[cigcommits] r15676  in doc/geodynamics.org/benchmarks/trunk: . geodyn long magma mc mc/2dcartesian short short/benchmarklanders short/benchmarkrs short/benchmarkrs/results short/benchmarkrsnog short/benchmarkrsnog/geofestinput short/benchmarkrsnog/plots short/benchmarkrsnog/pylith0.8input short/benchmarkrsnog/results short/benchmarkstrikeslip short/benchmarkstrikeslip/geofestinput short/benchmarkstrikeslip/plots short/benchmarkstrikeslip/pylith0.8input short/benchmarkstrikeslip/results short/utilities
luis at geodynamics.org
luis at geodynamics.org
Fri Sep 18 13:02:19 PDT 2009
Author: luis
Date: 20090918 13:02:16 0700 (Fri, 18 Sep 2009)
New Revision: 15676
Added:
doc/geodynamics.org/benchmarks/trunk/magma/index.rst
doc/geodynamics.org/benchmarks/trunk/magma/mckenzieequations.rst
doc/geodynamics.org/benchmarks/trunk/magma/milestone1.rst
doc/geodynamics.org/benchmarks/trunk/magma/milestone2.rst
doc/geodynamics.org/benchmarks/trunk/magma/milestone3.rst
doc/geodynamics.org/benchmarks/trunk/magma/milestone4.rst
doc/geodynamics.org/benchmarks/trunk/magma/milestone5.rst
doc/geodynamics.org/benchmarks/trunk/magma/runningstgmadds.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarklanders/descriptionlanders.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/descriptionrsnog.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/geofestinput/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/plots/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/pylith0.8input/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/results/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/descriptionrs.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/results/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/descriptionss.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/geofestinput/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/plots/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/pylith0.8input/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/results/index.rst
doc/geodynamics.org/benchmarks/trunk/short/index.rst
doc/geodynamics.org/benchmarks/trunk/short/overview.rst
doc/geodynamics.org/benchmarks/trunk/short/utilities/CUBITex.rst
doc/geodynamics.org/benchmarks/trunk/short/utilities/index.rst
Removed:
doc/geodynamics.org/benchmarks/trunk/magma/index.txt
doc/geodynamics.org/benchmarks/trunk/magma/mckenzieequations.txt
doc/geodynamics.org/benchmarks/trunk/magma/milestone1.txt
doc/geodynamics.org/benchmarks/trunk/magma/milestone2.txt
doc/geodynamics.org/benchmarks/trunk/magma/milestone3.txt
doc/geodynamics.org/benchmarks/trunk/magma/milestone4.txt
doc/geodynamics.org/benchmarks/trunk/magma/milestone5.txt
doc/geodynamics.org/benchmarks/trunk/magma/runningstgmadds.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarklanders/descriptionlanders.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/descriptionrsnog.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/geofestinput/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/plots/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/pylith0.8input/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/results/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/descriptionrs.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/results/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/descriptionss.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/geofestinput/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/plots/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/pylith0.8input/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/results/index.txt
doc/geodynamics.org/benchmarks/trunk/short/index.txt
doc/geodynamics.org/benchmarks/trunk/short/overview.txt
doc/geodynamics.org/benchmarks/trunk/short/utilities/CUBITex.txt
doc/geodynamics.org/benchmarks/trunk/short/utilities/index.txt
Modified:
doc/geodynamics.org/benchmarks/trunk/geodyn/index.rst
doc/geodynamics.org/benchmarks/trunk/index.rst
doc/geodynamics.org/benchmarks/trunk/long/circularinclusion.rst
doc/geodynamics.org/benchmarks/trunk/long/divergence.rst
doc/geodynamics.org/benchmarks/trunk/long/druckerprager.rst
doc/geodynamics.org/benchmarks/trunk/long/fallingsphere.rst
doc/geodynamics.org/benchmarks/trunk/long/geomod2004.rst
doc/geodynamics.org/benchmarks/trunk/long/geomod2008.rst
doc/geodynamics.org/benchmarks/trunk/long/index.rst
doc/geodynamics.org/benchmarks/trunk/long/relaxationtopography.rst
doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/index.rst
doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite1.rst
doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite2.rst
doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite3.rst
doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite4.rst
doc/geodynamics.org/benchmarks/trunk/mc/index.rst
doc/geodynamics.org/benchmarks/trunk/mc/notesonmantleconvectionbenchmarks.rst
Log:
Fix reST format in source files
Modified: doc/geodynamics.org/benchmarks/trunk/geodyn/index.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/geodyn/index.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/geodyn/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 2,7 +2,7 @@
Historical Benchmark Cases
==========================
 Historically, there are two cases defined in the benchmark study published
+Historically, there are two cases defined in the benchmark study published
in the 2001 paper by Christensen et al. [6]. Case 0 is a benchmark of rotating
nonmagnetic convection. Case 1 is a dynamo with an insulating inner core
corotating with the outer boundary. The regions outside the fluid shell are
@@ 10,25 +10,25 @@
appropriate potential fields in the exterior that imply no external sources
of the field.
 In both cases the Ekman number is $E = 10^{3}$ and the Prandtl number is
+In both cases the Ekman number is $E = 10^{3}$ and the Prandtl number is
$Pr = 1$. The Rayleigh number is set to $Ra = 100000$. Note that the
definition of the Rayleigh number differs from the one in the published
cases [6] by a factor of Ekman number, i.e., $Ra=\frac{Ra}{E}$. The
magnetic Prandtl number is zero in the nonmagnetic convection case 0, and
is $Pm = 5$ in case 1. The spherical harmonic expansion is truncated at
degree $\ell_{max}=32$ and a fourfold symmetry is assumed in the
longitudinal direction (`param.f` should be linked to `param32s4.f` when
you compile MAG). The input parameter files are `par.bench0` for case 0,
and `par.bench1` for case 1; both files reside in the `~/src` directory.
+longitudinal direction (``param.f`` should be linked to ``param32s4.f``
+when you compile MAG). The input parameter files are ``par.bench0``
+for case 0, and ``par.bench1`` for case 1; both files reside in the
+``~/src`` directory.
 The output files of the benchmark cases are stored n the directory
`~/benchdata/data_bench0` and `~/benchdata/databench1` respectively.
+The output files of the benchmark cases are stored n the directory
+``~/benchdata/data_bench0`` and ``~/benchdata/databench1`` respectively.
In the following table we see the solutions from MAG agree with the
benchmark suggested value with a small margin of difference. In both case 0
and case 1, the values listed were obtained with low resolution and a
relatively short run of MAG

++++++
  Case 0 Suggested value  Mag Case 0  Case 1 Suggested Value  Mag Case 1 
++++++
@@ 43,7 +43,6 @@
Reversal Dynamo Case
====================

In this benchmark, we produce a magnetic field reversal using MAG. The
input parameter in the source directory for this case is `~/src/par.Rev`.
There is no longitudinal symmetry in this case, so when you compile MAG,
@@ 51,9 +50,9 @@
Prandtl number is $Pr=1$ and the magnetic Prandtl number is $Pm=10$. The
Rayleigh number is $Ra=12000$.
+
Results and Discussions


This case was run on 32bit and 64bit Intel processors. Figure
[fig:FieldPlot1] shows a plot of mean velocity Vrms, mean magnetic
field Brms, the axial dipole and the dipole tilt on the outer boundary.
@@ 64,15 +63,17 @@
before the second field reversal and the bottom is the pole plot after the
second field reversal.
 image:: images/field64.ps
 Figure [fig:FieldPlot1]: Field Plot for Reversal Dynamo Case
+.. figure:: images/field64.ps
+ Figure [fig:FieldPlot1]:
+ Field Plot for Reversal Dynamo Case
+
+.. figure:: images/field64revR.ps
+ Figure [fig:FieldPlot2]:
+ Field Plot for Reversal Dynamo Case (longer run)
 image:: images/field64revR.ps
 Figure [fig:FieldPlot2]: Field Plot for Reversal Dynamo Case (longer run)

 image:: images/g1revR.ps
 image:: images/g7revR.ps
 Figure [fig:Thepole]: Magnetic Field Pole Plot. The top s the pole plot
+.. figure:: images/g1revR.ps
+.. figure:: images/g7revR.ps
+ Figure [fig:Thepole]: Magnetic Field Pole Plot. The top is the pole plot
at the beginning of the second field reversal; the bottom is the pole
plot at the end of the second field reversal.
Modified: doc/geodynamics.org/benchmarks/trunk/index.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/index.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 5,13 +5,15 @@
Benchmark Efforts by Working Group

 * "ShortTerm Crustal Dynamics":http://geodynamics.org/cig/software/benchmarks/short/
+* `ShortTerm Crustal Dynamics`__
+* `LongTerm Tectonics`__
+* `Mantle Convection`__
+* `Magma Migration`__
+* `Geodynamo`__
 * "LongTerm Tectonics":http://geodynamics.org/cig/software/benchmarks/long/
+__ http://geodynamics.org/cig/software/benchmarks/short/
+__ http://geodynamics.org/cig/software/benchmarks/long/
+__ http://geodynamics.org/cig/software/benchmarks/mc/
+__ http://geodynamics.org/cig/software/benchmarks/magma/
+__ http://geodynamics.org/cig/software/benchmarks/geodyn/
 * "Mantle Convection":http://geodynamics.org/cig/software/benchmarks/mc/

 * "Magma Migration":http://geodynamics.org/cig/software/benchmarks/magma/

 * "Geodynamo":http://geodynamics.org/cig/software/benchmarks/geodyn/

Modified: doc/geodynamics.org/benchmarks/trunk/long/circularinclusion.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/long/circularinclusion.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/circularinclusion.rst 20090918 20:02:16 UTC (rev 15676)
@@ 2,74 +2,74 @@
Circular Inclusion
==================
 Schmid and Podladchikov [Clast] derived a simple analytic solution for
 the pressure and velocity fields for a circular inclusion under simple
 shear as in Figure [fig:inclusionsetup].
+Schmid and Podladchikov [Clast] derived a simple analytic solution for
+the pressure and velocity fields for a circular inclusion under simple
+shear as in Figure [fig:inclusionsetup].
 image:: images/inclusion_setup.eps
 Figure [fig:inclusionsetup]
 Schematic for the circular inclusion benchmark
+.. figure:: images/inclusion_setup.eps
+ Figure [fig:inclusionsetup]
+ Schematic for the circular inclusion benchmark
 The file `input/benchmarks/circular_inclusion/README` has instructions
 on how to run this benchmark.
+The file ``input/benchmarks/circular_inclusion/README`` has instructions
+on how to run this benchmark.
 Because of the symmetry of the problem, we only have to solve over the
 topright quarter of the domain. For the velocity boundary conditions,
 the analytic solution is a bit complicated. So we used the simple
 relation $$v_x = \dot{\epsilon}y, v_y=\dot{\epsilon}x,$$ for the
 boundaries, where $\dot{\epsilon}$ is the magnitude of the shear and $x$
 and $y$ are the coordinates. This induces an error of order $r_i^2/r^2$,
 where $r_i=0.1$ is the radius of the inclusion, and $r$ is the radius. We
 have the boundaries at 80 times the radius of the inclusion, giving an
 error of about $0.01\%$, which is much smaller than the other errors we
 were looking at. Just to make sure, we did runs with boundaries at 40
 times the radius of the inclusion and got very similar results.
+Because of the symmetry of the problem, we only have to solve over the
+topright quarter of the domain. For the velocity boundary conditions,
+the analytic solution is a bit complicated. So we used the simple
+relation $$v_x = \dot{\epsilon}y, v_y=\dot{\epsilon}x,$$ for the
+boundaries, where $\dot{\epsilon}$ is the magnitude of the shear and $x$
+and $y$ are the coordinates. This induces an error of order $r_i^2/r^2$,
+where $r_i=0.1$ is the radius of the inclusion, and $r$ is the radius. We
+have the boundaries at 80 times the radius of the inclusion, giving an
+error of about $0.01\%$, which is much smaller than the other errors we
+were looking at. Just to make sure, we did runs with boundaries at 40
+times the radius of the inclusion and got very similar results.
 A characteristic of the analytic solution is that the pressure is zero
 inside the inclusion, while outside it follows the relation
 $$p_m=4\dot{\epsilon}\frac{\mu_m(\mu_i\mu_m)}{\mu_i+\mu_m}\frac{r_i^2}{r^2}\cos(2\theta),$$
 where $\mu_i=2$ is the viscosity of the inclusion and $\mu_m=1$ is the
 viscosity of the background media. Many numerical codes that solve Stokes
 flow (Eq. [eq:simple momentum conservation] and [eq:continuity]),
 including Gale, assume that pressure, velocity, and viscosity are
 continuous. The pressure discontinuity at the surface of the inclusion
 violates that assumption, so the error tends to concentrate near the
 surface of the inclusion.
+A characteristic of the analytic solution is that the pressure is zero
+inside the inclusion, while outside it follows the relation
+$$p_m=4\dot{\epsilon}\frac{\mu_m(\mu_i\mu_m)}{\mu_i+\mu_m}\frac{r_i^2}{r^2}\cos(2\theta),$$
+where $\mu_i=2$ is the viscosity of the inclusion and $\mu_m=1$ is the
+viscosity of the background media. Many numerical codes that solve Stokes
+flow (Eq. [eq:simple momentum conservation] and [eq:continuity]),
+including Gale, assume that pressure, velocity, and viscosity are
+continuous. The pressure discontinuity at the surface of the inclusion
+violates that assumption, so the error tends to concentrate near the
+surface of the inclusion.
 Figure [fig:Pressureinclusion] plots the error in the pressure along the
 line $y=x/2$ for different resolutions. Inside the inclusion near the
 surface, the pressure is consistently wrong. The pressure does not
 converge with higher resolution, giving us a clue that the default
 numerical scheme is not accurate.
+Figure [fig:Pressureinclusion] plots the error in the pressure along the
+line $y=x/2$ for different resolutions. Inside the inclusion near the
+surface, the pressure is consistently wrong. The pressure does not
+converge with higher resolution, giving us a clue that the default
+numerical scheme is not accurate.
 image:: images/inclusion_r8_p.png
 Figure [fig:Pressureinclusion]
 Pressure along the line $y=x/2$ for resolutions of $128 \times 128$
 (blue), $256 \times 256$ (red), and $512 \times 512$ (black). The
 inclusion has radius $r_i=0.1$. Note that the pressure should be zero
 inside the inclusion, but the numerical solutions consistently
 underestimate the pressure.
+.. figure:: images/inclusion_r8_p.png
+ Figure [fig:Pressureinclusion]
+ Pressure along the line $y=x/2$ for resolutions of $128 \times 128$
+ (blue), $256 \times 256$ (red), and $512 \times 512$ (black). The
+ inclusion has radius $r_i=0.1$. Note that the pressure should be zero
+ inside the inclusion, but the numerical solutions consistently
+ underestimate the pressure.
 Outside the inclusion, the error is better behaved. Figure
 [fig:Pressureerror] plots the error in the pressure along the line
 $y=x/2$ outside the inclusion for different resolutions. While there are
 still problems near the surface, away from the surface the solutions are
 quite good. Figure [fig:Scaledpressureerror] plots the error scaled
 with resolution, and we can see that the error scales linearly with
 resolution. This gives us confidence that, at least away from the
 inclusion, the code is giving the right answer. This kind of result,
 where the solution is bad close to the surface, but good otherwise, is
 typical for numerical solutions of this problem [FD Stokes].
+Outside the inclusion, the error is better behaved. Figure
+[fig:Pressureerror] plots the error in the pressure along the line
+$y=x/2$ outside the inclusion for different resolutions. While there are
+still problems near the surface, away from the surface the solutions are
+quite good. Figure [fig:Scaledpressureerror] plots the error scaled
+with resolution, and we can see that the error scales linearly with
+resolution. This gives us confidence that, at least away from the
+inclusion, the code is giving the right answer. This kind of result,
+where the solution is bad close to the surface, but good otherwise, is
+typical for numerical solutions of this problem [FD Stokes].
 image:: images/inclusion_r8_p_error.png
 Figure [fig:Pressureerror]
 Error in the pressure outside the inclusion along the line $y=x/2$ for
 resolutions of $128 \times 128$ (blue), $256 \times 256$ (red), and
 $512 \times 512$ (black). The inclusion has radius $r_i=0.1$.
+.. figure:: images/inclusion_r8_p_error.png
+ Figure [fig:Pressureerror]
+ Error in the pressure outside the inclusion along the line $y=x/2$ for
+ resolutions of $128 \times 128$ (blue), $256 \times 256$ (red), and
+ $512 \times 512$ (black). The inclusion has radius $r_i=0.1$.
 image:: images/inclusion_r8_p_scaled_error.png
 Figure [fig:Scaledpressureerror]
 As in Figure [fig:Pressureerror], but with the error scaled with $h$.
 So the mediumresolution error is multiplied by 2 and the
 highresolution error is multiplied by 4.
+.. figure:: images/inclusion_r8_p_scaled_error.png
+ Figure [fig:Scaledpressureerror]
+ As in Figure [fig:Pressureerror], but with the error scaled with $h$.
+ So the mediumresolution error is multiplied by 2 and the
+ highresolution error is multiplied by 4.
Modified: doc/geodynamics.org/benchmarks/trunk/long/divergence.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/long/divergence.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/divergence.rst 20090918 20:02:16 UTC (rev 15676)
@@ 2,39 +2,39 @@
Divergence
==========
 This benchmark tests the implementation of the divergence term in the
 equation [eq:divergence]. In 2D, a constant divergence is applied to a
 square domain, and the velocity on the corners is set to enforce a
 spreading from the center of the square. Figure [fig:Divergence_v_sri]
 shows the velocity and strain rate invariant for a numerical solution.
 For a constant divergence $d$, the analytic solution for this setup is
 $$v_x = x \cdot d/2, v_y = y \cdot d/2$$
+This benchmark tests the implementation of the divergence term in the
+equation [eq:divergence]. In 2D, a constant divergence is applied to a
+square domain, and the velocity on the corners is set to enforce a
+spreading from the center of the square. Figure [fig:Divergence_v_sri]
+shows the velocity and strain rate invariant for a numerical solution.
+For a constant divergence $d$, the analytic solution for this setup is
+$$v_x = x \cdot d/2, v_y = y \cdot d/2$$
 In 3D, the analytic solution is
 $$v_x = x \cdot d/3, v_y = y \cdot d/3, v_z = z \cdot d/3$$
+In 3D, the analytic solution is
+$$v_x = x \cdot d/3, v_y = y \cdot d/3, v_z = z \cdot d/3$$
 In both cases, the strain rate invariant equals $\sqrt{d/2}$. As shown in
 Figure [fig:Divergence_2D_error], the main source of error in 2D comes
 from inaccuracies in the solver. Figure [fig:Divergence_3D_error] paints
 a different picture in 3D, where the main source of error comes from
 having a finite number of particles.
+In both cases, the strain rate invariant equals $\sqrt{d/2}$. As shown in
+Figure [fig:Divergence_2D_error], the main source of error in 2D comes
+from inaccuracies in the solver. Figure [fig:Divergence_3D_error] paints
+a different picture in 3D, where the main source of error comes from
+having a finite number of particles.
 image:: images/divergence_v.png
 Figure [fig:Divergence_v_sri]
 Velocity and Strain Rate Invariant solution for the 2D Divergence
 benchmark. The variation in the strain rate invariant is uniformly
 small.
+.. figure:: images/divergence_v.png
+ Figure [fig:Divergence_v_sri]
+ Velocity and Strain Rate Invariant solution for the 2D Divergence
+ benchmark. The variation in the strain rate invariant is uniformly
+ small.
 image:: images/divergence_2D_error.eps
 Figure [fig:Divergence_2D_error]
 Maximum error in the strain rate invariant for the 2D Divergence
 benchmark vs. tolerance in the linear solver. The resolution is kept at
 $32 \times 32$, and the number of particles per cell is kept at 30.
+.. figure:: images/divergence_2D_error.eps
+ Figure [fig:Divergence_2D_error]
+ Maximum error in the strain rate invariant for the 2D Divergence
+ benchmark vs. tolerance in the linear solver. The resolution is kept at
+ $32 \times 32$, and the number of particles per cell is kept at 30.
 image:: images/divergence_3D_error.eps
 Figure [fig:Divergence_3D_error]
 Maximum error in the strain rate invariant for the 3D Divergence
 benchmark vs. the number of particles in each cell. The resolution is
 kept at $16 \times 16 \times 16$, and the tolerance in the linear
 solver is kept at $10^{7}$.
+.. figure:: images/divergence_3D_error.eps
+ Figure [fig:Divergence_3D_error]
+ Maximum error in the strain rate invariant for the 3D Divergence
+ benchmark vs. the number of particles in each cell. The resolution is
+ kept at $16 \times 16 \times 16$, and the tolerance in the linear
+ solver is kept at $10^{7}$.
Modified: doc/geodynamics.org/benchmarks/trunk/long/druckerprager.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/long/druckerprager.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/druckerprager.rst 20090918 20:02:16 UTC (rev 15676)
@@ 5,57 +5,58 @@
Analytic Treatment

 For the DruckerPrager rehology in 2D, we can write the yielding relation
 as $$\sigma_{ns}=\sigma_{nn}\tan\varphi+C,$$ where $\sigma_{ns}$ is the
 shear stress perpendicular to the fault plane, $\sigma_{nn}$ is the shear
 stress parallel to the fault plane, $\varphi$ is the internal angle of
 friction, and $C$ is the cohesion. Decomposing this into principal
 stresses $\sigma_{I}$, $\sigma_{II}$, and $\sigma_{III}$ gives
 $$\sin(2\Theta)(\sigma_{I}\sigma_{III})/2=\tan\varphi\left((\sigma_{I}+\sigma_{III})/2+\cos(2\Theta)(\sigma_{I}\sigma_{III})/2\right)+C,$$
 where $\Theta$ is the angle that the fault makes relative to the maximum
 shear stress. Assuming that the fault forms where the shear stress
 $\sigma_{I}\sigma_{III}$ is a minimum, a little algebra gives us
 $$\Theta=\pm\left(\frac{\pi}{4} + \frac{\varphi}{2}\right).$$
+For the DruckerPrager rehology in 2D, we can write the yielding relation
+as $$\sigma_{ns}=\sigma_{nn}\tan\varphi+C,$$ where $\sigma_{ns}$ is the
+shear stress perpendicular to the fault plane, $\sigma_{nn}$ is the shear
+stress parallel to the fault plane, $\varphi$ is the internal angle of
+friction, and $C$ is the cohesion. Decomposing this into principal
+stresses $\sigma_{I}$, $\sigma_{II}$, and $\sigma_{III}$ gives
+$$\sin(2\Theta)(\sigma_{I}\sigma_{III})/2=\tan\varphi\left((\sigma_{I}+\sigma_{III})/2+\cos(2\Theta)(\sigma_{I}\sigma_{III})/2\right)+C,$$
+where $\Theta$ is the angle that the fault makes relative to the maximum
+shear stress. Assuming that the fault forms where the shear stress
+$\sigma_{I}\sigma_{III}$ is a minimum, a little algebra gives us
+$$\Theta=\pm\left(\frac{\pi}{4} + \frac{\varphi}{2}\right).$$
 Using this, we can construct a simple plasticity experiment and make sure
 that Gale gives the correct faulting angle.
+Using this, we can construct a simple plasticity experiment and make sure
+that Gale gives the correct faulting angle.
+
Model Setup

