[cig-commits] r4400 - in
short/3D/PyLith/branches/pylith-0.8/doc/userguide: .
fileformats fileformats/data install intro materials
runpylith tutorials tutorials/reversenog tutorials/splittest
baagaard at geodynamics.org
baagaard at geodynamics.org
Tue Aug 22 14:42:48 PDT 2006
Author: baagaard
Date: 2006-08-22 14:42:48 -0700 (Tue, 22 Aug 2006)
New Revision: 4400
Added:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.bc
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.connect
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.coord
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.fuldat
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.hist
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.keyval
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.prop
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.skew
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.split
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.statevar
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.time
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.wink
short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splittest/splitcube.tex
Removed:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/bc.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/coord.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fuldat.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/hist.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/prop.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/skew.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/split.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/statevar.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/time.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/maxwell_linear.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splittest/splittest.tex
Modified:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/docdefs.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/makefile
short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/reversenog.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.tex
short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.tex
Log:
Continued docbook to LaTeX conversion. Cleaned up fileformats.
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/docdefs.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/docdefs.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/docdefs.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,34 +1,30 @@
% Miscellaneous
-\newcommand{\email}[1]{\tt #1}
+\newcommand{\email}[1]{{\tt #1}}
-
\newenvironment{warning}{Warning\par}{}
\newenvironment{tip}{Hint\par}{}
% GUI markup
-\newcommand{\guibutton}[1]{\fbox #1}
-\newcommand{\guimenu}[1]{\bf #1}
-\newcommand{\guimenuitem}[1]{\bf #1}
+\newcommand{\guibutton}[1]{{\bf\tt #1}}
+\newcommand{\guimenu}[1]{{\bf #1}}
+\newcommand{\guimenuitem}[1]{{\bf #1}}
\newcommand{\guiselect}{$\rightarrow$}
-\newcommand{\prompt}[1]{\tt\bf #1}
-\newcommand{\userinput}[1]{\tt #1}
-\newenvironment{screen}{}{}
+\newcommand{\prompt}[1]{{\tt #1}}
+\newcommand{\userinput}[1]{{\tt #1}}
+\newenvironment{screen}{\begin{alltt}}{\end{alltt}}
% Source code markup
-\newcommand{\application}[1]{\bf #1}
-\newcommand{\directory}[1]{\tt #1}
-\newcommand{\filename}[1]{\tt #1}
-\newcommand{\envvar}[1]{\tt #1}
-\newcommand{\replaceable}[1]{\it #1}
-\newcommand{\command}[1]{\tt #1}
-\newcommand{\option}[1]{\it\tt #1}
+\newcommand{\application}[1]{{\bf #1}}
+\newcommand{\directory}[1]{{\tt #1}}
+\newcommand{\filename}[1]{{\tt #1}}
+\newcommand{\envvar}[1]{{\tt #1}}
+\newcommand{\replaceable}[1]{{\it #1}}
+\newcommand{\command}[1]{{\tt #1}}
+\newcommand{\option}[1]{{\it\tt #1}}
-\newcommand{\classname}[1]{\em #1}
+\newcommand{\classname}[1]{{\em #1}}
-% temporary, should use hyperref
-\newcommand{\link}[2]{#1 ({\tt #2})}
-
% shortcuts
-\newcommand{\shellprompt}{\prompt{bash\$~}}
+\newcommand{\shellprompt}{\prompt{bash\$\ }}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/bc.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/bc.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/bc.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,47 +0,0 @@
-\subsection{xx.bc}
-
-The \filename{xx.bc} file specifies the displacements, velocity,
-and/or forces applied to vertices on the boundaries.
-
-\begin{figure}[htbp]
- \begin{center}
-\begin{verbatim}
-# File containing boundary conditions at vertices.
-#
-# Comment lines begin with '#'
-#
-# First, specify units of coordinates for each type of boundary
-# conditon. All three are required even if they are not all used.
-#
-displacement_units = m
-velocity_units = m/s
-force_units = newton
-#
-#
-# Boundary conditions applied to vertices. You must specify a flag and
-# value for each degree of freedom, even if some are free.
-#
-# Columns:
-# (1) Vertex number
-# (2) Boundary condition flag for x DOF
-# (3) Boundary condition flag for y DOF
-# (4) Boundary condition flag for z DOF
-# 0 = Free
-# 1 = Fixed displacement
-# 2 = Constant velocity
-# 3 = Constant force
-# A 2 or more digit code may be used for the boundary condition
-# flag. If used, the the final digit refers to the condition
-# type as defined above, while the beginning digit(s) refer to
-# the time history to be used.
-# (5) Boundary condition value for x DOF
-# (6) Boundary condition value for y DOF
-# (7) Boundary condition value for z DOF
-1 0 1 0 0.0000e+00 0.0000e+00 0.0000e+00
-3 0 1 0 0.0000e+00 0.0000e+00 0.0000e+00
-12 0 1 0 0.0000e+00 0.0000e+00 0.0000e+00
-\end{verbatim}
- \ldots
- \caption{Format of \filename{xx.bc} files.}
- \end{center}
-\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/connect.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,48 +0,0 @@
-\subsection{xx.connect}
-
-The \filename{xx.connect} file contains the finite-element mesh
-topology and material type information, including the element type,
-material type, and the lists of vertices for each element.
-
-\begin{figure}
- \begin{center}
-\begin{verbatim}
-# File containing finite-element mesh topology and material type
-# information.
-#
-# Comment lines begin with '#'
-#
-# Columns:
-# (1) Element number
-# (2) Element type
-# 1 = Linear hexahedron (8 vertices)
-# 2 = Linear hexahedron with 1 set of collapsed vertices
-# (7 vertices) [NOT IMPLEMENTED]
-# 3 = Linear hexahedron with 2 sets of collapsed vertices
-# (6 vertices) [NOT IMPLEMENTED]
-# 4 = Linear hexahedron with 4 vertices collapsed to a point
-# (5 vertices) [NOT IMPLEMENTED]
-# 5 = Linear tetrahedron (4 vertices)
-# 6 = Quadratix hexahedron (20 vertices) [NOT IMPLEMENTED]
-# 7 = Quadratic hexahedron with 3 vertices along one edge
-# collapsed to a point (18 vertices) [NOT IMPLEMENTED]
-# 8 = Quadratic hexahedron with 3 sets of collapsed vertices
-# (15 vertices) [NOT IMPLEMENTED]
-# 9 = Quadratic hexahedron with 9 vertices collapsed to a point
-# (13 vertices) [NOT IMPLEMENTED]
-# 10 = Quadratic tetrahedron (10 vertices) [NOT IMPLEMENTED]
-# (3) Material type, numbered consecutively beginning with '1'
-# (4) Infinite element flag, required but not currently implemented
-# 0 = only valid value
-# (5)+ Vertices in the element, identified by vertex number
-#
-# Note: No comments are allowed within the mesh information.
-#
-1 5 1 0 2911 2865 2886 2864
-2 5 2 0 843 3999 4029 3926
-3 5 1 0 684 8975 2346 6219
-\end{verbatim}
- \ldots
- \caption{Format of \filename{xx.connect} files.}
- \end{center}
-\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/coord.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/coord.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/coord.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,36 +0,0 @@
-\subsection{xx.coord}
-
-The \filename{xx.coord} file contains the coordinates of all of the
-vertices in the finite-element mesh.
-
-\begin{figure}
- \begin{center}
-\begin{verbatim}
-# File containing vertices of the finite-element mesh.
-#
-# Comment lines begin with '#'
-#
-# First, specify units of coordinates.
-#
-coord_unit = km
-#
-#
-# Now specify the coordinates of each vertex.
-#
-# Columns:
-# (1) Vertex number
-# (2) X coordinate
-# (3) Y coordinate
-# (4) Z coordinate
-#
-# Note: No comments are allowed within the list of vertex coordinates
-#
-1 0.000000e+00 0.000000e+00 0.000000e+00
-2 1.000000e+00 0.000000e+00 0.000000e+00
-3 0.000000e+00 2.000000e+00 0.000000e+00
-4 1.000000e+00 2.000000e+00 3.000000e+00
-\end{verbatim}
- \ldots
- \caption{Format of \filename{xx.coord} files.}
- \end{center}
-\end{figure}
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.bc
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.bc 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.bc 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,34 @@
+# File containing boundary conditions at vertices.
+#
+# Comment lines begin with '#'
+#
+# First, specify units of coordinates for each type of boundary
+# conditon. All three are required even if they are not all used.
+#
+displacement_units = m
+velocity_units = m/s
+force_units = newton
+#
+#
+# Boundary conditions applied to vertices. You must specify a flag and
+# value for each degree of freedom, even if some are free.
+#
+# Columns:
+# (1) Vertex number
+# (2) Boundary condition flag for x DOF
+# (3) Boundary condition flag for y DOF
+# (4) Boundary condition flag for z DOF
+# 0 = Free
+# 1 = Fixed displacement
+# 2 = Constant velocity
+# 3 = Constant force
+# A 2 or more digit code may be used for the boundary condition
+# flag. If used, the the final digit refers to the condition
+# type as defined above, while the beginning digit(s) refer to
+# the time history to be used.
+# (5) Boundary condition value for x DOF
+# (6) Boundary condition value for y DOF
+# (7) Boundary condition value for z DOF
+1 0 1 0 0.0000e+00 0.0000e+00 0.0000e+00
+3 0 1 0 0.0000e+00 0.0000e+00 0.0000e+00
+12 0 1 0 0.0000e+00 0.0000e+00 0.0000e+00
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.connect
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.connect 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.connect 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,34 @@
+# File containing finite-element mesh topology and material type
+# information.
+#
+# Comment lines begin with '#'
+#
+# Columns:
+# (1) Element number
+# (2) Element type
+# 1 = Linear hexahedron (8 vertices)
+# 2 = Linear hexahedron with 1 set of collapsed vertices
+# (7 vertices) [NOT IMPLEMENTED]
+# 3 = Linear hexahedron with 2 sets of collapsed vertices
+# (6 vertices) [NOT IMPLEMENTED]
+# 4 = Linear hexahedron with 4 vertices collapsed to a point
+# (5 vertices) [NOT IMPLEMENTED]
+# 5 = Linear tetrahedron (4 vertices)
+# 6 = Quadratix hexahedron (20 vertices) [NOT IMPLEMENTED]
+# 7 = Quadratic hexahedron with 3 vertices along one edge
+# collapsed to a point (18 vertices) [NOT IMPLEMENTED]
+# 8 = Quadratic hexahedron with 3 sets of collapsed vertices
+# (15 vertices) [NOT IMPLEMENTED]
+# 9 = Quadratic hexahedron with 9 vertices collapsed to a point
+# (13 vertices) [NOT IMPLEMENTED]
+# 10 = Quadratic tetrahedron (10 vertices) [NOT IMPLEMENTED]
+# (3) Material type, numbered consecutively beginning with '1'
+# (4) Infinite element flag, required but not currently implemented
+# 0 = only valid value
+# (5)+ Vertices in the element, identified by vertex number
+#
+# Note: No comments are allowed within the mesh information.
+#
+1 5 1 0 2911 2865 2886 2864
+2 5 2 0 843 3999 4029 3926
+3 5 1 0 684 8975 2346 6219
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.coord
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.coord 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.coord 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,23 @@
+# File containing vertices of the finite-element mesh.
+#
+# Comment lines begin with '#'
+#
+# First, specify units of coordinates.
+#
+coord_unit = km
+#
+#
+# Now specify the coordinates of each vertex.
+#
+# Columns:
+# (1) Vertex number
+# (2) X coordinate
+# (3) Y coordinate
+# (4) Z coordinate
+#
+# Note: No comments are allowed within the list of vertex coordinates
+#
+1 0.000000e+00 0.000000e+00 0.000000e+00
+2 1.000000e+00 0.000000e+00 0.000000e+00
+3 0.000000e+00 2.000000e+00 0.000000e+00
+4 1.000000e+00 2.000000e+00 3.000000e+00
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.fuldat
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.fuldat 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.fuldat 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,12 @@
+# File containing time steps at which full output is desired.
+#
+# Comment lines begin with '#'
+#
+# Note: Time step 0 (elastic solution) is always included in the
+# output.
+#
+# List the time steps, one per line.
+#
+ 10
+ 50
+ 100
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.hist
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.hist 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.hist 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,17 @@
+# File specifying time variation of boundary conditions.
+#
+# Comment lines begin with '#'
+#
+# Each time history consists of two or more lines. The first line
+# indicates the number of points in the history and the default load
+# value for the history. Subsequent lines define time/load pairs.
+#
+# Line 1, column 1: The number of points in the time history
+# Line 1, column 2: The value assigned to every point by default
+# (overridden by values in time history)
+# Line 2+, column 1: Time (in seconds) for a given load value
+# Line 2+, column 2: Load value at given time
+#
+ 2 1.0
+2.84014e+08 0.1
+3.15576e+08 0.5
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.keyval
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.keyval 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.keyval 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,61 @@
+# Simple parameter values for various PyLith settings. Defaults are
+# listed.
+#
+# Scaling factors applied to Winkler forces.
