[cig-commits] r20283 - in short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials: . greensfns2d

[willic3 at geodynamics.org]

Author: willic3
Date: 2012-06-01 16:26:01 -0700 (Fri, 01 Jun 2012)
New Revision: 20283

Added:
   short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/greensfns2d/
   short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/greensfns2d/figs/
   short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/greensfns2d/greensfns2d.lyx
Modified:
   short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/tutorials.lyx
Log:
Started creating manual section for Green's functions section.
Most of what's there right now is copied from another tutorial.



Added: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/greensfns2d/greensfns2d.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/greensfns2d/greensfns2d.lyx	                        (rev 0)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/greensfns2d/greensfns2d.lyx	2012-06-01 23:26:01 UTC (rev 20283)
@@ -0,0 +1,896 @@
+#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 1in
+\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 Section
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:Tutorial-Greensfns-2d"
+
+\end_inset
+
+Tutorial Generating and Using Green's Functions in Two Dimensions
+\end_layout
+
+\begin_layout Standard
+PyLith features discussed in this tutorial:
+\end_layout
+
+\begin_layout Itemize
+Green's functions
+\end_layout
+
+\begin_layout Itemize
+HDF5 output
+\end_layout
+
+\begin_layout Itemize
+Reading HDF5 output using h5py
+\end_layout
+
+\begin_layout Itemize
+Simple inversion procedure
+\end_layout
+
+\begin_layout Itemize
+Plotting results using matplotlib
+\end_layout
+
+\begin_layout Itemize
+Cubit mesh generation
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Variable mesh resolution
+\end_layout
+
+\begin_layout Itemize
+APREPRO programming language
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+Static solution
+\end_layout
+
+\begin_layout Itemize
+Linear triangular cells
+\end_layout
+
+\begin_layout Itemize
+Kinematic fault interface conditions
+\end_layout
+
+\begin_layout Itemize
+Plane strain linearly elastic material
+\end_layout
+
+\begin_layout Itemize
+SimpleDB spatial database
+\end_layout
+
+\begin_layout Itemize
+ZeroDispDB spatial database
+\end_layout
+
+\begin_layout Itemize
+UniformDB spatial database
+\end_layout
+
+\begin_layout Standard
+All of the files necessary to run the examples are contained in the directory
+ 
+\family typewriter
+examples/2d/greensfns.
+\end_layout
+
+\begin_layout Subsection
+Overview
+\end_layout
+
+\begin_layout Standard
+This tutorial is the simplest 2D example of a quasi-static finite element
+ problem (a simpler problem would consist of a 1D bar).
+ It is a mesh composed of two linear triangles subject to displacement boundary
+ conditions, assuming plane-strain linear elastic behavior.
+ Due to the simple geometry of the problem, the mesh may be constructed
+ by hand, using PyLith mesh ASCII format.
+ In this tutorial, we will walk through the steps necessary to construct,
+ run, and view three problems that use the same mesh.
+ In addition to this manual, each of the files for the example problem includes
+ extensive comments.
+\end_layout
+
+\begin_layout Subsection
+Mesh Description
+\end_layout
+
+\begin_layout Standard
+The mesh consists of two triangles forming a square with edge lengths of
+ one unit (Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:twotri3-mesh"
+
+\end_inset
+
+).
+ The mesh geometry and topology are described in the file 
+\family typewriter
+twotri3.mesh
+\family default
+, which is in PyLith mesh ASCII format.
+ This file format is described in Appendix 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "cha:File-Formats"
+
+\end_inset
+
+.
+ This file describes the dimensionality of the problem (1D, 2D, or 3D),
+ the coordinates of the vertices (nodes), the vertices composing each cell
+ (element), the material ID to be associated with each cell, and groups
+ of vertices that may be used to define faults or surfaces to which boundary
+ conditions may be applied.
