# [cig-commits] r15676 - in doc/geodynamics.org/benchmarks/trunk: . geodyn long magma mc mc/2d-cartesian short short/benchmark-landers short/benchmark-rs short/benchmark-rs/results short/benchmark-rs-nog short/benchmark-rs-nog/geofest-input short/benchmark-rs-nog/plots short/benchmark-rs-nog/pylith-0.8-input short/benchmark-rs-nog/results short/benchmark-strikeslip short/benchmark-strikeslip/geofest-input short/benchmark-strikeslip/plots short/benchmark-strikeslip/pylith-0.8-input short/benchmark-strikeslip/results short/utilities

luis at geodynamics.org luis at geodynamics.org
Fri Sep 18 13:02:19 PDT 2009

Author: luis
Date: 2009-09-18 13:02:16 -0700 (Fri, 18 Sep 2009)
New Revision: 15676

doc/geodynamics.org/benchmarks/trunk/magma/index.rst
doc/geodynamics.org/benchmarks/trunk/magma/mckenzie-equations.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/short/benchmark-landers/description-landers.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/description-rs-nog.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/geofest-input/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/plots/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/pylith-0.8-input/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/results/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/description-rs.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/results/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/description-ss.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/geofest-input/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/plots/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/pylith-0.8-input/index.rst
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/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/mckenzie-equations.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/short/benchmark-landers/description-landers.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/description-rs-nog.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/geofest-input/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/plots/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/pylith-0.8-input/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/results/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/description-rs.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/results/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/description-ss.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/geofest-input/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/plots/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/pylith-0.8-input/index.txt
doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/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/circular-inclusion.rst
doc/geodynamics.org/benchmarks/trunk/long/divergence.rst
doc/geodynamics.org/benchmarks/trunk/long/drucker-prager.rst
doc/geodynamics.org/benchmarks/trunk/long/falling-sphere.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/relaxation-topography.rst
doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/index.rst
doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite1.rst
doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite2.rst
doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite3.rst
doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite4.rst
doc/geodynamics.org/benchmarks/trunk/mc/index.rst
doc/geodynamics.org/benchmarks/trunk/mc/notes-on-mantle-convection-benchmarks.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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/geodyn/index.rst	2009-09-18 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
non-magnetic convection. Case 1 is a dynamo with an insulating inner core
co-rotating 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 non-magnetic convection case 0, and
is $Pm = 5$ in case 1. The spherical harmonic expansion is truncated at
degree $\ell_{max}=32$ and a four-fold 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
-~/bench-data/data_bench0 and ~/bench-data/data-bench1 respectively.
+The output files of the benchmark cases are stored n the directory
+~/bench-data/data_bench0 and ~/bench-data/data-bench1 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 32-bit and 64-bit Intel processors. Figure
[fig:Field-Plot1] 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/field-64.ps
-  Figure [fig:Field-Plot1]: Field Plot for Reversal Dynamo Case
+.. figure:: images/field-64.ps
+   Figure [fig:Field-Plot1]:
+   Field Plot for Reversal Dynamo Case
+
+.. figure:: images/field-64-revR.ps
+   Figure [fig:Field-Plot2]:
+   Field Plot for Reversal Dynamo Case (longer run)

-  image:: images/field-64-revR.ps
-  Figure [fig:Field-Plot2]: Field Plot for Reversal Dynamo Case (longer run)
-
-  image:: images/g1revR.ps
-  image:: images/g7revR.ps
-  Figure [fig:The-pole]: Magnetic Field Pole Plot. The top s the pole plot
+.. figure:: images/g1revR.ps
+.. figure:: images/g7revR.ps
+  Figure [fig:The-pole]: 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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/index.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -5,13 +5,15 @@
Benchmark Efforts by Working Group
----------------------------------

-  * "Short-Term Crustal Dynamics":http://geodynamics.org/cig/software/benchmarks/short/
+* Short-Term Crustal Dynamics__
+* Long-Term Tectonics__
+* Mantle Convection__
+* Magma Migration__
+* Geodynamo__

-  * "Long-Term 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/circular-inclusion.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/long/circular-inclusion.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/circular-inclusion.rst	2009-09-18 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:inclusion-setup].
+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:inclusion-setup].

-    image:: images/inclusion_setup.eps
-    Figure [fig:inclusion-setup]
-    Schematic for the circular inclusion benchmark
+.. figure:: images/inclusion_setup.eps
+   Figure [fig:inclusion-setup]
+   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
-  top-right 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
+top-right 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:Pressure-inclusion] 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:Pressure-inclusion] 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:Pressure-inclusion]
-    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:Pressure-inclusion]
+   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:Pressure-error] 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:Scaled-pressure-error] 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:Pressure-error] 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:Scaled-pressure-error] 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:Pressure-error]
-    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:Pressure-error]
+   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:Scaled-pressure-error]
-    As in Figure [fig:Pressure-error], but with the error scaled with $h$.
-    So the medium-resolution error is multiplied by 2 and the
-    high-resolution error is multiplied by 4.
+.. figure:: images/inclusion_r8_p_scaled_error.png
+   Figure [fig:Scaled-pressure-error]
+   As in Figure [fig:Pressure-error], but with the error scaled with $h$.
+   So the medium-resolution error is multiplied by 2 and the
+   high-resolution error is multiplied by 4.