+#
+winklerScaleX = 1.0
+winklerScaleY = 1.0
+winklerScaleZ = 1.0
+#
+# Scaling factors applied to differential Winkler forces.
+#
+winklerSlipScaleX = 1.0
+winklerSlipScaleY = 1.0
+winklerSlipScaleZ = 1.0
+#
+# Stress integration and numerical computation of the tangent
+# material matrix. Default values should be reasonable for most cases.
+#
+stressTolerance = 1.0e-12*Pa
+minimumStrainPerturbation = 1.0e-7
+initialStrainPerturbation = 1.0e-1
+#
+# Specify whether to use the solution from the previous time step as
+# the starting guess for the elastic solution in the current time step.
+# This feature has not been tested.
+#
+usePreviousDisplacementFlag = 0
+#
+# Quadrature order for the problem.
+#
+quadratureOrder = "Full"
+#
+# Gravitational acceleration in each direction.
+#
+gravityX = 0.0*m/(s*s)
+gravityY = 0.0*m/(s*s)
+gravityZ = 0.0*m/(s*s)
+#
+# Factors controlling computation of prestresses.
+#
+prestressAutoCompute = False
+prestressAutoChangeElasticProperties = False
+prestressAutoComputePoisson = 0.49
+prestressAutoComputeYoungs = 1.0e30*Pa
+#
+prestressScaleXx = 1.0
+prestressScaleYy = 1.0
+prestressScaleZz = 1.0
+prestressScaleXy = 1.0
+prestressScaleXz = 1.0
+prestressScaleYz = 1.0
+#
+# Unit numbers used in Fortran code. These defaults should work for
+# most Unix systems, but may be altered if necessary.
+#
+f77StandardInput = 5
+f77StandardOutput = 6
+f77FileInput = 10
+f77AsciiOutput = 11
+f77PlotOutput = 12
+f77UcdOutput = 13
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.prop
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.prop 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.prop 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,44 @@
+# File containing material properties.
+#
+# Comment lines begin with '#'
+#
+# The material type and material property values are specified using a
+# "keyword = value" syntax. The keywords for the different material
+# types are given below. Units for each of the values with dimensions
+# must follow the value as illustrated in the examples below.
+#
+# Materials and keywords:
+# Isotropic linear elastic
+# materialType ='IsotropicLinearElastic'
+# density
+# youngsModulus
+# poissonsRatio
+# endMaterial ='True' (flag indicating end of material)
+# Isotropic linear maxwell viscoelastic
+# materialType ='IsotropicLinearMaxwellViscoelastic'
+# density
+# youngsModulus
+# poissonsRatio
+# viscosity
+# endMaterial ='True' (flag indicating end of material)
+#
+# Material number 1
+materialType = 'IsotropicLinearMaxwellViscoelastic'
+density = 3000.0*kg/m**3
+youngsModulus = 7.5e10*Pa
+poissonsRatio = 0.25
+viscosity = 1.0e+18*Pa*s
+endMaterial = True
+# Material number 2
+materialType = 'IsotropicLinearElastic'
+density = 3000.0*kg/m**3
+youngsModulus = 7.5e10*Pa
+poissonsRatio = 0.25
+endMaterial = True
+# Material number 3
+materialType = 'IsotropicLinearMaxwellViscoelastic'
+density = 3000.0*kg/m**3
+youngsModulus = 7.5e10*Pa
+poissonsRatio = 0.25
+viscosity = 1.0e+18*Pa*s
+endMaterial = True
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.skew
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.skew 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.skew 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,16 @@
+# File containing local nodal coordinates.
+#
+# Comment lines begin with '#'
+#
+# First, specify units for rotations.
+#
+rotation_units = degree
+#
+#
+# Columns:
+# (1) Node number
+# (2) Euler angle for rotation in the x-y plane
+# (3) Euler angle for rotation in the x-z plane
+#
+68 12.3 4.2
+132 -12.3 -4.2
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.split
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.split 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.split 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,25 @@
+# File containing time stepping parameters.
+#
+# Comment lines begin with '#'
+#
+# Displacements are specified for each vertex on the fault for each
+# element containing the vertex. The displacements on each side of the
+# fault or dike should have opposite signs. The displacements
+# associated with a single side of the fault for each vertex should be
+# the same.
+#
+# Columns:
+# (1) Element number
+# (2) Vertex number
+# (3) Time history flag
+# 0 = Slip only in elastic solution
+# -1 = Slip at constant velocity
+# n = Slip according to load history n (requires xx.hist file)
+# (4) Displacement in x direction
+# (5) Displacement in y direction
+# (6) Displacement in z direction
+#
+ 14886 36 0 0.353500000 0.00000000 -0.353500000
+ 14887 36 0 0.353500000 0.00000000 -0.353500000
+ 14896 36 0 -0.353500000 0.00000000 0.353500000
+ 14981 36 0 -0.353500000 0.00000000 0.353500000
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.statevar
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.statevar 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.statevar 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,23 @@
+# File specifying which state variables to output.
+#
+# Comment lines begin with '#'
+#
+# State variables occur in groups of 6, corresponding to the number of
+# stress/strain components. The present groups are:
+# 1-6: Cauchy stress
+# 7-12: Total strain
+# 13-18: Viscous strain
+# 18-24: Plastic strain
+#
+# Lines:
+# (1) Total accumulated values for the current time step
+# (2) Incremental values (previous to current)
+# (3) Rate values (previous to current)
+#
+# Columns (per line):
+# (1) Number of state variables to output (0 ≤ value ≤ 24)
+# (2)+ State variable number to output (1 ≤ value ≤ 24)
+#
+ 12 1 2 3 4 5 6 7 8 9 10 11 12
+ 12 1 2 3 4 5 6 7 8 9 10 11 12
+ 0
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.time
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.time 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.time 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,42 @@
+# File containing time stepping parameters.
+#
+# Comment lines begin with '#'
+#
+# First, specify units used in values with dimensions of time.
+#
+time_units = year
+#
+#
+# Time stepping parameters are given in groups. The elastic solution
+# corresponds to group 0 and must always be defined. Although some of
+# the parameters do not have any meaning for the elastic solution,
+# they must be present anyway.
+#
+# Columns:
+# (1) Time step group number (=0 for elastic solution).
+# (2) The number of time steps in the group (=1 for elastic solution).
+# (3) Time step size (given in units of time_units).
+# (4) Amount of implicitness. Real dimensionless parameter that
+# ranges from 0.0 (fully explicit) to 1.0 (fully implicit). The
+# value is generally set to 0.5.
+# (5) Maximum number of equilibrium iterations before stiffness
+# matrix is reformed.
+# (6) Number of time steps between initial reformation of stiffness
+# matrix.
+# <0 Indicates that reformation should occur only for the first
+# step in each time step group.
+# =0 Indicates that reformation should never occur.
+# (7) Large deformation solution flag (only Linear strain is
+# presently available).
+# 0 = Linear strain
+# 1 = Large strain but use only linear contribution to the
+# stiffness matrix (sometimes results in better convergence)
+# 2 = Large strain and use nonlinear contribution to the
+# stiffness matrix
+# (8) Convergence tolerance for displacements (dimensionless value)
+# (9) Convergence tolerance for forces (dimensionless value)
+# (10) Convergence tolerance for energy (dimensionless value)
+# (11) Maximum number of equilibrium iterations
+#
+ 0 1 0.0 5.0e-01 1001 4 0 1.0e+00 1.0e+0 1.0e+00 1
+ 1 100 0.1 5.0e-01 1001 -1 0 1.0e+00 1.0e+0 1.0e+00 1
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.wink
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.wink 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/data/xx.wink 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,21 @@
+# File containing Winkler elements.
+#
+# Comment lines begin with '#'
+#
+# Flags for the degrees of freedom can have the following values:
+# 0 = no Winkler force
+# 1 = Winkler force applied at all times
+# -n = Winkler force applied according to load history n
+# (requires xx.hist file)
+#
+# Columns:
+# (1) Vertex number
+# (2) Flag for DOF in x-direction
+# (3) Flag for DOF in y-direction
+# (4) Flag for DOF in z-direction
+# (5) Magnitude of restoring force for x-direction
+# (6) Magnitude of restoring force for x-direction
+# (7) Magnitude of restoring force for x-direction
+#
+14 0 -1 0 0.0e+00 1.0e+25 0.0e+00
+18 0 1 0 1.0e+20 0.0e+00 0.0e+00
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -8,18 +8,209 @@
locations in some files (see the discussion of each file format for
more information).
-% Required input files
-\input{coord.tex}
-\input{connect.tex}
-\input{bc.tex}
-\input{time.tex}
-\input{prop.tex}
-\input{statevar.tex}
+% REQUIRED INPUT FILES
-% Optional input files
-\input{split.tex}
-\input{fuldat.tex}
-\input{skew.tex}
-\input{keyval.tex}
-\input{hist.tex}
-\input{wink.tex}
+\subsection{xx.coord}
+
+The \filename{xx.coord} file contains the coordinates of all of the
+vertices in the finite-element mesh.
+
+\begin{figure}[htbp]
+ \begin{center}
+ \verbatiminput{data/xx.coord}
+ \caption{Format of \filename{xx.coord} files.}
+ \end{center}
+\end{figure}
+
+\subsection{xx.connect}
+
+The \filename{xx.connect} file contains the finite-element mesh
+topology and material type information, including the element type,
+material type, and the lists of vertices for each element.
+
+\begin{figure}[htbp]
+ \begin{center}
+ \verbatiminput{data/xx.connect}
+ \caption{Format of \filename{xx.connect} files.}
+ \end{center}
+\end{figure}
+
+\subsection{xx.bc}
+
+The \filename{xx.bc} file specifies the displacements, velocity,
+and/or forces applied to vertices on the boundaries.
+
+\begin{figure}[htbp]
+ \begin{center}
+ \verbatiminput{data/xx.bc}
+ \caption{Format of \filename{xx.bc} files.}
+ \end{center}
+\end{figure}
+
+\subsection{xx.time}
+
+The \filename{xx.time} file specifies the time stepping parameters for
+the simulation.
+
+\begin{warning}
+ The convergence criteria depend on the type of solution and material
+ models. The time step for a linear elastic problem is much different
+ than that for a nonlinear or time-dependent problem.
+\end{warning}
+
+\begin{figure}[htbp]
+ \begin{center}
+ \verbatiminput{data/xx.time}
+ \caption{Format of \filename{xx.time} files.}
+ \end{center}
+\end{figure}
+
+\subsection{xx.prop}
+
+The \filename{xx.prop} file specifies the properties for each material
+model in the problem.
+
+\begin{warning}
+ The materials must be listed in order according to the material
+ number assigned to the elements in \filename{xx.connect}.
+\end{warning}
+
+\begin{figure}[htbp]
+ \begin{center}
+ \verbatiminput{data/xx.prop}
+ \caption{Format of \filename{xx.prop} files.}
+ \end{center}
+\end{figure}
+
+\subsection{xx.statevar}
+
+The \filename{xx.statevar} file specifies which state variables are to
+be included in the output of the elastic and time dependent solutions.
+
+\begin{figure}[htbp]
+ \begin{center}
+ \verbatiminput{data/xx.statevar}
+ \caption{Format of \filename{xx.statevar} files.}
+ \end{center}
+\end{figure}
+
+% OPTIONAL INPUT FILES
+
+\subsection{xx.split}
+
+The \filename{xx.split} file specifies the split node information for
+modeling dislocations. Dislocations may be used in simulating slip on
+faults as well as dike intrusions.
+
+\begin{figure}[htbp]
+ \begin{center}
+ \verbatiminput{xx.split}
+ \caption{Format of \filename{xx.split} files.}
+ \end{center}
+\end{figure}
+
+\subsection{xx.fuldat}
+
+The \filename{xx.fuldat} file lists the time step numbers at which
+full output is desired. The elastic solution (time step 0) is always
+included in the output. This file is required for time-dependent
+problems.
+
+\begin{figure}[htbp]
+ \begin{center}
+ \verbatiminput{xx.fuldat}
+ \caption{Format of \filename{xx.time} files.}
+ \end{center}
+\end{figure}
+
+\subsection{xx.skew}
+
+The \filename{xx.skew} file specifies local coordinate systems for
+nodes. The local coordinate system is specified using two Euler angles
+that rotate the local coordinate system to the global coordinate
+system.
+
+The applied coordinate rotations apply to all boundary conditions
+associated with the nodes listed in the file. These are useful, for
+example, if it is desired to apply boundary conditions in a direction
+normal or tangential to a side of the mesh when the side does not
+align with the global coordinate directions. Similarly, skew
+conditions could be used when specifying slip on a fault that lies at
+an angle to the global coordinates.
+
+\begin{figure}[htbp]
+ \begin{center}
+ \verbatiminput{xx.skew}
+ \caption{Format of \filename{xx.time} files.}
+ \end{center}
+\end{figure}
+
+\subsection{xx.keyval}
+
+The \filename{xx.keyval} file specifies some simple parameter
+settings.
+
+\subsubsection{Winkler forces}
+
+Scaling factors can be applied to Winkler forces, permitting a quick
+and easy way to change the density or gravitational acceleration when
+Winkler forces are used to simulate gravity.