+\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/twotri3-mesh.eps
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Mesh composed of two linear triangular cells used in the example problems.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotri3-mesh"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Additional Common Information
+\end_layout
+
+\begin_layout Standard
+In addition to the mesh, the three example problems share additional information.
+ For problems of this type, it is generally useful to create a file named
+ 
+\family typewriter
+pylithapp.cfg
+\family default
+ in the working directory, since this file is read automatically every time
+ PyLith is run.
+ Settings specific to a particular problem may be placed in other 
+\family typewriter
+.cfg
+\family default
+ files, as described later, and then those files are placed on the command
+ line.
+ The settings contained in 
+\family typewriter
+pylithapp.cfg
+\family default
+ for this problem consist of:
+\end_layout
+
+\begin_layout Description
+pylithapp.journal.info Settings that control the verbosity of the output for
+ the different components.
+\end_layout
+
+\begin_layout Description
+pylithapp.mesh_generator Settings that control mesh importing, such as the
+ importer type, the filename, and the spatial dimension of the mesh.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent Settings that control the problem, such as the total
+ time, time step size, and spatial dimension.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials Settings that control the material type,
+ specify which material IDs are to be associated with a particular material
+ type, and give the name of the spatial database containing the physical
+  properties for the material.
+ The quadrature information is also given.
+\end_layout
+
+\begin_layout Description
+pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
+ type.
+\end_layout
+
+\begin_layout Standard
+All of the problems in this directory use the same material database, as
+ specified under 
+\end_layout
+
+\begin_layout LyX-Code
+
+\family typewriter
+pylithapp.timedependent.materials
+\family default
+ 
+\end_layout
+
+\begin_layout Standard
+in 
+\family typewriter
+pylithapp.cfg
+\family default
+.
+ This information is contained in the file 
+\family typewriter
+matprops.spatialdb
+\family default
+.
+ Although the material model is specified in 
+\family typewriter
+pylithapp.cfg
+\family default
+, the values for the physical properties of the material are given in 
+\family typewriter
+matprops.spatialdb
+\family default
+.
+ For this example, values describing elastic plane strain material properties
+ are given at a single point, resulting in uniform material properties.
+\end_layout
+
+\begin_layout Subsection
+Axial Displacement Example
+\end_layout
+
+\begin_layout Standard
+The first example problem is extension of the mesh along the diagonal extending
+ from the lower left to the upper right of the square mesh.
+ Parameter settings that augment those in 
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file 
+\family typewriter
+axialdisp.cfg
+\family default
+.
+ These settings are:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent Specifies an implicit formulation for the problem
+ and specifies the array of boundary conditions.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.bc Defines which degrees of freedom are being constraine
+d (x and y), gives the label (defined in 
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points desired, assigns a label to the boundary condition
+ set, and gives the name of the spatial database with the values for the
+ Dirichlet boundary condition (
+\family typewriter
+axialdisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.problem.formulation.output.output.writer Gives the base filename for
+ VTK output 
+\begin_inset Newline newline
+\end_inset
+
+(
+\family typewriter
+axialdisp.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.materials.material.output Gives the base filename for
+ state variable output files (
+\family typewriter
+axialdisp-statevars.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The values for the Dirichlet boundary condition are given in the file 
+\family typewriter
+axialdisp.spatialdb
+\family default
+, as specified in 
+\family typewriter
+axialdisp.cfg
+\family default
+.
+ The format of all spatial database files is similar.
+ In this case, the desired displacement values are given at two points (lower
+ left and upper right).
+ Since data are being specified at points (rather than being uniform over
+ the mesh, for example), the data dimension is one.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twotri3.mesh
+\family default
+, 
+\family typewriter
+pylithapp.cfg
+\family default
+, 
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+axialdisp.cfg
+\family default
+, 
+\family typewriter
+axialdisp.spatialdb
+\family default
+) provide a complete description of the problem, and we can then run this
+ example by typing
+\end_layout
+
+\begin_layout LyX-Code
+pylith axialdisp.cfg
+\end_layout
+
+\begin_layout Standard
+Once the problem has run, three files will be produced.
