[cig-commits] r20087 - in short/3D/PyLith/branches/v1.7-trunk/doc/userguide: . benchmarks boundaryconditions fileformats install intro runpylith tutorials/shearwave
brad at geodynamics.org
brad at geodynamics.org
Fri May 11 16:00:45 PDT 2012
Author: brad
Date: 2012-05-11 16:00:45 -0700 (Fri, 11 May 2012)
New Revision: 20087
Modified:
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/TODO
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/benchmarks/benchmarks.lyx
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/components.lyx
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/fileformats/fileformats.lyx
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/install/install.lyx
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/intro.lyx
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/license.lyx
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/preface.lyx
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/runpylith/runpylith.lyx
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/shearwave/quad4.lyx
short/3D/PyLith/branches/v1.7-trunk/doc/userguide/userguide.lyx
Log:
Started working on updates for v1.7.
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/TODO
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/TODO 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/TODO 2012-05-11 23:00:45 UTC (rev 20087)
@@ -0,0 +1,5 @@
+Figures
+ Tikz for workflow
+ Dependencies
+ HDF5 layout
+ Replace fault implementation diagram
\ No newline at end of file
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/benchmarks/benchmarks.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/benchmarks/benchmarks.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/benchmarks/benchmarks.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -176,19 +176,21 @@
through a vertical strike-slip fault), TPV205 (vertical strike-slip fault
with high and low stress asperities), TPV210-2D (vertical slice through
a 60 degree dipping normal fault), TPV210 (60 degree dipping normal fault),
- TPV14-2D and TPV15-2D (horizontal slice through a verticel strike-slip
- fault with a branch) and TPV14 and TPV15 (vertical strike-slip fault with
- a branch).
+ TPV11, TPV12, TPV13, TPV14-2D and TPV15-2D (horizontal slice through a
+ verticel strike-slip fault with a branch), TPV14 and TPV15 (vertical strike-sli
+p fault with a branch), and TPV 16 and 17.
\end_layout
\begin_layout Standard
The benchmark results indicate that triangular and tetrahedral cells generate
less numerical noise than quadrilateral or hexahedral cells.
- TPV14-2D, TPV15-2D, TPV14, and TPV15 use the numerical damping via an artificia
-l viscosity available in PyLith v1.6 to these high-frequency oscillations.
- All of the other results without high frequency oscillations posted on
- the SCEC benchmarks web page employ damping via similar methods to reduce
- numerical artifacts.
+ Results for all of the benchmarks listed above except TPV14-2D, TPV15-2D,
+ TPV14, and TPV15 have been updated using PyLith 1.7, which provides much
+ closer agreement with the other codes comapred to previous versions of
+ PyLith.
+ We attribute the closer agreement to small adjustments of the fault implementat
+ion and some small bugfixes to the slip-weakening friction formulation.
+
\end_layout
\end_body
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/boundaryconditions/boundaryconditions.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -200,6 +200,12 @@
\end_layout
\begin_layout Section
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:Time:Dependent:BC"
+
+\end_inset
+
Time-Dependent Boundary Conditions
\end_layout
@@ -492,7 +498,7 @@
\begin_layout Plain Layout
\family typewriter
-initial-value
+displacement_initial
\end_layout
\end_inset
@@ -523,7 +529,7 @@
\begin_layout Plain Layout
\family typewriter
-rate-of-change
+velocity
\end_layout
\end_inset
@@ -554,7 +560,7 @@
\begin_layout Plain Layout
\family typewriter
-rate-start-time
+velocity_start_time
\end_layout
\end_inset
@@ -585,7 +591,7 @@
\begin_layout Plain Layout
\family typewriter
-change-in-value
+displacement_change
\end_layout
\end_inset
@@ -616,7 +622,7 @@
\begin_layout Plain Layout
\family typewriter
-change-start-time
+change_start_time
\end_layout
\end_inset
@@ -1049,7 +1055,7 @@
\begin_layout Plain Layout
\family typewriter
-initial-value
+tracton_initial
\end_layout
\end_inset
@@ -1080,7 +1086,7 @@
\begin_layout Plain Layout
\family typewriter
-rate-of-change
+traction_rate
\end_layout
\end_inset
@@ -1111,7 +1117,7 @@
\begin_layout Plain Layout
\family typewriter
-rate-start-time
+rate_start_time
\end_layout
\end_inset
@@ -1142,7 +1148,7 @@
\begin_layout Plain Layout
\family typewriter
-change-in-value
+traction_change
\end_layout
\end_inset
@@ -1173,7 +1179,7 @@
\begin_layout Plain Layout
\family typewriter
-change-start-time
+change_start_time
\end_layout
\end_inset
@@ -2348,8 +2354,15 @@
\end_inset
- and ?? list the fields available for output for a fault with kinematic
- (prescribed) earthquake rupture and a fault with dynamic rupture, respectively.
+ and
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "tab:fault:dyn:output"
+
+\end_inset
+
+ list the fields available for output for a fault with kinematic (prescribed)
+ earthquake rupture and a fault with dynamic rupture, respectively.