+
+\paragraph{Quadrature order}
+
+\begin{description}
+\item[Full] Quadrature order that should give the exact element
+ matrices when the elements are geometrically undistorted.
+\item[Reduced] Quadrature order that is one order less than full
+ quadrature. Note that for linear tetrahedra full and reduced
+ quadrature are equivalent (single integration point).
+
+ \begin{warning}
+ Use with caution as reduced quadrature can lead to numerical
+ instabilities.
+ \end{warning}
+
+\item[Selective] Uses Hughes' b-bar formulation to perform reduced
+ quadrature on the dilatational parts of the strain-displacement
+ matrix. This can be useful in nearly-incompressible problems.
+\end{description}
+
+\paragraph{Prestresses}
+
+Gravitational prestresses can be computed automatically. In such
+cases, the elastic properties in the prestress calculation can be set
+to uniform values independent of the parameters for any of the
+material models. When gravity is being used and prestresses are not
+computed automatically, each prestress component can be scaled
+independently. Reading prestresses from files is presently disabled.
+
+\begin{figure}[htbp]
+ \begin{center}
+ \verbatiminput{xx.keyval}
+ \caption{Format of \filename{xx.keyval} files.}
+ \end{center}
+\end{figure}
+
+\subsection{xx.hist}
+
+The \filename{xx.hist} files provide time histories for use in
+boundary conditions.
+
+\begin{figure}
+ \begin{center}
+ \verbatiminput{xx.hist}
+ \caption{Format of \filename{xx.hist} files.}
+ \end{center}
+\end{figure}
+
+\subsection{xx.wink}
+
+The \filename{xx.wink} file specifies Winkler elements, which may be
+used as spring foundations in the simulation of gravity.
+
+\begin{figure}
+ \begin{center}
+ \verbatiminput{xx.wink}
+ \caption{Format of \filename{xx.wink} files.}
+ \end{center}
+\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fuldat.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fuldat.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fuldat.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,27 +0,0 @@
-\subsection{xx.fuldat}
-
-The \filename{xx.fuldat} file lists the time step numbers at which
-full output is desired. The elastic solution (time step 0) is always
-included in the output. This file is required for time-dependent
-problems.
-
-\begin{figure}
- \begin{center}
-\begin{verbatim}
-# File containing time steps at which full output is desired.
-#
-# Comment lines begin with '#'
-#
-# Note: Time step 0 (elastic solution) is always included in the
-# output.
-#
-# List the time steps, one per line.
-#
- 10
- 50
- 100
-\end{verbatim}
-\ldots
- \caption{Format of \filename{xx.time} files.}
- \end{center}
-\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/hist.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/hist.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/hist.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,29 +0,0 @@
-\subsection{xx.hist}
-
-The \filename{xx.hist} files provide time histories for use in
-boundary conditions.
-
-\begin{figure}
- \begin{center}
-\begin{verbatim}
-# File specifying time variation of boundary conditions.
-#
-# Comment lines begin with '#'
-#
-# Each time history consists of two or more lines. The first line
-# indicates the number of points in the history and the default load
-# value for the history. Subsequent lines define time/load pairs.
-#
-# Line 1, column 1: The number of points in the time history
-# Line 1, column 2: The value assigned to every point by default
-# (overridden by values in time history)
-# Line 2+, column 1: Time (in seconds) for a given load value
-# Line 2+, column 2: Load value at given time
-#
- 2 1.0
-2.84014e+08 0.1
-3.15576e+08 0.5
-\end{verbatim}
- \caption{Format of \filename{xx.hist} files.}
- \end{center}
-\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/keyval.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,107 +0,0 @@
-\subsection{xx.keyval}
-
-The \filename{xx.keyval} file specifies some simple parameter
-settings.
-
-\subsubsection{Winkler forces}
-
-Scaling factors can be applied to Winkler forces, permitting a quick
-and easy way to change the density or gravitational acceleration when
-Winkler forces are used to simulate gravity.
-
-\paragraph{Quadrature order}
-
-\begin{description}
-\item[Full] Quadrature order that should give the exact element
- matrices when the elements are geometrically undistorted.
-\item[Reduced] Quadrature order that is one order less than full
- quadrature. Note that for linear tetrahedra full and reduced
- quadrature are equivalent (single integration point).
-
- \begin{warning}
- Use with caution as reduced quadrature can lead to numerical
- instabilities.
- \end{warning}
-
-\item[Selective] Uses Hughes' b-bar formulation to perform reduced
- quadrature on the dilatational parts of the strain-displacement
- matrix. This can be useful in nearly-incompressible problems.
-\end{description}
-
-\paragraph{Prestresses}
-
-Gravitational prestresses can be computed automatically. In such
-cases, the elastic properties in the prestress calculation can be set
-to uniform values independent of the parameters for any of the
-material models. When gravity is being used and prestresses are not
-computed automatically, each prestress component can be scaled
-independently. Reading prestresses from files is presently disabled.
-
-\begin{figure}
-\begin{center}
-\begin{verbatim}
-# Simple parameter values for various PyLith settings. Defaults are
-# listed.
-#
-# Scaling factors applied to Winkler forces.
-#
-winklerScaleX = 1.0
-winklerScaleY = 1.0
-winklerScaleZ = 1.0
-#
-# Scaling factors applied to differential Winkler forces.
-#
-winklerSlipScaleX = 1.0
-winklerSlipScaleY = 1.0
-winklerSlipScaleZ = 1.0
-#
-# Stress integration and numerical computation of the tangent
-# material matrix. Default values should be reasonable for most cases.
-#
-stressTolerance = 1.0e-12*Pa
-minimumStrainPerturbation = 1.0e-7
-initialStrainPerturbation = 1.0e-1
-#
-# Specify whether to use the solution from the previous time step as
-# the starting guess for the elastic solution in the current time step.
-# This feature has not been tested.
-#
-usePreviousDisplacementFlag = 0
-#
-# Quadrature order for the problem.
-#
-quadratureOrder = "Full"
-#
-# Gravitational acceleration in each direction.
-#
-gravityX = 0.0*m/(s*s)
-gravityY = 0.0*m/(s*s)
-gravityZ = 0.0*m/(s*s)
-#
-# Factors controlling computation of prestresses.
-#
-prestressAutoCompute = False
-prestressAutoChangeElasticProperties = False
-prestressAutoComputePoisson = 0.49
-prestressAutoComputeYoungs = 1.0e30*Pa
-#
-prestressScaleXx = 1.0
-prestressScaleYy = 1.0
-prestressScaleZz = 1.0
-prestressScaleXy = 1.0
-prestressScaleXz = 1.0
-prestressScaleYz = 1.0
-#
-# Unit numbers used in Fortran code. These defaults should work for
-# most Unix systems, but may be altered if necessary.
-#
-f77StandardInput = 5
-f77StandardOutput = 6
-f77FileInput = 10
-f77AsciiOutput = 11
-f77PlotOutput = 12
-f77UcdOutput = 13
-\end{verbatim}
- \caption{Format of \filename{xx.keyval} files.}
- \end{center}
-\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/prop.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/prop.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/prop.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,62 +0,0 @@
-\subsection{xx.prop}
-
-The \filename{xx.prop} file specifies the properties for each material
-model in the problem.
-
-\begin{warning}
- The materials must be listed in order according to the material
- number assigned to the elements in \filename{xx.connect}.
-\end{warning}
-
-\begin{figure}
- \begin{center}
-\begin{verbatim}
-# File containing material properties.
-#
-# Comment lines begin with '#'
-#
-# The material type and material property values are specified using a
-# "keyword = value" syntax. The keywords for the different material
-# types are given below. Units for each of the values with dimensions
-# must follow the value as illustrated in the examples below.
-#
-# Materials and keywords:
-# Isotropic linear elastic
-# materialType ='IsotropicLinearElastic'
-# density
-# youngsModulus
-# poissonsRatio
-# endMaterial ='True' (flag indicating end of material)
-# Isotropic linear maxwell viscoelastic
-# materialType ='IsotropicLinearMaxwellViscoelastic'
-# density
-# youngsModulus
-# poissonsRatio
-# viscosity
-# endMaterial ='True' (flag indicating end of material)
-#
-# Material number 1
-materialType = 'IsotropicLinearMaxwellViscoelastic'
-density = 3000.0*kg/m**3
-youngsModulus = 7.5e10*Pa
-poissonsRatio = 0.25
-viscosity = 1.0e+18*Pa*s
-endMaterial = True
-# Material number 2
-materialType = 'IsotropicLinearElastic'
-density = 3000.0*kg/m**3
-youngsModulus = 7.5e10*Pa
-poissonsRatio = 0.25
-endMaterial = True
-# Material number 3
-materialType = 'IsotropicLinearMaxwellViscoelastic'
-density = 3000.0*kg/m**3
-youngsModulus = 7.5e10*Pa
-poissonsRatio = 0.25
-viscosity = 1.0e+18*Pa*s
-endMaterial = True
-\end{verbatim}
- \ldots
- \caption{Format of \filename{xx.prop} files.}
- \end{center}
-\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/skew.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/skew.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/skew.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,39 +0,0 @@
-\subsection{xx.skew}
-
-The \filename{xx.skew} file specifies local coordinate systems for
-nodes. The local coordinate system is specified using two Euler angles
-that rotate the local coordinate system to the global coordinate
-system.
-
-The applied coordinate rotations apply to all boundary conditions
-associated with the nodes listed in the file. These are useful, for
-example, if it is desired to apply boundary conditions in a direction
-normal or tangential to a side of the mesh when the side does not
-align with the global coordinate directions. Similarly, skew
-conditions could be used when specifying slip on a fault that lies at
-an angle to the global coordinates.
-
-\begin{figure}
- \begin{center}
-\begin{verbatim}
-# File containing local nodal coordinates.
-#
-# Comment lines begin with '#'
-#
-# First, specify units for rotations.
-#
-rotation_units = degree
-#
-#
-# Columns:
-# (1) Node number
-# (2) Euler angle for rotation in the x-y plane
-# (3) Euler angle for rotation in the x-z plane
-#
-68 12.3 4.2
-132 -12.3 -4.2
-\end{verbatim}
- \ldots
- \caption{Format of \filename{xx.time} files.}
- \end{center}
-\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/split.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/split.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/split.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,39 +0,0 @@
-\subsection{xx.split}
-
-The \filename{xx.split} file specifies the split node information for
-modeling dislocations. Dislocations may be used in simulating slip on
-faults as well as dike intrusions.
-
-\begin{figure}
- \begin{center}
-\begin{verbatim}
-# File containing time stepping parameters.
-#
-# Comment lines begin with '#'
-#
-# Displacements are specified for each vertex on the fault for each
-# element containing the vertex. The displacements on each side of the
-# fault or dike should have opposite signs. The displacements
-# associated with a single side of the fault for each vertex should be
-# the same.
-#
-# Columns:
-# (1) Element number
-# (2) Vertex number
-# (3) Time history flag
-# 0 = Slip only in elastic solution
-# -1 = Slip at constant velocity
-# n = Slip according to load history n (requires xx.hist file)
-# (4) Displacement in x direction
-# (5) Displacement in y direction
-# (6) Displacement in z direction
-#
- 14886 36 0 0.353500000 0.00000000 -0.353500000
- 14887 36 0 0.353500000 0.00000000 -0.353500000
- 14896 36 0 -0.353500000 0.00000000 0.353500000
- 14981 36 0 -0.353500000 0.00000000 0.353500000
-\end{verbatim}
- \ldots
- \caption{Format of \filename{xx.split} files.}
- \end{center}
-\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/statevar.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/statevar.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/statevar.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,35 +0,0 @@
-\subsection{xx.statevar}
-
-The \filename{xx.statevar} file specifies which state variables are to
-be included in the output of the elastic and time dependent solutions.
-
-\begin{figure}
- \begin{center}
-\begin{verbatim}
-# File specifying which state variables to output.
-#
-# Comment lines begin with '#'
-#
-# State variables occur in groups of 6, corresponding to the number of
-# stress/strain components. The present groups are:
-# 1-6: Cauchy stress
-# 7-12: Total strain
-# 13-18: Viscous strain
-# 18-24: Plastic strain
-#
-# Lines:
-# (1) Total accumulated values for the current time step
-# (2) Incremental values (previous to current)
-# (3) Rate values (previous to current)
-#
-# Columns (per line):
-# (1) Number of state variables to output (0 ≤ value ≤ 24)
-# (2)+ State variable number to output (1 ≤ value ≤ 24)
-#
- 12 1 2 3 4 5 6 7 8 9 10 11 12
- 12 1 2 3 4 5 6 7 8 9 10 11 12
- 0
-\end{verbatim}
- \caption{Format of \filename{xx.statevar} files.}
- \end{center}
-\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/time.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/time.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/time.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,61 +0,0 @@
-\subsection{xx.time}
-
-The \filename{xx.time} file specifies the time stepping parameters for
-the simulation.
-
-\begin{warning}
- The convergence criteria depend on the type of solution and material
- models. The time step for a linear elastic problem is much different
- than that for a nonlinear or time-dependent problem.
-\end{warning}
-
-\begin{figure}
- \begin{center}
-\begin{verbatim}
-# File containing time stepping parameters.
