[cig-commits] r22105 - in short/3D/PyLith/trunk/doc/userguide: benchmarks/savageprescott/figs runpylith tutorials/3dhex8 tutorials/greensfns2d

[brad at geodynamics.org]

Author: brad
Date: 2013-05-17 18:12:14 -0700 (Fri, 17 May 2013)
New Revision: 22105

Modified:
   short/3D/PyLith/trunk/doc/userguide/benchmarks/savageprescott/figs/soln_profiles.pdf
   short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
   short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic.lyx
   short/3D/PyLith/trunk/doc/userguide/tutorials/greensfns2d/greensfns2d.lyx
Log:
Cleanup figures.

Modified: short/3D/PyLith/trunk/doc/userguide/benchmarks/savageprescott/figs/soln_profiles.pdf
===================================================================
(Binary files differ)

Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx	2013-05-18 00:23:27 UTC (rev 22104)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx	2013-05-18 01:12:14 UTC (rev 22105)
@@ -4922,7 +4922,7 @@
 \begin_inset Newline linebreak
 \end_inset
 
-DataWriterHDF5Mesh
+DataWriterHDF5
 \family default
 .
 \end_layout
@@ -5434,7 +5434,7 @@
 \end_layout
 
 \begin_layout LyX-Code
-writer = pylith.meshio.DataWriterHDF5ExtMesh
+writer = pylith.meshio.DataWriterHDF5Ext
 \end_layout
 
 \begin_layout LyX-Code

Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic.lyx	2013-05-18 00:23:27 UTC (rev 22104)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic.lyx	2013-05-18 01:12:14 UTC (rev 22105)
@@ -1,2501 +1,2492 @@
-#LyX 2.0 created this file. For more info see http://www.lyx.org/
-\lyxformat 413
-\begin_document
-\begin_header
-\textclass book
-\begin_preamble
-
-\end_preamble
-\use_default_options false
-\maintain_unincluded_children false
-\language english
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-\index Index
-\shortcut idx
-\color #008000
-\end_index
-\leftmargin 1in
-\topmargin 1in
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-\secnumdepth 3
-\tocdepth 3
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-\quotes_language english
-\papercolumns 1
-\papersides 1
-\paperpagestyle default
-\tracking_changes false
-\output_changes false
-\html_math_output 0
-\html_css_as_file 0
-\html_be_strict false
-\end_header
-
-\begin_body
-
-\begin_layout Subsection
-\begin_inset CommandInset label
-LatexCommand label
-name "sec:Tutorial-3d-hex8-quasistatic"
-
-\end_inset
-
-Quasi-Static Examples
-\end_layout
-
-\begin_layout Standard
-PyLith features discussed in this tutorial:
-\end_layout
-
-\begin_layout Itemize
-Quasi-static solution
-\end_layout
-
-\begin_layout Itemize
-Formatting timestamps of VTK output files
-\end_layout
-
-\begin_layout Itemize
-HDF5 output
-\end_layout
-
-\begin_layout Itemize
-Output of velocity field
-\end_layout
-
-\begin_layout Itemize
-Dirichlet displacement and velocity boundary conditions
-\end_layout
-
-\begin_layout Itemize
-Neumann traction boundary conditions and time-varying tractions
-\end_layout
-
-\begin_layout Itemize
-UniformDB spatial database
-\end_layout
-
-\begin_layout Itemize
-CompositeDB spatial database
-\end_layout
-
-\begin_layout Itemize
-Quasi-static fault rupture and fault creep
-\end_layout
-
-\begin_layout Itemize
-Multiple kinematic fault ruptures
-\end_layout
-
-\begin_layout Itemize
-Specifying more than one material
-\end_layout
-
-\begin_layout Itemize
-Nonlinear solver
-\end_layout
-
-\begin_layout Itemize
-Maxwell linear viscoelastic material
-\end_layout
-
-\begin_layout Itemize
-Power-law viscoelastic material
-\end_layout
-
-\begin_layout Itemize
-Drucker-Prager elastoplastic material
-\end_layout
-
-\begin_layout Itemize
-Adaptive time stepping
-\end_layout
-
-\begin_layout Subsubsection
-Overview
-\end_layout
-
-\begin_layout Standard
-This set of examples describes a set of quasi-static problems for PyLith.
- These quasi-static problems primarily demonstrate the usage of time-dependent
- boundary conditions and fault slip, as well as different rheologies.
- Some of the examples also demonstrate the usage of the nonlinear solver,
- which is required by the nonlinear rheologies (power-law viscoelastic and
- Drucker-Prager elastoplastic).
- Some of the examples also demonstrate the usage of HDF5 output, which is
- an alternative to the default VTK output.
- All of the examples are contained in the directory 
-\family typewriter
-examples/3d/hex8
-\family default
-, and the corresponding 
-\family typewriter
-.cfg
-\family default
- files are 
-\family typewriter
-step04.cfg
-\family default
-, 
-\family typewriter
-step05.cfg
-\family default
-, 
-\family typewriter
-step06.cfg
-\family default
-, 
-\family typewriter
-step07.cfg
-\family default
-, 
-\family typewriter
-step08.cfg
-\family default
-, and 
-\family typewriter
-step09.cfg
-\family default
-.
- Each example may be run as follows:
-\end_layout
-
-\begin_layout LyX-Code
-pylith stepXX.cfg
-\end_layout
-
-\begin_layout Standard
-This will cause PyLith to read the default parameters in 
-\family typewriter
-pylithapp.cfg
-\family default
-, and then override or augment them with the additional parameters in the
- 
-\family typewriter
-stepXX.cfg
-\family default
- file.
- Each 
-\family typewriter
-.cfg
-\family default
- file is extensively documented, to provide detailed information on the
- various parameters.
-\end_layout
-
-\begin_layout Subsubsection
-Step04 - Pure Dirichlet Velocity Boundary Conditions
-\end_layout
-
-\begin_layout Standard
-The 
-\family typewriter
-step04.cfg
-\family default
- file defines a problem with x-displacements fixed at zero on the positive
- and negative x-faces while velocity boundary conditions are applied in
- the y-directions on the same faces, yielding a left-lateral sense of movement.
- The bottom (negative z) boundary is held fixed in the z-direction.
- We also use a Maxwell viscoelastic material for the lower crust, and the
- simulation is run for 200 years using a constant time-step size of 20 years.
- The default time stepping behavior is 
-\family typewriter
-TimeStepUniform
-\family default
-.
- We retain that behavior for this problem and provide the total simulation
- time and the time-step size:
-\end_layout
-
-\begin_layout LyX-Code
-# Change the total simulation time to 200 years, and use a constant time
-\end_layout
-
-\begin_layout LyX-Code
-# step size of 20 years.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.implicit.time_step]
-\end_layout
-
-\begin_layout LyX-Code
-total_time = 200.0*year
-\end_layout
-
-\begin_layout LyX-Code
-dt = 20.0*year 
-\end_layout
-
-\begin_layout Standard
-We then change the material type of the lower crust, provide a spatial database
- from which to obtain the material properties (using the default 
-\family typewriter
-SimpleDB
-\family default
-), and request additional output information for the material:
-\end_layout
-
-\begin_layout LyX-Code
-# Change material type of lower crust to Maxwell viscoelastic.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent]
-\end_layout
-
-\begin_layout LyX-Code
-materials.lower_crust = pylith.materials.MaxwellIsotropic3D
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# Provide a spatial database from which to obtain property values.
-\end_layout
-
-\begin_layout LyX-Code
-# Since there are additional properties and state variables for the Maxwell
-\end_layout
-
-\begin_layout LyX-Code
-# model, we explicitly request that they be output.
- Properties are named in
-\end_layout
-
-\begin_layout LyX-Code
-# cell_info_fields and state variables are named in cell_data_fields.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.materials.lower_crust]
-\end_layout
-
-\begin_layout LyX-Code
-db_properties.iohandler.filename = spatialdb/mat_maxwell.spatialdb
-\end_layout
-
-\begin_layout LyX-Code
-output.cell_info_fields = [density,mu,lambda,maxwell_time]
-\end_layout
-
-\begin_layout LyX-Code
-output.cell_data_fields = [total_strain,stress,viscous_strain]
-\end_layout
-
-\begin_layout Standard
-Note that the default 
-\family typewriter
-output.cell_info_fields
-\family default
- are those corresponding to an elastic material (
-\family typewriter
-density
-\family default
-, 
-\family typewriter
-mu
-\family default
-, 
-\family typewriter
-lambda
-\family default
-), and the default 
-\family typewriter
-output.cell_data_fields
-\family default
- are 
-\family typewriter
-total_strain
-\family default
- and 
-\family typewriter
-stress
-\family default
-.
- For materials other than elastic, there are generally additional material
- properties and state variables, and the appropriate additional fields must
- be specifically requested for each material type.
-\end_layout
-
-\begin_layout Standard
-This example has no displacements in the elastic solution (t = 0), so we
- retain the default 
-\family typewriter
-ZeroDispDB
-\family default
- for all instances of 
-\family typewriter
-db_initial
-\family default
-.
- To apply the velocity boundary conditions, we must specify 
-\family typewriter
-db_rate
-\family default
-, which is zero by default.
- We use a 
-\family typewriter
-UniformDB
-\family default
- to assign the velocities:
-\end_layout
-
-\begin_layout LyX-Code
-# +x face
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.bc.x_pos]
-\end_layout
-
-\begin_layout LyX-Code
-bc_dof = [0, 1]
-\end_layout
-
-\begin_layout LyX-Code
-label = face_xpos
-\end_layout
-
-\begin_layout LyX-Code
-db_initial.label = Dirichlet BC on +x
-\end_layout
-
-\begin_layout LyX-Code
-db_rate = spatialdata.spatialdb.UniformDB
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.label = Dirichlet rate BC on +x
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.values = [displacement-rate-x,displacement-rate-y,rate-start-time]
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.data = [0.0*cm/year,1.0*cm/year,0.0*year]
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# -x face
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.bc.x_neg]
-\end_layout
-
-\begin_layout LyX-Code
-bc_dof = [0, 1]
-\end_layout
-
-\begin_layout LyX-Code
-label = face_xneg
-\end_layout
-
-\begin_layout LyX-Code
-db_initial.label = Dirichlet BC on -x
-\end_layout
-
-\begin_layout LyX-Code
-db_rate = spatialdata.spatialdb.UniformDB
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.label = Dirichlet rate BC on +x
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.values = [displacement-rate-x,displacement-rate-y,rate-start-time]
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.data = [0.0*cm/year,-1.0*cm/year,0.0*year]
-\end_layout
-
-\begin_layout Standard
-Note that 
-\family typewriter
-db_rate
-\family default
- requires a start time, which allows the condition to be applied at any
- time during the simulation.
- For this example, we start the velocity boundary conditions at t = 0.
-\end_layout
-
-\begin_layout Standard
-Finally, we must provide information on VTK output.
- This is slightly more complicated than the static case, because we must
- decide the frequency with which output occurs for each output manager.
- We also assign a more user-friendly format to the output file time stamp,
- and we request that the time stamp is in units of 1 year (rather than the
- default value of seconds):
-\end_layout
-
-\begin_layout LyX-Code
-# Give basename for VTK domain output of solution over domain.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.problem.formulation.output.domain]
-\end_layout
-
-\begin_layout LyX-Code
-# We specify that output occurs in terms of a given time frequency, and
-\end_layout
-
-\begin_layout LyX-Code
-# ask for output every 40 years.
- The time stamps of the output files are
-\end_layout
-
-\begin_layout LyX-Code
-# in years (rather than the default of seconds), and we give a format for
-\end_layout
-
-\begin_layout LyX-Code
-# the time stamp.
-\end_layout
-
-\begin_layout LyX-Code
-output_freq = time_step
-\end_layout
-
-\begin_layout LyX-Code
-time_step = 40.0*year
-\end_layout
-
-\begin_layout LyX-Code
-writer.filename = output/step04.vtk
-\end_layout
-
-\begin_layout LyX-Code
-writer.time_format = %04.0f
-\end_layout
-
-\begin_layout LyX-Code
-writer.time_constant = 1.0*year
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# Give basename for VTK domain output of solution over ground surface.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.problem.formulation.output.subdomain]
-\end_layout
-
-\begin_layout LyX-Code
-# Name of nodeset for ground surface.
-\end_layout
-
-\begin_layout LyX-Code
-label = face_zpos
-\end_layout
-
-\begin_layout LyX-Code
-# We keep the default output frequency behavior (skip every n steps), and
-\end_layout
-
-\begin_layout LyX-Code
-# ask to skip 0 steps between output, so that we get output every time step.
