[cig-commits] r17008 - in short/3D/PyLith/trunk/doc/userguide/tutorials: 3dhex8 3dhex8/friction 3dhex8/gravity 3dhex8/quasistatic 3dhex8/static 3dtet4 shearwave
brad at geodynamics.org
brad at geodynamics.org
Sun Jun 13 17:38:30 PDT 2010
Author: brad
Date: 2010-06-13 17:38:29 -0700 (Sun, 13 Jun 2010)
New Revision: 17008
Modified:
short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/friction/friction.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/gravity/gravity.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic/quasistatic.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/static/static.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/hex8.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/quad4.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/shearwave.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tet4.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tri3.lyx
Log:
Merge from v1.5-stable.
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/3dhex8.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -56,7 +56,7 @@
\end_inset
-Tutorial Using Hexahedral Mesh Created by CUBIT
+Tutorials Using Hexahedral Mesh Created by CUBIT
\end_layout
\begin_layout Standard
@@ -173,7 +173,7 @@
\begin_layout Standard
This tutorial is meant to demonstrate most of the important features of
- PyLith as a quasi-static finite element code, using a sequence of example
+ PyLith as a quasi-static finite-element code, using a sequence of example
problems.
All problems use the same 3D hexahedral mesh generated using the CUBIT
@@ -195,17 +195,17 @@
The tutorial demonstrates the usage of the CUBIT mesh generation package
to create a mesh, as well as describing how to use a CUBIT-generated mesh
in PyLith.
- Following the discussion of how to generate the mesh, there is a discussion
- of the
+ Following the discussion of how to generate the mesh, we discuss the
\family typewriter
pylithapp.cfg
\family default
file, which contains information common to all the simulations.
- The tutorial is then subdivided into four sections, each pertaining to
- a particular set of PyLith features.
- It is suggested that users go through each of these sections in order as
- the complexity increases at each step.
- All of the files to run the examples are contained in the directory
+ We group the examples into four sections, each pertaining to a particular
+ set of PyLith features.
+ We suggest users go through each of these sections in order as the complexity
+ increases at each step.
+ All of the files necessary to run the examples are contained in the directory
+
\family typewriter
examples/3d/hex8
\family default
@@ -226,8 +226,7 @@
).
Although it would be possible to generate this mesh by hand, it is much
- simpler to use a mesh generation package, and we use the CUBIT mesh generation
- package for this example.
+ simpler to use a mesh generation package, and we use CUBIT for this example.
We provide documented journal files in
\family typewriter
examples/3d/hex8/mesh.
@@ -402,7 +401,7 @@
pylithapp.cfg
\family default
.
- Since these examples use CUBIT format, in this file we set the importer
+ Since these examples use a mesh from CUBIT, in this file we set the importer
to
\family typewriter
MeshIOCubit
@@ -500,8 +499,8 @@
\end_layout
\begin_layout Standard
-The two material groups correspond to the two different colors in Figure
-
+The two material groups correspond to the two different colored regions
+ in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:3dhex8-mesh"
@@ -509,8 +508,8 @@
\end_inset
.
- The usage of two material groups allows us to specify different material
- types or material variations for the upper crust and lower crust, if desired.
+ Using two material groups allows us to specify different material types
+ or material variations for the upper crust and lower crust, if desired.
For now, we retain the default
\family typewriter
ElasticIsotropic3D
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/friction/friction.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/friction/friction.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/friction/friction.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -56,7 +56,7 @@
\end_inset
-Tutorial Using Hexahedral Mesh Created by CUBIT - Fault Friction Examples
+Fault Friction Examples
\end_layout
\begin_layout Standard
@@ -86,16 +86,21 @@
\begin_layout Standard
This set of examples provides an introduction to using fault friction in
static and quasi-static problems with PyLith.
+ Dynamic problems with fault friction are discussed in Section
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sec:tutorial:shearwave:quad4"
+
+\end_inset
+
+.
The boundary conditions are all either static or quasi-static Dirichlet
conditions, and only elastic materials are used.
- Thus, the only aspects that were not covered in previous examples involve
- the use of fault friction.
- Note that in all the fault friction examples we apply axial (x) displacements
- on both the positive and negative x-faces to maintain a compressive normal
- stress on the fault.