The fault coordinate system is shown in Figure
\begin_inset CommandInset ref
LatexCommand ref
@@ -3065,7 +3078,7 @@
\begin_layout Plain Layout
\family typewriter
-tractions_change
+traction_change
\end_layout
\end_inset
@@ -3311,7 +3324,7 @@
\begin_layout Plain Layout
\series bold
-Database
+Spatial database
\end_layout
\end_inset
@@ -3457,7 +3470,7 @@
\begin_layout Plain Layout
\family typewriter
-slip_time
+slip-time
\end_layout
\end_inset
@@ -3632,7 +3645,7 @@
\begin_layout Plain Layout
\series bold
-Database
+Spatial database
\end_layout
\end_inset
@@ -3778,7 +3791,7 @@
\begin_layout Plain Layout
\family typewriter
-slip_time
+slip-time
\end_layout
\end_inset
@@ -3973,7 +3986,7 @@
\begin_layout Plain Layout
\series bold
-Database
+Spatial database
\end_layout
\end_inset
@@ -4119,7 +4132,7 @@
\begin_layout Plain Layout
\family typewriter
-rise_time
+rise-time
\end_layout
\end_inset
@@ -4128,11 +4141,7 @@
\begin_inset Text
\begin_layout Plain Layout
-
-\family typewriter
-Rise time
-\family default
-(
+Rise time (
\begin_inset Formula $t_{r})$
\end_inset
@@ -4160,7 +4169,7 @@
\begin_layout Plain Layout
\family typewriter
-slip_time
+slip-time
\end_layout
\end_inset
@@ -4407,7 +4416,7 @@
\begin_layout Plain Layout
\series bold
-Database
+Spatial database
\end_layout
\end_inset
@@ -4553,7 +4562,7 @@
\begin_layout Plain Layout
\family typewriter
-rise_time
+rise-time
\end_layout
\end_inset
@@ -4562,11 +4571,7 @@
\begin_inset Text
\begin_layout Plain Layout
-
-\family typewriter
-Rise time
-\family default
-(
+Rise time (
\begin_inset Formula $t_{r})$
\end_inset
@@ -4594,7 +4599,7 @@
\begin_layout Plain Layout
\family typewriter
-slip_time
+slip-time
\end_layout
\end_inset
@@ -4844,11 +4849,22 @@
\end_layout
\begin_layout Description
-db_initial_tractions Spatial database specifying the initial tractions on
- the fault surface.
+open_free_surface If true, enforce traction free surface when the fault
+ opens, otherwise apply prescribed tractions even when the fault opens (default
+ is true); to mimic a dike opening use false.
\end_layout
\begin_layout Description
+zero_tolerance Tolerance for detecting zero values (default is 1.0e-10);
+ should be larger than absolute tolerance in KSP solves.
+\end_layout
+
+\begin_layout Description
+traction_perturbation Prescribed tractions on fault surface (generally used
+ for nucleating earthquake ruptures, default is none).
+\end_layout
+
+\begin_layout Description
friction Fault constitutive model.
\end_layout
@@ -4866,14 +4882,22 @@
\end_layout
\begin_layout LyX-Code
-db_initial_tractions = spatialdata.spatialdb.SimpleDB
+open_free_surface = True ; default
\end_layout
\begin_layout LyX-Code
-db_initial_tractions.iohandler.filename = tractions.spatialdb
+traction_perturbation = pylith.faults.TractPerturbation ; not default
\end_layout
\begin_layout LyX-Code
+traction_perturbation.db_initial = spatialdata.spatialdb.SimpleDB
+\end_layout
+
+\begin_layout LyX-Code
+traction_perturbation.db_initial.iohandler.filename = tractions.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
friction = pylith.friction.StaticFriction
\end_layout
@@ -4886,16 +4910,27 @@
\end_layout
\begin_layout Standard
-The initial tractions are specified using the same fault coordinate system
- as the slip directions in the kinematic ruptures.
+The prescribed traction perturbation is specified using the same fault coordinat
+e system as the slip directions in the kinematic ruptures.
+ The perurbation has the same functional form as the time-dependent boundary
+ conditions (and same spatial databases).
Table
\begin_inset CommandInset ref
LatexCommand ref
-reference "tab:fault:cohesive:dyn:initial:tractions"
+reference "tab:fault:cohesive:dyn:prescribed:tractions"
\end_inset
- gives the values in the spatial database for initial tractions.
+ gives the values in the spatial database for the prescribed tractions.
+ Table
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "tab:fault:dyn:output"
+
+\end_inset
+
+ shows the fields available for output.
+ Additional fields are available depending on the fault constitutive model.
\end_layout
\begin_layout Standard
@@ -4915,11 +4950,11 @@
\begin_layout Plain Layout
\begin_inset CommandInset label
LatexCommand label
-name "tab:fault:cohesive:dyn:initial:tractions"
+name "tab:fault:cohesive:dyn:prescribed:tractions"
\end_inset
-Values in spatial databases for initial tractions.
+Values in spatial databases for prescribed tractions.
