[cig-commits] r4409 - in
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube:
. figs
baagaard at geodynamics.org
baagaard at geodynamics.org
Wed Aug 23 16:27:13 PDT 2006
Author: baagaard
Date: 2006-08-23 16:27:13 -0700 (Wed, 23 Aug 2006)
New Revision: 4409
Added:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/geometry.eps
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/geometry.fig
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/workflow.eps
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/workflow.fig
Modified:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/splitcube.tex
Log:
User guide. Brought splitcube up to date. Added figures for splitcube tutorial.
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/geometry.eps
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/geometry.eps 2006-08-23 23:24:21 UTC (rev 4408)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/geometry.eps 2006-08-23 23:27:13 UTC (rev 4409)
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===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/geometry.fig 2006-08-23 23:24:21 UTC (rev 4408)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/geometry.fig 2006-08-23 23:27:13 UTC (rev 4409)
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+% here ends figure;
+$F2psEnd
+rs
+showpage
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/workflow.fig
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/workflow.fig 2006-08-23 23:24:21 UTC (rev 4408)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/figs/workflow.fig 2006-08-23 23:27:13 UTC (rev 4409)
@@ -0,0 +1,151 @@
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Modified: short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/splitcube.tex
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/splitcube.tex 2006-08-23 23:24:21 UTC (rev 4408)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/tutorials/splitcube/splitcube.tex 2006-08-23 23:27:13 UTC (rev 4409)
@@ -5,8 +5,8 @@
In this tutorial we will walk through the steps necessary to
construct, run, and view the results of a benchmark problem involving
a simple, vertical, through-going strike-slip fault. This problem
-examines the elastic deformation from a single, finite, right-lateral
-earthquake in 3-D without body forces.
+examines the elastic deformation from a left-lateral earthquake in
+3-D without body forces.
\subsection{Problem Description}
@@ -17,16 +17,17 @@
constants ($\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.
+distribution is 1.0 m of uniform left-lateral motion. The face of the
+cube on the plane x=0 is held fixed. The other lateral faces and top
+and bottom of the mesh are traction-free. The solution to this problem
+is zero stresses and strains with no displacements for the region
+$x<0.5$ km and a y-displacement of 1.0 m for $x>0.5$ km.
-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.}
+ \includegraphics{figs/geometry}
+ \caption{Geometry of model domain for simple model with
+ strike-slip fault.}
\end{center}
\end{figure}
@@ -105,13 +106,14 @@
\shellprompt\userinput{./tutor.py -m clean -s mesh}
\end{screen}
-\item Examine the \filename{splitcube.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 Examine the \filename{splitcube.geo} file to see how the
+ geometry for the problem is defined. Notice that the fault plane 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 have not flagged the face on the plane x=0
+ because we generate this boundary condition by hand. We also do not
+ have to flag the other faces 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}
@@ -123,7 +125,7 @@
\item Click on \guibutton{Generate Mesh}.
\item Export the mesh to a file named \filename{splitcube.netgen},
making sure the export filetype is "Neutral format".
-\item You can now exit \application{NETGEN}.
+\item You may now exit \application{NETGEN}.
\end{enumerate}
\subsection{Setup simulation input files}
@@ -151,7 +153,7 @@
\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{splitcube}. This
- utilitiy will generate the following files:
+ utility will generate the following files:
\filename{splitcube.w01.wink}, \filename{splitcube.coord},
\filename{splitcube.connect}, \filename{splitcube.bc},
\filename{splitcube.1.fcoord}, \filename{splitcube.1.fbc}.
@@ -166,7 +168,7 @@
\item The boundary conditions on the fault for this example are
very simple. As a result, the \filename{splitcube.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.
+ left-lateral slip of 1.0 m is applied to the fault surface.
\begin{warning}
If you make any changes to \filename{splitcube.geo} or change the
@@ -178,9 +180,17 @@
boundary conditions.
\end{warning}
-\item The external boundary conditions for this benchmark simply
- involve ... ADD STUFF HERE.
+\item The external boundary conditions for this benchmark are simply
+ pinned nodes on one face of the cube. Consequently, the boundary
+ condition file was created by hand. You need to remove the one
+ generated by the \command{readnetgen} utility which is empty and
+ copy the hand-generated file from the archive directory.
+ \begin{screen}
+ \shellprompt\userinput{rm splitcube.bc}
+ \shellprompt\userinput{cp ../archive/splitcube.bc .}
+ \end{screen}
+
\begin{warning}
If you make any changes to \filename{splitcube.geo} or change the
geometry within \application{NETGEN}, the boundary condition file
@@ -204,14 +214,15 @@
\shellprompt\userinput{./tutor.py -m retrieve -s run1}
\end{screen}
-\item In \filename{splitcube.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{splitcube.prop}. In \filename{splitcube.statevar} we choose to
- include total stress, total strain, incremental stress, and
- incremental strain in the output. As defined in
- \filename{splitcube.time}, the simulation will have 100 time steps of
- 0.1 year each.