+ In all the fault friction examples we apply axial (x) displacements on
+ both the positive and negative x-faces to maintain a compressive normal
+ tractions on the fault.
Otherwise, there would be no frictional resistance.
- All of the fault friction models are nonlinear, and they therefore require
- the usage of the nonlinear solver.
+ Fault friction generates nonlinear behavior, so we use the nonlinear solver.
All of the examples are contained in the directory
\family typewriter
examples/3d/hex8
@@ -129,7 +134,7 @@
\end_layout
\begin_layout LyX-Code
-pylith stepxx.cfg
+pylith stepXX.cfg
\end_layout
\begin_layout Standard
@@ -140,7 +145,7 @@
, and then override or augment them with the additional parameters in the
\family typewriter
-stepxx.cfg
+stepXX.cfg
\family default
file.
Each
@@ -160,11 +165,10 @@
\family typewriter
step10.cfg
\family default
- file describes a problem that is identical to example step01, except for
+ file defines a problem that is identical to example step01, except for
the presence of a vertical fault with static friction.
In this case, the applied displacements are insufficient to cause the fault
- to slip, so the solution should be identical to the results of example
- step01.
+ to slip, so the solution is identical to that in example step01.
As in previous examples involving faults, we must first provide an array
defining the fault interfaces:
\end_layout
@@ -211,7 +215,7 @@
\family typewriter
FaultCohesiveDyn
\family default
-, and we must also define the friction model to use:
+ and we set the friction model to use:
\end_layout
\begin_layout LyX-Code
@@ -248,7 +252,7 @@
StaticFriction
\family default
model requires values for the coefficient of friction and the cohesion
- (see
+ (see Section
\begin_inset CommandInset ref
LatexCommand ref
reference "sub:Fault-Constitutive-Models"
@@ -362,8 +366,8 @@
\family typewriter
step10
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step10-fault-traction-slip"
@@ -396,8 +400,7 @@
\begin_layout Plain Layout
Magnitude of tractions on the fault for example step10 visualized using
ParaView.
- Vectors of fault slip are also plotted; however, since slip does not occur
- for this example they do not appear.
+
\begin_inset CommandInset label
LatexCommand label
name "fig:step10-fault-traction-slip"
@@ -422,12 +425,7 @@
\end_layout
\begin_layout Standard
-The
-\family typewriter
-step11.cfg
-\family default
- file describes a problem that is nearly identical to example step10, except
- that for this example we apply twice as much shear displacement, which
+In step11 we apply twice as much shear displacement as in step10, which
is sufficient to induce slip on the fault.
All other settings are identical.
To change the amount of shear displacement, we change the spatial database
@@ -520,8 +518,8 @@
\family typewriter
step11
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step11-fault-traction-slip"
@@ -555,8 +553,11 @@
Magnitude of tractions on the fault for example step10 visualized using
ParaView.
Vectors of fault slip are also plotted.
- Note that to get the proper slip orientation it is necessary to use the
- Calculator in ParaView.
+ Note that PyLith outputs slip in the fault coordinate system, so we transform
+ them to the global coordinate system using the Calculator in ParaView.
+ A more general approach involves outputing the fault coordinate system
+ information and using these fields in the Calculator.
+
\begin_inset CommandInset label
LatexCommand label
name "fig:step11-fault-traction-slip"
@@ -751,8 +752,8 @@
\family typewriter
step12
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step12-displ-t200"
@@ -811,12 +812,8 @@
\end_layout
\begin_layout Standard
-The
-\family typewriter
-step13.cfg
-\family default
- file describes a problem that is identical to example step12, except that
- we use a slip-weakening friction model rather than a static friction model.
+In this example we replace the static friction fault constitutive model
+ in step12 with a slip-weakening friction fault constitutive model.
Fault friction is overcome at about t = 80 years, the fault slips in each
subsequent time step.
We again use a constant time step size of 5 years and apply the same intial
@@ -842,7 +839,7 @@
\begin_layout Standard
The slip-weakening constitutive model requires a static coefficient of friction,
a dynamic coefficient of friction, a slip weakening parameter, and a cohesion
- (see
+ (see Section
\begin_inset CommandInset ref
LatexCommand ref
reference "sub:Fault-Constitutive-Models"
@@ -911,8 +908,8 @@
\family typewriter
step1
\family default
-3), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+3).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step13-displ-t200"
@@ -971,13 +968,8 @@
\end_layout
\begin_layout Standard
-The
-\family typewriter
-step14.cfg
-\family default
- file describes a problem that is identical to example step13, except that
- we use a rate-and-state friction model with an aging law instead of a slip-weak
-ening friction model.