-\end_layout
-
-\begin_layout LyX-Code
-skip = 0
-\end_layout
-
-\begin_layout LyX-Code
-writer.filename = output/step04-groundsurf.vtk
-\end_layout
-
-\begin_layout LyX-Code
-writer.time_format = %04.0f
-\end_layout
-
-\begin_layout LyX-Code
-writer.time_constant = 1.0*year
-\end_layout
-
-\begin_layout Standard
-We provide similar output information for the two materials (
-\family typewriter
-upper_crust
-\family default
- and 
-\family typewriter
-lower_crust
-\family default
-).
- Note that for the domain output, we requested output in terms of a given
- time frequency, while for the subdomain we requested output in terms of
- number of time steps.
- When we have run the simulation, the output VTK files will be contained
- in 
-\family typewriter
-examples/3d/hex8/output
-\family default
- (all with a prefix of 
-\family typewriter
-step04
-\family default
-).
- Results using ParaView are shown in Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:step04-displ-t200"
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
-	filename figs/step04-displ-t200.jpg
-	lyxscale 50
-	width 10cm
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Plain Layout
-\begin_inset Caption
-
-\begin_layout Plain Layout
-Displacement field for example step04 at t = 200 years visualized using
- ParaView.
- The mesh has been distorted by the computed displacements (magnified by
- 500), and the vectors show the computed displacements.
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:step04-displ-t200"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsubsection
-Step05 - Time-Varying Dirichlet and Neumann Boundary Conditions
-\end_layout
-
-\begin_layout Standard
-The 
-\family typewriter
-step05.cfg
-\family default
- file describes a problem with time-varying Dirichlet and Neumann boundary
- conditions.
- The example is similar to example step04, with a few important differences:
-\end_layout
-
-\begin_layout Itemize
-The Dirichlet boundary conditions on the negative x-face include an initial
- displacement (applied in the elastic solution), as well as a constant velocity.
-\end_layout
-
-\begin_layout Itemize
-Neumann (traction) boundary conditions are applied in the negative x-direction
- on the positive x-face, giving a compressive stress.
- An initial traction is applied in the elastic solution, and then at t =
- 100 years it begins decreasing linearly until it reaches zero at the end
- of the simulation (t = 200 years).
-\end_layout
-
-\begin_layout Standard
-We again use a Maxwell viscoelastic material for the lower crust.
-\end_layout
-
-\begin_layout Standard
-For the boundary conditions, we must first change the boundary condition
- type for the positive x-face from the default Dirichlet to Neumann:
-\end_layout
-
-\begin_layout LyX-Code
-# +x face -- first change bc type to Neumann
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.bc]
-\end_layout
-
-\begin_layout LyX-Code
-x_pos = pylith.bc.Neumann 
-\end_layout
-
-\begin_layout Standard
-We provide quadrature information for this face as we did for example step02.
- We then use a 
-\family typewriter
-UniformDB
-\family default
- for both the initial tractions as well as the traction rates.
- We provide a start time of 100 years for the traction rates, and use a
- rate of 0.01 MPa/year, so that by the end of 200 years we have completely
- cancelled the initial traction of -1 MPa:
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.bc.x_pos]
-\end_layout
-
-\begin_layout LyX-Code
-# First specify a UniformDB for the initial tractions, along with the values.
-\end_layout
-
-\begin_layout LyX-Code
-db_initial = spatialdata.spatialdb.UniformDB
-\end_layout
-
-\begin_layout LyX-Code
-db_initial.label = Neumann BC on +x
-\end_layout
-
-\begin_layout LyX-Code
-db_initial.values = [traction-shear-horiz,traction-shear-vert,traction-normal]
-\end_layout
-
-\begin_layout LyX-Code
-db_initial.data = [0.0*MPa,0.0*MPa,-1.0*MPa]
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# Provide information on traction rates.
-\end_layout
-
-\begin_layout LyX-Code
-db_rate = spatialdata.spatialdb.UniformDB
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.label = Neumann rate BC on +x
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.values = [traction-rate-shear-horiz,traction-rate-shear-vert,
-\begin_inset Newline newline
-\end_inset
-
-traction-rate-normal,rate-start-time]
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.data = [0.0*MPa/year,0.0*MPa/year,0.01*MPa/year,100.0*year]
-\end_layout
-
-\begin_layout Standard
-The boundary conditions on the negative x-face are analogous, but we are
- instead using Dirichlet boundary conditions, and the initial displacement
- is in the same direction as the applied velocities:
-\end_layout
-
-\begin_layout LyX-Code
-# -x face
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.bc.x_neg]
-\end_layout
-
-\begin_layout LyX-Code
-bc_dof = [0, 1]
-\end_layout
-
-\begin_layout LyX-Code
-label = face_xneg
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# Initial displacements.
-\end_layout
-
-\begin_layout LyX-Code
-db_initial = spatialdata.spatialdb.UniformDB
-\end_layout
-
-\begin_layout LyX-Code
-db_initial.label = Dirichlet BC on -x
-\end_layout
-
-\begin_layout LyX-Code
-db_initial.values = [displacement-x,displacement-y]
-\end_layout
-
-\begin_layout LyX-Code
-db_initial.data = [0.0*cm,-0.5*cm]
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# Velocities.
-\end_layout
-
-\begin_layout LyX-Code
-db_rate = spatialdata.spatialdb.UniformDB
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.label = Dirichlet rate BC on -x
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.values = [displacement-rate-x,displacement-rate-y,rate-start-time]
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.data = [0.0*cm/year,-1.0*cm/year,0.0*year]
-\end_layout
-
-\begin_layout Standard
-The boundary conditions on the negative z-face are supplied in the same
- manner as for example step04.
- When we have run the simulation, the output VTK files will be contained
- in 
-\family typewriter
-examples/3d/hex8/output
-\family default
- (all with a prefix of 
-\family typewriter
-step05
-\family default
-).
- Results using ParaView are shown in Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:step05-displ-t40"
-
-\end_inset
-
-.
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
-	filename figs/step05-displ-t40.jpg
-	lyxscale 50
-	width 10cm
-
-\end_inset
-
-
-\begin_inset Caption
-
-\begin_layout Plain Layout
-Displacement field for example step05 at t = 40 years visualized using ParaView.
- The mesh has been distorted by the computed displacements (magnified by
- 500), and the vectors show the computed displacements.
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:step05-displ-t40"
-
-\end_inset
-
-.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsubsection
-Step06 - Dirichlet Boundary Conditions with Time-Dependent Kinematic Fault
- Slip
-\end_layout
-
-\begin_layout Standard
-The 
-\family typewriter
-step06.cfg
-\family default
- file defines a problem with Dirichlet (displacement) boundary conditions
- corresponding to zero x- and y-displacements applied on the negative and
- positive x-faces and a vertical fault that includes multiple earthquake
- ruptures as well as steady fault creep.
- The upper (locked) portion of the fault has 4 m of left-lateral slip every
- 200 years, while the lower (creeping) portion of the fault slips at a steady
- rate of 2 cm/year.
- The problem bears some similarity to the strike-slip fault model of Savage
- and Prescott 
-\begin_inset CommandInset citation
-LatexCommand cite
-key "Savage:Prescott:1978"
-
-\end_inset
-
-, except that the fault creep extends through the viscoelastic portion of
- the domain, and the far-field displacement boundary conditions are held
- fixed.
-\end_layout
-
-\begin_layout Standard
-In this example and the remainder of the examples in this section, we change
- the time stepping behavior from the default 
-\family typewriter
-TimeStepUniform
-\family default
- to 
-\family typewriter
-TimeStepAdapt
-\family default
-.
- For adaptive time stepping, we provide the maximum permissible time-step
- size, along with a stability factor.
- The stability factor controls the time-step size relative to the stable
- time-step size provided by the different materials in the model.
- A 
-\family typewriter
-stability_factor
-\family default
- of 1.0 means we should use the stable time-step size, while a 
-\family typewriter
-stability_factor
-\family default
- greater than 1.0 means we want to use a smaller time-step size.
- A 
-\family typewriter
-stability_factor
-\family default
- less than 1.0 allows time-step sizes greater than the stable time-step size,
- which may provide inaccurate results.
- The adaptive time stepping information is provided as:
-\end_layout
-
-\begin_layout LyX-Code
-# Change time stepping algorithm from uniform time step, to adaptive
-\end_layout
-
-\begin_layout LyX-Code
-# time stepping.
-\end_layout
-
-\begin_layout LyX-Code
-time_step = pylith.problems.TimeStepAdapt
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# Change the total simulation time to 700 years, and set the maximum time
-\end_layout
-
-\begin_layout LyX-Code
-# step size to 10 years.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.implicit.time_step]
-\end_layout
-
-\begin_layout LyX-Code
-total_time = 700.0*year
-\end_layout
-
-\begin_layout LyX-Code
-max_dt = 10.0*year
-\end_layout
-
-\begin_layout LyX-Code
-stability_factor = 1.0 ; use time step equal to stable value from materials
-\end_layout
-
-\begin_layout Standard
-In this example and the remainder of the examples in this section, we also
- make use of HDF5 output rather than the default VTK output.
- HDF5 output is a new feature beginning with PyLith version 1.6, and it is
- much more efficient with the additional advantage that multiple time steps
- can be contained in a single file.
- PyLith also produces Xdmf files describing the contents of the HDF5 files,
- which allows the files to be read easily by applications such as ParaView.
- Since VTK output is still the default, we must change the value from the
- default.
- Also note that the filename suffix is 
-\family typewriter
-.h5
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-# Give basename for output of solution over domain.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.problem.formulation.output.domain]
-\end_layout
-
-\begin_layout LyX-Code
-# We specify that output occurs in terms of a given time frequency, and
-\end_layout
-
-\begin_layout LyX-Code
-# ask for output every 50 years.
-\end_layout
-
-\begin_layout LyX-Code
-output_freq = time_step
-\end_layout
-
-\begin_layout LyX-Code
-time_step = 50.0*year
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# We are using HDF5 output so we must change the default writer.
-\end_layout
-
-\begin_layout LyX-Code
-writer = pylith.meshio.DataWriterHDF5
-\end_layout
-
-\begin_layout LyX-Code
-writer.filename = output/step06.h5  
-\end_layout
-
-\begin_layout Standard
-Note that we no longer need the 
-\family typewriter
-writer.time_format
-\family default
- or 
-\family typewriter
-writer.time_constant
-\family default
- properties, since all time steps are contained in a single file.
- The HDF5 writer does not have these properties, so if we attempt to define
- them an error will result.
-\end_layout
-
-\begin_layout Standard
-We also set the writer for other output as well, since it is not the default.
- For subdomain output we use:
-\end_layout
-
-\begin_layout LyX-Code
-# Give basename for output of solution over ground surface.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.problem.formulation.output.subdomain]
-\end_layout
-
-\begin_layout LyX-Code
-# Name of nodeset for ground surface.
-\end_layout
-
-\begin_layout LyX-Code
-label = face_zpos
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# We keep the default output frequency behavior (skip every n steps), and
-\end_layout
-
-\begin_layout LyX-Code
-# ask to skip 0 steps between output, so that we get output every time step.
-\end_layout
-
-\begin_layout LyX-Code
-# We again switch the writer to produce HDF5 output.
-\end_layout
-
-\begin_layout LyX-Code
-skip = 0
-\end_layout
-
-\begin_layout LyX-Code
-writer = pylith.meshio.DataWriterHDF5
-\end_layout
-
-\begin_layout LyX-Code
-writer.filename = output/step06-groundsurf.h5  
-\end_layout
-
-\begin_layout Standard
-For fault output we use:
-\end_layout
-
-\begin_layout LyX-Code
-# Give basename for fault rupture output.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.problem.interfaces.fault.output]
-\end_layout
-
-\begin_layout LyX-Code
-# We keep the default output frequency behavior (skip every n steps), and
-\end_layout
-
-\begin_layout LyX-Code
-# ask to skip 0 steps between output, so that we get output every time step.
-\end_layout
-
-\begin_layout LyX-Code
-# We again switch the writer to produce HDF5 output.
-\end_layout
-
-\begin_layout LyX-Code
-skip = 0
-\end_layout
-
-\begin_layout LyX-Code
-writer = pylith.meshio.DataWriterHDF5
-\end_layout
-
-\begin_layout LyX-Code
-writer.filename = output/step06-fault.h5
-\end_layout
-
-\begin_layout Standard
-\begin_inset Newline newline
-\end_inset
-
-pylith.meshio.DataWriterHDF5
-\family default
- for fault output.
-\end_layout
-
-\begin_layout Standard
-Due to the simplicity of the boundary conditions, we are able to use the
- default 
-\family typewriter
-ZeroDispBC
-\family default
- for the positive and negative x-faces, as well as the negative z-face.