 We performed a shortening experiment as shown in Figure
 [fig:MohrCoulombsetup]. We only solve the Stokes equation and look at
 the strain rate invariant to find incipient faults. We do not take any
 time steps, removing any confounding effects they may cause.
+We performed a shortening experiment as shown in Figure
+[fig:MohrCoulombsetup]. We only solve the Stokes equation and look at
+the strain rate invariant to find incipient faults. We do not take any
+time steps, removing any confounding effects they may cause.
 image:: images/Mohr_Coulomb_setup.eps
 Figure [fig:MohrCoulombsetup]
 The setup for the shortening experiment. The box is 1 unit on a side,
 and the low viscosity region has a radius of 0.01 (its size is
 exaggerated).
+.. figure:: images/Mohr_Coulomb_setup.eps
+ Figure [fig:MohrCoulombsetup]
+ The setup for the shortening experiment. The box is 1 unit on a side,
+ and the low viscosity region has a radius of 0.01 (its size is
+ exaggerated).
Numerical Results

 Figure [fig:MohrCoulombsri] shows the results for three different
 resolutions for $\varphi=45^{\deg}$. There is not much difference between
 the medium ($256 \times 256$) and high ($512 \times 512$) results,
 suggesting that we have sufficient resolution. Figure
 [fig:MohrCoulombcomparison] shows a plot of the numerical vs. analytic
 results for several different angles for medium resolution. This gives us
 confidence that, at least in compression(sp?) in 2D, our DruckerPrager
 implementation gives the correct results.
+Figure [fig:MohrCoulombsri] shows the results for three different
+resolutions for $\varphi=45^{\deg}$. There is not much difference between
+the medium ($256 \times 256$) and high ($512 \times 512$) results,
+suggesting that we have sufficient resolution. Figure
+[fig:MohrCoulombcomparison] shows a plot of the numerical vs. analytic
+results for several different angles for medium resolution. This gives us
+confidence that, at least in compression(sp?) in 2D, our DruckerPrager
+implementation gives the correct results.
 image:: images/Mohr_coulomb_resolutions.png
 Figure [fig:MohrCoulombsri]
 Strain rate invariant for the shortening experiment where
 $\varphi=45^{\deg}$ with three different resolutions:
 $128 \times 128$, $256 \times 256$, $512 \times 512$.
 Any differences between the medium and high resolution runs are swamped
 by uncertainties in determining the overall angle of faulting.
+.. figure:: images/Mohr_coulomb_resolutions.png
+ Figure [fig:MohrCoulombsri]
+ Strain rate invariant for the shortening experiment where
+ $\varphi=45^{\deg}$ with three different resolutions:
+ $128 \times 128$, $256 \times 256$, $512 \times 512$.
+ Any differences between the medium and high resolution runs are swamped
+ by uncertainties in determining the overall angle of faulting.
 image:: images/mohr_coulomb_angles.eps
 Figure [fig:MohrCoulombcomparison]
 Numerical vs. analytic results for fault angles as a function of
 internal angle of friction.
+.. figure:: images/mohr_coulomb_angles.eps
+ Figure [fig:MohrCoulombcomparison]
+ Numerical vs. analytic results for fault angles as a function of
+ internal angle of friction.
Modified: doc/geodynamics.org/benchmarks/trunk/long/fallingsphere.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/long/fallingsphere.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/fallingsphere.rst 20090918 20:02:16 UTC (rev 15676)
@@ 2,73 +2,73 @@
Falling Sphere
==============
 This benchmark simulates a rigid sphere falling through a cylinder filled
 with a viscous medium as in Figure [fig:SphereCylinder]
+This benchmark simulates a rigid sphere falling through a cylinder filled
+with a viscous medium as in Figure [fig:SphereCylinder]
 image:: sphere_cylinder.eps
 Figure [fig:SphereCylinder]
 Schematic of a Sphere falling through a Cylinder.
+.. figure:: sphere_cylinder.eps
+ Figure [fig:SphereCylinder]
+ Schematic of a Sphere falling through a Cylinder.
 The file `input/benchmarks/falling_sphere/README` has instructions on
 running this benchmark. In an infinitely large cylinder, the analytic
 solution for the drag on a sphere is $$F=6\pi\eta r u,$$ where $\eta$ is
 the viscosity of the medium, $r$ is the radius of the sphere, and $u$ is
 the velocity of the sphere. Conversely, the buoyancy force is
 $$F=\frac{4}{3}\pi{r^3}g\delta\rho,$$ where $g$ is the gravitational
 constant and $\delta\rho$ is the density difference between the sphere
 and the medium. Balancing these two forces and solving for the velocity
 gives $$u = \frac{2}{9}{r^2}g\delta\rho / \eta.$$
+The file ``input/benchmarks/falling_sphere/README`` has instructions on
+running this benchmark. In an infinitely large cylinder, the analytic
+solution for the drag on a sphere is $$F=6\pi\eta r u,$$ where $\eta$ is
+the viscosity of the medium, $r$ is the radius of the sphere, and $u$ is
+the velocity of the sphere. Conversely, the buoyancy force is
+$$F=\frac{4}{3}\pi{r^3}g\delta\rho,$$ where $g$ is the gravitational
+constant and $\delta\rho$ is the density difference between the sphere
+and the medium. Balancing these two forces and solving for the velocity
+gives $$u = \frac{2}{9}{r^2}g\delta\rho / \eta.$$
 Seetting $g=1$, $r=1$, $\delta\rho=0.01$, and $\eta=1$ gives a velocity
 of $$u=0.00222.$$
+Seetting $g=1$, $r=1$, $\delta\rho=0.01$, and $\eta=1$ gives a velocity
+of $$u=0.00222.$$
 In our case, we simulate a rigid sphere with a high viscosity sphere.
 This allows some internal circulation within the sphere, and so the
 expression for the velocity becomes [Landau & Lifschitz],
 $$u = \frac{1}{3}\frac{r^2{g}\delta\rho}{\eta}\frac{\eta+\eta'}{\eta+\frac{3}{2}\eta'},$$
 where $\eta'$ is the viscosity of the sphere. Four our case, the
 background medium's viscosity is 1 and the sphere's viscosity is 100, so
 the correction is about $1\%$. This turns out to be smaller than other
 effects for the cases we ran.
+In our case, we simulate a rigid sphere with a high viscosity sphere.
+This allows some internal circulation within the sphere, and so the
+expression for the velocity becomes [Landau & Lifschitz],
+$$u = \frac{1}{3}\frac{r^2{g}\delta\rho}{\eta}\frac{\eta+\eta'}{\eta+\frac{3}{2}\eta'},$$
+where $\eta'$ is the viscosity of the sphere. Four our case, the
+background medium's viscosity is 1 and the sphere's viscosity is 100, so
+the correction is about $1\%$. This turns out to be smaller than other
+effects for the cases we ran.
 when the boundaries are not infinitely far away, we can expand the
 solution in terms of the ratio of the radius of the sphere ($r$) to the
 radius of the cylinder ($R$). One solution by Habermann [Stokes Sphere]
 gives a drag force of
 $$F_H=6\pi\eta{ru}\frac{10.75857\left(\frac{r}{R}\right)^5}{1+f_H\left(\frac{r}{R}\right)},$$
 where
 $$f_H\left(\frac{r}{R}\right)=2.1050(r/R)+2.0865(r/R)^31.7068(r/R)^5+0.72603(r/R)^6.$$
+when the boundaries are not infinitely far away, we can expand the
+solution in terms of the ratio of the radius of the sphere ($r$) to the
+radius of the cylinder ($R$). One solution by Habermann [Stokes Sphere]
+gives a drag force of
+$$F_H=6\pi\eta{ru}\frac{10.75857\left(\frac{r}{R}\right)^5}{1+f_H\left(\frac{r}{R}\right)},$$
+where
+$$f_H\left(\frac{r}{R}\right)=2.1050(r/R)+2.0865(r/R)^31.7068(r/R)^5+0.72603(r/R)^6.$$
 For our case with $r=1$, $R=4$, this gives a velocity of
 $$u=1.122747319\cdot{10^{3}},$$ which agrees closely with the result
 from Habermann.
+For our case with $r=1$, $R=4$, this gives a velocity of
+$$u=1.122747319\cdot{10^{3}},$$ which agrees closely with the result
+from Habermann.
 Another possible artifact is that we do not simulate an infinitely long
 cylinder. This turns out to be a small effect. We use a cylinder with a
 height of 8, and place the sphere halfway down. We did runs where the
 cylinder was twice as tall, and the results were essentially unchanged.
+Another possible artifact is that we do not simulate an infinitely long
+cylinder. This turns out to be a small effect. We use a cylinder with a
+height of 8, and place the sphere halfway down. We did runs where the
+cylinder was twice as tall, and the results were essentially unchanged.
 The errors in the computed velocity compared to the Faxen solution are
 plotted in Figure [fig:Errorinvelocity]. These were done with
 resolutions of $8 \times 16 \times 8$, $16 \times 32 \times 16$, and
 $64 \times 128 \times 64$, corresponding to grid sizes ($h$) of $0.5$,
 $0.25$, $0.125$, and $0.0625$. Because of the symmetries of the problem
 we only have to simulate a quarter of the domain. As we increase the
 resolution (decrease $h$), the error decreases. Since we are simulating a
 high viscosity sphere rather than a completely rigid sphere, the velocity
 inside the sphere is not uniform. The error bars indicate the variation
 in velocity across the sphere.
+The errors in the computed velocity compared to the Faxen solution are
+plotted in Figure [fig:Errorinvelocity]. These were done with
+resolutions of $8 \times 16 \times 8$, $16 \times 32 \times 16$, and
+$64 \times 128 \times 64$, corresponding to grid sizes ($h$) of $0.5$,
+$0.25$, $0.125$, and $0.0625$. Because of the symmetries of the problem
+we only have to simulate a quarter of the domain. As we increase the
+resolution (decrease $h$), the error decreases. Since we are simulating a
+high viscosity sphere rather than a completely rigid sphere, the velocity
+inside the sphere is not uniform. The error bars indicate the variation
+in velocity across the sphere.
 image:: images/Sphere_Error.eps
 Figure [fig:Errorinvelocity]
 Error in computed velocity vs. resolution.
+.. figure:: images/Sphere_Error.eps
+ Figure [fig:Errorinvelocity]
+ Error in computed velocity vs. resolution.
 Scaling the error with resolution gives Figure [fig:Scalederrorvelocity].
 The error scales linearly with resolution, giving us confidence that we
 can accurately solve this problem.
+Scaling the error with resolution gives Figure [fig:Scalederrorvelocity].
+The error scales linearly with resolution, giving us confidence that we
+can accurately solve this problem.
 image:: images/Sphere_Scaled_Error.eps
 Figure [fig:Scalederrorvelocity]
 As in figure [fig:Errorinvelocity], but with the error scaled with $h$.
 So the higher resolution errors are multiplied by 2, 4, and 8.

+.. figure:: images/Sphere_Scaled_Error.eps
+ Figure [fig:Scalederrorvelocity]
+ As in figure [fig:Errorinvelocity], but with the error scaled with $h$.
+ So the higher resolution errors are multiplied by 2, 4, and 8.
+
Modified: doc/geodynamics.org/benchmarks/trunk/long/geomod2004.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/long/geomod2004.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/geomod2004.rst 20090918 20:02:16 UTC (rev 15676)
@@ 3,105 +3,106 @@
Geomod 2004
===========
 Two benchmarks were created to validate numerical codes against analog
 sandbox experiments [Buiter et al Numerical Sandbox]: one benchmark
 simulates extension, and the other simulates shortening. A number of
 investigators with different codes ran these benchmarks, giving us a good
 standard against which to compare.
+Two benchmarks were created to validate numerical codes against analog
+sandbox experiments [Buiter et al Numerical Sandbox]: one benchmark
+simulates extension, and the other simulates shortening. A number of
+investigators with different codes ran these benchmarks, giving us a good
+standard against which to compare.
+
Extension
=========
 This benchmark simulates a sandbox being extended as in Figure
 [fig:Extensionmodelsetup]. The right side and half of the bottom are
 translated to the right. This creates a velocity discontinuity at the
 center which is the initial seed for localization. Gale's implementation
 of this benchmark is in `input/benchmarks/extension.xml`.
+This benchmark simulates a sandbox being extended as in Figure
+[fig:Extensionmodelsetup]. The right side and half of the bottom are
+translated to the right. This creates a velocity discontinuity at the
+center which is the initial seed for localization. Gale's implementation
+of this benchmark is in ``input/benchmarks/extension.xml``.
 Like half of the codes in the benchmark, boundary friction was not
 included. Rather, the material is held fixed to the bottom boundary, and
 the velocity discontinuity is smoothed over 0.2 cm. In addition, the
 exact background viscosity is not prescribed by the benchmark. We have
 used $10^{12}\ Pa \cdot s$, the same as used in the I2ELVIS calculations.
 This value is somewhere in the middle of the range of values used in the
 calculations for other codes.
+Like half of the codes in the benchmark, boundary friction was not
+included. Rather, the material is held fixed to the bottom boundary, and
+the velocity discontinuity is smoothed over 0.2 cm. In addition, the
+exact background viscosity is not prescribed by the benchmark. We have
+used $10^{12}\ Pa \cdot s$, the same as used in the I2ELVIS calculations.
+This value is somewhere in the middle of the range of values used in the
+calculations for other codes.
 image:: images/Extension_setup.png
 Figure [fig:Extensionmodelsetup]
 Extension model setup. Reproduced, with permission, from Buiter et al.
 [Buiter et al Numerical Sandbox]
+.. figure:: images/Extension_setup.png
+ Figure [fig:Extensionmodelsetup]
+ Extension model setup. Reproduced, with permission, from Buiter et al.
+ [Buiter et al Numerical Sandbox]
 A comparison against the other codes is in Figure
 [fig:Comparisonextension]. While it is difficult to perform exact
 comparisons, Gale produces similar fault patterns. It is interesting to
 note that this qualitative comparison holds true even though the code is
 not exactly convergent. For example, Figure [fig:extensionconvergence]
 shows a run with varying resolution. Changing the resolution alters the
 details, but, after a certain minimum resolution, does not change the
 character of the solution.
+A comparison against the other codes is in Figure
+[fig:Comparisonextension]. While it is difficult to perform exact
+comparisons, Gale produces similar fault patterns. It is interesting to
+note that this qualitative comparison holds true even though the code is
+not exactly convergent. For example, Figure [fig:extensionconvergence]
+shows a run with varying resolution. Changing the resolution alters the
+details, but, after a certain minimum resolution, does not change the
+character of the solution.
 image:: images/Extension_comparision.png (sp?)
 Figure [fig:Comparisonextension]
 Strain rate invariant for the numerical extension models after 5 cm of
 extension. The resolutions of the various models are:
 I2ELVIS: $400 \times 75$
 LAPEX2D: $301 \times 71$
 Microfem: $201 \times 61$
 SloMo: $401 \times 71$
 Sopale: $401 \times 71$
 Gale: $1024 \times 128$
 Uper images reproduced, with permission, from Buiter et al.
 [Buiter et al Numerical Sandbox].
+.. figure:: images/Extension_comparision.png (sp?)
+ Figure [fig:Comparisonextension]
+ Strain rate invariant for the numerical extension models after 5 cm of
+ extension. The resolutions of the various models are:
+ I2ELVIS: $400 \times 75$
+ LAPEX2D: $301 \times 71$
+ Microfem: $201 \times 61$
+ SloMo: $401 \times 71$
+ Sopale: $401 \times 71$
+ Gale: $1024 \times 128$
+ Uper images reproduced, with permission, from Buiter et al.
+ [Buiter et al Numerical Sandbox].
 image:: images/extension_sensitivity.pdf
 Figure [fig:extensionconvergence]
 Strain rate invariant for the extension model after 5 cm of extension
 for four different resolutions: (a) 128x16, (b) 256x32, (c) 512x64,
 and (d) 1024x128.
+.. figure:: images/extension_sensitivity.pdf
+ Figure [fig:extensionconvergence]
+ Strain rate invariant for the extension model after 5 cm of extension
+ for four different resolutions: (a) 128x16, (b) 256x32, (c) 512x64,
+ and (d) 1024x128.
Shortening
==========
 This benchmark simulates a sandbox being shortened as in Figure
 [fig:Shorteningmodelsetup]. The right side is moved to the left,
 creating a velocity discontinuity at the bottom right corner. Gale's
 implementation of this benchmark is in `input/benchmarks/shortening.xml`.
+This benchmark simulates a sandbox being shortened as in Figure
+[fig:Shorteningmodelsetup]. The right side is moved to the left,
+creating a velocity discontinuity at the bottom right corner. Gale's
+implementation of this benchmark is in `input/benchmarks/shortening.xml`.
 Like most of the codes in the benchmark, we applied diffusion (diffusion
 coefficient $10^{6}\ m^2\ s^{1}$) to the top surface to smooth steep
 slope angles. This lies within the range used in calculations used by the
 other codes (LAPEX2D: $10^{6}\ m^2\ s^{1}$, Microfem: unspecified,
 Sopale: $10^{9}\ m^2\ s^{1}$). Again, the exact background viscosity is
 not prescribed by the benchmark, so we have used $10^{12}\ Pa \cdot s$.
+Like most of the codes in the benchmark, we applied diffusion (diffusion
+coefficient $10^{6}\ m^2\ s^{1}$) to the top surface to smooth steep
+slope angles. This lies within the range used in calculations used by the
+other codes (LAPEX2D: $10^{6}\ m^2\ s^{1}$, Microfem: unspecified,
+Sopale: $10^{9}\ m^2\ s^{1}$). Again, the exact background viscosity is
+not prescribed by the benchmark, so we have used $10^{12}\ Pa \cdot s$.
 image:: images/Shortening_setup.png
 Figure [fig:Shorteningmodelsetup]
 Shortening model setup. Reproduced, with permission, from Buiter et al.
 [Buiter et al Numerical Sandbox].
+.. figure:: images/Shortening_setup.png
+ Figure [fig:Shorteningmodelsetup]
+ Shortening model setup. Reproduced, with permission, from Buiter et al.
+ [Buiter et al Numerical Sandbox].
 A comparison against the other codes' calculations at 14 cm of cumulative
 shortening is in Figure [fig:shorteningcompare]. There is more variance
 among the different codes, so it is difficult to tell whether Gale's
 behavior agrees with the other codes. Figure [fig:shorteningconvergence]
 shows a run with a few different resolutions, and even there we see
 marked differences in behavior as we increase resolution.
+A comparison against the other codes' calculations at 14 cm of cumulative
+shortening is in Figure [fig:shorteningcompare]. There is more variance
+among the different codes, so it is difficult to tell whether Gale's
+behavior agrees with the other codes. Figure [fig:shorteningconvergence]
+shows a run with a few different resolutions, and even there we see
+marked differences in behavior as we increase resolution.
 image:: images/Shortening_comparison.png
 Figure [fig:shorteningcompare]
 Strain rate invariant for the numerical shortening models after 14 cm
 of shortening. The resolutions of the various models are:
 I2ELVIS: 900 x 75,
 LAPEX2D: 351 x 71,
 Microfem: 201 x 36,
 Sopale: 401 x 71,
 Gale: 512 x 128.
 The upper portion of the figure is reproduced, with permission, from
 Buiter et al. [Buiter et al Numerical Sandbox].
+.. figure:: images/Shortening_comparison.png
+ Figure [fig:shorteningcompare]
+ Strain rate invariant for the numerical shortening models after 14 cm
+ of shortening. The resolutions of the various models are:
+ I2ELVIS: 900 x 75,
+ LAPEX2D: 351 x 71,
+ Microfem: 201 x 36,
+ Sopale: 401 x 71,
+ Gale: 512 x 128.
+ The upper portion of the figure is reproduced, with permission, from
+ Buiter et al. [Buiter et al Numerical Sandbox].
 image:: images/shortening_sensitivity.pdf
 Figure [fig:shorteningconvergence]
 Strain rate invariant for the shortening model after 14 cm of
 shortening for three different resolutions: (a) 128 x 32,
 (b) 256 x 64, (c) 512 x 128.