+In step14 we use a rate-and-state friction model with an ageing law instead
+ of a slip-weakening friction model.
Slip begins to occur at about t = 45 years, and continues in each subsequent
time step.
We again use a constant time step size of 5 years and apply the same intial
@@ -1110,8 +1102,8 @@
\family typewriter
step1
\family default
-4), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+4).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step14-displ-t200"
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/gravity/gravity.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/gravity/gravity.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/gravity/gravity.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -56,7 +56,7 @@
\end_inset
-Tutorial Using Hexahedral Mesh Created by CUBIT - Gravity Examples
+Gravitational Body Force Examples
\end_layout
\begin_layout Standard
@@ -86,8 +86,7 @@
\begin_layout Standard
This set of examples describes a set of problems for PyLith involving gravitatio
nal body forces.
- All of the examples are quasi-static and all of them run for a time period
- of 200 years.
+ All of the examples are quasi-static and run for a time period of 200 years.
These examples also demonstrate the use of a generalized Maxwell viscoelastic
material, which is used for the lower crust in all examples.
The final example (step17) demonstrates the usage of a finite strain formulatio
@@ -117,7 +116,7 @@
\end_layout
\begin_layout LyX-Code
-pylith stepxx.cfg
+pylith stepXX.cfg
\end_layout
\begin_layout Standard
@@ -128,7 +127,7 @@
, and then override or augment them with the additional parameters in the
\family typewriter
-stepxx.cfg
+stepXX.cfg
\family default
file.
Each
@@ -148,13 +147,12 @@
\family typewriter
step15.cfg
\family default
- file describes a problem with extremely simple Dirichlet boundary conditions.
+ file defines a problem with extremely simple Dirichlet boundary conditions.
On the positive and negative x-faces, the positive and negative y-faces,
and the negative z-face, the displacements normal to the face are set to
zero.
- We then apply gravitational body forces.
- Since all the material in the example has the same density, for the elastic
- solution, the resultant stresses should be:
+ Because all of the materials in the example have the same density, the
+ elastic solution for loading via gravitational body forces is
\begin_inset Formula \begin{equation}
\sigma_{zz}=\rho gh;\:\sigma_{xx}=\sigma_{yy}=\frac{\nu\rho gh}{1-\nu}\:.\label{eq:1-1}\end{equation}
@@ -237,7 +235,7 @@
\end_layout
\begin_layout Standard
-We use a generalized Maxwell model for the lower crust (see
+We use a generalized Maxwell model for the lower crust (see Section
\begin_inset CommandInset ref
LatexCommand ref
reference "sub:Formulation-for-Gen-Max"
@@ -321,8 +319,8 @@
\family typewriter
step15
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step15-displ-t200"
@@ -389,7 +387,7 @@
\family typewriter
step16.cfg
\family default
- file describes a problem that is identical to example step15, except that
+ file defines a problem that is identical to example step15, except that
initial stresses are used to prevent the initial large displacements due
to 'turning on' gravity.
Since all normal stress components are given an initial stress of
@@ -397,7 +395,8 @@
\end_inset
, the initial stress state is lithostatic, which is an appropriate condition
- for many tectonic problems in the absence of tectonic stresses (e.g.,
+ for many tectonic problems in the absence of tectonic stresses (e.g., McGarr
+
\begin_inset CommandInset citation
LatexCommand cite
key "McGarr:1988"
@@ -411,10 +410,9 @@
\end_layout
\begin_layout Standard
-We set the gravity field, as for example step15, and we again use adaptive
- time stepping and use a generalized Maxwell rheology for the lower crust.
- We then must provide values for the initial stress for both the upper and
- lower crust.
+We set the gravity field, as in example step15, and we again use adaptive
+ time stepping with a generalized Maxwell rheology for the lower crust.
+ We provide values for the initial stress for both the upper and lower crust.