-#
-# Comment lines begin with '#'
-#
-# First, specify units used in values with dimensions of time.
-#
-time_units = year
-#
-#
-# Time stepping parameters are given in groups. The elastic solution
-# corresponds to group 0 and must always be defined. Although some of
-# the parameters do not have any meaning for the elastic solution,
-# they must be present anyway.
-#
-# Columns:
-# (1) Time step group number (=0 for elastic solution).
-# (2) The number of time steps in the group (=1 for elastic solution).
-# (3) Time step size (given in units of time_units).
-# (4) Amount of implicitness. Real dimensionless parameter that
-# ranges from 0.0 (fully explicit) to 1.0 (fully implicit). The
-# value is generally set to 0.5.
-# (5) Maximum number of equilibrium iterations before stiffness
-# matrix is reformed.
-# (6) Number of time steps between initial reformation of stiffness
-# matrix.
-# <0 Indicates that reformation should occur only for the first
-# step in each time step group.
-# =0 Indicates that reformation should never occur.
-# (7) Large deformation solution flag (only Linear strain is
-# presently available).
-# 0 = Linear strain
-# 1 = Large strain but use only linear contribution to the
-# stiffness matrix (sometimes results in better convergence)
-# 2 = Large strain and use nonlinear contribution to the
-# stiffness matrix
-# (8) Convergence tolerance for displacements (dimensionless value)
-# (9) Convergence tolerance for forces (dimensionless value)
-# (10) Convergence tolerance for energy (dimensionless value)
-# (11) Maximum number of equilibrium iterations
-#
- 0 1 0.0 5.0e-01 1001 4 0 1.0e+00 1.0e+0 1.0e+00 1
- 1 100 0.1 5.0e-01 1001 -1 0 1.0e+00 1.0e+0 1.0e+00 1
-\end{verbatim}
- \ldots
- \caption{Format of \filename{xx.time} files.}
- \end{center}
-\end{figure}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/wink.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,34 +0,0 @@
-\subsection{xx.wink}
-
-The \filename{xx.wink} file specifies Winkler elements, which may be
-used as spring foundations in the simulation of gravity.
-
-\begin{figure}
- \begin{center}
-\begin{verbatim}
-# File containing Winkler elements.
-#
-# Comment lines begin with '#'
-#
-# Flags for the degrees of freedom can have the following values:
-# 0 = no Winkler force
-# 1 = Winkler force applied at all times
-# -n = Winkler force applied according to load history n
-# (requires xx.hist file)
-#
-# Columns:
-# (1) Vertex number
-# (2) Flag for DOF in x-direction
-# (3) Flag for DOF in y-direction
-# (4) Flag for DOF in z-direction
-# (5) Magnitude of restoring force for x-direction
-# (6) Magnitude of restoring force for x-direction
-# (7) Magnitude of restoring force for x-direction
-#
-14 0 -1 0 0.0e+00 1.0e+25 0.0e+00
-18 0 1 0 1.0e+20 0.0e+00 0.0e+00
-\end{verbatim}
- \ldots
- \caption{Format of \filename{xx.wink} files.}
- \end{center}
-\end{figure}
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/install/install.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -20,18 +20,18 @@
\email{cig-short at geodynamics.org}, is a mailing list dedicated to CIG
issues associated with short-term crustal dynamics, including the use
of PyLith. You can subscribe to the mailing list and view messages at
-the \link{CIG website}{http://www.geodynamics.org}.
+the \href{http://www.geodynamics.org}{CIG website}.
\subsection{Reporting bugs and errors}
CIG uses the \application{Roundup} for bug tracking. If you find a bug
-in PyLith, please submit a bug report to the \link{CIG
-\application{Roundup} system}{http://www.geodynamics.org/roundup}. Of
-course, it is helpful to first check to see if someone else already
-submitted a report related to the issue; one of the CIG developers may
-have already posted a solution to the problem. You can reply to a
-current issue by clicking on the issue title. To submit a new issue,
-click on \guibutton{Create New} under \guimenu{Issues}.
+in PyLith, please submit a bug report to the
+\href{http://www.geodynamics.org/roundup}{CIG \application{Roundup}
+ system}. Of course, it is helpful to first check to see if someone
+else already submitted a report related to the issue; one of the CIG
+developers may have already posted a solution to the problem. You can
+reply to a current issue by clicking on the issue title. To submit a
+new issue, click on \guibutton{Create New} under \guimenu{Issues}.
\section{Installation}
@@ -46,10 +46,10 @@
compatible machine with GLIBC 2.2 or later.
\begin{enumerate}
-\item Download the \link{tarball}{http://crust.geodynamics.org/~leif/shipping/}
+\item Download the \href{http://crust.geodynamics.org/~leif/shipping/}{tarball}
\item Unpack the tarball in a suitable location.
\begin{screen}
- \prompt{bash~}\userinput{tar -zxvf pylith-0.8-linux-x86.tar.gz}
+ \shellprompt\userinput{tar -zxvf pylith-0.8-linux-x86.tar.gz}
\end{screen}
\item Add \directory{pylith-0.8-linux-x86/bin} to your \envvar{PATH}.
You will likely want to add something like
@@ -66,7 +66,7 @@
\replaceable{absolute\_path}/pylith-0.8-linux-x86/lib
\end{screen}
to your \filename{.bashrc} file (if you are using bash as your
- shell) or the equivalent to your \filename{.cshrc</filename} file
+ shell) or the equivalent to your \filename{.cshrc} file
(if you are using tcsh as your shell).
\item To uninstall PyLith, simply remove the \directory{pylith-0.8-linux-x86}
directory and all of its sub-directories.
@@ -80,7 +80,7 @@
rather slowly).
\begin{enumerate}
-\item Download the \link{disk image}{http://crust.geodynamics.org/~leif/shipping/}.
+\item Download the \href{http://crust.geodynamics.org/~leif/shipping/}{disk image}.
\item Double click on the disk image to mount the disk.
\item Double click on the disk and copy the \directory{PyLith} folder
to a suiteable location.
@@ -96,7 +96,7 @@
\begin{enumerate}
\item Download theq
- \link{installer}{http://crust.geodynamics.org/~leif/shipping/}.
+ \href{http://crust.geodynamics.org/~leif/shipping/}{installer}.
\item Double click on the \filename{setup.exe} file you just
downloaded and follow the instructions for installing.
\item To run PyLith, double click on the PyLith icon on the desktop or
@@ -113,9 +113,10 @@
PyLith depends on several other packages. In general, each package
must be compiled from source using compilers for each language that
are compatible with one another. The stable version of the PyLith
-source code is available from the \link{Geodynamics subversion
- repository}{http://www.geodynamics.org:8080/cig/software/Repository/}
-\directory{cig/short/3D/PyLith/branches/pylith-0.8}.
+source code is available from the
+\directory{cig/software/Repository/cig/short/3D/PyLith/branches/pylith-0.8}
+of the \href{http://www.geodynamics.org:8080/}{Geodynamics subversion
+ repository}.
\subsection{System Requirements}
@@ -160,10 +161,10 @@
experience building and installing software.
\end{warning}
-The PyLith-0.8 source code is available from the \link{Geodynamics
+The PyLith-0.8 source code is available from the \href{http://www.geodynamics.org:8080/cig/software/Repository}
+\directory{cig/short/3D/PyLith/branches/pylith-0.8}{Geodynamics
subversion
- repository}{http://www.geodynamics.org:8080/cig/software/Repository}
-\directory{cig/short/3D/PyLith/branches/pylith-0.8}.
+ repository}.
\subsection{System Requirements}
@@ -190,9 +191,9 @@
to build PyLith and the external packages on which it depends.
\begin{enumerate}
-\item Build \link{PETSc (developers
- version)}{http://www-unix.mcs.anl.gov/petsc/petsc-as/developers/index.html}
- and MPI.
+\item Build
+ \href{http://www-unix.mcs.anl.gov/petsc/petsc-as/developers/index.html}{PETSc
+ (developers version)} and MPI.
If you have an architecture optimized version of BLAS/LAPACK you
should use those instead of asking PETSc to download and build one
@@ -217,8 +218,7 @@
\begin{screen}
\shellprompt\userinput{hg clone http://mercurial.mcs.anl.gov/petsc/petsc-dev}
\shellprompt\userinput{cd petsc-dev/python}
- \shellprompt\userinput{hg clone http://mercurial.mcs.anl.gov/petsc/BuildSystem \
- BuildSystem}
+ \shellprompt\userinput{hg clone http://mercurial.mcs.anl.gov/petsc/BuildSystem BuildSystem}
\end{screen}
\item Set the \envvar{PETSC\_DIR} and \envvar{PETSC\_ARCH} environment
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/intro/intro.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -127,7 +127,7 @@
\subsection{PETSc}
-\link{PETSc}{http://www-unix.mcs.anl.gov/petsc/petsc-as/}, the
+\href{http://www-unix.mcs.anl.gov/petsc/petsc-as/}{PETSc}, the
Portable, Extensible Toolkit for Scientific computation, provides a
suite of routines for parallel, numerical solution of partial
differential equations for linear and nonlinear systems with large,
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/makefile
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/makefile 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/makefile 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,18 +1,8 @@
-#XSLSTYLESHEET_DIR=/usr/share/sgml/docbook/xsl-stylesheets
-XSLSTYLESHEET_DIR=/sw/share/xml/xsl/docbook-xsl
+default: userguide.dvi
-pylith_userguide.pdf pdf: pylith_userguide.fo
- fop $< pylith_userguide.pdf
+userguide.dvi:
+ latex userguide
-pylith_userguide.ps ps: pylith_userguide.fo
- fop -fo $< -ps pylith_userguide.ps
+again:
+ latex userguide
-pylith_userguide.xhtml xhtml:
- xsltproc --xinclude -o pylith_userguide.xhtml ${XSLSTYLESHEET_DIR}/xhtml/docbook.xsl pylith_userguide.xml
-
-pylith_userguide.fo:
- xsltproc --xinclude -o $@ ${XSLSTYLESHEET_DIR}/fo/docbook.xsl pylith_userguide.xml
-
-
-clean:
- -rm pylith_userguide.fo pylith_userguide.pdf
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/materials.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,3 +1,128 @@
\chapter{Material Models}
-\input{maxwell_linear.tex}
+\section{Effective Stress Function Formulation for a Maxwell Linear
+Viscoelastic Material}
+
+\subsection{Determination of stresses}
+
+The element stresses are
+\begin{equation}
+ \text{figs/ml-eq1.eps}
+\end{equation}
+where ?? is the total strain and $\text{ml-inlineeq1}$ is the initial
+stress. In terms of the deviatoric stress,
+\begin{equation}
+ \text{figs/ml-eq2.eps}
+\end{equation}
+where
+\begin{equation}
+ \text{figs/ml-eq3.eps}
+\end{equation}
+and the mean stress and strain are given by
+\begin{equation}
+ \text{figs/ml-eq4.eps}
+\end{equation}
+Equation~(2) [REPLACE WITH REF] may also be written as
+\begin{equation}
+ \text{figs/ml-eq4.eps}
+\end{equation}
+where
+\begin{equation}
+ \text{figs/ml-eq6.eps}
+\end{equation}
+The creep strain increment is approximated using
+\begin{equation}
+ \text{figs/ml-eq7.eps}
+\end{equation}
+where, using the $\alpha$-method of time integration,
+\begin{equation}
+ \text{figs/ml-eq8.eps}
+\end{equation}
+and
+\begin{equation}
+ \text{figs/ml-eq9.eps}
+\end{equation}
+where
+\begin{equation}
+ \text{figs/ml-eq10.eps}
+\end{equation}
+and
+\begin{equation}
+ \text{figs/ml-eq11.eps}
+\end{equation}
+For a linear Maxwell viscoelastic material
+\begin{equation}
+ \text{figs/ml-eq12.eps}
+\end{equation}
+Therefore,
+\begin{equation}
+ \text{figs/ml-eq13.eps}
+\end{equation}
+Subsituting (8), (12), and (13) into (5) [REPLACE WITH REFS], we obtain
+\begin{equation}
+ \text{figs/ml-eq14.eps}
+\end{equation}
+Solving for $\text{figs/ml-inlineeq2}$,
+\begin{equation}
+ \text{figs/ml-eq15.eps}
+\end{equation}
+In this case it is possible to solve directly for the deviatoric
+stresses, and the effective stress function approach is not needed. To
+obtain the total stress, we simply use
+\begin{equation}
+ \text{figs/ml-eq16.eps}
+\end{equation}
+
+\subsection{Tangent stress-strain relation}
+
+It is now necessary to provide a relationship for the viscoelastic
+tangent material matrix. If we use vectors composed of the stresses
+and tensor strains, this relationship is
+\begin{equation}
+ \text{figs/ml-eq17.eps}
+\end{equation}
+In terms of the vectors, we have
+\begin{equation}
+ \text{figs/ml-eq18.eps}
+\end{equation}
+Therefore,
+\begin{equation}
+ \text{figs/ml-eq19.eps}
+\end{equation}
+Using the chain rule,
+\begin{equation}
+ \text{figs/ml-eq20.eps}
+\end{equation}
+From (6) [REPLACE WITH REF], we obtain
+\begin{equation}
+ \text{figs/ml-eq21.eps}
+\end{equation}
+and from (3) [REPLACE WITH REF]
+\begin{equation}
+ \text{figs/ml-eq22.eps}
+\end{equation}
+Finally, from (15) [REPLACE WITH REF], we have
+\begin{equation}
+ \text{figs/ml-eq23.eps}
+\end{equation}
+From (19) [REPLACE WITH REF], the final material matrix relating
+stress and tensor strain is
+\begin{equation}
+ \text{figs/ml-eq24.eps}
+\end{equation}
+Note that the coefficient of the second matrix approaches $E/3(1+\nu)$
+as $\eta$ goes to infinity. Since finite element computations
+typically use engineering strain measures, the matrix that is actually
+used is
+\begin{equation}
+ \text{figs/ml-eq25.eps}
+\end{equation}
+To check the results we make sure that the regular elastic
+constitutive matrix is obtained for selected terms in the case where
+$\eta$ goes to infinity.
