>
     <!-- Two dimensional diffusion only problem. -->
   </problem_definition>
   <variables>

=== modified file 'tests/heat_2d_dg_ip/Makefile'
--- tests/heat_2d_dg_ip/Makefile	2012-08-13 11:42:30 +0000
+++ tests/heat_2d_dg_ip/Makefile	2013-10-16 12:23:45 +0000
@@ -1,6 +1,5 @@
 input: clean
 	../../bin/gmsh2triangle --2d src/square.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp
 
 clean:
 	rm -fr  *.ele *.edge *.node *.poly *.halo *.vtu *.pvtu fluidity.* *.s *.d.1 *.stat heat_[01] \

=== modified file 'tests/heat_2d_dg_ip/heat_2d_dg_ip.xml'
--- tests/heat_2d_dg_ip/heat_2d_dg_ip.xml	2012-08-13 11:42:30 +0000
+++ tests/heat_2d_dg_ip/heat_2d_dg_ip.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,9 @@
   <name>heat_2d_dg</name>
   <owner userid="dham"/>
   <tags>flml parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -np 2 ../../bin/fluidity -l heat_flredecomp.flml </command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp &amp;&amp;
+      mpiexec ../../bin/fluidity -l heat_flredecomp.flml </command_line>
     <!-- Two dimensional diffusion only problem. -->
   </problem_definition>
   <variables>

=== modified file 'tests/heat_2d_dg_local_assembly/Makefile'
--- tests/heat_2d_dg_local_assembly/Makefile	2012-11-08 17:26:18 +0000
+++ tests/heat_2d_dg_local_assembly/Makefile	2013-10-16 12:23:45 +0000
@@ -1,6 +1,5 @@
 input: clean
 	../../bin/gmsh2triangle --2d src/square.msh
-	mpiexec -n 8 ../../bin/flredecomp -i 1 -o 8 -v -l heat heat_flredecomp
 
 clean:
 	rm -f  *.ele *.edge *.node *.poly *.halo *.vtu *.pvtu fluidity.* *.s *.d.1 *.stat \

=== modified file 'tests/heat_2d_dg_local_assembly/heat_2d_dg_local_assembly.xml'
--- tests/heat_2d_dg_local_assembly/heat_2d_dg_local_assembly.xml	2012-08-13 11:42:30 +0000
+++ tests/heat_2d_dg_local_assembly/heat_2d_dg_local_assembly.xml	2013-10-16 12:23:45 +0000
@@ -5,8 +5,9 @@
   <name>heat_2d_dg</name>
   <owner userid="wence"/>
   <tags>flml parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -np 8 ../../bin/fluidity -l heat_flredecomp.flml </command_line>
+  <problem_definition length="short" nprocs="8">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 8 -v -l heat heat_flredecomp &amp;&amp;
+      mpiexec ../../bin/fluidity -l heat_flredecomp.flml </command_line>
     <!-- Two dimensional diffusion only problem. -->
   </problem_definition>
   <variables>

=== modified file 'tests/lagrangian_detectors/Makefile'
--- tests/lagrangian_detectors/Makefile	2012-07-24 16:34:10 +0000
+++ tests/lagrangian_detectors/Makefile	2013-10-16 12:23:45 +0000
@@ -1,7 +1,6 @@
 input: default
 default: clean
 	gmsh -2 -bin square.geo -o square.msh
-	mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l lagrangian_detectors_rk lagrangian_detectors_rk_flredecomp
 clean: 
 	rm -rf *.msh *.halo *.vtu *.pvtu *.log* *.err* *.stat blob_[012] *.detectors *.dat *flredecomp*
 

=== modified file 'tests/lagrangian_detectors/lagrangian_detectors.xml'
--- tests/lagrangian_detectors/lagrangian_detectors.xml	2012-07-24 16:34:10 +0000
+++ tests/lagrangian_detectors/lagrangian_detectors.xml	2013-10-16 12:23:45 +0000
@@ -4,9 +4,10 @@
   <name>lagrangian_detectors</name>
   <owner userid="colin"/>
   <tags>flml parallel nozoltan</tags>
-  <problem_definition length="short" nprocs="1">
+  <problem_definition length="short" nprocs="4">
     <command_line>
-mpirun -n 4 ../../bin/fluidity -v3 -l lagrangian_detectors_rk_flredecomp.flml
+mpiexec ../../bin/flredecomp -i 1 -o 4 -v -l lagrangian_detectors_rk lagrangian_detectors_rk_flredecomp;
+mpiexec ../../bin/fluidity -v3 -l lagrangian_detectors_rk_flredecomp.flml
     </command_line>
   </problem_definition>
   <variables>

=== modified file 'tests/lagrangian_detectors_3d/Makefile'
--- tests/lagrangian_detectors_3d/Makefile	2012-07-24 16:34:10 +0000
+++ tests/lagrangian_detectors_3d/Makefile	2013-10-16 12:23:45 +0000
@@ -1,6 +1,5 @@
 input: default
 default: clean
 	gmsh -3 -bin src/box.geo -o box.msh
-	mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l lagrangian_detectors_3d lagrangian_detectors_3d_flredecomp
 clean: 
 	rm -rf *.msh *.halo *.vtu *.pvtu *.log* *.err* *.stat blob_[012] *.detectors *.dat lagrangian_detectors_[01] *flredecomp*

=== modified file 'tests/lagrangian_detectors_3d/lagrangian_detectors_3d.xml'
--- tests/lagrangian_detectors_3d/lagrangian_detectors_3d.xml	2012-07-24 16:34:10 +0000
+++ tests/lagrangian_detectors_3d/lagrangian_detectors_3d.xml	2013-10-16 12:23:45 +0000
@@ -4,9 +4,9 @@
   <name>lagrangian_detectors_3d</name>
   <owner userid="colin"/>
   <tags>flml parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>
-mpirun -n 4 ../../bin/fluidity -v3 -l lagrangian_detectors_3d_flredecomp.flml
+  <problem_definition length="short" nprocs="4">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 4 -v -l lagrangian_detectors_3d lagrangian_detectors_3d_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v3 -l lagrangian_detectors_3d_flredecomp.flml
     </command_line>
   </problem_definition>
   <variables>

=== modified file 'tests/meshconv_test/meshconv_test.xml'
--- tests/meshconv_test/meshconv_test.xml	2013-04-11 19:08:05 +0000
+++ tests/meshconv_test/meshconv_test.xml	2013-10-16 12:23:45 +0000
@@ -8,8 +8,8 @@
     ../../bin/meshconv -i exodusii -o triangle rectangle; fluidity meshconv_exo2triangle.flml; rm rectangle.node rectangle.ele rectangle.edge;
     ../../bin/meshconv -i gmsh -o triangle rectangle; fluidity meshconv_gmsh2triangle.flml; rm rectangle.msh;
     ../../bin/meshconv -i triangle -o gmsh rectangle; fluidity meshconv_triangle2gmsh.flml; rm rectangle.*
-    mpiexec -n 2 ../../bin/meshconv -i gmsh -o triangle prectangle; mpiexec -n 2 fluidity meshconv_parallel_gmsh2triangle.flml; rm prectangle_?.msh;
-    mpiexec -n 2 ../../bin/meshconv -i triangle -o gmsh prectangle; mpiexec -n 2 fluidity meshconv_parallel_triangle2gmsh.flml; rm prectangle*;
+    mpiexec ../../bin/meshconv -i gmsh -o triangle prectangle; mpiexec fluidity meshconv_parallel_gmsh2triangle.flml; rm prectangle_?.msh;
+    mpiexec ../../bin/meshconv -i triangle -o gmsh prectangle; mpiexec fluidity meshconv_parallel_triangle2gmsh.flml; rm prectangle*;
     </command_line>
   </problem_definition>
   <variables>

=== modified file 'tests/mixing_stats_test/Makefile'
--- tests/mixing_stats_test/Makefile	2012-08-13 11:42:30 +0000
+++ tests/mixing_stats_test/Makefile	2013-10-16 12:23:45 +0000
@@ -2,7 +2,6 @@
 	sed  "s/mixing_stats_test/mixing_stats_test_serial/" mixing_stats_test.flml > mixing_stats_test_serial.flml
 	sed  "s/mixing_stats_test/mixing_stats_test_parallel/" mixing_stats_test.flml > mixing_stats_test_parallel.flml
 	gmsh  -bin -3 src/pseudo_2d_square.geo -o pseudo_2d_square.msh
-	mpiexec -n 3 ../../bin/flredecomp -i 1 -o 3 -v -l mixing_stats_test_parallel mixing_stats_test_parallel_flredecomp
 
 clean:
 	rm -f *.stat *.vtu *.pvtu *.convergence *checkpoint* *.err* *.log*  

=== modified file 'tests/mixing_stats_test/mixing_stats_test.xml'
--- tests/mixing_stats_test/mixing_stats_test.xml	2012-08-13 11:42:30 +0000
+++ tests/mixing_stats_test/mixing_stats_test.xml	2013-10-16 12:23:45 +0000
@@ -8,9 +8,10 @@
   
   <tags>flml parallel</tags>
   
-    <problem_definition length="medium" nprocs="1">
-    <command_line>fluidity -v3 -l mixing_stats_test_serial.flml;
-                  mpiexec -n 3 ../../bin/fluidity -v3 -l mixing_stats_test_parallel_flredecomp.flml;
+    <problem_definition length="medium" nprocs="3">
+      <command_line>mpiexec ../../bin/flredecomp -i 1 -o 3 -v -l mixing_stats_test_parallel mixing_stats_test_parallel_flredecomp &amp;&amp;
+        fluidity -v3 -l mixing_stats_test_serial.flml;
+                  mpiexec ../../bin/fluidity -v3 -l mixing_stats_test_parallel_flredecomp.flml;
      </command_line>
   </problem_definition> 
    

=== modified file 'tests/mmat-balancepressure-extrude-parallel/Makefile'
--- tests/mmat-balancepressure-extrude-parallel/Makefile	2012-07-24 16:34:10 +0000
+++ tests/mmat-balancepressure-extrude-parallel/Makefile	2013-10-16 12:23:45 +0000
@@ -1,9 +1,5 @@
 input: clean
 	../../bin/interval --dx 0.05 --reverse -- -0.5 0.5 line
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l mmat-balancepressure-p0p1cv-gpp2 mmat-balancepressure-p0p1cv-gpp2_flredecomp
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l mmat-balancepressure-p0p1cv-hpp2dg mmat-balancepressure-p0p1cv-hpp2dg_flredecomp
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l mmat-balancepressure-p0p1-rhop0-vfracp0 mmat-balancepressure-p0p1-rhop0-vfracp0_flredecomp
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv_flredecomp
 
 clean:
 	rm -rf *.stat *.vtu *.pvtu *.convergence *.node *.bound *.ele *.halo *.log-? *.err-? *checkpoint*

=== modified file 'tests/mmat-balancepressure-extrude-parallel/mmat-balancepressure-extrude-parallel.xml'
--- tests/mmat-balancepressure-extrude-parallel/mmat-balancepressure-extrude-parallel.xml	2012-07-24 16:34:10 +0000
+++ tests/mmat-balancepressure-extrude-parallel/mmat-balancepressure-extrude-parallel.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,30 @@
   <name>Control volume, multi-material surface integral pressure check</name>
   <owner userid="cwilson"/>
   <tags>flml parallel</tags>
-    <problem_definition length="medium" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/fluidity -v2 -l mmat-balancepressure-p0p1cv-gpp2_flredecomp.flml &amp;&amp; mv fluidity.log-0 mmat-balancepressure-p0p1cv-gpp2.log-0 &amp;&amp; mv fluidity.log-1 mmat-balancepressure-p0p1cv-gpp2.log-1 &amp;&amp; mv fluidity.err-0 mmat-balancepressure-p0p1cv-gpp2.err-0 &amp;&amp; mv fluidity.err-1 mmat-balancepressure-p0p1cv-gpp2.err-1 &amp;&amp; mpiexec -n 2 ../../bin/fluidity -v2 -l mmat-balancepressure-p0p1cv-hpp2dg_flredecomp.flml &amp;&amp; mv fluidity.log-0 mmat-balancepressure-p0p1cv-hpp2dg.log-0  &amp;&amp; mv fluidity.log-1 mmat-balancepressure-p0p1cv-hpp2dg.log-1  &amp;&amp; mv fluidity.err-0 mmat-balancepressure-p0p1cv-hpp2dg.err-0 &amp;&amp; mv fluidity.err-1 mmat-balancepressure-p0p1cv-hpp2dg.err-1 &amp;&amp; mpiexec -n 2 ../../bin/fluidity -v2 -l mmat-balancepressure-p0p1-rhop0-vfracp0_flredecomp.flml &amp;&amp; mv fluidity.log-0 mmat-balancepressure-p0p1-rhop0-vfracp0.log-0 &amp;&amp; mv fluidity.log-1 mmat-balancepressure-p0p1-rhop0-vfracp0.log-1 &amp;&amp; mv fluidity.err-0 mmat-balancepressure-p0p1-rhop0-vfracp0.err-0 &amp;&amp; mv fluidity.err-1 mmat-balancepressure-p0p1-rhop0-vfracp0.err-1 &amp;&amp; mpiexec -n 2 ../../bin/fluidity -v2 -l mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv_flredecomp.flml &amp;&amp; mv fluidity.log-0 mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv.log-0 &amp;&amp; mv fluidity.log-1 mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv.log-1 &amp;&amp; mv fluidity.err-0 mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv.err-0 &amp;&amp; mv fluidity.err-1 mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv.err-1</command_line>
+    <problem_definition length="medium" nprocs="2">
+      <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l mmat-balancepressure-p0p1cv-gpp2 mmat-balancepressure-p0p1cv-gpp2_flredecomp &amp;&amp;
+	mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l mmat-balancepressure-p0p1cv-hpp2dg mmat-balancepressure-p0p1cv-hpp2dg_flredecomp &amp;&amp;
+	mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l mmat-balancepressure-p0p1-rhop0-vfracp0 mmat-balancepressure-p0p1-rhop0-vfracp0_flredecomp &amp;&amp;
+	mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv_flredecomp &amp;&amp;
+        mpiexec ../../bin/fluidity -v2 -l mmat-balancepressure-p0p1cv-gpp2_flredecomp.flml &amp;&amp; mv fluidity.log-0 mmat-balancepressure-p0p1cv-gpp2.log-0 &amp;&amp;
+        mv fluidity.log-1 mmat-balancepressure-p0p1cv-gpp2.log-1 &amp;&amp;
+        mv fluidity.err-0 mmat-balancepressure-p0p1cv-gpp2.err-0 &amp;&amp;
+        mv fluidity.err-1 mmat-balancepressure-p0p1cv-gpp2.err-1 &amp;&amp;
+        mpiexec ../../bin/fluidity -v2 -l mmat-balancepressure-p0p1cv-hpp2dg_flredecomp.flml &amp;&amp;
+        mv fluidity.log-0 mmat-balancepressure-p0p1cv-hpp2dg.log-0  &amp;&amp;
+        mv fluidity.log-1 mmat-balancepressure-p0p1cv-hpp2dg.log-1  &amp;&amp; 
+        mv fluidity.err-0 mmat-balancepressure-p0p1cv-hpp2dg.err-0 &amp;&amp; 
+        mv fluidity.err-1 mmat-balancepressure-p0p1cv-hpp2dg.err-1 &amp;&amp; 
+        mpiexec ../../bin/fluidity -v2 -l mmat-balancepressure-p0p1-rhop0-vfracp0_flredecomp.flml &amp;&amp; 
+        mv fluidity.log-0 mmat-balancepressure-p0p1-rhop0-vfracp0.log-0 &amp;&amp; 
+        mv fluidity.log-1 mmat-balancepressure-p0p1-rhop0-vfracp0.log-1 &amp;&amp; 
+        mv fluidity.err-0 mmat-balancepressure-p0p1-rhop0-vfracp0.err-0 &amp;&amp; 
+        mv fluidity.err-1 mmat-balancepressure-p0p1-rhop0-vfracp0.err-1 &amp;&amp; 
+        mpiexec ../../bin/fluidity -v2 -l mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv_flredecomp.flml &amp;&amp; 
+        mv fluidity.log-0 mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv.log-0 &amp;&amp; 
+        mv fluidity.log-1 mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv.log-1 &amp;&amp; 
+        mv fluidity.err-0 mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv.err-0 &amp;&amp; 
+        mv fluidity.err-1 mmat-balancepressure-p1dgp2-rhop1dg-vfracp1cv.err-1</command_line>
   </problem_definition>  
   <variables>  
     <variable name="pressure_p0p1cv_gpp2" language="python">

=== modified file 'tests/mmat-interpolation-2d-parallel/Makefile'
--- tests/mmat-interpolation-2d-parallel/Makefile	2012-11-08 17:26:18 +0000
+++ tests/mmat-interpolation-2d-parallel/Makefile	2013-10-16 12:23:45 +0000
@@ -1,7 +1,6 @@
 input: clean
 	gmsh -2 src/2d_square.geo
 	../../bin/gmsh2triangle --2d src/2d_square.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l mmat-interpolation mmat-interpolation_flredecomp
 
 clean:
 	rm -rf *.stat *.msh *.vtu *.pvtu *.node *.ele *.halo *.edge *checkpoint* *convergence* matrixdump* *.log-? *.err-? src/2d_square.msh adapted_state_* mmat-interpolation_[0-3] *flredecomp*