Since the materials have the same density, we are able to use the same
\family typewriter
@@ -498,8 +496,8 @@
\family typewriter
step16
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step16-stress_xx-t200"
@@ -567,8 +565,8 @@
\family typewriter
step17.cfg
\family default
- file describes a problem that is identical to example step15, except that
- we now use a small strain formulation (see
+ file defines a problem that is identical to example step15, except that
+ we now use a small strain formulation (see Section
\begin_inset CommandInset ref
LatexCommand ref
reference "sec:Small-Strain-Formulation"
@@ -576,22 +574,22 @@
\end_inset
).
- All of the problems up to this point have assumed infinitesimal (linear)
- strain, meaning that the change in shape of the domain during deformation
- is not taken into account.
+ All of the problems up to this point have assumed infinitesimal strain,
+ meaning that the change in shape of the domain during deformation is not
+ taken into account.
In many problems it is important to consider the change in shape of the
domain.
This is particularly important in many problems involving gravitational
body forces, since a change in shape of the domain results in a different
- system of forces.
+ stress field.
By examining the stress and deformation fields for this example in comparison
with those of example step15, we can see what effect the infinitesimal
strain approximation has on our solution.
\end_layout
\begin_layout Standard
-We set the gravity field, as for example step15, and we again use adaptive
- time stepping and use a generalized Maxwell rheology for the lower crust.
+We set the gravity field, as in example step15 and again use adaptive time
+ stepping withs a generalized Maxwell rheology for the lower crust.
The only change is that we change the problem formulation from the default
\family typewriter
@@ -642,8 +640,8 @@
\family typewriter
step17
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step17-disp-t200"
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic/quasistatic.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic/quasistatic.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/quasistatic/quasistatic.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -56,7 +56,7 @@
\end_inset
-Tutorial Using Hexahedral Mesh Created by CUBIT - Quasi-static Examples
+Quasi-static Examples
\end_layout
\begin_layout Standard
@@ -84,6 +84,10 @@
\end_layout
\begin_layout Itemize
+UniformDB spatial database
+\end_layout
+
+\begin_layout Itemize
CompositeDB spatial database
\end_layout
@@ -167,7 +171,7 @@
\end_layout
\begin_layout LyX-Code
-pylith stepxx.cfg
+pylith stepXX.cfg
\end_layout
\begin_layout Standard
@@ -178,7 +182,7 @@
, and then override or augment them with the additional parameters in the
\family typewriter
-stepxx.cfg
+stepXX.cfg
\family default
file.
Each
@@ -198,10 +202,10 @@
\family typewriter
step04.cfg
\family default
- file describes a problem with x-displacements fixed at zero on the positive
+ file defines a problem with x-displacements fixed at zero on the positive
and negative x-faces while velocity boundary conditions are applied in
the y-directions on the same faces, yielding a left-lateral sense of movement.
- The bottom (minimum z) boundary is held fixed in the z-direction.
+ The bottom (negative z) boundary is held fixed in the z-direction.
We also use a Maxwell viscoelastic material for the lower crust, and the
simulation is run for 200 years using a constant time step size of 20 years.
The default time stepping behavior is
@@ -438,7 +442,7 @@
\begin_layout Standard
Finally, we must provide information on VTK output.
This is slightly more complicated than the static case, because we must
- decide the frequency with which output occurs for each output type.
+ decide the frequency with which output occurs for each output manager.
We also assign a more user-friendly format to the output file time stamp,
and we request that the time stamp is in units of 1 year (rather than the
default value of seconds):
@@ -555,8 +559,8 @@
\family typewriter
step04
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step04-displ-t200"
@@ -605,10 +609,6 @@
\end_layout
-\begin_layout Plain Layout
-
-\end_layout
-
\end_inset
@@ -797,8 +797,8 @@
\family typewriter
step05
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step05-displ-t40"
@@ -840,10 +840,6 @@
\end_layout
-\begin_layout Plain Layout
-
-\end_layout
-
\end_inset
@@ -859,14 +855,15 @@
\family typewriter
step06.cfg
\family default
- file describes a problem with Dirichlet (displacement) boundary conditions
+ file defines a problem with Dirichlet (displacement) boundary conditions
corresponding to zero x and y-displacements applied on the negative and
positive x-faces and a vertical fault that includes multiple earthquake
ruptures as well as steady fault creep.
The upper (locked) portion of the fault has 4 m of left-lateral slip every
200 years, while the lower (creeping) portion of the fault slips at a steady
rate of 2 cm/year.