+ The first file is named 
+\family typewriter
+axialdisp_t0000000.vtk
+\family default
+.
+ The 
+\family typewriter
+t0000000
+\family default
+ indicates that the output is for the first (and only) time step, corresponding
+ to an elastic solution.
+ This file contains mesh information as well as displacement values at the
+ mesh vertices.
+ The second file is named 
+\family typewriter
+axialdisp-statevars_t0000000.vtk
+\family default
+.
+ This file contains the state variables for each cell.
+ The default fields are the total strain and stress fields.
+ Since the cells are linear triangles, there is a single quadrature point
+ for each cell and thus a single set of stress and strain values for each
+ cell.
+ The final file (
+\family typewriter
+axialdisp-statevars_info.vtk
+\family default
+) gives the material properties used for the problem.
+ Since we have not specified which properties to write, the default properties
+ (
+\family typewriter
+mu
+\family default
+, 
+\family typewriter
+lambda
+\family default
+, 
+\family typewriter
+density
+\family default
+) are written.
+ All of the 
+\family typewriter
+.vtk
+\family default
+ files may be used with a number of visualization packages.
+ If the problem ran correctly, you should be able to generate a figure such
+ as Figure 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twotri3-axial"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename figs/axialdisp.jpg
+	lyxscale 50
+	scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the axial displacement example
+ using a mesh composed of two linear triangular cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotri3-axial"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Shear Displacement Example
+\end_layout
+
+\begin_layout Standard
+The next example problem is shearing of the mesh in the y direction using
+ displacements applied along the positive and negative x boundaries.
+ Parameter settings that augment those in 
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file 
+\family typewriter
+sheardisp.cfg
+\family default
+.
+ These settings include:
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_neg Specifies the boundary conditions for the
+ left side of the mesh, defining which degrees of freedom are being constrained
+ (x and y), giving the label (
+\family typewriter
+x_neg
+\family default
+, defined in 
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database with the values for the
+ Dirichlet boundary condition (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.x_pos Specifies the boundary conditions for the
+ left side of the mesh, defining which degrees of freedom are being constrained
+ (y only), giving the label (
+\family typewriter
+x_
+\family default
+pos, defined in 
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points desired, assigning a label to the boundary condition
+ set, and giving the name of the spatial database with the values for the
+ Dirichlet boundary condition (
+\family typewriter
+sheardisp.spatialdb
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twotri3.mesh
+\family default
+, 
+\family typewriter
+pylithapp.cfg
+\family default
+, 
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+sheardisp.cfg
+\family default
+, 
+\family typewriter
+sheardisp.spatialdb
+\family default
+) provide a complete description of the problem, and we can then run this
+ example by typing
+\end_layout
+
+\begin_layout LyX-Code
+pylith sheardisp.cfg
+\end_layout
+
+\begin_layout Standard
+Once the problem has run, three files will be produced as in the previous
+ example.
+ If the problem ran correctly, you should be able to generate a figure such
+ as Figure 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twotri-shear"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename figs/sheardisp.jpg
+	lyxscale 50
+	scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the shear displacement example
+ using a mesh composed of two linear triangular cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotri-shear"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Kinematic Fault Slip Example
+\end_layout
+
+\begin_layout Standard
+The next example problem is left-lateral fault slip applied between the
+ two triangular cells using kinematic cohesive cells.
+ The lower left and upper right boundaries are held fixed in the x and y
+ directions.
+ Parameter settings that augment those in 
+\family typewriter
+pylithapp.cfg
+\family default
+ are contained in the file 
+\family typewriter
+dislocation.cfg
+\family default
+.
+ The solution corresponds to rigid body rotation of each triangular cell.
+ As a result, the tractions on the fault are zero.
+ These settings include:
+\end_layout
+
+\begin_layout Description
+pylithapp.journal.info Turns on journaling for 1D quadrature (used for 2D
+ faults) and for cohesive kinematic faults.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.bc.bc Defines which degrees of freedom are being constraine
+d (x and y), gives the label (defined in 
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points desired, and assigns a label to the boundary condition
+ set.