- As for example step03, we define a fault interface, we identify the nodeset
- corresponding to the fault, and we provide quadrature information for the
- fault.
- We then define an array of earthquake sources and provide an origin time
- for each:
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.interfaces.fault]
-\end_layout
-
-\begin_layout LyX-Code
-# Set earthquake sources to an array consisting of creep and 3 ruptures.
-\end_layout
-
-\begin_layout LyX-Code
-eq_srcs = [creep,one,two,three]
-\end_layout
-
-\begin_layout LyX-Code
-eq_srcs.creep.origin_time = 00.0*year
-\end_layout
-
-\begin_layout LyX-Code
-eq_srcs.one.origin_time = 200.0*year
-\end_layout
-
-\begin_layout LyX-Code
-eq_srcs.two.origin_time = 400.0*year
-\end_layout
-
-\begin_layout LyX-Code
-eq_srcs.three.origin_time = 600.0*year
-\end_layout
-
-\begin_layout Standard
-Note that the creep begins at t = 0 years, while the ruptures (
-\family typewriter
-one
-\family default
-, 
-\family typewriter
-two
-\family default
-, 
-\family typewriter
-three
-\family default
-) occur at regular intervals of 200 years.
- We retain the default 
-\family typewriter
-StepSlipFn
-\family default
- for the ruptures.
- Each of the ruptures has the same amount of slip, and slip occurs simultaneousl
-y for the entire rupture region, so we can use the same 
-\family typewriter
-SimpleDB
-\family default
- files providing slip and slip time for each rupture:
-\end_layout
-
-\begin_layout LyX-Code
-# Define slip and origin time for first rupture.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.interfaces.fault.eq_srcs.one.slip_function]
-\end_layout
-
-\begin_layout LyX-Code
-slip.iohandler.filename = spatialdb/finalslip_rupture.spatialdb
-\end_layout
-
-\begin_layout LyX-Code
-slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# Define slip and origin time for second rupture.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.interfaces.fault.eq_srcs.two.slip_function]
-\end_layout
-
-\begin_layout LyX-Code
-slip.iohandler.filename = spatialdb/finalslip_rupture.spatialdb
-\end_layout
-
-\begin_layout LyX-Code
-slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# Define slip and origin time for third rupture.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.interfaces.fault.eq_srcs.three.slip_function]
-\end_layout
-
-\begin_layout LyX-Code
-slip.iohandler.filename = spatialdb/finalslip_rupture.spatialdb
-\end_layout
-
-\begin_layout LyX-Code
-slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
-\end_layout
-
-\begin_layout Standard
-For the creep source, we change the slip function to 
-\family typewriter
-ConstRateSlipFn
-\family default
-, and we use a 
-\family typewriter
-SimpleDB
-\family default
- for both the slip time and the slip rate:
-\end_layout
-
-\begin_layout LyX-Code
-# Define slip rate and origin time for fault creep.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.interfaces.fault.eq_srcs.creep]
-\end_layout
-
-\begin_layout LyX-Code
-slip_function = pylith.faults.ConstRateSlipFn
-\end_layout
-
-\begin_layout LyX-Code
-slip_function.slip_rate.iohandler.filename = spatialdb/sliprate_creep.spatialdb
-\end_layout
-
-\begin_layout LyX-Code
-slip_function.slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
-\end_layout
-
-\begin_layout Standard
-For all earthquake sources we provide both an 
-\family typewriter
-origin_time
-\family default
- and a 
-\family typewriter
-slip_function.slip_time
-\family default
-.
- The first provides the starting time for the entire earthquake source,
- while the second provides any spatial variation in the slip time with respect
- to the 
-\family typewriter
-origin_time
-\family default
- (if any).
- Since there are multiple earthquake sources of different types, there are
- a number of additional fault information fields available for output.
- We add these additional fields' output to the fault information file:
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.interfaces.fault]
-\end_layout
-
-\begin_layout LyX-Code
-output.vertex_info_fields = [normal_dir,strike_dir,dip_dir,final_slip_creep,
-\begin_inset Newline newline
-\end_inset
-
-final_slip_one,final_slip_two,final_slip_three,slip_time_creep,slip_time_one,
-\begin_inset Newline newline
-\end_inset
-
-slip_time_two,slip_time_three]
-\end_layout
-
-\begin_layout Standard
-This additional information will be contained in file 
-\family typewriter
-step06-fault_info.h5
-\family default
-.
- It will contain final slip information for each earthquake source along
- with slip time information.
- When we have run the simulation, the output HDF5 and Xdmf files will be
- contained in 
-\family typewriter
-examples/3d/hex8/output
-\family default
- (all with a prefix of 
-\family typewriter
-step06
-\family default
-).
- To open the files in ParaView, the Xdmf (
-\family typewriter
-.xmf
-\family default
-) files should be opened, as these files describe the HDF5 data structure.
- Results using ParaView are shown in Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:step06-displ-t300"
-
-\end_inset
-
-.
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
-	filename figs/step06-displ-t300.jpg
-	lyxscale 50
-	width 10cm
-
-\end_inset
-
-
-\begin_inset Caption
-
-\begin_layout Plain Layout
-Displacement field for example step06 at t = 300 years visualized using
- ParaView.
- The mesh has been distorted by the computed displacements (magnified by
- 500), and the vectors show the computed displacements.
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:step06-displ-t300"
-
-\end_inset
-
-.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsubsection
-Step07 - Dirichlet Velocity Boundary Conditions with Time-Dependent Kinematic
- Fault Slip
-\end_layout
-
-\begin_layout Standard
-In step07 we add velocity boundary conditions in the positive and negative
- y-directions on the positive and negative x-faces, so that the external
- boundaries keep pace with the average fault slip.
- This problem is nearly identical to the strike-slip fault model of Savage
- and Prescott 
-\begin_inset CommandInset citation
-LatexCommand cite
-key "Savage:Prescott:1978"
-
-\end_inset
-
-, except that the fault creep extends through the viscoelastic portion of
- the domain.
-\end_layout
-
-\begin_layout Standard
-We use the default 
-\family typewriter
-ZeroDispBC
-\family default
- for the initial displacements on the positive and negative x-faces, as
- well as the negative z-face.
- For the velocities on the positive and negative x-faces, we use a 
-\family typewriter
-UniformDB
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-# +x face
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.bc.x_pos]
-\end_layout
-
-\begin_layout LyX-Code
-bc_dof = [0, 1]
-\end_layout
-
-\begin_layout LyX-Code
-label = face_xpos
-\end_layout
-
-\begin_layout LyX-Code
-db_initial.label = Dirichlet BC on +x
-\end_layout
-
-\begin_layout LyX-Code
-db_rate = spatialdata.spatialdb.UniformDB
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.label = Dirichlet rate BC on +x
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.values = [displacement-rate-x,displacement-rate-y,rate-start-time]
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.data = [0.0*cm/year,1.0*cm/year,0.0*year]
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# -x face
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.bc.x_neg]
-\end_layout
-
-\begin_layout LyX-Code
-bc_dof = [0, 1]
-\end_layout
-
-\begin_layout LyX-Code
-label = face_xneg
-\end_layout
-
-\begin_layout LyX-Code
-db_initial.label = Dirichlet BC on -x
-\end_layout
-
-\begin_layout LyX-Code
-db_rate = spatialdata.spatialdb.UniformDB
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.label = Dirichlet rate BC on +x
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.values = [displacement-rate-x,displacement-rate-y,rate-start-time]
-\end_layout
-
-\begin_layout LyX-Code
-db_rate.data = [0.0*cm/year,-1.0*cm/year,0.0*year]
-\end_layout
-
-\begin_layout Standard
-The fault definition information is identical to example 
-\family typewriter
-step06
-\family default
-.
- In previous examples, we have just used the default output for the domain
- and subdomain (ground surface), which includes the displacements.
- In many cases, it is also useful to include the velocities.
- PyLith provides this information, computing the velocities for the current
- time step as the difference between the current displacements and the displacem
-ents from the previous time step, divided by the time-step size.
- This is more accurate than computing the velocities from the displacement
- field output that has been decimated in time.
- We can obtain this information by explicitly requesting it in 
-\family typewriter
-vertex_data_fields
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-# Give basename for output of solution over domain.
-\begin_inset Newline newline
-\end_inset
-
-[pylithapp.problem.formulation.output.domain]
-\end_layout
-
-\begin_layout LyX-Code
-# We specify that output occurs in terms of a given time frequency, and
-\end_layout
-
-\begin_layout LyX-Code
-# ask for output every 50 years.
-\end_layout
-
-\begin_layout LyX-Code
-# We also request velocity output in addition to displacements.
-\begin_inset Newline newline
-\end_inset
-
-vertex_data_fields = [displacement,velocity]
-\end_layout
-
-\begin_layout LyX-Code
-output_freq = time_step
-\end_layout
-
-\begin_layout LyX-Code
-time_step = 50.0*year
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# We are using HDF5 output so we must change the default writer.
-\end_layout
-
-\begin_layout LyX-Code
-writer = pylith.meshio.DataWriterHDF5
-\end_layout
-
-\begin_layout LyX-Code
-writer.filename = output/step07.h5
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# Give basename for output of solution over ground surface.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.problem.formulation.output.subdomain]
-\end_layout
-
-\begin_layout LyX-Code
-# Name of nodeset for ground surface.
-\end_layout
-
-\begin_layout LyX-Code
-label = face_zpos
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# We also request velocity output in addition to displacements.
-\end_layout
-
-\begin_layout LyX-Code
-vertex_data_fields = [displacement,velocity]
-\end_layout
-
-\begin_layout LyX-Code
-# We keep the default output frequency behavior (skip every n steps), and
-\end_layout
-
-\begin_layout LyX-Code
-# ask to skip 0 steps between output, so that we get output every time step.
-\end_layout
-
-\begin_layout LyX-Code
-skip = 0
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout LyX-Code
-# We again switch the writer to produce HDF5 output.
-\end_layout
-
-\begin_layout LyX-Code
-writer = pylith.meshio.DataWriterHDF5
-\end_layout
-
-\begin_layout LyX-Code
-writer.filename = output/step07-groundsurf.h5
-\end_layout
-
-\begin_layout Standard
-When we have run the simulation, the output HDF5 and Xdmf files will be
- contained in 
-\family typewriter
-examples/3d/hex8/output
-\family default
- (all with a prefix of 
-\family typewriter
-step07
-\family default
-).
- As for example step06, make sure to open the 
-\family typewriter
-.xmf
-\family default
- files rather than the 
-\family typewriter
-.h5
-\family default
- files.
- Results using ParaView are shown in Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:step07-displ-vel-t300"
-
-\end_inset
-
-.
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
-	filename figs/step07-displ-vel-t300.jpg
-	lyxscale 50
-	width 10cm
-
-\end_inset
-
-
-\begin_inset Caption
-
-\begin_layout Plain Layout
-Displacement field (color contours) and velocity field (vectors) for example
- step07 at t = 300 years visualized using ParaView.
- The mesh has been distorted by the computed displacements (magnified by
- 500), and the vectors show the computed velocities.
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:step07-displ-vel-t300"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsubsection
-Step08 - Dirichlet Velocity Boundary Conditions with Time-Dependent Kinematic
- Fault Slip and Power-Law Rheology
-\begin_inset CommandInset label
-LatexCommand label
-name "sub:Tutorial-Step08-Power-law"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-The 
-\family typewriter
-step08.cfg
-\family default
- file defines a problem that is identical to example step07, except the
- the lower crust is composed of a power-law viscoelastic material.
- Since the material behavior is now nonlinear, we must use the nonlinear
- solver:
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent]
-\end_layout
-
-\begin_layout LyX-Code
-# For this problem we must switch to a nonlinear solver.
-\end_layout
-
-\begin_layout LyX-Code
-implicit.solver = pylith.problems.SolverNonlinear
-\end_layout
-
-\begin_layout Standard
-Although we have not discussed the PyLith PETSc settings previously, note
- that the use of the nonlinear solver may require additional options if
- we wish to override the defaults.
- These settings are contained in 
-\family typewriter
-pylithapp.cfg
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.petsc]
-\end_layout
-
-\begin_layout LyX-Code
-# Nonlinear solver monitoring options.
-\end_layout
-
-\begin_layout LyX-Code
-snes_rtol = 1.0e-8
-\end_layout
-
-\begin_layout LyX-Code
-snes_atol = 1.0e-12
-\end_layout
-
-\begin_layout LyX-Code
-snes_max_it = 100
-\end_layout
-
-\begin_layout LyX-Code
-snes_monitor = true
-\end_layout
-
-\begin_layout LyX-Code
-snes_view = true
-\end_layout
-
-\begin_layout LyX-Code
-snes_converged_reason = true
-\end_layout
-
-\begin_layout Standard
-These settings are ignored unless we are using the nonlinear solver.