Modified: doc/geodynamics.org/benchmarks/trunk/long/divergence.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/long/divergence.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/divergence.rst	2009-09-18 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/drucker-prager.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/long/drucker-prager.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/drucker-prager.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -5,57 +5,58 @@
Analytic Treatment
------------------

-  For the Drucker-Prager 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 Drucker-Prager 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:Mohr-Coulomb-setup]. 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:Mohr-Coulomb-setup]. 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:Mohr-Coulomb-setup]
-    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:Mohr-Coulomb-setup]
+   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:Mohr-Coulomb-sri] 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:Mohr-Coulomb-comparison] 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 Drucker-Prager
-  implementation gives the correct results.
+Figure [fig:Mohr-Coulomb-sri] 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:Mohr-Coulomb-comparison] 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 Drucker-Prager
+implementation gives the correct results.

-    image:: images/Mohr_coulomb_resolutions.png
-    Figure [fig:Mohr-Coulomb-sri]
-    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:Mohr-Coulomb-sri]
+   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:Mohr-Coulomb-comparison]
-    Numerical vs. analytic results for fault angles as a function of
-    internal angle of friction.
+.. figure:: images/mohr_coulomb_angles.eps
+   Figure [fig:Mohr-Coulomb-comparison]
+   Numerical vs. analytic results for fault angles as a function of
+   internal angle of friction.

Modified: doc/geodynamics.org/benchmarks/trunk/long/falling-sphere.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/long/falling-sphere.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/falling-sphere.rst	2009-09-18 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:Sphere-Cylinder]
+This benchmark simulates a rigid sphere falling through a cylinder filled
+with a viscous medium as in Figure [fig:Sphere-Cylinder]

-    image:: sphere_cylinder.eps
-    Figure [fig:Sphere-Cylinder]
-    Schematic of a Sphere falling through a Cylinder.
+.. figure:: sphere_cylinder.eps
+   Figure [fig:Sphere-Cylinder]
+   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
-  $$F_H=6\pi\eta{ru}\frac{1-0.75857\left(\frac{r}{R}\right)^5}{1+f_H\left(\frac{r}{R}\right)},$$
-  where
-  $$f_H\left(\frac{r}{R}\right)=-2.1050(r/R)+2.0865(r/R)^3-1.7068(r/R)^5+0.72603(r/R)^6.$$
+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
+$$F_H=6\pi\eta{ru}\frac{1-0.75857\left(\frac{r}{R}\right)^5}{1+f_H\left(\frac{r}{R}\right)},$$
+where
+$$f_H\left(\frac{r}{R}\right)=-2.1050(r/R)+2.0865(r/R)^3-1.7068(r/R)^5+0.72603(r/R)^6.$$

-  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:Error-in-velocity]. 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:Error-in-velocity]. 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:Error-in-velocity]
-    Error in computed velocity vs. resolution.
+.. figure:: images/Sphere_Error.eps
+   Figure [fig:Error-in-velocity]
+   Error in computed velocity vs. resolution.

-  Scaling the error with resolution gives Figure [fig:Scaled-error-velocity].
-  The error scales linearly with resolution, giving us confidence that we
-  can accurately solve this problem.
+Scaling the error with resolution gives Figure [fig:Scaled-error-velocity].
+The error scales linearly with resolution, giving us confidence that we
+can accurately solve this problem.

-    image:: images/Sphere_Scaled_Error.eps
-    Figure [fig:Scaled-error-velocity]
-    As in figure [fig:Error-in-velocity], 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:Scaled-error-velocity]
+   As in figure [fig:Error-in-velocity], 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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/geomod2004.rst	2009-09-18 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:Extension-model-setup]. 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:Extension-model-setup]. 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:Extension-model-setup]
-    Extension model setup. Reproduced, with permission, from Buiter et al.
-    [Buiter et al Numerical Sandbox]
+.. figure:: images/Extension_setup.png
+   Figure [fig:Extension-model-setup]
+   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:Comparison-extension]. 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:extension-convergence]
-  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:Comparison-extension]. 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:extension-convergence]
+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:Comparison-extension]
-    Strain rate invariant for the numerical extension models after 5 cm of
-    extension. The resolutions of the various models are:
-    I2ELVIS:  $400 \times 75$
-    LAPEX-2D: $301 \times 71$
-    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:Comparison-extension]
+   Strain rate invariant for the numerical extension models after 5 cm of
+   extension. The resolutions of the various models are:
+   I2ELVIS:  $400 \times 75$
+   LAPEX-2D: $301 \times 71$
+   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:extension-convergence]
-    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:extension-convergence]
+   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:Shortening-model-setup]. 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:Shortening-model-setup]. 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 (LAPEX-2D: $10^{-6}\ m^2\ s^{-1}$, 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 (LAPEX-2D: $10^{-6}\ m^2\ s^{-1}$, 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:Shortening-model-setup]
-    Shortening model setup. Reproduced, with permission, from Buiter et al.
-    [Buiter et al Numerical Sandbox].
+.. figure:: images/Shortening_setup.png
+   Figure [fig:Shortening-model-setup]
+   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:shortening-compare]. 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:shortening-convergence]
-  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:shortening-compare]. 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:shortening-convergence]
+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:shortening-compare]
-    Strain rate invariant for the numerical shortening models after 14 cm
-    of shortening. The resolutions of the various models are:
-    I2ELVIS:  900 x 75,
-    LAPEX-2D: 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:shortening-compare]
+   Strain rate invariant for the numerical shortening models after 14 cm
+   of shortening. The resolutions of the various models are:
+   I2ELVIS:  900 x 75,
+   LAPEX-2D: 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:shortening-convergence]
-    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:shortening-convergence]
+   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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/geomod2008.rst	2009-09-18 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:Unstable-setup]. 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:Unstable-setup]. 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:Unstable-setup]
-    Setup for the unstable shortening benchmark.
-    Image courtesy of Susanne Buiter.
+.. figure:: images/Geomod2008_unstable_setup.eps
+   Figure [fig:Unstable-setup]
+   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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/index.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -3,36 +3,26 @@
==========