=== modified file 'tests/mmat-interpolation-2d-parallel/mmat-interpolation-2d-parallel.xml'
--- tests/mmat-interpolation-2d-parallel/mmat-interpolation-2d-parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/mmat-interpolation-2d-parallel/mmat-interpolation-2d-parallel.xml	2013-10-16 12:23:45 +0000
@@ -3,8 +3,9 @@
   <name>Multimaterial adaptivity and interpolation test</name>
   <owner userid="cwilson"/>
   <tags>flml 2dadapt zoltan parallel</tags>
-  <problem_definition length ="short" nprocs = "1">
-    <command_line>mpiexec -np 2 ../../bin/fluidity -v2 -l mmat-interpolation_flredecomp.flml &amp;&amp; mv fluidity.log-0 first.log-0 &amp;&amp; mv fluidity.log-1 first.log-1 &amp;&amp; mv fluidity.err-0 first.err-0 &amp;&amp; mv fluidity.err-1 first.err-1 &amp;&amp; ./change_options.py &amp;&amp; mpiexec -np 2 ../../bin/fluidity -v2 -l mmat-interpolation_2_checkpoint.flml &amp;&amp; mv fluidity.log-0 checkpoint.log-0 &amp;&amp; mv fluidity.log-1 checkpoint.log-1 &amp;&amp; mv fluidity.err-0 checkpoint.err-0 &amp;&amp; mv fluidity.err-1 checkpoint.err-1 </command_line>
+  <problem_definition length ="short" nprocs = "2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l mmat-interpolation mmat-interpolation_flredecomp &amp;&amp;
+      mpiexec ../../bin/fluidity -v2 -l mmat-interpolation_flredecomp.flml &amp;&amp; mv fluidity.log-0 first.log-0 &amp;&amp; mv fluidity.log-1 first.log-1 &amp;&amp; mv fluidity.err-0 first.err-0 &amp;&amp; mv fluidity.err-1 first.err-1 &amp;&amp; ./change_options.py &amp;&amp; mpiexec ../../bin/fluidity -v2 -l mmat-interpolation_2_checkpoint.flml &amp;&amp; mv fluidity.log-0 checkpoint.log-0 &amp;&amp; mv fluidity.log-1 checkpoint.log-1 &amp;&amp; mv fluidity.err-0 checkpoint.err-0 &amp;&amp; mv fluidity.err-1 checkpoint.err-1 </command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/mmat-interpolation-pseudo2d-parallel/Makefile'
--- tests/mmat-interpolation-pseudo2d-parallel/Makefile	2012-08-13 11:42:30 +0000
+++ tests/mmat-interpolation-pseudo2d-parallel/Makefile	2013-10-16 12:23:45 +0000
@@ -1,7 +1,6 @@
 input: clean
 	gmsh -3 src/2d_square.geo
 	../../bin/gmsh2triangle src/2d_square.msh
-	mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l mmat-interpolation mmat-interpolation_flredecomp
 
 clean:
 	rm -rf *.stat *.vtu *.pvtu *.msh *.node *.ele *.halo *.face *edge *checkpoint* *convergence* matrixdump* *.log-? *.err-? src/2d_square.msh adapted_state_* mmat-interpolation_[0-3] bounding_box* *metric* *flredecomp*

=== modified file 'tests/mmat-interpolation-pseudo2d-parallel/mmat-interpolation-pseudo2d-parallel.xml'
--- tests/mmat-interpolation-pseudo2d-parallel/mmat-interpolation-pseudo2d-parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/mmat-interpolation-pseudo2d-parallel/mmat-interpolation-pseudo2d-parallel.xml	2013-10-16 12:23:45 +0000
@@ -3,8 +3,9 @@
   <name>Multimaterial adaptivity and interpolation test</name>
   <owner userid="cwilson"/>
   <tags>flml 2dadapt parallel</tags>
-  <problem_definition length ="special" nprocs = "1">
-    <command_line>mpiexec -np 2 ../../bin/fluidity -v2 -l mmat-interpolation_flredecomp.flml &amp;&amp; mv fluidity.log-0 first.log-0 &amp;&amp; mv fluidity.log-1 first.log-1 &amp;&amp; mv fluidity.err-0 first.err-0 &amp;&amp; mv fluidity.err-1 first.err-1 &amp;&amp; ./change_options.py &amp;&amp; mpiexec -np 2 ../../bin/fluidity -v2 -l mmat-interpolation_2_checkpoint.flml &amp;&amp; mv fluidity.log-0 checkpoint.log-0 &amp;&amp; mv fluidity.log-1 checkpoint.log-1 &amp;&amp; mv fluidity.err-0 checkpoint.err-0 &amp;&amp; mv fluidity.err-1 checkpoint.err-1 </command_line>
+  <problem_definition length ="special" nprocs = "2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l mmat-interpolation mmat-interpolation_flredecomp &amp;&amp;
+      mpiexec ../../bin/fluidity -v2 -l mmat-interpolation_flredecomp.flml &amp;&amp; mv fluidity.log-0 first.log-0 &amp;&amp; mv fluidity.log-1 first.log-1 &amp;&amp; mv fluidity.err-0 first.err-0 &amp;&amp; mv fluidity.err-1 first.err-1 &amp;&amp; ./change_options.py &amp;&amp; mpiexec ../../bin/fluidity -v2 -l mmat-interpolation_2_checkpoint.flml &amp;&amp; mv fluidity.log-0 checkpoint.log-0 &amp;&amp; mv fluidity.log-1 checkpoint.log-1 &amp;&amp; mv fluidity.err-0 checkpoint.err-0 &amp;&amp; mv fluidity.err-1 checkpoint.err-1 </command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc/Makefile'
--- tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc/Makefile	2012-06-28 08:23:27 +0000
+++ tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc/Makefile	2013-10-16 12:23:45 +0000
@@ -1,10 +1,8 @@
-PROJECT = channel
-
 input: clean
 
 clean:
-	rm -f $(PROJECT) $(PROJECT)0 $(PROJECT).fld
-	rm -f $(PROJECT).s $(PROJECT).stat
+	rm -f channel channel0 channel.fld
+	rm -f channel.s channel.stat
 	rm -f *.d.* *.vtu
 	rm -f fluidity.err-0 fluidity.log-0
 	rm -f *.ele *.face *.node *.edge *.stat *.halo

=== modified file 'tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc/mms_tracer_P1dg_cdg_diff_steady_3d_cjc.xml'
--- tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc/mms_tracer_P1dg_cdg_diff_steady_3d_cjc.xml	2012-06-28 08:23:27 +0000
+++ tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc/mms_tracer_P1dg_cdg_diff_steady_3d_cjc.xml	2013-10-16 12:23:45 +0000
@@ -3,7 +3,7 @@
   <name>channel-flow-dg</name>
   <owner userid="colin"/>
   <problem_definition length="medium" nprocs="1">
-    <command_line>for layer in 5 10 20 30; do ./generate_mesh $layer; fluidity cdg_cjc.flml; cp cdg.stat cdg-$layer.stat; cp cdg_1.vtu cdg-$layer.vtu; done</command_line>
+    <command_line>./generate_mesh 5; fluidity cdg_cjc.flml; cp cdg.stat cdg-5.stat; cp cdg_1.vtu cdg-5.vtu; ./generate_mesh 10; fluidity cdg_cjc.flml; cp cdg.stat cdg-10.stat; cp cdg_1.vtu cdg-10.vtu; ./generate_mesh 20; fluidity cdg_cjc.flml; cp cdg.stat cdg-20.stat; cp cdg_1.vtu cdg-20.vtu; ./generate_mesh 30; fluidity cdg_cjc.flml; cp cdg.stat cdg-30.stat; cp cdg_1.vtu cdg-30.vtu</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc_inhNmnnbc/Makefile'
--- tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc_inhNmnnbc/Makefile	2012-09-05 18:33:14 +0000
+++ tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc_inhNmnnbc/Makefile	2013-10-16 12:23:45 +0000
@@ -1,10 +1,8 @@
-PROJECT = channel
-
 input: clean
 
 clean:
-	rm -f $(PROJECT) $(PROJECT)0 $(PROJECT).fld
-	rm -f $(PROJECT).s $(PROJECT).stat
+	rm -f channel channel0 channel.fld
+	rm -f channel.s channel.stat
 	rm -f *.d.* *.vtu
 	rm -f fluidity.err-0 fluidity.log-0
 	rm -f *.ele *.face *.node *.edge *.stat *.halo

=== modified file 'tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc_inhNmnnbc/mms_tracer_P1dg_cdg_diff_steady_3d_cjc_inhNmnnbc.xml'
--- tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc_inhNmnnbc/mms_tracer_P1dg_cdg_diff_steady_3d_cjc_inhNmnnbc.xml	2012-09-05 18:33:14 +0000
+++ tests/mms_tracer_P1dg_cdg_diff_steady_3d_cjc_inhNmnnbc/mms_tracer_P1dg_cdg_diff_steady_3d_cjc_inhNmnnbc.xml	2013-10-16 12:23:45 +0000
@@ -3,7 +3,7 @@
   <name>channel-flow-dg</name>
   <owner userid="avdis01"/>
   <problem_definition length="medium" nprocs="1">
-    <command_line>for layer in 5 10 20 30; do ./generate_mesh $layer; fluidity cdg_cjc.flml; cp cdg.stat cdg-$layer.stat; cp cdg_1.vtu cdg-$layer.vtu; done</command_line>
+    <command_line>./generate_mesh 5; fluidity cdg_cjc.flml; cp cdg.stat cdg-5.stat; cp cdg_1.vtu cdg-5.vtu; ./generate_mesh 10; fluidity cdg_cjc.flml; cp cdg.stat cdg-10.stat; cp cdg_1.vtu cdg-10.vtu; ./generate_mesh 20; fluidity cdg_cjc.flml; cp cdg.stat cdg-20.stat; cp cdg_1.vtu cdg-20.vtu; ./generate_mesh 30; fluidity cdg_cjc.flml; cp cdg.stat cdg-30.stat; cp cdg_1.vtu cdg-30.vtu</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/parallel_p0_consistent_interpolation/Makefile'
--- tests/parallel_p0_consistent_interpolation/Makefile	2012-08-13 11:42:30 +0000
+++ tests/parallel_p0_consistent_interpolation/Makefile	2013-10-16 12:23:45 +0000
@@ -1,17 +1,14 @@
-FLMLMODEL = parallel_p0_consistent_interpolation
-MESH = square-unstructured
-
 default: input
 
-input: src/$(MESH).tar.bz2
-	tar -xvjf src/$(MESH).tar.bz2
+input: src/square-unstructured.tar.bz2
+	tar -xvjf src/square-unstructured.tar.bz2
 
 clean: clean-mesh clean-run
 	rm -rf parallel_p0_consistent_interpolation_*
 clean-mesh:
-	rm -f $(MESH).edge $(MESH).ele $(MESH).node
-	rm -f $(MESH)_?*.edge $(MESH)_?*.ele $(MESH)_?*.node $(MESH)_?*.halo
+	rm -f square-unstructured.edge square-unstructured.ele square-unstructured.node
+	rm -f square-unstructured_?*.edge square-unstructured_?*.ele square-unstructured_?*.node square-unstructured_?*.halo
 clean-run:
-	rm -f $(FLMLMODEL)_?*.pvtu $(FLMLMODEL)_?*_?*.vtu $(FLMLMODEL).stat fluidity.err-* fluidity.log-* \
+	rm -f parallel_p0_consistent_interpolation_?*.pvtu parallel_p0_consistent_interpolation_?*_?*.vtu parallel_p0_consistent_interpolation.stat fluidity.err-* fluidity.log-* \
 	matrixdump matrixdump.info
 	rm -rf *flredecomp*

=== modified file 'tests/parallel_p0_consistent_interpolation/parallel_p0_consistent_interpolation.xml'
--- tests/parallel_p0_consistent_interpolation/parallel_p0_consistent_interpolation.xml	2012-08-13 11:42:30 +0000
+++ tests/parallel_p0_consistent_interpolation/parallel_p0_consistent_interpolation.xml	2013-10-16 12:23:45 +0000
@@ -3,8 +3,8 @@
   <name>parallel_p0_consistent_interpolation</name>
   <owner userid="cwilson"/>
   <tags>flml zoltan parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>make clean-run; mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l parallel_p0_consistent_interpolation parallel_p0_consistent_interpolation_flredecomp; mpiexec -n 2 ../../bin/fluidity -v2 -l parallel_p0_consistent_interpolation_flredecomp.flml</command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>make clean-run; mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l parallel_p0_consistent_interpolation parallel_p0_consistent_interpolation_flredecomp; mpiexec ../../bin/fluidity -v2 -l parallel_p0_consistent_interpolation_flredecomp.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/parallel_p0_consistent_interpolation_3d/parallel_p0_consistent_interpolation_3d.xml'
--- tests/parallel_p0_consistent_interpolation_3d/parallel_p0_consistent_interpolation_3d.xml	2012-08-13 11:42:30 +0000
+++ tests/parallel_p0_consistent_interpolation_3d/parallel_p0_consistent_interpolation_3d.xml	2013-10-16 12:23:45 +0000
@@ -3,8 +3,8 @@
   <name>parallel_p0_consistent_interpolation_3d</name>
   <owner userid="cwilson"/>
   <tags>flml zoltan parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>make clean-run; mpiexec -n 3 ../../bin/flredecomp -i 1 -o 3 -v -l parallel_p0_consistent_interpolation parallel_p0_consistent_interpolation_flredecomp; mpiexec -n 3 ../../bin/fluidity -v2 -l parallel_p0_consistent_interpolation_flredecomp.flml</command_line>
+  <problem_definition length="short" nprocs="3">
+    <command_line>make clean-run; mpiexec ../../bin/flredecomp -i 1 -o 3 -v -l parallel_p0_consistent_interpolation parallel_p0_consistent_interpolation_flredecomp; mpiexec ../../bin/fluidity -v2 -l parallel_p0_consistent_interpolation_flredecomp.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/parallel_p1_consistent_interpolation/parallel_p1_consistent_interpolation.xml'
--- tests/parallel_p1_consistent_interpolation/parallel_p1_consistent_interpolation.xml	2012-08-13 11:42:30 +0000
+++ tests/parallel_p1_consistent_interpolation/parallel_p1_consistent_interpolation.xml	2013-10-16 12:23:45 +0000
@@ -3,8 +3,8 @@
   <name>parallel_p1_consistent_interpolation</name>
   <owner userid="cwilson"/>
   <tags>flml zoltan parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>make clean-run; mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l parallel_p1_consistent_interpolation parallel_p1_consistent_interpolation_flredecomp; mpiexec -n 2 ../../bin/fluidity -v2 -l parallel_p1_consistent_interpolation_flredecomp.flml</command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>make clean-run; mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l parallel_p1_consistent_interpolation parallel_p1_consistent_interpolation_flredecomp; mpiexec ../../bin/fluidity -v2 -l parallel_p1_consistent_interpolation_flredecomp.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/parallel_p2_consistent_interpolation/parallel_p2_consistent_interpolation.xml'
--- tests/parallel_p2_consistent_interpolation/parallel_p2_consistent_interpolation.xml	2012-08-13 11:42:30 +0000
+++ tests/parallel_p2_consistent_interpolation/parallel_p2_consistent_interpolation.xml	2013-10-16 12:23:45 +0000
@@ -3,8 +3,8 @@
   <name>parallel_p2_consistent_interpolation</name>
   <owner userid="pef"/>
   <tags>flml zoltan parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>make clean-run; mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l parallel_p2_consistent_interpolation parallel_p2_consistent_interpolation_flredecomp; mpiexec -n 2 ../../bin/fluidity -v2 -l parallel_p2_consistent_interpolation_flredecomp.flml</command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>make clean-run; mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l parallel_p2_consistent_interpolation parallel_p2_consistent_interpolation_flredecomp; mpiexec ../../bin/fluidity -v2 -l parallel_p2_consistent_interpolation_flredecomp.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/periodic_2plus1_parallel/periodic_2plus1_parallel.xml'
--- tests/periodic_2plus1_parallel/periodic_2plus1_parallel.xml	2011-02-22 19:17:14 +0000
+++ tests/periodic_2plus1_parallel/periodic_2plus1_parallel.xml	2013-10-16 12:23:45 +0000
@@ -3,9 +3,8 @@
   <name>Periodic 2+1 parallel</name>
   <owner userid="am2008"/>
   <tags>flml zoltan parallel</tags>
-  <problem_definition length="short" nprocs="1">
+  <problem_definition length="short" nprocs="2">
     <command_line>
-    no_proc=2
     filename='periodic_2plus1_parallel';
     mesh='MMS_B';
     periodic_mesh='PeriodicMesh';
@@ -14,10 +13,10 @@
     ../../bin/periodise ${filename}.flml &amp;&amp;
     
     #flredecomp the flml
-    mpiexec -n 2 ../../bin/flredecomp -v -l -i 1 -o $no_proc ${filename}_periodised ${filename}_periodised_flredecomp &amp;&amp;
+    mpiexec ../../bin/flredecomp -v -l -i 1 -o 2 ${filename}_periodised ${filename}_periodised_flredecomp &amp;&amp;
         
     #run
-    mpiexec -n 2 ../../bin/fluidity -v3 -l ${filename}_periodised_flredecomp.flml 
+    mpiexec ../../bin/fluidity -v3 -l ${filename}_periodised_flredecomp.flml 
     </command_line>
   </problem_definition>
   <variables>

