Author: bugman
Date: Tue Oct 16 10:19:57 2012
New Revision: 17828
URL: http://svn.gna.org/viewcvs/relax?rev=17828&view=rev
Log:
Merged revisions 17391-17538 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
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r17391 | bugman | 2012-08-30 11:02:04 +0200 (Thu, 30 Aug 2012) | 3 lines
Added a paragraph to the model-free chapter of the user manual explaining
the J(w) equation forms.
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r17392 | bugman | 2012-08-30 11:03:23 +0200 (Thu, 30 Aug 2012) | 3 lines
Fixed some citations in the newly introduced model-free J(w) paragraph.
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r17393 | bugman | 2012-08-30 11:13:54 +0200 (Thu, 30 Aug 2012) | 3 lines
Added a LaTeX label to the NOE chapter of the user manual.
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r17394 | bugman | 2012-08-30 11:14:21 +0200 (Thu, 30 Aug 2012) | 3 lines
Fixes for the referencing in the J(w) mapping chapter of the user manual.
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r17395 | bugman | 2012-08-30 16:40:40 +0200 (Thu, 30 Aug 2012) | 3 lines
Small description edit for the relax_data.temp_control user function.
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r17396 | bugman | 2012-08-30 16:42:48 +0200 (Thu, 30 Aug 2012) | 3 lines
Spell fix for the relax_data.temp_calibration user function description.
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r17397 | bugman | 2012-08-30 16:49:41 +0200 (Thu, 30 Aug 2012) | 3 lines
Fix for the incomplete relax_data.temp_control user function description.
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r17398 | bugman | 2012-08-30 16:50:46 +0200 (Thu, 30 Aug 2012) | 3 lines
Another fix for the relax_data.temp_control description.
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r17399 | bugman | 2012-08-30 17:43:09 +0200 (Thu, 30 Aug 2012) | 3 lines
Added the Viles et al., 2001 reference.
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r17400 | bugman | 2012-08-30 18:07:51 +0200 (Thu, 30 Aug 2012) | 5 lines
Added a new section called 'From spectra to peak intensities' to the Rx
fitting chapter of the manual.
This adds a number of recommendations for high quality relaxation rates.
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r17401 | bugman | 2012-08-30 18:11:27 +0200 (Thu, 30 Aug 2012) | 3 lines
The NOE chapter now points to the recommendations in the Rx fitting chapter.
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r17402 | bugman | 2012-08-30 18:11:49 +0200 (Thu, 30 Aug 2012) | 3 lines
Added the nth package for the user manual LaTeX compilation.
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r17403 | bugman | 2012-08-31 22:05:56 +0200 (Fri, 31 Aug 2012) | 6 lines
Bug fix for the loading of peak intensities via spectrum.read_intensities.
The user function could not be applied twice, preventing the loading of
data from different spin
systems such as Trp indole NH data.
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r17404 | bugman | 2012-08-31 22:16:37 +0200 (Fri, 31 Aug 2012) | 6 lines
Bug fix for the reading of Sparky peak lists.
Spin names with numbers at the end were not being correctly identified.
This fix allows Trp indole
NE1-HE1 data to be loaded.
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r17405 | bugman | 2012-08-31 23:35:22 +0200 (Fri, 31 Aug 2012) | 3 lines
Allowed the raggedbottom LaTeX setting as this is better for the screenshot
layout in the user manual.
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r17406 | bugman | 2012-08-31 23:36:07 +0200 (Fri, 31 Aug 2012) | 3 lines
Added some Sparky info to the Rx curve-fitting chapter of the user manual.
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r17407 | bugman | 2012-08-31 23:36:17 +0200 (Fri, 31 Aug 2012) | 3 lines
Added a section label.
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r17408 | bugman | 2012-08-31 23:42:01 +0200 (Fri, 31 Aug 2012) | 5 lines
Added a step-by-step tutorial for the GUI NOE auto-analysis to the user
manual.
This includes 22 screenshots of all the steps!
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r17409 | bugman | 2012-08-31 23:53:41 +0200 (Fri, 31 Aug 2012) | 3 lines
Modified the NOE sample script to include Trp indole NH data.
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r17410 | bugman | 2012-09-01 10:09:08 +0200 (Sat, 01 Sep 2012) | 6 lines
Added some Trp peak data (backbone and indole N) to the Sparky steady-state
NOE peak lists.