+.. figure:: images/shortening_sensitivity.pdf
+ Figure [fig:shorteningconvergence]
+ Strain rate invariant for the shortening model after 14 cm of
+ shortening for three different resolutions: (a) 128 x 32,
+ (b) 256 x 64, (c) 512 x 128.
+
Modified: doc/geodynamics.org/benchmarks/trunk/long/geomod2008.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/long/geomod2008.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/geomod2008.rst 20090918 20:02:16 UTC (rev 15676)
@@ 3,185 +3,186 @@
Geomod 2008
===========
 Using the lessons learned from the Geomod 2004 benchmarks, new
 benchmarks were created that would make it easier to compare numerical
 experiments with each other and with analog experiments [Geomod 2008].
+Using the lessons learned from the Geomod 2004 benchmarks, new
+benchmarks were created that would make it easier to compare numerical
+experiments with each other and with analog experiments [Geomod 2008].
+
Stable Wedge
============
 This benchmark simulates a wall pushing a wedge as in Figure
 [fig:Wedge_setup]. There is an analytic solution [Dahlen Wedge] which
 details what the friction on the bottom and sides should be to provide
 enough resistance so that the wedge does not collapse under its own
 weight, but not so much as to cause any internal deformation as it
 slides. The derivation of the solution assumes that the friction along
 the sides has no cohesion. So the force at the tip will go to zero as the
 thickness of the material goes to zero. However, analog experiments
 suggest a finite cohesion, so this benchmark specifies a boundary
 cohesion.
+This benchmark simulates a wall pushing a wedge as in Figure
+[fig:Wedge_setup]. There is an analytic solution [Dahlen Wedge] which
+details what the friction on the bottom and sides should be to provide
+enough resistance so that the wedge does not collapse under its own
+weight, but not so much as to cause any internal deformation as it
+slides. The derivation of the solution assumes that the friction along
+the sides has no cohesion. So the force at the tip will go to zero as the
+thickness of the material goes to zero. However, analog experiments
+suggest a finite cohesion, so this benchmark specifies a boundary
+cohesion.
 We modeled the wedge using a relatively low viscosity ($1\ Pa \cdot s$)
 air layer on top. This low viscosity region does not, for the most part,
 affect the dynamics.
+We modeled the wedge using a relatively low viscosity ($1\ Pa \cdot s$)
+air layer on top. This low viscosity region does not, for the most part,
+affect the dynamics.
 We modeled boundary friction by first fixing the sand to the boundary. We
 then modify the material properties in the element next to the boundary
 so that it provides the correct resistance. So in the bulk, the sand's
 internal angle of friction is $36^{\deg}$ weakening to $31^{\deg}$, while
 in the element at the boundary the internal angle of friction is
 $16^{\deg}$ weakening to $14^{\deg}$. Similarly, in the bulk, the
 cohesion is $10\ Pa$, while at the boundary the cohesion is $10\ Pa$
 weakening to $0.01\ Pa$. If we do not weaken the cohesion, when we try to
 model an unstable wedge by reducing the internal angle of friction, the
 wedge never collapses on itself.
+We modeled boundary friction by first fixing the sand to the boundary. We
+then modify the material properties in the element next to the boundary
+so that it provides the correct resistance. So in the bulk, the sand's
+internal angle of friction is $36^{\deg}$ weakening to $31^{\deg}$, while
+in the element at the boundary the internal angle of friction is
+$16^{\deg}$ weakening to $14^{\deg}$. Similarly, in the bulk, the
+cohesion is $10\ Pa$, while at the boundary the cohesion is $10\ Pa$
+weakening to $0.01\ Pa$. If we do not weaken the cohesion, when we try to
+model an unstable wedge by reducing the internal angle of friction, the
+wedge never collapses on itself.
 Figure [fig:Stable_sri] shows the strain rate invariant after the wall
 has moved 4 cm, and Figure [fig:Stable_particles] shows the particles.
 The bulk translates with almost no deformation, although, as expected,
 the tip deforms. The odd structures at the tip are below the grid
 resolution. Figure [fig:Stable_unstable] shows a simulation when we
 reduce the boundary friction to $1^{\deg}$. The wedge quickly becomes
 unstable and collapses.
+Figure [fig:Stable_sri] shows the strain rate invariant after the wall
+has moved 4 cm, and Figure [fig:Stable_particles] shows the particles.
+The bulk translates with almost no deformation, although, as expected,
+the tip deforms. The odd structures at the tip are below the grid
+resolution. Figure [fig:Stable_unstable] shows a simulation when we
+reduce the boundary friction to $1^{\deg}$. The wedge quickly becomes
+unstable and collapses.
 image:: images/Geomod2008_wedge_setup.eps
 Figure [fig:Wedge_setup]
 Setup for the stable wedge benchmark. Image courtesy of Susanne Buiter.
+.. figure:: images/Geomod2008_wedge_setup.eps
+ Figure [fig:Wedge_setup]
+ Setup for the stable wedge benchmark. Image courtesy of Susanne Buiter.
 image:: images/Stable_wedge_sri.png
 Figure [fig:Stable_sri]
 Strain rate invariant for the stable wedge benchmark within the wedge.
 Outside the wedge, the strain rates are large because of the air's low
 viscosity. The resolution is 512.128, and the wedge has translated
 4 cm.
+.. figure:: images/Stable_wedge_sri.png
+ Figure [fig:Stable_sri]
+ Strain rate invariant for the stable wedge benchmark within the wedge.
+ Outside the wedge, the strain rates are large because of the air's low
+ viscosity. The resolution is 512.128, and the wedge has translated
+ 4 cm.
 image:: images/Stable_wedge_particles.png
 Figure [fig:Stable_particles]
 Material particles for the stable wedge benchmark. The deformation at
 the tip is caused by a finite boundary cohesion, although the actual
 structure is not resolved. The resolution is 512x128, and the wedge has
 translated 4 cm.
+.. figure:: images/Stable_wedge_particles.png
+ Figure [fig:Stable_particles]
+ Material particles for the stable wedge benchmark. The deformation at
+ the tip is caused by a finite boundary cohesion, although the actual
+ structure is not resolved. The resolution is 512x128, and the wedge has
+ translated 4 cm.
 image:: images/Stable_wedge_unstable.png
 Figure [fig:Stable_unstable]
 Strain rate invariant and velocity arrows for the stable wedge
 benchmark, but with the friction angle reduced to $1^{\deg}$. Note that
 the strain rates are much higher than in Figure [fig:Stable_sri]. The
 wedge collapses almost immediately. The resolution is 512x128, and the
 wedge has translated 0.17 cm.
+.. figure:: images/Stable_wedge_unstable.png
+ Figure [fig:Stable_unstable]
+ Strain rate invariant and velocity arrows for the stable wedge
+ benchmark, but with the friction angle reduced to $1^{\deg}$. Note that
+ the strain rates are much higher than in Figure [fig:Stable_sri]. The
+ wedge collapses almost immediately. The resolution is 512x128, and the
+ wedge has translated 0.17 cm.
Unstable Shortening
===================
 This benchmark simulates a wall pushing against a wall of sand as in
 Figure [fig:Unstablesetup]. There are three layers of sand, with the
 middle layer being a little heavier and sticking a little more to the
 boundary. Otherwise it is identical. Figures
 [fig:unstable_sri_128],
 [fig:unstable_sri_256],
 [fig:unstable_sri_512],
 [fig:unstable_particles_128],
 [fig:unstable_particles_256], and
 [fig:unstable_particles_512] show results at different times and
 different resolutions.
+This benchmark simulates a wall pushing against a wall of sand as in
+Figure [fig:Unstablesetup]. There are three layers of sand, with the
+middle layer being a little heavier and sticking a little more to the
+boundary. Otherwise it is identical. Figures
+[fig:unstable_sri_128],
+[fig:unstable_sri_256],
+[fig:unstable_sri_512],
+[fig:unstable_particles_128],
+[fig:unstable_particles_256], and
+[fig:unstable_particles_512] show results at different times and
+different resolutions.
 image:: images/Geomod2008_unstable_setup.eps
 Figure [fig:Unstablesetup]
 Setup for the unstable shortening benchmark.
 Image courtesy of Susanne Buiter.
+.. figure:: images/Geomod2008_unstable_setup.eps
+ Figure [fig:Unstablesetup]
+ Setup for the unstable shortening benchmark.
+ Image courtesy of Susanne Buiter.
 image:: images/Geomod2008_unstable_sri128x32.png
 Figure [fig:unstable_sri_128]
 Strain rate invariant for the unstable shortening benchmark with a
 resolution of 128x32. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_unstable_sri128x32.png
+ Figure [fig:unstable_sri_128]
+ Strain rate invariant for the unstable shortening benchmark with a
+ resolution of 128x32. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
 image:: images/Geomod2008_unstable_sri256x64.png
 Figure [fig:unstable_sri_256]
 Strain rate invariant for the unstable shortening benchmark with a
 resolution of 256x64. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_unstable_sri256x64.png
+ Figure [fig:unstable_sri_256]
+ Strain rate invariant for the unstable shortening benchmark with a
+ resolution of 256x64. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
 image:: images/Geomod2008_unstable_sri512x128.png
 Figure [fig:unstable_sri_512]
 Strain rate invariant for the unstable shortening benchmark with a
 resolution of 512x128. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_unstable_sri512x128.png
+ Figure [fig:unstable_sri_512]
+ Strain rate invariant for the unstable shortening benchmark with a
+ resolution of 512x128. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
 image:: images/Geomod2008_unstable_particles128x32.png
 Figure [fig:unstable_particles_128]
 Material particles for the unstable shortening benchmark with a
 resolution of 128x32. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_unstable_particles128x32.png
+ Figure [fig:unstable_particles_128]
+ Material particles for the unstable shortening benchmark with a
+ resolution of 128x32. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
 image:: images/Geomod2008_unstable_particles256x64.png
 Figure [fig:unstable_particles_256]
 Material particles for the unstable shortening benchmark with a
 resolution of 256x64. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_unstable_particles256x64.png
+ Figure [fig:unstable_particles_256]
+ Material particles for the unstable shortening benchmark with a
+ resolution of 256x64. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
 image:: images/Geomod2008_unstable_particles512x128.png
 Figure [fig:unstable_particles_512]
 Material particles for the unstable shortening benchmark with a
 resolution of 512x128. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_unstable_particles512x128.png
+ Figure [fig:unstable_particles_512]
+ Material particles for the unstable shortening benchmark with a
+ resolution of 512x128. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
Brittle Shortening
==================
 This benchmark is very similar to unstable shortening. The only
 difference is that part of the bottom is also moving along as shown in
 Figure [fig:Brittle_setup]. This causes the deformation to start from
 inside the sand box, rather than along the walls. F
 Figures
 [fig:brittle_sri_128],
 [fig:brittle_sri_256],
 [fig:brittle_sri_512],
 [fig:brittle_particles_128],
 [fig:brittle_particles_256], and
 [fig:brittle_particles_512] show results at different times and
 different resolutions.
+This benchmark is very similar to unstable shortening. The only
+difference is that part of the bottom is also moving along as shown in
+Figure [fig:Brittle_setup]. This causes the deformation to start from
+inside the sand box, rather than along the walls. F
+Figures
+[fig:brittle_sri_128],
+[fig:brittle_sri_256],
+[fig:brittle_sri_512],
+[fig:brittle_particles_128],
+[fig:brittle_particles_256], and
+[fig:brittle_particles_512] show results at different times and
+different resolutions.
 image:: images/Geomod2008_brittle_setup.eps
 Figure [fig:Brittle_setup]
 Setup for the brittle shortening benchmark.
 Image courtesy of Susanne Buiter.
+.. figure:: images/Geomod2008_brittle_setup.eps
+ Figure [fig:Brittle_setup]
+ Setup for the brittle shortening benchmark.
+ Image courtesy of Susanne Buiter.
 image:: images/Geomod2008_brittle_sri128x32.png
 Figure [fig:brittle_sri_128]
 Strain rate invariant for the brittle shortening benchmark with a
 resolution of 128x32. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_brittle_sri128x32.png
+ Figure [fig:brittle_sri_128]
+ Strain rate invariant for the brittle shortening benchmark with a
+ resolution of 128x32. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
 image:: images/Geomod2008_brittle_sri256x64.png
 Figure [fig:brittle_sri_256]
 Strain rate invariant for the brittle shortening benchmark with a
 resolution of 256x64. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_brittle_sri256x64.png
+ Figure [fig:brittle_sri_256]
+ Strain rate invariant for the brittle shortening benchmark with a
+ resolution of 256x64. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
 image:: images/Geomod2008_brittle_sri512x128.png
 Figure [fig:brittle_sri_512]
 Strain rate invariant for the brittle shortening benchmark with a
 resolution of 512x128. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_brittle_sri512x128.png
+ Figure [fig:brittle_sri_512]
+ Strain rate invariant for the brittle shortening benchmark with a
+ resolution of 512x128. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
 image:: images/Geomod2008_brittle_particles128x32.png
 Figure [fig:brittle_particles_128]
 Material particles for the brittle shortening benchmark with a
 resolution of 128x32. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_brittle_particles128x32.png
+ Figure [fig:brittle_particles_128]
+ Material particles for the brittle shortening benchmark with a
+ resolution of 128x32. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
 image:: images/Geomod2008_brittle_particles256x64.png
 Figure [fig:brittle_particles_256]
 Material particles for the brittle shortening benchmark with a
 resolution of 256x64. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.
+.. figure:: images/Geomod2008_brittle_particles256x64.png
+ Figure [fig:brittle_particles_256]
+ Material particles for the brittle shortening benchmark with a
+ resolution of 256x64. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
 image:: images/Geomod2008_brittle_particles512x128.png
 Figure [fig:brittle_particles_512]
 Material particles for the brittle shortening benchmark with a
 resolution of 512x128. The snapshots are taken at 0, 2.5, 5, 7.5, and
 10 cm of shortening.

+.. figure:: images/Geomod2008_brittle_particles512x128.png
+ Figure [fig:brittle_particles_512]
+ Material particles for the brittle shortening benchmark with a
+ resolution of 512x128. The snapshots are taken at 0, 2.5, 5, 7.5, and
+ 10 cm of shortening.
+
Modified: doc/geodynamics.org/benchmarks/trunk/long/index.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/long/index.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 3,36 +3,26 @@
==========
* Falling Sphere

* Circular Inclusion

* Relaxation of Topography

* Divergence

* DruckerPrager

* Geomod 2004

* Extension

* Shortening

* Geomod 2008

* Stable Wedge

* Unstable Shortening

* Brittle Shortening

Links
+
* "Four Gale Tutorials":http://geodynamics.org/cig/software/packages/long/gale/tutorials
+* `Four Gale Tutorials`__
+* `Original Work Area (currently empty)`__
* "Original Work Area (currently empty)":http://geodynamics.org/cig/workinggroups/long/workarea
+__ http://geodynamics.org/cig/software/packages/long/gale/tutorials
+__ http://geodynamics.org/cig/workinggroups/long/workarea

Modified: doc/geodynamics.org/benchmarks/trunk/long/relaxationtopography.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/long/relaxationtopography.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/relaxationtopography.rst 20090918 20:02:16 UTC (rev 15676)
@@ 2,43 +2,43 @@
Relaxation of Topography
========================
 Given an infinitely deep purely viscous medium with an infinitesimal
 sinusoidal height profile, the topography will decay exponentially
 with the timescale [Folds] $$t_r = \frac{4\pi\eta}{gL},$$ where
 $\eta$ is the viscosity, $g$ is the gravitational constant, and $L$ is
 the wavelength of the initial sinusoid.
+Given an infinitely deep purely viscous medium with an infinitesimal
+sinusoidal height profile, the topography will decay exponentially
+with the timescale [Folds] $$t_r = \frac{4\pi\eta}{gL},$$ where
+$\eta$ is the viscosity, $g$ is the gravitational constant, and $L$ is
+the wavelength of the initial sinusoid.
 In our case, we simulate a medium with finite depth and finite height.
 The internal fields decay exponentially with depth with a length scale of
 $L/{2\pi}$. The error in the solution due to a finite height is of order
 $(2\pi{A}/L)^2$, where $A$ is the amplitude of the sinusoid. We use $L=1$
 and $A=0.01$, giving errors of order $0.02\%$ and $0.4\%$.
+In our case, we simulate a medium with finite depth and finite height.
+The internal fields decay exponentially with depth with a length scale of
+$L/{2\pi}$. The error in the solution due to a finite height is of order
+$(2\pi{A}/L)^2$, where $A$ is the amplitude of the sinusoid. We use $L=1$
+and $A=0.01$, giving errors of order $0.02\%$ and $0.4\%$.
 The file `input/benchmarks/sinusoid/README` explains how to run this
 benchmark. Figure [fig:Straintopo] shows the results of a lowresolution
 run. Even this run is not particularly small ($128 \times 256$), because
 we need fairly high resolution to be able to accurately resolve the small
 ($1\%$) height difference. Also note that we use symmetry to only
 simulate half of the wavelength.
+The file `input/benchmarks/sinusoid/README` explains how to run this
+benchmark. Figure [fig:Straintopo] shows the results of a lowresolution
+run. Even this run is not particularly small ($128 \times 256$), because
+we need fairly high resolution to be able to accurately resolve the small
+($1\%$) height difference. Also note that we use symmetry to only
+simulate half of the wavelength.
 image:: images/Paraview_topography.png
 Figure [Straintopo]
 Strain rate and velocities for a sinusoidal topography relaxing under
 gravity.
+.. figure:: images/Paraview_topography.png
+ Figure [Straintopo]
+ Strain rate and velocities for a sinusoidal topography relaxing under
+ gravity.
 Running the code with multiple resolutions and measuring the error in the
 height in the trough gives Figure [fig:topoerror]. Scaling the error
 with resolution gives Figure [fig:scaledtopoerror]. The error decreases
 linearly with increasing resolution, giving us confidence in our ability
 to accurately track topography.
+Running the code with multiple resolutions and measuring the error in the
+height in the trough gives Figure [fig:topoerror]. Scaling the error
+with resolution gives Figure [fig:scaledtopoerror]. The error decreases
+linearly with increasing resolution, giving us confidence in our ability
+to accurately track topography.
 image:: images/topo_error.eps
 Figure [fig:topoerror]
 Error in the height at the trough
+.. figure:: images/topo_error.eps
+ Figure [fig:topoerror]
+ Error in the height at the trough
 image:: images/topo_scaled_error.eps
 Figure [fig:scaledtopoerror]
 As in Figure [fig:topoerror], but with the error scaled with $h$.
 So the mediumresolution error is multiplied by 2 and the
 highresolution error is multiplied by 4.

+.. figure:: images/topo_scaled_error.eps
+ Figure [fig:scaledtopoerror]
+ As in Figure [fig:topoerror], but with the error scaled with $h$.
+ So the mediumresolution error is multiplied by 2 and the
+ highresolution error is multiplied by 4.
+
Copied: doc/geodynamics.org/benchmarks/trunk/magma/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/magma/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,171 @@
+Benchmarks
+==========
+
+* An Introduction and Tutorial to the "McKenzie Equations" for Magma Migration
+ [last modified 20070115] > mckenzieequations.rst
+
+ A new formulation for the equations of magma migration in viscous materials
+ as originally derived by McKenzie is presented, as well as a set of
+ wellunderstood special case problems that form a useful benchmarksuite
+ for developing and testing new codes.
+
+
+* Running stgMADDs Benchmarks
+ [last modified 20090402] > runningstgmadds.rst
+
+ The Magma Development team has finished the alpha release of the
+ Magma Dynamics Demonstration Suite (MADDs). The initial code implements
+ the zero porosity / no melting magma benchmark for midocean ridge
+ solid flows in 2D and 3D built on the Underworld framework. The purpose
+ of this code is principally to validate accurate pressure solvers for
+ Stokes flow in current CIG supported software. The stgMADDs source
+ code is available in CIG's Mercurial Repository (geodynamics.org/hg).
+
+
+
+* Milestone1 Results and Analysis
+ [last modified 20080208] > milestone1.rst
+
+ Details how to run the first milestone of the MADDs project in 2D and 3D
+ and provides some results of those simulations. It also gives the rates
+ of convergence of the pressure gradient solutions as the resolution
+ is increased.
+
+ 2D Ridge Model
+ Velocity, pressure, and pressure gradients solutions and L2 errors
+ for a 2D ridge model with 120 x 60 elements.
+
+ 3D Ridge Model
+ Velocity, pressure, and pressure gradients solutions and L2 error fields
+ for 3D ridge model.
+
+ Global Pressure Gradient Errors for 2D Ridge Model
+ Normalized global L2 errors.
+
+ Global Pressure Gradient Errors for 3D Ridge Model
+ Global normalized L2 pressure gradient errors at varying resolutions.
+
+
+
+* Milestone2 Results and Analysis
+ [last modified 20080208] > milestone2.rst
+
+ Details the results of the Milestone2 simulations and analyzes the accuracy
+ of the advection scheme.
+
+ Gaussian Porosity Field Advection
+ Advection of Gaussian porosity field as a Stokes equation force term.
+ The lower density porosity region rises due to gravity.
+
+ Ridge Model with Gaussian Porosity Field
+ Stokes flow with 2D ridge model boundary conditions and Gaussian
+ porosity initial distribution, driven by a porosity dependent
+ force term.
+
+ Semi Lagrangian Advection Scheme Test  Step Function
+ Diagonal step function initial distribution subjected to a
+ shearing velocity field.
+
+ Semi Lagrangian Advection Scheme Test  Gaussian Distribution
+ Gaussian initial distribution subjected to a shearing velocity field.
+
+ Error Convergence for Advection Scheme  Step Function IC
+ Normalized global L2 errors for semi Lagrangian advection scheme
+ with a diagonal step function initial condition as a function
+ of resolution.
+
+ Error Convergence for Advection Scheme  Gaussian IC
+ Normalized global L2 errors for semi Lagrangian advection scheme
+ with Gaussian initial distribution as a function of resolution.
+
+
+
+* Milestone3 Results
+ [last modified 20080208] > milestone3.rst
+
+ Details the results for the third milestone, in which the melt velocity
+ was determined given the existing solid velocity and pressure fields.
+
+ Melt Model  2D Ridge with Constant Porosity
+ Solid and melt velocity, pressure, and pressure gradient fields
+ for 2D ridge model with constant porosity. Melt velocity magnitudes
+ are significantly larger near the point of discontinuity due to
+ their proportionality to the pressure gradients, which are largest
+ at these points.
+
+ Melt Model  Gaussian Porosity Driven Flow
+ Solid and melt velocity, pressure, and pressure gradient fields
+ for Stokes flow driven by a Gaussian initial porosity distribution.
+
+
+
+* Milestone4 Results and Analysis
+ [last modified 20080928] > milestone4.rst
+
+ Discussion of the system being modeled, and details of how to run the
+ model with different initial conditions in 2D and 3D.
+
+ 2D Solitary Wave
+ A 2D solitary wave with a wave speed of 7 rising through a solid
+ with a constant speed of 2. The wave shows no visible diffusive
+ behavior.
+
+ Noisy 1D Solitary Wave Initial Condition
+ Initial condition of a vertically changing 1D solitary wave with
+ a certain amount of introduced noise, which allows 2D solitary
+ waves to emerge over time.
+
+ Emerging 2D Solitary Waves
+ Solitary waves emerging from a noisy 1D solitary wave initial condition.
+
+ Emergent 2D Solitary Waves
+ Solitary waves having emerged from a noisy 1D solitary wave initial distribution.
+
+
+
+* Milestone5 Results and Analysis
+ [last modified 20090326] > milestone5.rst
+
+ Results and analysis for the isoviscous McKenzie equations (with melting)
+ driven by a corner flow velocity BC.
+
+ Isoviscous McKenzie System with Corner Flow BC  1
+ After 1 time step
+
+ Isoviscous McKenzie System with Corner Flow BC  50
+ After 50 time steps
+
+ Isoviscous McKenzie System with Corner Flow BC  3200
+ After 3200 time steps
+
+ Velocity  x component
+ xcomponent of the velocity field for the 3D isoviscous McKenzie model
+ with ridge BCs at time step 150.
+
+ Velocity  y component
+ ycomponent of the velocity field for the 3D isoviscous McKenzie model
+ with ridge BCs at time step 150.
+
+ Porosity
+ Porosity field for the 3D isoviscous McKenzie model with ridge BCs
+ at time step 150.
+
+ Compaction pressure
+ Compaction pressure due to compressibility of the solid phase for the
+ 3D isoviscous McKenzie model with ridge BCs at time step 150.
+
+ Melt fraction
+ Melt fraction field representing the melt to solid phase of the
+ 3D isoviscous McKenzie model with ridge BCs at time step 150.
+
+ Melt velocity  x component
+ xcomponent of the melt velocity field for the 3D isoviscous McKenzie model
+ with ridge BCs at time step 150.
+
+ Melt velocity  y component
+ ycomponent of the melt velocity field for the 3D isoviscous McKenzie model
+ with ridge BCs at time step 150.
+
+
+
+URL http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/
Deleted: doc/geodynamics.org/benchmarks/trunk/magma/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,171 +0,0 @@
Benchmarks

* An Introduction and Tutorial to the "McKenzie Equations" for Magma Migration
 [last modified 20070115] > mckenzieequations.txt

 A new formulation for the equations of magma migration in viscous materials
 as originally derived by McKenzie is presented, as well as a set of
 wellunderstood special case problems that form a useful benchmarksuite
 for developing and testing new codes.