+ In this case, rather than specifying a spatial database file with the values
+ for the Dirichlet boundary condition.
+ The default database (ZeroDispDB) for Dirichlet boundary conditions is
+ used, which sets the displacements to zero.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.interfaces Gives the label (defined in 
+\family typewriter
+twotri3.mesh
+\family default
+) defining the points on the fault, provides quadrature information, and
+ then gives database names for material properties (needed for conditioning),
+ fault slip, peak fault slip rate, and fault slip time.
+\end_layout
+
+\begin_layout Description
+pylithapp.timedependent.interfaces.fault.output.writer Gives the base filename
+ for cohesive cell output files (
+\family typewriter
+dislocation-fault.vtk
+\family default
+).
+\end_layout
+
+\begin_layout Standard
+Rather than specifying the displacement boundary conditions in a spatial
+ database file, we use the default behavior for Dirichlet boundary conditions,
+ which is a uniform, constant displacement of zero.
+\end_layout
+
+\begin_layout Standard
+The fault example requires three additional database files that were not
+ needed for the simple displacement examples.
+ The first file (
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+) specifies 0.01 m of left-lateral fault slip for the entire fault.
+ The data dimension is zero since the same data are applied to all points
+ in the set.
+ The default slip time function is a step-function, so we also must provide
+ the time at which slip begins.
+ The elastic solution is associated with advancing from 
+\begin_inset Formula $t=-dt$
+\end_inset
+
+ to 
+\begin_inset Formula $t=0$
+\end_inset
+
+, so we set the slip initiation time for the step-function to 0 in 
+\family typewriter
+dislocation_sliptime.spatialdb
+\family default
+.
+\end_layout
+
+\begin_layout Standard
+The files containing common information (
+\family typewriter
+twotri3.mesh
+\family default
+, 
+\family typewriter
+pylithapp.cfg
+\family default
+, 
+\family typewriter
+matprops.spatialdb
+\family default
+) along with the problem-specific files (
+\family typewriter
+\size small
+dislocation.cfg
+\family default
+, 
+\family typewriter
+dislocation_slip.spatialdb
+\family default
+, 
+\family typewriter
+dislocation_sliptime.spatialdb
+\family default
+\size default
+) provide a complete description of the problem, and we can then run this
+ example by typing
+\end_layout
+
+\begin_layout LyX-Code
+pylith dislocation.cfg
+\end_layout
+
+\begin_layout Standard
+Once the problem has run, five files are produced.
+ In addition to the files produced in the previous two examples, this example
+ produces two files associated with the fault interface.
+ The file 
+\family typewriter
+dislocation-fault_t0000000.vtk
+\family default
+ gives the fault slip for each vertex on the fault along with the computed
+ traction change for the cohesive cell.
+ The file 
+\family typewriter
+dislocation-fault_info.vtk
+\family default
+ provides information such as the normal direction, final slip, and slip
+ time for each vertex on the fault.
+ If the problem ran correctly, you should be able to generate a figure such
+ as Figure 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "fig:twotri-disloc"
+
+\end_inset
+
+, which was generated using ParaView.
+\end_layout
+
+\begin_layout Standard
+\noindent
+\align center
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename figs/dislocation.jpg
+	lyxscale 50
+	scale 33
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Color contours and vectors of displacement for the kinematic fault example
+ using a mesh composed of two linear triangular cells.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:twotri-disloc"
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document

Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/tutorials.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/tutorials.lyx	2012-06-01 23:02:29 UTC (rev 20282)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/tutorials.lyx	2012-06-01 23:26:01 UTC (rev 20283)
@@ -256,6 +256,13 @@
 \end_inset
 
 
+\begin_inset CommandInset include
+LatexCommand input
+filename "greensfns2d/greensfns2d.lyx"
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Section