[cig-commits] r16717 - in short/3D/PyLith/trunk/doc/userguide: benchmarks boundaryconditions install intro runpylith tutorials
brad at geodynamics.org
brad at geodynamics.org
Sat May 15 13:04:12 PDT 2010
Author: brad
Date: 2010-05-15 13:04:12 -0700 (Sat, 15 May 2010)
New Revision: 16717
Modified:
short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx
short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx
short/3D/PyLith/trunk/doc/userguide/install/install.lyx
short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
Log:
Added comments on what areas need updated, revision, or addition.
Modified: short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx 2010-05-15 18:25:37 UTC (rev 16716)
+++ short/3D/PyLith/trunk/doc/userguide/benchmarks/benchmarks.lyx 2010-05-15 20:04:12 UTC (rev 16717)
@@ -1,4 +1,4 @@
-#LyX 1.6.0 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -143,5 +143,9 @@
\end_layout
+\begin_layout Subsection
+ADD SCEC DYNAMIC RUPTURE BENCHMARKS
+\end_layout
+
\end_body
\end_document
Modified: short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx 2010-05-15 18:25:37 UTC (rev 16716)
+++ short/3D/PyLith/trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx 2010-05-15 20:04:12 UTC (rev 16717)
@@ -1,4 +1,4 @@
-#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -1821,9 +1821,8 @@
For fault interfaces, dislocations in 1D correspond to fault-opening (and
closing), in 2D lateral-slip and fault opening, and in 3D lateral-slip,
reverse-slip, and fault opening.
- The current release of PyLith only supports kinematic (prescribed) slip.
- Support for fault constitutive models for frictional interface conditions
- will be supported in a future release (December 2008).
+ PyLith supports kinematic (prescribed) slip and dynamic (spontaneous) rupture
+ simulations.
\end_layout
\begin_layout Subsection
@@ -1991,7 +1990,7 @@
\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename figs/quad4cohesive.eps
+ filename figs/quad4cohesivekin.eps
\end_inset
@@ -2025,58 +2024,6 @@
\end_layout
-\begin_layout Standard
-\noindent
-\align center
-\begin_inset Float figure
-placement H
-wide false
-sideways false
-status open
-
-\begin_layout Plain Layout
-\align center
-\begin_inset Graphics
- filename figs/quad4cohesivekin.eps
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Plain Layout
-\begin_inset Caption
-
-\begin_layout Plain Layout
-Example of cohesive cell using Lagrange multipliers inserted into a mesh
- of two quadrilateral cells.
- The zero thickness cohesive cell (shown with dashed lines) controls slip
- on the fault.
- The Lagrange multipliers for a kinematic earthquake source are associated
- with the degrees of freedom for vertices 8 and 9.
- The constraint associated with vertex 8 controls the relative motion between
- vertices 2 and 6, and the constraint associated with vertex 9 controls
- the relative motion between vertices 3 and 7.
-
-\begin_inset CommandInset label
-LatexCommand label
-name "fig:fault:cohesive:quad4:kin"
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
\begin_layout Subsection
Fault Parameters
\end_layout
@@ -2667,7 +2614,7 @@
\end_layout
\begin_layout Subsubsection
-Kinematic Earthquake Rupture Parameters
+Kinematic Rupture Parameters
\end_layout
\begin_layout Standard
@@ -3752,6 +3699,22 @@
\end_layout
+\begin_layout Subsection
+Dynamic Earthquake Rupture
+\end_layout
+
+\begin_layout Subsubsection
+Governing Equations
+\end_layout
+
+\begin_layout Subsubsection
+Dynamic Rupture Parameters
+\end_layout
+
+\begin_layout Subsubsection
+Fault Constitutive Models
+\end_layout
+
\begin_layout Section
Gravitational Body Forces
\end_layout
Modified: short/3D/PyLith/trunk/doc/userguide/install/install.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2010-05-15 18:25:37 UTC (rev 16716)
+++ short/3D/PyLith/trunk/doc/userguide/install/install.lyx 2010-05-15 20:04:12 UTC (rev 16717)
@@ -1,4 +1,4 @@
-#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -224,7 +224,7 @@
\begin_deeper
\begin_layout LyX-Code
-$ tar -xzf pylith-1.4.2-linux-i686.tgz
+$ tar -xzf pylith-1.5.0-linux-i686.tgz
\end_layout
\end_deeper
@@ -298,7 +298,7 @@
\begin_deeper
\begin_layout LyX-Code
-$ tar -xzf pylith-1.4.2-darwin-powerpc.tgz
+$ tar -xzf pylith-1.5.0-darwin-powerpc.tgz
\end_layout
\end_deeper
@@ -516,6 +516,8 @@
\family default
projects offer pre-built binaries for a variety of systems, including Mac
OS X.