* Running stgMADDs Benchmarks
 [last modified 20090402] > runningstgmadds.txt

 The Magma Development team has finished the alpha release of the
 Magma Dynamics Demonstration Suite (MADDs). The initial code implements
 the zero porosity / no melting magma benchmark for midocean ridge
 solid flows in 2D and 3D built on the Underworld framework. The purpose
 of this code is principally to validate accurate pressure solvers for
 Stokes flow in current CIG supported software. The stgMADDs source
 code is available in CIG's Mercurial Repository (geodynamics.org/hg).



* Milestone1 Results and Analysis
 [last modified 20080208] > milestone1.txt

 Details how to run the first milestone of the MADDs project in 2D and 3D
 and provides some results of those simulations. It also gives the rates
 of convergence of the pressure gradient solutions as the resolution
 is increased.

 2D Ridge Model
 Velocity, pressure, and pressure gradients solutions and L2 errors
 for a 2D ridge model with 120 x 60 elements.

 3D Ridge Model
 Velocity, pressure, and pressure gradients solutions and L2 error fields
 for 3D ridge model.

 Global Pressure Gradient Errors for 2D Ridge Model
 Normalized global L2 errors.

 Global Pressure Gradient Errors for 3D Ridge Model
 Global normalized L2 pressure gradient errors at varying resolutions.



* Milestone2 Results and Analysis
 [last modified 20080208] > milestone2.txt

 Details the results of the Milestone2 simulations and analyzes the accuracy
 of the advection scheme.

 Gaussian Porosity Field Advection
 Advection of Gaussian porosity field as a Stokes equation force term.
 The lower density porosity region rises due to gravity.

 Ridge Model with Gaussian Porosity Field
 Stokes flow with 2D ridge model boundary conditions and Gaussian
 porosity initial distribution, driven by a porosity dependent
 force term.

 Semi Lagrangian Advection Scheme Test  Step Function
 Diagonal step function initial distribution subjected to a
 shearing velocity field.

 Semi Lagrangian Advection Scheme Test  Gaussian Distribution
 Gaussian initial distribution subjected to a shearing velocity field.

 Error Convergence for Advection Scheme  Step Function IC
 Normalized global L2 errors for semi Lagrangian advection scheme
 with a diagonal step function initial condition as a function
 of resolution.

 Error Convergence for Advection Scheme  Gaussian IC
 Normalized global L2 errors for semi Lagrangian advection scheme
 with Gaussian initial distribution as a function of resolution.



* Milestone3 Results
 [last modified 20080208] > milestone3.txt

 Details the results for the third milestone, in which the melt velocity
 was determined given the existing solid velocity and pressure fields.

 Melt Model  2D Ridge with Constant Porosity
 Solid and melt velocity, pressure, and pressure gradient fields
 for 2D ridge model with constant porosity. Melt velocity magnitudes
 are significantly larger near the point of discontinuity due to
 their proportionality to the pressure gradients, which are largest
 at these points.

 Melt Model  Gaussian Porosity Driven Flow
 Solid and melt velocity, pressure, and pressure gradient fields
 for Stokes flow driven by a Gaussian initial porosity distribution.



* Milestone4 Results and Analysis
 [last modified 20080928] > milestone4.txt

 Discussion of the system being modeled, and details of how to run the
 model with different initial conditions in 2D and 3D.

 2D Solitary Wave
 A 2D solitary wave with a wave speed of 7 rising through a solid
 with a constant speed of 2. The wave shows no visible diffusive
 behavior.

 Noisy 1D Solitary Wave Initial Condition
 Initial condition of a vertically changing 1D solitary wave with
 a certain amount of introduced noise, which allows 2D solitary
 waves to emerge over time.

 Emerging 2D Solitary Waves
 Solitary waves emerging from a noisy 1D solitary wave initial condition.

 Emergent 2D Solitary Waves
 Solitary waves having emerged from a noisy 1D solitary wave initial distribution.



* Milestone5 Results and Analysis
 [last modified 20090326] > milestone5.txt

 Results and analysis for the isoviscous McKenzie equations (with melting)
 driven by a corner flow velocity BC.

 Isoviscous McKenzie System with Corner Flow BC  1
 After 1 time step

 Isoviscous McKenzie System with Corner Flow BC  50
 After 50 time steps

 Isoviscous McKenzie System with Corner Flow BC  3200
 After 3200 time steps

 Velocity  x component
 xcomponent of the velocity field for the 3D isoviscous McKenzie model
 with ridge BCs at time step 150.

 Velocity  y component
 ycomponent of the velocity field for the 3D isoviscous McKenzie model
 with ridge BCs at time step 150.

 Porosity
 Porosity field for the 3D isoviscous McKenzie model with ridge BCs
 at time step 150.

 Compaction pressure
 Compaction pressure due to compressibility of the solid phase for the
 3D isoviscous McKenzie model with ridge BCs at time step 150.

 Melt fraction
 Melt fraction field representing the melt to solid phase of the
 3D isoviscous McKenzie model with ridge BCs at time step 150.

 Melt velocity  x component
 xcomponent of the melt velocity field for the 3D isoviscous McKenzie model
 with ridge BCs at time step 150.

 Melt velocity  y component
 ycomponent of the melt velocity field for the 3D isoviscous McKenzie model
 with ridge BCs at time step 150.



URL
 http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/
Copied: doc/geodynamics.org/benchmarks/trunk/magma/mckenzieequations.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/magma/mckenzieequations.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/mckenzieequations.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/mckenzieequations.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,10 @@
+
+An Introduction and Tutorial to the "McKenzie Equations" for Magma Migration
+ [last modified 20070115]
+
+ A new formulation for the equations of magma migration in viscous materials
+ as originally derived by McKenzie is presented, as well as a set of wellunderstood
+ special case problems that form a useful benchmarksuite for developing and
+ testing new codes.
+
+URL http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/McKenzieIntroBenchmarks.pdf/view
Deleted: doc/geodynamics.org/benchmarks/trunk/magma/mckenzieequations.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/mckenzieequations.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/mckenzieequations.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,11 +0,0 @@

An Introduction and Tutorial to the "McKenzie Equations" for Magma Migration
 [last modified 20070115]

 A new formulation for the equations of magma migration in viscous materials
 as originally derived by McKenzie is presented, as well as a set of wellunderstood
 special case problems that form a useful benchmarksuite for developing and
 testing new codes.

URL
 http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/McKenzieIntroBenchmarks.pdf/view
Added: doc/geodynamics.org/benchmarks/trunk/magma/milestone1.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/milestone1.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone1.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,62 @@
+.. Plone Metadata
+..
+.. milestone1results
+..
+.. Milestone 1 Results and Analysis
+..
+.. Details how to run the first milestone of the MADDs project in 2D and 3D
+.. and provides some results of these simulations. It also gives the rates
+.. of convergence of the pressure gradient solutions as the resolution is
+.. increased.
+
+Running the code
+================
+
+In order to run the simulations for milestone 1 of the MADDs project
+(in 2D), first::
+
+ cd Magma/Models/Milestone1/Ridge2D_Quadratic
+
+Then make a symbolic link to the executable binary (assuming the code
+has been successfully built)::
+
+ ln s ../../../../build/bin/StGermain .
+
+The simulation may then be run (in parallel), passing the respective XML
+file as input::
+
+ mpiexec np <#ofprocs> ./StGermain Ridge2D.xml
+
+Alternatively, the 3D simulation may be run as::
+
+ cd Magma/Models/Milestone1/Ridge3D_Quadratic
+ ln s ../../../../build/bin/StGermain .
+ mpiexec np <#ofprocs> ./StGermain Ridge3D.xml
+
+
+Simulation results and error convergence
+========================================
+
+These simulations will produce graphical output of the velocity,
+pressure, and pressure gradient solutions, as well as the analytic
+reference solutions and the elementwise normalized L2 error fields for
+the pressure and pressure gradients, as shown below. It will also
+generate text files to the output directory giving the nodewise results
+for the respective fields.
+
+As the resolution is increased, the normalized global L2 errors are
+observed to decrease. This decrease is approximately linear for the 2D
+ridge mode and slightly poorer for the 3D model. Graphs detailing the
+global errors as a function of resolution are given below.
+
+
+Related Item(s)
+
+ 2D Ridge Model
+ 3D Ridge Model
+ Global Pressure Gradient Errors for 2D Ridge Model
+ Global Pressure Gradient Errors for 3D Ridge Model
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/milestone1results/
Deleted: doc/geodynamics.org/benchmarks/trunk/magma/milestone1.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/milestone1.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone1.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,60 +0,0 @@
Plone Metadata

 milestone1results

 Milestone 1 Results and Analysis

 Details how to run the first milestone of the MADDs project in 2D and 3D
 and provides some results of these simulations. It also gives the rates
 of convergence of the pressure gradient solutions as the resolution is
 increased.

Running the code

 In order to run the simulations for milestone 1 of the MADDs project
 (in 2D), first::

 cd Magma/Models/Milestone1/Ridge2D_Quadratic

 Then make a symbolic link to the executable binary (assuming the code
 has been successfully built)::

 ln s ../../../../build/bin/StGermain .

 The simulation may then be run (in parallel), passing the respective XML
 file as input::

 mpiexec np <#ofprocs> ./StGermain Ridge2D.xml

 Alternatively, the 3D simulation may be run as::

 cd Magma/Models/Milestone1/Ridge3D_Quadratic
 ln s ../../../../build/bin/StGermain .
 mpiexec np <#ofprocs> ./StGermain Ridge3D.xml


Simulation results and error convergence

 These simulations will produce graphical output of the velocity,
 pressure, and pressure gradient solutions, as well as the analytic
 reference solutions and the elementwise normalized L2 error fields for
 the pressure and pressure gradients, as shown below. It will also
 generate text files to the output directory giving the nodewise results
 for the respective fields.

 As the resolution is increased, the normalized global L2 errors are
 observed to decrease. This decrease is approximately linear for the 2D
 ridge mode and slightly poorer for the 3D model. Graphs detailing the
 global errors as a function of resolution are given below.


Related Item(s)

 2D Ridge Model
 3D Ridge Model
 Global Pressure Gradient Errors for 2D Ridge Model
 Global Pressure Gradient Errors for 3D Ridge Model


URL
 http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/milestone1results/
Added: doc/geodynamics.org/benchmarks/trunk/magma/milestone2.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/milestone2.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone2.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,92 @@
+.. Plone Metadata
+..
+.. milestone2results
+..
+.. Milestone 2 Results and Analysis
+..
+.. Details the results of the Milestone 2 simulations and analyzes the
+.. accuracy of the advection scheme.
+
+Model Descriptions
+==================
+
+The second milestone contains several different models. In each a
+porosity distribution has been supplied, which acts as a force term on
+the stokes equation. The porosity is advected according to a semi
+Lagrangian scheme, with no natural diffusion. Details of these models are
+given below.
+
+Simple Gaussian porosity field
+
+
+The first model is a simple demonstration of how the porosity dependent
+force term drives the porosity distribution up through the domain. The
+domain is subjected to free slip boundary conditions, which also distort
+the porosity distribution as it is advected. This model is housed in
+the directory::
+
+ Magma/Models/Milestone2/ZPNM_SemiLagrangianPorosity/
+
+with the XML file to be passed at run time being the 'Porridge.xml' file.
+
+
+Ridge model with Gaussian porosity distribution
+
+
+The second model is an extension of the first milestone, that is a ridge
+model with the intial boundary conditions loaded from a reference
+solution. However in this case a Gaussian porosity distribution has been
+added. The porosity distribution is distorted as it moves up through the
+domain in accordance with the velocity field generated from the boundary
+conditions. This model can be found in::
+
+ Magma/Models/Milestone2/RidgeModelWithGaussianPorosity/
+
+with the XML file to be passed being 'Ridge2D.xml'
+
+
+Validation of the advection scheme
+
+
+As well as the models, a test is also supplied for validating the
+accuracy of the semi Lagrangian advection scheme. This involves an
+initial porosity distribution (either Gaussian or diagonal line step
+function, as determined from the XML), which is subjected to a static
+shearing velocity field. The porosity distribution is subjected to the
+velocity field for a finite number of time steps (as determined from the
+XML input file), before the velocity field is reversed and the
+distribution advected back for the same number of time steps. The
+normalized global L2 error between the initial and final distributions is
+then calculated. This test is housed in the directory::
+
+ Magma/Models/Milestone2/tests/
+
+and may be run using the input file 'testSemiLagrangianAdvection.xml'.
+
+Running this simulation at varying resolutions, the convergence of the
+errors for the advection scheme were determined using both the Gaussian
+distribution and diagonal step function as initial conditions. The errors
+were recorded for schemes which used a cubid method as well as a
+quadratic method based on the element shape functions for interpolating
+the value at the end point of the characteristic. As can be observed from
+the convergence error plots below, the quadratic and cubic interpolation
+method schemes converged at comparable (less than linear) rates using the
+step function initial condition, with an improvement in those results
+obtained using the cubic interpolation method. When the Gaussian initial
+distribution was applied (which was easier to solve accurately on account
+of the smoother gradients involved), both interpolation methods converged
+at a rate much better than linear, with the cubic interpolation method
+proving far superior to the quadratic method.
+
+Related Item(s)
+
+ Gaussian Porosity Field Advection
+ Ridge Model With Gaussian Porosity Field
+ Semi Lagrangian Advection Scheme Test  Step Function
+ Semi Lagrangian Advection Scheme Test  Gaussian Distribution
+ Error Convergence for Advection Scheme  Step Function IC
+ Error Convergence for Advection Scheme  Gaussian IC
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/milestone2results/
Deleted: doc/geodynamics.org/benchmarks/trunk/magma/milestone2.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/milestone2.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone2.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,87 +0,0 @@
Plone Metadata

 milestone2results

 Milestone 2 Results and Analysis

 Details the results of the Milestone 2 simulations and analyzes the
 accuracy of the advection scheme.

Model Descriptions

 The second milestone contains several different models. In each a
 porosity distribution has been supplied, which acts as a force term on
 the stokes equation. The porosity is advected according to a semi
 Lagrangian scheme, with no natural diffusion. Details of these models are
 given below.

Simple Gaussian porosity field

 The first model is a simple demonstration of how the porosity dependent
 force term drives the porosity distribution up through the domain. The
 domain is subjected to free slip boundary conditions, which also distort
 the porosity distribution as it is advected. This model is housed in
 the directory::

 Magma/Models/Milestone2/ZPNM_SemiLagrangianPorosity/

 with the XML file to be passed at run time being the 'Porridge.xml' file.

Ridge model with Gaussian porosity distribution

 The second model is an extension of the first milestone, that is a ridge
 model with the intial boundary conditions loaded from a reference
 solution. However in this case a Gaussian porosity distribution has been
 added. The porosity distribution is distorted as it moves up through the
 domain in accordance with the velocity field generated from the boundary
 conditions. This model can be found in::

 Magma/Models/Milestone2/RidgeModelWithGaussianPorosity/

 with the XML file to be passed being 'Ridge2D.xml'


Validation of the advection scheme

 As well as the models, a test is also supplied for validating the
 accuracy of the semi Lagrangian advection scheme. This involves an
 initial porosity distribution (either Gaussian or diagonal line step
 function, as determined from the XML), which is subjected to a static
 shearing velocity field. The porosity distribution is subjected to the
 velocity field for a finite number of time steps (as determined from the
 XML input file), before the velocity field is reversed and the
 distribution advected back for the same number of time steps. The
 normalized global L2 error between the initial and final distributions is
 then calculated. This test is housed in the directory::

 Magma/Models/Milestone2/tests/

 and may be run using the input file 'testSemiLagrangianAdvection.xml'.

 Running this simulation at varying resolutions, the convergence of the
 errors for the advection scheme were determined using both the Gaussian
 distribution and diagonal step function as initial conditions. The errors
 were recorded for schemes which used a cubid method as well as a
 quadratic method based on the element shape functions for interpolating
 the value at the end point of the characteristic. As can be observed from
 the convergence error plots below, the quadratic and cubic interpolation
 method schemes converged at comparable (less than linear) rates using the
 step function initial condition, with an improvement in those results
 obtained using the cubic interpolation method. When the Gaussian initial
 distribution was applied (which was easier to solve accurately on account
 of the smoother gradients involved), both interpolation methods converged
 at a rate much better than linear, with the cubic interpolation method
 proving far superior to the quadratic method.

Related Item(s)

 Gaussian Porosity Field Advection
 Ridge Model With Gaussian Porosity Field
 Semi Lagrangian Advection Scheme Test  Step Function
 Semi Lagrangian Advection Scheme Test  Gaussian Distribution
 Error Convergence for Advection Scheme  Step Function IC
 Error Convergence for Advection Scheme  Gaussian IC


URL
 http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/milestone2results/
Added: doc/geodynamics.org/benchmarks/trunk/magma/milestone3.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/milestone3.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone3.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,40 @@
+.. Plone Metadata
+..
+.. milestone3results
+..
+.. Milestone 3 Results
+..
+.. Details the results for the third milestone, in which melt velocity was
+.. determined given the existing solid velocity and pressure fields.
+
+Model descriptions
+==================
+
+Two different models were implemented for which the melt velocity was
+determined. The first of these was an extension of the ridge model
+implemented in Milestone 1, but with a constant porosity field, such that
+the solution was static in time. This model can be found in::
+
+ /Magma/Models/Milestone3/Ridge2D_Field_BasedConstantPorosity
+
+The second model was an extension of the porosity driven Stokes flow with
+a Gaussian intial distribution implemented in Milestone 2. This model
+resides at::
+
+ /Magma/Models/Milestone3/FieldBasedPorosityDrivenFlow2D
+
+Since the melt velocity is decoupled from the McKenzie equations, it is
+relatively simple to calculate, provided that the pressure and solid
+velocity fields have already been accurately determined. As such no tests
+were applied to validate its accuracy, however qualitatively their
+behavior is observed to be correct.
+
+
+Related Item(s)
+
+ Melt Model  Gaussian Porosity Driven Flow
+ Melt Model  2D Ridge with Constant Porosity
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/milestone3results/
Deleted: doc/geodynamics.org/benchmarks/trunk/magma/milestone3.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/milestone3.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone3.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,39 +0,0 @@
Plone Metadata

 milestone3results

 Milestone 3 Results

 Details the results for the third milestone, in which melt velocity was
 determined given the existing solid velocity and pressure fields.

Model descriptions

 Two different models were implemented for which the melt velocity was
 determined. The first of these was an extension of the ridge model
 implemented in Milestone 1, but with a constant porosity field, such that
 the solution was static in time. This model can be found in::

 /Magma/Models/Milestone3/Ridge2D_Field_BasedConstantPorosity

 The second model was an extension of the porosity driven Stokes flow with
 a Gaussian intial distribution implemented in Milestone 2. This model
 resides at::

 /Magma/Models/Milestone3/FieldBasedPorosityDrivenFlow2D

 Since the melt velocity is decoupled from the McKenzie equations, it is
 relatively simple to calculate, provided that the pressure and solid
 velocity fields have already been accurately determined. As such no tests
 were applied to validate its accuracy, however qualitatively their
 behavior is observed to be correct.


Related Item(s)

 Melt Model  Gaussian Porosity Driven Flow
 Melt Model  2D Ridge with Constant Porosity


URL
 http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/milestone3results/
Added: doc/geodynamics.org/benchmarks/trunk/magma/milestone4.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/milestone4.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone4.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,73 @@
+.. Plone Metadata
+..
+.. milestone4results
+..
+.. Milestone 4  Results and Analysis
+..
+.. Discussion of the system being modeled, and details of how to run the
+.. model with different initial conditions in 2D and 3D.
+
+Problem Description
+===================
+
+This milestone solves a porosity pressure system which involves the
+coupling of a Darcy flow to describe the compressibility of the permeable
+solid matrix and a time dependent advection equation for the porosity
+field. Together these equations allow for nonlinear dispersive porosity
+waves. Given an initial porosity distribution which is itself a porosity
+wave, this wave should advect at a speed determined by the amplitude and
+the power used to determine the permeability from the porosity (as well
+as the velocity of the background solid), without any diffusion. If the
+initial porosity distribution is not itself a solitary porosity wave,
+with time these should emerge from the porosity field.
+
+Running the Simulations
+
+
+In order to run the solitary waves model, (in 2D) first::
+
+ cd Magma/Models/Milestone4/SolitaryWaves2D
+
+Then make a symbolic link to the executable binary as::
+
+ ln s ../../../../build/bin/StGermain .
+
+The simulation may then be run in parallel as::
+
+ mpirun np <#ofprocs> ./StGermain SolitaryWaves.xml
+
+This will run the code with the default initial porosity distribution of
+a solitary wave with a wave speed of 7 and a porosity exponent of 3. The
+background solid velocity has been set in the file 'VelocityField.xml' as
+2, such that the wave should rise with a speed of 5. In order to verify
+that the wave is advecting at the correct speed, this may be changed to
+7, which should then show the wave to be stationary.
+
+An alternative initial porosity distribution of a vertically changing
+noisy 1D solitary wave may be set from the file 'sWaveSetup.xml' by
+modifying the 'referenceSolutionFileName' parameter to
+'./input/solitaryWaves1DGlobal.dat'. This should then show a set of 2D
+solitary porosity waves emerging from the 1D distribution with time.
+
+A 3D model may also be run by changing directories to::
+
+ cd Magma/Models/Milestone4/SolitaryWaves3D
+
+and then repeating the procedures detailed above for the 2D system. The
+initial condition, read in from the file
+'./input/solitaryWaves3DGlobal.dat', is that of a single 1D solitary wave
+in the vertical direction set against a noisy background distribution
+which evolves with time into a set of 3D solitary waves.
+
+
+Related item(s)
+
+ Emerging 2D Solitary Waves
+ 2D Solitary Wave
+ Noisy 1D Solitary Wave Initial Condition
+ Emergent 2D Solitary Waves
+ Emergent 3D Solitary Waves
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/milestone4results/
Deleted: doc/geodynamics.org/benchmarks/trunk/magma/milestone4.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/milestone4.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone4.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,71 +0,0 @@
Plone Metadata

 milestone4results

 Milestone 4  Results and Analysis

 Discussion of the system being modeled, and details of how to run the
 model with different initial conditions in 2D and 3D.

Problem Description

 This milestone solves a porosity pressure system which involves the
 coupling of a Darcy flow to describe the compressibility of the permeable
 solid matrix and a time dependent advection equation for the porosity
 field. Together these equations allow for nonlinear dispersive porosity
 waves. Given an initial porosity distribution which is itself a porosity
 wave, this wave should advect at a speed determined by the amplitude and
 the power used to determine the permeability from the porosity (as well
 as the velocity of the background solid), without any diffusion. If the
 initial porosity distribution is not itself a solitary porosity wave,
 with time these should emerge from the porosity field.