* Falling Sphere
-
* Circular Inclusion
-
* Relaxation of Topography
-
* Divergence
-
* Drucker-Prager
-
* Geomod 2004
-
* Extension
-
* Shortening
-
* Geomod 2008
-
* Stable Wedge
-
* Unstable Shortening
-
* Brittle Shortening

-

+-----

-* "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/relaxation-topography.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/long/relaxation-topography.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/long/relaxation-topography.rst	2009-09-18 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:Strain-topo] shows the results of a low-resolution
-  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:Strain-topo] shows the results of a low-resolution
+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 [Strain-topo]
-    Strain rate and velocities for a sinusoidal topography relaxing under
-    gravity.
+.. figure:: images/Paraview_topography.png
+   Figure [Strain-topo]
+   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:topo-error]. Scaling the error
-  with resolution gives Figure [fig:scaled-topo-error]. 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:topo-error]. Scaling the error
+with resolution gives Figure [fig:scaled-topo-error]. The error decreases
+linearly with increasing resolution, giving us confidence in our ability
+to accurately track topography.

-    image:: images/topo_error.eps
-    Figure [fig:topo-error]
-    Error in the height at the trough
+.. figure:: images/topo_error.eps
+   Figure [fig:topo-error]
+   Error in the height at the trough

-    image:: images/topo_scaled_error.eps
-    Figure [fig:scaled-topo-error]
-    As in Figure [fig:topo-error], but with the error scaled with $h$.
-    So the medium-resolution error is multiplied by 2 and the
-    high-resolution error is multiplied by 4.
-
+.. figure:: images/topo_scaled_error.eps
+   Figure [fig:scaled-topo-error]
+   As in Figure [fig:topo-error], but with the error scaled with $h$.
+   So the medium-resolution error is multiplied by 2 and the
+   high-resolution 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	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,171 @@
+Benchmarks
+==========
+
+* An Introduction and Tutorial to the "McKenzie Equations" for Magma Migration
+
+    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
+    well-understood special case problems that form a useful benchmark-suite
+    for developing and testing new codes.
+
+
+
+    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 mid-ocean 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
+
+    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
+
+    Details the results of the Milestone2 simulations and analyzes the accuracy
+
+        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
+
+    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
+
+    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
+
+    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
+        x-component of the velocity field for the 3D isoviscous McKenzie model
+        with ridge BCs at time step 150.
+
+      Velocity - y component
+        y-component 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
+        x-component of the melt velocity field for the 3D isoviscous McKenzie model
+        with ridge BCs at time step 150.
+
+      Melt velocity - y component
+        y-component 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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/index.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,171 +0,0 @@
-Benchmarks
-
-* An Introduction and Tutorial to the "McKenzie Equations" for Magma Migration
-
-    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
-    well-understood special case problems that form a useful benchmark-suite
-    for developing and testing new codes.
-
-
-
-    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 mid-ocean 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
-
-    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
-
-    Details the results of the Milestone2 simulations and analyzes the accuracy
-
-        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
-
-    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
-
-    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
-
-    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
-        x-component of the velocity field for the 3D isoviscous McKenzie model
-        with ridge BCs at time step 150.
-
-      Velocity - y component
-        y-component 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
-        x-component of the melt velocity field for the 3D isoviscous McKenzie model
-        with ridge BCs at time step 150.
-
-      Melt velocity - y component
-        y-component 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/mckenzie-equations.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/magma/mckenzie-equations.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/magma/mckenzie-equations.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/mckenzie-equations.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,10 @@
+
+An Introduction and Tutorial to the "McKenzie Equations" for Magma Migration
+
+  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 well-understood
+  special case problems that form a useful benchmark-suite 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/mckenzie-equations.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/magma/mckenzie-equations.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/mckenzie-equations.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,11 +0,0 @@
-
-An Introduction and Tutorial to the "McKenzie Equations" for Magma Migration
-
-  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 well-understood
-  special case problems that form a useful benchmark-suite for developing and
-  testing new codes.
-
-URL
-  http://geodynamics.org/cig/workinggroups/magma/workarea/benchmark/McKenzieIntroBenchmarks.pdf/view

===================================================================
--- doc/geodynamics.org/benchmarks/trunk/magma/milestone1.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone1.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,62 @@
+..
+..  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::
+
+
+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 <#-of-procs> ./StGermain Ridge2D.xml
+
+Alternatively, the 3D simulation may be run as::
+
+    ln -s ../../../../build/bin/StGermain .
+    mpiexec -np <#-of-procs> ./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 element-wise 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 node-wise 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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone1.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,60 +0,0 @@
-
-  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::
-
-
-  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 <#-of-procs> ./StGermain Ridge2D.xml
-
-  Alternatively, the 3D simulation may be run as::
-
-        ln -s ../../../../build/bin/StGermain .
-        mpiexec -np <#-of-procs> ./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 element-wise 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 node-wise 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/

===================================================================
--- doc/geodynamics.org/benchmarks/trunk/magma/milestone2.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone2.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,92 @@
+..
+..  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'
+
+
+----------------------------------
+
+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)
+
+  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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone2.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,87 +0,0 @@
-
-  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'
-
-
-
-  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)
-
-  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/

===================================================================
--- doc/geodynamics.org/benchmarks/trunk/magma/milestone3.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone3.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,40 @@
+..
+..  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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone3.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,39 +0,0 @@
-
-  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/