+ A number of optional PETSc packages that provide additional preconditioners
+ and solvers require a Fortran compiler.
\end_layout
\begin_layout Subsubsection
@@ -952,7 +954,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf petsc-dev-pylith-1.4.2.tgz
+$ tar xzf petsc-dev-pylith-1.5.0.tgz
\end_layout
\begin_layout Standard
@@ -960,7 +962,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c petsc-dev-pylith-1.4.2.tgz | tar xf -
+$ gunzip -c petsc-dev-pylith-1.5.0.tgz | tar xf -
\end_layout
\begin_layout Standard
@@ -1569,7 +1571,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf nemesis-1.0.tar.gz
+$ tar xzf nemesis-1.0.1.tar.gz
\end_layout
\begin_layout Standard
@@ -1577,7 +1579,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c nemesis-1.0.tar.gz | tar xf -
+$ gunzip -c nemesis-1.0.1.tar.gz | tar xf -
\end_layout
\begin_layout Subsubsection
@@ -1649,7 +1651,7 @@
\begin_inset Newline newline
\end_inset
-$ cd nemesis-1.0
+$ cd nemesis-1.0.1
\end_layout
\begin_layout Enumerate
@@ -1782,7 +1784,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf proj-4.6.1.tar.gz
+$ tar xzf proj-4.7.0.tar.gz
\end_layout
\begin_layout Standard
@@ -1790,13 +1792,13 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c proj-4.6.1.tar.gz | tar xf -
+$ gunzip -c proj-4.7.0.tar.gz | tar xf -
\end_layout
\begin_layout Standard
Download the datum shift archive and unpack it in the
\family typewriter
-proj-4.6.0/nad
+proj-4.7.0/nad
\family default
directory using the
\family typewriter
@@ -1806,7 +1808,7 @@
\end_layout
\begin_layout LyX-Code
-$ cd proj-4.6.1/nad$ unzip proj-datumgrid-1.4.zip
+$ cd proj-4.6.1/nad$ unzip proj-datumgrid-1.5.zip
\end_layout
\begin_layout Standard
@@ -1839,7 +1841,7 @@
\begin_inset Newline newline
\end_inset
-$ cd proj-4.6.1
+$ cd proj-4.7.0
\end_layout
\begin_layout Enumerate
@@ -1965,7 +1967,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf numpy-1.3.0.tar.gz
+$ tar xzf numpy-1.4.1.tar.gz
\end_layout
\begin_layout Standard
@@ -1973,7 +1975,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c numpy-1.3.0.tar.gz | tar xf -
+$ gunzip -c numpy-1.4.1.tar.gz | tar xf -
\end_layout
\begin_layout Subsubsection
@@ -1999,7 +2001,7 @@
\begin_inset Newline newline
\end_inset
-$ cd numpy-1.3.0
+$ cd numpy-1.4.1
\end_layout
\begin_layout Enumerate
@@ -2039,6 +2041,8 @@
PATH
\family default
.
+ You can customize the BLAS and LAPACK libraries used in building numpy
+ by editing the site.cfg file.
\end_layout
\begin_layout Subsection
@@ -2080,6 +2084,7 @@
\end_inset
.
+ Versions newer than v0.3.5 have are not compatible with PyLith.
Download the source archive and unpack it using the
\family typewriter
tar
@@ -2088,7 +2093,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf FIAT-0.3.4.tar.gz
+$ tar xzf FIAT-0.3.5.tar.gz
\end_layout
\begin_layout Standard
@@ -2096,7 +2101,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c FIAT-0.3.4.tar.gz | tar xf -
+$ gunzip -c FIAT-0.3.5.tar.gz | tar xf -
\end_layout
\begin_layout Subsubsection
@@ -2122,7 +2127,7 @@
\begin_inset Newline newline
\end_inset
-$ cd FIAT-0.3.4
+$ cd FIAT-0.3.5
\end_layout
\begin_layout Enumerate
@@ -2215,7 +2220,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf spatialdata-0.5.tgz
+$ tar xzf spatialdata-0.5.2.tgz
\end_layout
\begin_layout Standard
@@ -2223,7 +2228,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c spatialdata-0.5.tgz | tar xf -
+$ gunzip -c spatialdata-0.5.2.tgz | tar xf -
\end_layout
\begin_layout Subsubsection
@@ -2431,7 +2436,7 @@
\end_layout
\begin_layout LyX-Code
-$ tar xzf pylith-1.4.2.tgz
+$ tar xzf pylith-1.5.0.tgz
\end_layout
\begin_layout Standard
@@ -2439,7 +2444,7 @@
\end_layout
\begin_layout LyX-Code
-$ gunzip -c pylith-1.4.2.tgz | tar xf -
+$ gunzip -c pylith-1.5.0.tgz | tar xf -
\end_layout
\begin_layout Subsubsection
@@ -2511,7 +2516,7 @@
\begin_inset Newline newline
\end_inset
-$ cd pylith-1.4.2
+$ cd pylith-1.5.0
\end_layout
\begin_layout Enumerate
Modified: short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2010-05-15 18:25:37 UTC (rev 16716)
+++ short/3D/PyLith/trunk/doc/userguide/intro/intro.lyx 2010-05-15 20:04:12 UTC (rev 16717)
@@ -1,4 +1,4 @@
-#LyX 1.6.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -106,31 +106,27 @@
At present, mesh information may be provided using a simple ASCII file
(PyLith mesh ASCII format) or imported from CUBIT or LaGriT, two widely-used
meshing packages.