\end_layout
\end_inset
@@ -4930,10 +4965,11 @@
\begin_inset Tabular
-<lyxtabular version="3" rows="7" columns="3">
+<lyxtabular version="3" rows="22" columns="4">
<features tabularvalignment="middle">
<column alignment="left" valignment="top" width="0">
<column alignment="left" valignment="top" width="0">
+<column alignment="left" valignment="top" width="0">
<column alignment="left" valignment="top" width="2.5in">
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
@@ -4942,6 +4978,17 @@
\begin_layout Plain Layout
\series bold
+Spatial database
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\series bold
Dimension
\end_layout
@@ -4975,6 +5022,17 @@
\begin_inset Text
\begin_layout Plain Layout
+
+\family typewriter
+db_initial
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
1-D
\end_layout
@@ -5002,6 +5060,15 @@
</cell>
</row>
<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
@@ -5042,6 +5109,15 @@
\end_inset
</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
@@ -5064,6 +5140,15 @@
</cell>
</row>
<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
@@ -5104,6 +5189,15 @@
\end_inset
</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
@@ -5135,12 +5229,346 @@
\end_inset
</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-normal
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Normal traction (tension is positive)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+db_rate
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+1-D
+\end_layout
+
+\end_inset
+</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\family typewriter
+traction-rate-normal
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Rate of change of normal traction (tension is positive)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+2-D
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-rate-shear
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Rate of change of left-lateral shear traction (reverse shear for dipping
+ faults)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-rate-normal
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Rate of change of normal traction (tension is positive)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+3-D
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-rate-leftlateral
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Rate of change of eft-lateral shear traction
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-rate-shear-updip
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Rate of change of reverse shear traction
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-rate-normal
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Rate of change of normal traction (tension is positive)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+all
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+rate-start-time
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Time at which rate of change begins
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+db_change
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+1-D
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
traction-normal
\end_layout
@@ -5150,12 +5578,292 @@
\begin_inset Text
\begin_layout Plain Layout
-Normal traction (tension is positive)
+Change in normal traction (tension is positive)
\end_layout
\end_inset
</cell>
</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+2-D
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-shear
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Change in left-lateral shear traction (reverse shear for dipping faults)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-normal
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Change in normal traction (tension is positive)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+3-D
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-leftlateral
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Change in left-lateral shear traction
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-shear-updip
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Change in reverse shear traction
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction-normal
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Change in normal traction (tension is positive)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+all
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+change-start-time
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Time at which change begins
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+th_change
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+all
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+None
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Time history for change
+\end_layout
+
+\end_inset
+</cell>
+</row>
</lyxtabular>
\end_inset
@@ -5166,13 +5874,406 @@
\end_inset
+\begin_inset Float table
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\noindent
+\align center
+\begin_inset Caption
+
+\begin_layout Plain Layout
+\begin_inset CommandInset label
+LatexCommand label
+name "tab:fault:dyn:output"
+
+\end_inset
+
+Fields available in output of fault information.
\end_layout
+\end_inset
+
+
+\begin_inset VSpace defskip
+\end_inset
+
+
+\begin_inset Tabular
+<lyxtabular version="3" rows="11" columns="3">
+<features tabularvalignment="middle">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="3.5in">
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\series bold
+Field Type
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\series bold
+Field
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\series bold
+Description
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+vertex_info_fields
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+normal_dir
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Direction of fault normal in global coordinate system
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+strike_dir
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Direction of fault strike in global coordinate system
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+dip_dir
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Up-dip direction on hanging wall in global coordinate system
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction_initial
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Initial tractions (if specified) in fault coordinate system
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction_rate
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Rate of change in tractions (if specified) in fault coordinate system
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+rate_start_time
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Time at which rate of change begins (if specified)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction_change
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Change in tractions (if specified) in fault coordinate system
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+change_start_time
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Time at which change occurs (if specified)
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+vertex_data_fields
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+slip
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Slip vector at time step (in fault coordinate system) in meters
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+
+\family typewriter
+traction
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" bottomline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Fault tractions (in fault coordinate system) in Pa
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
\begin_layout Subsubsection
Fault Constitutive Models
\begin_inset CommandInset label
LatexCommand label
-name "sub:Fault-Constitutive-Models"
+name "sec:fault:constitutive:models"
\end_inset
@@ -5366,6 +6467,12 @@
\end_layout
\begin_layout Paragraph
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:friction:slip:weakening"
+
+\end_inset
+
Slip-Weakening Friction
\end_layout
@@ -5397,9 +6504,53 @@
.
As long as the fault is locked, the initial state variables are zero, so
specifying the initial state variables for slip-weakening friction is rare.
+ The slip-weakening friction also includes a parameter,
+\family typewriter
+force_healing
+\family default
+, to control healing.
+ In quasi-static simulations, one usually wants slip confined to a single
+ time step (
+\family typewriter
+force_healing
+\family default
+ = True), whereas in a dynamic simulation slip occurs over many time steps
+ (
+\family typewriter
+force_healing
+\family default
+ = False; default behavior) and fault healing is often neglected.
+ The properties include:
\end_layout
+\begin_layout Description
+force_healing Flag indicating whether healing (cumalative slip state variable
+ reset to zero) is forced after every time step.