-\end_layout
-
-\begin_layout Standard
-When setting the physical properties for the power-law material in PyLith,
- the parameters (see Section 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "sub:Power-Law-Maxwell-Viscoelastic"
-
-\end_inset
-
-) do not generally correspond to the values provided in laboratory results.
- PyLith includes a utility code, 
-\family typewriter
-powerlaw_gendb.py
-\family default
-, to simplify the process of using laboratory results with PyLith.
- This utility code is installed in the same location as PyLith.
- An example of how to use it is in 
-\family typewriter
-examples/3d/hex8/spatialdb/powerlaw
-\family default
-.
- The user must provide a spatial database defining the spatial distribution
- of laboratory-derived parameters (contained in 
-\family typewriter
-powerlaw_params.
-\begin_inset Newline linebreak
-\end_inset
-
-spatialdb
-\family default
-), another spatial database defining the temperature field in degrees K
- (contained in 
-\family typewriter
-temperature.spatialdb
-\family default
-), and a set of points for which values are desired (
-\family typewriter
-powerlaw_points.txt
-\family default
-).
- The parameters for the code are defined in 
-\family typewriter
-powerlaw_gendb.cfg
-\family default
-.
- The properties expected by PyLith are 
-\family typewriter
-reference_strain_rate
-\family default
-, 
-\family typewriter
-reference_stress
-\family default
-, and 
-\family typewriter
-power_law_exponent
-\family default
-.
- The user must specify either 
-\family typewriter
-reference_strain_rate
-\family default
- or 
-\family typewriter
-reference_stress
-\family default
- so that 
-\family typewriter
-powerlaw_gendb.py
-\family default
- can compute the other property.
- Default values of 1.0e-6 1/s and 1 MPa are provided.
- In this example, the same database was used for all parameters, and a separate
- database was used to define the temperature distribution.
- In practice, the user can provide any desired thermal model to provide
- the spatial database for the temperature.
- In this example, a simple 1D (vertically-varying) distribution was used.
- The utility code can be used by simply executing it from the 
-\family typewriter
-examples/3d/hex8/spatialdb/powerlaw
-\family default
- directory:
-\end_layout
-
-\begin_layout LyX-Code
-powerlaw_gendb.py
-\end_layout
-
-\begin_layout Standard
-This code will automatically read the parameters in 
-\family typewriter
-powerlaw_gendb.cfg
-\family default
- in creating the file
-\begin_inset Newline newline
-\end_inset
-
- 
-\family typewriter
-examples/3d/hex8/spatialdb/mat_powerlaw.spatialdb
-\family default
-.
-\end_layout
-
-\begin_layout Standard
-We first change the material type of the lower crust to 
-\family typewriter
-PowerLaw3D
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-# Change material type of lower crust to power-law viscoelastic.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent]
-\end_layout
-
-\begin_layout LyX-Code
-materials.lower_crust = pylith.materials.PowerLaw3D
-\end_layout
-
-\begin_layout Standard
-In many cases, it is useful to obtain the material properties from two different
- sources.
- For example, the elastic properties may come from a seismic velocity model
- while the viscous properties may be derived from a thermal model.
- In such a case we can use a 
-\family typewriter
-CompositeDB
-\family default
-, which allows a different spatial database to be used for a subset of the
- properties.
- We do this as follows:
-\end_layout
-
-\begin_layout LyX-Code
-# Provide a spatial database from which to obtain property values.
-\end_layout
-
-\begin_layout LyX-Code
-# In this case, we prefer to obtain the power-law properties from one
-\end_layout
-
-\begin_layout LyX-Code
-# database and the elastic properties from another database, so we use
-\end_layout
-
-\begin_layout LyX-Code
-# a CompositeDB.
- Each part of the CompositeDB is a SimpleDB.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.materials.lower_crust]
-\end_layout
-
-\begin_layout LyX-Code
-db_properties = spatialdata.spatialdb.CompositeDB
-\end_layout
-
-\begin_layout LyX-Code
-db_properties.db_A = spatialdata.spatialdb.SimpleDB
-\end_layout
-
-\begin_layout LyX-Code
-db_properties.db_B = spatialdata.spatialdb.SimpleDB
-\end_layout
-
-\begin_layout Standard
-We must define the properties that come from each spatial database and then
- provide the database parameters:
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-# Provide the values to be obtained from each database and the database
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-# name.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-[pylithapp.timedependent.materials.lower_crust.db_properties]
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-values_A = [density,vs,vp]   ; Elastic properties.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-db_A.label = Elastic properties
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-db_A.iohandler.filename = spatialdb/mat_elastic.spatialdb
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-values_B = [reference-stress,reference-strain-rate,power-law-exponent] 
-  ; Power-law properties.
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-db_B.label = Power-law properties
-\end_layout
-
-\begin_layout LyX-Code
-
-\size small
-db_B.iohandler.filename = spatialdb/mat_powerlaw.spatialdb
-\end_layout
-
-\begin_layout Standard
-The 
-\family typewriter
-PowerLaw3D
-\family default
- material has additional properties and state variables with respect to
- the default 
-\family typewriter
-ElasticIsotropic3D
-\family default
- material, so we request that these properties be written to the 
-\family typewriter
-lower_crust
-\family default
- material files:
-\end_layout
-
-\begin_layout LyX-Code
-# Since there are additional properties and state variables for the
-\end_layout
-
-\begin_layout LyX-Code
-# power-law model, we explicitly request that they be output.
- Properties are
-\end_layout
-
-\begin_layout LyX-Code
-# named in cell_info_fields and state variables are named in
-\end_layout
-
-\begin_layout LyX-Code
-# cell_data_fields.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.materials.lower_crust]
-\end_layout
-
-\begin_layout LyX-Code
-output.cell_info_fields = [density,mu,lambda,reference_strain_rate,reference_stre
-ss,
-\begin_inset Newline newline
-\end_inset
-
-power_law_exponent]
-\end_layout
-
-\begin_layout LyX-Code
-output.cell_data_fields = [total_strain,stress,viscous_strain]
-\end_layout
-
-\begin_layout Standard
-When we have run the simulation, the output HDF5 and Xdmf files will be
- contained in 
-\family typewriter
-examples/3d/hex8/output
-\family default
- (all with a prefix of 
-\family typewriter
-step08
-\family default
-).
- Results using ParaView are shown in Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:step08-strain-displ-t150"
-
-\end_inset
-
-.
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
-	filename figs/step08-strain-displ-t150.jpg
-	lyxscale 50
-	width 10cm
-
-\end_inset
-
-
-\begin_inset Caption
-
-\begin_layout Plain Layout
-The XY-component of strain (color contours) and displacement field (vectors)
- for example step08 at t = 150 years visualized using ParaView.
- For this visualization, we loaded both the 
-\family typewriter
-step08-lower_crust.xmf
-\family default
- and 
-\family typewriter
-step08-upper_crust.xmf
-\family default
- files to contour the strain field, and superimposed on it the displacement
- field vectors from 
-\family typewriter
-step08.xmf
-\family default
-.
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:step08-strain-displ-t150"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsubsection
-Step09 - Dirichlet Velocity Boundary Conditions with Time-Dependent Kinematic
- Fault Slip and Drucker-Prager Elastoplastic Rheology
-\end_layout
-
-\begin_layout Standard
-In this example we use a Drucker-Prager elastoplastic rheology in the lower
- crust.
- As in example step08, the material behavior is nonlinear so we again use
- the nonlinear solver.
- The material is elastoplastic, there is no inherent time-dependent response
- and the stable time-step size for the material depends on the loading condition
-s.
- To avoid this, we set the maximum time-step size to 5 years rather than
- the value of 10 years used in example 
-\family typewriter
-step08
-\family default
-:
-\end_layout
-
-\begin_layout LyX-Code
-# Change the total simulation time to 700 years, and set the maximum time
-\end_layout
-
-\begin_layout LyX-Code
-# step size to 5 years.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.implicit.time_step]
-\end_layout
-
-\begin_layout LyX-Code
-total_time = 700.0*year
-\end_layout
-
-\begin_layout LyX-Code
-max_dt = 5.0*year
-\end_layout
-
-\begin_layout LyX-Code
-stability_factor = 1.0 ; use time step equal to stable value from materials
-\end_layout
-
-\begin_layout LyX-Code
-# For this problem we set adapt_skip to zero so that the time step size
- is
-\end_layout
-
-\begin_layout LyX-Code
-# readjusted every time step.
-\end_layout
-
-\begin_layout LyX-Code
-adapt_skip = 0
-\end_layout
-
-\begin_layout Standard
-We change the material type of the lower crust to 
-\family typewriter
-DruckerPrager3D
-\family default
-, and we again use a 
-\family typewriter
-CompositeDB
-\family default
- to assign the material properties:
-\end_layout
-
-\begin_layout LyX-Code
-# Change material type of lower crust to Drucker-Prager.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent]
-\end_layout
-
-\begin_layout LyX-Code
-materials.lower_crust = pylith.materials.DruckerPrager3D
-\end_layout
-
-\begin_layout LyX-Code
-
-\end_layout
-
-\begin_layout LyX-Code
-# Provide a spatial database from which to obtain property values.
-\end_layout
-
-\begin_layout LyX-Code
-# In this case, we prefer to obtain the Drucker-Prager properties from one
-\end_layout
-
-\begin_layout LyX-Code
-# database and the elastic properties from another database, so we use
-\end_layout
-
-\begin_layout LyX-Code
-# a CompositeDB.
- Each part of the CompositeDB is a SimpleDB.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.materials.lower_crust]
-\end_layout
-
-\begin_layout LyX-Code
-db_properties = spatialdata.spatialdb.CompositeDB
-\end_layout
-
-\begin_layout LyX-Code
-db_properties.db_A = spatialdata.spatialdb.SimpleDB
-\end_layout
-
-\begin_layout LyX-Code
-db_properties.db_B = spatialdata.spatialdb.SimpleDB
-\end_layout
-
-\begin_layout Standard
-As for the step08 example, we first define the properties that come from
- each spatial database and then provide the database filename:
-\end_layout
-
-\begin_layout LyX-Code
-# Provide the values to be obtained from each database and the database
-\end_layout
-
-\begin_layout LyX-Code
-# name.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.materials.lower_crust.db_properties]
-\end_layout
-
-\begin_layout LyX-Code
-values_A = [density,vs,vp]   ; Elastic properties.
-\end_layout
-
-\begin_layout LyX-Code
-db_A.label = Elastic properties
-\end_layout
-
-\begin_layout LyX-Code
-db_A.iohandler.filename = spatialdb/mat_elastic.spatialdb
-\end_layout
-
-\begin_layout LyX-Code
-values_B = [friction-angle,cohesion,dilatation-angle]   ; Drucker-Prager
- properties.
-\end_layout
-
-\begin_layout LyX-Code
-db_B.label = Drucker-Prager properties
-\end_layout
-
-\begin_layout LyX-Code
-db_B.iohandler.filename = spatialdb/mat_druckerprager.spatialdb
-\end_layout
-
-\begin_layout Standard
-We also request output of the properties and state variables that are unique
- to the 
-\family typewriter
-DruckerPrager3D
-\family default
- material:
-\end_layout
-
-\begin_layout LyX-Code
-# Since there are additional properties and state variables for the
-\end_layout
-
-\begin_layout LyX-Code
-# Drucker-Prager model, we explicitly request that they be output.
-\end_layout
-
-\begin_layout LyX-Code
-# Properties are named in cell_info_fields and state variables are named
- in
-\end_layout
-
-\begin_layout LyX-Code
-# cell_data_fields.
-\end_layout
-
-\begin_layout LyX-Code
-[pylithapp.timedependent.materials.lower_crust]
-\end_layout
-
-\begin_layout LyX-Code
-output.cell_info_fields = [density,mu,lambda,alpha_yield,beta,alpha_flow]
-\end_layout
-
-\begin_layout LyX-Code
-output.cell_data_fields = [total_strain,stress,plastic_strain]
-\end_layout
-
-\begin_layout Standard
-When we have run the simulation, the output HDF5 and Xdmf files will be
- contained in 
-\family typewriter
-examples/3d/hex8/output
-\family default
- (all with a prefix of 
-\family typewriter
-step09
-\family default
-).
- Results using ParaView are shown in Figure 
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "fig:step09-strain-displ-t150"
-
-\end_inset
-
-.
