Define the equation systems object and the system we are going -to solve. See Example 2 for more details. +to solve. See Introduction Example 2 for more details.
@@ -232,7 +232,7 @@
-Objects for error estimation, see Example 10 for more details. +Error estimation objects, see Adaptivity Example 2 for details
@@ -294,7 +294,7 @@
```-          GnuPlotIO plot(mesh,"Example 0", GnuPlotIO::GRID_ON);
+          GnuPlotIO plot(mesh,"Adaptivity Example 1", GnuPlotIO::GRID_ON);

```
@@ -646,7 +646,7 @@
This is a function call that is necessary when using adaptive -mesh refinement. See Example 10 for more details. +mesh refinement. See Adaptivity Example 2 for more details.
Index: doc/html/adaptivity_ex3.php =================================================================== --- doc/html/adaptivity_ex3.php (revision 5986) +++ doc/html/adaptivity_ex3.php (working copy) @@ -25,15 +25,15 @@ Element 1: [ 0,1]x[ 0,1] Element 2: [-1,0]x[-1,0] The mesh is provided in the standard libMesh ASCII format file -named "lshaped.xda". In addition, an input file named "ex14.in" +named "lshaped.xda". In addition, an input file named "adaptivity_ex3.in" is provided which allows the user to set several parameters for the solution so that the problem can be re-run without a re-compile. The solution technique employed is to have a refinement loop with a linear solve inside followed by a refinement of the grid and projection of the solution to the new grid In the final loop iteration, there is no additional -refinement after the solve. In the input file "ex14.in", the variable -"max_r_steps" controls the number of refinement steps, +refinement after the solve. In the input file "adaptivity_ex3.in", +the variable "max_r_steps" controls the number of refinement steps, "max_r_level" controls the maximum element refinement level, and "refine_percentage" / "coarsen_percentage" determine the number of elements which will be refined / coarsened at each step. Index: doc/html/subdomains_ex1.php =================================================================== --- doc/html/subdomains_ex1.php (revision 5986) +++ doc/html/subdomains_ex1.php (working copy) @@ -641,7 +641,7 @@
```           if(dim == 1)
{
-            GnuPlotIO plot(mesh,"Example 4, 1D",GnuPlotIO::GRID_ON);
+            GnuPlotIO plot(mesh,"Subdomains Example 1, 1D",GnuPlotIO::GRID_ON);
plot.write_equation_systems("out_1",equation_systems);
}
else
Index: doc/html/subdomains_ex2.php
===================================================================
--- doc/html/subdomains_ex2.php	(revision 5986)
+++ doc/html/subdomains_ex2.php	(working copy)
@@ -515,8 +515,8 @@
if(dim == 1)
{
-            GnuPlotIO plot(mesh,"Example 4, 1D",GnuPlotIO::GRID_ON);
-            plot.write_equation_systems("out_1",equation_systems);
+            GnuPlotIO plot(mesh,"Subdomains Example 2, 1D",GnuPlotIO::GRID_ON);
+            plot.write_equation_systems("gnuplot_script",equation_systems);
}
else
{
Index: doc/html/miscellaneous_ex5.php
===================================================================
--- doc/html/miscellaneous_ex5.php	(revision 5986)
+++ doc/html/miscellaneous_ex5.php	(working copy)
@@ -16,8 +16,8 @@

By Lorenzo Botti

-This example is based on example 14, but uses an Interior Penalty
-Discontinuous Galerkin formulation.
+This example is based on Adaptivity Example 3, but uses an
+Interior Penalty Discontinuous Galerkin formulation.

```
Index: doc/html/vector_fe_ex1.php =================================================================== --- doc/html/vector_fe_ex1.php (revision 5986) +++ doc/html/vector_fe_ex1.php (working copy) @@ -270,12 +270,12 @@ controlled from the command line. For example, you can invoke conjugate gradient with: -

./ex3 -ksp_type cg +

./vector_fe_ex1 -ksp_type cg

You can also get a nice X-window that monitors the solver convergence with: -

./ex3 -ksp_xmonitor +

./vector_fe_ex1 -ksp_xmonitor

if you linked against the appropriate X libraries when you built PETSc. Index: doc/html/introduction_ex2.php =================================================================== --- doc/html/introduction_ex2.php (revision 5986) +++ doc/html/introduction_ex2.php (working copy) @@ -27,11 +27,11 @@ command line arguments to PETSc. For example, you might try running this example as: -

./ex2 -log_info +

./introduction_ex2 -log_info

to see what PETSc is doing behind the scenes or -

./ex2 -log_summary +

./introduction_ex2 -log_summary

to get a summary of what PETSc did. Among other things, libMesh::init() initializes the MPI Index: doc/html/introduction_ex3.php =================================================================== --- doc/html/introduction_ex3.php (revision 5986) +++ doc/html/introduction_ex3.php (working copy) @@ -274,12 +274,12 @@ controlled from the command line. For example, you can invoke conjugate gradient with: -