- The problem bears some similarity to the strike-slip fault model of
+ The problem bears some similarity to the strike-slip fault model of Savange
+ and Prescott
\begin_inset CommandInset citation
LatexCommand cite
key "Savage:Prescott:1978"
@@ -891,9 +888,8 @@
.
For adaptive time stepping, we provide the maximum permissible time step
size, along with a stability factor.
- The stability factor controls how the time step size is allowed to deviate
- from the stable time step size provided by the different materials in the
- model.
+ The stability factor controls the time step size relative to the stable
+ time step size provided by the different materials in the model.
A
\family typewriter
stability_factor
@@ -1110,7 +1106,7 @@
\end_layout
\begin_layout Standard
-Note that for all earthquake sources we provide both an
+For all earthquake sources we provide both an
\family typewriter
origin_time
\family default
@@ -1128,8 +1124,7 @@
(if any).
Since there are multiple earthquake sources of different types, there are
a number of additional fault information fields available for output.
- We therefore request that these additional fields be output to the fault
- information file:
+ We add these additional fields be output to the fault information file:
\end_layout
\begin_layout LyX-Code
@@ -1165,8 +1160,8 @@
\family typewriter
step06
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step06-displ-t300"
@@ -1220,15 +1215,11 @@
\end_layout
\begin_layout Standard
-The
-\family typewriter
-step07.cfg
-\family default
- file describes a problem nearly identical to example step06.
- The only difference is that velocity boundary conditions in the positive
- and negative y-directions on the positive and negative x-faces, so that
- the external boundaries keep pace with the average fault slip.
- This problem is nearly identical to the strike-slip fault model of
+In step07 we add velocity boundary conditions in the positive and negative
+ y-directions on the positive and negative x-faces, so that the external
+ boundaries keep pace with the average fault slip.
+ This problem is nearly identical to the strike-slip fault model of Savage
+ and Prescott
\begin_inset CommandInset citation
LatexCommand cite
key "Savage:Prescott:1978"
@@ -1332,12 +1323,13 @@
\begin_layout Standard
The fault definition information is identical to example step06.
In previous examples, we have just used the default output for the domain
- and subdomain (ground surface), which just provides the displacements.
- In many cases, it is also useful to provide the velocities.
- PyLith is able to provide this information, approximating the velocities
- for the current time step as the difference between the current displacements
- and the displacements from the previous time step, divided by the time
- step size.
+ and subdomain (ground surface), which includes the displacements.
+ In many cases, it is also useful to include the velocities.
+ PyLith provides this information, computing the velocities for the current
+ time step as the difference between the current displacements and the displacem
+ents from the previous time step, divided by the time step size.
+ This is more accurate than computing the velocities from the displacement
+ field output that has been decimated in time.
We can obtain this information by explicitly requesting it in
\family typewriter
vertex_data_fields
@@ -1460,8 +1452,8 @@
\family typewriter
step07
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step07-displ-vel-t300"
@@ -1526,8 +1518,8 @@
\family typewriter
step08.cfg
\family default
- file describes a problem that is identical to example step07, except the
- the lower crust is composed of power-law viscoelastic material.
+ file defines a problem that is identical to example step07, except the
+ the lower crust is composed of a power-law viscoelastic material.
Since the material behavior is now nonlinear, we must use the nonlinear
solver:
\end_layout
@@ -1588,27 +1580,25 @@
\end_layout
\begin_layout Standard
-These settings are unused unless we are using the nonlinear solver.
+These settings are ignored unless we are using the nonlinear solver.
\end_layout
\begin_layout Standard
-When using laboratory results for power-law viscoelastic materials, the
- properties provided do not generally match those expected by PyLith (see
-
+When setting the physical properties for the power-law material in PyLith,
+ the parameters (see Section
\begin_inset CommandInset ref
LatexCommand ref
reference "sub:Power-Law-Maxwell-Viscoelastic"
\end_inset
-).
- A utility code,
+) do not generally correspond to the values provided in laboratory results.
+ PyLith include a utility code,
\family typewriter
powerlaw_gendb.py
\family default
-, has been provided to simplify the process of using laboratory results
- with PyLith.
- This utility code should be installed in the same location as PyLith.
+, to simplify the process of using laboratory results with PyLith.
+ This utility code is installed in the same location as PyLith.