- The elements currently available include a linear bar in 1D, linear triangles
- and quadrilaterals in 2D, and linear tetrahedra and hexahedra in 3D.
+ The elements currently available include a linear bar in 1-D, linear triangles
+ and quadrilaterals in 2-D, and linear tetrahedra and hexahedra in 3-D.
Higher-order (quadratic) elements are also supported, but it is not presently
possible to create a quadratic mesh from the linear meshes provided by
most meshing packages.
Materials presently available include isotropic elastic, linear Maxwell
- viscoelastic (3D only), generalized Maxwell viscoelastic (3D only), and
- power-law viscoelastic (3D only).
+ viscoelastic (2-D and 3-D), generalized Maxwell viscoelastic (3-D only),
+ power-law viscoelastic (3-D only), and Drucker-Prager elastoplastic (3-D
+ only).
Boundary conditions include Dirichlet (prescribed displacements and velocities)
, Neumann (traction), point forces, and absorbing boundaries.
- Cohesive elements are used to implement slip across interior surfaces (faults).
- At present, only kinematically-specified fault slip is available.
- In the near future, we will provide several constitutive models for cohesive
- elements, which will allow slip to occur using various fault constitutive
- models.
+ Cohesive elements are used to implement slip across interior surfaces (faults)
+ with both kinematically-specified fault slip and slip governed by fault
+ constitutive models.
\end_layout
\begin_layout Standard
PyLith is under active development and we expect a number of additions and
improvements in the near future.
- Likely enhancements will include fault constitutive models with cohesive
- (fault) cells, additional bulk constitutive models, automatic generation
- of higher-order elements from linear elements, and the generation of Green's
- functions to be used in inversions.
- Several of these features should be available by Jan 2010.
+ Likely enhancements will include additional bulk and fault constitutive
+ models and generation of Green's functions to be used in inversions.
\end_layout
\begin_layout Section
@@ -333,8 +329,9 @@
simple shear, and slip on through-going faults, have been used to test
the code.
Additionally, we have run the Southern California Earthquake Center crustal
- deformation benchmarks for strike-slip and reverse-slip to determine the
- relative local and global error (see Chapter
+ deformation and several of the spontaneous rupture benchmarks for strike-slip
+ and reverse-slip to determine the relative local and global error (see
+ Chapter
\begin_inset CommandInset ref
LatexCommand ref
reference "cha:Benchmarks"
Modified: short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2010-05-15 18:25:37 UTC (rev 16716)
+++ short/3D/PyLith/trunk/doc/userguide/runpylith/runpylith.lyx 2010-05-15 20:04:12 UTC (rev 16717)
@@ -1,4 +1,4 @@
-#LyX 1.6.3 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -813,6 +813,20 @@
\end_layout
\begin_layout Standard
+ADD STUFF HERE
+\begin_inset Note Greyedout
+status open
+
+\begin_layout Plain Layout
+ADD STUFF HERE ABOUT reorder_mesh AND OTHER MESH GENERATOR SETTINGS
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
Geometrical and topological information for the finite element mesh may
be provided by exporting an EXODUS format file from CUBIT, by exporting
a GMV file and an accompanying Pset file from LaGriT, or by specifying
@@ -1726,7 +1740,7 @@
<lyxtabular version="3" rows="9" columns="3">
<features>
<column alignment="left" valignment="top" width="2in">
-<column alignment="center" valignment="middle" width="0.6in">
+<column alignment="center" valignment="middle" width="0.75in">
<column alignment="left" valignment="top" width="3in">
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
@@ -1807,7 +1821,7 @@
\begin_inset Newline newline
\end_inset
-positive_definite
+type
\end_layout
\end_inset
@@ -1817,8 +1831,8 @@
\begin_layout Plain Layout
-\shape italic
-0
+\emph on
+nonzero
\end_layout
\end_inset
@@ -1827,7 +1841,7 @@
\begin_inset Text
\begin_layout Plain Layout
-Turn off positive definite shifting.