+\end_layout
+
\begin_layout Standard
+An example of setting the properties for the rate and state friction component
+ in a
+\family typewriter
+.cfg
+\family default
+ file is:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.problem.interfaces.fault]
+\end_layout
+
+\begin_layout LyX-Code
+friction = pylith.friction.SlipWeakening ; Change friction model from the
+ default
+\end_layout
+
+\begin_layout LyX-Code
+friction.force_healing = False ; default value
+\end_layout
+
+\begin_layout Standard
\noindent
\align center
\begin_inset Float table
@@ -5443,7 +6594,7 @@
\begin_layout Plain Layout
\series bold
-Database
+Spatial database
\end_layout
\end_inset
@@ -5476,6 +6627,8 @@
\begin_inset Text
\begin_layout Plain Layout
+
+\family typewriter
db_properties
\end_layout
@@ -5616,6 +6769,8 @@
\begin_inset Text
\begin_layout Plain Layout
+
+\family typewriter
db_initial_state
\end_layout
@@ -5988,6 +7143,12 @@
\end_layout
\begin_layout Paragraph
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:friction:rate:state:ageing"
+
+\end_inset
+
Rate- and State-Friction with Ageing Law
\end_layout
@@ -6001,7 +7162,10 @@
T_{c}-\mu_{f}T_{n} & T_{n}\leq0\\
0 & T_{n}>0
\end{cases}\\
-\mu_{f}=a\sinh^{-1}\left(\frac{1}{2}\frac{V}{V_{0}}\exp\left(\frac{1}{a}\left(\mu_{0}+b\ln\left(\frac{V_{0}\theta}{L}\right)\right)\right)\right)\\
+\mu_{f}=\begin{cases}
+\mu_{0}+a\ln\left(\frac{V}{V_{0}}\right)+b\ln\left(\frac{V_{0}\theta}{L}\right) & V\ge V_{\mathit{min}}\\
+\mu_{0}+a\ln\left(\frac{V_{min}}{V}\right)+b\ln\left(\frac{V_{0}\theta}{L}\right)-a\left(1-\frac{V}{V_{min}}\right) & V<V_{min}
+\end{cases}\\
\frac{d\theta}{dt}=1-\frac{V\theta}{L}
\end{gather}
@@ -6012,6 +7176,10 @@
\end_inset
is slip rate,
+\begin_inset Formula $V_{min}$
+\end_inset
+
+ is a minimum slip rate,
\begin_inset Formula $a$
\end_inset
@@ -6028,15 +7196,31 @@
\end_inset
is a state variable.
- We have used the regularization of the coefficient of friction proposed
- by Ben-Zion and Rice
+ With an interative solver in quasi-static simulations with a small, but
+ nonzero residual tolerance we never encounter zero slip rates in quasi-static
+ simulations.
+ Instead we want to avoid significant variations in the coefficient of friction
+ for slip rates on the same order as our residual tolerance.
+ We regularize the rate and state friction model by iposing a linearization
+ of the variation of the coefficient of friction with slip rate when the
+ slip rate drops below a minimum slip rate,
+\begin_inset Formula $V_{min}$
+\end_inset
+
+ (
+\family typewriter
+min_slip_rate
+\family default
+ property with a default value of 1.0e-12).
+ Note that this is different than the popular inverse hypoerbolic sine regulariz
+ation proposed by Ben-Zion and Rice
\begin_inset CommandInset citation
LatexCommand cite
key "BenZion:Rice:1997"
\end_inset
- to permit zero slip rate.
+ to permit zero slip rates.
Following Kaneko
\shape italic
et al.
@@ -6076,6 +7260,42 @@
\end_layout
\begin_layout Standard
+The properties include:
+\end_layout
+
+\begin_layout Description
+min_slip_rate Slip rate at which linearization occurs,
+\begin_inset Formula $V_{min}$
+\end_inset
+
+.
+ Should be about one order of magnitude larger than absolute tolerance in
+ solve.
+\end_layout
+
+\begin_layout Standard
+An example of setting the properties for the rate and state friction component
+ in a
+\family typewriter
+.cfg
+\family default
+ file is:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.problem.interfaces.fault]
+\end_layout
+
+\begin_layout LyX-Code
+friction = pylith.friction.RateStateAgeing ; Change friction model from the
+ default
+\end_layout
+
+\begin_layout LyX-Code
+friction.min_slip_rate = 1.0e-12 ; default value
+\end_layout
+
+\begin_layout Standard
The spatial database files for the rate and state friction model properties
and state variables specify the spatial variation of the fault constitutive
model parameters given in Table
@@ -6429,6 +7649,83 @@
\end_layout
+\begin_layout Subsection
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:fault:cohesive:impulses"
+
+\end_inset
+
+Slip Impulses for Green's Functions
+\end_layout
+
+\begin_layout Standard
+Computing static Green's functions using the GreensFns problem requires
+ a specialized fault implementation, FaultCohesiveImpulses, to setup the
+ slip impulses.
+ The parameters controlling the slip impulses include the components involved
+ (lateral, reverse, and/or fault opening) and the amplitude of the pulses
+ (e.g., selecting a subset of a fault or including a spatial variation).
+ The GreensFns properties and facilities include:
+\end_layout
+
+\begin_layout Description
+threshold Threshold for non-zero amplitude; impulses will only be generated
+ at locations on the fault where the amplitude excees this threshold.
+\end_layout
+
+\begin_layout Description
+impulse_dof Array of components associated with impulses, e.g., [0, 1] for
+ slip involving the lateral and up-dip components.
+\end_layout
+
+\begin_layout Description
+db_impulse_amplitude Spatial database for amplitude of slip impulse (scalar
+ field).
+ Default is SimpleDB.
+\end_layout
+
+\begin_layout Standard
+An example of setting the properties and facilities for FaultCohesiveImpulses
+ in a
+\family typewriter
+.cfg
+\family default
+ file is:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.problem.interfaces]
+\end_layout
+
+\begin_layout LyX-Code
+fault = pylith.faults.FaultCohesiveImpulses ; Change from the default
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.problem.interfaces.fault]
+\end_layout
+
+\begin_layout LyX-Code
+threshold = 1.0e-6*m ; default
+\end_layout
+
+\begin_layout LyX-Code
+impulse_dof = [0] ; lateral slip-only
+\end_layout
+
+\begin_layout LyX-Code
+db_impulse_amplitude.iohandler.filename = myimpulse.spatialdb
+\end_layout
+
+\begin_layout LyX-Code
+db_impulse_amplitude.label = Impulse amplitude
+\end_layout
+
\begin_layout Section
Gravitational Body Forces
\end_layout
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/components.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/components.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/components.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -122,6 +122,18 @@
\begin_layout Description
\family typewriter
+GreensFns pylith.problems.GreensFns
+\family default
+
+\begin_inset Newline newline
+\end_inset
+
+Static Green's function problem with slip impulses.