+\begin{equation}
+ \text{figs/ml-eq26.eps}
+\end{equation}
+This is consistent with the regular elasticity matrix, and equation
+(25) [REPLACE WITH REF] should thus be used when forming the stiffness
+matrix.
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/maxwell_linear.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/maxwell_linear.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/materials/maxwell_linear.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,127 +0,0 @@
-\section{Effective Stress Function Formulation for a Maxwell Linear
-Viscoelastic Material}
-
-\subsection{Determination of stresses}
-
-The element stresses are
-\begin{equation}
- \text{figs/ml-eq1.eps}
-\end{equation}
-where ?? is the total strain and $\text{ml-inlineeq1}$ is the initial
-stress. In terms of the deviatoric stress,
-\begin{equation}
- \text{figs/ml-eq2.eps}
-\end{equation}
-where
-\begin{equation}
- \text{figs/ml-eq3.eps}
-\end{equation}
-and the mean stress and strain are given by
-\begin{equation}
- \text{figs/ml-eq4.eps}
-\end{equation}
-Equation~(2) [REPLACE WITH REF] may also be written as
-\begin{equation}
- \text{figs/ml-eq4.eps}
-\end{equation}
-where
-\begin{equation}
- \text{figs/ml-eq6.eps}
-\end{equation}
-The creep strain increment is approximated using
-\begin{equation}
- \text{figs/ml-eq7.eps}
-\end{equation}
-where, using the $\alpha$-method of time integration,
-\begin{equation}
- \text{figs/ml-eq8.eps}
-\end{equation}
-and
-\begin{equation}
- \text{figs/ml-eq9.eps}
-\end{equation}
-where
-\begin{equation}
- \text{figs/ml-eq10.eps}
-\end{equation}
-and
-\begin{equation}
- \text{figs/ml-eq11.eps}
-\end{equation}
-For a linear Maxwell viscoelastic material
-\begin{equation}
- \text{figs/ml-eq12.eps}
-\end{equation}
-Therefore,
-\begin{equation}
- \text{figs/ml-eq13.eps}
-\end{equation}
-Subsituting (8), (12), and (13) into (5) [REPLACE WITH REFS], we obtain
-\begin{equation}
- \text{figs/ml-eq14.eps}
-\end{equation}
-Solving for $\text{figs/ml-inlineeq2}$,
-\begin{equation}
- \text{figs/ml-eq15.eps}
-\end{equation}
-In this case it is possible to solve directly for the deviatoric
-stresses, and the effective stress function approach is not needed. To
-obtain the total stress, we simply use
-\begin{equation}
- \text{figs/ml-eq16.eps}
-\end{equation}
-
-\subsection{Tangent stress-strain relation}
-
-It is now necessary to provide a relationship for the viscoelastic
-tangent material matrix. If we use vectors composed of the stresses
-and tensor strains, this relationship is
-\begin{equation}
- \text{figs/ml-eq17.eps}
-\end{equation}
-In terms of the vectors, we have
-\begin{equation}
- \text{figs/ml-eq18.eps}
-\end{equation}
-Therefore,
-\begin{equation}
- \text{figs/ml-eq19.eps}
-\end{equation}
-Using the chain rule,
-\begin{equation}
- \text{figs/ml-eq20.eps}
-\end{equation}
-From (6) [REPLACE WITH REF], we obtain
-\begin{equation}
- \text{figs/ml-eq21.eps}
-\end{equation}
-and from (3) [REPLACE WITH REF]
-\begin{equation}
- \text{figs/ml-eq22.eps}
-\end{equation}
-Finally, from (15) [REPLACE WITH REF], we have
-\begin{equation}
- \text{figs/ml-eq23.eps}
-\end{equation}
-From (19) [REPLACE WITH REF], the final material matrix relating
-stress and tensor strain is
-\begin{equation}
- \text{figs/ml-eq24.eps}
-\end{equation}
-Note that the coefficient of the second matrix approaches $E/3(1+\nu)$
-as $\eta$ goes to infinity. Since finite element computations
-typically use engineering strain measures, the matrix that is actually
-used is
-\begin{equation}
- \text{figs/ml-eq25.eps}
-\end{equation}
-To check the results we make sure that the regular elastic
-constitutive matrix is obtained for selected terms in the case where
-$\eta$ goes to infinity.
-\begin{equation}
- \text{figs/ml-eq26.eps}
-\end{equation}
-This is consistent with the regular elasticity matrix, and equation
-(25) [REPLACE WITH REF] should thus be used when forming the stiffness
-matrix.
-
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/preface.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -32,11 +32,10 @@
Current PyLith development is supported by the Southern California
Earthquake Center, the National Science Foundation, the CIG, and
internal U.S. Geological Survey funding. Pyre development is funded by
-the \link{Department of
- Energy's}{http://www.doe.gov/engine/content.do} Advanced Simulation
-and Computing program and the \link{National Science
- Foundation's}{http://www.nsf.gov} Information Technology Research
-(ITR) program.
+the \href{http://www.doe.gov/engine/content.do}{Department of
+ Energy's} Advanced Simulation and Computing program and the
+\href{http://www.nsf.gov}{National Science Foundation's} Information
+Technology Research (ITR) program.
\section{Request for Comments}
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/runpylith/runpylith.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,188 @@
+\chapter{Running PyLith}
+
+\section{Supported Finite Elements}
+
+PyLith currently only supports the 4-node linear tetrahedral and
+8-node linear hexahedral elements. The node ordering must follow the
+convention shown in figures~\ref{fig:tet4} and~ref{fig:hex8}.
+
+\begin{figure}[htbp]
+ \begin{center}
+ \includegraphics{figs/tet4}
+ \caption{Linear tetrahedral finite element.}
+ \label{fig:tet4}
+ \end{center}
+\end{figure}
+
+\begin{figure}[htbp]
+ \begin{center}
+ \includegraphics{figs/hex8}
+ \caption{Linear hexahedral finite element.}
+ \label{fig:hex8}
+ \end{center}
+\end{figure}
+
+\section{Input Files}
+
+PyLith gets its input from a variety of files. Most of these are
+associated with different kinds of boundary conditions. As a result
+only six files are required. The remaining files are only used when
+the associated boundary condition is used. See
+Appendix~\ref{app:file:formats} for a detailed discussion of the file
+formats.
+
+The first step in the simulation process involves partitioning the
+mesh among the processors. In this phase, PyLith reads in the entire
+mesh and then writes out processor specific pieces with one file for
+each processor. The filenames for these follow the convention
+\filename{xx.PROC.ext} where \filename{PROC}
+refers to the processor number and \filename{xx.ext} was the
+original filename. This procedure is applied to files with the
+following extensions: \filename{coord},
+\filename{connect}, \filename{split}, and
+\filename{bc}.
+
+The remaining files provide information common to all processors. As a
+result, the user must create copies of each one for each of the
+processors. By default PyLith expects the names of these files to
+follow the same form, \filename{xx.PROC.ext}. Setting up this naming
+scheme is most easily done using symbolic links or copying files to
+local directories on each machine using a shell script that starts a
+simulation. See \filename{runbm.py} in
+section~\ref{sec:tutorial:reversenog} for a simple example. You can
+also choose your own filename template by setting the appropriate
+command-line argument. See ~\ref{sec:commandline:args} for more
+information.
+
+
+\subsection{Required Input Files}
+
+The required input files define the finite-element mesh, boundary
+conditions, time step information, output, and material properties.
+
+\begin{description}
+\item[\filename{xx.coord}] Coordinates of finite-element vertices.
+\item[\filename{xx.connect}] Topology and material information for
+ the finite-element mesh.
+\item[\filename{xx.bc}] Boundary conditions at vertices on external
+ boundaries.
+\item[\filename{xx.time}] Time stepping information.
+\item[\filename{xx.statevar}] State variables to be output for the
+ elastic and (time-dependent) viscoelastic solution.
+\item[\filename{xx.prop}] Properties for each material.
+\end{description}
+
+\subsection{Optional Input Files}
+
+The optional input files are only read when a file exists matching the
+name of an input file PyLith expects to read. Note that explicit
+filenames for each of the files can be specified using command-line
+arguments as discussed in section~\ref{sec:commandline:args}.
+
+\begin{description}
+\item[\filename{xx.fuldat}] Time steps for which full output is
+ requested.
+\item[\filename{xx.split}] Dislocation boundary condition information
+ (implemented using split nodes).
+\item[\filename{xx.skew}] Local coordinate rotation information for
+ boundary conditions.
+\item[\filename{xx.keyval}] File for changing default parameters.
+\item[\filename{xx.wink}] Winkler spring element boundary condition
+ information. {\em Not yet tested.}
+\item[\filename{xx.hist}] Time histories for split node and Winkler boundary
+ conditions (if necessary). {\em Not yet
+ tested.}
+\end{description}
+
+\section{Command-line Arguments}
+\label{sec:commandline:args}
+
+In general, PyLith's command-line arguments fall into three
+categories: MPI settings, Pyre properties and facilities, and PETSc
+settings.
+
+If using the MPICH implementation of the Message Passing Interface
+(MPI), as is done for the CIG distributed binaries, the synopsis for
+running PyLith is \\
+\command{mpirun} -np \replaceable{NPROCS} pylith3dapp.py
+\replaceable{PyLith settings} \replaceable{PETSc settings}
+
+\subsection{MPI Settings}
+
+\begin{warning}
+ This section applies only to PyLith compiled using the MPICH
+ implementation of the Message Passing Interface (MPI).
+\end{warning}
+
+
+The MPI settings define how many processors are used and other
+parallel processing parameters. The number of processors is specified
+using \option{-np NPROCS}, where \replaceable{NPROCS} corresponds to
+the number of processors.
+
+\subsection{Properties and Facilities}
+
+PyLith gathers many simulation parameters and settings using Pyre
+properties and facilities. Properties correspond to simple settings in
+the form of strings, integers, and real numbers. Facilities
+corresponds to software modules. Both facilities and properties have
+default values provided, so you only need to set values when you want
+to deviate from the default behavior. Unless you write a module that
+extends PyLith's functionality, you will never need to change any of
+the facilities from the defaults.
+
+In the current version of PyLith, all of the properties are associated
+with the scanner component. You can get a list of all of these
+properties along with a description of what they do by running PyLith
+with the \option{--scanner.help-properties} command-line argument.
+
+\begin{figure}
+ \begin{center}
+ \begin{screen}
+ mpirun -np \replaceable{1} pylith3dapp.py\\
+ --scanner.help-properties --scanner.asciiOutput=\replaceable{none}\\
+ --scanner.title=\replaceable{"My simulation"}
+ \end{screen}
+ \caption{Setting scanner properties from the command line.}
+ \end{center}
+\end{figure}
+
+\subsection{PETSc Settings}
+
+PyLith relies on PETSc for the linear algebra computations. Many of
+PETSc options can be set using command-line arguments. The ones of
+primary interest in the case of PyLith are shown in
+table~\ref{tab:petsc:options}.
+
+\begin{table}[htbp]
+ \begin{center}
+ \begin{tabular}{ll}
+ Argument & Description \\ \hline
+ \option{-log\_summary}
+ & Print logging objects and events \\
+ \option{-pc\_type \replaceable{bjacobi}}
+ & Set preconditioner type to block Jacobi. See PETSc
+ documentation for a list of all preconditioner types. \\
+ \option{-sub\_pc\_type \replaceable{ilu}}
+ & Set preconditioner to incomplete factorization for
+ each block. See PETSc documentation for a list of all
+ preconditioners. \\
+ \option{-ksp\_monitor \replaceable{stdout}}
+ & Dump preconditioned residual norm to stdout. If only
+ \option{-ksp\_monitor} is given, the default is
+ to use stdout. \\
+ \option{-ksp\_view}
+ & Print linear solver parameters. \\
+ \option{-ksp\_rtol \replaceable{1.0e-09}}
+ & Tolerance for relative decrease in residual norm
+ \end{tabular}
+ \caption{Useful command-line arguments for setting PETSc options.}
+ \end{center}
+\end{table}
+
+\section{Setting Pyre properties using pml files}
+
+PyLith's Pyre properties can also be set using \filename{pml} files.
+These are XML files that follow a special Pyre XML schema.