Running the Simulations

 In order to run the solitary waves model, (in 2D) first::

 cd Magma/Models/Milestone4/SolitaryWaves2D

 Then make a symbolic link to the executable binary as::

 ln s ../../../../build/bin/StGermain .

 The simulation may then be run in parallel as::

 mpirun np <#ofprocs> ./StGermain SolitaryWaves.xml

 This will run the code with the default initial porosity distribution of
 a solitary wave with a wave speed of 7 and a porosity exponent of 3. The
 background solid velocity has been set in the file 'VelocityField.xml' as
 2, such that the wave should rise with a speed of 5. In order to verify
 that the wave is advecting at the correct speed, this may be changed to
 7, which should then show the wave to be stationary.

 An alternative initial porosity distribution of a vertically changing
 noisy 1D solitary wave may be set from the file 'sWaveSetup.xml' by
 modifying the 'referenceSolutionFileName' parameter to
 './input/solitaryWaves1DGlobal.dat'. This should then show a set of 2D
 solitary porosity waves emerging from the 1D distribution with time.

 A 3D model may also be run by changing directories to::

 cd Magma/Models/Milestone4/SolitaryWaves3D

 and then repeating the procedures detailed above for the 2D system. The
 initial condition, read in from the file
 './input/solitaryWaves3DGlobal.dat', is that of a single 1D solitary wave
 in the vertical direction set against a noisy background distribution
 which evolves with time into a set of 3D solitary waves.


Related item(s)

 Emerging 2D Solitary Waves
 2D Solitary Wave
 Noisy 1D Solitary Wave Initial Condition
 Emergent 2D Solitary Waves
 Emergent 3D Solitary Waves


URL
 http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/milestone4results/
Added: doc/geodynamics.org/benchmarks/trunk/magma/milestone5.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/milestone5.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone5.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,70 @@
+.. Plone Metadata
+..
+.. milestone5results
+..
+.. Milestone 5  Results and Analysis
+..
+.. Results and analysis for the isoviscous McKenzie equations (with melting)
+.. driven by a corner flow velocity BC.
+
+
+Problem Description
+===================
+
+This model describes the full isoviscous McKenzie equations (with
+melting), for a system driven by a corner flow velocity boundary
+condition for the solid phase. These equations couple a Stokes system for
+the solid phase with a Darcy flow for the melt moving through the
+permeable solid, and an advection term for the porosity field. The flow
+is driven by a corner flow boundary condition for the solid, which
+creates a region of low dynamic pressure about the area of discontinuity,
+and a linear ramp in the melting function.
+
+Running the Simulation
+
+
+The model is run from the directory::
+
+ Magma/Models/Milestone4/IsoviscousMcKenzieRidge2D/
+
+and executing as::
+
+ ./StGermain IsoviscousMcKenzieRidge2D.xml
+
+taking care to create a soft link to the StGermain binary in the build
+directory as before.
+
+
+3D Model with Ridge Velocity Boundary Conditions
+
+
+A 3D model was also implemented, which is driven by Direchlet BCs on the
+velocity field, which are interpolated onto the prescribed domain from an
+input file (the same one as for Milestone 1). The directory and execution
+command for running this model are given as::
+
+ Magma/Models/Milestone5/IsoviscousMcKenzieRidge3D
+ ./StGermain IsoviscousMcKenzieRidge3D.xml
+
+Some images for the x and y velocity components, the dynamic and
+compaction pressures, the porosity, the melt fraction, and the x and y
+melt velocity components are attached below.
+
+
+Related Item(s)
+
+ Isoviscous McKenzie System with Corner Flow BC  1
+ Isoviscous McKenzie System with Corner Flow BC  50
+ Isoviscous McKenzie System with Corner Flow BC  3200
+ Velocity  x component
+ Velocity  y component
+ Dynamic (Stokes) pressure
+ Porosity
+ Compaction pressure
+ Melt fraction
+ Melt velocity  x component
+ Melt velocity  y component
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/milestone5results/
Deleted: doc/geodynamics.org/benchmarks/trunk/magma/milestone5.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/milestone5.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone5.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,66 +0,0 @@
Plone Metadata

 milestone5results

 Milestone 5  Results and Analysis

 Results and analysis for the isoviscous McKenzie equations (with melting)
 driven by a corner flow velocity BC.


Problem Description

 This model describes the full isoviscous McKenzie equations (with
 melting), for a system driven by a corner flow velocity boundary
 condition for the solid phase. These equations couple a Stokes system for
 the solid phase with a Darcy flow for the melt moving through the
 permeable solid, and an advection term for the porosity field. The flow
 is driven by a corner flow boundary condition for the solid, which
 creates a region of low dynamic pressure about the area of discontinuity,
 and a linear ramp in the melting function.

Running the Simulation

 The model is run from the directory::

 Magma/Models/Milestone4/IsoviscousMcKenzieRidge2D/

 and executing as::

 ./StGermain IsoviscousMcKenzieRidge2D.xml

 taking care to create a soft link to the StGermain binary in the build
 directory as before.

3D Model with Ridge Velocity Boundary Conditions

 A 3D model was also implemented, which is driven by Direchlet BCs on the
 velocity field, which are interpolated onto the prescribed domain from an
 input file (the same one as for Milestone 1). The directory and execution
 command for running this model are given as::

 Magma/Models/Milestone5/IsoviscousMcKenzieRidge3D
 ./StGermain IsoviscousMcKenzieRidge3D.xml

 Some images for the x and y velocity components, the dynamic and
 compaction pressures, the porosity, the melt fraction, and the x and y
 melt velocity components are attached below.


Related Item(s)

 Isoviscous McKenzie System with Corner Flow BC  1
 Isoviscous McKenzie System with Corner Flow BC  50
 Isoviscous McKenzie System with Corner Flow BC  3200
 Velocity  x component
 Velocity  y component
 Dynamic (Stokes) pressure
 Porosity
 Compaction pressure
 Melt fraction
 Melt velocity  x component
 Melt velocity  y component


URL
 http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/milestone5results/
Added: doc/geodynamics.org/benchmarks/trunk/magma/runningstgmadds.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/runningstgmadds.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/runningstgmadds.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,43 @@
+.. Plone Metadata
+..
+.. stgmadds
+..
+
+
+===========================
+Running stgMADDs Benchmarks
+===========================
+
+The Magma Development team has finished the alpha release of the Magma
+Dynamics Demonstration Suite (MADDs). The initial code implements the
+zero porosity/no melting magma benchmark for midocean ridge solid flows
+in 2D and 3D built on the Underworld framework. The purpose of this code
+is principally to validate accurate pressure solvers for Stokes flow in
+current CIG supported software. The stgMADDs source code is available in
+CIG's Mercurial Repository (geodynamics.org/hg).
+
+Download and Install stgMADDs
+=============================
+
+For a first time download of the stgMADDs repository, do the following:
+
+1 Create the topmost repository with::
+
+ hg clone http://geodynamics.org/hg/magma/3D/stgMADDs
+
+2 Then obtain all the other repositories using::
+
+ ./obtainRepositories.py
+
+4 To push, you may have to use the ssh syntax, e.g.::
+
+ hg push ssh://hg@geodynamics.org/hg/magma/3D/stgMADDs
+
+Caveat Emptor: This is very much an alpha release code for
+experimentation with the accuracy of different mixed FEM pressure
+solvers. Questions, complaints and bug reports should be directed to
+"cigmagma at geodynamics.org":mailto:cigmagma at geodynamics.org
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/stgmadds/
Deleted: doc/geodynamics.org/benchmarks/trunk/magma/runningstgmadds.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/magma/runningstgmadds.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/runningstgmadds.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,38 +0,0 @@
Plone Metadata

 stgmadds

 Running stgMADDs Benchmarks

 The Magma Development team has finished the alpha release of the Magma
 Dynamics Demonstration Suite (MADDs). The initial code implements the
 zero porosity/no melting magma benchmark for midocean ridge solid flows
 in 2D and 3D built on the Underworld framework. The purpose of this code
 is principally to validate accurate pressure solvers for Stokes flow in
 current CIG supported software. The stgMADDs source code is available in
 CIG's Mercurial Repository (geodynamics.org/hg).

Download and Install stgMADDs

 For a first time download of the stgMADDs repository, do the following:

 1 Create the topmost repository with::

 hg clone http://geodynamics.org/hg/magma/3D/stgMADDs

 2 Then obtain all the other repositories using::

 ./obtainRepositories.py

 4 To push, you may have to use the ssh syntax, e.g.::

 hg push ssh://hg@geodynamics.org/hg/magma/3D/stgMADDs

 Caveat Emptor: This is very much an alpha release code for
 experimentation with the accuracy of different mixed FEM pressure
 solvers. Questions, complaints and bug reports should be directed to
 "cigmagma at geodynamics.org":mailto:cigmagma at geodynamics.org


URL
 http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/stgmadds/
Modified: doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/index.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/index.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 2,103 +2,106 @@
General Description of the Benchmark Problem
============================================
 The benchmark will be similar to the benchmark of Blankenbach *et al.*
 (1989) in methodology.
+The benchmark will be similar to the benchmark of Blankenbach *et al.*
+(1989) in methodology.
 The benchmark problem is 2D thermal convection of a nonrotating
 anelastic liquid of infinite Prandtl number in a Cartesian, closed, unit
 cell. The governing equations is based on Truncated AnElastic
 Approximation (TALA).
+The benchmark problem is 2D thermal convection of a nonrotating
+anelastic liquid of infinite Prandtl number in a Cartesian, closed, unit
+cell. The governing equations is based on Truncated AnElastic
+Approximation (TALA).
 (attach equations as image here...)
+(attach equations as image here...)
 We will have several cases, steady or unsteady, constant or variable
 viscosity, bottom or internal heated, heat or mechanically driven.
+We will have several cases, steady or unsteady, constant or variable
+viscosity, bottom or internal heated, heat or mechanically driven.
Grids

 Each case will be run at **3 different resolutions** (grid resolution
 32x32, 64x64, 128x128, or higher if needed) to quantify the convergence
 asymptotically. By comparing the asymptotically converged result, we
 probably can negate the need of mesh refinement near the boundary and
 reduce the uncertainty associated with various
 interpolation/extrapolation schemes in calculating derived information
 (e.g. geoid).
+Each case will be run at **3 different resolutions** (grid resolution
+32x32, 64x64, 128x128, or higher if needed) to quantify the convergence
+asymptotically. By comparing the asymptotically converged result, we
+probably can negate the need of mesh refinement near the boundary and
+reduce the uncertainty associated with various interpolation/extrapolation
+schemes in calculating derived information (e.g. geoid).
+
Velocity BC's

 All boundaries (top, bottom, left, right) are **impermeable** (i.e., zero
 normal velocity) and **freeslip** (i.e., zero tangential stress), except
 for the mechanically driven case, where the top boundary is impermeble
 and zeroslip (i.e. fixed horizontal velocity).
+All boundaries (top, bottom, left, right) are **impermeable** (i.e., zero
+normal velocity) and **freeslip** (i.e., zero tangential stress), except
+for the mechanically driven case, where the top boundary is impermeble
+and zeroslip (i.e. fixed horizontal velocity).
+
Temperature BC's

 All nondimensional numbers are defined at the top surface. There are
 five nondimensional numbers:
+All nondimensional numbers are defined at the top surface. There are
+five nondimensional numbers:
 * **Ra**: Rayleigh number
+* **Ra**: Rayleigh number
 * **H**: volumentric heat production number, **H = 0**, except for
 internal heated cases.
+* **H**: volumentric heat production number, **H = 0**, except for
+ internal heated cases.
 * **Di**: Dissipation number
+* **Di**: Dissipation number
 * **Gamma**: Gruneisen parameter
+* **Gamma**: Gruneisen parameter
 * **T_0**: Surface temperature, **T_0 = 0.1** for all cases.
+* **T_0**: Surface temperature, **T_0 = 0.1** for all cases.
+
Reference State

 The reference density profile is $rho_ref(z) = exp((1z)*Di/Gamma)$
+The reference density profile is $rho_ref(z) = exp((1z)*Di/Gamma)$
 The reference temperature profile is $T_ref(z) = T_0 * exp((1z) * Di) T_0$
+The reference temperature profile is $T_ref(z) = T_0 * exp((1z) * Di) T_0$
 These physical properties are constant: thermal diffusivity, coefficient
 of thermal expansion, gravitational acceleration.
+These physical properties are constant: thermal diffusivity, coefficient
+of thermal expansion, gravitational acceleration.
Required Information (all quantities are nondimensional unless specified)

 * Nusselt number
+* Nusselt number
 * Mean Temperature
+* Mean Temperature
 * Total Kinetic Energy
+* Total Kinetic Energy
 * RMS(V_x at top surface)
+* RMS(V_x at top surface)
 * Max(V_x at top surface)
+* Max(V_x at top surface)
 * Total Dissipation Heating
+* Total Dissipation Heating
 * Total Adiabatic Cooling
+* Total Adiabatic Cooling
 * Dynamic Topography: Values required at 4 corners.
+* Dynamic Topography: Values required at 4 corners.
 * Geoid Anomaly (dimensional): values required at the upper corners.
 The following dimensional constants (in SI units) are used for the
 calculation of geoid:
+* Geoid Anomaly (dimensional): values required at the upper corners.
 * Gravitational constant **G** = 6.673x10^11
+ The following dimensional constants (in SI units) are used for the
+ calculation of geoid:
 * depth of the box **R** = 3x10^6
+ * Gravitational constant **G** = 6.673x10^11
 * density at surface **rho_0** = 4000
+ * depth of the box **R** = 3x10^6
 * coefficient of thermal expansion **alpha_0** = 3x10^5
+ * density at surface **rho_0** = 4000
 * temperature contrast **Delta_T** = 3000
+ * coefficient of thermal expansion **alpha_0** = 3x10^5
 * viscosity **visc_0** = 10^21
+ * temperature contrast **Delta_T** = 3000
 * thermal diffusivity **kappa_0** = 10^6
+ * viscosity **visc_0** = 10^21
 The density is 0 above the top of the box and is 2 below the bottom of
 the box.
+ * thermal diffusivity **kappa_0** = 10^6
+
+The density is 0 above the top of the box and is 2 below the bottom of
+the box.
Modified: doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite1.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite1.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite1.rst 20090918 20:02:16 UTC (rev 15676)
@@ 2,49 +2,52 @@
Suite 1
=======
 Testing the implementation of driving forces, isoviscous, comparing with
 analytical solutions.
+Testing the implementation of driving forces, isoviscous, comparing with
+analytical solutions.
 The nondimensional numbers are moderately low in this case (Ra=10^5,
 Di=0.25, gamma=1.5). The viscosity is constant. The purpose of this suite
 is to ensure the driving forces are implemented correctly. This set of
 nondimensional numbers will give low compressibility and slow
 convection. Therefore, most of the codes should behave well in this
 parameter range.
+The nondimensional numbers are moderately low in this case (Ra=10^5,
+Di=0.25, gamma=1.5). The viscosity is constant. The purpose of this suite
+is to ensure the driving forces are implemented correctly. This set of
+nondimensional numbers will give low compressibility and slow
+convection. Therefore, most of the codes should behave well in this
+parameter range.
+
Case 1a: Bottom Heated

 The temperature at the bottom is fixed at 1. The initial temperature
 condition is
+The temperature at the bottom is fixed at 1. The initial temperature
+condition is
 T = 0.5 everwhere, except at z = 0.5,
 where T = 0.5 + cos(pi * x) * 0.001 * elz
+ T = 0.5 everwhere, except at z = 0.5,
+ where T = 0.5 + cos(pi * x) * 0.001 * elz
 where elz is the number of elements in the zdirection.
+where elz is the number of elements in the zdirection.
 The initial temperature perturbation mimics a delta function. However,
 the amplitude of the perturbation, with a factor of 1/1000, doesn't match
 with a delta function. A comparison with analytical solution is possible
 for the 0thstep velocity.
+The initial temperature perturbation mimics a delta function. However,
+the amplitude of the perturbation, with a factor of 1/1000, doesn't match
+with a delta function. A comparison with analytical solution is possible
+for the 0thstep velocity.
+
Case 1b: Internal Heated

 The temperature BC at the bottom is noheatflux. The initial temperature
 is the same as Case 1a. H = 1.
+The temperature BC at the bottom is noheatflux. The initial temperature
+is the same as Case 1a. H = 1.
+
Case 1c: Mechanically Driven

 The temperature at the bottom is fixed at 0. The initial temperature is
 zero everywhere. The horizontal velocity BC at the top boundary is
+The temperature at the bottom is fixed at 0. The initial temperature is
+zero everywhere. The horizontal velocity BC at the top boundary is
 V_x = 1000 * x^2 * (x1)^2
+ V_x = 1000 * x^2 * (x1)^2
 so that V_x = 0 at x = 0 and 1, and dV_x/dx = 0 at x = 0 and 1.
 (This case is optional.)
+so that V_x = 0 at x = 0 and 1, and dV_x/dx = 0 at x = 0 and 1.
+(This case is optional.)
 image:: Vx.png
 "Horizontal velocity boundary condition"
+.. figure:: Vx.png
+ Horizontal velocity boundary condition
Modified: doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite2.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite2.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite2.rst 20090918 20:02:16 UTC (rev 15676)
@@ 7,24 +7,26 @@
Steady state, basal heated
==========================
 Gamma = 1.1 in this suite.
+Gamma = 1.1 in this suite.
 Temperature dependent viscosity: eta = exp(5 * T)
+Temperature dependent viscosity: eta = exp(5 * T)
+
Case 2a

 * Ra = 3x10^5, Di = 0.5
+* Ra = 3x10^5, Di = 0.5
Case 2b

 * Ra = 10^6, Di = 0.75 (not sure whether this case can reach steady state)
+* Ra = 10^6, Di = 0.75 (not sure whether this case can reach steady state)
+
Case 2c

 * Ra = 3x10^6, Di = 1.0 (not sure whether this case can reach steady state)
+* Ra = 3x10^6, Di = 1.0 (not sure whether this case can reach steady state)
Modified: doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite3.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite3.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite3.rst 20090918 20:02:16 UTC (rev 15676)
@@ 6,7 +6,7 @@
Steady state, internal heated
=============================
 This suite will have several cases taken from Jarvis and McKenzie (1980)
+This suite will have several cases taken from Jarvis and McKenzie (1980)
 H = 1, noheatflux for the bottom boundary.
+H = 1, noheatflux for the bottom boundary.
Modified: doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite4.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite4.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/2dcartesian/suite4.rst 20090918 20:02:16 UTC (rev 15676)
@@ 6,5 +6,5 @@
Timedependent, unstead convection
==================================
 Parameters to be determined ...
+Parameters to be determined ...
Modified: doc/geodynamics.org/benchmarks/trunk/mc/index.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/mc/index.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 1,5 +1,4 @@

============================
Mantle Convection Benchmarks
============================
@@ 7,35 +6,33 @@
Benchmarks
==========
+
2D Cartesian Compressible Convection Benchmarks

 * Suite 1
+* Suite 1
+* Suite 2
+* Suite 3
+* Suite 4
 * Suite 2
 * Suite 3

 * Suite 4


3D Spherical Mantle Convection Benchmarks

 * BM1{AH}
+* BM1{AH}
+* BM2{AH}
+* BM3{AD}
 * BM2{AH}
 * Bm3{AD}


Links

 * "Mantle Convection Benchmarks":http://geodynamics.org/cig/workinggroups/mc/workarea/benchmark/
+* `Mantle Convection Benchmarks`__
+* `Benchmarks for 2D Cartesian Compressible Convection`__
+* `3D Spherical Mantle Convection Benchmarks`__
 * "Benchmarks for 2D Cartesian compressible convection":http://geodynamics.org/cig/Members/tan2/benchmarks/
+__ http://geodynamics.org/cig/workinggroups/mc/workarea/benchmark/
+__ http://geodynamics.org/cig/Members/tan2/benchmarks/
+__ http://geodynamics.org/cig/workinggroups/mc/workarea/benchmark/3dconvention/
 * "3D Spherical Mantle Convection Benchmarks":http://geodynamics.org/cig/workinggroups/mc/workarea/benchmark/3dconvention/