./ex3 -ksp_type cg +

./introduction_ex3 -ksp_type cg

You can also get a nice X-window that monitors the solver convergence with: -

./ex3 -ksp_xmonitor +

./introduction_ex3 -ksp_xmonitor

if you linked against the appropriate X libraries when you built PETSc. @@ -405,7 +405,7 @@ Build a Finite Element object of the specified type. Since the FEBase::build() member dynamically creates memory we will store the object as an AutoPtr. This can be thought -of as a pointer that will clean up after itself. Example 4 +of as a pointer that will clean up after itself. Introduction Example 4 describes some advantages of AutoPtr's in the context of quadrature rules. Index: doc/html/introduction_ex4.php =================================================================== --- doc/html/introduction_ex4.php (revision 5986) +++ doc/html/introduction_ex4.php (working copy) @@ -599,7 +599,7 @@
```           if(dim == 1)
{
-            GnuPlotIO plot(mesh,"Example 4, 1D",GnuPlotIO::GRID_ON);
+            GnuPlotIO plot(mesh,"Introduction Example 4, 1D",GnuPlotIO::GRID_ON);
plot.write_equation_systems("out_1",equation_systems);
}
#ifdef LIBMESH_HAVE_EXODUS_API
Index: doc/html/systems_of_equations_ex2.php
===================================================================
--- doc/html/systems_of_equations_ex2.php	(revision 5986)
+++ doc/html/systems_of_equations_ex2.php	(working copy)
@@ -292,7 +292,7 @@

-          PerfLog perf_log("Example 13");
+          PerfLog perf_log("Systems Example 2");

Index: doc/html/systems_of_equations_ex3.php
===================================================================
--- doc/html/systems_of_equations_ex3.php	(revision 5986)
+++ doc/html/systems_of_equations_ex3.php	(working copy)
@@ -292,7 +292,7 @@

-          PerfLog perf_log("Example 13");
+          PerfLog perf_log("Systems Example 3");

Index: examples/introduction/introduction_ex2/introduction_ex2.C
===================================================================
--- examples/introduction/introduction_ex2/introduction_ex2.C	(revision 5986)
+++ examples/introduction/introduction_ex2/introduction_ex2.C	(working copy)
@@ -30,11 +30,11 @@
// command line arguments to PETSc.  For example, you might
// try running this example as:
//
- // ./ex2 -log_info
+ // ./introduction_ex2 -log_info
//
// to see what PETSc is doing behind the scenes or
//
- // ./ex2 -log_summary
+ // ./introduction_ex2 -log_summary
//
// to get a summary of what PETSc did.
// Among other things, libMesh::init() initializes the MPI
Index: examples/introduction/introduction_ex3/introduction_ex3.C
===================================================================
--- examples/introduction/introduction_ex3/introduction_ex3.C	(revision 5986)
+++ examples/introduction/introduction_ex3/introduction_ex3.C	(working copy)
@@ -137,12 +137,12 @@
// controlled from the command line.  For example,
// you can invoke conjugate gradient with:
//
-  // ./ex3 -ksp_type cg
+  // ./introduction_ex3 -ksp_type cg
//
// You can also get a nice X-window that monitors the solver
// convergence with:
//
-  // ./ex3 -ksp_xmonitor
+  // ./introduction-ex3 -ksp_xmonitor
//
// if you linked against the appropriate X libraries when you
// built PETSc.
@@ -198,7 +198,7 @@
// Build a Finite Element object of the specified type.  Since the
// FEBase::build() member dynamically creates memory we will
// store the object as an AutoPtr.  This can be thought
-  // of as a pointer that will clean up after itself.  Example 4
+  // of as a pointer that will clean up after itself.  Introduction Example 4
// describes some advantages of  AutoPtr's in the context of
AutoPtr fe (FEBase::build(dim, fe_type));
Index: examples/introduction/introduction_ex4/introduction_ex4.C
===================================================================
--- examples/introduction/introduction_ex4/introduction_ex4.C	(revision 5986)
+++ examples/introduction/introduction_ex4/introduction_ex4.C	(working copy)
@@ -301,7 +301,7 @@
// to a GMV-formatted plot file.
if(dim == 1)
{
-    GnuPlotIO plot(mesh,"Example 4, 1D",GnuPlotIO::GRID_ON);
+    GnuPlotIO plot(mesh,"Introduction Example 4, 1D",GnuPlotIO::GRID_ON);
plot.write_equation_systems("gnuplot_script",equation_systems);
}
#ifdef LIBMESH_HAVE_EXODUS_API
Index: examples/miscellaneous/miscellaneous_ex5/miscellaneous_ex5.C
===================================================================
--- examples/miscellaneous/miscellaneous_ex5/miscellaneous_ex5.C	(revision 5986)
+++ examples/miscellaneous/miscellaneous_ex5/miscellaneous_ex5.C	(working copy)
@@ -19,8 +19,8 @@
//
// By Lorenzo Botti
//
- // This example is based on example 14, but uses an Interior Penalty
- // Discontinuous Galerkin formulation.
+ // This example is based on Adaptivity Example 3, but uses an
+ // Interior Penalty Discontinuous Galerkin formulation.