+\end_layout
+
+\begin_layout Description
+
+\family typewriter
Implicit pylith.problems.Implicit
\family default
@@ -497,62 +509,62 @@
\begin_layout Description
\family typewriter
-MaxwellPlaneStrain pylith.materials.MaxwellPlaneStrain
+ElasticIsotropic3D pylith.materials.ElasticIsotropic3D
\family default
\begin_inset Newline newline
\end_inset
-Linear Maxwell viscoelastic bulk constitutive model for plane strain problems.
+Linearly elastic 3-D bulk constitutive model.
\end_layout
\begin_layout Description
\family typewriter
-GenMaxwellPlaneStrain pylith.materials.GenMaxwellPlaneStrain
+MaxwellIsotropic3D pylith.materials.MaxwellIsotropic3D
\family default
\begin_inset Newline newline
\end_inset
-Generalized Maxwell viscoelastic bulk constitutive model for plane strain
- problems.
+Linear Maxwell viscoelastic bulk constitutive model.
\end_layout
\begin_layout Description
\family typewriter
-ElasticIsotropic3D pylith.materials.ElasticIsotropic3D
+MaxwellPlaneStrain pylith.materials.MaxwellPlaneStrain
\family default
\begin_inset Newline newline
\end_inset
-Linearly elastic 3-D bulk constitutive model.
+Linear Maxwell viscoelastic bulk constitutive model for plane strain problems.
\end_layout
\begin_layout Description
\family typewriter
-MaxwellIsotropic3D pylith.materials.MaxwellIsotropic3D
+GenMaxwellIsotropic3D pylith.materials.GenMaxwellIsotropic3D
\family default
\begin_inset Newline newline
\end_inset
-Linear Maxwell viscoelastic bulk constitutive model.
+Generalized Maxwell viscoelastic bulk constitutive model.
\end_layout
\begin_layout Description
\family typewriter
-GenMaxwellIsotropic3D pylith.materials.GenMaxwellIsotropic3D
+GenMaxwellPlaneStrain pylith.materials.GenMaxwellPlaneStrain
\family default
\begin_inset Newline newline
\end_inset
-Generalized Maxwell viscoelastic bulk constitutive model.
+Generalized Maxwell viscoelastic bulk constitutive model for plane strain
+ problems.
\end_layout
\begin_layout Description
@@ -570,6 +582,18 @@
\begin_layout Description
\family typewriter
+PowerLawPlaneStrain pylith.materials.PowerLawPlaneStrain
+\family default
+
+\begin_inset Newline newline
+\end_inset
+
+Power-law viscoelastic bulk constitutive model for plane strain problems.
+\end_layout
+
+\begin_layout Description
+
+\family typewriter
DruckerPrage3D pylith.materials.DruckerPrager3D
\family default
@@ -582,6 +606,18 @@
\begin_layout Description
\family typewriter
+DruckerPragePlaneStrain pylith.materials.DruckerPragerPlaneStrain
+\family default
+
+\begin_inset Newline newline
+\end_inset
+
+Drucker-Prager elastoplastic bulk constitutive model for plane strain problems.
+\end_layout
+
+\begin_layout Description
+
+\family typewriter
Homogeneous pylith.materials.Homogeneous
\family default
@@ -701,6 +737,19 @@
\begin_layout Description
\family typewriter
+FaultCohesiveImpulses pylith.faults.FaultCohesive
+\family default
+Impulses
+\begin_inset Newline newline
+\end_inset
+
+Fault surface with Green's functions slip impulses implemented using cohesive
+ elements.
+\end_layout
+
+\begin_layout Description
+
+\family typewriter
EqKinSrc pylith.faults.EqKinSrc
\family default
@@ -784,6 +833,20 @@
Slip-time function with a user-defined slip time function.
\end_layout
+\begin_layout Description
+
+\family typewriter
+TractPerturbation pylith.faults.TractPerturbation
+\family default
+
+\begin_inset Newline newline
+\end_inset
+
+Prescribed traction perturbation applied to fault with constitituve model
+ in additional to tractions from deformation (generally used to nucleate
+ a rupture).
+\end_layout
+
\begin_layout Subsection
Friction components
\end_layout
@@ -959,6 +1022,18 @@
\begin_layout Description
\family typewriter
+OutputSolnPoints pylith.meshio.OutputSoln
+\family default
+Points
+\begin_inset Newline newline
+\end_inset
+
+Output manager for solution data at arbitrary points in the domain.
+\end_layout
+
+\begin_layout Description
+
+\family typewriter
OutputDirichlet pylith.meshio.OutputDirichlet
\family default
@@ -1007,6 +1082,18 @@
\begin_layout Description
\family typewriter
+OutputFaultImpulses pylith.meshio.OutputFaultImpulses
+\family default
+
+\begin_inset Newline newline
+\end_inset
+
+Output manager for fault with static slip impulses.
+\end_layout
+
+\begin_layout Description
+
+\family typewriter
OutputMatElastic pylith.meshio.OutputMatElastic
\family default
@@ -1031,6 +1118,22 @@
\begin_layout Description
\family typewriter
+PointsList pylith.meshio.PointsList
+\family default
+
+\begin_inset Newline newline
+\end_inset
+
+Manager for text file container points for
+\family typewriter
+OutputSolnPoints
+\family default
+.