Modified: doc/geodynamics.org/benchmarks/trunk/mc/notesonmantleconvectionbenchmarks.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/mc/notesonmantleconvectionbenchmarks.rst 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/notesonmantleconvectionbenchmarks.rst 20090918 20:02:16 UTC (rev 15676)
@@ 2,77 +2,77 @@
Notes On Mantle Convection Benchmarks
=====================================
 (1) Ra = 3x10**6 (I think this is high enough to give some real time
 dependence without pushing available resolution very much).
+(1) Ra = 3x10**6 (I think this is high enough to give some real time
+dependence without pushing available resolution very much).
 (2) Constaint properties (thermal expansivity, thermal diffusivity,
 density, gravity, viscosity, internal heat generation) to keep things
 very simple.
+(2) Constaint properties (thermal expansivity, thermal diffusivity,
+density, gravity, viscosity, internal heat generation) to keep things
+very simple.
 (3) Free slip upper and lower boundaries.
+(3) Free slip upper and lower boundaries.
 (4) Radius ratio = 0.546 (cmb/surface radius)
+(4) Radius ratio = 0.546 (cmb/surface radius)
 (5) purely internally heated
+(5) purely internally heated
 (6) insulating at cmb, constant temperature at surface
+(6) insulating at cmb, constant temperature at surface
 (7) model resolution: 65 nodes (64 layers) radially, with some packing of
 nodes near the top and bottom boundaries. (We'll send you the actual
 radii we use, assuming you can vary them at will.)
+(7) model resolution: 65 nodes (64 layers) radially, with some packing of
+nodes near the top and bottom boundaries. (We'll send you the actual
+radii we use, assuming you can vary them at will.)
 (8) initial diagnostics: (basically, these are just to get started and
 see if we're in the same universe)
+(8) initial diagnostics: (basically, these are just to get started and
+see if we're in the same universe)
 * (a) Nu vs. time (this should square with the internal heating in a
 timeaverage sense)
+* (a) Nu vs. time (this should square with the internal heating in a
+ timeaverage sense)
 * (b) Radial temperature profile vs. time  this is effectively a
 measure of the efficiency of heat transfer, or equivalent of Nu for
 bottom heated cases.
+* (b) Radial temperature profile vs. time  this is effectively a
+ measure of the efficiency of heat transfer, or equivalent of Nu for
+ bottom heated cases.
 * (c) Spherical harmonic expansion of temperature field at all radial
 levels at beginning and ending time (see below).
+* (c) Spherical harmonic expansion of temperature field at all radial
+ levels at beginning and ending time (see below).
 * (d) peak velocity and peak temperature in each radial layer vs. time
+* (d) peak velocity and peak temperature in each radial layer vs. time
 * (e) for now, let's ignore dynamic topography, since it's derived from
 primitive results
+* (e) for now, let's ignore dynamic topography, since it's derived from
+ primitive results
 (9) Initial conditions and run time: This is a bit thorny, so here's a
 proposal. We can run TERRA to equilibrium under the specified model
 conditions. Equilibrium is where Nu has settled down to fluctuations
 about a steady mean value. At some point, call it time = 0.0, we'll stop
 the code and output the full temperature field in the form of a spherical
 harmonic expansion up to degree 128, which corresponds to the highest
 model resolution. We can then restart both TERRA and CitcomS using this
 spherical harmonic expansion (NOT the full temperature field at each
 node, since this would prejudice things with regard to the particular
 horizontal discretization.) Then both codes can run for a defined amount
 of model time, keeping track of Nu, peak T, and peak V as a function of
 time as indicated above. At the end of this time, or at several times
 along the way, we can output spherical harmonic representations of T at
 each layer for comparison.
+(9) Initial conditions and run time: This is a bit thorny, so here's a
+proposal. We can run TERRA to equilibrium under the specified model
+conditions. Equilibrium is where Nu has settled down to fluctuations
+about a steady mean value. At some point, call it time = 0.0, we'll stop
+the code and output the full temperature field in the form of a spherical
+harmonic expansion up to degree 128, which corresponds to the highest
+model resolution. We can then restart both TERRA and CitcomS using this
+spherical harmonic expansion (NOT the full temperature field at each
+node, since this would prejudice things with regard to the particular
+horizontal discretization.) Then both codes can run for a defined amount
+of model time, keeping track of Nu, peak T, and peak V as a function of
+time as indicated above. At the end of this time, or at several times
+along the way, we can output spherical harmonic representations of T at
+each layer for comparison.
 I added the following comments:
+I added the following comments:
 (1) We use some analytic expressions for initial conditions (e.g., some
 radial profile superimposed with a small perturbation of a given harmonic
 function). In this way, others, if they want to benchmark their codes, do
 not need to get the Terra output. Also in case some summary report comes
 out of this effort, we can simply write down the initial conditions.
+(1) We use some analytic expressions for initial conditions (e.g., some
+radial profile superimposed with a small perturbation of a given harmonic
+function). In this way, others, if they want to benchmark their codes, do
+not need to get the Terra output. Also in case some summary report comes
+out of this effort, we can simply write down the initial conditions.
 (2) We aim to reproduce four benchmark cases in steady of just one. The
 four cases at the moment in my mind can be: three constant property cases
 with purely basal heating at Ra=1e5 (case 1), and Ra=1e6 (case 2), and
 purely internal heating at Ra=1e6 (case 3), and one temperature dependent
 viscosity and purely basal heating at Ra=1e6 (case 4).
+(2) We aim to reproduce four benchmark cases in steady of just one. The
+four cases at the moment in my mind can be: three constant property cases
+with purely basal heating at Ra=1e5 (case 1), and Ra=1e6 (case 2), and
+purely internal heating at Ra=1e6 (case 3), and one temperature dependent
+viscosity and purely basal heating at Ra=1e6 (case 4).
 Case 1 will likely reach to a steady state, which is always a good thing
 for a benchmark. Cases 2 and 3 are almost identical to what you have
 suggested recently, and they are most likely timedependent. The 1e6 Ra
 is smaller than what you suggested today but is consistent with your
 earlier suggestion. With Ra=1e6, we may not need grid refinement, which
 is also good for benchmark purposes (again, others can do it later).
 Case 4 is obviously of interest too.
+Case 1 will likely reach to a steady state, which is always a good thing
+for a benchmark. Cases 2 and 3 are almost identical to what you have
+suggested recently, and they are most likely timedependent. The 1e6 Ra
+is smaller than what you suggested today but is consistent with your
+earlier suggestion. With Ra=1e6, we may not need grid refinement, which
+is also good for benchmark purposes (again, others can do it later).
+Case 4 is obviously of interest too.
Added: doc/geodynamics.org/benchmarks/trunk/short/benchmarklanders/descriptionlanders.rst
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarklanders/descriptionlanders.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarklanders/descriptionlanders.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,79 @@
+.. Plone Metadata
+.. descriptionlanders
+.. Benchmark Description
+.. Benchmark problem description
+
+Summary
+=======
+
+Viscoelastic (Maxwell) relaxation of stresses from the 1992 M7.3 Landers earthquake,
+focusing on the deformation in the area of the 1999 M7.1 Hector Mine earthquake.
+
+Problem Specification
+
+
+Model size  [NEED SPECS FOR CARL'S MESH]
+``````````````````````````````````````````
+
+Material properties
+```````````````````
+
+Elastic
+ The material properties are a simplified 1D version of the
+ 3D SCEC Community Velocity Model. The 1D model contains 11 layers with
+ uniform material properties within each layer and a minimum layer thickness
+ of 2 km. The elastic properties are given in an "ASCII":materials_layers2km.txt
+ file.
+
+ Viscoelastic  Maxwell linear viscoelasticity (based on values in Pollitz, EPSL, 2003)
+ Upper crust (19 km ≤ z)  η = 1.0e+25 Pas (essentially elastic)
+ Lower crust (30 km ≤ z <  19 km)  η = 32.2e+18 Pas
+ Mantle (z < 30 km)  η = 4.6e+18 Pas
+
+Fault geometry and slip distribution
+ The Landers and Hector Mine fault geometries and slip distribution
+ for Landers are incorporated into the LaGriT mesh.
+
+Boundary conditions
+ Bottom and side displacements are pinned. Top of the model is a free surface.
+
+Discretization
+ [GET SPECS FROM CARL'S MESH]
+
+Element types
+ Linear and/or quadratic tetrahedral elements
+
+
+Requested Output
+
+
+Solution
+````````
+
+Displacements at all nodes at times of 0, 0.5, 1, 2, 4, and 7 years
+as well as the mesh topology (i.e., element connectivity arrays and
+coordinates of vertices) and basis functions. Also compute the traction
+vector computed at the quadrature points of the faces making up the
+Hector Mine faults.
+
+June 30, 2006  Use ASCII output for now. In the future we will
+switch to using HDF5 files.
+
+
+Performance
+```````````
+
+ * CPU time
+ * Wallclock time
+ * Memory usage
+ * Compiler and platform info
+
+"Truth"
+
+
+ You can't handle the truth
+
+
+URL
+
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarklanders/descriptionlanders
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarklanders/descriptionlanders.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarklanders/descriptionlanders.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarklanders/descriptionlanders.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,77 +0,0 @@
Plone Metadata
 descriptionlanders
 Benchmark Description
 Benchmark problem description

Summary

 Viscoelastic (Maxwell) relaxation of stresses from the 1992 M7.3 Landers earthquake,
 focusing on the deformation in the area of the 1999 M7.1 Hector Mine earthquake.

Problem Specification

 Model size  [NEED SPECS FOR CARL'S MESH]

 Material properties

 Elastic  The material properties are a simplified 1D version of the
 3D SCEC Community Velocity Model. The 1D model contains 11 layers with
 uniform material properties within each layer and a minimum layer thickness
 of 2 km. The elastic properties are given in an "ASCII":materials_layers2km.txt
 file.

 Viscoelastic  Maxwell linear viscoelasticity (based on values in Pollitz, EPSL, 2003)

 Upper crust (19 km ≤ z)  η = 1.0e+25 Pas (essentially elastic)

 Lower crust (30 km ≤ z <  19 km)  η = 32.2e+18 Pas

 Mantle (z < 30 km)  η = 4.6e+18 Pas

 Fault geometry and slip distribution

 The Landers and Hector Mine fault geometries and slip distribution
 for Landers are incorporated into the LaGriT mesh.

 Boundary conditions

 Bottom and side displacements are pinned. Top of the model is a free surface.

 Discretization

 [GET SPECS FROM CARL'S MESH]

 Element types

 Linear and/or quadratic tetrahedral elements

Requested Output

 Solution

 Displacements at all nodes at times of 0, 0.5, 1, 2, 4, and 7 years
 as well as the mesh topology (i.e., element connectivity arrays and
 coordinates of vertices) and basis functions. Also compute the traction
 vector computed at the quadrature points of the faces making up the
 Hector Mine faults.

 June 30, 2006  Use ASCII output for now. In the future we will
 switch to using HDF5 files.

 Performance

 * CPU time

 * Wallclock time

 * Memory usage

 * Compiler and platform info

"Truth"

 You can't handle the truth


URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarklanders/descriptionlanders
Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/descriptionrs.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/descriptionrs.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/descriptionrs.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/descriptionrs.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,104 @@
+Plone Metadata
+ descriptionrs
+ Benchmark Description
+ Benchmark problem description. Formerly known as benchmark 6b.
+
+Summary
+
+ Viscoelastic (Maxwell) relaxation of stresses from a single, finite, reverseslip
+ earthquake in 3D with gravity. Evaluate results with imposed displacement boundary
+ conditions on a cube with sides of length 24 km. The displacements imposed are
+ the analytic elastic solutions. Symmetry boundary conditions are imposed at y = 0,
+ so the solution is equivalent to that for a domain with a 48 km length in the
+ y direction.
+
+ The effects of gravitational loading should be relaxed before the fault slip is
+ imposed. Alternatively, Winkler nodes could be used to calculate the gravitational
+ restoring forces resulting from the deformed upper surface.
+
+Problem Specificaqtion
+
+ Model size  0 km ≤ x ≤ 24 km; 0 km ≤ y ≤ 24 km; 24 km ≤ z ≤ 0 km
+
+ Top layer  12 km ≤ z ≤ 0 km
+
+ Bottom layer  24 km ≤ z ≤ 12 km
+
+ Material properties  The top layer is nearly elastic whereas the bottom layer
+ is viscoelastic.
+
+ Elastic  Poisson solid, G = 30 GPa, ρ = 3000 kg/m^3; g = 9.80665 m/s^2
+
+ Maxwell viscoelastic material properties
+
+ Top layer  η = 1.0e+25 Pas (essentially elastic)
+
+ Bottom layer  η = 1.0e+18 Pas
+
+ Boundary conditions
+
+ Bottom and side displacements set to analytic solution. (Note: the side
+ at y = 0 km has zero ydisplacements because of the symmetry.) Top of the
+ model is a free surface.
+
+ Discretization
+
+ The model should be discretized with a nominal spatial resolution of 1000m,
+ 500m, and 250m. If possible, also run the models with a nominal spatial
+ resolution of 125 m. Optionally, use meshes with variable (optimal)
+ spatial resolution with the same number of nodes as the uniform resolution
+ meshes.
+
+ Element types
+
+ Linear and/or quadratic and tetrahedral and/or hexahedral
+
+ Fault specifications
+
+ Type  45 degree dipping reverse fault.
+
+ Location  Strike parallel to ydirection with top edge at x = 4 km
+ and bottom edge at x = 12 km. 0 km ≤ y ≤ 16 km; 16 km ≤ z ≤ 0 km
+
+ Slip distribution  1 m of uniform thrust slip motion for 0 km ≤ y ≤ 12 km
+ and 12 km ≤ z ≤ 0 km with a linear taper to 0 slip at y = 16 km and z = 16 km.
+ In the region where the two tapers overlap, each slip value is the minimum
+ of the two tapers (so that the taper remains linear).
+
+ Boundary conditions
+
+ Lateral and bottom displacements are set to analytic elastic solution.
+ Note that the side at y = 0 km has zero ydisplacements because of the
+ imposed symmetry at y = 0 km.
+
+Requested Output
+
+ Solution
+
+ Displacements at all nodes at times of 0, 1, 5, and 10 years
+ as well as the mesh topology (i.e., element connectivity arrays and
+ coordinates of vertices) and basis functions.
+
+ June 30, 2006  Use ASCII output for now. In the future we will switch
+ to using HDF5 files.
+
+ Performance
+
+ * CPU time
+
+ * Wallclock time
+
+ * Memory usage
+
+ * Compiler and platform info
+
+"Truth"
+
+ Okada routines are available to generate an elastic solution. The 'best'
+ viscoelastic answer will be derived via mesh refinement. Analytical
+ solutions to the viscoelastic problem are being sought if anyone has
+ any information.
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrs/descriptionrs
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/descriptionrs.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/descriptionrs.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/descriptionrs.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,104 +0,0 @@
Plone Metadata
 descriptionrs
 Benchmark Description
 Benchmark problem description. Formerly known as benchmark 6b.

Summary

 Viscoelastic (Maxwell) relaxation of stresses from a single, finite, reverseslip
 earthquake in 3D with gravity. Evaluate results with imposed displacement boundary
 conditions on a cube with sides of length 24 km. The displacements imposed are
 the analytic elastic solutions. Symmetry boundary conditions are imposed at y = 0,
 so the solution is equivalent to that for a domain with a 48 km length in the
 y direction.

 The effects of gravitational loading should be relaxed before the fault slip is
 imposed. Alternatively, Winkler nodes could be used to calculate the gravitational
 restoring forces resulting from the deformed upper surface.

Problem Specificaqtion

 Model size  0 km ≤ x ≤ 24 km; 0 km ≤ y ≤ 24 km; 24 km ≤ z ≤ 0 km

 Top layer  12 km ≤ z ≤ 0 km

 Bottom layer  24 km ≤ z ≤ 12 km

 Material properties  The top layer is nearly elastic whereas the bottom layer
 is viscoelastic.

 Elastic  Poisson solid, G = 30 GPa, ρ = 3000 kg/m^3; g = 9.80665 m/s^2

 Maxwell viscoelastic material properties

 Top layer  η = 1.0e+25 Pas (essentially elastic)

 Bottom layer  η = 1.0e+18 Pas

 Boundary conditions

 Bottom and side displacements set to analytic solution. (Note: the side
 at y = 0 km has zero ydisplacements because of the symmetry.) Top of the
 model is a free surface.

 Discretization

 The model should be discretized with a nominal spatial resolution of 1000m,
 500m, and 250m. If possible, also run the models with a nominal spatial
 resolution of 125 m. Optionally, use meshes with variable (optimal)
 spatial resolution with the same number of nodes as the uniform resolution
 meshes.

 Element types

 Linear and/or quadratic and tetrahedral and/or hexahedral

 Fault specifications

 Type  45 degree dipping reverse fault.

 Location  Strike parallel to ydirection with top edge at x = 4 km
 and bottom edge at x = 12 km. 0 km ≤ y ≤ 16 km; 16 km ≤ z ≤ 0 km

 Slip distribution  1 m of uniform thrust slip motion for 0 km ≤ y ≤ 12 km
 and 12 km ≤ z ≤ 0 km with a linear taper to 0 slip at y = 16 km and z = 16 km.
 In the region where the two tapers overlap, each slip value is the minimum
 of the two tapers (so that the taper remains linear).

 Boundary conditions

 Lateral and bottom displacements are set to analytic elastic solution.
 Note that the side at y = 0 km has zero ydisplacements because of the
 imposed symmetry at y = 0 km.

Requested Output

 Solution

 Displacements at all nodes at times of 0, 1, 5, and 10 years
 as well as the mesh topology (i.e., element connectivity arrays and
 coordinates of vertices) and basis functions.

 June 30, 2006  Use ASCII output for now. In the future we will switch
 to using HDF5 files.

 Performance

 * CPU time

 * Wallclock time

 * Memory usage

 * Compiler and platform info

"Truth"

 Okada routines are available to generate an elastic solution. The 'best'
 viscoelastic answer will be derived via mesh refinement. Analytical
 solutions to the viscoelastic problem are being sought if anyone has
 any information.


URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrs/descriptionrs
Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/results/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/results/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/results/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/results/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,11 @@
+Plone Metadata
+ results
+
+ Results
+
+ Results from benchmark runs. Place tarballs containing the requested results
+ in this folder and describe the run in the `description` field.
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrs/results
+
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/results/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/results/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrs/results/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,11 +0,0 @@
Plone Metadata
 results

 Results

 Results from benchmark runs. Place tarballs containing the requested results
 in this folder and describe the run in the `description` field.

URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrs/results

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/descriptionrsnog.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/descriptionrsnog.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/descriptionrsnog.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/descriptionrsnog.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,93 @@
+Plone Metadata
+ descriptionrsnog
+ Benchmark Description
+ Benchmark problem description. Formerly known as benchmark 5b.
+
+Summary
+
+ Viscoelastic (Maxwell) relaxation of stresses from a single finite, reverseslip
+earthquake in 3D without gravity. Evaluate results with imposed displacement boundary
+conditions on a cube with sides of length 24 km. The displacements imposed are the
+analytic elastic solutions. Symmetry boundary conditions are imposed at y = 0,
+so the solution is equivalent to that for a domain with a 48 km length in the
+y direction.
+
+Problem Specification
+
+ Model size  0 km ≤ x ≤ 24 km; 0 km ≤ y ≤ 24 km; 24 km ≤ z ≤ 0 km
+
+ Top layer  12 km ≤ z ≤ 0 km
+
+ Bottom layer  24 km ≤ z ≤ 12 km
+
+ Material properties  The top layer is nearly elastic whereas the bottom layer is viscoelastic.
+
+ Elastic  Poisson solid, G = 30 GPa
+
+ Viscoelasticity  Maxwell linear viscoelasticity
+
+ Top layer  η = 1.0e+25 Pas (essentially elastic)
+
+ Bottom layer  η = 1.0e+18 Pas
+
+ Fault specifications
+
+ Type  45 degree dipping reverse fault.
+
+ Location  Strike parallel to ydirection with top edge at x = 4 km,
+ and bottom edge at x = 20 km. 0 km ≤ y ≤ 16 km; 16 km ≤ z ≤ 0 km
+
+ Slip distribution  1 m of uniform thrust slip motion for 0 km ≤ y ≤ 12 km
+ and 12 km ≤ z ≤ 0 km with a linear taper to 0 slip at y = 16 km and
+ z = 16 km. In the region where the two tapers overlap, each slip value
+ is the minimum of the two tapers (so that the taper remains linear).
+
+ Boundary conditions
+
+ Bottom and side displacements set to analytic solution. (Note: the side
+ at y = 0 km has zero ydisplacements because of symmetry). Top of the
+ model is a free surface.
+
+ Discretization
+
+ The model should be discretized with nominal spatial resolutions of
+ 1000 m, 500 m, 250 m. If possible, also run the models with a nominal
+ spatial resolution of 125 m. Optionally, use meshes with variable (optimal)
+ spatial resolution with the same number of nodes as the uniform resolution
+ meshes.
+
+ Element types
+
+ Linear and/or quadratic and tetrahedral and/or hexahedral.
+
+
+Requested Output
+
+ Solution
+
+ Displacements at all nodes at times of 0, 1, 5, and 10 years as well as
+ the mesh topology (i.e., element connectivity arrays and coordinates of
+ vertices) and basis functions.
+
+ June 30, 2006  Use ASCII output for now. In the future we will switch
+ to using HDF5 files.
+
+ Performance
+
+ * CPU time
+
+ * Wallclock time
+
+ * Memory usage
+
+ * Compiler and platform info
+
+"Truth"
+
+ Okada routines are available to generate an elastic solution. The 'best'
+ viscoelastic answer will be derived via mesh refinement. Analytical solutions
+ to the viscoelastic solution are being sought if anyone has information.
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrsnog/descriptionrsnog
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/descriptionrsnog.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/descriptionrsnog.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/descriptionrsnog.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,93 +0,0 @@
Plone Metadata
 descriptionrsnog
 Benchmark Description
 Benchmark problem description. Formerly known as benchmark 5b.

Summary

 Viscoelastic (Maxwell) relaxation of stresses from a single finite, reverseslip
earthquake in 3D without gravity. Evaluate results with imposed displacement boundary
conditions on a cube with sides of length 24 km. The displacements imposed are the
analytic elastic solutions. Symmetry boundary conditions are imposed at y = 0,
so the solution is equivalent to that for a domain with a 48 km length in the
y direction.

Problem Specification

 Model size  0 km ≤ x ≤ 24 km; 0 km ≤ y ≤ 24 km; 24 km ≤ z ≤ 0 km

 Top layer  12 km ≤ z ≤ 0 km

 Bottom layer  24 km ≤ z ≤ 12 km

 Material properties  The top layer is nearly elastic whereas the bottom layer is viscoelastic.

 Elastic  Poisson solid, G = 30 GPa

 Viscoelasticity  Maxwell linear viscoelasticity

 Top layer  η = 1.0e+25 Pas (essentially elastic)

 Bottom layer  η = 1.0e+18 Pas

 Fault specifications

 Type  45 degree dipping reverse fault.

 Location  Strike parallel to ydirection with top edge at x = 4 km,
 and bottom edge at x = 20 km. 0 km ≤ y ≤ 16 km; 16 km ≤ z ≤ 0 km

 Slip distribution  1 m of uniform thrust slip motion for 0 km ≤ y ≤ 12 km
 and 12 km ≤ z ≤ 0 km with a linear taper to 0 slip at y = 16 km and
 z = 16 km. In the region where the two tapers overlap, each slip value
 is the minimum of the two tapers (so that the taper remains linear).

 Boundary conditions

 Bottom and side displacements set to analytic solution. (Note: the side
 at y = 0 km has zero ydisplacements because of symmetry). Top of the
 model is a free surface.

 Discretization

 The model should be discretized with nominal spatial resolutions of
 1000 m, 500 m, 250 m. If possible, also run the models with a nominal
 spatial resolution of 125 m. Optionally, use meshes with variable (optimal)
 spatial resolution with the same number of nodes as the uniform resolution
 meshes.

 Element types

 Linear and/or quadratic and tetrahedral and/or hexahedral.


Requested Output

 Solution

 Displacements at all nodes at times of 0, 1, 5, and 10 years as well as
 the mesh topology (i.e., element connectivity arrays and coordinates of
 vertices) and basis functions.

 June 30, 2006  Use ASCII output for now. In the future we will switch
 to using HDF5 files.

 Performance

 * CPU time

 * Wallclock time

 * Memory usage

 * Compiler and platform info

"Truth"

 Okada routines are available to generate an elastic solution. The 'best'
 viscoelastic answer will be derived via mesh refinement. Analytical solutions
 to the viscoelastic solution are being sought if anyone has information.


URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrsnog/descriptionrsnog
Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/geofestinput/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/geofestinput/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/geofestinput/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/geofestinput/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,23 @@
+GeoFEST Input
+
+ Input files for GeoFEST
+
+ * bmrsnog_tet4_1000m.gft.gz (20060831)
+ Gzipped GeoFEST input file for benchmark using linear tetrahedral elements
+ with a 1000m nominal node spacing.
+
+ * bmrsnog_tet4_0500m.gft.gz (20060831)
+ Gzipped GeoFEST input file for benchmark using linear tetrahedral elements
+ with a 500m nominal node spacing.
+
+ * reverse slip (no grav), refined grid 01, no smoothing (GeoFEST 4.5)
+ (20060906) Carl Gable's mesh,
+ see http://meshing.lanl.gov/proj/crustal_dyn_reverse_fault_bm/catalog.html
+
+ * reverse slip (no grav), refined grid 02, no smoothing (GeoFEST 4.5)
+ (20060906) Carl Gable's mesh #02,
+ see http://meshing.lanl.gov/proj/crustal_dyn_reverse_fault_bm/catalog.html
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrsnog/geofestinput
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/geofestinput/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/geofestinput/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/geofestinput/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,23 +0,0 @@
GeoFEST Input

 Input files for GeoFEST

 * bmrsnog_tet4_1000m.gft.gz (20060831)
 Gzipped GeoFEST input file for benchmark using linear tetrahedral elements
 with a 1000m nominal node spacing.