An example of how to use it is in
\family typewriter
examples/3d/hex8/spatialdb/powerlaw
@@ -1661,8 +1651,6 @@
\family default
can compute the other property.
Default values of 1.0e-6 1/s and 1 MPa are provided.
- A spatial database must then be provided for each laboratory-derived parameter
- and for the temperature.
In this example, the same database was used for all parameters, and a separate
database was used to define the temperature distribution.
In practice, the user can provide any desired thermal model to provide
@@ -1680,8 +1668,8 @@
\end_layout
\begin_layout Standard
-This will cause the code to automatically read the parameters in powerlaw_gendb.c
-fg, and the file
+This code will automatically read the parameters in powerlaw_gendb.cfg in
+ creating the file
\begin_inset Newline newline
\end_inset
@@ -1689,7 +1677,7 @@
\family typewriter
examples/3d/hex8/spatialdb/mat_powerlaw.spatialdb
\family default
- will be created.
+.
\end_layout
\begin_layout Standard
@@ -1760,12 +1748,8 @@
\end_layout
\begin_layout Standard
-Each subset of properties comes from a
-\family typewriter
-SimpleDB
-\family default
-, so we must first define the properties that come from each spatial database
- and then provide the database filename:
+We must define the properties that come from each spatial database and then
+ provide the database parameters:
\end_layout
\begin_layout LyX-Code
@@ -1866,8 +1850,8 @@
\family typewriter
step08
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step08-strain-displ-t150"
@@ -1933,18 +1917,13 @@
\end_layout
\begin_layout Standard
-The
-\family typewriter
-step09.cfg
-\family default
- file describes a problem that is nearly identical to example step08, except
- the the lower crust is composed of Drucker-Prager elastoplastic material.
- As for example step08, the material behavior is nonlinear so we again use
+In this example we use a Drucker-Prager elastoplastic rheology in the lower
+ crust.
+ As in example step08, the material behavior is nonlinear so we again use
the nonlinear solver.
- Since the material is elastoplastic, there is no inherent time-dependence,
- which means that there is no stable time step size for the material.
- Depending on the loading conditions, this may make it difficult to obtain
- convergence.
+ The material is elastoplastic, there is no inherent time-dependent response
+ and the stable time step size for the material depends on the loading condition
+s.
To avoid this, we set the maximum time step size to 5 years rather than
the value of 10 years used in example step08:
\end_layout
@@ -2137,8 +2116,8 @@
\family typewriter
step09
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step09-strain-displ-t150"
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/static/static.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/static/static.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dhex8/static/static.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -56,7 +56,7 @@
\end_inset
-Tutorial Using Hexahedral Mesh Created by CUBIT - Static Examples
+Static Examples
\end_layout
\begin_layout Standard
@@ -138,7 +138,7 @@
\end_layout
\begin_layout LyX-Code
-pylith stepxx.cfg
+pylith stepXX.cfg
\end_layout
\begin_layout Standard
@@ -149,15 +149,15 @@
, and then override or augment them with the additional parameters in the
\family typewriter
-stepxx.cfg
+stepXX.cfg
\family default
file.
Each
\family typewriter
.cfg
\family default
- file is extensively documented, to provide detailed information on the
- various parameters.
+ file is extensively documented to provide detailed information on the various
+ parameters.
\end_layout
\begin_layout Subsubsection
@@ -169,14 +169,15 @@
\family typewriter
step01.cfg
\family default
- file describes a problem with pure Dirichlet (displacement) boundary conditions
+ file defines a problem with pure Dirichlet (displacement) boundary conditions
corresponding to compression in the x-direction and shear in the y-direction.
The bottom (minimum z) boundary is held fixed in the z-direction.
On the positive and negative x-faces, compressional displacements of 1
m are applied in the x-direction and shear displacements yielding a left-latera
l sense of shear are applied in the y-direction.
- In this example and in subsequent examples we would like to output a subset
- of the displacement solution corresponding to the ground surface.
+ In this example and in subsequent examples we would like to output the
+ displacement solution over a subset of the domain corresponding to the
+ ground surface.