===================================================================
--- doc/geodynamics.org/benchmarks/trunk/magma/milestone4.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone4.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,73 @@
+..
+..   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 non-linear 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 <#-of-procs> ./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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone4.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,71 +0,0 @@
-
-  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 non-linear 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 <#-of-procs> ./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/

===================================================================
--- doc/geodynamics.org/benchmarks/trunk/magma/milestone5.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone5.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,70 @@
+..
+..   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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/milestone5.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,66 +0,0 @@
-
-  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/

===================================================================
+++ doc/geodynamics.org/benchmarks/trunk/magma/running-stgmadds.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,43 @@
+..
+..
+
+
+===========================
+===========================
+
+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 mid-ocean 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).
+
+=============================
+
+
+1 Create the topmost repository with::
+
+
+2 Then obtain all the other repositories using::
+
+ ./obtainRepositories.py
+
+4 To push, you may have to use the ssh syntax, e.g.::
+
+
+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
+"cig-magma at geodynamics.org":mailto:cig-magma at geodynamics.org
+
+
+URL

===================================================================
--- doc/geodynamics.org/benchmarks/trunk/magma/running-stgmadds.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/magma/running-stgmadds.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,38 +0,0 @@
-
-
-
-  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 mid-ocean 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).
-
-
-
-  1 Create the topmost repository with::
-
-
-  2 Then obtain all the other repositories using::
-
-     ./obtainRepositories.py
-
-  4 To push, you may have to use the ssh syntax, e.g.::
-
-
-  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
-  "cig-magma at geodynamics.org":mailto:cig-magma at geodynamics.org
-
-
-URL

Modified: doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/index.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/index.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/index.rst	2009-09-18 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 2-D thermal convection of a non-rotating
-  anelastic liquid of infinite Prandtl number in a Cartesian, closed, unit
-  cell. The governing equations is based on Truncated An-Elastic
-  Approximation (TALA).
+The benchmark problem is 2-D thermal convection of a non-rotating
+anelastic liquid of infinite Prandtl number in a Cartesian, closed, unit
+cell. The governing equations is based on Truncated An-Elastic
+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.
+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 **free-slip** (i.e., zero tangential stress), except
-  for the mechanically driven case, where the top boundary is impermeble
-  and zero-slip (i.e. fixed horizontal velocity).
+All boundaries (top, bottom, left, right) are **impermeable** (i.e., zero
+normal velocity) and **free-slip** (i.e., zero tangential stress), except
+for the mechanically driven case, where the top boundary is impermeble
+and zero-slip (i.e. fixed horizontal velocity).

+
Temperature BC's
----------------

-  All non-dimensional numbers are defined at the top surface. There are
-  five non-dimensional numbers:
+All non-dimensional numbers are defined at the top surface. There are
+five non-dimensional 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 $rho_ref(z) = exp((1-z)*Di/Gamma)$
+The reference density profile is $rho_ref(z) = exp((1-z)*Di/Gamma)$

-  The reference temperature profile is $T_ref(z) = T_0 * exp((1-z) * Di) T_0$
+The reference temperature profile is $T_ref(z) = T_0 * exp((1-z) * Di) T_0$

-  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 non-dimensional 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

-  * 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/2d-cartesian/suite1.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite1.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite1.rst	2009-09-18 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 non-dimensional 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
-  non-dimensional numbers will give low compressibility and slow
-  convection. Therefore, most of the codes should behave well in this
-  parameter range.
+The non-dimensional 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
+non-dimensional 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 z-direction.
+where elz is the number of elements in the z-direction.

-  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 0th-step 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 0th-step velocity.

+
Case 1b: Internal Heated
------------------------

-  The temperature BC at the bottom is no-heatflux. The initial temperature
-  is the same as Case 1a. H = 1.
+The temperature BC at the bottom is no-heatflux. 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 * (x-1)^2
+  V_x = 1000 * x^2 * (x-1)^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/2d-cartesian/suite2.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite2.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite2.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -7,24 +7,26 @@
==========================

-  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/2d-cartesian/suite3.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite3.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite3.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -6,7 +6,7 @@
=============================

-  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, no-heatflux for the bottom boundary.
+H = 1, no-heatflux for the bottom boundary.

Modified: doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite4.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite4.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/2d-cartesian/suite4.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -6,5 +6,5 @@
==================================

-  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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/index.rst	2009-09-18 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{A-H}
+* BM1{A-H}
+* BM2{A-H}
+* BM3{A-D}

-  * BM2{A-H}

-  * Bm3{A-D}

-
-
-----

-  * "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/notes-on-mantle-convection-benchmarks.rst
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/mc/notes-on-mantle-convection-benchmarks.rst	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/mc/notes-on-mantle-convection-benchmarks.rst	2009-09-18 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.

-  (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
-      time-average sense)
+* (a) Nu vs. time (this should square with the internal heating in a
+  time-average 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.

-  (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 time-dependent. 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 time-dependent. 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.