 * bmrsnog_tet4_0500m.gft.gz (20060831)
 Gzipped GeoFEST input file for benchmark using linear tetrahedral elements
 with a 500m nominal node spacing.

 * reverse slip (no grav), refined grid 01, no smoothing (GeoFEST 4.5)
 (20060906) Carl Gable's mesh,
 see http://meshing.lanl.gov/proj/crustal_dyn_reverse_fault_bm/catalog.html

 * reverse slip (no grav), refined grid 02, no smoothing (GeoFEST 4.5)
 (20060906) Carl Gable's mesh #02,
 see http://meshing.lanl.gov/proj/crustal_dyn_reverse_fault_bm/catalog.html


URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrsnog/geofestinput
Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/plots/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/plots/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/plots/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/plots/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,45 @@
+Plone Metadata
+ Plots of ReverseSlip No Gravity Benchmark Results
+ Plots of global and local errors for reverseslip no gravity benchmark
+
+Displacement Field
+
+ "PyLith soln":img:tet4_1000m_pylith_disp_t00.png
+
+ "GeoFEST soln":img:tet4_1000m_geofest_disp_t00.png
+
+Global Error
+
+ "Plot of global error":img:globalerror.png
+
+Local Error
+
+ Elastic solution: Code versus Analytic
+
+ 1000m resolution
+
+ "PyLith error":img:tet4_1000m_pylith_analytic_t00.png
+
+ "GeoFEST error":img:tet4_1000m_geofest_analytic_t00.png
+
+ "COMSOL error":img:tet10_2000m_femlab_analytic_t00.png
+
+ 500m resolution
+
+ "PyLith error":img:tet4_0500m_pylith_analytic_t00.png
+
+ "GeoFEST error":img:tet4_0500m_geofest_analytic_t00.png
+
+ Viscoelastic solution: PyLith versus GeoFEST
+
+ "t0yr":img:tet4_0500m_pylith_geofest_t00.png
+
+ "t1yr":img:tet4_0500m_pylith_geofest_t01.png
+
+ "t5yr":img:tet4_0500m_pylith_geofest_t05.png
+
+ "t10yr":img:tet4_0500m_pylith_geofest_t10.png
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrsnog/plots
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/plots/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/plots/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/plots/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,45 +0,0 @@
Plone Metadata
 Plots of ReverseSlip No Gravity Benchmark Results
 Plots of global and local errors for reverseslip no gravity benchmark

Displacement Field

 "PyLith soln":img:tet4_1000m_pylith_disp_t00.png

 "GeoFEST soln":img:tet4_1000m_geofest_disp_t00.png

Global Error

 "Plot of global error":img:globalerror.png

Local Error

 Elastic solution: Code versus Analytic

 1000m resolution

 "PyLith error":img:tet4_1000m_pylith_analytic_t00.png

 "GeoFEST error":img:tet4_1000m_geofest_analytic_t00.png

 "COMSOL error":img:tet10_2000m_femlab_analytic_t00.png

 500m resolution

 "PyLith error":img:tet4_0500m_pylith_analytic_t00.png

 "GeoFEST error":img:tet4_0500m_geofest_analytic_t00.png

 Viscoelastic solution: PyLith versus GeoFEST

 "t0yr":img:tet4_0500m_pylith_geofest_t00.png

 "t1yr":img:tet4_0500m_pylith_geofest_t01.png

 "t5yr":img:tet4_0500m_pylith_geofest_t05.png

 "t10yr":img:tet4_0500m_pylith_geofest_t10.png


URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrsnog/plots
Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/pylith0.8input/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/pylith0.8input/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/pylith0.8input/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/pylith0.8input/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,30 @@
+PyLith0.8 Input
+
+ Input files for PyLith0.8
+
+ * bmrsnog_hex_1000m.tgz (20060720)
+ Tarball containing PyLith0.8 input files for benchmark using linear hexahedral
+ elements with a 1000m nominal node spacing.
+
+ * bmrsnog_tet4_1000m.tgz (20060720)
+ Tarball containing PyLith0.8 input files for benchmark using linear tetrahedral
+ elements with a 1000m nominal node spacing.
+
+ * bmrsnog_tet4_0500m.tgz (20060720)
+ Tarball containing PyLith0.8 input files for benchmark using linear tetrahedral
+ elements with a 500m nominal node spacing.
+
+ * bmrsnog_tet4_0250m.tgz (20060720)
+ Tarball containing PyLith0.8 input files for benchmark using linear tetrahedral
+ elements with a 250m nominal node spacing.
+
+ * reverse slip (no grav), refined grid 01, no smoothing (20060906)
+ Carl Gable's mesh,
+ see http://meshing.lanl.gov/proj/crustal_dyn_reverse_fault_bm/catalog.html
+
+ * reverse slip (no grav), refined grid 02, no smoothing (20060906)
+ Carl Gable's mesh #2,
+ see http://meshing.lanl.gov/proj/crustal_dyn_reverse_fault_bm/catalog.html
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrsnog/pylith0.8input
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/pylith0.8input/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/pylith0.8input/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/pylith0.8input/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,30 +0,0 @@
PyLith0.8 Input

 Input files for PyLith0.8

 * bmrsnog_hex_1000m.tgz (20060720)
 Tarball containing PyLith0.8 input files for benchmark using linear hexahedral
 elements with a 1000m nominal node spacing.

 * bmrsnog_tet4_1000m.tgz (20060720)
 Tarball containing PyLith0.8 input files for benchmark using linear tetrahedral
 elements with a 1000m nominal node spacing.

 * bmrsnog_tet4_0500m.tgz (20060720)
 Tarball containing PyLith0.8 input files for benchmark using linear tetrahedral
 elements with a 500m nominal node spacing.

 * bmrsnog_tet4_0250m.tgz (20060720)
 Tarball containing PyLith0.8 input files for benchmark using linear tetrahedral
 elements with a 250m nominal node spacing.

 * reverse slip (no grav), refined grid 01, no smoothing (20060906)
 Carl Gable's mesh,
 see http://meshing.lanl.gov/proj/crustal_dyn_reverse_fault_bm/catalog.html

 * reverse slip (no grav), refined grid 02, no smoothing (20060906)
 Carl Gable's mesh #2,
 see http://meshing.lanl.gov/proj/crustal_dyn_reverse_fault_bm/catalog.html

URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrsnog/pylith0.8input
Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/results/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/results/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/results/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/results/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,69 @@
+Results
+
+ Results from benchmark runs. Place tarballs containing the requested results
+ in this folder and describe the run in the description field.
+
+ * GeoFEST reverse fault results  1 km (20060817)
+ Tarball contains input and output files as well as text file
+ containing runtime information
+
+ * GeoFEST reverse fault results  500 m (20060817)
+ Tarball contains input and output files as well as text file
+ containing runtime information
+
+ * Geofest reverse slip var_res_mesh_01_soln (20060905)
+ fixed the BCs, Geofest 4.5, dt=0.1 constant
+
+ * PyLith, 1 proc, linear hex, 1 km resolution, dt=0.1yr (20060829)
+ PyLith results run on 1 processor of a Power Mac G5.
+ Linear hexahedral mesh at 1 km resolution.
+ Constant time step size of 0.1 years.
+
+ * PyLith, 1 proc, linear tet, 1 km resolution, dt=0.1yr (20060829)
+ PyLith results run on 1 processor of a Power Mac G5.
+ Linear tetrahedral mesh at 1 km resolution.
+ Constant time step size of 0.1 years.
+
+ * PyLith, 1 proc, linear tet, 500 m resolution, dt=0.1yr (20060829)
+ PyLith results run on 1 processor of a Power Mac G5.
+ Linear tetrahedral mesh at 500 m resolution.
+ Constant time step size of 0.1 years.
+
+ * PyLith, 1 proc, linear tet, 250 m resolution, dt=0.1yr (20060829)
+ PyLith results run on 1 processor of a Power Mac G5.
+ Linear tetrahedral mesh at 250 m resolution.
+ Constant time step size of 0.1 years.
+
+ * tet_var_res_01_pylith_soln.tgz (20060904)
+ PyLith0.8 results for Carl Gable's variable resolution (no smoothing)
+ mesh 01 for the reverse slip benchmark  constant dt=0.1yr
+
+ * Femlab 2 km resolution, elastic (20061016)
+ This model has 19544 quadratic tetrahedral elements and is twice the
+ size in y of the model description, since there is no symmetric boundary.
+ This yields a resolution close to 2 km. The model and solver require
+ about 800 MB and is solved in about 10 minutes on a 1.8 GHz AMD Opteron.
+
+ * Femlab 1 km resolution, t = 0 years (20061018)
+ This model has ~162000 linear tetrahedral elements and is twice the size
+ in y of the model description, since there is no symmetric boundary.
+ This yields a resolution close to 1 km. The model and the solver require
+ about 800MB and is solved in about 3 minutes on a 1.8 GHz AMD Opteron.
+ An iterative solver was used, which uses the Incomplete LU preconditioner
+ with a drop tolerance of 0.01
+
+ * Femlab 1 km resolution, t = 1 year
+ Viscoelastic problem requires ~3.5GB and takes about 4.5 hrs to run.
+ Drop tolerance is 0.01
+
+ * Femlab 1 km resolution, t = 5 years
+ Viscoelastic problem requires ~3.5GB and takes about 4.5 hrs to run.
+ Drop tolerance is 0.01
+
+ * Femlab 1 km resolution, t = 10 years
+ Viscoelastic problem requires ~3.5GB and takes about 4.5 hrs to run.
+ Drop tolerance is 0.01
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrsnog/results
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/results/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/results/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkrsnog/results/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,69 +0,0 @@
Results

 Results from benchmark runs. Place tarballs containing the requested results
 in this folder and describe the run in the description field.

 * GeoFEST reverse fault results  1 km (20060817)
 Tarball contains input and output files as well as text file
 containing runtime information

 * GeoFEST reverse fault results  500 m (20060817)
 Tarball contains input and output files as well as text file
 containing runtime information

 * Geofest reverse slip var_res_mesh_01_soln (20060905)
 fixed the BCs, Geofest 4.5, dt=0.1 constant

 * PyLith, 1 proc, linear hex, 1 km resolution, dt=0.1yr (20060829)
 PyLith results run on 1 processor of a Power Mac G5.
 Linear hexahedral mesh at 1 km resolution.
 Constant time step size of 0.1 years.

 * PyLith, 1 proc, linear tet, 1 km resolution, dt=0.1yr (20060829)
 PyLith results run on 1 processor of a Power Mac G5.
 Linear tetrahedral mesh at 1 km resolution.
 Constant time step size of 0.1 years.

 * PyLith, 1 proc, linear tet, 500 m resolution, dt=0.1yr (20060829)
 PyLith results run on 1 processor of a Power Mac G5.
 Linear tetrahedral mesh at 500 m resolution.
 Constant time step size of 0.1 years.

 * PyLith, 1 proc, linear tet, 250 m resolution, dt=0.1yr (20060829)
 PyLith results run on 1 processor of a Power Mac G5.
 Linear tetrahedral mesh at 250 m resolution.
 Constant time step size of 0.1 years.

 * tet_var_res_01_pylith_soln.tgz (20060904)
 PyLith0.8 results for Carl Gable's variable resolution (no smoothing)
 mesh 01 for the reverse slip benchmark  constant dt=0.1yr

 * Femlab 2 km resolution, elastic (20061016)
 This model has 19544 quadratic tetrahedral elements and is twice the
 size in y of the model description, since there is no symmetric boundary.
 This yields a resolution close to 2 km. The model and solver require
 about 800 MB and is solved in about 10 minutes on a 1.8 GHz AMD Opteron.

 * Femlab 1 km resolution, t = 0 years (20061018)
 This model has ~162000 linear tetrahedral elements and is twice the size
 in y of the model description, since there is no symmetric boundary.
 This yields a resolution close to 1 km. The model and the solver require
 about 800MB and is solved in about 3 minutes on a 1.8 GHz AMD Opteron.
 An iterative solver was used, which uses the Incomplete LU preconditioner
 with a drop tolerance of 0.01

 * Femlab 1 km resolution, t = 1 year
 Viscoelastic problem requires ~3.5GB and takes about 4.5 hrs to run.
 Drop tolerance is 0.01

 * Femlab 1 km resolution, t = 5 years
 Viscoelastic problem requires ~3.5GB and takes about 4.5 hrs to run.
 Drop tolerance is 0.01

 * Femlab 1 km resolution, t = 10 years
 Viscoelastic problem requires ~3.5GB and takes about 4.5 hrs to run.
 Drop tolerance is 0.01


URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkrsnog/results
Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/descriptionss.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/descriptionss.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/descriptionss.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/descriptionss.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,103 @@
+Plone Metadata
+
+ descriptionss
+ Benchmark Description
+ Benchmark problem description. Formerly known as benchmark 4b.
+
+Summary
+
+ Viscoelastic (Maxwell) relaxation of stresses from a single, finite,
+strikeslip earthquake in 3D without gravity. Evaluate results with imposed
+displacement boundary conditions on a cube with sides of length 24 km. The
+displacements imposed are the analytic elastic solutions. Antiplane strain
+boundary conditions are imposed at y = 0, so the solution is equivalent
+to that for a domain with a 48 km length in the y direction.
+
+Problem Specification
+
+ "Problem geometry":img:benchmark_geometry.png
+
+ Model size  0 km ≤ x ≤ 24 km; 0 km ≤ y ≤ 24 km; 24 ≤ z ≤ 0 km
+
+ Top layer  12 km ≤ z ≤ 0 km
+
+ Bottom layer  24 km ≤ z ≤ 12 km
+
+ Material properties  The top layer is nearly elastic whereas the bottom layer
+ is viscoelastic.
+
+ Elastic  Poisson solid, G = 30 GPa
+
+ Viscoelasticity  Maxwell linear viscoelasticity
+
+ Top layer  η = 1.0e+25 Pas (essentially elastic)
+
+ Bottom layer  η = 1.0e+18 Pas
+
+ Fault specifications
+
+ Type  Vertical rightlateral strikeslip fault.
+
+ Location 
+ Strike parallel to ydirection at center of model (x = 12 km)
+ 0 km ≤ y ≤ 16 km; 16 km ≤ z ≤ 0 km.
+
+ Slip distribution 
+ 1 m of uniform strike slip motion for 0 km ≤ y ≤ 12 km
+ and 12 km ≤ z ≤ 0 km with a linear taper to 0 slip
+ at y = 16 km and z = 16 km. In the region where the two
+ tapers overlap, each slip value is the minimum of the
+ two tapers (so that the taper remains linear).
+
+ Boundary conditions
+
+ Bottom and side displacements are set to the elastic analytical solution,
+ and the top of the model is a free surface. There are two exceptions to
+ these applied boundary conditions. The first is on the y = 0 plane, where
+ ydisplacements are left free to preserve symmetry, and the x and
+ zdisplacements are set to zero. The second is along the line segment
+ between (12, 0, 24) and (12, 24, 24), where the analytical solution
+ blows up in some cases. Along this line segment, all 3 displacement
+ components are left free.
+
+ Discretization
+
+ The model should be discretized with nominal spatial resolutions of
+ 1000 m, 500 m, and 250 m. If possible, also run the models with a nomial
+ spatial resolution of 125 m. Optionally, use meshes with variable
+ (optimal) spatial resolution with the same number of nodes as the
+ uniform resolution meshes.
+
+ Element types
+
+ Linear and/or quadratic and tetrahedral and/or hexahedral.
+
+
+Requested Output
+
+ Solution
+
+ Displacement at all nodes at times of 0, 1, 5, and 10 years as well
+ as the mesh topology (i.e., element connectivity arrays and coordinates
+ of vertices) and basis functions.
+
+ June 30, 2006  Use ASCII output for now. In the future we will switch
+ to using HDF5 files.
+
+ Performance
+
+ * CPU time
+
+ * Wallclock time
+
+ * Memory usage
+
+ * Compiler and platform info
+
+"Truth"
+
+ Okada routines are available to generate an elastic solution. The 'best'
+ viscoelastic answer will be derived via mesh refinement. Analytical solutions
+ to the viscoelastic solution are being sought if anyone has information.
+
+
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/descriptionss.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/descriptionss.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/descriptionss.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,103 +0,0 @@
Plone Metadata

 descriptionss
 Benchmark Description
 Benchmark problem description. Formerly known as benchmark 4b.

Summary

 Viscoelastic (Maxwell) relaxation of stresses from a single, finite,
strikeslip earthquake in 3D without gravity. Evaluate results with imposed
displacement boundary conditions on a cube with sides of length 24 km. The
displacements imposed are the analytic elastic solutions. Antiplane strain
boundary conditions are imposed at y = 0, so the solution is equivalent
to that for a domain with a 48 km length in the y direction.

Problem Specification

 "Problem geometry":img:benchmark_geometry.png

 Model size  0 km ≤ x ≤ 24 km; 0 km ≤ y ≤ 24 km; 24 ≤ z ≤ 0 km

 Top layer  12 km ≤ z ≤ 0 km

 Bottom layer  24 km ≤ z ≤ 12 km

 Material properties  The top layer is nearly elastic whereas the bottom layer
 is viscoelastic.

 Elastic  Poisson solid, G = 30 GPa

 Viscoelasticity  Maxwell linear viscoelasticity

 Top layer  η = 1.0e+25 Pas (essentially elastic)

 Bottom layer  η = 1.0e+18 Pas

 Fault specifications

 Type  Vertical rightlateral strikeslip fault.

 Location 
 Strike parallel to ydirection at center of model (x = 12 km)
 0 km ≤ y ≤ 16 km; 16 km ≤ z ≤ 0 km.

 Slip distribution 
 1 m of uniform strike slip motion for 0 km ≤ y ≤ 12 km
 and 12 km ≤ z ≤ 0 km with a linear taper to 0 slip
 at y = 16 km and z = 16 km. In the region where the two
 tapers overlap, each slip value is the minimum of the
 two tapers (so that the taper remains linear).

 Boundary conditions

 Bottom and side displacements are set to the elastic analytical solution,
 and the top of the model is a free surface. There are two exceptions to
 these applied boundary conditions. The first is on the y = 0 plane, where
 ydisplacements are left free to preserve symmetry, and the x and
 zdisplacements are set to zero. The second is along the line segment
 between (12, 0, 24) and (12, 24, 24), where the analytical solution
 blows up in some cases. Along this line segment, all 3 displacement
 components are left free.

 Discretization

 The model should be discretized with nominal spatial resolutions of
 1000 m, 500 m, and 250 m. If possible, also run the models with a nomial
 spatial resolution of 125 m. Optionally, use meshes with variable
 (optimal) spatial resolution with the same number of nodes as the
 uniform resolution meshes.

 Element types

 Linear and/or quadratic and tetrahedral and/or hexahedral.


Requested Output

 Solution

 Displacement at all nodes at times of 0, 1, 5, and 10 years as well
 as the mesh topology (i.e., element connectivity arrays and coordinates
 of vertices) and basis functions.

 June 30, 2006  Use ASCII output for now. In the future we will switch
 to using HDF5 files.

 Performance

 * CPU time

 * Wallclock time

 * Memory usage

 * Compiler and platform info

"Truth"

 Okada routines are available to generate an elastic solution. The 'best'
 viscoelastic answer will be derived via mesh refinement. Analytical solutions
 to the viscoelastic solution are being sought if anyone has information.


Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/geofestinput/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/geofestinput/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/geofestinput/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/geofestinput/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,28 @@
+
+GeoFEST Input
+
+ Input files for GeoFEST
+
+ * GeoFEST linear tet 1km resolution dt = 0.1 year
+
+ * GeoFEST linear tet 500m resolution dt = 0.1 year
+
+ * GeoFEST linear tet 250m resolution input file
+
+ * GeoFEST / PYRAMID 1km
+ PYRAMID input file for parallel 1km run.
+
+ * GeoFEST / PYRAMID 500m
+ PYRAMID input file for parallel GeoFEST run.
+
+ * GeoFEST / PYRAMID 250m
+ PYRAMID input file for parallel GeoFEST run.
+
+ * GeoFEST linear tet 500m dt = 0.1 year (NEW)
+ The taper problem has been fixed
+
+ * GeoFEST linear tet 250m dt = 0.1 year (NEW)
+ The taper problem has been fixed.
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkstrikeslip/geofestinput
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/geofestinput/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/geofestinput/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/geofestinput/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,28 +0,0 @@

GeoFEST Input

 Input files for GeoFEST

 * GeoFEST linear tet 1km resolution dt = 0.1 year

 * GeoFEST linear tet 500m resolution dt = 0.1 year

 * GeoFEST linear tet 250m resolution input file

 * GeoFEST / PYRAMID 1km
 PYRAMID input file for parallel 1km run.

 * GeoFEST / PYRAMID 500m
 PYRAMID input file for parallel GeoFEST run.

 * GeoFEST / PYRAMID 250m
 PYRAMID input file for parallel GeoFEST run.

 * GeoFEST linear tet 500m dt = 0.1 year (NEW)
 The taper problem has been fixed

 * GeoFEST linear tet 250m dt = 0.1 year (NEW)
 The taper problem has been fixed.

URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkstrikeslip/geofestinput
Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,29 @@
+
+StrikeSlip Benchmark (no gravity)
+
+ Benchmark for strikeslip fault without gravity.
+
+ * Benchmark Description
+ Benchmark problem description. Formerly known as benchmark 4b.
+
+ * PyLith0.8 Input
+ Input files for PyLith0.8
+
+ * GeoFEST Input
+ Input files for GeoFEST
+
+ * Results
+ Results from benchmark runs. Place tarballs containing the
+ requested results in this folder and describe the run in the
+ description field.
+
+ * Plots of Benchmarking Results
+ Plots of benchmarking results showing global and local errors.
+
+ * Geometry for StrikeSlip Benchmark
+ Domain and fault geometry for the strikeslip benchmark.
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks
+
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,29 +0,0 @@

StrikeSlip Benchmark (no gravity)

 Benchmark for strikeslip fault without gravity.

 * Benchmark Description
 Benchmark problem description. Formerly known as benchmark 4b.

 * PyLith0.8 Input
 Input files for PyLith0.8

 * GeoFEST Input
 Input files for GeoFEST

 * Results
 Results from benchmark runs. Place tarballs containing the
 requested results in this folder and describe the run in the
 description field.

 * Plots of Benchmarking Results
 Plots of benchmarking results showing global and local errors.

 * Geometry for StrikeSlip Benchmark
 Domain and fault geometry for the strikeslip benchmark.


URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/plots/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/plots/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/plots/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/plots/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,48 @@
+Plots of StrikeSlip No Gravity Benchmark Results
+ Plots of global and local errors for strikeslip no gravity benchmark
+
+Displacement Field
+
+ "PyLith soln":img:tet4_1000m_pylith_disp_t00.png
+
+ "GeoFEST soln":img:tet4_1000m_geofest_disp_t00.png
+
+Global Error
+
+ "Plot of global error":img:globalerror.png
+
+Local Error
+
+ Elastic solution: Code versus Analytic
+
+ 250m resolution
+
+ "PyLith error":img:tet4_0250m_pylith_analytic_t00.png
+
+ "GeoFEST error":img:tet4_0250m_geofest_analytic_t00.png
+
+ 500m resolution
+
+ "PyLith error":img:tet4_0500m_pylith_analytic_t00.png
+
+ "GeoFEST error":img:tet4_0500m_geofest_analytic_t00.png
+
+ Viscoelastic solution: PyLith versus GeoFEST
+
+ 250m resolution
+
+ "t0yr":img:tet4_0250m_pylith_geofest_t00.png
+
+ 500m resolution
+
+ "t0yr":img:tet4_0500m_pylith_geofest_t00.png
+
+ "t1yr":img:tet4_0500m_pylith_geofest_t01.png
+
+ "t5yr":img:tet4_0500m_pylith_geofest_t05.png
+
+ "t10yr":img:tet4_0500m_pylith_geofest_t10.png
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkstrikeslip/plots
+
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/plots/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/plots/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/plots/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,48 +0,0 @@
Plots of StrikeSlip No Gravity Benchmark Results
 Plots of global and local errors for strikeslip no gravity benchmark

Displacement Field

 "PyLith soln":img:tet4_1000m_pylith_disp_t00.png

 "GeoFEST soln":img:tet4_1000m_geofest_disp_t00.png

Global Error

 "Plot of global error":img:globalerror.png

Local Error

 Elastic solution: Code versus Analytic

 250m resolution

 "PyLith error":img:tet4_0250m_pylith_analytic_t00.png

 "GeoFEST error":img:tet4_0250m_geofest_analytic_t00.png

 500m resolution

 "PyLith error":img:tet4_0500m_pylith_analytic_t00.png

 "GeoFEST error":img:tet4_0500m_geofest_analytic_t00.png

 Viscoelastic solution: PyLith versus GeoFEST

 250m resolution

 "t0yr":img:tet4_0250m_pylith_geofest_t00.png

 500m resolution

 "t0yr":img:tet4_0500m_pylith_geofest_t00.png

 "t1yr":img:tet4_0500m_pylith_geofest_t01.png

 "t5yr":img:tet4_0500m_pylith_geofest_t05.png

 "t10yr":img:tet4_0500m_pylith_geofest_t10.png

URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkstrikeslip/plots

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/pylith0.8input/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/pylith0.8input/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/pylith0.8input/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/pylith0.8input/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,19 @@
+PyLith0.8 Input
+
+ Input files for PyLith0.8
+
+ * bmssnog_tet4_1000m.tgz
+ Tarball containing PyLith0.8 input files for benchmark using
+ linear tetrahedral elements with a 1000m nominal node spacing.
+
+ * bmssnog_tet4_0500m.tgz
+ Tarball containing PyLith0.8 input files for benchmark using
+ linear tetrahedral elements with a 500m nominal node spacing.
+
+ * bmssnog_tet4_0250m.tgz
+ Tarball containing PyLith0.8 input files for benchmark using
+ linear tetrahedral elements with a 250m nominal node spacing.
+
+Original URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkstrikeslip/pylith0.8input/
+
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/pylith0.8input/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/pylith0.8input/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/pylith0.8input/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,19 +0,0 @@
PyLith0.8 Input

 Input files for PyLith0.8

 * bmssnog_tet4_1000m.tgz
 Tarball containing PyLith0.8 input files for benchmark using
 linear tetrahedral elements with a 1000m nominal node spacing.

 * bmssnog_tet4_0500m.tgz
 Tarball containing PyLith0.8 input files for benchmark using
 linear tetrahedral elements with a 500m nominal node spacing.

 * bmssnog_tet4_0250m.tgz
 Tarball containing PyLith0.8 input files for benchmark using
 linear tetrahedral elements with a 250m nominal node spacing.

Original URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkstrikeslip/pylith0.8input/

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/results/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/results/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/results/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/results/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,84 @@
+Results
+
+ Results from benchmark runs. Place tarballs containing the requested results
+ in this folder, and describe the run in the description field.
+
+ * PyLith, 1 proc, linear tet, 1km resolution, dt=0.1yr (20060829)
+ PyLith results run on 1 processor of a Power Mac G5.
+ Linear tetrahedral mesh at 1km resolution.
+ Constant time step size of 0.1 year.
+
+ * PyLith, 1 proc, linear hex, 1km resolution, dt=0.1yr (20060829)
+ PyLith results on 1 processor of a Power Mac G5.
+ Linear hexahedral mesh at 1km resolution.
+ Constant time step size of 0.1 year.
+
+ * PyLith, 1 proc, linear tet, 500m resolution, dt=0.1yr (20060829)
+ PyLith results run on 1 processor of a Power Mac G5.
+ Linear tetrahedral mesh at 500m resolution.
+ Constant time step size of 0.1 year.
+
+ * PyLith Revised Results, 500m, New BC and Split Node Input (20070130)
+ New solution using revised BC and split node inputs. The revised BC
+ take care of the problems of defining BC on the fault plane (or in
+ some cases the projected fault plane). The new split node inputs
+ no longer assume a bilinear slip distribution in the region where
+ the fault tapers overlap, and now assumes a taper consistent with
+ what is used for the analytical solution.
+
+ * PyLith Revised Results, 500m, Altered BC for Viscoelastic Solution (20070206)
+ New version where BC have been altered from those of previous version
+ to make viscoelastic results consistent with those from GeoFEST.
+ The revised BC do not pin ycomponent on the y=0 plane, and no BC
+ are applied along the intersection of the fault plane (or its projection)
+ along y=0 and z=24.
+
+ * PyLith, 1 proc, linear tet, 250m resolution, dt=0.1yr (20060907)
+ PyLith results run on 1 processor of an Opteron 2.4GHz Linux machine.
+ Linear tetrahedral mesh at 250m resolution.
+ Constant time step size of 0.1 year.
+
+ * GeoFEST / PYRAMID 1km (20060906)
+ Parallel results using 64 processors of Intel/Linux Cluster
+ with GeoFEST4.5 and Pyramid2.1.3
+
+ * GeoFEST / PYRAMID 500m (20060906)
+ Parallel results using 64 processors of Intel/Linux Cluster
+ with GeoFEST4.5 and Pyramid2.1.3
+
+ * GeoFEST / PYRAMID 250m (20060906)
+ Parallel results using 128 processors of Intel/Linux Cluster
+ with GeoFEST4.5 and Pyramid2.1.3
+
+ * GeoFEST linear tet 1km resolution dt=0.1yr (updated) (20060921)
+ The taper error has been fixed.
+
+ * GeoFEST LinearTet 500m ReRun (20061129)
+
+ * GeoFEST LinearTet 250m ReRun (20061129)
+
+ * Femlab 1km resolution, t = 0 years (20061017)
+ This model has ~162,000 linear tetrahedral elements and is twice the
+ size in y of the model description, since there is no symmetric boundary.
+ This yields a resolution close to 1km. The model and solver require
+ almost 800MB and is solved in about 3 minutes on a 1.8 GHz AMD Opteron.
+ An iterative solver was used, which uses the Incomplete LU preconditioner
+ with a drop tolerance of 0.01. Decreasing this value has very little
+ effect on the error but takes longer to solve.
+
+ * Femlab 1km resolution, t = 1 year (20061017)
+ Viscoelastic problem requires ~3.5GB and takes about 4.5 hours to run.
+ Drop tolerance is 0.01.
+
+ * Femlab 1km resolution, t = 5 years (20061017)
+ Viscoelastic problem requires ~3.5GB and takes about 4.5 hours to run.
+ Drop tolerance is 0.01.
+
+ * Femlab 1km resolution, t = 10 years (20061017)
+ Viscoelastic problem requires ~3.5GB and takes about 4.5 hours to run.
+ Drop tolerance is 0.01.
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkstrikeslip/results
+
Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/results/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/results/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmarkstrikeslip/results/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,84 +0,0 @@
Results

 Results from benchmark runs. Place tarballs containing the requested results
 in this folder, and describe the run in the description field.

 * PyLith, 1 proc, linear tet, 1km resolution, dt=0.1yr (20060829)
 PyLith results run on 1 processor of a Power Mac G5.
 Linear tetrahedral mesh at 1km resolution.
 Constant time step size of 0.1 year.

 * PyLith, 1 proc, linear hex, 1km resolution, dt=0.1yr (20060829)
 PyLith results on 1 processor of a Power Mac G5.
 Linear hexahedral mesh at 1km resolution.
 Constant time step size of 0.1 year.

 * PyLith, 1 proc, linear tet, 500m resolution, dt=0.1yr (20060829)
 PyLith results run on 1 processor of a Power Mac G5.
 Linear tetrahedral mesh at 500m resolution.
 Constant time step size of 0.1 year.

 * PyLith Revised Results, 500m, New BC and Split Node Input (20070130)
 New solution using revised BC and split node inputs. The revised BC
 take care of the problems of defining BC on the fault plane (or in
 some cases the projected fault plane). The new split node inputs
 no longer assume a bilinear slip distribution in the region where
 the fault tapers overlap, and now assumes a taper consistent with
 what is used for the analytical solution.

 * PyLith Revised Results, 500m, Altered BC for Viscoelastic Solution (20070206)
 New version where BC have been altered from those of previous version
 to make viscoelastic results consistent with those from GeoFEST.
 The revised BC do not pin ycomponent on the y=0 plane, and no BC
 are applied along the intersection of the fault plane (or its projection)
 along y=0 and z=24.

 * PyLith, 1 proc, linear tet, 250m resolution, dt=0.1yr (20060907)
 PyLith results run on 1 processor of an Opteron 2.4GHz Linux machine.
 Linear tetrahedral mesh at 250m resolution.
 Constant time step size of 0.1 year.

 * GeoFEST / PYRAMID 1km (20060906)
 Parallel results using 64 processors of Intel/Linux Cluster
 with GeoFEST4.5 and Pyramid2.1.3

 * GeoFEST / PYRAMID 500m (20060906)
 Parallel results using 64 processors of Intel/Linux Cluster
 with GeoFEST4.5 and Pyramid2.1.3

 * GeoFEST / PYRAMID 250m (20060906)
 Parallel results using 128 processors of Intel/Linux Cluster
 with GeoFEST4.5 and Pyramid2.1.3

 * GeoFEST linear tet 1km resolution dt=0.1yr (updated) (20060921)
 The taper error has been fixed.

 * GeoFEST LinearTet 500m ReRun (20061129)

 * GeoFEST LinearTet 250m ReRun (20061129)

 * Femlab 1km resolution, t = 0 years (20061017)
 This model has ~162,000 linear tetrahedral elements and is twice the
 size in y of the model description, since there is no symmetric boundary.
 This yields a resolution close to 1km. The model and solver require
 almost 800MB and is solved in about 3 minutes on a 1.8 GHz AMD Opteron.
 An iterative solver was used, which uses the Incomplete LU preconditioner
 with a drop tolerance of 0.01. Decreasing this value has very little
 effect on the error but takes longer to solve.

 * Femlab 1km resolution, t = 1 year (20061017)
 Viscoelastic problem requires ~3.5GB and takes about 4.5 hours to run.
 Drop tolerance is 0.01.

 * Femlab 1km resolution, t = 5 years (20061017)
 Viscoelastic problem requires ~3.5GB and takes about 4.5 hours to run.
 Drop tolerance is 0.01.

 * Femlab 1km resolution, t = 10 years (20061017)
 Viscoelastic problem requires ~3.5GB and takes about 4.5 hours to run.
 Drop tolerance is 0.01.


URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmarkstrikeslip/results

Copied: doc/geodynamics.org/benchmarks/trunk/short/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,52 @@
+
+ShortTerm Tectonics Benchmarks
+
+"Overview":overview
+
+Benchmarks
+
+ Strikeslip (no gravity)
+
+ * "Description":benchmarkstrikeslip/descriptionss
+
+ * "PyLith input":benchmarkstrikeslip/pylith0.8input
+
+ * "GeoFEST input":benchmarkstrikeslip/geofestinput
+
+ * "Submitted results":benchmarkstrikeslip/result
+
+ * "Plots of results":benchmarkstrikeslip/plots
+
+ Reverseslip (no gravity)
+
+ * "Description":benchmarkrsnog/descriptionrsnog
+
+ * "PyLith input":benchmarkrsnog/pylith0.8input
+
+ * "GeoFEST input":benchmarkrsnog/geofestinput
+
+ * "Submitted results":benchmarkrsnog/results
+
+ * "Plots of results":benchmarkrsnog/plots
+
+ Reverseslip (with gravity)
+
+ * "Description":benchmarkrs/descriptionrs
+
+ * PyLith input (coming soon)
+
+ * GeoFEST input (coming soon)
+
+ * "Submitted results":benchmarkrs/results
+
+ LandersHector Mine
+
+ * "Description":benchmarklanders/descriptionlanders
+
+ * Mesh constructed with LaGriT (coming soon)
+
+Utilities
+
+ * "Analytic and SemiAnalytic Codes":utilities
+
+ * "CUBIT examples":utilities/CUBITex
Deleted: doc/geodynamics.org/benchmarks/trunk/short/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,52 +0,0 @@

ShortTerm Tectonics Benchmarks

"Overview":overview

Benchmarks

 Strikeslip (no gravity)

 * "Description":benchmarkstrikeslip/descriptionss

 * "PyLith input":benchmarkstrikeslip/pylith0.8input

 * "GeoFEST input":benchmarkstrikeslip/geofestinput

 * "Submitted results":benchmarkstrikeslip/result

 * "Plots of results":benchmarkstrikeslip/plots

 Reverseslip (no gravity)

 * "Description":benchmarkrsnog/descriptionrsnog

 * "PyLith input":benchmarkrsnog/pylith0.8input

 * "GeoFEST input":benchmarkrsnog/geofestinput

 * "Submitted results":benchmarkrsnog/results

 * "Plots of results":benchmarkrsnog/plots

 Reverseslip (with gravity)

 * "Description":benchmarkrs/descriptionrs

 * PyLith input (coming soon)

 * GeoFEST input (coming soon)

 * "Submitted results":benchmarkrs/results

 LandersHector Mine

 * "Description":benchmarklanders/descriptionlanders

 * Mesh constructed with LaGriT (coming soon)

Utilities

 * "Analytic and SemiAnalytic Codes":utilities

 * "CUBIT examples":utilities/CUBITex
Copied: doc/geodynamics.org/benchmarks/trunk/short/overview.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/overview.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/overview.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/overview.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,69 @@
+Short Name: overview
+Title: Overview
+Description: Overview of benchmark suite
+
+Overview of Goals and Objectives
+
+ In order to test the accuracy and speed of various elastic and viscoelastic
+finite element calculations using different codes on different platforms, we
+have developed the following benchmark comparisons. Information resulting from
+the benchmark comparisons will be used for the following purposes.
+
+ 1 Confirming proper numerical implementation of the physics include
+ rheological laws, fault constitutive laws, etc.
+
+ 1 Testing the accuracy of the numerical implementations as a function
+ of meshing scheme, number of nodes, element type, timestepping scheme,
+ code, etc.
+
+ 1 Testing the computational efficiency of different codes, solvers, and
+ modeling techniques as a function of meshing scheme, number of nodes,
+ element type, timestepping scheme, code, etc.
+
+ 1 Comparing and evaluating available finite element codes.
+
+ Based on the comparisons, we would like to be able to (1) identify and correct any
+errors in numerical implementation which currently exist in any of the considered
+codes, (2) quantify differences in numerical solutions as a function of meshing
+scheme, number of nodes, element type, timestepping scheme, code, etc., and (3)
+quantify and, if possible, minimize model induced uncertainties resulting from
+discretization, model boundaries, unexpected transients in timedependent materials,
+etc.
+
+General Methodology
+
+ All benchmark descriptions assume a righthanded Cartesian coordinate system
+with the xdirection running east, the ydirection running north, and the
+zdirection running up. If a boundary condition is applied at a depth, d, this
+will correspond to z = d. The surface is always assumed to be at z = 0.
+Use whatever coordinate system is most convienient for your program, but please
+convert the results to the one defined here.
+
+ Benchmark meshes will be described at the coarsest level to be run. Because meshes
+may be either structured or unstructured, the mesh nodal spacing described refers
+to the average. If memory, time, and patience allow, also run models at 1/2, 1/4,
+1/8, etc. the original coarse node spacing. This will make it possible to see how
+accuracy and speed scale with mesh spacing. If your code permits a variety of
+element types, also run models using various types of elements (linear vs.
+quadrilateral; hexahedral vs. tetrahedral, full vs. reduced integration). This
+will make it possible to see how accuracy and speed change with element type.
+Finally, variable mesh spacing degrades accuracy, but, for economy, we would like
+to employ a variable mesh (e.g., to resolve stress variations at the fault tips,
+etc.) If time permits, investigate the tradeoffs involved in using variable
+resolution meshes.
+
+ With regard to output, there are a number of parameters which should be noted
+for each model. For the purposes of determining accuracy, please record displacements
+at all nodes and stresses (all 6 independent components) at all Gauss points
+at each specified time. For the purposes of evaluating performance, please try
+to keep track of memory usage (including the size of stiffness matrix and mean
+execution time, etc.) More details regarding the submission of your results for
+inclusion in the summary analysis can be found at this document. To ease the
+burden on those who are compiling the data, your results will not be accepted
+unless they are in the specified format.
+
+ When available, analytical solutions for the various benchmarks will be given
+on the CIG website at http://XXXXXXXX. Whenever possible, please check to make
+sure your results are essentially correct before submitting them for the summary
+analysis.
+
Deleted: doc/geodynamics.org/benchmarks/trunk/short/overview.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/overview.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/overview.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,69 +0,0 @@
Short Name: overview
Title: Overview
Description: Overview of benchmark suite

Overview of Goals and Objectives

 In order to test the accuracy and speed of various elastic and viscoelastic
finite element calculations using different codes on different platforms, we
have developed the following benchmark comparisons. Information resulting from
the benchmark comparisons will be used for the following purposes.

 1 Confirming proper numerical implementation of the physics include
 rheological laws, fault constitutive laws, etc.

 1 Testing the accuracy of the numerical implementations as a function
 of meshing scheme, number of nodes, element type, timestepping scheme,
 code, etc.

 1 Testing the computational efficiency of different codes, solvers, and
 modeling techniques as a function of meshing scheme, number of nodes,
 element type, timestepping scheme, code, etc.

 1 Comparing and evaluating available finite element codes.

 Based on the comparisons, we would like to be able to (1) identify and correct any
errors in numerical implementation which currently exist in any of the considered
codes, (2) quantify differences in numerical solutions as a function of meshing
scheme, number of nodes, element type, timestepping scheme, code, etc., and (3)
quantify and, if possible, minimize model induced uncertainties resulting from
discretization, model boundaries, unexpected transients in timedependent materials,
etc.

General Methodology

 All benchmark descriptions assume a righthanded Cartesian coordinate system
with the xdirection running east, the ydirection running north, and the
zdirection running up. If a boundary condition is applied at a depth, d, this
will correspond to z = d. The surface is always assumed to be at z = 0.
Use whatever coordinate system is most convienient for your program, but please
convert the results to the one defined here.

 Benchmark meshes will be described at the coarsest level to be run. Because meshes
may be either structured or unstructured, the mesh nodal spacing described refers
to the average. If memory, time, and patience allow, also run models at 1/2, 1/4,
1/8, etc. the original coarse node spacing. This will make it possible to see how
accuracy and speed scale with mesh spacing. If your code permits a variety of
element types, also run models using various types of elements (linear vs.
quadrilateral; hexahedral vs. tetrahedral, full vs. reduced integration). This
will make it possible to see how accuracy and speed change with element type.
Finally, variable mesh spacing degrades accuracy, but, for economy, we would like
to employ a variable mesh (e.g., to resolve stress variations at the fault tips,
etc.) If time permits, investigate the tradeoffs involved in using variable
resolution meshes.

 With regard to output, there are a number of parameters which should be noted
for each model. For the purposes of determining accuracy, please record displacements
at all nodes and stresses (all 6 independent components) at all Gauss points
at each specified time. For the purposes of evaluating performance, please try
to keep track of memory usage (including the size of stiffness matrix and mean
execution time, etc.) More details regarding the submission of your results for
inclusion in the summary analysis can be found at this document. To ease the
burden on those who are compiling the data, your results will not be accepted
unless they are in the specified format.

 When available, analytical solutions for the various benchmarks will be given
on the CIG website at http://XXXXXXXX. Whenever possible, please check to make
sure your results are essentially correct before submitting them for the summary
analysis.

Copied: doc/geodynamics.org/benchmarks/trunk/short/utilities/CUBITex.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/utilities/CUBITex.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/utilities/CUBITex.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/utilities/CUBITex.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,17 @@
+
+Example Journal Files for CUBIT
+
+ From the 2009 NMCDEF meeting in Golden, CO
+
+ * Meshing example (20090623)
+ Very short example of meshing a pyramid and displaying mesh
+
+ * Geometry test (20090623)
+ Example of building geometrical shapes with merging, subtracting, moving, etc.
+
+ * Fault example (20090623)
+ Example of building and meshing (coarsely) a region around a dipping fault patch.
+
+
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/utilities/CUBITex
Deleted: doc/geodynamics.org/benchmarks/trunk/short/utilities/CUBITex.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/utilities/CUBITex.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/utilities/CUBITex.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,17 +0,0 @@

Example Journal Files for CUBIT

 From the 2009 NMCDEF meeting in Golden, CO

 * Meshing example (20090623)
 Very short example of meshing a pyramid and displaying mesh

 * Geometry test (20090623)
 Example of building geometrical shapes with merging, subtracting, moving, etc.

 * Fault example (20090623)
 Example of building and meshing (coarsely) a region around a dipping fault patch.


URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/utilities/CUBITex
Copied: doc/geodynamics.org/benchmarks/trunk/short/utilities/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/utilities/index.txt)
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/utilities/index.rst (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/utilities/index.rst 20090918 20:02:16 UTC (rev 15676)
@@ 0,0 +1,2 @@
+URL
+ http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/utilities
Deleted: doc/geodynamics.org/benchmarks/trunk/short/utilities/index.txt
===================================================================
 doc/geodynamics.org/benchmarks/trunk/short/utilities/index.txt 20090918 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/utilities/index.txt 20090918 20:02:16 UTC (rev 15676)
@@ 1,2 +0,0 @@
URL
 http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/utilities
More information about the CIGCOMMITS
mailing list