-\begin_inset Float figure
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
-	filename figs/step08-strain-displ-t150.jpg
-	lyxscale 50
-	width 10cm
-
-\end_inset
-
-
-\begin_inset Caption
-
-\begin_layout Plain Layout
-The XY-component of strain (color contours) and displacement field (vectors)
- for example step09 at t = 150 years visualized using ParaView.
- For this visualization, we loaded both the 
-\family typewriter
-step09-lower_crust.xmf
-\family default
- and 
-\family typewriter
-step09-upper_crust.xmf
-\family default
- files to contour the strain field, and superimposed on it the displacement
- field vectors from 
-\family typewriter
-step09.xmf
-\family default
-.
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:step09-strain-displ-t150"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_body
-\end_document
+#LyX 2.0 created this file. For more info see http://www.lyx.org/
+\lyxformat 413
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+
+\end_preamble
+\use_default_options false
+\maintain_unincluded_children false
+\language english
+\language_package default
+\inputencoding latin1
+\fontencoding global
+\font_roman default
+\font_sans default
+\font_typewriter default
+\font_default_family default
+\use_non_tex_fonts false
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+
+\graphics default
+\default_output_format default
+\output_sync 0
+\bibtex_command default
+\index_command default
+\paperfontsize default
+\spacing single
+\use_hyperref false
+\papersize default
+\use_geometry true
+\use_amsmath 0
+\use_esint 0
+\use_mhchem 1
+\use_mathdots 1
+\cite_engine basic
+\use_bibtopic false
+\use_indices false
+\paperorientation portrait
+\suppress_date false
+\use_refstyle 0
+\index Index
+\shortcut idx
+\color #008000
+\end_index
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 2in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\paragraph_indentation default
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\html_math_output 0
+\html_css_as_file 0
+\html_be_strict false
+\end_header
+
+\begin_body
+
+\begin_layout Subsection
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:Tutorial-3d-hex8-quasistatic"
+
+\end_inset
+
+Quasi-Static Examples
+\end_layout
+
+\begin_layout Standard
+PyLith features discussed in this tutorial:
+\end_layout
+
+\begin_layout Itemize
+Quasi-static solution
+\end_layout
+
+\begin_layout Itemize
+Formatting timestamps of VTK output files
+\end_layout
+
+\begin_layout Itemize
+HDF5 output
+\end_layout
+
+\begin_layout Itemize
+Output of velocity field
+\end_layout
+
+\begin_layout Itemize
+Dirichlet displacement and velocity boundary conditions
+\end_layout
+
+\begin_layout Itemize
+Neumann traction boundary conditions and time-varying tractions
+\end_layout
+
+\begin_layout Itemize
+UniformDB spatial database
+\end_layout
+
+\begin_layout Itemize
+CompositeDB spatial database
+\end_layout
+
+\begin_layout Itemize
+Quasi-static fault rupture and fault creep
+\end_layout
+
+\begin_layout Itemize
+Multiple kinematic fault ruptures
+\end_layout
+
+\begin_layout Itemize
+Specifying more than one material
+\end_layout
+
+\begin_layout Itemize
+Nonlinear solver
+\end_layout
+
+\begin_layout Itemize
+Maxwell linear viscoelastic material
+\end_layout
+
+\begin_layout Itemize
+Power-law viscoelastic material
+\end_layout
+
+\begin_layout Itemize
+Drucker-Prager elastoplastic material
+\end_layout
+
+\begin_layout Itemize
+Adaptive time stepping
+\end_layout
+
+\begin_layout Subsubsection
+Overview
+\end_layout
+
+\begin_layout Standard
+This set of examples describes a set of quasi-static problems for PyLith.
+ These quasi-static problems primarily demonstrate the usage of time-dependent
+ boundary conditions and fault slip, as well as different rheologies.
+ Some of the examples also demonstrate the usage of the nonlinear solver,
+ which is required by the nonlinear rheologies (power-law viscoelastic and
+ Drucker-Prager elastoplastic).
+ Some of the examples also demonstrate the usage of HDF5 output, which is
+ an alternative to the default VTK output.
+ All of the examples are contained in the directory 
+\family typewriter
+examples/3d/hex8
+\family default
+, and the corresponding 
+\family typewriter
+.cfg
+\family default
+ files are 
+\family typewriter
+step04.cfg
+\family default
+, 
+\family typewriter
+step05.cfg
+\family default
+, 
+\family typewriter
+step06.cfg
+\family default
+, 
+\family typewriter
+step07.cfg
+\family default
+, 
+\family typewriter
+step08.cfg
+\family default
+, and 
+\family typewriter
+step09.cfg
+\family default
+.
+ Each example may be run as follows:
+\end_layout
+
+\begin_layout LyX-Code
+pylith stepXX.cfg
+\end_layout
+
+\begin_layout Standard
+This will cause PyLith to read the default parameters in 
+\family typewriter
+pylithapp.cfg
+\family default
+, and then override or augment them with the additional parameters in the
+ 
+\family typewriter
+stepXX.cfg
+\family default
+ file.
+ Each 
+\family typewriter
+.cfg
+\family default
+ file is extensively documented, to provide detailed information on the
+ various parameters.
+\end_layout
+
+\begin_layout Subsubsection
+Step04 - Pure Dirichlet Velocity Boundary Conditions
+\end_layout
+
+\begin_layout Standard
+The 
+\family typewriter
+step04.cfg
+\family default
+ file defines a problem with x-displacements fixed at zero on the positive
+ and negative x-faces while velocity boundary conditions are applied in
+ the y-directions on the same faces, yielding a left-lateral sense of movement.
+ The bottom (negative z) boundary is held fixed in the z-direction.
+ We also use a Maxwell viscoelastic material for the lower crust, and the
+ simulation is run for 200 years using a constant time-step size of 20 years.
+ The default time stepping behavior is 
+\family typewriter
+TimeStepUniform
+\family default
+.
+ We retain that behavior for this problem and provide the total simulation
+ time and the time-step size:
+\end_layout
+
+\begin_layout LyX-Code
+# Change the total simulation time to 200 years, and use a constant time
+\end_layout
+
+\begin_layout LyX-Code
+# step size of 20 years.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.implicit.time_step]
+\end_layout
+
+\begin_layout LyX-Code
+total_time = 200.0*year
+\end_layout
+
+\begin_layout LyX-Code
+dt = 20.0*year 
+\end_layout
+
+\begin_layout Standard
+We then change the material type of the lower crust, provide a spatial database
+ from which to obtain the material properties (using the default 
+\family typewriter
+SimpleDB
+\family default
+), and request additional output information for the material:
+\end_layout
+
+\begin_layout LyX-Code
+# Change material type of lower crust to Maxwell viscoelastic.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent]
+\end_layout
+
+\begin_layout LyX-Code
+materials.lower_crust = pylith.materials.MaxwellIsotropic3D
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# Provide a spatial database from which to obtain property values.
+\end_layout
+
+\begin_layout LyX-Code
+# Since there are additional properties and state variables for the Maxwell
+\end_layout
+
+\begin_layout LyX-Code
+# model, we explicitly request that they be output.
+ Properties are named in
+\end_layout
+
+\begin_layout LyX-Code
+# cell_info_fields and state variables are named in cell_data_fields.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.lower_crust]
+\end_layout
+
+\begin_layout LyX-Code
+db_properties.iohandler.filename = spatialdb/mat_maxwell.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+output.cell_info_fields = [density,mu,lambda,maxwell_time]
+\end_layout
+
+\begin_layout LyX-Code
+output.cell_data_fields = [total_strain,stress,viscous_strain]
+\end_layout
+
+\begin_layout Standard
+Note that the default 
+\family typewriter
+output.cell_info_fields
+\family default
+ are those corresponding to an elastic material (
+\family typewriter
+density
+\family default
+, 
+\family typewriter
+mu
+\family default
+, 
+\family typewriter
+lambda
+\family default
+), and the default 
+\family typewriter
+output.cell_data_fields
+\family default
+ are 
+\family typewriter
+total_strain
+\family default
+ and 
+\family typewriter
+stress
+\family default
+.
+ For materials other than elastic, there are generally additional material
+ properties and state variables, and the appropriate additional fields must
+ be specifically requested for each material type.
+\end_layout
+
+\begin_layout Standard
+This example has no displacements in the elastic solution (t = 0), so we
+ retain the default 
+\family typewriter
+ZeroDispDB
+\family default
+ for all instances of 
+\family typewriter
+db_initial
+\family default
+.
+ To apply the velocity boundary conditions, we must specify 
+\family typewriter
+db_rate
+\family default
+, which is zero by default.
+ We use a 
+\family typewriter
+UniformDB
+\family default
+ to assign the velocities:
+\end_layout
+
+\begin_layout LyX-Code
+# +x face
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.bc.x_pos]
+\end_layout
+
+\begin_layout LyX-Code
+bc_dof = [0, 1]
+\end_layout
+
+\begin_layout LyX-Code
+label = face_xpos
+\end_layout
+
+\begin_layout LyX-Code
+db_initial.label = Dirichlet BC on +x
+\end_layout
+
+\begin_layout LyX-Code
+db_rate = spatialdata.spatialdb.UniformDB
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.label = Dirichlet rate BC on +x
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.values = [displacement-rate-x,displacement-rate-y,rate-start-time]
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.data = [0.0*cm/year,1.0*cm/year,0.0*year]
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# -x face
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.bc.x_neg]
+\end_layout
+
+\begin_layout LyX-Code
+bc_dof = [0, 1]
+\end_layout
+
+\begin_layout LyX-Code
+label = face_xneg
+\end_layout
+
+\begin_layout LyX-Code
+db_initial.label = Dirichlet BC on -x
+\end_layout
+
+\begin_layout LyX-Code
+db_rate = spatialdata.spatialdb.UniformDB
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.label = Dirichlet rate BC on +x
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.values = [displacement-rate-x,displacement-rate-y,rate-start-time]
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.data = [0.0*cm/year,-1.0*cm/year,0.0*year]
+\end_layout
+
+\begin_layout Standard
+Note that 
+\family typewriter
+db_rate
+\family default
+ requires a start time, which allows the condition to be applied at any
+ time during the simulation.
+ For this example, we start the velocity boundary conditions at t = 0.
+\end_layout
+
+\begin_layout Standard
+Finally, we must provide information on VTK output.
+ This is slightly more complicated than the static case, because we must
+ decide the frequency with which output occurs for each output manager.
+ We also assign a more user-friendly format to the output file time stamp,
+ and we request that the time stamp is in units of 1 year (rather than the
+ default value of seconds):
+\end_layout
+
+\begin_layout LyX-Code
+# Give basename for VTK domain output of solution over domain.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.problem.formulation.output.domain]
+\end_layout
+
+\begin_layout LyX-Code
+# We specify that output occurs in terms of a given time frequency, and
+\end_layout
+
+\begin_layout LyX-Code
+# ask for output every 40 years.
+ The time stamps of the output files are
+\end_layout
+
+\begin_layout LyX-Code
+# in years (rather than the default of seconds), and we give a format for
+\end_layout
+
+\begin_layout LyX-Code
+# the time stamp.
+\end_layout
+
+\begin_layout LyX-Code
+output_freq = time_step
+\end_layout
+
+\begin_layout LyX-Code
+time_step = 40.0*year
+\end_layout
+
+\begin_layout LyX-Code
+writer.filename = output/step04.vtk
+\end_layout
+
+\begin_layout LyX-Code
+writer.time_format = %04.0f
+\end_layout
+
+\begin_layout LyX-Code
+writer.time_constant = 1.0*year
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# Give basename for VTK domain output of solution over ground surface.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.problem.formulation.output.subdomain]
+\end_layout
+
+\begin_layout LyX-Code
+# Name of nodeset for ground surface.
+\end_layout
+
+\begin_layout LyX-Code
+label = face_zpos
+\end_layout
+
+\begin_layout LyX-Code
+# We keep the default output frequency behavior (skip every n steps), and
+\end_layout
+
+\begin_layout LyX-Code
+# ask to skip 0 steps between output, so that we get output every time step.
+\end_layout
+
+\begin_layout LyX-Code
+skip = 0
+\end_layout
+
+\begin_layout LyX-Code
+writer.filename = output/step04-groundsurf.vtk
+\end_layout
+
+\begin_layout LyX-Code
+writer.time_format = %04.0f
+\end_layout
+
+\begin_layout LyX-Code
+writer.time_constant = 1.0*year
+\end_layout
+
+\begin_layout Standard
+We provide similar output information for the two materials (
+\family typewriter
+upper_crust
+\family default
+ and 
+\family typewriter
+lower_crust
+\family default
+).