=== modified file 'tests/petsc_readnsolve/petsc_readnsolve.xml'
--- tests/petsc_readnsolve/petsc_readnsolve.xml	2012-08-14 16:26:46 +0000
+++ tests/petsc_readnsolve/petsc_readnsolve.xml	2013-10-16 12:23:45 +0000
@@ -3,24 +3,24 @@
   <name>petsc_readnsolve</name>
   <owner userid="skramer"/>
   <tags> parallel </tags>
-  <problem_definition length="short" nprocs="1">
-    <comment>This is a lie: we're actually using nprocs=4.  First make a common flredecomped mesh and edit the flml files to use this, then do the actual test.</comment>
-    <command_line>mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l standing_wave_failing_velocity standing_wave_failing_velocity_flredecomp;
-mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l standing_wave_failing_pressure standing_wave_failing_pressure_flredecomp;
-mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l standing_wave standing_wave_flredecomp;
+  <problem_definition length="short" nprocs="4">
+    <comment>First make a common flredecomped mesh and edit the flml files to use this, then do the actual test.</comment>
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 4 -v -l standing_wave_failing_velocity standing_wave_failing_velocity_flredecomp;
+mpiexec ../../bin/flredecomp -i 1 -o 4 -v -l standing_wave_failing_pressure standing_wave_failing_pressure_flredecomp;
+mpiexec ../../bin/flredecomp -i 1 -o 4 -v -l standing_wave standing_wave_flredecomp;
 sed --in-place s/failing_velocity_flredecomp_CoordinateMesh/flredecomp_CoordinateMesh/g standing_wave_failing_velocity_flredecomp.flml;
 sed --in-place s/failing_pressure_flredecomp_CoordinateMesh/flredecomp_CoordinateMesh/g standing_wave_failing_pressure_flredecomp.flml;
 rm -f *failing_velocity_flredecomp_CoordinateMesh* *failing_pressure_flredecomp_CoordinateMesh*
-( mpiexec -n 4 fluidity -v2 -l standing_wave_failing_velocity_flredecomp.flml 2&gt;&amp;1 ) &gt; /dev/null;
+( mpiexec fluidity -v2 -l standing_wave_failing_velocity_flredecomp.flml 2&gt;&amp;1 ) &gt; /dev/null;
 mv matrixdump velocity_matrixdump;
 mkdir -p velocity_logs;
 mv fluidity.log* fluidity.err* velocity_logs/;
-( mpiexec -n 4 fluidity -v2 -l standing_wave_failing_pressure_flredecomp.flml 2&gt;&amp;1 ) &gt; /dev/null;
+( mpiexec fluidity -v2 -l standing_wave_failing_pressure_flredecomp.flml 2&gt;&amp;1 ) &gt; /dev/null;
 mv matrixdump pressure_matrixdump;
 rm matrixdump.info;
-mpiexec -n 4 petsc_readnsolve -v -l -prns_filename velocity_matrixdump  standing_wave_flredecomp.flml Velocity;
+mpiexec petsc_readnsolve -v -l -prns_filename velocity_matrixdump  standing_wave_flredecomp.flml Velocity;
 mv petsc_readnsolve.err* petsc_readnsolve.log* velocity_logs/;
-mpiexec -n 4 petsc_readnsolve -v -l -prns_filename pressure_matrixdump  standing_wave_flredecomp.flml Pressure;
+mpiexec petsc_readnsolve -v -l -prns_filename pressure_matrixdump  standing_wave_flredecomp.flml Pressure;
 rm -rf fluidity.err-*<comment>Note we use ; and no &amp;&amp; as most of these commands will actually fail (on purpose). Also removing fluidity.err-* from "failing solve runs" to prevent noise in testharness output. For same reason redirecting mpiexec output of failing fluidity runs to the bin.</comment></command_line>
   </problem_definition>
   <variables>

=== modified file 'tests/photosynthetic_radiation/photosynthetic_radiation.xml'
--- tests/photosynthetic_radiation/photosynthetic_radiation.xml	2012-08-22 16:12:59 +0000
+++ tests/photosynthetic_radiation/photosynthetic_radiation.xml	2013-10-16 12:23:45 +0000
@@ -4,8 +4,8 @@
   <name>photosynthetic_radiation</name>
   <owner userid="jhill1"/>
   <tags>flml biology par</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -n 2 flredecomp -i 1 -o 2 photosynthetic_radiation photosynthetic_radiation_flredecomp &amp;&amp; mpiexec -n 2 fluidity photosynthetic_radiation_flredecomp.flml </command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec flredecomp -i 1 -o 2 photosynthetic_radiation photosynthetic_radiation_flredecomp &amp;&amp; mpiexec fluidity photosynthetic_radiation_flredecomp.flml </command_line>
     <!-- Calculate the amount of light in the ocean. This version is DG. -->
   </problem_definition>
   <variables>

=== removed directory 'tests/pressure_fs_topbottom'
=== removed file 'tests/pressure_fs_topbottom/Makefile'
--- tests/pressure_fs_topbottom/Makefile	2013-07-11 11:35:02 +0000
+++ tests/pressure_fs_topbottom/Makefile	1970-01-01 00:00:00 +0000
@@ -1,5 +0,0 @@
-input: clean
-	gmsh -2 -bin src/square.geo
-
-clean:
-	rm -rf src/*.msh *.stat *.vtu *.log-0 *.err-0 *checkpoint *.convergence

=== removed file 'tests/pressure_fs_topbottom/pressure_fs_topbottom.flml'
--- tests/pressure_fs_topbottom/pressure_fs_topbottom.flml	2012-03-16 05:00:48 +0000
+++ tests/pressure_fs_topbottom/pressure_fs_topbottom.flml	1970-01-01 00:00:00 +0000
@@ -1,387 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<fluidity_options>
-  <simulation_name>
-    <string_value lines="1">pressure_fs_topbottom</string_value>
-  </simulation_name>
-  <problem_type>
-    <string_value lines="1">stokes</string_value>
-  </problem_type>
-  <geometry>
-    <dimension>
-      <integer_value rank="0">2</integer_value>
-    </dimension>
-    <mesh name="CoordinateMesh">
-      <from_file file_name="src/square">
-        <format name="gmsh"/>
-        <stat>
-          <include_in_stat/>
-        </stat>
-      </from_file>
-    </mesh>
-    <mesh name="VelocityMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <quadrature>
-      <degree>
-        <integer_value rank="0">5</integer_value>
-      </degree>
-    </quadrature>
-  </geometry>
-  <io>
-    <dump_format>
-      <string_value>vtk</string_value>
-    </dump_format>
-    <dump_period_in_timesteps>
-      <constant>
-        <integer_value rank="0">1</integer_value>
-      </constant>
-    </dump_period_in_timesteps>
-    <output_mesh name="CoordinateMesh"/>
-    <stat>
-      <output_at_start/>
-      <output_before_adapts/>
-      <output_after_adapts/>
-    </stat>
-  </io>
-  <timestepping>
-    <current_time>
-      <real_value rank="0">0.0</real_value>
-    </current_time>
-    <timestep>
-      <real_value rank="0">100.0</real_value>
-    </timestep>
-    <finish_time>
-      <real_value rank="0">1000</real_value>
-    </finish_time>
-    <steady_state>
-      <tolerance>
-        <real_value rank="0">1.e-6</real_value>
-        <infinity_norm/>
-      </tolerance>
-    </steady_state>
-  </timestepping>
-  <physical_parameters>
-    <gravity>
-      <magnitude>
-        <real_value rank="0">1.0</real_value>
-      </magnitude>
-      <vector_field name="GravityDirection" rank="1">
-        <prescribed>
-          <mesh name="CoordinateMesh"/>
-          <value name="WholeMesh">
-            <constant>
-              <real_value shape="2" dim1="dim" rank="1">0.0 -1.0</real_value>
-            </constant>
-          </value>
-          <output/>
-          <stat>
-            <include_in_stat/>
-          </stat>
-          <detectors>
-            <exclude_from_detectors/>
-          </detectors>
-        </prescribed>
-      </vector_field>
-    </gravity>
-  </physical_parameters>
-  <material_phase name="Fluid">
-    <equation_of_state>
-      <fluids>
-        <linear>
-          <reference_density>
-            <real_value rank="0">1.0</real_value>
-          </reference_density>
-          <temperature_dependency>
-            <reference_temperature>
-              <real_value rank="0">0.0</real_value>
-            </reference_temperature>
-            <thermal_expansion_coefficient>
-              <real_value rank="0">1.0</real_value>
-            </thermal_expansion_coefficient>
-          </temperature_dependency>
-          <subtract_out_hydrostatic_level/>
-        </linear>
-      </fluids>
-    </equation_of_state>
-    <scalar_field name="Pressure" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <remove_stabilisation_term/>
-            <integrate_continuity_by_parts/>
-          </continuous_galerkin>
-        </spatial_discretisation>
-        <scheme>
-          <poisson_pressure_solution>
-            <string_value lines="1">never</string_value>
-          </poisson_pressure_solution>
-          <use_projection_method>
-            <full_schur_complement>
-              <inner_matrix name="FullMomentumMatrix">
-                <solver>
-                  <iterative_method name="cg"/>
-                  <preconditioner name="mg"/>
-                  <relative_error>
-                    <real_value rank="0">1.e-12</real_value>
-                  </relative_error>
-                  <max_iterations>
-                    <integer_value rank="0">1000</integer_value>
-                  </max_iterations>
-                  <never_ignore_solver_failures/>
-                  <diagnostics>
-                    <monitors/>
-                  </diagnostics>
-                </solver>
-              </inner_matrix>
-              <preconditioner_matrix name="ScaledPressureMassMatrix"/>
-            </full_schur_complement>
-          </use_projection_method>
-        </scheme>
-        <solver>
-          <iterative_method name="fgmres"/>
-          <preconditioner name="ksp">
-            <solver>
-              <iterative_method name="cg"/>
-              <preconditioner name="sor"/>
-              <relative_error>
-                <real_value rank="0">1.e-12</real_value>
-              </relative_error>
-              <max_iterations>
-                <integer_value rank="0">1000</integer_value>
-              </max_iterations>
-              <never_ignore_solver_failures/>
-              <diagnostics>
-                <monitors/>
-              </diagnostics>
-            </solver>
-          </preconditioner>
-          <relative_error>
-            <real_value rank="0">1.e-10</real_value>
-          </relative_error>
-          <absolute_error>
-            <real_value rank="0">1.e-16</real_value>
-          </absolute_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <no_interpolation/>
-      </prognostic>
-    </scalar_field>
-    <scalar_field name="Density" rank="0">
-      <diagnostic>
-        <algorithm name="Internal" material_phase_support="multiple"/>
-        <mesh name="VelocityMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-    <vector_field name="Velocity" rank="1">
-      <prognostic>
-        <mesh name="VelocityMesh"/>
-        <equation name="LinearMomentum"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <stabilisation>
-              <no_stabilisation/>
-            </stabilisation>
-            <mass_terms>
-              <exclude_mass_terms/>
-            </mass_terms>
-            <advection_terms>
-              <exclude_advection_terms/>
-            </advection_terms>
-            <stress_terms>
-              <partial_stress_form/>
-            </stress_terms>
-          </continuous_galerkin>
-          <conservative_advection>
-            <real_value rank="0">1.0</real_value>
-          </conservative_advection>
-        </spatial_discretisation>
-        <temporal_discretisation>
-          <theta>
-            <real_value rank="0">1.0</real_value>
-          </theta>
-          <relaxation>
-            <real_value rank="0">1.0</real_value>
-          </relaxation>
-        </temporal_discretisation>
-        <reference_coordinates>
-          <real_value shape="2" dim1="dim" rank="1">0.25 0.5</real_value>
-          <specify_components>
-            <y_component/>
-          </specify_components>
-        </reference_coordinates>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="mg"/>
-          <relative_error>
-            <real_value rank="0">1.e-12</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <initial_condition name="WholeMesh">
-          <constant>
-            <real_value shape="2" dim1="dim" rank="1">0.0 0.0</real_value>
-          </constant>
-        </initial_condition>
-        <boundary_conditions name="Sides">
-          <surface_ids>
-            <integer_value shape="2" rank="1">7 9</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <x_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </x_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Bottom">
-          <surface_ids>
-            <integer_value shape="1" rank="1">6</integer_value>
-          </surface_ids>
-          <type name="free_surface">
-            <external_density>
-              <real_value rank="0">2.0</real_value>
-            </external_density>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Top">
-          <surface_ids>
-            <integer_value shape="1" rank="1">8</integer_value>
-          </surface_ids>
-          <type name="free_surface"/>
-        </boundary_conditions>
-        <tensor_field name="Viscosity" rank="2">
-          <prescribed>
-            <value name="WholeMesh">
-              <anisotropic_symmetric>
-                <constant>
-                  <real_value symmetric="true" dim2="dim" shape="2 2" dim1="dim" rank="2">1.0 1.0 1.0 1.0</real_value>
-                </constant>
-              </anisotropic_symmetric>
-            </value>
-            <output/>
-          </prescribed>
-        </tensor_field>
-        <output/>
-        <stat>
-          <include_in_stat/>
-          <previous_time_step>
-            <exclude_from_stat/>
-          </previous_time_step>
-          <nonlinear_field>
-            <exclude_from_stat/>
-          </nonlinear_field>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </vector_field>
-    <scalar_field name="Temperature" rank="0">
-      <prescribed>
-        <mesh name="CoordinateMesh"/>
-        <value name="WholeMesh">
-          <python>
-            <string_value lines="20" type="code" language="python">def val(X,t):
-   from math import pi, cos
-   dx = 1./80.
-   zprime = 0.5
-   wavelength = 1.0
-   k = 2.0*pi/wavelength
-   if((X[1]&lt;=zprime+dx/2.)and(X[1]&gt;zprime-dx/2.)):
-      return 1.0*cos(k*X[0])/dx
-   else:
-      return 0.0</string_value>
-          </python>
-        </value>
-        <output/>
-        <stat>
-          <surface_integral type="value" name="Left">
-            <surface_ids>
-              <integer_value shape="1" rank="1">7</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="Right">
-            <surface_ids>
-              <integer_value shape="1" rank="1">9</integer_value>
-            </surface_ids>
-          </surface_integral>
-        </stat>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-      </prescribed>
-    </scalar_field>
-    <scalar_field name="FreeSurface" rank="0">
-      <diagnostic>
-        <algorithm name="Internal" material_phase_support="multiple"/>
-        <mesh name="CoordinateMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-  </material_phase>
-</fluidity_options>

=== removed file 'tests/pressure_fs_topbottom/pressure_fs_topbottom.xml'
--- tests/pressure_fs_topbottom/pressure_fs_topbottom.xml	2011-08-10 02:27:04 +0000
+++ tests/pressure_fs_topbottom/pressure_fs_topbottom.xml	1970-01-01 00:00:00 +0000
@@ -1,16 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<testproblem>
-  <name>pressure_fs_topbottom</name>
-  <owner userid="cwilson"/>
-  <tags>flml</tags>
-  <problem_definition length="special" nprocs="1">
-    <command_line>fluidity -v2 -l pressure_fs_topbottom.flml</command_line>
-  </problem_definition>
-  <variables>
-    <variable name="freesurfacemaxend" language="python">from fluidity_tools import stat_parser as stat
-freesurfacemaxend = stat("pressure_fs_topbottom.stat")["Fluid"]["FreeSurface"]["max"][-1]</variable>
-  </variables>
-  <pass_tests>
-    <test name="check_fs_at_end" language="python">assert abs(freesurfacemaxend-0.178135683326) &lt; 0.001</test>
-  </pass_tests>
-</testproblem>

=== removed directory 'tests/pressure_fs_topbottom/src'
=== removed file 'tests/pressure_fs_topbottom/src/square.geo'
--- tests/pressure_fs_topbottom/src/square.geo	2011-08-10 02:27:04 +0000
+++ tests/pressure_fs_topbottom/src/square.geo	1970-01-01 00:00:00 +0000
@@ -1,14 +0,0 @@
-Point(1) = {0, 0, 0};
-Extrude {1, 0, 0} {
-  Point{1}; Layers{80};
-}
-Extrude {0, 1, 0} {
-  Line{1}; Layers{80};
-}
-// Bottom
-Physical Line(6) = {1};
-Physical Line(7) = {4};
-// Top
-Physical Line(8) = {2};
-Physical Line(9) = {3};
-Physical Surface(10) = {5};

=== modified file 'tests/sigma_layer_sphere_parallel/sigma_layer_sphere_parallel.xml'
--- tests/sigma_layer_sphere_parallel/sigma_layer_sphere_parallel.xml	2013-01-31 17:06:32 +0000
+++ tests/sigma_layer_sphere_parallel/sigma_layer_sphere_parallel.xml	2013-10-16 12:23:45 +0000
@@ -6,9 +6,9 @@
          depth of the layers is correct at each end (should be the same) and at the centre -->
   <owner userid="jhill1"/>
   <tags>flml</tags>
-  <problem_definition length="short" nprocs="1">
-      <command_line>mpiexec -n 2 flredecomp -i 1 -o 2  sphere_sigma  sphere_sigma_flredecomp;
-                    mpiexec -n 2 fluidity sphere_sigma_flredecomp.flml</command_line>
+  <problem_definition length="short" nprocs="2">
+      <command_line>mpiexec flredecomp -i 1 -o 2  sphere_sigma  sphere_sigma_flredecomp;
+                    mpiexec fluidity sphere_sigma_flredecomp.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== removed directory 'tests/simple_vector_null_space'
=== removed file 'tests/simple_vector_null_space/Makefile'
--- tests/simple_vector_null_space/Makefile	2013-07-11 11:35:02 +0000
+++ tests/simple_vector_null_space/Makefile	1970-01-01 00:00:00 +0000
@@ -1,5 +0,0 @@
-input: clean
-	gmsh -2 -bin src/smallsquare.geo
-
-clean:
-	rm -rf src/*.msh *.stat *.vtu *.log-0 *.err-0 *checkpoint *.convergence

