plugin for initial temperature condition for ellipsoid chunk geometry #720

trajaona · 2016-01-18T16:46:01Z

This is a plugin for initial conditions.

bangerth · 2016-01-19T01:17:05Z

include/aspect/initial_conditions/adiabatic_boundary.h

+
+/** This initial condition is designed for the 3D ellipsoid chunk geometry
+ * model. It discretizes the model domain into two regions separated by an
+ * isotherm below with the temperature increases adiabatically. The user


with -> which

bangerth · 2016-01-20T04:12:31Z

include/aspect/initial_conditions/adiabatic_boundary.h

+ * temperature increases adiabatically while above the adiabatic 
+ * boundary the temperature linearly increases from a surface temperature
+ * (273.15 K or 0 degree C) to an isotherm (1673.15 K or 1600 degree C)
+ * that is the adiabatic boundary.


I meant to move this documentation to the class declaration, not to the namespace declaration. I think it would also be useful if you merged the documentation, not just collated it.

bangerth · 2016-01-22T01:27:57Z

include/aspect/initial_conditions/adiabatic_boundary.h

+          double initial_temperature (const Point<dim> &position) const;
+
+    	  /**
+    	   * declare the parameters that this class needs


bangerth · 2016-01-22T02:51:28Z

Some other comments:

We usually try to name the class and the section of the parameter file with the same words. Can you adapt this? (We also try to keep class name and file name in sync.)
I think the name "adiabatic boundary isotherm" may not be the best. It doesn't actually mean anything to me. Is this a standard technical term? If so, maybe it'd be worth explaining it in the descriptive section at the bottom of the .cc file. If it isn't, maybe we can find a better name?

I (or others) might have other comments once the current ones are addressed.

trajaona · 2016-01-22T02:58:22Z

The adiabatic boundary isotherm is not a standard technical term. I will think about a better name for it.

bangerth · 2016-01-22T20:19:07Z

source/initial_conditions/adiabatic_boundary.cc

+         {
+           prm.enter_subsection("Adiabatic boundary isotherm");
+           {
+             prm.declare_entry("Adiabatic Boundary Filename",


We typically capitalize only the first word of an option (just like for section names).

bangerth · 2016-01-27T03:48:44Z

Let me know when you're done rewriting things and we'll give it another once-over.

Every patch is currently checked whether it satisfies the correct indentation, simply because that makes the entire code base look uniform. We do this using a program called astyle, which you can find here: http://astyle.sourceforge.net/

Can you install version 2.04 (NOT the newer versions) on your machine in a place where it will be found when calling astyle on the command line, and then call ./doc/indent in the aspect directory? This indents all files using the default indentation style, after which you can commit and push the patch once again. This should make the auto-checker happy.

trajaona · 2016-01-31T03:27:59Z

Just to let you know that I pushed the updated patch.

trajaona · 2016-02-18T21:32:22Z

Just a reminder that I have made these changes.

On Jan 26, 2016, at 10:48 PM, Wolfgang Bangerth notifications@github.com wrote:

Let me know when you're done rewriting things and we'll give it another once-over.

Every patch is currently checked whether it satisfies the correct indentation, simply because that makes the entire code base look uniform. We do this using a program called astyle, which you can find here: http://astyle.sourceforge.net/ http://astyle.sourceforge.net/
Can you install version 2.04 (NOT the newer versions) on your machine in a place where it will be found when calling astyle on the command line, and then call ./doc/indent in the aspect directory? This indents all files using the default indentation style, after which you can commit and push the patch once again. This should make the auto-checker happy.

—
Reply to this email directly or view it on GitHub #720 (comment).

bangerth · 2016-03-24T12:34:09Z

@gassmoeller -- talking to @trajaona he says that he's made some changes and would appreciate if you could take another look.

gassmoeller · 2016-03-24T14:29:42Z

source/initial_conditions/adiabatic_boundary.cc

@@ -144,27 +109,21 @@ namespace aspect
    double
    AdiabaticBoundary<dim>::initial_temperature (const Point<dim> &) const
    {
-      Assert (false, ExcNotImplemented());
+      AssertThrow (false, ExcMessage ("The 'adiabatic boundary' initial temperature plugin is only implemented for 3d cases."));


This function is a bit confusing, because it is not a template specialization (I guess it is only called in 2d, because you provide a specialization for 3d below). Can you change it to the same format as the AdiabaticBoundary<2>::get_isotherm_depth() function above? I.e. please make this function a template specialization for dim==2.

gassmoeller · 2016-03-24T14:43:10Z

Sorry for the delay, I did not see this PR was updated (I only get messages when somebody writes a comment, not when commits are pushed here).
I left some minor comments at the individual commit, I hope you see them although they do not show up in the conversation here. In general I think this PR has improved a lot. Please address the minor issues and take a look at why the test is failing (it seems it can not read the test data file, did you check that in?).
When that is done, please post me a note, and I will take a final look.