+ Note that for the domain output, we requested output in terms of a given
+ time frequency, while for the subdomain we requested output in terms of
+ number of time steps.
+ When we have run the simulation, the output VTK files will be contained
+ in 
+\family typewriter
+examples/3d/hex8/output
+\family default
+ (all with a prefix of 
+\family typewriter
+step04
+\family default
+).
+ Results using ParaView are shown in Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:step04-displ-t200"
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename figs/step04-displ-t200.jpg
+	lyxscale 50
+	width 10cm
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Displacement field for example step04 at t = 200 years visualized using
+ ParaView.
+ The mesh has been distorted by the computed displacements (magnified by
+ 500), and the vectors show the computed displacements.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:step04-displ-t200"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsubsection
+Step05 - Time-Varying Dirichlet and Neumann Boundary Conditions
+\end_layout
+
+\begin_layout Standard
+The 
+\family typewriter
+step05.cfg
+\family default
+ file describes a problem with time-varying Dirichlet and Neumann boundary
+ conditions.
+ The example is similar to example step04, with a few important differences:
+\end_layout
+
+\begin_layout Itemize
+The Dirichlet boundary conditions on the negative x-face include an initial
+ displacement (applied in the elastic solution), as well as a constant velocity.
+\end_layout
+
+\begin_layout Itemize
+Neumann (traction) boundary conditions are applied in the negative x-direction
+ on the positive x-face, giving a compressive stress.
+ An initial traction is applied in the elastic solution, and then at t =
+ 100 years it begins decreasing linearly until it reaches zero at the end
+ of the simulation (t = 200 years).
+\end_layout
+
+\begin_layout Standard
+We again use a Maxwell viscoelastic material for the lower crust.
+\end_layout
+
+\begin_layout Standard
+For the boundary conditions, we must first change the boundary condition
+ type for the positive x-face from the default Dirichlet to Neumann:
+\end_layout
+
+\begin_layout LyX-Code
+# +x face -- first change bc type to Neumann
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.bc]
+\end_layout
+
+\begin_layout LyX-Code
+x_pos = pylith.bc.Neumann 
+\end_layout
+
+\begin_layout Standard
+We provide quadrature information for this face as we did for example step02.
+ We then use a 
+\family typewriter
+UniformDB
+\family default
+ for both the initial tractions as well as the traction rates.
+ We provide a start time of 100 years for the traction rates, and use a
+ rate of 0.01 MPa/year, so that by the end of 200 years we have completely
+ cancelled the initial traction of -1 MPa:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.bc.x_pos]
+\end_layout
+
+\begin_layout LyX-Code
+# First specify a UniformDB for the initial tractions, along with the values.
+\end_layout
+
+\begin_layout LyX-Code
+db_initial = spatialdata.spatialdb.UniformDB
+\end_layout
+
+\begin_layout LyX-Code
+db_initial.label = Neumann BC on +x
+\end_layout
+
+\begin_layout LyX-Code
+db_initial.values = [traction-shear-horiz,traction-shear-vert,traction-normal]
+\end_layout
+
+\begin_layout LyX-Code
+db_initial.data = [0.0*MPa,0.0*MPa,-1.0*MPa]
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# Provide information on traction rates.
+\end_layout
+
+\begin_layout LyX-Code
+db_rate = spatialdata.spatialdb.UniformDB
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.label = Neumann rate BC on +x
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.values = [traction-rate-shear-horiz,traction-rate-shear-vert,
+\begin_inset Newline newline
+\end_inset
+
+traction-rate-normal,rate-start-time]
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.data = [0.0*MPa/year,0.0*MPa/year,0.01*MPa/year,100.0*year]
+\end_layout
+
+\begin_layout Standard
+The boundary conditions on the negative x-face are analogous, but we are
+ instead using Dirichlet boundary conditions, and the initial displacement
+ is in the same direction as the applied velocities:
+\end_layout
+
+\begin_layout LyX-Code
+# -x face
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.bc.x_neg]
+\end_layout
+
+\begin_layout LyX-Code
+bc_dof = [0, 1]
+\end_layout
+
+\begin_layout LyX-Code
+label = face_xneg
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# Initial displacements.
+\end_layout
+
+\begin_layout LyX-Code
+db_initial = spatialdata.spatialdb.UniformDB
+\end_layout
+
+\begin_layout LyX-Code
+db_initial.label = Dirichlet BC on -x
+\end_layout
+
+\begin_layout LyX-Code
+db_initial.values = [displacement-x,displacement-y]
+\end_layout
+
+\begin_layout LyX-Code
+db_initial.data = [0.0*cm,-0.5*cm]
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# Velocities.
+\end_layout
+
+\begin_layout LyX-Code
+db_rate = spatialdata.spatialdb.UniformDB
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.label = Dirichlet rate BC on -x
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.values = [displacement-rate-x,displacement-rate-y,rate-start-time]
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.data = [0.0*cm/year,-1.0*cm/year,0.0*year]
+\end_layout
+
+\begin_layout Standard
+The boundary conditions on the negative z-face are supplied in the same
+ manner as for example step04.
+ When we have run the simulation, the output VTK files will be contained
+ in 
+\family typewriter
+examples/3d/hex8/output
+\family default
+ (all with a prefix of 
+\family typewriter
+step05
+\family default
+).
+ Results using ParaView are shown in Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:step05-displ-t40"
+
+\end_inset
+
+.
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename figs/step05-displ-t40.jpg
+	lyxscale 50
+	width 10cm
+
+\end_inset
+
+
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Displacement field for example step05 at t = 40 years visualized using ParaView.
+ The mesh has been distorted by the computed displacements (magnified by
+ 500), and the vectors show the computed displacements.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:step05-displ-t40"
+
+\end_inset
+
+.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsubsection
+Step06 - Dirichlet Boundary Conditions with Time-Dependent Kinematic Fault
+ Slip
+\end_layout
+
+\begin_layout Standard
+The 
+\family typewriter
+step06.cfg
+\family default
+ file defines a problem with Dirichlet (displacement) boundary conditions
+ corresponding to zero x- and y-displacements applied on the negative and
+ positive x-faces and a vertical fault that includes multiple earthquake
+ ruptures as well as steady fault creep.
+ The upper (locked) portion of the fault has 4 m of left-lateral slip every
+ 200 years, while the lower (creeping) portion of the fault slips at a steady
+ rate of 2 cm/year.
+ The problem bears some similarity to the strike-slip fault model of Savage
+ and Prescott 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "Savage:Prescott:1978"
+
+\end_inset
+
+, except that the fault creep extends through the viscoelastic portion of
+ the domain, and the far-field displacement boundary conditions are held
+ fixed.
+\end_layout
+
+\begin_layout Standard
+In this example and the remainder of the examples in this section, we change
+ the time stepping behavior from the default 
+\family typewriter
+TimeStepUniform
+\family default
+ to 
+\family typewriter
+TimeStepAdapt
+\family default
+.
+ For adaptive time stepping, we provide the maximum permissible time-step
+ size, along with a stability factor.
+ The stability factor controls the time-step size relative to the stable
+ time-step size provided by the different materials in the model.
+ A 
+\family typewriter
+stability_factor
+\family default
+ of 1.0 means we should use the stable time-step size, while a 
+\family typewriter
+stability_factor
+\family default
+ greater than 1.0 means we want to use a smaller time-step size.
+ A 
+\family typewriter
+stability_factor
+\family default
+ less than 1.0 allows time-step sizes greater than the stable time-step size,
+ which may provide inaccurate results.
+ The adaptive time stepping information is provided as:
+\end_layout
+
+\begin_layout LyX-Code
+# Change time stepping algorithm from uniform time step, to adaptive
+\end_layout
+
+\begin_layout LyX-Code
+# time stepping.
+\end_layout
+
+\begin_layout LyX-Code
+time_step = pylith.problems.TimeStepAdapt
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# Change the total simulation time to 700 years, and set the maximum time
+\end_layout
+
+\begin_layout LyX-Code
+# step size to 10 years.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.implicit.time_step]
+\end_layout
+
+\begin_layout LyX-Code
+total_time = 700.0*year
+\end_layout
+
+\begin_layout LyX-Code
+max_dt = 10.0*year
+\end_layout
+
+\begin_layout LyX-Code
+stability_factor = 1.0 ; use time step equal to stable value from materials
+\end_layout
+
+\begin_layout Standard
+In this example and the remainder of the examples in this section, we also
+ make use of HDF5 output rather than the default VTK output.
+ HDF5 output is a new feature beginning with PyLith version 1.6, and it is
+ much more efficient with the additional advantage that multiple time steps
+ can be contained in a single file.
+ PyLith also produces Xdmf files describing the contents of the HDF5 files,
+ which allows the files to be read easily by applications such as ParaView.
+ Since VTK output is still the default, we must change the value from the
+ default.
+ Also note that the filename suffix is 
+\family typewriter
+.h5
+\family default
+:
+\end_layout
+
+\begin_layout LyX-Code
+# Give basename for output of solution over domain.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.problem.formulation.output.domain]
+\end_layout
+
+\begin_layout LyX-Code
+# We specify that output occurs in terms of a given time frequency, and
+\end_layout
+
+\begin_layout LyX-Code
+# ask for output every 50 years.
+\end_layout
+
+\begin_layout LyX-Code
+output_freq = time_step
+\end_layout
+
+\begin_layout LyX-Code
+time_step = 50.0*year
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# We are using HDF5 output so we must change the default writer.
+\end_layout
+
+\begin_layout LyX-Code
+writer = pylith.meshio.DataWriterHDF5
+\end_layout
+
+\begin_layout LyX-Code
+writer.filename = output/step06.h5  
+\end_layout
+
+\begin_layout Standard
+Note that we no longer need the 
+\family typewriter
+writer.time_format
+\family default
+ or 
+\family typewriter
+writer.time_constant
+\family default
+ properties, since all time steps are contained in a single file.
+ The HDF5 writer does not have these properties, so if we attempt to define
+ them an error will result.
+\end_layout
+
+\begin_layout Standard
+We also set the writer for other output as well, since it is not the default.
+ For subdomain output we use:
+\end_layout
+
+\begin_layout LyX-Code
+# Give basename for output of solution over ground surface.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.problem.formulation.output.subdomain]
+\end_layout
+
+\begin_layout LyX-Code
+# Name of nodeset for ground surface.
+\end_layout
+
+\begin_layout LyX-Code
+label = face_zpos
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# We keep the default output frequency behavior (skip every n steps), and
+\end_layout
+
+\begin_layout LyX-Code
+# ask to skip 0 steps between output, so that we get output every time step.
+\end_layout
+
+\begin_layout LyX-Code
+# We again switch the writer to produce HDF5 output.
+\end_layout
+
+\begin_layout LyX-Code
+skip = 0
+\end_layout
+
+\begin_layout LyX-Code
+writer = pylith.meshio.DataWriterHDF5
+\end_layout
+
+\begin_layout LyX-Code
+writer.filename = output/step06-groundsurf.h5  
+\end_layout
+
+\begin_layout Standard
+For fault output we use:
+\end_layout
+
+\begin_layout LyX-Code
+# Give basename for fault rupture output.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.problem.interfaces.fault.output]
+\end_layout
+
+\begin_layout LyX-Code
+# We keep the default output frequency behavior (skip every n steps), and
+\end_layout
+
+\begin_layout LyX-Code
+# ask to skip 0 steps between output, so that we get output every time step.
+\end_layout
+
+\begin_layout LyX-Code
+# We again switch the writer to produce HDF5 output.
+\end_layout
+
+\begin_layout LyX-Code
+skip = 0
+\end_layout
+
+\begin_layout LyX-Code
+writer = pylith.meshio.DataWriterHDF5
+\end_layout
+
+\begin_layout LyX-Code
+writer.filename = output/step06-fault.h5
+\end_layout
+
+\begin_layout Standard
+Due to the simplicity of the boundary conditions, we are able to use the
+ default 
+\family typewriter
+ZeroDispBC
+\family default
+ for the positive and negative x-faces, as well as the negative z-face.
+ As for example step03, we define a fault interface, we identify the nodeset
+ corresponding to the fault, and we provide quadrature information for the
+ fault.
+ We then define an array of earthquake sources and provide an origin time
+ for each:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.interfaces.fault]
+\end_layout
+
+\begin_layout LyX-Code
+# Set earthquake sources to an array consisting of creep and 3 ruptures.
