2012/8/23 John Peterson <jwpeter...@gmail.com>:
> On Thu, Aug 23, 2012 at 9:18 AM, Geordie McBain <gdmcb...@freeshell.org>
> wrote:
>> 2012/8/23 John Peterson <jwpeter...@gmail.com>:
>>> On Thu, Aug 23, 2012 at 2:34 AM, Geordie McBain <gdmcb...@freeshell.org>
>>> wrote:
>>>> 2012/8/22 Geordie McBain <gdmcb...@freeshell.org>:
>>>>> 2012/8/22 Subramanya Gautam Sadasiva <ssada...@purdue.edu>:
>>>>>> Hi,
>>>>>> I am new to libmesh, but there seems to have been some sort of
>>>>>> rearrangement of the example numbers. Is there somewhere I can find
>>>>>> which old example numbers correspond to the current examples?
>>>>>
>>>>> Hello. I had hoped that this would be a simple exercise in svn log,
>>>>> but after finding the relevant revision easily enough
>>>>>
>>>>> %<---
>>>>> $ svn log -r 5000
>>>>> ------------------------------------------------------------------------
>>>>> r5000 | knezed01 | 2011-12-05 05:49:39 +0100 (Mon, 05 Dec 2011) | 1 line
>>>>>
>>>>> Reorganized the examples into subdirectories. The comments in each
>>>>> example still need to be updated to reflect the new numbering scheme.
>>>>> ------------------------------------------------------------------------
>>>>> --->%
>>>>>
>>>>> I was quickly reminded that Subversion ("svn diff --summarize -c
>>>>> 5000") only tracks renames as deletes and additions, but not which
>>>>> addition was related to which deletion.
>>>>> However, the second sentence in the log comment means the (42000
>>>>> line!) output of "svn diff -c 5000" can be searched for "Example 0",
>>>>> "Example 1", ... so
>>>>>
>>>>> svn diff -c 5000 | grep -E '(<h1>Example [0-9]|\+\+\+ .*\.C)'
>>>>>
>>>>> gives the attached 72 line output which pretty much pairs up the old &
>>>>> new.
>>>>
>>>> After that I noticed a few cross-references in comments or string
>>>> literals still using the old numerotation, so I tried to find and
>>>> update them all; patch attached.
>>>
>>> Geordie, thanks for taking the time to produce this mapping.
>>>
>>> Subramanya, was there some specific example you were curious about?
>>>
>>> The libmesh examples documentation page
>>> (http://libmesh.sourceforge.net/examples.php) appears to be in good
>>> shape to me...
>>
>> Yes but subpages contain things like "This example is based on example 14"
>>
>> http://libmesh.sourceforge.net/miscellaneous_ex5.php
>>
>> The attached patch (which replaces this morning's, adding a couple of
>> other catches from the example sources, and being against the later
>> r5983) doesn't touch the doc/html/*.php. (I had thought, without
>> looking into it, they might be generated from the example sources
>> somehow.)
>
> Thanks for the patch. I never got the one you sent earlier; I think
> libmesh-users drops all? attachments.
Oh, right, sorry. I think I've seen some here with the .txt suffix,
but I guess the idea is to copy patches to libmesh-devel?
Here it is again, this time (against r5986 and) with the corresponding
changes to doc/html/*.php. (I gather these are kept in step thus
manually with the examples/*/*/*.C?)
Index: doc/html/adaptivity_ex1.php
===================================================================
--- doc/html/adaptivity_ex1.php (revision 5986)
+++ doc/html/adaptivity_ex1.php (working copy)
@@ -113,7 +113,7 @@
</div>
<div class = "comment">
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.
</div>
<div class ="fragment">
@@ -232,7 +232,7 @@
</pre>
</div>
<div class = "comment">
-Objects for error estimation, see Example 10 for more details.
+Error estimation objects, see Adaptivity Example 2 for details
</div>
<div class ="fragment">
@@ -294,7 +294,7 @@
<div class ="fragment">
<pre>
- GnuPlotIO plot(mesh,"Example 0", GnuPlotIO::GRID_ON);
+ GnuPlotIO plot(mesh,"Adaptivity Example 1", GnuPlotIO::GRID_ON);
</pre>
</div>
@@ -646,7 +646,7 @@
</div>
<div class = "comment">
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.
</div>
<div class ="fragment">
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 @@
<pre>
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 @@
<pre>
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 @@
<br><br>By Lorenzo Botti
-<br><br>This example is based on example 14, but uses an Interior Penalty
-Discontinuous Galerkin formulation.
+<br><br>This example is based on Adaptivity Example 3, but uses an
+Interior Penalty Discontinuous Galerkin formulation.
<br><br></div>
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:
-<br><br>./ex3 -ksp_type cg
+<br><br>./vector_fe_ex1 -ksp_type cg
<br><br>You can also get a nice X-window that monitors the solver
convergence with:
-<br><br>./ex3 -ksp_xmonitor
+<br><br>./vector_fe_ex1 -ksp_xmonitor
<br><br>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:
-<br><br>./ex2 -log_info
+<br><br>./introduction_ex2 -log_info
<br><br>to see what PETSc is doing behind the scenes or
-<br><br>./ex2 -log_summary
+<br><br>./introduction_ex2 -log_summary
<br><br>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:
-<br><br>./ex3 -ksp_type cg
+<br><br>./introduction_ex3 -ksp_type cg
<br><br>You can also get a nice X-window that monitors the solver
convergence with:
-<br><br>./ex3 -ksp_xmonitor
+<br><br>./introduction_ex3 -ksp_xmonitor
<br><br>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<FEBase>. 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.
</div>
Index: doc/html/introduction_ex4.php
===================================================================
--- doc/html/introduction_ex4.php (revision 5986)
+++ doc/html/introduction_ex4.php (working copy)
@@ -599,7 +599,7 @@
<pre>
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 @@
<div class ="fragment">
<pre>
- PerfLog perf_log("Example 13");
+ PerfLog perf_log("Systems Example 2");
</pre>
</div>
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 @@
<div class ="fragment">
<pre>
- PerfLog perf_log("Example 13");
+ PerfLog perf_log("Systems Example 3");
</pre>
</div>
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<FEBase>. 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.
AutoPtr<FEBase> 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 <iostream>
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.
Index: examples/adaptivity/adaptivity_ex1/adaptivity_ex1.C
===================================================================
--- examples/adaptivity/adaptivity_ex1/adaptivity_ex1.C (revision 5986)
+++ examples/adaptivity/adaptivity_ex1/adaptivity_ex1.C (working copy)
@@ -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);
LinearImplicitSystem& system = equation_systems.add_system
<LinearImplicitSystem>("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.
Index: examples/adaptivity/adaptivity_ex3/adaptivity_ex3.C
===================================================================
--- examples/adaptivity/adaptivity_ex3/adaptivity_ex3.C (revision 5986)
+++ examples/adaptivity/adaptivity_ex3/adaptivity_ex3.C (working copy)
@@ -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"
+ // 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.
------------------------------------------------------------------------------
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