Wed Nov 5 15:42:35 PST 2014

Repository : https://github.com/geodynamics/pylith

On branches: baagaard/add-examples-debugging,baagaard/add-release-2.0.3,baagaard/add-release-2.1.0,baagaard/dynrup-new-lagrange,baagaard/feature-output-station-names,baagaard/feature-progress-monitor,baagaard/fix-custom-faultpc,baagaard/fix-error-messages,baagaard/fix-faults-intersect,baagaard/fix-friction-initial-state,baagaard/update-autoconf,knepley/feature-petsc-fe,knepley/upgrade-petsc-3.5,knepley/upgrade-petsc-master,maint,master,next,willic3/fix-plasticity
Link       : https://github.com/geodynamics/pylith/compare/f33c75b19fd60eedb2a3405db76a1fee333bb1d7...5b6d812b1612809fea3bd331c4e5af98c25a536a

>---------------------------------------------------------------

commit 3426804affbf3baa9d92a75776c62f7211aad7a4
Author: Brad Aagaard <baagaard at usgs.gov>
Date:   Mon Jun 23 21:33:00 2014 -0700

    Finished setting up files with error and correct files. Moved correct files to correct directory.


>---------------------------------------------------------------

3426804affbf3baa9d92a75776c62f7211aad7a4
 .../correct}/mat_elastic.spatialdb                 |  0
 examples/debugging/{ => correct}/pylithapp.cfg     |  6 ++--
 .../{step01_correct.cfg => correct/step01.cfg}     |  0
 .../{step02_correct.cfg => correct/step02.cfg}     |  5 ++++
 .../{step03_correct.cfg => correct/step03.cfg}     | 15 +++++-----
 examples/debugging/mat_elastic_correct.spatialdb   | 26 ----------------
 examples/debugging/pylithapp.cfg                   | 35 ++--------------------
 examples/debugging/step02.cfg                      | 11 +++++--
 examples/debugging/step03.cfg                      | 15 +++-------
 9 files changed, 33 insertions(+), 80 deletions(-)

diff --git a/examples/3d/hex8/spatialdb/mat_elastic.spatialdb b/examples/debugging/correct/mat_elastic.spatialdb
similarity index 100%
copy from examples/3d/hex8/spatialdb/mat_elastic.spatialdb
copy to examples/debugging/correct/mat_elastic.spatialdb
diff --git a/examples/debugging/pylithapp.cfg b/examples/debugging/correct/pylithapp.cfg
similarity index 98%
copy from examples/debugging/pylithapp.cfg
copy to examples/debugging/correct/pylithapp.cfg
index 57a06d4..b672a92 100644
--- a/examples/debugging/pylithapp.cfg
+++ b/examples/debugging/correct/pylithapp.cfg
@@ -18,6 +18,7 @@ solverlinear = 1
 meshiocubit = 1
 implicitelasticity = 1
 faultcohesivekin = 1
+fault = 1
 fiatlagrange = 1
 materials = 1
 
@@ -88,7 +89,6 @@ sub_pc_factor_shift_type = nonzero
 
 # Convergence parameters.
 ksp_rtol = 1.0e-10
-ksp_atol = 1.0e-20
 ksp_max_it = 100
 ksp_gmres_restart = 50
 
@@ -100,7 +100,6 @@ ksp_error_if_not_converged = true
 
 # Nonlinear solver monitoring options.
 snes_rtol = 1.0e-10
-snes_atol = 1.0e-9
 snes_max_it = 100
 snes_monitor = true
 #snes_view = true
@@ -109,3 +108,6 @@ snes_error_if_not_converged = true
 
 # PETSc summary -- useful for performance information.
 log_summary = true
+
+
+# End of file
diff --git a/examples/debugging/step01_correct.cfg b/examples/debugging/correct/step01.cfg
similarity index 100%
rename from examples/debugging/step01_correct.cfg
rename to examples/debugging/correct/step01.cfg
diff --git a/examples/debugging/step02_correct.cfg b/examples/debugging/correct/step02.cfg
similarity index 97%
rename from examples/debugging/step02_correct.cfg
rename to examples/debugging/correct/step02.cfg
index defcfd1..278fe20 100644
--- a/examples/debugging/step02_correct.cfg
+++ b/examples/debugging/correct/step02.cfg
@@ -24,6 +24,11 @@
 # ----------------------------------------------------------------------
 # problem
 # ----------------------------------------------------------------------
+[pylithapp.problem.normalizer]
+length_scale = 1.0*km
+shear_modulus = 30.0*GPa
+relaxation_time = 2.0*year
+
 [pylithapp.timedependent.formulation.time_step]
 # Define the total time for the simulation and the default time step size.
 total_time = 0.0*s ; total time of simulation
diff --git a/examples/debugging/step03_correct.cfg b/examples/debugging/correct/step03.cfg
similarity index 94%
rename from examples/debugging/step03_correct.cfg
rename to examples/debugging/correct/step03.cfg
index b92a021..9421e59 100644
--- a/examples/debugging/step03_correct.cfg
+++ b/examples/debugging/correct/step03.cfg
@@ -71,16 +71,16 @@ bc_dof = [0, 1]
 label = face_xpos
 db_initial = spatialdata.spatialdb.UniformDB
 db_initial.label = Dirichlet BC on +x
-db_initial.values = [displacement-x,displacement-y]
-db_initial.data = [-1.0*m,3.0*m]
+db_initial.values = [displacement-x,displacement-y,displacement-z]
+db_initial.data = [-1.0*m,3.0*m,0.0*m]
 