#include

Index: examples/systems_of_equations/systems_of_equations_ex2/systems_of_equations_ex2.C
===================================================================
--- examples/systems_of_equations/systems_of_equations_ex2/systems_of_equations_ex2.C	(revision 5986)
+++ examples/systems_of_equations/systems_of_equations_ex2/systems_of_equations_ex2.C	(working copy)
@@ -143,7 +143,7 @@
equation_systems.print_info();

// Create a performance-logging object for this example
-  PerfLog perf_log("Example 13");
+  PerfLog perf_log("Systems Example 2");

// Get a reference to the Stokes system to use later.
TransientLinearImplicitSystem&  navier_stokes_system =
Index: examples/systems_of_equations/systems_of_equations_ex3/systems_of_equations_ex3.C
===================================================================
--- examples/systems_of_equations/systems_of_equations_ex3/systems_of_equations_ex3.C	(revision 5986)
+++ examples/systems_of_equations/systems_of_equations_ex3/systems_of_equations_ex3.C	(working copy)
@@ -136,7 +136,7 @@
equation_systems.print_info();

// Create a performance-logging object for this example
-  PerfLog perf_log("Example 13");
+  PerfLog perf_log("Systems Example 3");

// Get a reference to the Stokes system to use later.
TransientLinearImplicitSystem&  navier_stokes_system =
Index: examples/subdomains/subdomains_ex1/subdomains_ex1.C
===================================================================
--- examples/subdomains/subdomains_ex1/subdomains_ex1.C	(revision 5986)
+++ examples/subdomains/subdomains_ex1/subdomains_ex1.C	(working copy)
@@ -329,7 +329,7 @@
// to a GMV-formatted plot file.
if(dim == 1)
{
-    GnuPlotIO plot(mesh,"Example 4, 1D",GnuPlotIO::GRID_ON);
+    GnuPlotIO plot(mesh,"Subdomains Example 1, 1D",GnuPlotIO::GRID_ON);
plot.write_equation_systems("gnuplot_script",equation_systems);
}
else
Index: examples/subdomains/subdomains_ex2/subdomains_ex2.C
===================================================================
--- examples/subdomains/subdomains_ex2/subdomains_ex2.C	(revision 5986)
+++ examples/subdomains/subdomains_ex2/subdomains_ex2.C	(working copy)
@@ -267,7 +267,7 @@
// to a GMV-formatted plot file.
if(dim == 1)
{
-    GnuPlotIO plot(mesh,"Example 4, 1D",GnuPlotIO::GRID_ON);
+    GnuPlotIO plot(mesh,"Subdomains Example 2, 1D",GnuPlotIO::GRID_ON);
plot.write_equation_systems("gnuplot_script",equation_systems);
}
else
Index: examples/vector_fe/vector_fe_ex1/vector_fe_ex1.C
===================================================================
--- examples/vector_fe/vector_fe_ex1/vector_fe_ex1.C	(revision 5986)
+++ examples/vector_fe/vector_fe_ex1/vector_fe_ex1.C	(working copy)
@@ -133,12 +133,12 @@
// controlled from the command line.  For example,
// you can invoke conjugate gradient with:
//
-  // ./ex3 -ksp_type cg
+  // ./vector_fe_ex1 -ksp_type cg
//
// You can also get a nice X-window that monitors the solver
// convergence with:
//
-  // ./ex3 -ksp_xmonitor
+  // ./vector_fe_ex1 -ksp_xmonitor
//
// if you linked against the appropriate X libraries when you
// built PETSc.
===================================================================
@@ -80,7 +80,7 @@
MeshTools::Generation::build_line(mesh,n,0.,1.,EDGE3);

// Define the equation systems object and the system we are going
-  // to solve. See Example 2 for more details.
+  // to solve. See Introduction Example 2 for more details.
EquationSystems equation_systems(mesh);
("1D");
@@ -122,7 +122,7 @@
// going to solve the equation system for that refined mesh.
if(r_step != max_r_steps)
{
-          // Objects for error estimation, see Example 10 for more details.
+          // Error estimation objects, see Adaptivity Example 2 for details
ErrorVector error;
KellyErrorEstimator error_estimator;

@@ -145,7 +145,7 @@
// Construct gnuplot plotting object, pass in mesh, title of plot
// and boolean to indicate use of grid in plot. The grid is used to
// show the edges of each element in the mesh.
-  GnuPlotIO plot(mesh,"Example 0", GnuPlotIO::GRID_ON);
+  GnuPlotIO plot(mesh,"Adaptivity Example 1", GnuPlotIO::GRID_ON);

// Write out script to be called from within gnuplot:
// Load gnuplot, then type "call 'gnuplot_script'" from gnuplot prompt
@@ -296,7 +296,7 @@
}

// This is a function call that is necessary when using adaptive
-    // mesh refinement. See Example 10 for more details.
+    // mesh refinement. See Adaptivity Example 2 for more details.
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);

// Add Ke and Fe to the global matrix and right-hand-side.
===================================================================
@@ -28,15 +28,15 @@
// Element 1: [ 0,1]x[ 0,1]
// Element 2: [-1,0]x[-1,0]
// The mesh is provided in the standard libMesh ASCII format file
- // named "lshaped.xda".  In addition, an input file named "ex14.in"