To do this, we first set the output to an array of two output managers
as follows:
\end_layout
@@ -199,7 +200,7 @@
\begin_layout Standard
We then define the subdomain output manager to correspond to a subset of
- the solution:
+ the domain:
\end_layout
\begin_layout LyX-Code
@@ -241,8 +242,8 @@
\family typewriter
bc_dof
\family default
-), we must provide a label that describes the Cubit nodeset to which to
- apply the BC, and we must specify what type of spatial database is being
+), we must provide a the label associated with the CUBIT nodeset associated
+ with the BC, and we must specify the type of spatial database is being
used to describe the boundary conditions.
For the x-faces, we use a
\family typewriter
@@ -360,8 +361,8 @@
\family typewriter
step01
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step01-displ"
@@ -409,10 +410,6 @@
\end_layout
-\begin_layout Plain Layout
-
-\end_layout
-
\end_inset
@@ -427,11 +424,11 @@
\family typewriter
step02.cfg
\family default
- file describes a problem with Dirichlet (displacement) boundary conditions
+ file defines a problem with Dirichlet (displacement) boundary conditions
corresponding to zero x and y-displacements applied on the negative x-face
and Neumann (traction) boundary conditions corresponding to normal compression
and horizontal shear applied on the positive x-face.
- The bottom (minimum z) boundary is held fixed in the z-direction.
+ The bottom (negative z) boundary is held fixed in the z-direction.
The problem is similar to example step01, except that 1 MPa of normal compressi
on and 1 MPa of shear (in a left-lateral sense) are applied on the positive
x-face, and the negative x-face is pinned in both the x and y-directions.
@@ -560,8 +557,8 @@
\family typewriter
step02
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step02-displ"
@@ -603,10 +600,6 @@
\end_layout
-\begin_layout Plain Layout
-
-\end_layout
-
\end_inset
@@ -745,6 +738,10 @@
\end_layout
\begin_layout LyX-Code
+slip.query_type = linear
+\end_layout
+
+\begin_layout LyX-Code
slip_time.iohandler.filename = spatialdb/sliptime.spatialdb
\end_layout
@@ -788,8 +785,8 @@
\family typewriter
step03
\family default
-), and the results may be visualized using a tool such as ParaView or mayavi2.
- Results using ParaView are shown in
+).
+ Results using ParaView are shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:step03-displ"
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/3dtet4/3dtet4.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -1,4 +1,4 @@
-#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -384,7 +384,7 @@
\end_layout
\begin_layout Standard
-Since these examples use LaGriT format, we set the importer to
+Since these examples use a mesh from LaGriT, we set the importer to
\family typewriter
MeshIO
\family default
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/hex8.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/hex8.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/hex8.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -175,8 +175,8 @@
\begin_layout Standard
The simulation parameters match those in the tri3 and tet4 examples.
- As in the tet4 example, we both the longitudinal degree of freedom and
- the out-of-plane transverse degree of freedom.
+ As in the tet4 example, we fix both the longitudinal degree of freedom
+ and the out-of-plane transverse degree of freedom.
Using eight-point quadrature permits use of a time step of 1/20 s, which
is slightly larger than the time step of 1/30 s used in the tri3 and tet4
simulations.
@@ -202,7 +202,7 @@
If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset CommandInset ref
-LatexCommand vref
+LatexCommand ref
reference "fig:shearwave:hex8:deform"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/quad4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/quad4.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/quad4.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -120,8 +120,6 @@
\end_inset
).
- This mesh could be generated via a simple script, but it is even easier
- to generate this mesh using CUBIT.
We provide documented CUBIT journal files in
\family typewriter
examples/bar_shearwave/quad4.
@@ -228,7 +226,7 @@
If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset CommandInset ref
-LatexCommand vref
+LatexCommand ref
reference "fig:shearwave:quad4:kinematic"
\end_inset
@@ -289,6 +287,15 @@
In this set of examples we replace the kinematic fault interface with the
dynamic fault interface, resulting in fault slip controlled by a fault-constitu
tive model.
+ See Section
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sub:Fault-Constitutive-Models"
+
+\end_inset
+
+ for detailed information about the fault constitutive models available
+ in PyLith.
Because this is a dynamic simulation we want the generated shear wave to
continue to be absorbed at the ends of the bar, so we drive the fault by
imposing initial tractions directly on the fault surface rather than through
@@ -319,7 +326,7 @@
\begin_layout Standard
The parameters specific to this example are related to the use of the static
- friction fault constitutive model (see Section ??).
+ friction fault constitutive model.
