Merge branch 'baagaard/update-tests'

* baagaard/update-tests:
  Small updates to developer doc.
  Remove obsolete plasticity test (tests/3d/plasticity/threehex8).
  Upgraded tests/2d/slipdir to full-scale test (tests_auto/2d/slipdir).
  Collapse tests/3d/plasticity/threehex8 into one directory.
  Remove obsolete tests.
  Switch to HDF5 output.
  Update nonplanar example.
  Switch from PyTables to h5py in plotting.
  Increase number of procs for several examples.

configure.ac

@@ -335,6 +335,7 @@ AC_CONFIG_FILES([Makefile
 		tests_auto/2d/Makefile
 		tests_auto/2d/tri3/Makefile
 		tests_auto/2d/quad4/Makefile
+		tests_auto/2d/slipdir/Makefile
 		tests_auto/3d/Makefile
 		tests_auto/3d/tet4/Makefile
 		tests_auto/3d/hex8/Makefile
@@ -344,7 +345,6 @@ AC_CONFIG_FILES([Makefile
 		tests/2d/Makefile
 		tests/2d/maxwell/Makefile
 		tests/2d/powerlaw/Makefile
-		tests/2d/slipdir/Makefile
 		tests/2d/frictionslide/Makefile
 		tests/2d/plasticity/Makefile
 		tests/2d/plasticity/initialstress/Makefile
@@ -354,15 +354,8 @@ AC_CONFIG_FILES([Makefile
 		tests/3d/cyclicfriction/Makefile
 		tests/3d/cyclicfriction/output/Makefile
 		tests/3d/plasticity/Makefile
-		tests/3d/plasticity/threehex8/Makefile
-		tests/3d/plasticity/threehex8/config/Makefile
-		tests/3d/plasticity/threehex8/mesh/Makefile
-		tests/3d/plasticity/threehex8/results/Makefile
-		tests/3d/plasticity/threehex8/spatialdb/Makefile
 		tests/3d/plasticity/dynamic/Makefile
 		tests/3d/plasticity/initialstress/Makefile
-		tests/topology/Makefile
-		tests/refinefaulttip/Makefile
                 doc/Makefile
 		doc/developer/Makefile
 		doc/install/Makefile

doc/developer/general

@@ -7,13 +7,12 @@ for EVERY method, member, and argument to a member function.
 go in .cc files, and inline methods go in .icc files. Use an include
 directive in header files for inline methods.
 
-3. Files checked in to the repository trunk should at least compile.
+3. ALL development should be done in developer branches. Merge to the
+'next' branch for integration testing. Once testing is complete, merge
+to master. See PETSc development documentation for how we use
+branches.
 
-4. Changes to the code that fix bugs in released code should be done
-in the stable branch. Those changes are then merged into the trunk
-(this is tricky, so please notify Brad and he will do it for you).
-
-5. C++ and Python classes should have corresponding unit tests in
+4. C++ and Python classes should have corresponding unit tests in
 libtests and pytests. High-level functionality should be verified
 using a full-scale test.
 

examples/run_examples.py

@@ -96,7 +96,7 @@ def run_pylith(dir, examples, nprocs=1):
     run_pylith(dir, examples, nprocs=2)
     run_pylith(dir, examples, nprocs=3)
     run_pylith(dir, examples, nprocs=4)
-    run_pylith(dir, examples, nprocs=5)
+    run_pylith(dir, examples, nprocs=6)
 
 
 # ----------------------------------------------------------------------
@@ -149,7 +149,7 @@ def run_pylith(dir, examples, nprocs=1):
     run_pylith(dir, examples, nprocs=1)
     run_pylith(dir, examples, nprocs=2)
     run_pylith(dir, examples, nprocs=4)
-    run_pylith(dir, examples, nprocs=5)
+    run_pylith(dir, examples, nprocs=6)
 
 
 # ----------------------------------------------------------------------
@@ -194,6 +194,7 @@ def run_pylith(dir, examples, nprocs=1):
     run_pylith(dir, examples, nprocs=1)
     run_pylith(dir, examples, nprocs=2)
     run_pylith(dir, examples, nprocs=4)
+    run_pylith(dir, examples, nprocs=6)
 
     dir = "2d/greensfns/reverse"
     examples = ("eqsim.cfg",
@@ -202,3 +203,4 @@ def run_pylith(dir, examples, nprocs=1):
     run_pylith(dir, examples, nprocs=1)
     run_pylith(dir, examples, nprocs=2)
     run_pylith(dir, examples, nprocs=4)
+    run_pylith(dir, examples, nprocs=6)

tests/2d/Makefile.am

@@ -19,7 +19,6 @@
 SUBDIRS = \
 	maxwell \
 	powerlaw \
-	slipdir \
 	frictionslide \
 	plasticity
 

tests/2d/frictionslide/plot_friction.py

@@ -11,7 +11,7 @@
     raise ValueError("Unknown sim '%s'." % sim)
 