+\end_layout
+
+\begin_layout LyX-Code
+eq_srcs = [creep,one,two,three]
+\end_layout
+
+\begin_layout LyX-Code
+eq_srcs.creep.origin_time = 00.0*year
+\end_layout
+
+\begin_layout LyX-Code
+eq_srcs.one.origin_time = 200.0*year
+\end_layout
+
+\begin_layout LyX-Code
+eq_srcs.two.origin_time = 400.0*year
+\end_layout
+
+\begin_layout LyX-Code
+eq_srcs.three.origin_time = 600.0*year
+\end_layout
+
+\begin_layout Standard
+Note that the creep begins at t = 0 years, while the ruptures (
+\family typewriter
+one
+\family default
+, 
+\family typewriter
+two
+\family default
+, 
+\family typewriter
+three
+\family default
+) occur at regular intervals of 200 years.
+ We retain the default 
+\family typewriter
+StepSlipFn
+\family default
+ for the ruptures.
+ Each of the ruptures has the same amount of slip, and slip occurs simultaneousl
+y for the entire rupture region, so we can use the same 
+\family typewriter
+SimpleDB
+\family default
+ files providing slip and slip time for each rupture:
+\end_layout
+
+\begin_layout LyX-Code
+# Define slip and origin time for first rupture.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.interfaces.fault.eq_srcs.one.slip_function]
+\end_layout
+
+\begin_layout LyX-Code
+slip.iohandler.filename = spatialdb/finalslip_rupture.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# Define slip and origin time for second rupture.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.interfaces.fault.eq_srcs.two.slip_function]
+\end_layout
+
+\begin_layout LyX-Code
+slip.iohandler.filename = spatialdb/finalslip_rupture.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# Define slip and origin time for third rupture.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.interfaces.fault.eq_srcs.three.slip_function]
+\end_layout
+
+\begin_layout LyX-Code
+slip.iohandler.filename = spatialdb/finalslip_rupture.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
+\end_layout
+
+\begin_layout Standard
+For the creep source, we change the slip function to 
+\family typewriter
+ConstRateSlipFn
+\family default
+, and we use a 
+\family typewriter
+SimpleDB
+\family default
+ for both the slip time and the slip rate:
+\end_layout
+
+\begin_layout LyX-Code
+# Define slip rate and origin time for fault creep.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.interfaces.fault.eq_srcs.creep]
+\end_layout
+
+\begin_layout LyX-Code
+slip_function = pylith.faults.ConstRateSlipFn
+\end_layout
+
+\begin_layout LyX-Code
+slip_function.slip_rate.iohandler.filename = spatialdb/sliprate_creep.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+slip_function.slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
+\end_layout
+
+\begin_layout Standard
+For all earthquake sources we provide both an 
+\family typewriter
+origin_time
+\family default
+ and a 
+\family typewriter
+slip_function.slip_time
+\family default
+.
+ The first provides the starting time for the entire earthquake source,
+ while the second provides any spatial variation in the slip time with respect
+ to the 
+\family typewriter
+origin_time
+\family default
+ (if any).
+ Since there are multiple earthquake sources of different types, there are
+ a number of additional fault information fields available for output.
+ We add these additional fields' output to the fault information file:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.interfaces.fault]
+\end_layout
+
+\begin_layout LyX-Code
+output.vertex_info_fields = [normal_dir,strike_dir,dip_dir,final_slip_creep,
+\begin_inset Newline newline
+\end_inset
+
+final_slip_one,final_slip_two,final_slip_three,slip_time_creep,slip_time_one,
+\begin_inset Newline newline
+\end_inset
+
+slip_time_two,slip_time_three]
+\end_layout
+
+\begin_layout Standard
+This additional information will be contained in file 
+\family typewriter
+step06-fault_info.h5
+\family default
+.
+ It will contain final slip information for each earthquake source along
+ with slip time information.
+ When we have run the simulation, the output HDF5 and Xdmf files will be
+ contained in 
+\family typewriter
+examples/3d/hex8/output
+\family default
+ (all with a prefix of 
+\family typewriter
+step06
+\family default
+).
+ To open the files in ParaView, the Xdmf (
+\family typewriter
+.xmf
+\family default
+) files should be opened, as these files describe the HDF5 data structure.
+ Results using ParaView are shown in Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:step06-displ-t300"
+
+\end_inset
+
+.
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename figs/step06-displ-t300.jpg
+	lyxscale 50
+	width 10cm
+
+\end_inset
+
+
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Displacement field for example step06 at t = 300 years visualized using
+ ParaView.
+ The mesh has been distorted by the computed displacements (magnified by
+ 500), and the vectors show the computed displacements.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:step06-displ-t300"
+
+\end_inset
+
+.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsubsection
+Step07 - Dirichlet Velocity Boundary Conditions with Time-Dependent Kinematic
+ Fault Slip
+\end_layout
+
+\begin_layout Standard
+In step07 we add velocity boundary conditions in the positive and negative
+ y-directions on the positive and negative x-faces, so that the external
+ boundaries keep pace with the average fault slip.
+ This problem is nearly identical to the strike-slip fault model of Savage
+ and Prescott 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "Savage:Prescott:1978"
+
+\end_inset
+
+, except that the fault creep extends through the viscoelastic portion of
+ the domain.
+\end_layout
+
+\begin_layout Standard
+We use the default 
+\family typewriter
+ZeroDispBC
+\family default
+ for the initial displacements on the positive and negative x-faces, as
+ well as the negative z-face.
+ For the velocities on the positive and negative x-faces, we use a 
+\family typewriter
+UniformDB
+\family default
+:
+\end_layout
+
+\begin_layout LyX-Code
+# +x face
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.bc.x_pos]
+\end_layout
+
+\begin_layout LyX-Code
+bc_dof = [0, 1]
+\end_layout
+
+\begin_layout LyX-Code
+label = face_xpos
+\end_layout
+
+\begin_layout LyX-Code
+db_initial.label = Dirichlet BC on +x
+\end_layout
+
+\begin_layout LyX-Code
+db_rate = spatialdata.spatialdb.UniformDB
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.label = Dirichlet rate BC on +x
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.values = [displacement-rate-x,displacement-rate-y,rate-start-time]
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.data = [0.0*cm/year,1.0*cm/year,0.0*year]
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# -x face
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.bc.x_neg]
+\end_layout
+
+\begin_layout LyX-Code
+bc_dof = [0, 1]
+\end_layout
+
+\begin_layout LyX-Code
+label = face_xneg
+\end_layout
+
+\begin_layout LyX-Code
+db_initial.label = Dirichlet BC on -x
+\end_layout
+
+\begin_layout LyX-Code
+db_rate = spatialdata.spatialdb.UniformDB
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.label = Dirichlet rate BC on +x
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.values = [displacement-rate-x,displacement-rate-y,rate-start-time]
+\end_layout
+
+\begin_layout LyX-Code
+db_rate.data = [0.0*cm/year,-1.0*cm/year,0.0*year]
+\end_layout
+
+\begin_layout Standard
+The fault definition information is identical to example 
+\family typewriter
+step06
+\family default
+.
+ In previous examples, we have just used the default output for the domain
+ and subdomain (ground surface), which includes the displacements.
+ In many cases, it is also useful to include the velocities.
+ PyLith provides this information, computing the velocities for the current
+ time step as the difference between the current displacements and the displacem
+ents from the previous time step, divided by the time-step size.
+ This is more accurate than computing the velocities from the displacement
+ field output that has been decimated in time.
+ We can obtain this information by explicitly requesting it in 
+\family typewriter
+vertex_data_fields
+\family default
+:
+\end_layout
+
+\begin_layout LyX-Code
+# Give basename for output of solution over domain.
+\begin_inset Newline newline
+\end_inset
+
+[pylithapp.problem.formulation.output.domain]
+\end_layout
+
+\begin_layout LyX-Code
+# We specify that output occurs in terms of a given time frequency, and
+\end_layout
+
+\begin_layout LyX-Code
+# ask for output every 50 years.
+\end_layout
+
+\begin_layout LyX-Code
+# We also request velocity output in addition to displacements.
+\begin_inset Newline newline
+\end_inset
+
+vertex_data_fields = [displacement,velocity]
+\end_layout
+
+\begin_layout LyX-Code
+output_freq = time_step
+\end_layout
+
+\begin_layout LyX-Code
+time_step = 50.0*year
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# We are using HDF5 output so we must change the default writer.
+\end_layout
+
+\begin_layout LyX-Code
+writer = pylith.meshio.DataWriterHDF5
+\end_layout
+
+\begin_layout LyX-Code
+writer.filename = output/step07.h5
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# Give basename for output of solution over ground surface.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.problem.formulation.output.subdomain]
+\end_layout
+
+\begin_layout LyX-Code
+# Name of nodeset for ground surface.
+\end_layout
+
+\begin_layout LyX-Code
+label = face_zpos
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# We also request velocity output in addition to displacements.
+\end_layout
+
+\begin_layout LyX-Code
+vertex_data_fields = [displacement,velocity]
+\end_layout
+
+\begin_layout LyX-Code
+# We keep the default output frequency behavior (skip every n steps), and
+\end_layout
+
+\begin_layout LyX-Code
+# ask to skip 0 steps between output, so that we get output every time step.
+\end_layout
+
+\begin_layout LyX-Code
+skip = 0
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+# We again switch the writer to produce HDF5 output.
+\end_layout
+
+\begin_layout LyX-Code
+writer = pylith.meshio.DataWriterHDF5
+\end_layout
+
+\begin_layout LyX-Code
+writer.filename = output/step07-groundsurf.h5
+\end_layout
+
+\begin_layout Standard
+When we have run the simulation, the output HDF5 and Xdmf files will be
+ contained in 
+\family typewriter
+examples/3d/hex8/output
+\family default
+ (all with a prefix of 
+\family typewriter
+step07
+\family default
+).
+ As for example step06, make sure to open the 
+\family typewriter
+.xmf
+\family default
+ files rather than the 
+\family typewriter
+.h5
+\family default
+ files.
+ Results using ParaView are shown in Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:step07-displ-vel-t300"
+
+\end_inset
+
+.
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename figs/step07-displ-vel-t300.jpg
+	lyxscale 50
+	width 10cm
+
+\end_inset
+
+
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Displacement field (color contours) and velocity field (vectors) for example
+ step07 at t = 300 years visualized using ParaView.
+ The mesh has been distorted by the computed displacements (magnified by
+ 500), and the vectors show the computed velocities.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:step07-displ-vel-t300"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsubsection
+Step08 - Dirichlet Velocity Boundary Conditions with Time-Dependent Kinematic
+ Fault Slip and Power-Law Rheology
+\begin_inset CommandInset label
+LatexCommand label
+name "sub:Tutorial-Step08-Power-law"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+The 
+\family typewriter
+step08.cfg
+\family default
+ file defines a problem that is identical to example step07, except the
+ the lower crust is composed of a power-law viscoelastic material.
+ Since the material behavior is now nonlinear, we must use the nonlinear
+ solver:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent]
+\end_layout
+
+\begin_layout LyX-Code
+# For this problem we must switch to a nonlinear solver.
+\end_layout
+
+\begin_layout LyX-Code
+implicit.solver = pylith.problems.SolverNonlinear
+\end_layout
+
+\begin_layout Standard
+Although we have not discussed the PyLith PETSc settings previously, note
+ that the use of the nonlinear solver may require additional options if
+ we wish to override the defaults.
+ These settings are contained in 
+\family typewriter
+pylithapp.cfg
+\family default
+:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.petsc]
+\end_layout
+
+\begin_layout LyX-Code
+# Nonlinear solver monitoring options.
+\end_layout
+
+\begin_layout LyX-Code
+snes_rtol = 1.0e-8
+\end_layout
+
+\begin_layout LyX-Code
+snes_atol = 1.0e-12
+\end_layout
+
+\begin_layout LyX-Code
+snes_max_it = 100
+\end_layout
+
+\begin_layout LyX-Code
+snes_monitor = true
+\end_layout
+
+\begin_layout LyX-Code
+snes_view = true
+\end_layout
+
+\begin_layout LyX-Code
+snes_converged_reason = true
+\end_layout
+
+\begin_layout Standard
+These settings are ignored unless we are using the nonlinear solver.
+\end_layout
+
+\begin_layout Standard
+When setting the physical properties for the power-law material in PyLith,
+ the parameters (see Section 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sub:Power-Law-Maxwell-Viscoelastic"
+
+\end_inset
+
+) do not generally correspond to the values provided in laboratory results.
+ PyLith includes a utility code, 
+\family typewriter
+powerlaw_gendb.py
+\family default
+, to simplify the process of using laboratory results with PyLith.
+ This utility code is installed in the same location as PyLith.
+ An example of how to use it is in 
+\family typewriter
+examples/3d/hex8/spatialdb/powerlaw
+\family default
+.
+ The user must provide a spatial database defining the spatial distribution
+ of laboratory-derived parameters (contained in 
+\family typewriter
+powerlaw_params.