This is in preparation for the modification of the NOE system test to catch
bug #20119
(https://gna.org/bugs/index.php?20119).
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r17411 | bugman | 2012-09-01 10:17:30 +0200 (Sat, 01 Sep 2012) | 5 lines
Modified the NOE system test to test the usage of Trp indole 15N data.
This is to catch bug #20119 (https://gna.org/bugs/index.php?20119).
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r17412 | bugman | 2012-09-01 10:18:22 +0200 (Sat, 01 Sep 2012) | 5 lines
Significant update of the NOE chapter of the user manual.
The sample script used in this chapter was incredibly out of date!
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r17413 | bugman | 2012-09-01 11:05:16 +0200 (Sat, 01 Sep 2012) | 3 lines
Lots of editing of the NOE chapter of the user manual.
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r17414 | bugman | 2012-09-01 11:20:30 +0200 (Sat, 01 Sep 2012) | 3 lines
Modified the NOE system test to catch bug #20120
(https://gna.org/bugs/?20120).
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r17415 | bugman | 2012-09-01 11:21:54 +0200 (Sat, 01 Sep 2012) | 3 lines
Removed a debugging print out.
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r17416 | bugman | 2012-09-01 11:27:10 +0200 (Sat, 01 Sep 2012) | 6 lines
Fix for bug #20120 (https://gna.org/bugs/?20120), the bad Grace plots with
multiple spin types.
The grace data assembly function was not setting the correct index for when
a spin type changes to a
preexisting type.
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r17417 | bugman | 2012-09-01 13:13:01 +0200 (Sat, 01 Sep 2012) | 6 lines
Bug fix for the generic_fns.grace.get_data() function.
This was just recently introduced and was triggered by the
Relax_fit.test_bug_12670_12679 system
test.
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r17418 | bugman | 2012-09-01 14:58:49 +0200 (Sat, 01 Sep 2012) | 5 lines
Created the GUI wizard _apply() method for executing the current page's
_apply() method.
This is for the GUI tests to simulate a click on the 'Apply' button.
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r17419 | bugman | 2012-09-01 15:13:43 +0200 (Sat, 01 Sep 2012) | 5 lines
The spectrum.read_intensities user function now prints out a list of the
intensities read in.
This is for better user feedback as to what the user function has actually
done.
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r17420 | bugman | 2012-09-01 15:14:32 +0200 (Sat, 01 Sep 2012) | 3 lines
The NOE auto-analysis GUI test now checks the support for Trp indole N data
as well.
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r17421 | bugman | 2012-09-03 10:19:35 +0200 (Mon, 03 Sep 2012) | 3 lines
Fix for the spin.create user function documentation - the prompt examples
were wrong.
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r17422 | bugman | 2012-09-03 10:23:39 +0200 (Mon, 03 Sep 2012) | 3 lines
Created a directory for screenshots of the spin viewer window operation.
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r17423 | bugman | 2012-09-03 10:48:57 +0200 (Mon, 03 Sep 2012) | 3 lines
Changed the "View->Spin view" menu item to "View->Spin viewer".
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r17424 | bugman | 2012-09-03 11:11:48 +0200 (Mon, 03 Sep 2012) | 3 lines
Shifted the spin viewer screenshots into their own directory.
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r17425 | bugman | 2012-09-03 11:16:01 +0200 (Mon, 03 Sep 2012) | 5 lines
Redesign of the data model chapter of the user manual.
This includes the moving of all of the spin viewer window text and
screenshots from the NOE chapter.
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r17426 | bugman | 2012-09-03 11:28:42 +0200 (Mon, 03 Sep 2012) | 3 lines
Added screenshots of the spin viewer spin loading wizard sequence.read page.
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r17427 | bugman | 2012-09-03 11:43:36 +0200 (Mon, 03 Sep 2012) | 6 lines
More rearrangements of data model and NOE chapters of the relax manual.
The GUI spin deselection part of the NOE chapter has been shifted into the
data model chapter. And
the GUI loading of spins from a sequence file section has been completed.
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r17428 | bugman | 2012-09-03 12:06:00 +0200 (Mon, 03 Sep 2012) | 6 lines
Defined a new set of LaTeX commands for prompt/script/GUI strings and
elements for the user manual.