=== removed file 'tests/simple_vector_null_space/simple.flml'
--- tests/simple_vector_null_space/simple.flml	2012-03-16 05:00:48 +0000
+++ tests/simple_vector_null_space/simple.flml	1970-01-01 00:00:00 +0000
@@ -1,318 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<fluidity_options>
-  <simulation_name>
-    <string_value lines="1">simple</string_value>
-  </simulation_name>
-  <problem_type>
-    <string_value lines="1">stokes</string_value>
-  </problem_type>
-  <geometry>
-    <dimension>
-      <integer_value rank="0">2</integer_value>
-    </dimension>
-    <mesh name="CoordinateMesh">
-      <from_file file_name="src/smallsquare">
-        <format name="gmsh"/>
-        <stat>
-          <include_in_stat/>
-        </stat>
-      </from_file>
-    </mesh>
-    <mesh name="VelocityMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <stat>
-          <include_in_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <quadrature>
-      <degree>
-        <integer_value rank="0">5</integer_value>
-      </degree>
-    </quadrature>
-  </geometry>
-  <io>
-    <dump_format>
-      <string_value>vtk</string_value>
-    </dump_format>
-    <dump_period_in_timesteps>
-      <constant>
-        <integer_value rank="0">1</integer_value>
-      </constant>
-    </dump_period_in_timesteps>
-    <output_mesh name="CoordinateMesh"/>
-    <checkpointing>
-      <checkpoint_period_in_dumps>
-        <integer_value rank="0">10</integer_value>
-      </checkpoint_period_in_dumps>
-      <checkpoint_at_start/>
-      <checkpoint_at_end/>
-    </checkpointing>
-    <stat>
-      <output_at_start/>
-      <output_before_adapts/>
-      <output_after_adapts/>
-    </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">1000</real_value>
-    </finish_time>
-    <final_timestep>
-      <integer_value rank="0">1</integer_value>
-    </final_timestep>
-  </timestepping>
-  <material_phase name="Fluid">
-    <vector_field name="Velocity" rank="1">
-      <prognostic>
-        <mesh name="VelocityMesh"/>
-        <equation name="Boussinesq"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <stabilisation>
-              <no_stabilisation/>
-            </stabilisation>
-            <mass_terms>
-              <exclude_mass_terms/>
-            </mass_terms>
-            <advection_terms>
-              <exclude_advection_terms/>
-            </advection_terms>
-            <stress_terms>
-              <tensor_form/>
-            </stress_terms>
-          </continuous_galerkin>
-          <conservative_advection>
-            <real_value rank="0">1.0</real_value>
-          </conservative_advection>
-        </spatial_discretisation>
-        <temporal_discretisation>
-          <theta>
-            <real_value rank="0">1.0</real_value>
-          </theta>
-          <relaxation>
-            <real_value rank="0">1.0</real_value>
-          </relaxation>
-        </temporal_discretisation>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="sor"/>
-          <relative_error>
-            <real_value rank="0">1.e-12</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors>
-              <iteration_vtus/>
-            </monitors>
-          </diagnostics>
-        </solver>
-        <initial_condition name="WholeMesh">
-          <constant>
-            <real_value shape="2" dim1="dim" rank="1">0.0 0.0</real_value>
-          </constant>
-        </initial_condition>
-        <boundary_conditions name="Side1">
-          <surface_ids>
-            <integer_value shape="1" rank="1">7</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <x_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </x_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Side2">
-          <surface_ids>
-            <integer_value shape="1" rank="1">9</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <x_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </x_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Top">
-          <surface_ids>
-            <integer_value shape="1" rank="1">8</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <y_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </y_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <tensor_field name="Viscosity" rank="2">
-          <prescribed>
-            <value name="WholeMesh">
-              <isotropic>
-                <constant>
-                  <real_value rank="0">1.0</real_value>
-                </constant>
-              </isotropic>
-            </value>
-            <output/>
-          </prescribed>
-        </tensor_field>
-        <vector_field name="Source" rank="1">
-          <prescribed>
-            <value name="WholeMesh">
-              <python>
-                <string_value lines="20" type="code" language="python">def val(x,t):
-  from math import sin, pi
-  return [0, sin(2*x[1]/pi)]</string_value>
-              </python>
-            </value>
-            <output/>
-            <stat>
-              <include_in_stat/>
-            </stat>
-            <detectors>
-              <exclude_from_detectors/>
-            </detectors>
-          </prescribed>
-        </vector_field>
-        <output/>
-        <stat>
-          <include_in_stat/>
-          <previous_time_step>
-            <exclude_from_stat/>
-          </previous_time_step>
-          <nonlinear_field>
-            <exclude_from_stat/>
-          </nonlinear_field>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </vector_field>
-    <scalar_field name="Elliptic" rank="0">
-      <prognostic>
-        <mesh name="VelocityMesh"/>
-        <equation name="AdvectionDiffusion"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <stabilisation>
-              <no_stabilisation/>
-            </stabilisation>
-            <advection_terms>
-              <exclude_advection_terms/>
-            </advection_terms>
-            <mass_terms>
-              <exclude_mass_terms/>
-            </mass_terms>
-          </continuous_galerkin>
-          <conservative_advection>
-            <real_value rank="0">0.0</real_value>
-          </conservative_advection>
-        </spatial_discretisation>
-        <temporal_discretisation>
-          <theta>
-            <real_value rank="0">1.0</real_value>
-          </theta>
-        </temporal_discretisation>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="sor"/>
-          <relative_error>
-            <real_value rank="0">1.e-12</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors>
-              <iteration_vtus/>
-            </monitors>
-          </diagnostics>
-        </solver>
-        <initial_condition name="WholeMesh">
-          <constant>
-            <real_value rank="0">0.0</real_value>
-          </constant>
-        </initial_condition>
-        <boundary_conditions name="Top">
-          <surface_ids>
-            <integer_value shape="1" rank="1">8</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <constant>
-              <real_value rank="0">0.0</real_value>
-            </constant>
-          </type>
-        </boundary_conditions>
-        <tensor_field name="Diffusivity" rank="2">
-          <prescribed>
-            <value name="WholeMesh">
-              <isotropic>
-                <constant>
-                  <real_value rank="0">1.0</real_value>
-                </constant>
-              </isotropic>
-            </value>
-            <output/>
-          </prescribed>
-        </tensor_field>
-        <scalar_field name="Source" rank="0">
-          <prescribed>
-            <value name="WholeMesh">
-              <python>
-                <string_value lines="20" type="code" language="python">def val(x,t):
-  from math import sin, pi
-  return sin(2*x[1]/pi)</string_value>
-              </python>
-            </value>
-            <output/>
-            <stat/>
-            <detectors>
-              <exclude_from_detectors/>
-            </detectors>
-          </prescribed>
-        </scalar_field>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </scalar_field>
-  </material_phase>
-</fluidity_options>

=== removed file 'tests/simple_vector_null_space/simple_vector_null_space.xml'
--- tests/simple_vector_null_space/simple_vector_null_space.xml	2011-08-11 00:18:05 +0000
+++ tests/simple_vector_null_space/simple_vector_null_space.xml	1970-01-01 00:00:00 +0000
@@ -1,12 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<testproblem>
-  <name>simple_vector_null_space</name>
-  <owner userid="cwilson"/>
-  <tags>flml</tags>
-  <problem_definition length="special" nprocs="1">
-    <command_line>fluidity -v2 -l simple.flml</command_line>
-  </problem_definition>
-  <variables>
-  </variables>
-  <pass_tests/>
-</testproblem>

=== removed directory 'tests/simple_vector_null_space/src'
=== removed file 'tests/simple_vector_null_space/src/smallsquare.geo'
--- tests/simple_vector_null_space/src/smallsquare.geo	2011-08-11 00:18:05 +0000
+++ tests/simple_vector_null_space/src/smallsquare.geo	1970-01-01 00:00:00 +0000
@@ -1,14 +0,0 @@
-Point(1) = {0, 0, 0};
-Extrude {1, 0, 0} {
-  Point{1}; Layers{4};
-}
-Extrude {0, 1, 0} {
-  Line{1}; Layers{4};
-}
-// Bottom
-Physical Line(6) = {1};
-Physical Line(7) = {4};
-// Top
-Physical Line(8) = {2};
-Physical Line(9) = {3};
-Physical Surface(10) = {5};

=== modified file 'tests/spherical_patch/spherical_patch.xml'
--- tests/spherical_patch/spherical_patch.xml	2013-06-12 14:27:18 +0000
+++ tests/spherical_patch/spherical_patch.xml	2013-10-16 12:23:45 +0000
@@ -2,10 +2,10 @@
 <testproblem>
   <name>spherical patch<comment>Tests gmsh reading and writing on the sphere with 2d horizontal spherical input mesh, checkpointing and flredecomp.</comment></name>
   <owner userid="skramer"/>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -n 3 ../../bin/flredecomp -i 1 -o 3 -v -l spherical_segment spherical_segment_flredecomp &amp;&amp;
-mpirun -np 3 fluidity -v2 -l spherical_segment_flredecomp.flml &amp;&amp;
-mpirun -np 3 ../../bin/flredecomp -v -l -i 3 -o 1 spherical_segment_2_checkpoint serial &amp;&amp;
+  <problem_definition length="short" nprocs="3">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 3 -v -l spherical_segment spherical_segment_flredecomp &amp;&amp;
+mpiexec fluidity -v2 -l spherical_segment_flredecomp.flml &amp;&amp;
+mpiexec ../../bin/flredecomp -v -l -i 3 -o 1 spherical_segment_2_checkpoint serial &amp;&amp;
 fluidity -v2 -l serial.flml</command_line>
   </problem_definition>
   <variables>

=== modified file 'tests/square-convection-parallel-trivial/square-convection-parallel-trivial.xml'
--- tests/square-convection-parallel-trivial/square-convection-parallel-trivial.xml	2012-08-13 11:42:30 +0000
+++ tests/square-convection-parallel-trivial/square-convection-parallel-trivial.xml	2013-10-16 12:23:45 +0000
@@ -3,9 +3,9 @@
   <name>Square convection (Adaptive CG-test version)</name>
   <owner userid="pfarrell"/>
   <tags>flml parallel</tags>
-  <problem_definition length = "short" nprocs = "1">
-    <command_line>mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l square-convection square-convection_flredecomp &amp;&amp;
-mpiexec -n 2 ../../bin/fluidity -v2 -l square-convection_flredecomp.flml</command_line>
+  <problem_definition length = "short" nprocs = "2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l square-convection square-convection_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v2 -l square-convection_flredecomp.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/square-convection-parallel/square-convection-parallel.xml'
--- tests/square-convection-parallel/square-convection-parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/square-convection-parallel/square-convection-parallel.xml	2013-10-16 12:23:45 +0000
@@ -3,9 +3,9 @@
   <name>Square convection (Adaptive CG-test version)</name>
   <owner userid="pfarrell"/>
   <tags>flml parallel 2dadapt</tags>
-  <problem_definition length = "medium" nprocs = "1">
-    <command_line>mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l square-convection square-convection_flredecomp &amp;&amp;
-mpiexec -n 2 ../../bin/fluidity -v2 -l square-convection_flredecomp.flml</command_line>
+  <problem_definition length = "medium" nprocs = "2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l square-convection square-convection_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v2 -l square-convection_flredecomp.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/standing_wave-parallel/standing_wave-parallel.xml'
--- tests/standing_wave-parallel/standing_wave-parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/standing_wave-parallel/standing_wave-parallel.xml	2013-10-16 12:23:45 +0000
@@ -3,14 +3,14 @@
   <name>Standing free surface wave in channel using P1DG-P2.</name>
   <owner userid="skramer"/>
   <tags>flml parallel</tags>
-  <problem_definition length="medium" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l standing_wave standing_wave_flredecomp
+  <problem_definition length="medium" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l standing_wave standing_wave_flredecomp
 
-mpiexec -n 2 ../../bin/fluidity -v3 -l  standing_wave_flredecomp.flml;
+mpiexec ../../bin/fluidity -v3 -l  standing_wave_flredecomp.flml;
 mkdir -p run1_logs; 
 mv fluidity.* run1_logs; 
 spud-set standing_wave_1_checkpoint.flml /material_phase::water/scalar_field::Pressure/prognostic/scheme/poisson_pressure_solution never;
-mpiexec -n 2 ../../bin/fluidity -v3 -l standing_wave_1_checkpoint.flml</command_line>
+mpiexec ../../bin/fluidity -v3 -l standing_wave_1_checkpoint.flml</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/test_adapt-at-first-time-step/test_adapt-at-first-time-step.xml'
--- tests/test_adapt-at-first-time-step/test_adapt-at-first-time-step.xml	2012-08-13 11:42:30 +0000
+++ tests/test_adapt-at-first-time-step/test_adapt-at-first-time-step.xml	2013-10-16 12:23:45 +0000
@@ -4,9 +4,9 @@
   <name>Test adapt_at_first_timestep</name>
   <owner userid="skramer"/>
   <tags>flml nozoltan parallel</tags>
-    <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l test_adapt-at-first-time-step test_adapt-at-first-time-step_flredecomp &amp;&amp;
-mpiexec -n 2 ../../bin/fluidity -v3 -l test_adapt-at-first-time-step_flredecomp.flml </command_line>
+    <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l test_adapt-at-first-time-step test_adapt-at-first-time-step_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v3 -l test_adapt-at-first-time-step_flredecomp.flml </command_line>
   </problem_definition>  
   <variables>  
     <variable name="solvers_converged" language="python">

=== modified file 'tests/test_energy_stats/test_energy_stats.xml'
--- tests/test_energy_stats/test_energy_stats.xml	2012-08-13 11:42:30 +0000
+++ tests/test_energy_stats/test_energy_stats.xml	2013-10-16 12:23:45 +0000
@@ -3,11 +3,11 @@
   <name>test energy stats and compare parallel and serial</name>
   <owner userid="skramer"/>
   <tags> parallel 2dadapt </tags>
-  <problem_definition length="medium" nprocs="1">
+  <problem_definition length="medium" nprocs="3">
     <command_line>
-    mpiexec  -np 1 ../../bin/fluidity -v3 -l lock_exchange_2d.flml &amp;&amp;
-    mpiexec -n 3 ../../bin/flredecomp -i 1 -o 3 -v -l lock_exchange_2d_parallel lock_exchange_2d_parallel_flredecomp &amp;&amp;
-    mpiexec -np 3 ../../bin/fluidity -v3 -l lock_exchange_2d_parallel_flredecomp.flml
+    ../../bin/fluidity -v3 -l lock_exchange_2d.flml &amp;&amp;
+    mpiexec ../../bin/flredecomp -i 1 -o 3 -v -l lock_exchange_2d_parallel lock_exchange_2d_parallel_flredecomp &amp;&amp;
+    mpiexec ../../bin/fluidity -v3 -l lock_exchange_2d_parallel_flredecomp.flml
     </command_line> 
   </problem_definition>
   <variables>

=== modified file 'tests/test_metric_advection_parallel/test_metric_advection_parallel.xml'
--- tests/test_metric_advection_parallel/test_metric_advection_parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/test_metric_advection_parallel/test_metric_advection_parallel.xml	2013-10-16 12:23:45 +0000
@@ -3,9 +3,9 @@
   <name>Metric advection test, parallel</name>
   <owner userid="pef"/>
   <tags>flml parallel 2dadapt</tags>
-  <problem_definition length = "medium" nprocs = "1">
-    <command_line>mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l test_metric_advection_parallel test_metric_advection_parallel_flredecomp &amp;&amp;
-mpiexec -n 2 ../../bin/fluidity -v3 -l test_metric_advection_parallel_flredecomp.flml
+  <problem_definition length = "medium" nprocs = "2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l test_metric_advection_parallel test_metric_advection_parallel_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v3 -l test_metric_advection_parallel_flredecomp.flml
     </command_line>
   </problem_definition>
   <variables>