 [pylithapp.timedependent.bc.x_neg]
 bc_dof = [0, 1]
 label = face_xneg
 db_initial = spatialdata.spatialdb.UniformDB
 db_initial.label = Dirichlet BC on -x
-db_initial.values = [displacement-x,displacement-y]
-db_initial.data = [1.0*m,-3.0*m]
+db_initial.values = [displacement-x,displacement-y,displacement-z]
+db_initial.data = [1.0*m,-3.0*m,0.0*m]
 
 [pylithapp.timedependent.bc.z_neg]
 bc_dof = [2]
@@ -105,7 +105,7 @@ label = fault_ext
 friction = pylith.friction.StaticFriction
 friction.label = Static friction
 
-zero_tolerance = 1.0e-12
+zero_tolerance = 1.0e-10
 
 # We must define the quadrature information for fault cells.
 # The fault cells are 2D (surface).
@@ -126,10 +126,10 @@ friction.db_properties.data = [0.6,0.0*Pa]
 [pylithapp.petsc]
 
 ksp_rtol = 1.0e-20
-ksp_atol = 1.0e-13
+ksp_atol = 1.0e-12
 
 snes_rtol = 1.0e-20
-snes_atol = 1.0e-10
+snes_atol = 1.0e-8
 
 # Friction sensitivity solve used to compute the increment in slip
 # associated with changes in the Lagrange multiplier imposed by the
@@ -153,6 +153,7 @@ writer.filename = output/step03-groundsurf.vtk
 
 [pylithapp.problem.interfaces.fault.output]
 writer.filename = output/step03-fault.vtk
+vertex_data_fields = [traction,slip,slip_rate]
 
 [pylithapp.timedependent.materials.uppercrust.output]
 writer.filename = output/step03-uppercrust.vtk
diff --git a/examples/debugging/mat_elastic_correct.spatialdb b/examples/debugging/mat_elastic_correct.spatialdb
deleted file mode 100644
index 526fab2..0000000
--- a/examples/debugging/mat_elastic_correct.spatialdb
+++ /dev/null
@@ -1,26 +0,0 @@
-// -*- C++ -*- (tell Emacs to use C++ mode for syntax highlighting)
-//
-// This spatial database specifies the distribution of material
-// properties. In this case, the material properties are uniform.
-//
-#SPATIAL.ascii 1
-SimpleDB {
-  num-values = 3 // number of material property values
-  value-names =  density vs vp // names of the material property values
-  value-units =  kg/m**3  m/s  m/s // units
-  num-locs = 1 // number of locations
-  data-dim = 0
-  space-dim = 3
-  cs-data = cartesian {
-    to-meters = 1.0
-    space-dim = 3
-  }
-}
-// Columns are
-// (1) x coordinate (m)
-// (2) y coordinate (m)
-// (3) z coordinate (m)
-// (4) density (kg/m^3)
-// (5) vs (m/s)
-// (6) vp (m/s)
-0.0  0.0  0.0   2500.0  3000.0  5291.502622129181
diff --git a/examples/debugging/pylithapp.cfg b/examples/debugging/pylithapp.cfg
index 57a06d4..7a24110 100644
--- a/examples/debugging/pylithapp.cfg
+++ b/examples/debugging/pylithapp.cfg
@@ -5,23 +5,6 @@
 # in this directory.
 
 # ----------------------------------------------------------------------
-# journal
-# ----------------------------------------------------------------------
-# Turn on some journals to show progress.
-[pylithapp.journal.info]
-pylithapp = 1
-timedependent = 1
-greensfns = 1
-implicit = 1
-petsc = 1
-solverlinear = 1
-meshiocubit = 1
-implicitelasticity = 1
-faultcohesivekin = 1
-fiatlagrange = 1
-materials = 1
-
-# ----------------------------------------------------------------------
 # mesh_generator
 # ----------------------------------------------------------------------
 [pylithapp.mesh_generator]
@@ -87,25 +70,13 @@ pc_type = asm
 sub_pc_factor_shift_type = nonzero
 