These will be used to regularize the text throughout the manual, as this is
currently quite mixed
up.
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r17429 | bugman | 2012-09-03 12:16:00 +0200 (Mon, 03 Sep 2012) | 3 lines
Added some more LaTeX functions for formatting consistency.
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r17430 | bugman | 2012-09-03 13:29:09 +0200 (Mon, 03 Sep 2012) | 3 lines
Removed some '()' text from the end of the user functions in the user
function documentation.
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r17431 | bugman | 2012-09-03 14:13:37 +0200 (Mon, 03 Sep 2012) | 6 lines
Improved the consistency on the user manual by using the new LaTeX commands.
These changes are throughout the manual and affect all the text of user
functions, menu items,
prompt examples, GUI elements, files, directories, etc.
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r17432 | bugman | 2012-09-03 14:22:16 +0200 (Mon, 03 Sep 2012) | 3 lines
Clean up of a paragraph of the data model chapter of the user manual.
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r17433 | bugman | 2012-09-03 14:24:13 +0200 (Mon, 03 Sep 2012) | 6 lines
Changed the order of the Rx curve-fitting and NOE chapters in the relax
manual.
This is because the NOE chapter references passages from the Rx
curve-fitting chapter, so it's more
logical to have the Rx curve-fitting chapter first.
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r17434 | bugman | 2012-09-03 14:51:11 +0200 (Mon, 03 Sep 2012) | 3 lines
Fix for the Farrow et al., 1995 DOI number.
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r17435 | bugman | 2012-09-03 15:03:36 +0200 (Mon, 03 Sep 2012) | 3 lines
Added the Fushman et al., 1998 reference.
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r17436 | bugman | 2012-09-03 15:06:25 +0200 (Mon, 03 Sep 2012) | 3 lines
Added the other consistency testing references to the citation chapter of
the manual.
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r17437 | bugman | 2012-09-03 15:06:52 +0200 (Mon, 03 Sep 2012) | 3 lines
Added a LaTeX label to the J(w) mapping chapter.
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r17438 | bugman | 2012-09-03 15:13:16 +0200 (Mon, 03 Sep 2012) | 3 lines
Activated the consistency testing chapter of the user manual.
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r17439 | bugman | 2012-09-03 15:13:38 +0200 (Mon, 03 Sep 2012) | 3 lines
Large edits of the consistency testing chapter of the user manual.
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r17440 | bugman | 2012-09-03 17:37:14 +0200 (Mon, 03 Sep 2012) | 3 lines
Added trp indole NH loading into the relaxation curve-fitting sample script.
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r17441 | bugman | 2012-09-03 22:34:03 +0200 (Mon, 03 Sep 2012) | 6 lines
Editing of the relaxation curve-fitting and NOE chapters of the user manual.
This is to synchronise the format of the two chapters, and includes the
swapping of text between
them.
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r17442 | bugman | 2012-09-03 23:07:07 +0200 (Mon, 03 Sep 2012) | 3 lines
Small edits of the relax data model chapter of the user manual.
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r17443 | bugman | 2012-09-04 11:52:07 +0200 (Tue, 04 Sep 2012) | 3 lines
Added some Grace plots from an NOE analysis for use in the user manual.
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r17444 | bugman | 2012-09-04 16:51:24 +0200 (Tue, 04 Sep 2012) | 5 lines
Added a tonne of GUI screenshots of an R1 analysis.
These will be used in the relaxation curve-fitting chapter of the user
manual.
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r17445 | bugman | 2012-09-04 16:51:25 +0200 (Tue, 04 Sep 2012) | 7 lines
Large expansion and lots of editing of the relaxation curve-fitting chapter
of the user manual.
The GUI section has been added which includes step-by-step instructions on
how to use relax,
illustrated with screenshots at each step. There has been general editing
of the whole of the
chapter as well.
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r17446 | bugman | 2012-09-04 16:52:00 +0200 (Tue, 04 Sep 2012) | 3 lines
Editing of the relax data model chapter of the user manual.
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r17447 | bugman | 2012-09-04 16:52:34 +0200 (Tue, 04 Sep 2012) | 3 lines
The old R1 and R2 analysis screenshots have been shifted to the intro
chapter.
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r17448 | bugman | 2012-09-04 16:53:06 +0200 (Tue, 04 Sep 2012) | 3 lines
Some editing of the NOE chapter of the relax user manual.