===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-landers/description-landers.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-landers/description-landers.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,79 @@
+..  description-landers
+..  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 1-D version of the
+    3-D SCEC Community Velocity Model. The 1-D 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 Pa-s (essentially elastic)
+      Lower crust (-30 km ≤ z < - 19 km) -- η = 32.2e+18 Pa-s
+      Mantle (z < -30 km) -- η = 4.6e+18 Pa-s
+
+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/benchmark-landers/description-landers

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-landers/description-landers.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-landers/description-landers.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-landers/description-landers.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,77 +0,0 @@
-  description-landers
-  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 1-D version of the
-    3-D SCEC Community Velocity Model. The 1-D 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 Pa-s (essentially elastic)
-
-      Lower crust (-30 km ≤ z < - 19 km) -- η = 32.2e+18 Pa-s
-
-      Mantle (z < -30 km) -- η = 4.6e+18 Pa-s
-
-    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/benchmark-landers/description-landers

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/description-rs.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/description-rs.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/description-rs.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/description-rs.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,104 @@
+  description-rs
+  Benchmark Description
+  Benchmark problem description. Formerly known as benchmark 6b.
+
+Summary
+
+  Viscoelastic (Maxwell) relaxation of stresses from a single, finite, reverse-slip
+  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 Pa-s (essentially elastic)
+
+      Bottom layer -- η = 1.0e+18 Pa-s
+
+    Boundary conditions
+
+      Bottom and side displacements set to analytic solution. (Note: the side
+      at y = 0 km has zero y-displacements 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 y-direction 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 y-displacements 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/benchmark-rs/description-rs

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/description-rs.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/description-rs.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/description-rs.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,104 +0,0 @@
-  description-rs
-  Benchmark Description
-  Benchmark problem description. Formerly known as benchmark 6b.
-
-Summary
-
-  Viscoelastic (Maxwell) relaxation of stresses from a single, finite, reverse-slip
-  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 Pa-s (essentially elastic)
-
-      Bottom layer -- η = 1.0e+18 Pa-s
-
-    Boundary conditions
-
-      Bottom and side displacements set to analytic solution. (Note: the side
-      at y = 0 km has zero y-displacements 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 y-direction 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 y-displacements 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/benchmark-rs/description-rs

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/results/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/results/index.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/results/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/results/index.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,11 @@
+    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/benchmark-rs/results
+

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/results/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/results/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs/results/index.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,11 +0,0 @@
-    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/benchmark-rs/results
-

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/description-rs-nog.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/description-rs-nog.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/description-rs-nog.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/description-rs-nog.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,93 @@
+    description-rs-nog
+    Benchmark Description
+    Benchmark problem description. Formerly known as benchmark 5b.
+
+Summary
+
+  Viscoelastic (Maxwell) relaxation of stresses from a single finite, reverse-slip
+earthquake in 3-D 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 Pa-s (essentially elastic)
+
+      Bottom layer -- η = 1.0e+18 Pa-s
+
+    Fault specifications
+
+      Type -- 45 degree dipping reverse fault.
+
+      Location -- Strike parallel to y-direction 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 y-displacements 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/benchmark-rs-nog/description-rs-nog

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/description-rs-nog.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/description-rs-nog.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/description-rs-nog.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,93 +0,0 @@
-    description-rs-nog
-    Benchmark Description
-    Benchmark problem description. Formerly known as benchmark 5b.
-
-Summary
-
-  Viscoelastic (Maxwell) relaxation of stresses from a single finite, reverse-slip
-earthquake in 3-D 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 Pa-s (essentially elastic)
-
-      Bottom layer -- η = 1.0e+18 Pa-s
-
-    Fault specifications
-
-      Type -- 45 degree dipping reverse fault.
-
-      Location -- Strike parallel to y-direction 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 y-displacements 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/benchmark-rs-nog/description-rs-nog

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/geofest-input/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/geofest-input/index.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/geofest-input/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/geofest-input/index.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,23 @@
+GeoFEST Input
+
+  Input files for GeoFEST
+
+    * bmrsnog_tet4_1000m.gft.gz (2006-08-31)
+        Gzipped GeoFEST input file for benchmark using linear tetrahedral elements
+        with a 1000m nominal node spacing.
+
+    * bmrsnog_tet4_0500m.gft.gz (2006-08-31)
+        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)
+        (2006-09-06) 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)
+        (2006-09-06) 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/benchmark-rs-nog/geofest-input

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/geofest-input/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/geofest-input/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/geofest-input/index.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,23 +0,0 @@
-GeoFEST Input
-
-  Input files for GeoFEST
-
-    * bmrsnog_tet4_1000m.gft.gz (2006-08-31)
-        Gzipped GeoFEST input file for benchmark using linear tetrahedral elements
-        with a 1000m nominal node spacing.
-
-    * bmrsnog_tet4_0500m.gft.gz (2006-08-31)
-        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)
-        (2006-09-06) 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)
-        (2006-09-06) 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/benchmark-rs-nog/geofest-input

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/plots/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/plots/index.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/plots/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/plots/index.rst	2009-09-18 20:02:16 UTC (rev 15676)
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+    Plots of Reverse-Slip No Gravity Benchmark Results
+    Plots of global and local errors for reverse-slip 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/benchmark-rs-nog/plots

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/plots/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/plots/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/plots/index.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,45 +0,0 @@
-    Plots of Reverse-Slip No Gravity Benchmark Results
-    Plots of global and local errors for reverse-slip 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/benchmark-rs-nog/plots

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/pylith-0.8-input/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/pylith-0.8-input/index.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/pylith-0.8-input/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/pylith-0.8-input/index.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,30 @@
+PyLith-0.8 Input
+
+  Input files for PyLith-0.8
+
+    * bmrsnog_hex_1000m.tgz (2006-07-20)
+        Tarball containing PyLith-0.8 input files for benchmark using linear hexahedral
+        elements with a 1000m nominal node spacing.
+
+    * bmrsnog_tet4_1000m.tgz (2006-07-20)
+        Tarball containing PyLith-0.8 input files for benchmark using linear tetrahedral
+        elements with a 1000m nominal node spacing.
+
+    * bmrsnog_tet4_0500m.tgz (2006-07-20)
+        Tarball containing PyLith-0.8 input files for benchmark using linear tetrahedral
+        elements with a 500m nominal node spacing.
+
+    * bmrsnog_tet4_0250m.tgz (2006-07-20)
+        Tarball containing PyLith-0.8 input files for benchmark using linear tetrahedral
+        elements with a 250m nominal node spacing.
+
+    * reverse slip (no grav), refined grid 01, no smoothing (2006-09-06)
+        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 (2006-09-06)
+        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/benchmark-rs-nog/pylith-0.8-input