+
+ADD STUFF HERE
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/reversenog.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/reversenog.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/reversenog/reversenog.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -61,8 +61,8 @@
We will start by downloading the tutorial tarball and unpacking it.
\begin{enumerate}
-\item Download the \link{tutorial
- tarball}{http://www.geodynamics.org:8080/cig/Members/willic3/pylithusers/pylith0.8/pylith-0.8\_tutorials.tgz}
+\item Download the \href{http://www.geodynamics.org:8080/cig/Members/willic3/pylithusers/pylith0.8/pylith-0.8\_tutorials.tgz}{tutorial
+ tarball}
and unpack it in a location of your choosing.
\begin{screen}
@@ -172,8 +172,8 @@
\begin{screen}
\shellprompt\userinput{../../utils/readnetgen}
- \prompt{~Enter root name for all files. Both input and}\\
- \prompt{~output files will all have this prefix:}\\
+ \prompt{\ Enter root name for all files. Both input and}
+ \prompt{\ output files will all have this prefix:}
\userinput{bmrsnog}
\end{screen}
@@ -190,8 +190,8 @@
PyLith needs as input.
\begin{screen}
- \shellprompt\userinput{../../utils/faultcalc p=bmrsnog.fault.par n=bmrsnog.coord\\
- i=bmrsnog.1.fbc o=bmrsnog.split}
+ \shellprompt\userinput{../../utils/faultcalc p=bmrsnog.fault.par n=bmrsnog.coord \(\backslash\)}
+ \userinput{i=bmrsnog.1.fbc o=bmrsnog.split}
\end{screen}
\item The external boundary conditions for this benchmark are also
@@ -256,11 +256,11 @@
\subsection{Visualize the single processor run}
Now it is time to visualize the results of the simulation. By default,
-PyLith writes simulation output using \link{\application{AVS} UCD
- files}{http://help.avs.com/Express/doc/help/reference/dvmac/UCD\_Form.htm}.
-These can be read by several other visualization tools besides
-\application{AVS}, e.g., \application{ParaView} and \application{Iris
- Explorer}. We will use the open-source application
+PyLith writes simulation output using
+\href{http://help.avs.com/Express/doc/help/reference/dvmac/UCD\_Form.htm}{\application{AVS}
+ UCD files}. These can be read by several other visualization tools
+besides \application{AVS}, e.g., \application{ParaView} and
+\application{Iris Explorer}. We will use the open-source application
\application{ParaView} to visualize the results.
\begin{enumerate}
@@ -280,8 +280,8 @@
\filename{bmrsnog\_1.0.mesh.t00010.inp}.
\begin{screen}
- \shellprompt\userinput{cat bmrsnog\_1.0.mesh.inp bmrsnog\_1.0.mesh.time.00010.inp \ \\
-> bmrsnog\_1.0.mesh.t00010.inp}
+ \shellprompt\userinput{cat bmrsnog\_1.0.mesh.inp bmrsnog\_1.0.mesh.time.00010.inp \(\backslash\)}
+ \userinput{> bmrsnog\_1.0.mesh.t00010.inp}
\end{screen}
\item Start \application{ParaView} by executing \command{paraview}.
@@ -313,19 +313,21 @@
interpolating colors, and changing the color map.
\item Let's show the displacements as vectors. Click on the calculator
icon, and add the three displacement components together. Enter
- "XDispl*iHat+YDispl*jHat+ZDispl*kHat" in the \guimenuitem{Calculator}
- box. Note the variable names are available by clicking on the
- \guibutton{scalars} button and the \guibutton{iHat},
- \guibutton{jHat}, \guibutton{kHat} buttons are on the right side of
- the top row. Click on the \guibutton{Accept} button. To show the
- dataset as vectors, click on the \guibutton{glyph} button (looks
- like several dots) in the toolbar. After clicking the
- \guibutton{Accept} button, you should have a vector plot. You can
- turn on/off other datasets by clicking on the eye icon to the left
- of the dataset name. If you color the surfaces using the
- x-displacements field while also making the displacement vectors
- visible (colored using property), you should see an image similar to
- the one in figure~\ref{fig:bmrsnog:xdisp:vec:t10}.
+ \begin{screen}
+ XDispl*iHat+YDispl*jHat+ZDispl*kHat
+ \end{screen}
+ in the \guimenuitem{Calculator} box. Note the variable names are
+ available by clicking on the \guibutton{scalars} button and the
+ \guibutton{iHat}, \guibutton{jHat}, \guibutton{kHat} buttons are on
+ the right side of the top row. Click on the \guibutton{Accept}
+ button. To show the dataset as vectors, click on the
+ \guibutton{glyph} button (looks like several dots) in the toolbar.
+ After clicking the \guibutton{Accept} button, you should have a
+ vector plot. You can turn on/off other datasets by clicking on the
+ eye icon to the left of the dataset name. If you color the surfaces
+ using the x-displacements field while also making the displacement
+ vectors visible (colored using property), you should see an image
+ similar to the one in figure~\ref{fig:bmrsnog:xdisp:vec:t10}.
\begin{figure}[htbp]
\begin{center}
@@ -391,10 +393,10 @@
twice to create UCD files for each processor.
\begin{screen}
- \shellprompt\userinput{cat bmrsnog\_2.0.mesh.inp bmrsnog\_2.0.mesh.time.00010.inp \\
- > bmrsnog\_2.0.mesh.t00010.inp} \\
- \shellprompt\userinput{cat bmrsnog\_2.1.mesh.inp bmrsnog\_2.1.mesh.time.00010.inp \\
- > bmrsnog\_2.1.mesh.t00010.inp}
+ \shellprompt\userinput{cat bmrsnog\_2.0.mesh.inp bmrsnog\_2.0.mesh.time.00010.inp \(\backslash\)}
+ \userinput{> bmrsnog\_2.0.mesh.t00010.inp}
+ \shellprompt\userinput{cat bmrsnog\_2.1.mesh.inp bmrsnog\_2.1.mesh.time.00010.inp \(\backslash\)}
+ \userinput{> bmrsnog\_2.1.mesh.t00010.inp}
\end{screen}
\item Start \application{ParaView} by executing \command{paraview}.
Copied: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splittest/splitcube.tex (from rev 4398, short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splittest/splittest.tex)
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splittest/splittest.tex 2006-08-22 15:30:52 UTC (rev 4398)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splittest/splitcube.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -0,0 +1,396 @@
+\section{Tutorial For Simple Strike-Slip Fault}
+
+\subsection{Overview}
+
+In this tutorial we will walk through the steps necessary to
+construct, run, and view the results of a benchmark problem involving
+a simple, vertical, through-going strike-slip fault. This problem
+examines the elastic deformation from a single, finite, right-lateral
+earthquake in 3-D without body forces.
+
+\subsection{Problem Description}
+
+The model domain is a cube with edges 1 km long (0 km $\leq$ x $\leq$
+1 km; 0 km $\leq$ y $\leq$ 1 km; 0 km $\leq$ z $\leq$ 1 km) and is
+composed of two materials. The fault separates two materials that have
+the same properties. Both materials are Poisson solids with Lame's
+constants ($\mu$ and $\lambda$) equal to 30 GPa.
+
+The strike-slip fault dips at an angle of 90 degrees. The slip
+distribution is 1.0 m of uniform right-lateral motion.
+
+The plane y=0 is a plane of symmetry, so the y-DOF displacements on
+this face are zero. The other lateral faces and bottom of the mesh are
+traction-free.
+
+\begin{figure}
+ \begin{center}
+ %\includegraphics{figs/geometry}
+ \caption{Geometry of model domain for simple model with strike-slip fault.}
+ \end{center}
+\end{figure}
+
+\subsubsection{Workflow}
+
+The complete workflow used to create the input files for this tutorial
+is shown in figure~\ref{fig:splittest:workflow}.
+
+\begin{figure}[htbp]
+ \begin{center}
+ \includegraphics{figs/workflow}
+ \caption{Workflow for setting up input files for example with
+ simple strike-slip faylt.}
+ \label{fig:splittest:workflow}
+ \end{center}
+\end{figure}
+
+\subsection{Download and unpack}
+
+We will start by downloading the tutorial tarball and unpacking it.
+
+\begin{enumerate}
+\item Download the \href{http://www.geodynamics.org:8080/cig/Members/willic3/pylithusers/pylith0.8/pylith-0.8\_tutorials.tgz}{tutorial tarball}
+ and unpack it in a location of your choosing.
+
+ \begin{screen}
+ \shellprompt\userinput{tar -zxvf pylith-0.8\_tutorials.tgz}
+ \end{screen}
+
+\item Go to the \directory{tutorials/splittest} directory.
+ The \directory{archive} directory contains all of the input and
+ output files associated with this tutorial. We will copy input files
+ from this directory into the \directory{workarea} directory. At each
+ step, you can check to make sure your input and output agree with
+ the files in the \directory{archive} directory. These files also
+ allow you to start at an intermediate step as described in the next
+ section.
+
+ \begin{screen}
+ \shellprompt\userinput{cd tutorials/splittest}
+ \end{screen}
+
+\end{enumerate}
+
+\subsection{Tutor}
+
+Copy the \filename{tutor.py} script from the \directory{archive}
+directory into the \directory{workarea} directory.
+
+\begin{tip}
+ If you have run this tutorial previously, you may want to run
+ \command{tutor.py} in mode "clean" with step "all" to clear out all
+ old tutorial files.
+\end{tip}
+
+\begin{screen}
+\shellprompt\userinput{cd workarea}
+\shellprompt\userinput{cp ../archive/tutor.py .}
+\shellprompt\userinput{./tutor.py -m clean -s all}
+\end{screen}
+
+\subsection{Generate the mesh}
+
+In this step we will generate the finite-element mesh for the
+benchmark problem using \application{NETGEN}.
+
+\begin{enumerate}
+\item In the \directory{splittest/workarea} directory, run
+ \command{tutor.py} for step "mesh" with mode "retrieve" to fetch the
+ geometry file for \application{NETGEN}. You may also want to run
+ \command{tutor.py} for this step with mode "clean" to clean out old
+ files.
+
+ \begin{screen}
+ \shellprompt\userinput{./tutor.py -m retrieve -s mesh}
+ \shellprompt\userinput{./tutor.py -m clean -s mesh}
+ \end{screen}
+
+\item Examine the \filename{splittest.geo} file to see how the geometry
+ for the problem is defined. Notice that the fault plan has
+ been flagged with a boundary condition code. This will be
+ used to associate boundary conditions with the fault surface and the
+ associated nodes. We do not have to flag the lateral faces and top
+ and bottom of the mesh because they are traction-free, which is a
+ natural boundary condition in the finite-element formulation.
+\item Start up \application{NETGEN} by running \command{ng}.
+
+ \begin{screen}
+ \shellprompt\userinput{ng}
+ \end{screen}
+
+\item Select \guimenu{File}\guiselect\guimenuitem{Load Geometry}
+ and select \filename{splittest.geo}.
+\item Click on \guibutton{Generate Mesh}.
+\item Export the mesh to a file named \filename{splittest.netgen},
+ making sure the export filetype is "Neutral format".
+\item You can now exit \application{NETGEN}.
+\end{enumerate}
+
+\subsection{Setup simulation input files}
+
+In this step we will setup the PyLith input files for the mesh and
+boundary conditions.
+
+\begin{enumerate}
+\item Run \command{tutor.py} for step "setup" with mode "retrieve" to
+ fetch files from the archive.
+
+ \begin{screen}
+ \shellprompt\userinput{./tutor.py -m retrieve -s setup}
+ \end{screen}
+
+\item We will use a simple Fortran utility to generate PyLith
+ input files from the \application{NETGEN} output.
+
+ \begin{description}
+ \item[\command{readnetgen}] A Fortran program to read
+ \application{NETGEN} neutral format and create several of the
+ input files needed by PyLith.
+ \end{description}
+
+\item Run the \command{readnetgen} utility program to process the
+ \application{NETGEN} output file into PyLith compatible input files.
+ It will ask for a root filename, enter \filename{splittest}. This
+ utilitiy will generate the following files:
+ \filename{splittest.w01.wink}, \filename{splittest.coord},
+ \filename{splittest.connect}, \filename{splittest.bc},
+ \filename{splittest.1.fcoord}, \filename{splittest.1.fbc}.
+
+ \begin{screen}
+ \shellprompt\userinput{../../utils/readnetgen}
+ \prompt{\ Enter root name for all files. Both input and}
+ \prompt{\ output files will all have this prefix:}
+ \userinput{splittest}
+ \end{screen}
+
+\item The boundary conditions on the fault for this example are
+ very simple. As a result, the \filename{splittest.split} file was
+ generated by hand. You should examine this file to see how a uniform
+ right-lateral slip of 1.0 m is applied to the fault surface.
+
+ \begin{warning}
+ If you make any changes to \filename{splittest.geo} or change the
+ geometry within \application{NETGEN}, the split-node file
+ \filename{splittest.split} will no longer be correct and you will
+ have to generate one yourself. Note that it is also possible that
+ a different version of \application{NETGEN} may provide a slightly
+ different mesh, which would also be incompatible with the provided
+ boundary conditions.
+ \end{warning}
+
+\item The external boundary conditions for this benchmark simply
+ involve ... ADD STUFF HERE.