=== modified file 'tests/test_source_absorption/test_source_absorption.xml'
--- tests/test_source_absorption/test_source_absorption.xml	2012-06-28 08:23:27 +0000
+++ tests/test_source_absorption/test_source_absorption.xml	2013-10-16 12:23:45 +0000
@@ -4,7 +4,7 @@
   <owner userid="avire"/>
   <tags>flml</tags>
   <problem_definition length="medium" nprocs="1">
-    <command_line>mpiexec -np 1 fluidity -v2 test_no_source_absorption.flml &gt; test_no_source_absorption.log &amp;&amp; mpiexec -np 1 fluidity -v2 test_source_absorption.flml &gt; test_source_absorption.log</command_line>
+    <command_line>mpiexec fluidity -v2 test_no_source_absorption.flml &gt; test_no_source_absorption.log &amp;&amp; mpiexec fluidity -v2 test_source_absorption.flml &gt; test_source_absorption.log</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/vb_parallel/vb_parallel.xml'
--- tests/vb_parallel/vb_parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/vb_parallel/vb_parallel.xml	2013-10-16 12:23:45 +0000
@@ -4,9 +4,9 @@
   <name>vb_parallel</name>
   <owner userid="colin"/>
   <tags>flml parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l blob blob_flredecomp &amp;&amp;
-mpiexec -n 2 ../../bin/fluidity blob_flredecomp.flml; ../../bin/pvtu2vtu blob 1</command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l blob blob_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity blob_flredecomp.flml; ../../bin/pvtu2vtu blob 1</command_line>
   </problem_definition>
   <variables>
     <variable name="solvers_converged" language="python">

=== modified file 'tests/viscosity_2d_p0_parallel/viscosity_2d_p0_parallel.xml'
--- tests/viscosity_2d_p0_parallel/viscosity_2d_p0_parallel.xml	2012-08-13 11:42:30 +0000
+++ tests/viscosity_2d_p0_parallel/viscosity_2d_p0_parallel.xml	2013-10-16 12:23:45 +0000
@@ -4,9 +4,9 @@
   <name>heat_2d_dg</name>
   <owner userid="cwilson"/>
   <tags>flml parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp &amp;&amp;
-mpiexec -np 2 ../../bin/fluidity -v2 -l heat_flredecomp.flml </command_line>
+  <problem_definition length="short" nprocs="2">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v2 -l heat_flredecomp.flml </command_line>
     <!-- Two dimensional diffusion only problem. -->
   </problem_definition>
   <variables>

=== modified file 'tests/viscosity_2d_p0_parallel_local_assembly/viscosity_2d_p0_parallel_local_assembly.xml'
--- tests/viscosity_2d_p0_parallel_local_assembly/viscosity_2d_p0_parallel_local_assembly.xml	2012-08-13 11:42:30 +0000
+++ tests/viscosity_2d_p0_parallel_local_assembly/viscosity_2d_p0_parallel_local_assembly.xml	2013-10-16 12:23:45 +0000
@@ -5,9 +5,9 @@
   <name>heat_2d_dg</name>
   <owner userid="wence"/>
   <tags>flml parallel</tags>
-  <problem_definition length="short" nprocs="1">
-    <command_line>mpiexec -n 16 ../../bin/flredecomp -i 1 -o 16 -v -l heat heat_flredecomp &amp;&amp;
-mpiexec -np 16 ../../bin/fluidity -v2 -l heat_flredecomp.flml </command_line>
+  <problem_definition length="short" nprocs="16">
+    <command_line>mpiexec ../../bin/flredecomp -i 1 -o 16 -v -l heat heat_flredecomp &amp;&amp;
+mpiexec ../../bin/fluidity -v2 -l heat_flredecomp.flml </command_line>
     <!-- Two dimensional diffusion only problem. -->
   </problem_definition>
   <variables>

=== removed directory 'tests/viscous_fs_top'
=== removed file 'tests/viscous_fs_top/Makefile'
--- tests/viscous_fs_top/Makefile	2013-07-11 11:39:00 +0000
+++ tests/viscous_fs_top/Makefile	1970-01-01 00:00:00 +0000
@@ -1,5 +0,0 @@
-input: clean
-	gmsh -2 -bin src/square.geo
-
-clean:
-	rm -rf src/*.msh *.stat *.vtu *.log-0 *.err-0 *checkpoint *.convergence

=== removed directory 'tests/viscous_fs_top/src'
=== removed file 'tests/viscous_fs_top/src/square.geo'
--- tests/viscous_fs_top/src/square.geo	2011-08-10 22:28:30 +0000
+++ tests/viscous_fs_top/src/square.geo	1970-01-01 00:00:00 +0000
@@ -1,14 +0,0 @@
-Point(1) = {0, 0, 0};
-Extrude {1, 0, 0} {
-  Point{1}; Layers{80};
-}
-Extrude {0, 1, 0} {
-  Line{1}; Layers{80};
-}
-// Bottom
-Physical Line(6) = {1};
-Physical Line(7) = {4};
-// Top
-Physical Line(8) = {2};
-Physical Line(9) = {3};
-Physical Surface(10) = {5};

=== removed file 'tests/viscous_fs_top/viscous_fs_top.xml'
--- tests/viscous_fs_top/viscous_fs_top.xml	2011-08-11 19:51:20 +0000
+++ tests/viscous_fs_top/viscous_fs_top.xml	1970-01-01 00:00:00 +0000
@@ -1,390 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<testproblem>
-  <name>viscous_fs_top</name>
-  <owner userid="cwilson"/>
-  <tags>flml</tags>
-  <problem_definition length="special" nprocs="1">
-    <command_line>fluidity -v2 viscous_fs_top_A.flml &gt;&amp; A.log &amp;&amp; fluidity -v2 viscous_fs_top_B.flml &gt;&amp; B.log &amp;&amp; fluidity -v2 viscous_fs_top_C.flml &gt;&amp; C.log &amp;&amp; fluidity -v2 viscous_fs_top_D.flml &gt;&amp; D.log &amp;&amp; fluidity -v2 viscous_fs_top_E.flml &gt;&amp; E.log &amp;&amp; fluidity -v2 viscous_fs_top_F.flml &gt;&amp; F.log &amp;&amp; fluidity -v2 viscous_fs_top_G.flml &gt;&amp; G.log &amp;&amp; fluidity -v2 viscous_fs_top_H.flml &gt;&amp; H.log</command_line>
-  </problem_definition>
-  <variables>
-    <variable name="ab_convergence_fs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, sqrt
-
-file1 = "viscous_fs_top_A.stat"
-file2 = "viscous_fs_top_B.stat"
-
-error1 = sqrt(sum(stat(file1)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file1)["dt"]["value"][1:]))
-error2 = sqrt(sum(stat(file2)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file2)["dt"]["value"][1:]))
-
-error_inf1 = stat(file1)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-error_inf2 = stat(file2)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-
-print error1
-print error2
-
-print error_inf1
-print error_inf2
-
-ratio = error1 / error2
-ratio_inf = error_inf1 / error_inf2
-ab_convergence_fs = [log(ratio, 2), log(ratio_inf, 2)]
-    </variable>
-    <variable name="ab_convergence_maxfs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, pi, cos, sin, cosh, sinh, exp
-from numpy import sqrt, interp
-from scipy.integrate import quad
-
-file1 = "viscous_fs_top_A.stat"
-file2 = "viscous_fs_top_B.stat"
-
-stat1 = stat(file1)
-stat2 = stat(file2)
-
-def analytical(t):
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  D=1.0
-  rhog=1.0
-  amp = 0.1
-  F0 = amp
-  relaxation_time = 2.0*(D*k + sinh(D*k)*cosh(D*k))*k/(rhog*sinh(D*k)**2)
-  return exp(-t/relaxation_time)*F0
-
-def numerical(statn, t):
-  return interp([t], statn["ElapsedTime"]["value"], statn["Fluid"]["FreeSurface"]["max"])[0]
-
-def error(statn, t):
-  return abs(analytical(t)-numerical(statn, t))
-
-quad1 = quad(lambda t: error(stat1, t)**2, stat1["ElapsedTime"]["value"][0], stat1["ElapsedTime"]["value"][-1], limit=1000)
-quad2 = quad(lambda t: error(stat2, t)**2, stat2["ElapsedTime"]["value"][0], stat2["ElapsedTime"]["value"][-1], limit=1000)
-
-error1 = sqrt(quad1[0])
-error2 = sqrt(quad2[0])
-
-print error1, quad1[-1]
-print error2, quad2[-1]
-
-ratio = error1 / error2
-ab_convergence_maxfs = log(ratio, 2)
-    </variable>
-    <variable name="bc_convergence_fs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, sqrt
-
-file1 = "viscous_fs_top_B.stat"
-file2 = "viscous_fs_top_C.stat"
-
-error1 = sqrt(sum(stat(file1)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file1)["dt"]["value"][1:]))
-error2 = sqrt(sum(stat(file2)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file2)["dt"]["value"][1:]))
-
-error_inf1 = stat(file1)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-error_inf2 = stat(file2)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-
-print error1
-print error2
-
-print error_inf1
-print error_inf2
-
-ratio = error1 / error2
-ratio_inf = error_inf1 / error_inf2
-bc_convergence_fs = [log(ratio, 2), log(ratio_inf, 2)]
-    </variable>
-    <variable name="bc_convergence_maxfs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, pi, cos, sin, cosh, sinh, exp
-from numpy import sqrt, interp
-from scipy.integrate import quad
-
-file1 = "viscous_fs_top_B.stat"
-file2 = "viscous_fs_top_C.stat"
-
-stat1 = stat(file1)
-stat2 = stat(file2)
-
-def analytical(t):
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  D=1.0
-  rhog=1.0
-  amp = 0.1
-  F0 = amp
-  relaxation_time = 2.0*(D*k + sinh(D*k)*cosh(D*k))*k/(rhog*sinh(D*k)**2)
-  return exp(-t/relaxation_time)*F0
-
-def numerical(statn, t):
-  return interp([t], statn["ElapsedTime"]["value"], statn["Fluid"]["FreeSurface"]["max"])[0]
-
-def error(statn, t):
-  return abs(analytical(t)-numerical(statn, t))
-
-quad1 = quad(lambda t: error(stat1, t)**2, stat1["ElapsedTime"]["value"][0], stat1["ElapsedTime"]["value"][-1], limit=1000)
-quad2 = quad(lambda t: error(stat2, t)**2, stat2["ElapsedTime"]["value"][0], stat2["ElapsedTime"]["value"][-1], limit=1000)
-
-error1 = sqrt(quad1[0])
-error2 = sqrt(quad2[0])
-
-print error1, quad1[-1]
-print error2, quad2[-1]
-
-ratio = error1 / error2
-bc_convergence_maxfs = log(ratio, 2)
-    </variable>
-    <variable name="cd_convergence_fs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, sqrt
-
-file1 = "viscous_fs_top_C.stat"
-file2 = "viscous_fs_top_D.stat"
-
-error1 = sqrt(sum(stat(file1)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file1)["dt"]["value"][1:]))
-error2 = sqrt(sum(stat(file2)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file2)["dt"]["value"][1:]))
-
-error_inf1 = stat(file1)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-error_inf2 = stat(file2)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-
-print error1
-print error2
-
-print error_inf1
-print error_inf2
-
-ratio = error1 / error2
-ratio_inf = error_inf1 / error_inf2
-cd_convergence_fs = [log(ratio, 2), log(ratio_inf, 2)]
-    </variable>
-    <variable name="cd_convergence_maxfs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, pi, cos, sin, cosh, sinh, exp
-from numpy import sqrt, interp
-from scipy.integrate import quad
-
-file1 = "viscous_fs_top_C.stat"
-file2 = "viscous_fs_top_D.stat"
-
-stat1 = stat(file1)
-stat2 = stat(file2)
-
-def analytical(t):
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  D=1.0
-  rhog=1.0
-  amp = 0.1
-  F0 = amp
-  relaxation_time = 2.0*(D*k + sinh(D*k)*cosh(D*k))*k/(rhog*sinh(D*k)**2)
-  return exp(-t/relaxation_time)*F0
-
-def numerical(statn, t):
-  return interp([t], statn["ElapsedTime"]["value"], statn["Fluid"]["FreeSurface"]["max"])[0]
-
-def error(statn, t):
-  return abs(analytical(t)-numerical(statn, t))
-
-quad1 = quad(lambda t: error(stat1, t)**2, stat1["ElapsedTime"]["value"][0], stat1["ElapsedTime"]["value"][-1], limit=1000)
-quad2 = quad(lambda t: error(stat2, t)**2, stat2["ElapsedTime"]["value"][0], stat2["ElapsedTime"]["value"][-1], limit=1000)
-
-error1 = sqrt(quad1[0])
-error2 = sqrt(quad2[0])
-
-print error1, quad1[-1]
-print error2, quad2[-1]
-
-ratio = error1 / error2
-cd_convergence_maxfs = log(ratio, 2)
-    </variable>
-    <variable name="de_convergence_fs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, sqrt
-
-file1 = "viscous_fs_top_D.stat"
-file2 = "viscous_fs_top_E.stat"
-
-error1 = sqrt(sum(stat(file1)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file1)["dt"]["value"][1:]))
-error2 = sqrt(sum(stat(file2)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file2)["dt"]["value"][1:]))
-
-error_inf1 = stat(file1)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-error_inf2 = stat(file2)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-
-print error1
-print error2
-
-print error_inf1
-print error_inf2
-
-ratio = error1 / error2
-ratio_inf = error_inf1 / error_inf2
-de_convergence_fs = [log(ratio, 2), log(ratio_inf, 2)]
-    </variable>
-    <variable name="de_convergence_maxfs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, pi, cos, sin, cosh, sinh, exp
-from numpy import sqrt, interp
-from scipy.integrate import quad
-
-file1 = "viscous_fs_top_D.stat"
-file2 = "viscous_fs_top_E.stat"
-
-stat1 = stat(file1)
-stat2 = stat(file2)
-
-def analytical(t):
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  D=1.0
-  rhog=1.0
-  amp = 0.1
-  F0 = amp
-  relaxation_time = 2.0*(D*k + sinh(D*k)*cosh(D*k))*k/(rhog*sinh(D*k)**2)
-  return exp(-t/relaxation_time)*F0
-
-def numerical(statn, t):
-  return interp([t], statn["ElapsedTime"]["value"], statn["Fluid"]["FreeSurface"]["max"])[0]
-
-def error(statn, t):
-  return abs(analytical(t)-numerical(statn, t))
-
-quad1 = quad(lambda t: error(stat1, t)**2, stat1["ElapsedTime"]["value"][0], stat1["ElapsedTime"]["value"][-1], limit=1000)
-quad2 = quad(lambda t: error(stat2, t)**2, stat2["ElapsedTime"]["value"][0], stat2["ElapsedTime"]["value"][-1], limit=1000)
-
-error1 = sqrt(quad1[0])
-error2 = sqrt(quad2[0])
-
-print error1, quad1[-1]
-print error2, quad2[-1]
-
-ratio = error1 / error2
-de_convergence_maxfs = log(ratio, 2)
-    </variable>
-    <variable name="ef_convergence_fs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, sqrt
-
-file1 = "viscous_fs_top_E.stat"
-file2 = "viscous_fs_top_F.stat"
-
-error1 = sqrt(sum(stat(file1)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file1)["dt"]["value"][1:]))
-error2 = sqrt(sum(stat(file2)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file2)["dt"]["value"][1:]))
-
-error_inf1 = stat(file1)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-error_inf2 = stat(file2)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-
-print error1
-print error2
-
-print error_inf1
-print error_inf2
-
-ratio = error1 / error2
-ratio_inf = error_inf1 / error_inf2
-ef_convergence_fs = [log(ratio, 2), log(ratio_inf, 2)]
-    </variable>
-    <variable name="ef_convergence_maxfs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, pi, cos, sin, cosh, sinh, exp
-from numpy import sqrt, interp
-from scipy.integrate import quad
-
-file1 = "viscous_fs_top_E.stat"
-file2 = "viscous_fs_top_F.stat"
-
-stat1 = stat(file1)
-stat2 = stat(file2)
-
-def analytical(t):
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  D=1.0
-  rhog=1.0
-  amp = 0.1
-  F0 = amp
-  relaxation_time = 2.0*(D*k + sinh(D*k)*cosh(D*k))*k/(rhog*sinh(D*k)**2)
-  return exp(-t/relaxation_time)*F0
-
-def numerical(statn, t):
-  return interp([t], statn["ElapsedTime"]["value"], statn["Fluid"]["FreeSurface"]["max"])[0]
-
-def error(statn, t):
-  return abs(analytical(t)-numerical(statn, t))
-
-quad1 = quad(lambda t: error(stat1, t)**2, stat1["ElapsedTime"]["value"][0], stat1["ElapsedTime"]["value"][-1], limit=1000)
-quad2 = quad(lambda t: error(stat2, t)**2, stat2["ElapsedTime"]["value"][0], stat2["ElapsedTime"]["value"][-1], limit=1000)
-
-error1 = sqrt(quad1[0])
-error2 = sqrt(quad2[0])
-
-print error1, quad1[-1]
-print error2, quad2[-1]
-
-ratio = error1 / error2
-ef_convergence_maxfs = log(ratio, 2)
-    </variable>
-    <variable name="gh_convergence_fs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, sqrt
-
-file1 = "viscous_fs_top_G.stat"
-file2 = "viscous_fs_top_H.stat"
-
-error1 = sqrt(sum(stat(file1)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file1)["dt"]["value"][1:]))
-error2 = sqrt(sum(stat(file2)["Fluid"]["DifferenceSquared"]["surface_integral%SurfaceL2Norm"][1:]*stat(file2)["dt"]["value"][1:]))
-
-error_inf1 = stat(file1)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-error_inf2 = stat(file2)["Fluid"]["FreeSurfaceDifference"]["max"].max()
-
-print error1
-print error2
-
-print error_inf1
-print error_inf2
-
-ratio = error1 / error2
-ratio_inf = error_inf1 / error_inf2
-gh_convergence_fs = [log(ratio, 2), log(ratio_inf, 2)]
-    </variable>
-    <variable name="gh_convergence_maxfs" language="python">
-from fluidity_tools import stat_parser as stat
-from math import log, pi, cos, sin, cosh, sinh, exp
-from numpy import sqrt, interp
-from scipy.integrate import quad
-
-file1 = "viscous_fs_top_G.stat"
-file2 = "viscous_fs_top_H.stat"
-
-stat1 = stat(file1)
-stat2 = stat(file2)
-
-def analytical(t):
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  D=1.0
-  rhog=1.0
-  amp = 0.1
-  F0 = amp
-  relaxation_time = 2.0*(D*k + sinh(D*k)*cosh(D*k))*k/(rhog*sinh(D*k)**2)
-  return exp(-t/relaxation_time)*F0
-
-def numerical(statn, t):
-  return interp([t], statn["ElapsedTime"]["value"], statn["Fluid"]["FreeSurface"]["max"])[0]
-
-def error(statn, t):
-  return abs(analytical(t)-numerical(statn, t))
-
-quad1 = quad(lambda t: error(stat1, t)**2, stat1["ElapsedTime"]["value"][0], stat1["ElapsedTime"]["value"][-1], limit=1000)
-quad2 = quad(lambda t: error(stat2, t)**2, stat2["ElapsedTime"]["value"][0], stat2["ElapsedTime"]["value"][-1], limit=1000)
-
-error1 = sqrt(quad1[0])
-error2 = sqrt(quad2[0])
-
-print error1, quad1[-1]
-print error2, quad2[-1]
-
-ratio = error1 / error2
-gh_convergence_maxfs = log(ratio, 2)
-    </variable>
-  </variables>
-  <pass_tests/>
-</testproblem>