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/pylith-0.8-input/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/pylith-0.8-input/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/pylith-0.8-input/index.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,30 +0,0 @@
-PyLith-0.8 Input
-
-  Input files for PyLith-0.8
-
-    * bmrsnog_hex_1000m.tgz (2006-07-20)
-        Tarball containing PyLith-0.8 input files for benchmark using linear hexahedral
-        elements with a 1000m nominal node spacing.
-
-    * bmrsnog_tet4_1000m.tgz (2006-07-20)
-        Tarball containing PyLith-0.8 input files for benchmark using linear tetrahedral
-        elements with a 1000m nominal node spacing.
-
-    * bmrsnog_tet4_0500m.tgz (2006-07-20)
-        Tarball containing PyLith-0.8 input files for benchmark using linear tetrahedral
-        elements with a 500m nominal node spacing.
-
-    * bmrsnog_tet4_0250m.tgz (2006-07-20)
-        Tarball containing PyLith-0.8 input files for benchmark using linear tetrahedral
-        elements with a 250m nominal node spacing.
-
-    * reverse slip (no grav), refined grid 01, no smoothing (2006-09-06)
-        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 (2006-09-06)
-        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/benchmark-rs-nog/pylith-0.8-input

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/results/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/results/index.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/results/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/results/index.rst	2009-09-18 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 (2006-08-17)
+        Tarball contains input and output files as well as text file
+        containing run-time information
+
+    * GeoFEST reverse fault results - 500 m (2006-08-17)
+        Tarball contains input and output files as well as text file
+        containing run-time information
+
+    * Geofest reverse slip var_res_mesh_01_soln (2006-09-05)
+        fixed the BCs, Geofest 4.5, dt=0.1 constant
+
+    * PyLith, 1 proc, linear hex, 1 km resolution, dt=0.1yr (2006-08-29)
+        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 (2006-08-29)
+        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 (2006-08-29)
+        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 (2006-08-29)
+        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 (2006-09-04)
+        PyLith-0.8 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 (2006-10-16)
+        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 (2006-10-18)
+        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/benchmark-rs-nog/results

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/results/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/results/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-rs-nog/results/index.txt	2009-09-18 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 (2006-08-17)
-        Tarball contains input and output files as well as text file
-        containing run-time information
-
-    * GeoFEST reverse fault results - 500 m (2006-08-17)
-        Tarball contains input and output files as well as text file
-        containing run-time information
-
-    * Geofest reverse slip var_res_mesh_01_soln (2006-09-05)
-        fixed the BCs, Geofest 4.5, dt=0.1 constant
-
-    * PyLith, 1 proc, linear hex, 1 km resolution, dt=0.1yr (2006-08-29)
-        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 (2006-08-29)
-        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 (2006-08-29)
-        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 (2006-08-29)
-        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 (2006-09-04)
-        PyLith-0.8 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 (2006-10-16)
-        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 (2006-10-18)
-        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/benchmark-rs-nog/results

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/description-ss.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/description-ss.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/description-ss.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/description-ss.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,103 @@
+
+    description-ss
+    Benchmark Description
+    Benchmark problem description. Formerly known as benchmark 4b.
+
+Summary
+
+  Viscoelastic (Maxwell) relaxation of stresses from a single, finite,
+strike-slip earthquake in 3-D 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. Anti-plane 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 Pa-s (essentially elastic)
+
+      Bottom layer -- η = 1.0e+18 Pa-s
+
+  Fault specifications
+
+    Type -- Vertical right-lateral strike-slip fault.
+
+    Location --
+      Strike parallel to y-direction 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
+    y-displacements are left free to preserve symmetry, and the x- and
+    z-displacements 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/benchmark-strikeslip/description-ss.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/description-ss.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/description-ss.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,103 +0,0 @@
-
-    description-ss
-    Benchmark Description
-    Benchmark problem description. Formerly known as benchmark 4b.
-
-Summary
-
-  Viscoelastic (Maxwell) relaxation of stresses from a single, finite,
-strike-slip earthquake in 3-D 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. Anti-plane 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 Pa-s (essentially elastic)
-
-      Bottom layer -- η = 1.0e+18 Pa-s
-
-  Fault specifications
-
-    Type -- Vertical right-lateral strike-slip fault.
-
-    Location --
-      Strike parallel to y-direction 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
-    y-displacements are left free to preserve symmetry, and the x- and
-    z-displacements 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/benchmark-strikeslip/geofest-input/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/geofest-input/index.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/geofest-input/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/geofest-input/index.rst	2009-09-18 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/benchmark-strikeslip/geofest-input

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/geofest-input/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/geofest-input/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/geofest-input/index.txt	2009-09-18 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/benchmark-strikeslip/geofest-input

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/index.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/index.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,29 @@
+
+Strike-Slip Benchmark (no gravity)
+
+  Benchmark for strike-slip fault without gravity.
+
+    * Benchmark Description
+        Benchmark problem description. Formerly known as benchmark 4b.
+
+    * PyLith-0.8 Input
+        Input files for PyLith-0.8
+
+    * 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 Strike-Slip Benchmark
+        Domain and fault geometry for the strike-slip benchmark.
+
+
+URL
+    http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks
+