+
+ \begin{warning}
+ If you make any changes to \filename{splittest.geo} or change the
+ geometry within \application{NETGEN}, the boundary condition file
+ \filename{splittest.bc} will no longer be correct and you will
+ have to generate one yourself. Note that it is also possible that
+ a different version of \application{NETGEN} may provide a slightly
+ different mesh, which would also be incompatible with the provided
+ boundary conditions.
+ \end{warning}
+\end{enumerate}
+
+\subsection{Run the simulation on one processor}
+
+In this step we will run the simulation on a single processor.
+
+\begin{enumerate}
+\item Run \command{tutor.py} for step "run1" with mode "retrieve" to
+ fetch some parameter files from the archive.
+
+ \begin{screen}
+ \shellprompt\userinput{./tutor.py -m retrieve -s run1}
+ \end{screen}
+
+\item In \filename{splittest.fuldat}, we have specified that we want
+ full output at time steps 10, 50, and 100. We define two materials
+ with elastic behavior in
+ \filename{splittest.prop}. In \filename{splittest.statevar} we choose to
+ include total stress, total strain, incremental stress, and
+ incremental strain in the output. As defined in
+ \filename{splittest.time}, the simulation will have 100 time steps of
+ 0.1 year each.
+\item Run the simulation by executing \userinput{runbm.py -n 1}, where
+ the 1 refers to the number of processors.
+
+ \begin{tip}
+ All of the input is echoed in the file \filename{splittest.ascii}.
+ You can check to make sure your input is digested correctly by
+ examining this file. For large problems, this file can be quite
+ large. You can suppress creation of this file using the command
+ line argument \option{--scanner.asciiOutput=none} flag. On the
+ other hand, for debugging purposes in small problems, you may wish
+ to output everything, including the computed results, in this file
+ using \option{--scanner.asciiOutput=full}.
+ \end{tip}
+
+ \begin{screen}
+ \shellprompt\userinput{./runbm.py -n 1}
+ \end{screen}
+\end{enumerate}
+
+\subsection{Visualize the single processor run}
+
+Now it is time to visualize the results of the simulation. By default,
+PyLith writes simulation output using \href{http://help.avs.com/Express/doc/help/reference/dvmac/UCD\_Form.htm}{\application{AVS} UCD
+ files}.
+These can be read by several other visualization tools besides
+\application{AVS}, e.g., \application{ParaView} and \application{Iris
+ Explorer}. We will use the open-source application
+\application{ParaView} to visualize the results.
+
+\begin{enumerate}
+\item If necessary, run \command{tutor.py} for step "viz1" with mode
+ "retrieve" to fetch the simulation output from the archive.
+
+ \begin{screen}
+ \shellprompt\userinput{./tutor.py -m retrieve -s viz1}
+ \end{screen}
+
+\item PyLith does not write complete UCD files. So the first step is
+ to combine the mesh topology information with the output at a given
+ time step into a complete UCD file. For example, use \command{cat}
+ to merge the nodal coordinates file
+ (\filename{splittest\_1.0.mesh.inp}) and the nodal displacements at
+ time step 10 file (\filename{splittest\_1.0.mesh.time.00010.inp}) into
+ \filename{splittest\_1.0.mesh.t00010.inp}.
+
+ \begin{screen}
+ \shellprompt\userinput{cat splittest\_1.0.mesh.inp splittest\_1.0.mesh.time.00010.inp \(\backslash\)}
+ \userinput{> splittest\_1.0.mesh.t00010.inp}
+\end{screen}
+
+\item Start \application{ParaView} by executing \command{paraview}.
+
+ \begin{screen}
+ \shellprompt\userinput{paraview}
+ \end{screen}
+
+\item Load the UCD file that you just created by selecting
+ \guimenu{File}\guiselect\guimenuitem{Open Data}. Select the file in
+ the dialog box and the click the \guibutton{Open} button. Click the
+ \guibutton{Accept} button. You should see a color rendering of the x
+ displacements. You can use the mouse to rotate, translate, and zoom.
+ Your image should look similar to the one in
+ figure~\ref{fig::splittest:xdisp:t10}.
+
+ \begin{figure}[htbp]
+ \begin{center}
+ %\includegraphics{figs/xdisp_t10}
+ \caption{ParaView rendering of displacement in x-direction at
+ time step 10 (10 yrs after imposed dislocation) for the
+ simple strike-slip example.}
+ \label{fig:splittest:xdisp:t10}
+ \end{center}
+ \end{figure}
+
+\item In the \guibutton{Display} tab, you can change several options,
+ such as including a color bar, coloring a different component,
+ interpolating colors, and changing the color map.
+\item Let's show the displacements as vectors. Click on the calculator
+ icon, and add the three displacement components together. Enter
+ \begin{screen}
+ XDispl*iHat + YDispl*jHat + ZDispl*kHat
+ \end{screen}
+ in the \guimenuitem{Calculator}
+ box. Note the variable names are available by clicking on the
+ \guibutton{scalars} button and the \guibutton{iHat},
+ \guibutton{jHat}, \guibutton{kHat} buttons are on the right side of
+ the top row. Click on the \guibutton{Accept} button. To show the
+ dataset as vectors, click on the \guibutton{glyph} button (looks
+ like several dots) in the toolbar. After clicking the
+ \guibutton{Accept} button, you should have a vector plot. You can
+ turn on/off other datasets by clicking on the eye icon to the left
+ of the dataset name. If you color the surfaces using the
+ x-displacements field while also making the displacement vectors
+ visible (colored using property), you should see an image similar to
+ the one in figure~\ref{fig:splittest:xdisp:vec:t10}.
+
+ \begin{figure}[htbp]
+ \begin{center}
+ %\includegraphics{figs/splittest_xdisp_vec_t10}
+ \caption{ParaView rendering of displacement in x-direction and
+ displacement vectors at time step 10 (10 yrs after imposed
+ dislocation) for the simple strike-slip example.}
+ \label{fig:splittest:xdisp:vec:t10}
+ \end{center}
+ \end{figure}
+
+\end{enumerate}
+
+\subsection{Run the simulation on two processors}
+
+In this step we will run the simulation on two processors. Even if
+your machine only has one processor, a "multprocessor" job will run as
+multiple processes on the single processor. In such cases, the job
+will run slightly slower than the single processor run, but the two
+processes will behave independently as if they are on different
+processors.
+
+\begin{enumerate}
+\item Run \command{tutor.py} for step "run2" with mode "retrieve" to
+ make sure all parameter files are available.
+
+ \begin{screen}
+ \shellprompt\userinput{./tutor.py -m retrieve -s run2}
+ \end{screen}
+
+\item The parameter files are the same as those in the single
+ processor run. The \command{runbm} script will automatically take
+ care of duplicating these files so that there is one for each
+ processor.
+\item Run the simulation by executing \command{runbm.py -n 2}, where
+ the 2 refers to the number of processors.
+
+ \begin{screen}
+ \shellprompt\userinput{./runbm.py -n 2}
+ \end{screen}
+\end{enumerate}
+
+\subsection{Visualize the two processor run}
+
+PyLith does not currently support parallel output, so each processor
+writes its UCD output to a different file. This means that you need to
+form complete UCD files for each processor and then load each one into
+\application{ParaView}.
+
+\begin{enumerate}
+\item If necessary, run \command{tutor.py} for step "viz2" with mode
+ "retrieve" to fetch the simulation output from the archive.
+
+ \begin{screen}
+ \shellprompt\userinput{./tutor.py -m retrieve -s viz2}
+ \end{screen}
+
+\item As in the case of the single processor run, the first step is to
+ combine the mesh topology information with the output at a given
+ time step into a complete UCD file. Because PyLith writes the output
+ from each processor into a different file, we must run \command{cat}
+ twice to create UCD files for each processor.
+
+ \begin{screen}
+ \shellprompt\userinput{cat splittest\_2.0.mesh.inp splittest\_2.0.mesh.time.00010.inp \(\backslash\)}
+ \userinput{> splittest\_2.0.mesh.t00010.inp}
+ \shellprompt\userinput{cat splittest\_2.1.mesh.inp splittest\_2.1.mesh.time.00010.inp \(\backslash\)}
+ \userinput{> splittest\_2.1.mesh.t00010.inp}
+ \end{screen}
+
+\item Start \application{ParaView} by executing \command{paraview}.
+
+ \begin{screen}
+ \shellprompt\userinput{paraview}
+ \end{screen}
+
+\item Load the UCD files that you just created by selecting
+ \guimenu{File}\guiselect\guimenuitem{Open Data}. Select the file in
+ the dialog box and the click the \guibutton{Open} button. Click the
+ \guibutton{Accept} button. You can now visualize the datasets just
+ like you did for the single processor case.
+\item You can merge the datasets from the different processors by
+ selecting \guimenu{Filter}\guiselect\guimenuitem{Append}. Doing so
+ will allow you to operate on the data from all of the processors
+ simultaneously instead of having to repeat any processing for every
+ processor.
+\end{enumerate}
Deleted: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splittest/splittest.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splittest/splittest.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splittest/splittest.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,394 +0,0 @@
-\section{Tutorial For Simple Strike-Slip Fault}
-
-\subsection{Overview}
-
-In this tutorial we will walk through the steps necessary to
-construct, run, and view the results of a benchmark problem involving
-a simple, vertical, through-going strike-slip fault. This problem
-examines the elastic deformation from a single, finite, right-lateral
-earthquake in 3-D without body forces.
-
-\subsection{Problem Description}
-
-The model domain is a cube with edges 1 km long (0 km $\leq$ x $\leq$
-1 km; 0 km $\leq$ y $\leq$ 1 km; 0 km $\leq$ z $\leq$ 1 km) and is
-composed of two materials. The fault separates two materials that have
-the same properties. Both materials are Poisson solids with Lame's
-constants ($\mu$ and $\lambda$) equal to 30 GPa.
-
-The strike-slip fault dips at an angle of 90 degrees. The slip
-distribution is 1.0 m of uniform right-lateral motion.
-
-The plane y=0 is a plane of symmetry, so the y-DOF displacements on
-this face are zero. The other lateral faces and bottom of the mesh are
-traction-free.
-
-\begin{figure}
- \begin{center}
- %\includegraphics{figs/geometry}
- \caption{Geometry of model domain for simple model with strike-slip fault.}
- \end{center}
-\end{figure}
-
-\subsubsection{Workflow}
-
-The complete workflow used to create the input files for this tutorial
-is shown in figure~\ref{fig:splittest:workflow}.
-
-\begin{figure}[htbp]
- \begin{center}
- \includegraphics{figs/workflow}
- \caption{Workflow for setting up input files for example with
- simple strike-slip faylt.}
- \label{fig:splittest:workflow}
- \end{center}
-\end{figure}
-
-\subsection{Download and unpack}
-
-We will start by downloading the tutorial tarball and unpacking it.
-
-\begin{enumerate}
-\item Download the \link{tutorial
- tarball}{http://www.geodynamics.org:8080/cig/Members/willic3/pylithusers/pylith0.8/pylith-0.8\_tutorials.tgz}
- and unpack it in a location of your choosing.
-
- \begin{screen}
- \shellprompt\userinput{tar -zxvf pylith-0.8\_tutorials.tgz}
- \end{screen}
-
-\item Go to the \directory{tutorials/splittest} directory.
- The \directory{archive} directory contains all of the input and
- output files associated with this tutorial. We will copy input files
- from this directory into the \directory{workarea} directory. At each
- step, you can check to make sure your input and output agree with
- the files in the \directory{archive} directory. These files also
- allow you to start at an intermediate step as described in the next
- section.
-
- \begin{screen}
- \shellprompt\userinput{cd tutorials/splittest}
- \end{screen}
-
-\end{enumerate}
-
-\subsection{Tutor}
-
-Copy the \filename{tutor.py} script from the \directory{archive}
-directory into the \directory{workarea} directory.
-
-\begin{tip}
- If you have run this tutorial previously, you may want to run
- \command{tutor.py} in mode "clean" with step "all" to clear out all
- old tutorial files.
-\end{tip}
-
-\begin{screen}
-\shellprompt\userinput{cd workarea}
-\shellprompt\userinput{cp ../archive/tutor.py .}
-\shellprompt\userinput{./tutor.py -m clean -s all}
-\end{screen}
-
-\subsection{Generate the mesh}
-
-In this step we will generate the finite-element mesh for the
-benchmark problem using \application{NETGEN}.
-
-\begin{enumerate}
-\item In the \directory{splittest/workarea} directory, run
- \command{tutor.py} for step "mesh" with mode "retrieve" to fetch the
- geometry file for \application{NETGEN}. You may also want to run
- \command{tutor.py} for this step with mode "clean" to clean out old
- files.
-
- \begin{screen}
- \shellprompt\userinput{./tutor.py -m retrieve -s mesh}
- \shellprompt\userinput{./tutor.py -m clean -s mesh}
- \end{screen}
-
-\item Examine the \filename{splittest.geo} file to see how the geometry
- for the problem is defined. Notice that the fault plan has
- been flagged with a boundary condition code. This will be
- used to associate boundary conditions with the fault surface and the
- associated nodes. We do not have to flag the lateral faces and top
- and bottom of the mesh because they are traction-free, which is a
- natural boundary condition in the finite-element formulation.