+Turn on nonzero shifting.
\end_layout
\end_inset
@@ -1840,11 +1854,7 @@
\begin_layout Plain Layout
\family typewriter
-sub_pc_factor_shift_
-\begin_inset Newline newline
-\end_inset
-
-nonzero
+ksp_max_it
\end_layout
\end_inset
@@ -1853,7 +1863,9 @@
\begin_inset Text
\begin_layout Plain Layout
-n/a
+
+\emph on
+100
\end_layout
\end_inset
@@ -1862,7 +1874,7 @@
\begin_inset Text
\begin_layout Plain Layout
-Turn on nonzero shifting.
+Maximum number of iterations.
\end_layout
\end_inset
@@ -1875,7 +1887,7 @@
\begin_layout Plain Layout
\family typewriter
-ksp_max_it
+ksp_gmres_restart
\end_layout
\end_inset
@@ -1884,9 +1896,7 @@
\begin_inset Text
\begin_layout Plain Layout
-
-\emph on
-100
+50
\end_layout
\end_inset
@@ -1895,7 +1905,7 @@
\begin_inset Text
\begin_layout Plain Layout
-Maximum number of iterations.
+Number of iterations after which Gram-Schmidt orthogonalization is restarted.
\end_layout
\end_inset
@@ -1908,7 +1918,7 @@
\begin_layout Plain Layout
\family typewriter
-ksp_gmres_restart
+ksp_rtol
\end_layout
\end_inset
@@ -1917,7 +1927,9 @@
\begin_inset Text
\begin_layout Plain Layout
-50
+
+\shape italic
+1.0e-08
\end_layout
\end_inset
@@ -1926,7 +1938,7 @@
\begin_inset Text
\begin_layout Plain Layout
-Number of iterations after which Gram-Schmidt orthogonalization is restarted.
+Convergence tolerance for relative decrease in residual norm.
\end_layout
\end_inset
@@ -1937,9 +1949,7 @@
\begin_inset Text
\begin_layout Plain Layout
-
-\family typewriter
-ksp_rtol
+ksp_atol
\end_layout
\end_inset
@@ -1949,8 +1959,8 @@
\begin_layout Plain Layout
-\shape italic
-1.0e-08
+\emph on
+1.0e-15
\end_layout
\end_inset
@@ -1959,7 +1969,7 @@
\begin_inset Text
\begin_layout Plain Layout
-Convergence tolerance for relative decrease in residual norm.
+Convergence tolerance for absolute value in residual norm.
\end_layout
\end_inset
@@ -2060,7 +2070,15 @@
Implicit time stepping should be used for quasi-static problems, whereas
explicit time stepping should be used for dynamic problems which include
inertial terms.
- An example of setting the formulation facility to the implicit time stepping
+ Two options for explicit time-stepping are available: using a full, consistent
+ Jacobian matrix and a lumped Jacobian matrix.
+ In the lumped Jacobian formulation, the Jacobian is a diagonal matrix and
+ stored as a vector, and PyLith employs an optimized built-in solver rather
+ than a PETSc solver.
+\end_layout
+
+\begin_layout Standard
+An example of setting the formulation facility to the implicit time stepping
component is:
\end_layout
@@ -2085,6 +2103,19 @@
formulation = pylith.problems.Explicit
\end_layout
+\begin_layout Standard
+An example of setting the formulation facility to the lumped explicit time
+ stepping component is:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.timedependent]
+\end_layout
+
+\begin_layout LyX-Code
+formulation = pylith.problems.ExplicitLumped
+\end_layout
+
\begin_layout Subsection
Time-Stepping Formulation
\end_layout
@@ -2127,9 +2158,10 @@
\end_layout
\begin_layout Description
-split_fields Split solution field into a displacement portion (field 0)
- and a Lagrange multiplier portion (field 1) to permit application of sophistica
-ted PETSc preconditions (default is false; for expert users only).
+split_fields Split solution field into a displacement portion (fields 0..ndim-1)
+ and a Lagrange multiplier portion (field ndim) to permit application of
+ sophisticated PETSc preconditioners (default is false; for expert users
+ only).
\end_layout
\begin_layout Standard
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2010-05-15 18:25:37 UTC (rev 16716)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/tutorials.lyx 2010-05-15 20:04:12 UTC (rev 16717)
@@ -1,4 +1,4 @@
-#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
+#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
@@ -222,6 +222,10 @@
\end_layout
+\begin_layout Subsection
+ADD bar_shearwave
+\end_layout
+
\begin_layout Section
Additional Examples
\end_layout
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