=== removed file 'tests/viscous_fs_top/viscous_fs_top_A.flml'
--- tests/viscous_fs_top/viscous_fs_top_A.flml	2012-03-16 05:00:48 +0000
+++ tests/viscous_fs_top/viscous_fs_top_A.flml	1970-01-01 00:00:00 +0000
@@ -1,484 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<fluidity_options>
-  <simulation_name>
-    <string_value lines="1">viscous_fs_top_A</string_value>
-  </simulation_name>
-  <problem_type>
-    <string_value lines="1">stokes</string_value>
-  </problem_type>
-  <geometry>
-    <dimension>
-      <integer_value rank="0">2</integer_value>
-    </dimension>
-    <mesh name="CoordinateMesh">
-      <from_file file_name="src/square">
-        <format name="gmsh"/>
-        <stat>
-          <include_in_stat/>
-        </stat>
-      </from_file>
-    </mesh>
-    <mesh name="VelocityMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <mesh name="FreeSurfaceSquaredMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <quadrature>
-      <degree>
-        <integer_value rank="0">5</integer_value>
-      </degree>
-    </quadrature>
-  </geometry>
-  <io>
-    <dump_format>
-      <string_value>vtk</string_value>
-    </dump_format>
-    <dump_period_in_timesteps>
-      <constant>
-        <integer_value rank="0">1</integer_value>
-      </constant>
-    </dump_period_in_timesteps>
-    <output_mesh name="CoordinateMesh"/>
-    <stat>
-      <output_at_start/>
-      <output_before_adapts/>
-      <output_after_adapts/>
-    </stat>
-  </io>
-  <timestepping>
-    <current_time>
-      <real_value rank="0">0.0</real_value>
-    </current_time>
-    <timestep>
-      <real_value rank="0">64.0</real_value>
-    </timestep>
-    <finish_time>
-      <real_value rank="0">500</real_value>
-    </finish_time>
-  </timestepping>
-  <physical_parameters>
-    <gravity>
-      <magnitude>
-        <real_value rank="0">1.0</real_value>
-      </magnitude>
-      <vector_field name="GravityDirection" rank="1">
-        <prescribed>
-          <mesh name="CoordinateMesh"/>
-          <value name="WholeMesh">
-            <constant>
-              <real_value shape="2" dim1="dim" rank="1">0.0 -1.0</real_value>
-            </constant>
-          </value>
-          <output/>
-          <stat>
-            <include_in_stat/>
-          </stat>
-          <detectors>
-            <exclude_from_detectors/>
-          </detectors>
-        </prescribed>
-      </vector_field>
-    </gravity>
-  </physical_parameters>
-  <material_phase name="Fluid">
-    <equation_of_state>
-      <fluids>
-        <linear>
-          <reference_density>
-            <real_value rank="0">1.0</real_value>
-          </reference_density>
-          <subtract_out_hydrostatic_level/>
-        </linear>
-      </fluids>
-    </equation_of_state>
-    <scalar_field name="Pressure" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <remove_stabilisation_term/>
-            <integrate_continuity_by_parts/>
-          </continuous_galerkin>
-        </spatial_discretisation>
-        <scheme>
-          <poisson_pressure_solution>
-            <string_value lines="1">never</string_value>
-          </poisson_pressure_solution>
-          <use_projection_method>
-            <full_schur_complement>
-              <inner_matrix name="FullMomentumMatrix">
-                <solver>
-                  <iterative_method name="cg"/>
-                  <preconditioner name="mg"/>
-                  <relative_error>
-                    <real_value rank="0">1.e-12</real_value>
-                  </relative_error>
-                  <max_iterations>
-                    <integer_value rank="0">1000</integer_value>
-                  </max_iterations>
-                  <never_ignore_solver_failures/>
-                  <diagnostics>
-                    <monitors/>
-                  </diagnostics>
-                </solver>
-              </inner_matrix>
-              <preconditioner_matrix name="ScaledPressureMassMatrix"/>
-            </full_schur_complement>
-          </use_projection_method>
-        </scheme>
-        <solver>
-          <iterative_method name="fgmres"/>
-          <preconditioner name="ksp">
-            <solver>
-              <iterative_method name="cg"/>
-              <preconditioner name="sor"/>
-              <relative_error>
-                <real_value rank="0">1.e-12</real_value>
-              </relative_error>
-              <max_iterations>
-                <integer_value rank="0">1000</integer_value>
-              </max_iterations>
-              <never_ignore_solver_failures/>
-              <diagnostics>
-                <monitors/>
-              </diagnostics>
-            </solver>
-          </preconditioner>
-          <relative_error>
-            <real_value rank="0">1.e-10</real_value>
-          </relative_error>
-          <absolute_error>
-            <real_value rank="0">1.e-16</real_value>
-          </absolute_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <no_interpolation/>
-      </prognostic>
-    </scalar_field>
-    <scalar_field name="Density" rank="0">
-      <diagnostic>
-        <algorithm name="Internal" material_phase_support="multiple"/>
-        <mesh name="CoordinateMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-    <vector_field name="Velocity" rank="1">
-      <prognostic>
-        <mesh name="VelocityMesh"/>
-        <equation name="LinearMomentum"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <stabilisation>
-              <no_stabilisation/>
-            </stabilisation>
-            <mass_terms>
-              <exclude_mass_terms/>
-            </mass_terms>
-            <advection_terms>
-              <exclude_advection_terms/>
-            </advection_terms>
-            <stress_terms>
-              <partial_stress_form/>
-            </stress_terms>
-          </continuous_galerkin>
-          <conservative_advection>
-            <real_value rank="0">1.0</real_value>
-          </conservative_advection>
-        </spatial_discretisation>
-        <temporal_discretisation>
-          <theta>
-            <real_value rank="0">1.0</real_value>
-          </theta>
-          <relaxation>
-            <real_value rank="0">1.0</real_value>
-          </relaxation>
-        </temporal_discretisation>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="mg"/>
-          <relative_error>
-            <real_value rank="0">1.e-12</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <initial_condition name="WholeMesh">
-          <constant>
-            <real_value shape="2" dim1="dim" rank="1">0.0 0.0</real_value>
-          </constant>
-        </initial_condition>
-        <boundary_conditions name="Sides">
-          <surface_ids>
-            <integer_value shape="2" rank="1">7 9</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <x_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </x_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Bottom">
-          <surface_ids>
-            <integer_value shape="1" rank="1">6</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <y_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </y_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Top">
-          <surface_ids>
-            <integer_value shape="1" rank="1">8</integer_value>
-          </surface_ids>
-          <type name="free_surface">
-            <no_normal_stress/>
-          </type>
-        </boundary_conditions>
-        <tensor_field name="Viscosity" rank="2">
-          <prescribed>
-            <value name="WholeMesh">
-              <anisotropic_symmetric>
-                <constant>
-                  <real_value symmetric="true" dim2="dim" shape="2 2" dim1="dim" rank="2">1.0 1.0 1.0 1.0</real_value>
-                </constant>
-              </anisotropic_symmetric>
-            </value>
-            <output/>
-          </prescribed>
-        </tensor_field>
-        <output/>
-        <stat>
-          <include_in_stat/>
-          <previous_time_step>
-            <exclude_from_stat/>
-          </previous_time_step>
-          <nonlinear_field>
-            <exclude_from_stat/>
-          </nonlinear_field>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </vector_field>
-    <scalar_field name="FreeSurface" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <initial_condition name="WholeMesh">
-          <python>
-            <string_value lines="20" type="code" language="python">def val(X,t):
-  from math import pi, cos, sin, cosh, sinh, exp
-  dx = 1./80.
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  amp = 0.1
-  
-  F0 = amp*cos(k*X[0])
-  if(X[1]&gt;(1.-dx/2.)):
-    return F0
-  else:
-    return 0.0</string_value>
-          </python>
-        </initial_condition>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="sor"/>
-          <relative_error>
-            <real_value rank="0">1.e-6</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <output/>
-        <stat>
-          <surface_integral type="value" name="Top">
-            <surface_ids>
-              <integer_value shape="1" rank="1">8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="Bottom">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6</integer_value>
-            </surface_ids>
-          </surface_integral>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </scalar_field>
-    <scalar_field name="AnalyticalFreeSurface" rank="0">
-      <prescribed>
-        <mesh name="CoordinateMesh"/>
-        <value name="WholeMesh">
-          <python>
-            <string_value lines="20" type="code" language="python">def val(X,t):
-  from math import pi, cos, sin, cosh, sinh, exp
-  dx = 1./80.
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  D=1.0
-  rhog=1.0
-  amp = 0.1
-  
-  F0 = amp*cos(k*X[0])
-  relaxation_time = 2.0*(D*k + sinh(D*k)*cosh(D*k))*k/(rhog*sinh(D*k)**2)
-  F = exp(-t/relaxation_time)*F0
-  if(X[1]&gt;(1.-dx/2.)):
-    return F
-  else:
-    return 0.0</string_value>
-          </python>
-        </value>
-        <output/>
-        <stat/>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-      </prescribed>
-    </scalar_field>
-    <scalar_field name="FreeSurfaceDifference" rank="0">
-      <diagnostic>
-        <algorithm source_field_2_type="scalar" name="scalar_difference" source_field_1_name="FreeSurface" source_field_2_name="AnalyticalFreeSurface" material_phase_support="single" source_field_1_type="scalar">
-          <absolute_difference/>
-        </algorithm>
-        <mesh name="FreeSurfaceSquaredMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-    <scalar_field name="DifferenceSquared" rank="0">
-      <diagnostic>
-        <algorithm name="scalar_python_diagnostic" material_phase_support="single">
-          <string_value lines="20" type="code" language="python">fsd = state.scalar_fields["FreeSurfaceDifference"]
-
-assert(field.node_count==fsd.node_count)
-
-for i in range(field.node_count):
-  field.set(i, fsd.node_val(i)*fsd.node_val(i))</string_value>
-          <depends>
-            <string_value lines="1">FreeSurfaceDifference</string_value>
-          </depends>
-        </algorithm>
-        <mesh name="FreeSurfaceSquaredMesh"/>
-        <output/>
-        <stat>
-          <surface_integral type="value" name="SurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6 8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="TopSurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="BottomSurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6</integer_value>
-            </surface_ids>
-          </surface_integral>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-  </material_phase>
-</fluidity_options>

=== removed file 'tests/viscous_fs_top/viscous_fs_top_B.flml'
--- tests/viscous_fs_top/viscous_fs_top_B.flml	2012-03-16 05:00:48 +0000
+++ tests/viscous_fs_top/viscous_fs_top_B.flml	1970-01-01 00:00:00 +0000
@@ -1,484 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<fluidity_options>
-  <simulation_name>
-    <string_value lines="1">viscous_fs_top_B</string_value>
-  </simulation_name>
-  <problem_type>
-    <string_value lines="1">stokes</string_value>
-  </problem_type>
-  <geometry>
-    <dimension>
-      <integer_value rank="0">2</integer_value>
-    </dimension>
-    <mesh name="CoordinateMesh">
-      <from_file file_name="src/square">
-        <format name="gmsh"/>
-        <stat>
-          <include_in_stat/>
-        </stat>
-      </from_file>
-    </mesh>
-    <mesh name="VelocityMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <mesh name="FreeSurfaceSquaredMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <quadrature>
-      <degree>
-        <integer_value rank="0">5</integer_value>
-      </degree>
-    </quadrature>
-  </geometry>
-  <io>
-    <dump_format>
-      <string_value>vtk</string_value>
-    </dump_format>
-    <dump_period_in_timesteps>
-      <constant>
-        <integer_value rank="0">1</integer_value>
-      </constant>
-    </dump_period_in_timesteps>
-    <output_mesh name="CoordinateMesh"/>
-    <stat>
-      <output_at_start/>
-      <output_before_adapts/>
-      <output_after_adapts/>
-    </stat>
-  </io>
-  <timestepping>
-    <current_time>
-      <real_value rank="0">0.0</real_value>
-    </current_time>
-    <timestep>
-      <real_value rank="0">32.0</real_value>
-    </timestep>
-    <finish_time>
-      <real_value rank="0">500</real_value>
-    </finish_time>
-  </timestepping>
-  <physical_parameters>
-    <gravity>
-      <magnitude>
-        <real_value rank="0">1.0</real_value>
-      </magnitude>
-      <vector_field name="GravityDirection" rank="1">
-        <prescribed>
-          <mesh name="CoordinateMesh"/>
-          <value name="WholeMesh">
-            <constant>
-              <real_value shape="2" dim1="dim" rank="1">0.0 -1.0</real_value>
-            </constant>
-          </value>
-          <output/>
-          <stat>
-            <include_in_stat/>
-          </stat>
-          <detectors>
-            <exclude_from_detectors/>
-          </detectors>
-        </prescribed>
-      </vector_field>
-    </gravity>
-  </physical_parameters>
-  <material_phase name="Fluid">
-    <equation_of_state>
-      <fluids>
-        <linear>
-          <reference_density>
-            <real_value rank="0">1.0</real_value>
-          </reference_density>
-          <subtract_out_hydrostatic_level/>
-        </linear>
-      </fluids>
-    </equation_of_state>
-    <scalar_field name="Pressure" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <remove_stabilisation_term/>
-            <integrate_continuity_by_parts/>
-          </continuous_galerkin>
-        </spatial_discretisation>
-        <scheme>
-          <poisson_pressure_solution>
-            <string_value lines="1">never</string_value>
-          </poisson_pressure_solution>
-          <use_projection_method>
-            <full_schur_complement>
-              <inner_matrix name="FullMomentumMatrix">
-                <solver>
-                  <iterative_method name="cg"/>
-                  <preconditioner name="mg"/>
-                  <relative_error>
-                    <real_value rank="0">1.e-12</real_value>
-                  </relative_error>
-                  <max_iterations>
-                    <integer_value rank="0">1000</integer_value>
-                  </max_iterations>
-                  <never_ignore_solver_failures/>
-                  <diagnostics>
-                    <monitors/>
-                  </diagnostics>
-                </solver>
-              </inner_matrix>
-              <preconditioner_matrix name="ScaledPressureMassMatrix"/>
-            </full_schur_complement>
-          </use_projection_method>
-        </scheme>
-        <solver>
-          <iterative_method name="fgmres"/>
-          <preconditioner name="ksp">
-            <solver>
-              <iterative_method name="cg"/>
-              <preconditioner name="sor"/>
-              <relative_error>
-                <real_value rank="0">1.e-12</real_value>
-              </relative_error>
-              <max_iterations>
-                <integer_value rank="0">1000</integer_value>
-              </max_iterations>
-              <never_ignore_solver_failures/>
-              <diagnostics>
-                <monitors/>
-              </diagnostics>
-            </solver>
-          </preconditioner>
-          <relative_error>
-            <real_value rank="0">1.e-10</real_value>
-          </relative_error>
-          <absolute_error>
-            <real_value rank="0">1.e-16</real_value>
-          </absolute_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <no_interpolation/>
-      </prognostic>
-    </scalar_field>
-    <scalar_field name="Density" rank="0">
-      <diagnostic>
-        <algorithm name="Internal" material_phase_support="multiple"/>
-        <mesh name="CoordinateMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-    <vector_field name="Velocity" rank="1">
-      <prognostic>
-        <mesh name="VelocityMesh"/>
-        <equation name="LinearMomentum"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <stabilisation>
-              <no_stabilisation/>
-            </stabilisation>
-            <mass_terms>
-              <exclude_mass_terms/>
-            </mass_terms>
-            <advection_terms>
-              <exclude_advection_terms/>
-            </advection_terms>
-            <stress_terms>
-              <partial_stress_form/>
-            </stress_terms>
-          </continuous_galerkin>
-          <conservative_advection>
-            <real_value rank="0">1.0</real_value>
-          </conservative_advection>
-        </spatial_discretisation>
-        <temporal_discretisation>
-          <theta>
-            <real_value rank="0">1.0</real_value>
-          </theta>
-          <relaxation>
-            <real_value rank="0">1.0</real_value>
-          </relaxation>
-        </temporal_discretisation>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="mg"/>
-          <relative_error>
-            <real_value rank="0">1.e-12</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <initial_condition name="WholeMesh">
-          <constant>
-            <real_value shape="2" dim1="dim" rank="1">0.0 0.0</real_value>
-          </constant>
-        </initial_condition>
-        <boundary_conditions name="Sides">
-          <surface_ids>
-            <integer_value shape="2" rank="1">7 9</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <x_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </x_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Bottom">
-          <surface_ids>
-            <integer_value shape="1" rank="1">6</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <y_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </y_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Top">
-          <surface_ids>
-            <integer_value shape="1" rank="1">8</integer_value>
-          </surface_ids>
-          <type name="free_surface">
-            <no_normal_stress/>
-          </type>
-        </boundary_conditions>
-        <tensor_field name="Viscosity" rank="2">
-          <prescribed>
-            <value name="WholeMesh">
-              <anisotropic_symmetric>
-                <constant>
-                  <real_value symmetric="true" dim2="dim" shape="2 2" dim1="dim" rank="2">1.0 1.0 1.0 1.0</real_value>
-                </constant>
-              </anisotropic_symmetric>
-            </value>
-            <output/>
-          </prescribed>
-        </tensor_field>
-        <output/>
-        <stat>
-          <include_in_stat/>
-          <previous_time_step>
-            <exclude_from_stat/>
-          </previous_time_step>
-          <nonlinear_field>
-            <exclude_from_stat/>
-          </nonlinear_field>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </vector_field>
-    <scalar_field name="FreeSurface" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <initial_condition name="WholeMesh">
-          <python>
-            <string_value lines="20" type="code" language="python">def val(X,t):
-  from math import pi, cos, sin, cosh, sinh, exp
-  dx = 1./80.
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  amp = 0.1
-  
-  F0 = amp*cos(k*X[0])
-  if(X[1]&gt;(1.-dx/2.)):
-    return F0
-  else:
-    return 0.0</string_value>
-          </python>
-        </initial_condition>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="sor"/>
-          <relative_error>
-            <real_value rank="0">1.e-6</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <output/>
-        <stat>
-          <surface_integral type="value" name="Top">
-            <surface_ids>
-              <integer_value shape="1" rank="1">8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="Bottom">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6</integer_value>
-            </surface_ids>
-          </surface_integral>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </scalar_field>
-    <scalar_field name="AnalyticalFreeSurface" rank="0">
-      <prescribed>
-        <mesh name="CoordinateMesh"/>
-        <value name="WholeMesh">
-          <python>
-            <string_value lines="20" type="code" language="python">def val(X,t):
-  from math import pi, cos, sin, cosh, sinh, exp
-  dx = 1./80.
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  D=1.0
-  rhog=1.0
-  amp = 0.1
-  
-  F0 = amp*cos(k*X[0])
-  relaxation_time = 2.0*(D*k + sinh(D*k)*cosh(D*k))*k/(rhog*sinh(D*k)**2)
-  F = exp(-t/relaxation_time)*F0
-  if(X[1]&gt;(1.-dx/2.)):
-    return F
-  else:
-    return 0.0</string_value>
-          </python>
-        </value>
-        <output/>
-        <stat/>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-      </prescribed>
-    </scalar_field>
-    <scalar_field name="FreeSurfaceDifference" rank="0">
-      <diagnostic>
-        <algorithm source_field_2_type="scalar" name="scalar_difference" source_field_1_name="FreeSurface" source_field_2_name="AnalyticalFreeSurface" material_phase_support="single" source_field_1_type="scalar">
-          <absolute_difference/>
-        </algorithm>
-        <mesh name="FreeSurfaceSquaredMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-    <scalar_field name="DifferenceSquared" rank="0">
-      <diagnostic>
-        <algorithm name="scalar_python_diagnostic" material_phase_support="single">
-          <string_value lines="20" type="code" language="python">fsd = state.scalar_fields["FreeSurfaceDifference"]
-
-assert(field.node_count==fsd.node_count)
-
-for i in range(field.node_count):
-  field.set(i, fsd.node_val(i)*fsd.node_val(i))</string_value>
-          <depends>
-            <string_value lines="1">FreeSurfaceDifference</string_value>
-          </depends>
-        </algorithm>
-        <mesh name="FreeSurfaceSquaredMesh"/>
-        <output/>
-        <stat>
-          <surface_integral type="value" name="SurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6 8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="TopSurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="BottomSurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6</integer_value>
-            </surface_ids>
-          </surface_integral>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-  </material_phase>
-</fluidity_options>