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/index.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,29 +0,0 @@
-
-Strike-Slip Benchmark (no gravity)
-
-  Benchmark for strike-slip fault without gravity.
-
-    * Benchmark Description
-        Benchmark problem description. Formerly known as benchmark 4b.
-
-    * PyLith-0.8 Input
-        Input files for PyLith-0.8
-
-    * 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 Strike-Slip Benchmark
-        Domain and fault geometry for the strike-slip benchmark.
-
-
-URL
-    http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks
-

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/plots/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/plots/index.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/plots/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/plots/index.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,48 @@
+Plots of Strike-Slip No Gravity Benchmark Results
+  Plots of global and local errors for strike-slip 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/benchmark-strikeslip/plots
+

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/plots/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/plots/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/plots/index.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,48 +0,0 @@
-Plots of Strike-Slip No Gravity Benchmark Results
-  Plots of global and local errors for strike-slip 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/benchmark-strikeslip/plots
-

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/pylith-0.8-input/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/pylith-0.8-input/index.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/pylith-0.8-input/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/pylith-0.8-input/index.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,19 @@
+PyLith-0.8 Input
+
+  Input files for PyLith-0.8
+
+    * bmssnog_tet4_1000m.tgz
+        Tarball containing PyLith-0.8 input files for benchmark using
+        linear tetrahedral elements with a 1000m nominal node spacing.
+
+    * bmssnog_tet4_0500m.tgz
+        Tarball containing PyLith-0.8 input files for benchmark using
+        linear tetrahedral elements with a 500m nominal node spacing.
+
+    * bmssnog_tet4_0250m.tgz
+        Tarball containing PyLith-0.8 input files for benchmark using
+        linear tetrahedral elements with a 250m nominal node spacing.
+
+Original URL
+    http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmark-strikeslip/pylith-0.8-input/
+

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/pylith-0.8-input/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/pylith-0.8-input/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/pylith-0.8-input/index.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,19 +0,0 @@
-PyLith-0.8 Input
-
-  Input files for PyLith-0.8
-
-    * bmssnog_tet4_1000m.tgz
-        Tarball containing PyLith-0.8 input files for benchmark using
-        linear tetrahedral elements with a 1000m nominal node spacing.
-
-    * bmssnog_tet4_0500m.tgz
-        Tarball containing PyLith-0.8 input files for benchmark using
-        linear tetrahedral elements with a 500m nominal node spacing.
-
-    * bmssnog_tet4_0250m.tgz
-        Tarball containing PyLith-0.8 input files for benchmark using
-        linear tetrahedral elements with a 250m nominal node spacing.
-
-Original URL
-    http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/benchmark-strikeslip/pylith-0.8-input/
-

Copied: doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/results/index.rst (from rev 15673, doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/results/index.txt)
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/results/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/results/index.rst	2009-09-18 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 (2006-08-29)
+        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 (2006-08-29)
+        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 (2006-08-29)
+        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 (2007-01-30)
+        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 (2007-02-06)
+        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 y-component 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 (2006-09-07)
+        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 (2006-09-06)
+        Parallel results using 64 processors of Intel/Linux Cluster
+        with GeoFEST-4.5 and Pyramid-2.1.3
+
+    * GeoFEST / PYRAMID 500m (2006-09-06)
+        Parallel results using 64 processors of Intel/Linux Cluster
+        with GeoFEST-4.5 and Pyramid-2.1.3
+
+    * GeoFEST / PYRAMID 250m (2006-09-06)
+        Parallel results using 128 processors of Intel/Linux Cluster
+        with GeoFEST-4.5 and Pyramid-2.1.3
+
+    * GeoFEST linear tet 1km resolution dt=0.1yr (updated) (2006-09-21)
+        The taper error has been fixed.
+
+    * GeoFEST Linear-Tet 500m Re-Run (2006-11-29)
+
+    * GeoFEST Linear-Tet 250m Re-Run (2006-11-29)
+
+    * Femlab 1km resolution, t = 0 years (2006-10-17)
+        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 (2006-10-17)
+        Viscoelastic problem requires ~3.5GB and takes about 4.5 hours to run.
+        Drop tolerance is 0.01.
+
+    * Femlab 1km resolution, t = 5 years (2006-10-17)
+        Viscoelastic problem requires ~3.5GB and takes about 4.5 hours to run.
+        Drop tolerance is 0.01.
+
+    * Femlab 1km resolution, t = 10 years (2006-10-17)
+        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/benchmark-strikeslip/results
+

Deleted: doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/results/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/results/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/benchmark-strikeslip/results/index.txt	2009-09-18 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 (2006-08-29)
-        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 (2006-08-29)
-        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 (2006-08-29)
-        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 (2007-01-30)
-        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 (2007-02-06)
-        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 y-component 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 (2006-09-07)
-        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 (2006-09-06)
-        Parallel results using 64 processors of Intel/Linux Cluster
-        with GeoFEST-4.5 and Pyramid-2.1.3
-
-    * GeoFEST / PYRAMID 500m (2006-09-06)
-        Parallel results using 64 processors of Intel/Linux Cluster
-        with GeoFEST-4.5 and Pyramid-2.1.3
-
-    * GeoFEST / PYRAMID 250m (2006-09-06)
-        Parallel results using 128 processors of Intel/Linux Cluster
-        with GeoFEST-4.5 and Pyramid-2.1.3
-
-    * GeoFEST linear tet 1km resolution dt=0.1yr (updated) (2006-09-21)
-        The taper error has been fixed.
-
-    * GeoFEST Linear-Tet 500m Re-Run (2006-11-29)
-
-    * GeoFEST Linear-Tet 250m Re-Run (2006-11-29)
-
-    * Femlab 1km resolution, t = 0 years (2006-10-17)
-        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 (2006-10-17)
-        Viscoelastic problem requires ~3.5GB and takes about 4.5 hours to run.
-        Drop tolerance is 0.01.
-
-    * Femlab 1km resolution, t = 5 years (2006-10-17)
-        Viscoelastic problem requires ~3.5GB and takes about 4.5 hours to run.
-        Drop tolerance is 0.01.
-
-    * Femlab 1km resolution, t = 10 years (2006-10-17)
-        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/benchmark-strikeslip/results
-