+\item As defined in \filename{splitcube.time}, the simulation will
+ only solve for the elastic solution. In \filename{splitcube.fuldat},
+ we have not specified any time steps for output because in this
+ problem we only compute the elastic solution, which is always
+ included in the output. We define two materials with elastic
+ behavior in \filename{splitcube.prop}. In
+ \filename{splitcube.statevar} we choose to include total stress,
+ total strain, incremental stress, and incremental strain in the
+ output.
\item Run the simulation by executing \userinput{runbm.py -n 1}, where
the 1 refers to the number of processors.
@@ -234,11 +245,11 @@
\subsection{Visualize the single processor run}
Now it is time to visualize the results of the simulation. By default,
-PyLith writes simulation output using \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
+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}
@@ -254,12 +265,12 @@
time step into a complete UCD file. For example, use \command{cat}
to merge the nodal coordinates file
(\filename{splitcube\_1.0.mesh.inp}) and the nodal displacements at
- time step 10 file (\filename{splitcube\_1.0.mesh.time.00010.inp}) into
- \filename{splitcube\_1.0.mesh.t00010.inp}.
+ time step 10 file (\filename{splitcube\_1.0.mesh.time.00000.inp}) into
+ \filename{splitcube\_1.0.mesh.t00000.inp}.
\begin{screen}
- \shellprompt\userinput{cat splitcube\_1.0.mesh.inp splitcube\_1.0.mesh.time.00010.inp \(\backslash\)}
- \userinput{> splitcube\_1.0.mesh.t00010.inp}
+ \shellprompt\userinput{cat splitcube\_1.0.mesh.inp splitcube\_1.0.mesh.time.00000.inp \(\backslash\)}
+ \userinput{> splitcube\_1.0.mesh.t00000.inp}
\end{screen}
\item Start \application{ParaView} by executing \command{paraview}.
@@ -274,15 +285,15 @@
\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::splitcube:xdisp:t10}.
+ figure~\ref{fig::splitcube:xdisp:t0}.
\begin{figure}[htbp]
\begin{center}
- %\includegraphics{figs/xdisp_t10}
+ %\includegraphics{figs/xdisp_0}
\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:splitcube:xdisp:t10}
+ time step 0 (elastic solution to the imposed dislocation) for
+ the simple strike-slip example.}
+ \label{fig:splitcube:xdisp:00}
\end{center}
\end{figure}
@@ -294,27 +305,26 @@
\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:splitcube:xdisp:vec:t10}.
+ 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:splitcube:xdisp:vec:t0}.
\begin{figure}[htbp]
\begin{center}
- %\includegraphics{figs/splitcube_xdisp_vec_t10}
+ %\includegraphics{figs/splitcube_xdisp_vec_t0}
\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:splitcube:xdisp:vec:t10}
+ displacement vectors at time step 0 (elastic solution to the
+ imposed dislocation) for the simple strike-slip example.}
+ \label{fig:splitcube:xdisp:vec:t0}
\end{center}
\end{figure}
@@ -325,9 +335,8 @@
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.
+will run 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
@@ -338,7 +347,7 @@
\end{screen}
\item The parameter files are the same as those in the single
- processor run. The \command{runbm} script will automatically take
+ processor run. The \command{runbm.py} 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
@@ -371,10 +380,10 @@
twice to create UCD files for each processor.
\begin{screen}
- \shellprompt\userinput{cat splitcube\_2.0.mesh.inp splitcube\_2.0.mesh.time.00010.inp \(\backslash\)}
- \userinput{> splitcube\_2.0.mesh.t00010.inp}
- \shellprompt\userinput{cat splitcube\_2.1.mesh.inp splitcube\_2.1.mesh.time.00010.inp \(\backslash\)}
- \userinput{> splitcube\_2.1.mesh.t00010.inp}
+ \shellprompt\userinput{cat splitcube\_2.0.mesh.inp splitcube\_2.0.mesh.time.00000.inp \(\backslash\)}
+ \userinput{> splitcube\_2.0.mesh.t00000.inp}
+ \shellprompt\userinput{cat splitcube\_2.1.mesh.inp splitcube\_2.1.mesh.time.00000.inp \(\backslash\)}
+ \userinput{> splitcube\_2.1.mesh.t00000.inp}
\end{screen}
\item Start \application{ParaView} by executing \command{paraview}.
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