+\end_layout
+
+\begin_layout Description
+
+\family typewriter
DataWriterVTKMesh pylith.meshio.DataWriterVTKMesh
\family default
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/fileformats/fileformats.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/fileformats/fileformats.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/fileformats/fileformats.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -1,5 +1,5 @@
-#LyX 1.6.2 created this file. For more info see http://www.lyx.org/
-\lyxformat 345
+#LyX 2.0 created this file. For more info see http://www.lyx.org/
+\lyxformat 413
\begin_document
\begin_header
\textclass book
@@ -7,18 +7,26 @@
\end_preamble
\use_default_options false
+\maintain_unincluded_children false
\language english
+\language_package default
\inputencoding latin1
+\fontencoding global
\font_roman default
\font_sans default
\font_typewriter default
\font_default_family default
+\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
\graphics default
+\default_output_format default
+\output_sync 0
+\bibtex_command default
+\index_command default
\paperfontsize default
\spacing single
\use_hyperref false
@@ -26,9 +34,18 @@
\use_geometry true
\use_amsmath 1
\use_esint 0
+\use_mhchem 1
+\use_mathdots 1
\cite_engine basic
\use_bibtopic false
+\use_indices false
\paperorientation portrait
+\suppress_date false
+\use_refstyle 0
+\index Index
+\shortcut idx
+\color #008000
+\end_index
\leftmargin 1in
\topmargin 1in
\rightmargin 1in
@@ -36,15 +53,16 @@
\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
-\defskip medskip
+\paragraph_indentation default
\quotes_language english
\papercolumns 1
\papersides 2
\paperpagestyle default
\tracking_changes false
\output_changes false
-\author ""
-\author ""
+\html_math_output 0
+\html_css_as_file 0
+\html_be_strict false
\end_header
\begin_body
@@ -1581,5 +1599,96 @@
\end_layout
+\begin_layout Section
+\begin_inset CommandInset label
+LatexCommand label
+name "sec:FileFormat:PointsList"
+
+\end_inset
+
+Points List File
+\end_layout
+
+\begin_layout Standard
+This file lists the coordinates of the locations where output is requested
+ for the
+\family typewriter
+OutputSolnPoints
+\family default
+ component.
+ The coordinate system is specified in the
+\family typewriter
+OutputSolnPoints
+\family default
+ component.
+
+\end_layout
+
+\begin_layout LyX-Code
+# This time step file specifies five time steps with the units in years.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comments are limited to complete lines.
+ The default delimiter for comments
+\end_layout
+
+\begin_layout LyX-Code
+# is '#', which can be changed via parameters.
+ Additionally, the delimiter
+\end_layout
+
+\begin_layout LyX-Code
+# separating values can also be customized (default is whitespace).
+\end_layout
+
+\begin_layout LyX-Code
+1.0 -2.0 0.0
+\end_layout
+
+\begin_layout LyX-Code
+2.0 -4.0 -0.1
+\end_layout
+
+\begin_layout LyX-Code
+0.0 +2.0 0.0
+\end_layout
+
+\begin_layout LyX-Code
+2.5 -0.2 -0.2
+\end_layout
+
+\begin_layout LyX-Code
+0.0 2.0 +0.2
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\begin_inset Caption
+
+\begin_layout Plain Layout
+Format of files with coordinates of points for output.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
\end_body
\end_document
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/install/install.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/install/install.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/install/install.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -190,8 +190,8 @@
\end_layout
\begin_layout Standard
-Binary executables are available for Linux, Mac OS X (Intel 10.4/10.5 and
- Intel 10.6), and Windows from the PyLith web page
+Binary executables are available for Linux, Mac OS X (Intel 10.5 and Intel
+ 10.6/10.7), and Windows from the PyLith web page
\begin_inset Flex URL
status collapsed
@@ -253,7 +253,7 @@
\begin_deeper
\begin_layout LyX-Code
-$ tar -xzf pylith-1.6.1-linux-i686.tgz
+$ tar -xzf pylith-1.7.0-linux-i686.tgz
\end_layout
\end_deeper
@@ -323,12 +323,12 @@
\begin_layout Enumerate
Unpack the tarball.
- For 10.4.x or 10.5.x operating system,
+ For the 10.5.x operating system
\end_layout
\begin_deeper
\begin_layout LyX-Code
-$ tar -xzf pylith-1.6.1-darwin-10.4.tgz
+$ tar -xzf pylith-1.7.0-darwin-10.5.tgz
\end_layout
\end_deeper
@@ -453,7 +453,7 @@
pylith
\family default
command automatically submits jobs to the batch queue.
- Pyre contains support for the LSF, PBS, and Globus batch systems.
+ Pyre contains support for the LSF, PBS, SGE, and Globus batch systems.
\end_layout
\begin_layout Standard
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/intro.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/intro.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/intro/intro.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -127,21 +127,23 @@
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.
Materials presently available include isotropic elastic, linear Maxwell
- viscoelastic (2-D and 3-D), generalized Maxwell viscoelastic (2-D and 3-D),
- power-law viscoelastic (3-D only), and Drucker-Prager elastoplastic (3-D
- only).
+ viscoelastic, generalized Maxwell viscoelastic, power-law viscoelastic,
+ and Drucker-Prager elastoplastic.
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)
with both kinematically-specified fault slip and slip governed by fault
constitutive models.
+ PyLith also includes an interface for computing static Green's functions
+ for fault slip.