=== removed file 'tests/viscous_fs_top/viscous_fs_top_C.flml'
--- tests/viscous_fs_top/viscous_fs_top_C.flml	2012-03-16 05:00:48 +0000
+++ tests/viscous_fs_top/viscous_fs_top_C.flml	1970-01-01 00:00:00 +0000
@@ -1,484 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<fluidity_options>
-  <simulation_name>
-    <string_value lines="1">viscous_fs_top_C</string_value>
-  </simulation_name>
-  <problem_type>
-    <string_value lines="1">stokes</string_value>
-  </problem_type>
-  <geometry>
-    <dimension>
-      <integer_value rank="0">2</integer_value>
-    </dimension>
-    <mesh name="CoordinateMesh">
-      <from_file file_name="src/square">
-        <format name="gmsh"/>
-        <stat>
-          <include_in_stat/>
-        </stat>
-      </from_file>
-    </mesh>
-    <mesh name="VelocityMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <mesh name="FreeSurfaceSquaredMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <quadrature>
-      <degree>
-        <integer_value rank="0">5</integer_value>
-      </degree>
-    </quadrature>
-  </geometry>
-  <io>
-    <dump_format>
-      <string_value>vtk</string_value>
-    </dump_format>
-    <dump_period_in_timesteps>
-      <constant>
-        <integer_value rank="0">1</integer_value>
-      </constant>
-    </dump_period_in_timesteps>
-    <output_mesh name="CoordinateMesh"/>
-    <stat>
-      <output_at_start/>
-      <output_before_adapts/>
-      <output_after_adapts/>
-    </stat>
-  </io>
-  <timestepping>
-    <current_time>
-      <real_value rank="0">0.0</real_value>
-    </current_time>
-    <timestep>
-      <real_value rank="0">16.0</real_value>
-    </timestep>
-    <finish_time>
-      <real_value rank="0">500</real_value>
-    </finish_time>
-  </timestepping>
-  <physical_parameters>
-    <gravity>
-      <magnitude>
-        <real_value rank="0">1.0</real_value>
-      </magnitude>
-      <vector_field name="GravityDirection" rank="1">
-        <prescribed>
-          <mesh name="CoordinateMesh"/>
-          <value name="WholeMesh">
-            <constant>
-              <real_value shape="2" dim1="dim" rank="1">0.0 -1.0</real_value>
-            </constant>
-          </value>
-          <output/>
-          <stat>
-            <include_in_stat/>
-          </stat>
-          <detectors>
-            <exclude_from_detectors/>
-          </detectors>
-        </prescribed>
-      </vector_field>
-    </gravity>
-  </physical_parameters>
-  <material_phase name="Fluid">
-    <equation_of_state>
-      <fluids>
-        <linear>
-          <reference_density>
-            <real_value rank="0">1.0</real_value>
-          </reference_density>
-          <subtract_out_hydrostatic_level/>
-        </linear>
-      </fluids>
-    </equation_of_state>
-    <scalar_field name="Pressure" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <remove_stabilisation_term/>
-            <integrate_continuity_by_parts/>
-          </continuous_galerkin>
-        </spatial_discretisation>
-        <scheme>
-          <poisson_pressure_solution>
-            <string_value lines="1">never</string_value>
-          </poisson_pressure_solution>
-          <use_projection_method>
-            <full_schur_complement>
-              <inner_matrix name="FullMomentumMatrix">
-                <solver>
-                  <iterative_method name="cg"/>
-                  <preconditioner name="mg"/>
-                  <relative_error>
-                    <real_value rank="0">1.e-12</real_value>
-                  </relative_error>
-                  <max_iterations>
-                    <integer_value rank="0">1000</integer_value>
-                  </max_iterations>
-                  <never_ignore_solver_failures/>
-                  <diagnostics>
-                    <monitors/>
-                  </diagnostics>
-                </solver>
-              </inner_matrix>
-              <preconditioner_matrix name="ScaledPressureMassMatrix"/>
-            </full_schur_complement>
-          </use_projection_method>
-        </scheme>
-        <solver>
-          <iterative_method name="fgmres"/>
-          <preconditioner name="ksp">
-            <solver>
-              <iterative_method name="cg"/>
-              <preconditioner name="sor"/>
-              <relative_error>
-                <real_value rank="0">1.e-12</real_value>
-              </relative_error>
-              <max_iterations>
-                <integer_value rank="0">1000</integer_value>
-              </max_iterations>
-              <never_ignore_solver_failures/>
-              <diagnostics>
-                <monitors/>
-              </diagnostics>
-            </solver>
-          </preconditioner>
-          <relative_error>
-            <real_value rank="0">1.e-10</real_value>
-          </relative_error>
-          <absolute_error>
-            <real_value rank="0">1.e-16</real_value>
-          </absolute_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <no_interpolation/>
-      </prognostic>
-    </scalar_field>
-    <scalar_field name="Density" rank="0">
-      <diagnostic>
-        <algorithm name="Internal" material_phase_support="multiple"/>
-        <mesh name="CoordinateMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-    <vector_field name="Velocity" rank="1">
-      <prognostic>
-        <mesh name="VelocityMesh"/>
-        <equation name="LinearMomentum"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <stabilisation>
-              <no_stabilisation/>
-            </stabilisation>
-            <mass_terms>
-              <exclude_mass_terms/>
-            </mass_terms>
-            <advection_terms>
-              <exclude_advection_terms/>
-            </advection_terms>
-            <stress_terms>
-              <partial_stress_form/>
-            </stress_terms>
-          </continuous_galerkin>
-          <conservative_advection>
-            <real_value rank="0">1.0</real_value>
-          </conservative_advection>
-        </spatial_discretisation>
-        <temporal_discretisation>
-          <theta>
-            <real_value rank="0">1.0</real_value>
-          </theta>
-          <relaxation>
-            <real_value rank="0">1.0</real_value>
-          </relaxation>
-        </temporal_discretisation>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="mg"/>
-          <relative_error>
-            <real_value rank="0">1.e-12</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <initial_condition name="WholeMesh">
-          <constant>
-            <real_value shape="2" dim1="dim" rank="1">0.0 0.0</real_value>
-          </constant>
-        </initial_condition>
-        <boundary_conditions name="Sides">
-          <surface_ids>
-            <integer_value shape="2" rank="1">7 9</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <x_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </x_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Bottom">
-          <surface_ids>
-            <integer_value shape="1" rank="1">6</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <y_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </y_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Top">
-          <surface_ids>
-            <integer_value shape="1" rank="1">8</integer_value>
-          </surface_ids>
-          <type name="free_surface">
-            <no_normal_stress/>
-          </type>
-        </boundary_conditions>
-        <tensor_field name="Viscosity" rank="2">
-          <prescribed>
-            <value name="WholeMesh">
-              <anisotropic_symmetric>
-                <constant>
-                  <real_value symmetric="true" dim2="dim" shape="2 2" dim1="dim" rank="2">1.0 1.0 1.0 1.0</real_value>
-                </constant>
-              </anisotropic_symmetric>
-            </value>
-            <output/>
-          </prescribed>
-        </tensor_field>
-        <output/>
-        <stat>
-          <include_in_stat/>
-          <previous_time_step>
-            <exclude_from_stat/>
-          </previous_time_step>
-          <nonlinear_field>
-            <exclude_from_stat/>
-          </nonlinear_field>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </vector_field>
-    <scalar_field name="FreeSurface" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <initial_condition name="WholeMesh">
-          <python>
-            <string_value lines="20" type="code" language="python">def val(X,t):
-  from math import pi, cos, sin, cosh, sinh, exp
-  dx = 1./80.
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  amp = 0.1
-  
-  F0 = amp*cos(k*X[0])
-  if(X[1]&gt;(1.-dx/2.)):
-    return F0
-  else:
-    return 0.0</string_value>
-          </python>
-        </initial_condition>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="sor"/>
-          <relative_error>
-            <real_value rank="0">1.e-6</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <output/>
-        <stat>
-          <surface_integral type="value" name="Top">
-            <surface_ids>
-              <integer_value shape="1" rank="1">8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="Bottom">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6</integer_value>
-            </surface_ids>
-          </surface_integral>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </scalar_field>
-    <scalar_field name="AnalyticalFreeSurface" rank="0">
-      <prescribed>
-        <mesh name="CoordinateMesh"/>
-        <value name="WholeMesh">
-          <python>
-            <string_value lines="20" type="code" language="python">def val(X,t):
-  from math import pi, cos, sin, cosh, sinh, exp
-  dx = 1./80.
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  D=1.0
-  rhog=1.0
-  amp = 0.1
-  
-  F0 = amp*cos(k*X[0])
-  relaxation_time = 2.0*(D*k + sinh(D*k)*cosh(D*k))*k/(rhog*sinh(D*k)**2)
-  F = exp(-t/relaxation_time)*F0
-  if(X[1]&gt;(1.-dx/2.)):
-    return F
-  else:
-    return 0.0</string_value>
-          </python>
-        </value>
-        <output/>
-        <stat/>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-      </prescribed>
-    </scalar_field>
-    <scalar_field name="FreeSurfaceDifference" rank="0">
-      <diagnostic>
-        <algorithm source_field_2_type="scalar" name="scalar_difference" source_field_1_name="FreeSurface" source_field_2_name="AnalyticalFreeSurface" material_phase_support="single" source_field_1_type="scalar">
-          <absolute_difference/>
-        </algorithm>
-        <mesh name="FreeSurfaceSquaredMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-    <scalar_field name="DifferenceSquared" rank="0">
-      <diagnostic>
-        <algorithm name="scalar_python_diagnostic" material_phase_support="single">
-          <string_value lines="20" type="code" language="python">fsd = state.scalar_fields["FreeSurfaceDifference"]
-
-assert(field.node_count==fsd.node_count)
-
-for i in range(field.node_count):
-  field.set(i, fsd.node_val(i)*fsd.node_val(i))</string_value>
-          <depends>
-            <string_value lines="1">FreeSurfaceDifference</string_value>
-          </depends>
-        </algorithm>
-        <mesh name="FreeSurfaceSquaredMesh"/>
-        <output/>
-        <stat>
-          <surface_integral type="value" name="SurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6 8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="TopSurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="BottomSurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6</integer_value>
-            </surface_ids>
-          </surface_integral>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-  </material_phase>
-</fluidity_options>