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===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/index.rst	                        (rev 0)
+++ doc/geodynamics.org/benchmarks/trunk/short/index.rst	2009-09-18 20:02:16 UTC (rev 15676)
@@ -0,0 +1,52 @@
+
+Short-Term Tectonics Benchmarks
+
+"Overview":overview
+
+Benchmarks
+
+  Strike-slip (no gravity)
+
+    * "Description":benchmark-strikeslip/description-ss
+
+    * "PyLith input":benchmark-strikeslip/pylith-0.8-input
+
+    * "GeoFEST input":benchmark-strikeslip/geofest-input
+
+    * "Submitted results":benchmark-strikeslip/result
+
+    * "Plots of results":benchmark-strikeslip/plots
+
+  Reverse-slip (no gravity)
+
+    * "Description":benchmark-rs-nog/description-rs-nog
+
+    * "PyLith input":benchmark-rs-nog/pylith-0.8-input
+
+    * "GeoFEST input":benchmark-rs-nog/geofest-input
+
+    * "Submitted results":benchmark-rs-nog/results
+
+    * "Plots of results":benchmark-rs-nog/plots
+
+  Reverse-slip (with gravity)
+
+    * "Description":benchmark-rs/description-rs
+
+    * PyLith input (coming soon)
+
+    * GeoFEST input (coming soon)
+
+    * "Submitted results":benchmark-rs/results
+
+  Landers-Hector Mine
+
+    * "Description":benchmark-landers/description-landers
+
+    * Mesh constructed with LaGriT (coming soon)
+
+Utilities
+
+  * "Analytic and Semi-Analytic Codes":utilities
+
+  * "CUBIT examples":utilities/CUBITex

Deleted: doc/geodynamics.org/benchmarks/trunk/short/index.txt
===================================================================
--- doc/geodynamics.org/benchmarks/trunk/short/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/index.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,52 +0,0 @@
-
-Short-Term Tectonics Benchmarks
-
-"Overview":overview
-
-Benchmarks
-
-  Strike-slip (no gravity)
-
-    * "Description":benchmark-strikeslip/description-ss
-
-    * "PyLith input":benchmark-strikeslip/pylith-0.8-input
-
-    * "GeoFEST input":benchmark-strikeslip/geofest-input
-
-    * "Submitted results":benchmark-strikeslip/result
-
-    * "Plots of results":benchmark-strikeslip/plots
-
-  Reverse-slip (no gravity)
-
-    * "Description":benchmark-rs-nog/description-rs-nog
-
-    * "PyLith input":benchmark-rs-nog/pylith-0.8-input
-
-    * "GeoFEST input":benchmark-rs-nog/geofest-input
-
-    * "Submitted results":benchmark-rs-nog/results
-
-    * "Plots of results":benchmark-rs-nog/plots
-
-  Reverse-slip (with gravity)
-
-    * "Description":benchmark-rs/description-rs
-
-    * PyLith input (coming soon)
-
-    * GeoFEST input (coming soon)
-
-    * "Submitted results":benchmark-rs/results
-
-  Landers-Hector Mine
-
-    * "Description":benchmark-landers/description-landers
-
-    * Mesh constructed with LaGriT (coming soon)
-
-Utilities
-
-  * "Analytic and Semi-Analytic 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	2009-09-18 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, time-stepping 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, time-stepping 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, time-stepping scheme, code, etc., and (3)
+quantify and, if possible, minimize model induced uncertainties resulting from
+discretization, model boundaries, unexpected transients in time-dependent materials,
+etc.
+
+General Methodology
+
+  All benchmark descriptions assume a right-handed Cartesian coordinate system
+with the x-direction running east, the y-direction running north, and the
+z-direction 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 trade-offs 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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/overview.txt	2009-09-18 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, time-stepping 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, time-stepping 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, time-stepping scheme, code, etc., and (3)
-quantify and, if possible, minimize model induced uncertainties resulting from
-discretization, model boundaries, unexpected transients in time-dependent materials,
-etc.
-
-General Methodology
-
-  All benchmark descriptions assume a right-handed Cartesian coordinate system
-with the x-direction running east, the y-direction running north, and the
-z-direction 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 trade-offs 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	2009-09-18 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 (2009-06-23)
+        Very short example of meshing a pyramid and displaying mesh
+
+    * Geometry test (2009-06-23)
+        Example of building geometrical shapes with merging, subtracting, moving, etc.
+
+    * Fault example (2009-06-23)
+        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	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/utilities/CUBITex.txt	2009-09-18 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 (2009-06-23)
-        Very short example of meshing a pyramid and displaying mesh
-
-    * Geometry test (2009-06-23)
-        Example of building geometrical shapes with merging, subtracting, moving, etc.
-
-    * Fault example (2009-06-23)
-        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	2009-09-18 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
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--- doc/geodynamics.org/benchmarks/trunk/short/utilities/index.txt	2009-09-18 18:41:30 UTC (rev 15675)
+++ doc/geodynamics.org/benchmarks/trunk/short/utilities/index.txt	2009-09-18 20:02:16 UTC (rev 15676)
@@ -1,2 +0,0 @@
-URL
-  http://geodynamics.org/cig/workinggroups/short/workarea/benchmarks/utilities