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r17449 | bugman | 2012-09-04 17:11:43 +0200 (Tue, 04 Sep 2012) | 3 lines
Fix for bug #20133 (https://gna.org/bugs/?20133) - this was simply a
missing import.
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r17450 | bugman | 2012-09-05 12:12:02 +0200 (Wed, 05 Sep 2012) | 3 lines
Editing of the nmrPipe script in the Rx curve-fitting chapter of the manual.
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r17451 | semor | 2012-09-05 13:52:36 +0200 (Wed, 05 Sep 2012) | 6 lines
Added some text and a reference to the consistency testing chapter.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id:
<CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@xxxxxxxxxxxxxx>)
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r17452 | bugman | 2012-09-05 13:52:45 +0200 (Wed, 05 Sep 2012) | 5 lines
Bug fix for the creation of 2D graphs via grace.write for when many data
sets exist.
The algorithm for setting the Grace symbol number to be between 1 and 10
was broken!
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r17453 | semor | 2012-09-05 14:16:17 +0200 (Wed, 05 Sep 2012) | 8 lines
Added text to detail the usage of the consistency testing script.
This text was modified from the corresponding text for jw_mapping.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id:
<CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@xxxxxxxxxxxxxx>)
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r17454 | bugman | 2012-09-05 14:18:38 +0200 (Wed, 05 Sep 2012) | 3 lines
Deletion of the relax version LaTeX file - this is automatically created
anyway.
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r17455 | semor | 2012-09-05 14:20:52 +0200 (Wed, 05 Sep 2012) | 8 lines
Added the DOI to reference Morin11 and fixed indentation.
10.1016/j.pnmrs.2010.12.003
This follows a comment by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00022.html
(Message-id:
<CAED9pY-ikjPvGaRPADHRJpLGFGnoeu+yNp5D1hLLm1U70maAwA@xxxxxxxxxxxxxx>)
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r17456 | semor | 2012-09-05 14:25:48 +0200 (Wed, 05 Sep 2012) | 3 lines
Made some corrections to the formatting of math symbols in Latex.
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r17457 | semor | 2012-09-05 14:48:42 +0200 (Wed, 05 Sep 2012) | 8 lines
Corrected the bibliography entries whih were still in plain text and not as
a Latex \cite call...
Also renamed the MorinGagne09 entry to MorinGagne09a as there is now also
MorinGagne09b.
This was proposed by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2012-09/msg00025.html
(Message-id:
<CAED9pY9uKUd_OesCvDLqv2fGPoLDHB4ftrbW1-y6df4oQtbWyg@xxxxxxxxxxxxxx>)
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r17458 | semor | 2012-09-05 15:08:57 +0200 (Wed, 05 Sep 2012) | 6 lines
Added a directory for placing consistency testing graphics.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id:
<CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@xxxxxxxxxxxxxx>)
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r17459 | semor | 2012-09-05 15:23:32 +0200 (Wed, 05 Sep 2012) | 10 lines
Added a modified version of figure 1 from Morin and Gagne (JBNMR, 2009).
http://dx.doi.org/10.1007/s10858-009-9381-4
File formats are .agr (xmgrace), eps (gzipped), and png.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id:
<CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@xxxxxxxxxxxxxx>)
........
r17460 | semor | 2012-09-05 15:33:12 +0200 (Wed, 05 Sep 2012) | 6 lines
Added some text to describe the consistency testing example figure.
This follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id:
<CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@xxxxxxxxxxxxxx>)
........
r17461 | semor | 2012-09-05 16:00:48 +0200 (Wed, 05 Sep 2012) | 12 lines
Added more text to describe the consistency testing approach.
Also includes a very basic point by point protocol for consistency testing.
This was proposed by by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00028.html
(Message-id:
<CAED9pY_YTDj8SX8crQu9on4LqA=pLzQwwyaz9kMLWD96xg-d0g@xxxxxxxxxxxxxx>)
This also follows a discussion started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00019.html
(Message-id:
<CAED9pY8XhmmvyfBS7mZA8XZ=4mJZe9TuGjARHoV2tVcjjV9SrQ@xxxxxxxxxxxxxx>)
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r17462 | semor | 2012-09-05 17:02:41 +0200 (Wed, 05 Sep 2012) | 12 lines
Reverted r17456.