…d fix directory not found

trajaona · 2016-04-29T17:21:34Z

@gassmoeller-- My apologize for late reply. Our cluster was down for a while so I could not test the changes I have made on the PR. I have done the edits according to your comments. I have also increased the grid size the lithospheric thickness data to 0.5x0.5 degree since I think this resolution will be enough for the test.

gassmoeller · 2016-05-02T08:25:05Z

source/initial_conditions/adiabatic_boundary.cc

@@ -135,10 +137,13 @@ namespace aspect
      {
        prm.enter_subsection("Adiabatic boundary");
        {
+          prm.declare_entry ("Data directory", "$ASPECT_SOURCE_DIR/tests/adiabatic_boundary/",


I would prefer if the default value could be set to "$ASPECT_SOURCE_DIR/data/initial-conditions/adiabatic-boundary/", and you would move the test data file there as well. This is how we handle it for all the other tests that need data files, and then all data is in one subfolder (aspect/data).

gassmoeller · 2016-05-02T08:35:40Z

No apologies needed 😄. I have two last minor details and a few typos, after that this is good to go.

gassmoeller · 2016-05-04T09:23:38Z

Ok, great. The code is good to go. There are two small things left (I had not noticed before, or they just came up with your latest commits): You will need to update your test results to succeed with a current master (I think Timo changed some output format for the number of iterations and updated all already merged tests). And you commited a file 'tests/adiabatic_boundary/.DS_Store' that does not belong there, probably it is something your operating system or file manager created and you accidentally added it, please remove that. After that we are ready to go, thanks for all the work 👍

gassmoeller · 2016-05-04T12:41:59Z

Sorry for all the comments, but two more things: There is another .DS_Store in source/initial_conditions/.DS_Store, please remove that as well. And please add an entry to doc/module/changes.h to document your addition. This way we can properly anounce the new feature at the next release. Just copy one of the other entries and write a sentence or two about your plugin. Thanks!

gassmoeller · 2016-05-12T10:27:04Z

Ok, looks great. Thanks a lot 👍

plugin for initial temperature condition for ellipsoid chunk geometry

2a433a6

bangerth reviewed Jan 19, 2016
View reviewed changes

some edits to adiabatic_boundary.h and adiabatic_boundary.cc

3fc4fef

bangerth reviewed Jan 20, 2016
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Tahiry Andriantsoa Rajaonarison added 3 commits January 20, 2016 18:21

correction of adiabatic_boundary.h and upload of screen-output

79ad8e8

edits of adiabatic_boundary.h

0f0a48b

some corrections to adiabatic_boundary.cc

c08bad6

bangerth reviewed Jan 22, 2016
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Tahiry Andriantsoa Rajaonarison added 2 commits January 24, 2016 21:19

corrected adiabatic_boundary.cc and adiabatic_boundary.h

3e4e716

small edit of adiabatic_boundary.cc

9fdb1ad

corrected indentation

b3ab2f2

Tahiry Andriantsoa Rajaonarison added 2 commits March 12, 2016 19:51

Merge branch 'master' into adiabatic_boundary_plugin

7ee8b84

Correct indentation of adiabatic_boundary.cc

a774912

bangerth self-assigned this Mar 24, 2016

gassmoeller reviewed Mar 24, 2016
View reviewed changes

Tahiry Andriantsoa Rajaonarison added 3 commits April 18, 2016 20:59

minor edit of adiabatic_boundary.cc

bd120a1

Merge branch 'master' into adiabatic_boundary_plugin

db3a887

Minor edits of adiabatic_boundary.cc, smoothed isotherm depth data an…

6552e50

…d fix directory not found

gassmoeller reviewed May 2, 2016
View reviewed changes

Tahiry Andriantsoa Rajaonarison added 2 commits May 2, 2016 17:52

Merge branch 'master' into adiabatic_boundary_plugin

a0b4704

replace file reading code and minor edits

66c01a7

Tahiry Andriantsoa Rajaonarison added 4 commits May 9, 2016 13:22

delete .DS_Store files

d353ce5

Merge branch 'master' into adiabatic_boundary_plugin

03f734d

Update screen-output and changes.h

cbed6dc

fixe mistake

3c3fd49

gassmoeller merged commit 3d733a0 into geodynamics:master May 12, 2016

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plugin for initial temperature condition for ellipsoid chunk geometry #720

plugin for initial temperature condition for ellipsoid chunk geometry #720

trajaona commented Jan 18, 2016

bangerth Jan 19, 2016

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gassmoeller commented May 12, 2016

plugin for initial temperature condition for ellipsoid chunk geometry #720

plugin for initial temperature condition for ellipsoid chunk geometry #720

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