We set the fault constitutive model via
\end_layout
@@ -334,9 +341,9 @@
\begin_layout Standard
and use a UniformDB to set the static friction parameters.
We use a coefficient of friction of 0.6 and no cohesion (0 MPa).
- The parameters specific to this example are in dynamic_
+ The parameters specific to this example are in
\family typewriter
-staticfriction.cfg
+dynamic_staticfriction.cfg
\family default
, so we run the problem via:
\end_layout
@@ -363,16 +370,16 @@
If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset CommandInset ref
-LatexCommand vref
+LatexCommand ref
reference "fig:shearwave:quad4:staticfriction"
\end_inset
, which was generated using ParaView.
- The steady-state solution is a constant slip rate of 0.08 m/s and shear
- traction of 6.0 MPa on the fault surface, a uniform shear strain of 2e-5
- in the bar with uniform, constant velocities in the y-direction of +0.04
- m/s and -0.04 m/s on the -x and +x sides of the fault, respectively.
+ The steady-state solution is a constant slip rate of 0.08 m/s, a shear traction
+ of 6.0 MPa on the fault surface, and a uniform shear strain of 2e-5 in the
+ bar with uniform, constant velocities in the y-direction of +0.04 m/s and
+ -0.04 m/s on the -x and +x sides of the fault, respectively.
\end_layout
\begin_layout Standard
@@ -466,9 +473,9 @@
\end_layout
\begin_layout Standard
-The parameters specific to this example are in dynamic_
+The parameters specific to this example are in
\family typewriter
-slipweakening.cfg
+dynamic_slipweakening.cfg
\family default
, so we run the problem via:
\end_layout
@@ -490,7 +497,7 @@
If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset CommandInset ref
-LatexCommand vref
+LatexCommand ref
reference "fig:shearwave:quad4:slipweakening"
\end_inset
@@ -572,9 +579,9 @@
We use a reference coefficient of friction of 0.6, reference slip rate of
1.0e-6 m/s, characteristic slip distance of 0.037 m, coefficients a and b
of 0.0125 and 0.0172, and no cohesion (0 MPa).
- The parameters specific to this example are in dynamic_
+ The parameters specific to this example are in
\family typewriter
-ratestateageing.cfg
+dynamic_ratestateageing.cfg
\family default
, so we run the problem via:
\end_layout
@@ -596,7 +603,7 @@
If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset CommandInset ref
-LatexCommand vref
+LatexCommand ref
reference "fig:shearwave:quad4:ratestateageing"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/shearwave.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/shearwave.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/shearwave.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -62,9 +62,9 @@
using a kinematic fault rupture with simultaneous slip over the fault surface,
which we place at the center of the bar.
The discretization size is 200 m in all cases.
- The slip time histories follows the integral of Brune's far-field time
- function with slip initiating at 0.1 s, a left-lateral final slip of 1.0
- m, and a rise time of 2.0 s.
+ The slip time histories follow the integral of Brune's far-field time function
+ with slip initiating at 0.1 s, a left-lateral final slip of 1.0 m, and a
+ rise time of 2.0 s.
The shear wave speed in the bar is 1.0 km/s, so the shear wave reaches each
end of the bar at 4.1 s.
Absorbing boundaries on the ends of the bar prevent significant reflections.
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tet4.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tet4.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tet4.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -202,7 +202,7 @@
If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset CommandInset ref
-LatexCommand vref
+LatexCommand ref
reference "fig:shearwave:tet4:deform"
\end_inset
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tri3.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tri3.lyx 2010-06-14 00:35:28 UTC (rev 17007)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/shearwave/tri3.lyx 2010-06-14 00:38:29 UTC (rev 17008)
@@ -1,4 +1,4 @@
-#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -220,7 +220,7 @@
\end_inset
.
- We simulation 12.0 s of motion with a time step of 1/30 s.
+ We simulate 12.0 s of motion with a time step of 1/30 s.
This time step must follow the Courant–Friedrichs–Lewy condition; that
is, the time step must be smaller than the time it takes the P wave to
propagate across the shortest edge of a cell.
@@ -266,8 +266,8 @@
If the problem ran correctly, you should be able to generate a figure such
as Figure
\begin_inset CommandInset ref
-LatexCommand vref
-reference "fig:shearwave:tet4:deform"
+LatexCommand ref
+reference "fig:shearwave:tri3:deform"
\end_inset
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