\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 additional bulk and fault constitutive
- models and generation of Green's functions to be used in inversions.
+ models, coupled quasi-static and dynamic simulations for earthquake cycle
+ modeling, and coupling between elasticity, heat flow, and/or fluid flow.
\end_layout
\begin_layout Section
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/license.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/license.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/license.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -72,7 +72,7 @@
\end_layout
\begin_layout Standard
-Copyright (C) 2010-2011 University of California, Davis
+Copyright (C) 2010-2012 University of California, Davis
\end_layout
\begin_layout Standard
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/preface.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/preface.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/preface.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -190,14 +190,14 @@
Strand, and C.
Williams (2011),
\emph on
-PyLith User Manual, Version 1.6.1.
+PyLith User Manual, Version 1.7.0.
\emph default
Davis, CA: Computational Infrastructure of Geodynamics.
\begin_inset Newline newline
\end_inset
-URL: geodynamics.org/cig/software/pylith/pylith_manual-1.6.pdf
+URL: geodynamics.org/cig/software/pylith/pylith_manual-1.7.pdf
\end_layout
\begin_layout Section
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/runpylith/runpylith.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/runpylith/runpylith.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/runpylith/runpylith.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -1400,13 +1400,15 @@
The problem component specifies the basic parameters of the simulation,
including the physical properties, the boundary conditions, and interface
conditions (faults).
- The current release of PyLith contains one type of problem,
+ The current release of PyLith contains two types of problem,
\family typewriter
TimeDependent
\family default
- for use in static, quasi-static, and dynamic simulations.
- Future releases may contain multiple types of problems, for example, computing
- Green's functions, as additional applications are developed.
+ for use in static, quasi-static, and dynamic simulations and
+\family typewriter
+GreensFns
+\family default
+ for computing static Green's functions.
The general facilities include:
\end_layout
@@ -2836,8 +2838,8 @@
\end_layout
\begin_layout Standard
-PyLith currently only contains this one type of problem which is used for
- static, quasi-static, and dynamic simulations.
+This type of problem applies to transient static, quasi-static, and dynamic
+ simulations.
The time-dependent problem adds the
\family typewriter
formulation
@@ -2847,8 +2849,6 @@
elasticity equation.
PyLith provides several alternative formulations, each specific to a different
type of problem.
- Future versions of PyLith will likely include support for additional formulatio
-ns, such as large deformations with a lumped Jacobian matrix.
\end_layout
\begin_layout Description
@@ -3167,10 +3167,14 @@
\end_layout
\begin_layout Description
-total_time Time duration for simulation.
+total_time Time duration for simulation (default is 0.0 s).
\end_layout
\begin_layout Description
+start_time Start time for simulation (default is 0.0 s)
+\end_layout
+
+\begin_layout Description
dt Time step for simulation.
\end_layout
@@ -3351,6 +3355,109 @@
\end_layout
\begin_layout Section
+Green's Functions Problem
+\end_layout
+
+\begin_layout Standard
+This type of problem applies to computing static Green's functions for elastic
+ deformation.
+ The
+\family typewriter
+GreensFns
+\family default
+ problem specializes the time-dependent facility to the case of static simulatio
+ns with slip impulses on a fault.
+ The default formulation is the Implicit formulation and should not be changed
+ as the other formulations are not applicable to static Green's functions.
+ In the output files, the deformation at each
+\begin_inset Quotes eld
+\end_inset
+
+time step
+\begin_inset Quotes erd
+\end_inset
+
+ is the deformation for a different slip impulse.
+ The properties provide the ability to select which fault to use for slip
+ impulses.
+ The only fault component available for use with the
+\family typewriter
+GreensFns
+\family default
+ problem is the
+\family typewriter
+FaultCohesiveImpulses
+\family default
+ component discussed in Section
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sec:fault:cohesive:impulses"
+
+\end_inset
+
+.
+ The
+\family typewriter
+GreensFns
+\family default
+ properties include:
+\end_layout
+
+\begin_layout Description
+fault_id Id of fault on which to impose slip impulses.
+\end_layout
+
+\begin_layout Standard
+An example of setting the properties for the GreensFns problem in a
+\family typewriter
+.cfg
+\family default
+ file is:
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp]
+\end_layout
+
+\begin_layout LyX-Code
+problem = pylith.problems.GreensFns ; Change problem type from the default
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+[pylithapp.greensfns]
+\end_layout
+
+\begin_layout LyX-Code
+fault_id = 100 ; Default value
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+\color red
+Warning:
+\series default
+\color none
+
+\color inherit
+The
+\family typewriter
+GreensFns
+\family default
+ problem generates slip impulses on a fault.
+ The current version of PyLith requires that impulses can only be applied
+ to a single fault and the fault facility must be set to
+\family typewriter
+FaultCohesiveImpulses
+\family default
+.
+\end_layout
+
+\begin_layout Section
\begin_inset CommandInset label
LatexCommand label
name "sec:spatial:databases"
@@ -3881,7 +3988,7 @@
\end_layout
\begin_layout LyX-Code
-quadrature.cell.shape = tetrahedron
+quadrature.cell.dimension = 3
\end_layout
\begin_layout LyX-Code
@@ -4254,9 +4361,21 @@
the surface of the boundary.
As with several of the boundary conditions, the boundary must be a simply-conne
cted surface.
- The OutputSolnSubset is the specialized OutputManager that implements this
- feature and, by default, includes the displacement field in the output.