+\begin_inset Newline linebreak
+\end_inset
+
+spatialdb
+\family default
+), another spatial database defining the temperature field in degrees K
+ (contained in 
+\family typewriter
+temperature.spatialdb
+\family default
+), and a set of points for which values are desired (
+\family typewriter
+powerlaw_points.txt
+\family default
+).
+ The parameters for the code are defined in 
+\family typewriter
+powerlaw_gendb.cfg
+\family default
+.
+ The properties expected by PyLith are 
+\family typewriter
+reference_strain_rate
+\family default
+, 
+\family typewriter
+reference_stress
+\family default
+, and 
+\family typewriter
+power_law_exponent
+\family default
+.
+ The user must specify either 
+\family typewriter
+reference_strain_rate
+\family default
+ or 
+\family typewriter
+reference_stress
+\family default
+ so that 
+\family typewriter
+powerlaw_gendb.py
+\family default
+ can compute the other property.
+ Default values of 1.0e-6 1/s and 1 MPa are provided.
+ In this example, the same database was used for all parameters, and a separate
+ database was used to define the temperature distribution.
+ In practice, the user can provide any desired thermal model to provide
+ the spatial database for the temperature.
+ In this example, a simple 1D (vertically-varying) distribution was used.
+ The utility code can be used by simply executing it from the 
+\family typewriter
+examples/3d/hex8/spatialdb/powerlaw
+\family default
+ directory:
+\end_layout
+
+\begin_layout LyX-Code
+powerlaw_gendb.py
+\end_layout
+
+\begin_layout Standard
+This code will automatically read the parameters in 
+\family typewriter
+powerlaw_gendb.cfg
+\family default
+ in creating the file
+\begin_inset Newline newline
+\end_inset
+
+ 
+\family typewriter
+examples/3d/hex8/spatialdb/mat_powerlaw.spatialdb
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+We first change the material type of the lower crust to 
+\family typewriter
+PowerLaw3D
+\family default
+:
+\end_layout
+
+\begin_layout LyX-Code
+# Change material type of lower crust to power-law viscoelastic.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent]
+\end_layout
+
+\begin_layout LyX-Code
+materials.lower_crust = pylith.materials.PowerLaw3D
+\end_layout
+
+\begin_layout Standard
+In many cases, it is useful to obtain the material properties from two different
+ sources.
+ For example, the elastic properties may come from a seismic velocity model
+ while the viscous properties may be derived from a thermal model.
+ In such a case we can use a 
+\family typewriter
+CompositeDB
+\family default
+, which allows a different spatial database to be used for a subset of the
+ properties.
+ We do this as follows:
+\end_layout
+
+\begin_layout LyX-Code
+# Provide a spatial database from which to obtain property values.
+\end_layout
+
+\begin_layout LyX-Code
+# In this case, we prefer to obtain the power-law properties from one
+\end_layout
+
+\begin_layout LyX-Code
+# database and the elastic properties from another database, so we use
+\end_layout
+
+\begin_layout LyX-Code
+# a CompositeDB.
+ Each part of the CompositeDB is a SimpleDB.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.lower_crust]
+\end_layout
+
+\begin_layout LyX-Code
+db_properties = spatialdata.spatialdb.CompositeDB
+\end_layout
+
+\begin_layout LyX-Code
+db_properties.db_A = spatialdata.spatialdb.SimpleDB
+\end_layout
+
+\begin_layout LyX-Code
+db_properties.db_B = spatialdata.spatialdb.SimpleDB
+\end_layout
+
+\begin_layout Standard
+We must define the properties that come from each spatial database and then
+ provide the database parameters:
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+# Provide the values to be obtained from each database and the database
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+# name.
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+[pylithapp.timedependent.materials.lower_crust.db_properties]
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+values_A = [density,vs,vp]   ; Elastic properties.
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+db_A.label = Elastic properties
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+db_A.iohandler.filename = spatialdb/mat_elastic.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+values_B = [reference-stress,reference-strain-rate,power-law-exponent] 
+  ; Power-law properties.
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+db_B.label = Power-law properties
+\end_layout
+
+\begin_layout LyX-Code
+
+\size small
+db_B.iohandler.filename = spatialdb/mat_powerlaw.spatialdb
+\end_layout
+
+\begin_layout Standard
+The 
+\family typewriter
+PowerLaw3D
+\family default
+ material has additional properties and state variables with respect to
+ the default 
+\family typewriter
+ElasticIsotropic3D
+\family default
+ material, so we request that these properties be written to the 
+\family typewriter
+lower_crust
+\family default
+ material files:
+\end_layout
+
+\begin_layout LyX-Code
+# Since there are additional properties and state variables for the
+\end_layout
+
+\begin_layout LyX-Code
+# power-law model, we explicitly request that they be output.
+ Properties are
+\end_layout
+
+\begin_layout LyX-Code
+# named in cell_info_fields and state variables are named in
+\end_layout
+
+\begin_layout LyX-Code
+# cell_data_fields.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.lower_crust]
+\end_layout
+
+\begin_layout LyX-Code
+output.cell_info_fields = [density,mu,lambda,reference_strain_rate,reference_stre
+ss,
+\begin_inset Newline newline
+\end_inset
+
+power_law_exponent]
+\end_layout
+
+\begin_layout LyX-Code
+output.cell_data_fields = [total_strain,stress,viscous_strain]
+\end_layout
+
+\begin_layout Standard
+When we have run the simulation, the output HDF5 and Xdmf files will be
+ contained in 
+\family typewriter
+examples/3d/hex8/output
+\family default
+ (all with a prefix of 
+\family typewriter
+step08
+\family default
+).
+ Results using ParaView are shown in Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:step08-strain-displ-t150"
+
+\end_inset
+
+.
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename figs/step08-strain-displ-t150.jpg
+	lyxscale 50
+	width 10cm
+
+\end_inset
+
+
+\begin_inset Caption
+
+\begin_layout Plain Layout
+The XY-component of strain (color contours) and displacement field (vectors)
+ for example step08 at t = 150 years visualized using ParaView.
+ For this visualization, we loaded both the 
+\family typewriter
+step08-lower_crust.xmf
+\family default
+ and 
+\family typewriter
+step08-upper_crust.xmf
+\family default
+ files to contour the strain field, and superimposed on it the displacement
+ field vectors from 
+\family typewriter
+step08.xmf
+\family default
+.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:step08-strain-displ-t150"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsubsection
+Step09 - Dirichlet Velocity Boundary Conditions with Time-Dependent Kinematic
+ Fault Slip and Drucker-Prager Elastoplastic Rheology
+\end_layout
+
+\begin_layout Standard
+In this example we use a Drucker-Prager elastoplastic rheology in the lower
+ crust.
+ As in example step08, the material behavior is nonlinear so we again use
+ the nonlinear solver.
+ The material is elastoplastic, there is no inherent time-dependent response
+ and the stable time-step size for the material depends on the loading condition
+s.
+ To avoid this, we set the maximum time-step size to 5 years rather than
+ the value of 10 years used in example 
+\family typewriter
+step08
+\family default
+:
+\end_layout
+
+\begin_layout LyX-Code
+# Change the total simulation time to 700 years, and set the maximum time
+\end_layout
+
+\begin_layout LyX-Code
+# step size to 5 years.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.implicit.time_step]
+\end_layout
+
+\begin_layout LyX-Code
+total_time = 700.0*year
+\end_layout
+
+\begin_layout LyX-Code
+max_dt = 5.0*year
+\end_layout
+
+\begin_layout LyX-Code
+stability_factor = 1.0 ; use time step equal to stable value from materials
+\end_layout
+
+\begin_layout LyX-Code
+# For this problem we set adapt_skip to zero so that the time step size
+ is
+\end_layout
+
+\begin_layout LyX-Code
+# readjusted every time step.
+\end_layout
+
+\begin_layout LyX-Code
+adapt_skip = 0
+\end_layout
+
+\begin_layout Standard
+We change the material type of the lower crust to 
+\family typewriter
+DruckerPrager3D
+\family default
+, and we again use a 
+\family typewriter
+CompositeDB
+\family default
+ to assign the material properties:
+\end_layout
+
+\begin_layout LyX-Code
+# Change material type of lower crust to Drucker-Prager.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent]
+\end_layout
+
+\begin_layout LyX-Code
+materials.lower_crust = pylith.materials.DruckerPrager3D
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+# Provide a spatial database from which to obtain property values.
+\end_layout
+
+\begin_layout LyX-Code
+# In this case, we prefer to obtain the Drucker-Prager properties from one
+\end_layout
+
+\begin_layout LyX-Code
+# database and the elastic properties from another database, so we use
+\end_layout
+
+\begin_layout LyX-Code
+# a CompositeDB.
+ Each part of the CompositeDB is a SimpleDB.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.lower_crust]
+\end_layout
+
+\begin_layout LyX-Code
+db_properties = spatialdata.spatialdb.CompositeDB
+\end_layout
+
+\begin_layout LyX-Code
+db_properties.db_A = spatialdata.spatialdb.SimpleDB
+\end_layout
+
+\begin_layout LyX-Code
+db_properties.db_B = spatialdata.spatialdb.SimpleDB
+\end_layout
+
+\begin_layout Standard
+As for the step08 example, we first define the properties that come from
+ each spatial database and then provide the database filename:
+\end_layout
+
+\begin_layout LyX-Code
+# Provide the values to be obtained from each database and the database
+\end_layout
+
+\begin_layout LyX-Code
+# name.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.lower_crust.db_properties]
+\end_layout
+
+\begin_layout LyX-Code
+values_A = [density,vs,vp]   ; Elastic properties.
+\end_layout
+
+\begin_layout LyX-Code
+db_A.label = Elastic properties
+\end_layout
+
+\begin_layout LyX-Code
+db_A.iohandler.filename = spatialdb/mat_elastic.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+values_B = [friction-angle,cohesion,dilatation-angle]   ; Drucker-Prager
+ properties.
+\end_layout
+
+\begin_layout LyX-Code
+db_B.label = Drucker-Prager properties
+\end_layout
+
+\begin_layout LyX-Code
+db_B.iohandler.filename = spatialdb/mat_druckerprager.spatialdb
+\end_layout
+
+\begin_layout Standard
+We also request output of the properties and state variables that are unique
+ to the 
+\family typewriter
+DruckerPrager3D
+\family default
+ material:
+\end_layout
+
+\begin_layout LyX-Code
+# Since there are additional properties and state variables for the
+\end_layout
+
+\begin_layout LyX-Code
+# Drucker-Prager model, we explicitly request that they be output.
+\end_layout
+
+\begin_layout LyX-Code
+# Properties are named in cell_info_fields and state variables are named
+ in
+\end_layout
+
+\begin_layout LyX-Code
+# cell_data_fields.
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent.materials.lower_crust]
+\end_layout
+
+\begin_layout LyX-Code
+output.cell_info_fields = [density,mu,lambda,alpha_yield,beta,alpha_flow]
+\end_layout
+
+\begin_layout LyX-Code
+output.cell_data_fields = [total_strain,stress,plastic_strain]
+\end_layout
+
+\begin_layout Standard
+When we have run the simulation, the output HDF5 and Xdmf files will be
+ contained in 
+\family typewriter
+examples/3d/hex8/output
+\family default
+ (all with a prefix of 
+\family typewriter
+step09
+\family default
+).
+ Results using ParaView are shown in Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:step09-strain-displ-t150"
+
+\end_inset
+
+.
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename figs/step08-strain-displ-t150.jpg
+	lyxscale 50
+	width 10cm
+
+\end_inset
+
+
+\begin_inset Caption
+
+\begin_layout Plain Layout
+The XY-component of strain (color contours) and displacement field (vectors)
+ for example step09 at t = 150 years visualized using ParaView.
+ For this visualization, we loaded both the 
+\family typewriter
+step09-lower_crust.xmf
+\family default
+ and 
+\family typewriter
+step09-upper_crust.xmf
+\family default
+ files to contour the strain field, and superimposed on it the displacement
+ field vectors from 
+\family typewriter
+step09.xmf
+\family default
+.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:step09-strain-displ-t150"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document

Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/greensfns2d/greensfns2d.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/greensfns2d/greensfns2d.lyx	2013-05-18 00:23:27 UTC (rev 22104)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/greensfns2d/greensfns2d.lyx	2013-05-18 01:12:14 UTC (rev 22105)
@@ -395,7 +395,7 @@
 \end_layout
 
 \begin_layout LyX-Code
-writer = pylith.meshio.DataWriterHDF5Mesh
+writer = pylith.meshio.DataWriterHDF5
 \end_layout
 
 \begin_layout LyX-Code