 # ======================================================================
-import tables
+import h5py
 import pylab
 import numpy
 from math import exp
@@ -72,12 +72,12 @@ def integrateStateVar(theta, v, t0):
 
 # ----------------------------------------------------------------------
 
-h5 = tables.openFile("output/ratestate_%s-fault.h5" % sim, "r")
-time = h5.root.time[:].ravel()
-slip = h5.root.vertex_fields.slip[:]
-slipRate = h5.root.vertex_fields.slip_rate[:]
-stateVar = h5.root.vertex_fields.state_variable[:]
-traction = h5.root.vertex_fields.traction[:]
+h5 = h5py.File("output/ratestate_%s-fault.h5" % sim, "r")
+time = h5['time'][:].ravel()
+slip = h5['vertex_fields/slip'][:]
+slipRate = h5['vertex_fields/slip_rate'][:]
+stateVar = h5['vertex_fields/state_variable'][:]
+traction = h5['vertex_fields/traction'][:]
 h5.close()
 
 fig = pylab.Figure()

tests/2d/nonplanar/bc.jou

@@ -30,16 +30,25 @@ block 1 name "inner"
 block 2 surface surf_outer
 block 2 name "outer"
 
+# ----------------------------------------------------------------------
+# Create nodeset for fault interfaces
+# ----------------------------------------------------------------------
+group "fault" add node in curve 5
+nodeset 20 group fault
+nodeset 20 name "fault"
+
 # ----------------------------------------------------------------------
 # Create nodeset for boundaries
 # ----------------------------------------------------------------------
 group "bndry_south" add node in curve 6
 group "bndry_south" add node in curve 7
+group "bndry_south" remove node in group fault
 nodeset 11 group bndry_south
 nodeset 11 name "bndry_south"
 
 group "bndry_north" add node in curve 9
 group "bndry_north" add node in curve 8
+group "bndry_north" remove node in group fault
 nodeset 12 group bndry_north
 nodeset 12 name "bndry_north"
 
@@ -51,16 +60,8 @@ group "bndry_east" add node in curve 2
 nodeset 14 group bndry_east
 nodeset 14 name "bndry_east"
 
-# ----------------------------------------------------------------------
-# Create nodeset for fault interfaces
-# ----------------------------------------------------------------------
-group "fault" add node in curve 5
-group "fault" remove node in bndry_north
-group "fault" remove node in bndry_south
-nodeset 20 group fault
-nodeset 20 name "fault"
-
 # End of file
 
 
 
+

tests/2d/nonplanar/geometry.jou

@@ -19,7 +19,7 @@
 # ----------------------------------------------------------------------
 # Set units to SI.
 # ----------------------------------------------------------------------
-# {Units('si')}
+${Units('si')}
 #
 # ----------------------------------------------------------------------
 # Reset geometry.
@@ -73,4 +73,3 @@ imprint all
 merge all
 
 # End of file
-

tests/2d/nonplanar/mesh.jou

@@ -27,7 +27,7 @@ playback 'geometry.jou'
 # ----------------------------------------------------------------------
 surface all scheme trimesh
 curve all scheme default
-#{dx=600.0*m}
+${dx=600.0*m}
 surface all size {600*m}
 
 # ----------------------------------------------------------------------
@@ -52,6 +52,3 @@ playback 'bc.jou'
 export mesh "mesh.exo" dimension 2 overwrite
 
 # End of file
-
-
-

tests/2d/nonplanar/pylithapp.cfg

@@ -185,7 +185,7 @@ writer = pylith.meshio.DataWriterHDF5
 writer.filename = output/nonplanar.h5
 
 [pylithapp.timedependent.interfaces.fault.output]
-vertex_info_fields=[traction_initial_value]
+vertex_info_fields=[normal_dir,strike_dir,traction_initial_value]
 vertex_data_fields=[slip,slip_rate,traction]
 skip = 2
 writer = pylith.meshio.DataWriterHDF5