 # Convergence parameters.
-ksp_rtol = 1.0e-10
-ksp_atol = 1.0e-20
+ksp_rtol = 1.0e-8
 ksp_max_it = 100
 ksp_gmres_restart = 50
 
-# Linear solver monitoring options.
-ksp_monitor = true
-#ksp_view = true
-ksp_converged_reason = true
-ksp_error_if_not_converged = true
-
 # Nonlinear solver monitoring options.
 snes_rtol = 1.0e-10
-snes_atol = 1.0e-9
 snes_max_it = 100
-snes_monitor = true
-#snes_view = true
-snes_converged_reason = true
-snes_error_if_not_converged = true
 
-# PETSc summary -- useful for performance information.
-log_summary = true
+
+# End of file
diff --git a/examples/debugging/step02.cfg b/examples/debugging/step02.cfg
index 0788860..90891dc 100644
--- a/examples/debugging/step02.cfg
+++ b/examples/debugging/step02.cfg
@@ -24,6 +24,11 @@
 # ----------------------------------------------------------------------
 # problem
 # ----------------------------------------------------------------------
+[pylithapp.problem.normalizer]
+length_scale = 1.0*km
+shear_modulus = 30.0*GPa
+relaxation_time = 2.0*year
+
 [pylithapp.timedependent.formulation.time_step]
 # Define the total time for the simulation and the default time step size.
 total_time = 0.0*s ; total time of simulation
@@ -88,17 +93,19 @@ fault = pylith.faults.FaultCohesiveKin
 # Set the parameters for the fault interface condition.
 [pylithapp.timedependent.interfaces.fault]
 # The label corresponds to the name of the nodeset in CUBIT.
-label = fault_ext
+label = fault
+edge = fault_edge
 
 # We must define the quadrature information for fault cells.
 # The fault cells are 2D (surface).
+quadrature.cell = pylith.feassemble.FIATLagrange
 quadrature.cell.dimension = 2
 
 # The slip time and final slip are defined in spatial databases.
 [pylithapp.timedependent.interfaces.fault.eq_srcs.rupture.slip_function]
 slip = spatialdata.spatialdb.UniformDB
 slip.label = Final slip
-slip.values = [lateral-slip, reverse-slip, fault-opening]
+slip.values = [left-lateral-slip, reverse-slip, fault-opening]
 slip.data = [+2.0*m, 0.0*m, 0.0*m]
 
 slip_time = spatialdata.spatialdb.UniformDB
diff --git a/examples/debugging/step03.cfg b/examples/debugging/step03.cfg
index 4e1895f..2af6962 100644
--- a/examples/debugging/step03.cfg
+++ b/examples/debugging/step03.cfg
@@ -72,7 +72,7 @@ label = face_xpos
 db_initial = spatialdata.spatialdb.UniformDB
 db_initial.label = Dirichlet BC on +x
 db_initial.values = [displacement-x,displacement-y,displacement-z]
-db_initial.data = [-1.0*m,3.0*m,0.0*m]
+db_initial.data = [-1.0*m,3.0*cm,0.0*m]
 
 [pylithapp.timedependent.bc.x_neg]
 bc_dof = [0, 1, 2]
@@ -80,7 +80,7 @@ label = face_xneg
 db_initial = spatialdata.spatialdb.UniformDB
 db_initial.label = Dirichlet BC on -x
 db_initial.values = [displacement-x,displacement-y,displacement-z]
-db_initial.data = [1.0*m,-3.0*m,0.0*m]
+db_initial.data = [1.0*m,-3.0*cm,0.0*m]
 
 [pylithapp.timedependent.bc.z_neg]
 bc_dof = [2]
@@ -105,8 +105,6 @@ label = fault_ext
 friction = pylith.friction.StaticFriction
 friction.label = Static friction
 
-zero_tolerance = 1.0e-12
-
 # We must define the quadrature information for fault cells.
 # The fault cells are 2D (surface).
 quadrature.cell = pylith.feassemble.FIATLagrange
@@ -125,11 +123,8 @@ friction.db_properties.data = [0.6,0.0*Pa]
 # NOTE: There are additional settings specific to fault friction.
 [pylithapp.petsc]
 
-ksp_rtol = 1.0e-20
-ksp_atol = 1.0e-10
-
-snes_rtol = 1.0e-20
-snes_atol = 1.0e-8
+ksp_atol = 1.0e-8
+snes_atol = 1.0e-6
 
 # Friction sensitivity solve used to compute the increment in slip
 # associated with changes in the Lagrange multiplier imposed by the
@@ -139,8 +134,6 @@ friction_sub_pc_factor_shift_type = nonzero
 friction_ksp_max_it = 25
 friction_ksp_gmres_restart = 30
 
-friction_ksp_converged_reason = true
-
 # ----------------------------------------------------------------------
 # output
 # ----------------------------------------------------------------------