- In addition to the OutputManager parameters, the OutputSolnSubset includes:
+ The
+\family typewriter
+OutputSolnSubset
+\family default
+ is the specialized OutputManager that implements this feature and, by default,
+ includes the displacement field in the output.
+ In addition to the
+\family typewriter
+OutputManager
+\family default
+ parameters, the
+\family typewriter
+OutputSolnSubset
+\family default
+ includes:
\end_layout
\begin_layout Description
@@ -4269,6 +4388,90 @@
\end_layout
\begin_layout Subsection
+Output at Arbitrary Points
+\end_layout
+
+\begin_layout Standard
+In many situations with recorded observations, one would like to extract
+ the solution at the same locations as the recorded observation.
+ Rather than forcing the finite-element discretization to be consistent
+ with the observation points, PyLith includes a specialized output manager,
+
+\family typewriter
+OutputSolnPoints
+\family default
+, to interpolate the solution to arbitrary points.
+ By default, the output manager will include the displaceent time histories
+ in the output.
+ The locations are specified in a text file.
+ In addition to the
+\family typewriter
+OutputManager
+\family default
+ parameters, the
+\family typewriter
+OutputSolnSubset
+\family default
+ includes:
+\end_layout
+
+\begin_layout Description
+vertex_data_fields Names of vertex data fields to output (default is [``displace
+ments'']).
+\end_layout
+
+\begin_layout Description
+reader Reader for points list (default is
+\family typewriter
+PointsList
+\family default
+).
+\end_layout
+
+\begin_layout Description
+writer Writer for output (default is
+\family typewriter
+DataWriterVTKPoints
+\family default
+).
+ In most cases users will want to use the
+\family typewriter
+DataWriterHDF5Mesh
+\family default
+.
+\end_layout
+
+\begin_layout Subsubsection
+PointsList Reader
+\end_layout
+
+\begin_layout Standard
+This object corresponds to a simple text file containing a list of points
+ (one per line) where output is desired.
+ The points are specified in the coordinate system specified by OutputSolnPoints.
+ The coordinates will be transformed into the coordinate system of the mesh
+ prior to interpolation.
+ The properties available to customize the behavior of
+\family typewriter
+PointsList
+\family default
+ are:
+\end_layout
+
+\begin_layout Description
+filename Names of file containing list of points.
+\end_layout
+
+\begin_layout Description
+comment_delimiter Delimiter at beginning of line to identify comments (default
+ is #).
+\end_layout
+
+\begin_layout Description
+value_delimiter Delimiter used to separate values (default is whitespace).
+\end_layout
+
+\begin_layout Subsection
Output Field Filters
\end_layout
@@ -4448,9 +4651,11 @@
\end_inset
for an example).
- Accessing the datasets in the HDF5 files using tools such as PyTables with
- visualization through MayaVi circumvents this problem, but requires writing
- Python scripts and a deeper knowledge of the visualization interface.
+ Accessing the datasets in the HDF5 files using tools such as h5py (included
+ with the PyLith binary and installed by default with the PyLith Installer)
+ and PyTables with visualization through MayaVi circumvents this problem,
+ but requires writing Python scripts and a deeper knowledge of the visualization
+ interface.
\end_layout
\begin_layout Standard
@@ -4716,8 +4921,8 @@
\begin_layout Itemize
Merge materials using the same material model.
- This will result in only one VTK file for each material model rather than
- several files.
+ This will result in only one VTK or HDF5 file for each material model rather
+ than several files.
\end_layout
\begin_layout Itemize
@@ -4790,7 +4995,12 @@
\end_layout
\begin_layout Itemize
+Consult the PyLith FAQ webpage (ADD URL HERE) which contains a growing list
+ of common problems and their corresponding solutions.
+\end_layout
+\begin_layout Itemize
+
\family typewriter
ImportError: liblapack.so.2: cannot open shared object file: No such file
or directory
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/shearwave/quad4.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/shearwave/quad4.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/tutorials/shearwave/quad4.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -315,7 +315,7 @@
See Section
\begin_inset CommandInset ref
LatexCommand ref
-reference "sub:Fault-Constitutive-Models"
+reference "sec:fault:constitutive:models"
\end_inset
@@ -459,7 +459,14 @@
\begin_layout Standard
The parameters specific to this example are related to the use of the slip-weake
-ning friction fault constitutive model (see Section ??).
+ning friction fault constitutive model (see Section
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sec:fault:constitutive:models"
+
+\end_inset
+
+).
We set the fault constitutive model via
\end_layout
@@ -586,7 +593,14 @@
\begin_layout Standard
The parameters specific to this example are related to the use of the rate-
- and state-friction fault constitutive model (see Section ??).
+ and state-friction fault constitutive model (see Section
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "sec:fault:constitutive:models"
+
+\end_inset
+
+).
The evolution of the state variable uses the ageing law.
We set the fault constitutive model via
\end_layout
Modified: short/3D/PyLith/branches/v1.7-trunk/doc/userguide/userguide.lyx
===================================================================
--- short/3D/PyLith/branches/v1.7-trunk/doc/userguide/userguide.lyx 2012-05-11 22:51:16 UTC (rev 20086)
+++ short/3D/PyLith/branches/v1.7-trunk/doc/userguide/userguide.lyx 2012-05-11 23:00:45 UTC (rev 20087)
@@ -136,7 +136,7 @@
\begin_inset Newline newline
\end_inset
-Version 1.6.1
+Version 1.7.0
\end_layout
\begin_layout Date
More information about the CIG-COMMITS
mailing list