=== removed file 'tests/viscous_fs_top/viscous_fs_top_D.flml'
--- tests/viscous_fs_top/viscous_fs_top_D.flml	2012-03-16 05:00:48 +0000
+++ tests/viscous_fs_top/viscous_fs_top_D.flml	1970-01-01 00:00:00 +0000
@@ -1,484 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<fluidity_options>
-  <simulation_name>
-    <string_value lines="1">viscous_fs_top_D</string_value>
-  </simulation_name>
-  <problem_type>
-    <string_value lines="1">stokes</string_value>
-  </problem_type>
-  <geometry>
-    <dimension>
-      <integer_value rank="0">2</integer_value>
-    </dimension>
-    <mesh name="CoordinateMesh">
-      <from_file file_name="src/square">
-        <format name="gmsh"/>
-        <stat>
-          <include_in_stat/>
-        </stat>
-      </from_file>
-    </mesh>
-    <mesh name="VelocityMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <mesh name="FreeSurfaceSquaredMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <quadrature>
-      <degree>
-        <integer_value rank="0">5</integer_value>
-      </degree>
-    </quadrature>
-  </geometry>
-  <io>
-    <dump_format>
-      <string_value>vtk</string_value>
-    </dump_format>
-    <dump_period_in_timesteps>
-      <constant>
-        <integer_value rank="0">1</integer_value>
-      </constant>
-    </dump_period_in_timesteps>
-    <output_mesh name="CoordinateMesh"/>
-    <stat>
-      <output_at_start/>
-      <output_before_adapts/>
-      <output_after_adapts/>
-    </stat>
-  </io>
-  <timestepping>
-    <current_time>
-      <real_value rank="0">0.0</real_value>
-    </current_time>
-    <timestep>
-      <real_value rank="0">8</real_value>
-    </timestep>
-    <finish_time>
-      <real_value rank="0">500</real_value>
-    </finish_time>
-  </timestepping>
-  <physical_parameters>
-    <gravity>
-      <magnitude>
-        <real_value rank="0">1.0</real_value>
-      </magnitude>
-      <vector_field name="GravityDirection" rank="1">
-        <prescribed>
-          <mesh name="CoordinateMesh"/>
-          <value name="WholeMesh">
-            <constant>
-              <real_value shape="2" dim1="dim" rank="1">0.0 -1.0</real_value>
-            </constant>
-          </value>
-          <output/>
-          <stat>
-            <include_in_stat/>
-          </stat>
-          <detectors>
-            <exclude_from_detectors/>
-          </detectors>
-        </prescribed>
-      </vector_field>
-    </gravity>
-  </physical_parameters>
-  <material_phase name="Fluid">
-    <equation_of_state>
-      <fluids>
-        <linear>
-          <reference_density>
-            <real_value rank="0">1.0</real_value>
-          </reference_density>
-          <subtract_out_hydrostatic_level/>
-        </linear>
-      </fluids>
-    </equation_of_state>
-    <scalar_field name="Pressure" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <remove_stabilisation_term/>
-            <integrate_continuity_by_parts/>
-          </continuous_galerkin>
-        </spatial_discretisation>
-        <scheme>
-          <poisson_pressure_solution>
-            <string_value lines="1">never</string_value>
-          </poisson_pressure_solution>
-          <use_projection_method>
-            <full_schur_complement>
-              <inner_matrix name="FullMomentumMatrix">
-                <solver>
-                  <iterative_method name="cg"/>
-                  <preconditioner name="mg"/>
-                  <relative_error>
-                    <real_value rank="0">1.e-12</real_value>
-                  </relative_error>
-                  <max_iterations>
-                    <integer_value rank="0">1000</integer_value>
-                  </max_iterations>
-                  <never_ignore_solver_failures/>
-                  <diagnostics>
-                    <monitors/>
-                  </diagnostics>
-                </solver>
-              </inner_matrix>
-              <preconditioner_matrix name="ScaledPressureMassMatrix"/>
-            </full_schur_complement>
-          </use_projection_method>
-        </scheme>
-        <solver>
-          <iterative_method name="fgmres"/>
-          <preconditioner name="ksp">
-            <solver>
-              <iterative_method name="cg"/>
-              <preconditioner name="sor"/>
-              <relative_error>
-                <real_value rank="0">1.e-12</real_value>
-              </relative_error>
-              <max_iterations>
-                <integer_value rank="0">1000</integer_value>
-              </max_iterations>
-              <never_ignore_solver_failures/>
-              <diagnostics>
-                <monitors/>
-              </diagnostics>
-            </solver>
-          </preconditioner>
-          <relative_error>
-            <real_value rank="0">1.e-10</real_value>
-          </relative_error>
-          <absolute_error>
-            <real_value rank="0">1.e-16</real_value>
-          </absolute_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <no_interpolation/>
-      </prognostic>
-    </scalar_field>
-    <scalar_field name="Density" rank="0">
-      <diagnostic>
-        <algorithm name="Internal" material_phase_support="multiple"/>
-        <mesh name="CoordinateMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-    <vector_field name="Velocity" rank="1">
-      <prognostic>
-        <mesh name="VelocityMesh"/>
-        <equation name="LinearMomentum"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <stabilisation>
-              <no_stabilisation/>
-            </stabilisation>
-            <mass_terms>
-              <exclude_mass_terms/>
-            </mass_terms>
-            <advection_terms>
-              <exclude_advection_terms/>
-            </advection_terms>
-            <stress_terms>
-              <partial_stress_form/>
-            </stress_terms>
-          </continuous_galerkin>
-          <conservative_advection>
-            <real_value rank="0">1.0</real_value>
-          </conservative_advection>
-        </spatial_discretisation>
-        <temporal_discretisation>
-          <theta>
-            <real_value rank="0">1.0</real_value>
-          </theta>
-          <relaxation>
-            <real_value rank="0">1.0</real_value>
-          </relaxation>
-        </temporal_discretisation>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="mg"/>
-          <relative_error>
-            <real_value rank="0">1.e-12</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <initial_condition name="WholeMesh">
-          <constant>
-            <real_value shape="2" dim1="dim" rank="1">0.0 0.0</real_value>
-          </constant>
-        </initial_condition>
-        <boundary_conditions name="Sides">
-          <surface_ids>
-            <integer_value shape="2" rank="1">7 9</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <x_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </x_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Bottom">
-          <surface_ids>
-            <integer_value shape="1" rank="1">6</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <y_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </y_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Top">
-          <surface_ids>
-            <integer_value shape="1" rank="1">8</integer_value>
-          </surface_ids>
-          <type name="free_surface">
-            <no_normal_stress/>
-          </type>
-        </boundary_conditions>
-        <tensor_field name="Viscosity" rank="2">
-          <prescribed>
-            <value name="WholeMesh">
-              <anisotropic_symmetric>
-                <constant>
-                  <real_value symmetric="true" dim2="dim" shape="2 2" dim1="dim" rank="2">1.0 1.0 1.0 1.0</real_value>
-                </constant>
-              </anisotropic_symmetric>
-            </value>
-            <output/>
-          </prescribed>
-        </tensor_field>
-        <output/>
-        <stat>
-          <include_in_stat/>
-          <previous_time_step>
-            <exclude_from_stat/>
-          </previous_time_step>
-          <nonlinear_field>
-            <exclude_from_stat/>
-          </nonlinear_field>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </vector_field>
-    <scalar_field name="FreeSurface" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <initial_condition name="WholeMesh">
-          <python>
-            <string_value lines="20" type="code" language="python">def val(X,t):
-  from math import pi, cos, sin, cosh, sinh, exp
-  dx = 1./80.
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  amp = 0.1
-  
-  F0 = amp*cos(k*X[0])
-  if(X[1]&gt;(1.-dx/2.)):
-    return F0
-  else:
-    return 0.0</string_value>
-          </python>
-        </initial_condition>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="sor"/>
-          <relative_error>
-            <real_value rank="0">1.e-6</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <output/>
-        <stat>
-          <surface_integral type="value" name="Top">
-            <surface_ids>
-              <integer_value shape="1" rank="1">8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="Bottom">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6</integer_value>
-            </surface_ids>
-          </surface_integral>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </scalar_field>
-    <scalar_field name="AnalyticalFreeSurface" rank="0">
-      <prescribed>
-        <mesh name="CoordinateMesh"/>
-        <value name="WholeMesh">
-          <python>
-            <string_value lines="20" type="code" language="python">def val(X,t):
-  from math import pi, cos, sin, cosh, sinh, exp
-  dx = 1./80.
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  D=1.0
-  rhog=1.0
-  amp = 0.1
-  
-  F0 = amp*cos(k*X[0])
-  relaxation_time = 2.0*(D*k + sinh(D*k)*cosh(D*k))*k/(rhog*sinh(D*k)**2)
-  F = exp(-t/relaxation_time)*F0
-  if(X[1]&gt;(1.-dx/2.)):
-    return F
-  else:
-    return 0.0</string_value>
-          </python>
-        </value>
-        <output/>
-        <stat/>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-      </prescribed>
-    </scalar_field>
-    <scalar_field name="FreeSurfaceDifference" rank="0">
-      <diagnostic>
-        <algorithm source_field_2_type="scalar" name="scalar_difference" source_field_1_name="FreeSurface" source_field_2_name="AnalyticalFreeSurface" material_phase_support="single" source_field_1_type="scalar">
-          <absolute_difference/>
-        </algorithm>
-        <mesh name="FreeSurfaceSquaredMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-    <scalar_field name="DifferenceSquared" rank="0">
-      <diagnostic>
-        <algorithm name="scalar_python_diagnostic" material_phase_support="single">
-          <string_value lines="20" type="code" language="python">fsd = state.scalar_fields["FreeSurfaceDifference"]
-
-assert(field.node_count==fsd.node_count)
-
-for i in range(field.node_count):
-  field.set(i, fsd.node_val(i)*fsd.node_val(i))</string_value>
-          <depends>
-            <string_value lines="1">FreeSurfaceDifference</string_value>
-          </depends>
-        </algorithm>
-        <mesh name="FreeSurfaceSquaredMesh"/>
-        <output/>
-        <stat>
-          <surface_integral type="value" name="SurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6 8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="TopSurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">8</integer_value>
-            </surface_ids>
-          </surface_integral>
-          <surface_integral type="value" name="BottomSurfaceL2Norm">
-            <surface_ids>
-              <integer_value shape="1" rank="1">6</integer_value>
-            </surface_ids>
-          </surface_integral>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-  </material_phase>
-</fluidity_options>

=== removed file 'tests/viscous_fs_top/viscous_fs_top_E.flml'
--- tests/viscous_fs_top/viscous_fs_top_E.flml	2012-03-16 05:00:48 +0000
+++ tests/viscous_fs_top/viscous_fs_top_E.flml	1970-01-01 00:00:00 +0000
@@ -1,484 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<fluidity_options>
-  <simulation_name>
-    <string_value lines="1">viscous_fs_top_E</string_value>
-  </simulation_name>
-  <problem_type>
-    <string_value lines="1">stokes</string_value>
-  </problem_type>
-  <geometry>
-    <dimension>
-      <integer_value rank="0">2</integer_value>
-    </dimension>
-    <mesh name="CoordinateMesh">
-      <from_file file_name="src/square">
-        <format name="gmsh"/>
-        <stat>
-          <include_in_stat/>
-        </stat>
-      </from_file>
-    </mesh>
-    <mesh name="VelocityMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <mesh name="FreeSurfaceSquaredMesh">
-      <from_mesh>
-        <mesh name="CoordinateMesh"/>
-        <mesh_shape>
-          <polynomial_degree>
-            <integer_value rank="0">2</integer_value>
-          </polynomial_degree>
-        </mesh_shape>
-        <stat>
-          <exclude_from_stat/>
-        </stat>
-      </from_mesh>
-    </mesh>
-    <quadrature>
-      <degree>
-        <integer_value rank="0">5</integer_value>
-      </degree>
-    </quadrature>
-  </geometry>
-  <io>
-    <dump_format>
-      <string_value>vtk</string_value>
-    </dump_format>
-    <dump_period_in_timesteps>
-      <constant>
-        <integer_value rank="0">1</integer_value>
-      </constant>
-    </dump_period_in_timesteps>
-    <output_mesh name="CoordinateMesh"/>
-    <stat>
-      <output_at_start/>
-      <output_before_adapts/>
-      <output_after_adapts/>
-    </stat>
-  </io>
-  <timestepping>
-    <current_time>
-      <real_value rank="0">0.0</real_value>
-    </current_time>
-    <timestep>
-      <real_value rank="0">4</real_value>
-    </timestep>
-    <finish_time>
-      <real_value rank="0">500</real_value>
-    </finish_time>
-  </timestepping>
-  <physical_parameters>
-    <gravity>
-      <magnitude>
-        <real_value rank="0">1.0</real_value>
-      </magnitude>
-      <vector_field name="GravityDirection" rank="1">
-        <prescribed>
-          <mesh name="CoordinateMesh"/>
-          <value name="WholeMesh">
-            <constant>
-              <real_value shape="2" dim1="dim" rank="1">0.0 -1.0</real_value>
-            </constant>
-          </value>
-          <output/>
-          <stat>
-            <include_in_stat/>
-          </stat>
-          <detectors>
-            <exclude_from_detectors/>
-          </detectors>
-        </prescribed>
-      </vector_field>
-    </gravity>
-  </physical_parameters>
-  <material_phase name="Fluid">
-    <equation_of_state>
-      <fluids>
-        <linear>
-          <reference_density>
-            <real_value rank="0">1.0</real_value>
-          </reference_density>
-          <subtract_out_hydrostatic_level/>
-        </linear>
-      </fluids>
-    </equation_of_state>
-    <scalar_field name="Pressure" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <remove_stabilisation_term/>
-            <integrate_continuity_by_parts/>
-          </continuous_galerkin>
-        </spatial_discretisation>
-        <scheme>
-          <poisson_pressure_solution>
-            <string_value lines="1">never</string_value>
-          </poisson_pressure_solution>
-          <use_projection_method>
-            <full_schur_complement>
-              <inner_matrix name="FullMomentumMatrix">
-                <solver>
-                  <iterative_method name="cg"/>
-                  <preconditioner name="mg"/>
-                  <relative_error>
-                    <real_value rank="0">1.e-12</real_value>
-                  </relative_error>
-                  <max_iterations>
-                    <integer_value rank="0">1000</integer_value>
-                  </max_iterations>
-                  <never_ignore_solver_failures/>
-                  <diagnostics>
-                    <monitors/>
-                  </diagnostics>
-                </solver>
-              </inner_matrix>
-              <preconditioner_matrix name="ScaledPressureMassMatrix"/>
-            </full_schur_complement>
-          </use_projection_method>
-        </scheme>
-        <solver>
-          <iterative_method name="fgmres"/>
-          <preconditioner name="ksp">
-            <solver>
-              <iterative_method name="cg"/>
-              <preconditioner name="sor"/>
-              <relative_error>
-                <real_value rank="0">1.e-12</real_value>
-              </relative_error>
-              <max_iterations>
-                <integer_value rank="0">1000</integer_value>
-              </max_iterations>
-              <never_ignore_solver_failures/>
-              <diagnostics>
-                <monitors/>
-              </diagnostics>
-            </solver>
-          </preconditioner>
-          <relative_error>
-            <real_value rank="0">1.e-10</real_value>
-          </relative_error>
-          <absolute_error>
-            <real_value rank="0">1.e-16</real_value>
-          </absolute_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <exclude_from_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <no_interpolation/>
-      </prognostic>
-    </scalar_field>
-    <scalar_field name="Density" rank="0">
-      <diagnostic>
-        <algorithm name="Internal" material_phase_support="multiple"/>
-        <mesh name="CoordinateMesh"/>
-        <output/>
-        <stat/>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-      </diagnostic>
-    </scalar_field>
-    <vector_field name="Velocity" rank="1">
-      <prognostic>
-        <mesh name="VelocityMesh"/>
-        <equation name="LinearMomentum"/>
-        <spatial_discretisation>
-          <continuous_galerkin>
-            <stabilisation>
-              <no_stabilisation/>
-            </stabilisation>
-            <mass_terms>
-              <exclude_mass_terms/>
-            </mass_terms>
-            <advection_terms>
-              <exclude_advection_terms/>
-            </advection_terms>
-            <stress_terms>
-              <partial_stress_form/>
-            </stress_terms>
-          </continuous_galerkin>
-          <conservative_advection>
-            <real_value rank="0">1.0</real_value>
-          </conservative_advection>
-        </spatial_discretisation>
-        <temporal_discretisation>
-          <theta>
-            <real_value rank="0">1.0</real_value>
-          </theta>
-          <relaxation>
-            <real_value rank="0">1.0</real_value>
-          </relaxation>
-        </temporal_discretisation>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="mg"/>
-          <relative_error>
-            <real_value rank="0">1.e-12</real_value>
-          </relative_error>
-          <max_iterations>
-            <integer_value rank="0">1000</integer_value>
-          </max_iterations>
-          <never_ignore_solver_failures/>
-          <diagnostics>
-            <monitors/>
-          </diagnostics>
-        </solver>
-        <initial_condition name="WholeMesh">
-          <constant>
-            <real_value shape="2" dim1="dim" rank="1">0.0 0.0</real_value>
-          </constant>
-        </initial_condition>
-        <boundary_conditions name="Sides">
-          <surface_ids>
-            <integer_value shape="2" rank="1">7 9</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <x_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </x_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Bottom">
-          <surface_ids>
-            <integer_value shape="1" rank="1">6</integer_value>
-          </surface_ids>
-          <type name="dirichlet">
-            <align_bc_with_cartesian>
-              <y_component>
-                <constant>
-                  <real_value rank="0">0.0</real_value>
-                </constant>
-              </y_component>
-            </align_bc_with_cartesian>
-          </type>
-        </boundary_conditions>
-        <boundary_conditions name="Top">
-          <surface_ids>
-            <integer_value shape="1" rank="1">8</integer_value>
-          </surface_ids>
-          <type name="free_surface">
-            <no_normal_stress/>
-          </type>
-        </boundary_conditions>
-        <tensor_field name="Viscosity" rank="2">
-          <prescribed>
-            <value name="WholeMesh">
-              <anisotropic_symmetric>
-                <constant>
-                  <real_value symmetric="true" dim2="dim" shape="2 2" dim1="dim" rank="2">1.0 1.0 1.0 1.0</real_value>
-                </constant>
-              </anisotropic_symmetric>
-            </value>
-            <output/>
-          </prescribed>
-        </tensor_field>
-        <output/>
-        <stat>
-          <include_in_stat/>
-          <previous_time_step>
-            <exclude_from_stat/>
-          </previous_time_step>
-          <nonlinear_field>
-            <exclude_from_stat/>
-          </nonlinear_field>
-        </stat>
-        <convergence>
-          <include_in_convergence/>
-        </convergence>
-        <detectors>
-          <include_in_detectors/>
-        </detectors>
-        <steady_state>
-          <include_in_steady_state/>
-        </steady_state>
-        <consistent_interpolation/>
-      </prognostic>
-    </vector_field>
-    <scalar_field name="FreeSurface" rank="0">
-      <prognostic>
-        <mesh name="CoordinateMesh"/>
-        <initial_condition name="WholeMesh">
-          <python>
-            <string_value lines="20" type="code" language="python">def val(X,t):
-  from math import pi, cos, sin, cosh, sinh, exp
-  dx = 1./80.
-  wavelength=1.0
-  k=2.0*pi/wavelength
-  amp = 0.1
-  
-  F0 = amp*cos(k*X[0])
-  if(X[1]&gt;(1.-dx/2.)):
-    return F0
-  else:
-    return 0.0</string_value>
-          </python>
-        </initial_condition>
-        <solver>
-          <iterative_method name="cg"/>
-          <preconditioner name="sor"/>
-          <relative_error>