-\item Start up \application{NETGEN} by running \command{ng}.
-
- \begin{screen}
- \shellprompt\userinput{ng}
- \end{screen}
-
-\item Select \guimenu{File}\guiselect\guimenuitem{Load Geometry}
- and select \filename{splittest.geo}.
-\item Click on \guibutton{Generate Mesh}.
-\item Export the mesh to a file named \filename{splittest.netgen},
- making sure the export filetype is "Neutral format".
-\item You can now exit \application{NETGEN}.
-\end{enumerate}
-
-\subsection{Setup simulation input files}
-
-In this step we will setup the PyLith input files for the mesh and
-boundary conditions.
-
-\begin{enumerate}
-\item Run \command{tutor.py} for step "setup" with mode "retrieve" to
- fetch files from the archive.
-
- \begin{screen}
- \shellprompt\userinput{./tutor.py -m retrieve -s setup}
- \end{screen}
-
-\item We will use a simple Fortran utility to generate PyLith
- input files from the \application{NETGEN} output.
-
- \begin{description}
- \item[\command{readnetgen}] A Fortran program to read
- \application{NETGEN} neutral format and create several of the
- input files needed by PyLith.
- \end{description}
-
-\item Run the \command{readnetgen} utility program to process the
- \application{NETGEN} output file into PyLith compatible input files.
- It will ask for a root filename, enter \filename{splittest}. This
- utilitiy will generate the following files:
- \filename{splittest.w01.wink}, \filename{splittest.coord},
- \filename{splittest.connect}, \filename{splittest.bc},
- \filename{splittest.1.fcoord}, \filename{splittest.1.fbc}.
-
- \begin{screen}
- \shellprompt\userinput{../../utils/readnetgen}
- \prompt{~Enter root name for all files. Both input and}\\
- \prompt{~output files will all have this prefix:}\\
- \userinput{splittest}
- \end{screen}
-
-\item The boundary conditions on the fault for this example are
- very simple. As a result, the \filename{splittest.split} file was
- generated by hand. You should examine this file to see how a uniform
- right-lateral slip of 1.0 m is applied to the fault surface.
-
- \begin{warning}
- If you make any changes to \filename{splittest.geo} or change the
- geometry within \application{NETGEN}, the split-node file
- \filename{splittest.split} will no longer be correct and you will
- have to generate one yourself. Note that it is also possible that
- a different version of \application{NETGEN} may provide a slightly
- different mesh, which would also be incompatible with the provided
- boundary conditions.
- \end{warning}
-
-\item The external boundary conditions for this benchmark simply
- involve ... ADD STUFF HERE.
-
- \begin{warning}
- If you make any changes to \filename{splittest.geo} or change the
- geometry within \application{NETGEN}, the boundary condition file
- \filename{splittest.bc} will no longer be correct and you will
- have to generate one yourself. Note that it is also possible that
- a different version of \application{NETGEN} may provide a slightly
- different mesh, which would also be incompatible with the provided
- boundary conditions.
- \end{warning}
-\end{enumerate}
-
-\subsection{Run the simulation on one processor}
-
-In this step we will run the simulation on a single processor.
-
-\begin{enumerate}
-\item Run \command{tutor.py} for step "run1" with mode "retrieve" to
- fetch some parameter files from the archive.
-
- \begin{screen}
- \shellprompt\userinput{./tutor.py -m retrieve -s run1}
- \end{screen}
-
-\item In \filename{splittest.fuldat}, we have specified that we want
- full output at time steps 10, 50, and 100. We define two materials
- with elastic behavior in
- \filename{splittest.prop}. In \filename{splittest.statevar} we choose to
- include total stress, total strain, incremental stress, and
- incremental strain in the output. As defined in
- \filename{splittest.time}, the simulation will have 100 time steps of
- 0.1 year each.
-\item Run the simulation by executing \userinput{runbm.py -n 1}, where
- the 1 refers to the number of processors.
-
- \begin{tip}
- All of the input is echoed in the file \filename{splittest.ascii}.
- You can check to make sure your input is digested correctly by
- examining this file. For large problems, this file can be quite
- large. You can suppress creation of this file using the command
- line argument \option{--scanner.asciiOutput=none} flag. On the
- other hand, for debugging purposes in small problems, you may wish
- to output everything, including the computed results, in this file
- using \option{--scanner.asciiOutput=full}.
- \end{tip}
-
- \begin{screen}
- \shellprompt\userinput{./runbm.py -n 1}
- \end{screen}
-\end{enumerate}
-
-\subsection{Visualize the single processor run}
-
-Now it is time to visualize the results of the simulation. By default,
-PyLith writes simulation output using \link{\application{AVS} UCD
- files}{http://help.avs.com/Express/doc/help/reference/dvmac/UCD\_Form.htm}.
-These can be read by several other visualization tools besides
-\application{AVS}, e.g., \application{ParaView} and \application{Iris
- Explorer}. We will use the open-source application
-\application{ParaView} to visualize the results.
-
-\begin{enumerate}
-\item If necessary, run \command{tutor.py} for step "viz1" with mode
- "retrieve" to fetch the simulation output from the archive.
-
- \begin{screen}
- \shellprompt\userinput{./tutor.py -m retrieve -s viz1}
- \end{screen}
-
-\item PyLith does not write complete UCD files. So the first step is
- to combine the mesh topology information with the output at a given
- time step into a complete UCD file. For example, use \command{cat}
- to merge the nodal coordinates file
- (\filename{splittest\_1.0.mesh.inp}) and the nodal displacements at
- time step 10 file (\filename{splittest\_1.0.mesh.time.00010.inp}) into
- \filename{splittest\_1.0.mesh.t00010.inp}.
-
- \begin{screen}
- \shellprompt\userinput{cat splittest\_1.0.mesh.inp splittest\_1.0.mesh.time.00010.inp \ \\
-> splittest\_1.0.mesh.t00010.inp}
-\end{screen}
-
-\item Start \application{ParaView} by executing \command{paraview}.
-
- \begin{screen}
- \shellprompt\userinput{paraview}
- \end{screen}
-
-\item Load the UCD file that you just created by selecting
- \guimenu{File}\guiselect\guimenuitem{Open Data}. Select the file in
- the dialog box and the click the \guibutton{Open} button. Click the
- \guibutton{Accept} button. You should see a color rendering of the x
- displacements. You can use the mouse to rotate, translate, and zoom.
- Your image should look similar to the one in
- figure~\ref{fig::splittest:xdisp:t10}.
-
- \begin{figure}[htbp]
- \begin{center}
- %\includegraphics{figs/xdisp_t10}
- \caption{ParaView rendering of displacement in x-direction at
- time step 10 (10 yrs after imposed dislocation) for the
- simple strike-slip example.}
- \label{fig:splittest:xdisp:t10}
- \end{center}
- \end{figure}
-
-\item In the \guibutton{Display} tab, you can change several options,
- such as including a color bar, coloring a different component,
- interpolating colors, and changing the color map.
-\item Let's show the displacements as vectors. Click on the calculator
- icon, and add the three displacement components together. Enter
- "XDispl*iHat+YDispl*jHat+ZDispl*kHat" in the \\guimenuitem{Calculator}
- box. Note the variable names are available by clicking on the
- \guibutton{scalars} button and the \guibutton{iHat},
- \guibutton{jHat}, \guibutton{kHat} buttons are on the right side of
- the top row. Click on the \guibutton{Accept} button. To show the
- dataset as vectors, click on the \guibutton{glyph} button (looks
- like several dots) in the toolbar. After clicking the
- \guibutton{Accept} button, you should have a vector plot. You can
- turn on/off other datasets by clicking on the eye icon to the left
- of the dataset name. If you color the surfaces using the
- x-displacements field while also making the displacement vectors
- visible (colored using property), you should see an image similar to
- the one in figure~\ref{fig:splittest:xdisp:vec:t10}.
-
- \begin{figure}[htbp]
- \begin{center}
- %\includegraphics{figs/splittest_xdisp_vec_t10}
- \caption{ParaView rendering of displacement in x-direction and
- displacement vectors at time step 10 (10 yrs after imposed
- dislocation) for the simple strike-slip example.}
- \label{fig:splittest:xdisp:vec:t10}
- \end{center}
- \end{figure}
-
-\end{enumerate}
-
-\subsection{Run the simulation on two processors}
-
-In this step we will run the simulation on two processors. Even if
-your machine only has one processor, a "multprocessor" job will run as
-multiple processes on the single processor. In such cases, the job
-will run slightly slower than the single processor run, but the two
-processes will behave independently as if they are on different
-processors.
-
-\begin{enumerate}
-\item Run \command{tutor.py} for step "run2" with mode "retrieve" to
- make sure all parameter files are available.
-
- \begin{screen}
- \shellprompt\userinput{./tutor.py -m retrieve -s run2}
- \end{screen}
-
-\item The parameter files are the same as those in the single
- processor run. The \command{runbm} script will automatically take
- care of duplicating these files so that there is one for each
- processor.
-\item Run the simulation by executing \command{runbm.py -n 2}, where
- the 2 refers to the number of processors.
-
- \begin{screen}
- \shellprompt\userinput{./runbm.py -n 2}
- \end{screen}
-\end{enumerate}
-
-\subsection{Visualize the two processor run}
-
-PyLith does not currently support parallel output, so each processor
-writes its UCD output to a different file. This means that you need to
-form complete UCD files for each processor and then load each one into
-\application{ParaView}.
-
-\begin{enumerate}
-\item If necessary, run \command{tutor.py} for step "viz2" with mode
- "retrieve" to fetch the simulation output from the archive.
-
- \begin{screen}
- \shellprompt\userinput{./tutor.py -m retrieve -s viz2}
- \end{screen}
-
-\item As in the case of the single processor run, the first step is to
- combine the mesh topology information with the output at a given
- time step into a complete UCD file. Because PyLith writes the output
- from each processor into a different file, we must run \command{cat}
- twice to create UCD files for each processor.
-
- \begin{screen}
- \shellprompt\userinput{cat splittest\_2.0.mesh.inp splittest\_2.0.mesh.time.00010.inp \\
- > splittest\_2.0.mesh.t00010.inp} \\
- \shellprompt\userinput{cat splittest\_2.1.mesh.inp splittest\_2.1.mesh.time.00010.inp \\
- > splittest\_2.1.mesh.t00010.inp}
- \end{screen}
-
-\item Start \application{ParaView} by executing \command{paraview}.
-
- \begin{screen}
- \shellprompt\userinput{paraview}
- \end{screen}
-
-\item Load the UCD files that you just created by selecting
- \guimenu{File}\guiselect\guimenuitem{Open Data}. Select the file in
- the dialog box and the click the \guibutton{Open} button. Click the
- \guibutton{Accept} button. You can now visualize the datasets just
- like you did for the single processor case.
-\item You can merge the datasets from the different processors by
- selecting \guimenu{Filter}\guiselect\guimenuitem{Append}. Doing so
- will allow you to operate on the data from all of the processors
- simultaneously instead of having to repeat any processing for every
- processor.
-\end{enumerate}
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/tutorials.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -10,8 +10,8 @@
Before you begin any of the tutorials, you will need to install PyLith
following the instructions in section~\ref{sec:install}. In order to
work through a full tutorial, in addition to \application{PyLith} you
-will need \link{\application{NETGEN}}{http://www.hpfem.jku.at/netgen/}
-to generate the mesh and \link{ParaView}{http://www.paraview.org} to
+will need \href{http://www.hpfem.jku.at/netgen/}{\application{NETGEN}}
+to generate the mesh and \href{http://www.paraview.org}{ParaView} to
view simulation results. You may use other packages, but some adaption
from what is described here will be necessary. Alternatively, you can
just complete a subset of the tutorial using files provided (as
@@ -43,5 +43,5 @@
you should remove them and let the tutor retrieve clean copies.
\end{tip}
-\input{splittest/splittest.tex}
+\input{splittest/splitcube.tex}
\input{reversenog/reversenog.tex}
Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.tex 2006-08-22 18:24:20 UTC (rev 4399)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/userguide.tex 2006-08-22 21:42:48 UTC (rev 4400)
@@ -1,9 +1,12 @@
% -*- TeX -*-
-\documentclass{report}
+\documentclass{book}
\usepackage{amsmath}
\usepackage{graphicx}
+\usepackage{alltt}
+%\usepackage{url}
+\usepackage{hyperref}
+\usepackage{moreverb}
-
\input{docdefs.tex}
\begin{document}
@@ -16,24 +19,26 @@
Cassie Ferguson\\
Sue Kientz}
\date{\today}
-
+%\titlepage{pylith_cover}
+
\maketitle
-\part{Preface}
+\frontmatter
\input{preface.tex}
-\part{PyLith}
+\mainmatter
\input{intro/intro.tex}
\input{install/install.tex}
+\input{runpylith/runpylith.tex}
\input{tutorials/tutorials.tex}
-\part{Appendices}
+\appendix
\input{fileformats/fileformats.tex}
\input{materials/materials.tex}
\input{license.tex}
\end{document}
-% End of file
\ No newline at end of file
+% End of file
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