This follows a remark by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00029.html
(Message-id:
<CAED9pY9jMXUyUsRv_FDcoen-_3SOu3oyrYK_egyw89dgH5-ESQ@xxxxxxxxxxxxxx>)
The command used was:
svn merge -r17456:17455 .
Then, the file was manually adjusted since there were apparently conflicts
with svn...
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r17463 | semor | 2012-09-05 17:09:25 +0200 (Wed, 05 Sep 2012) | 13 lines
Added the bounding box and a centerline command to the code for the figure
for consistency testing...
This follows two remark by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2012-09/msg00030.html
(Message-id:
<CAED9pY_DzNvTcCjD0NzzkW_Zy-xdHrUe4q6ooqrSF17ySnj_Tg@xxxxxxxxxxxxxx>)
and
https://mail.gna.org/public/relax-devel/2012-09/msg00032.html
(Message-id:
<CAED9pY-aymMGvmo=JMC_nWYSeLd-HAsCirv7so5P3OhJBNFY5Q@xxxxxxxxxxxxxx>)
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r17464 | semor | 2012-09-05 17:15:23 +0200 (Wed, 05 Sep 2012) | 3 lines
Made a small correction to a reference such that a superscript is correctly
displayed.
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r17465 | semor | 2012-09-05 21:07:58 +0200 (Wed, 05 Sep 2012) | 7 lines
Fixed a bibliography entry label problem.
This was spotted by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2012-09/msg00040.html
(Message-id:
<CAED9pY-pvtpE69tqXqb30fj9aWL1_wU8yaM4u44rMXY1LEQbag@xxxxxxxxxxxxxx>)
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r17466 | semor | 2012-09-05 21:11:24 +0200 (Wed, 05 Sep 2012) | 6 lines
Fixed the bounding box for the consistency testing figure and also fixed
some Latex unfriendly code...
Problems were spotted by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2012-09/msg00039.html
(Message-id:
<CAED9pY9pucoVrGzDvKs0u6hdUb94-Db8ixvno7MFN1QZsQDonA@xxxxxxxxxxxxxx>)
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r17467 | bugman | 2012-09-06 08:17:08 +0200 (Thu, 06 Sep 2012) | 3 lines
Fixed the newlines in the sample script in the consistency testing chapter.
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r17468 | bugman | 2012-09-06 10:59:01 +0200 (Thu, 06 Sep 2012) | 7 lines
Editing of the "Values, gradients, and Hessians" chapter of the user manual
to make it fit better.
The context of this chapter has been specified by changing the title to
"Optimisation of relaxation
data -- values, gradients, and Hessians" and the intro text has been
updated. As this chapter is no
longer straight after the model-free chapter, this is needed.
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r17469 | bugman | 2012-09-06 11:19:43 +0200 (Thu, 06 Sep 2012) | 3 lines
Editing and a number of fixes/cleanups for the consistency testing chapter
of the user manual.
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r17470 | bugman | 2012-09-06 11:30:04 +0200 (Thu, 06 Sep 2012) | 3 lines
Small edits of the consistency testing figure caption in the relax user
manual.
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r17471 | bugman | 2012-09-06 11:47:49 +0200 (Thu, 06 Sep 2012) | 3 lines
Big clean up of the Bibtex bibliography file for the relax user manual.
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r17472 | semor | 2012-09-06 11:48:22 +0200 (Thu, 06 Sep 2012) | 6 lines
Added some text to explain why test only J(0) is discussed whereas the
script also calculated F_R2 and F_eta.
This was suggested by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2012-09/msg00044.html
(Message-id:
<CAED9pY9U46ga6_j245peX1ETNZc_Lw0f5cz+5xx5rGVhee29YA@xxxxxxxxxxxxxx>)
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r17473 | bugman | 2012-09-06 16:07:04 +0200 (Thu, 06 Sep 2012) | 5 lines
A few small edits of the relaxation curve-fitting chapter.
This is to reinforce the exact time of the relaxation time period.
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r17474 | bugman | 2012-09-06 17:14:43 +0200 (Thu, 06 Sep 2012) | 3 lines
[... 624 lines stripped ...]
r17828 - in /branches/frame_order_testing: ./ docs/html/ docs/latex/ generic_fns/ graphics/ graphics/analyses/consistency_te...