Author: bugman
Date: Thu May 29 14:12:42 2014
New Revision: 23596
URL: http://svn.gna.org/viewcvs/relax?rev=23596&view=rev
Log:
Merged revisions 23348-23351,23356-23359,23364,23413-23420 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_speed
........
r23348 | tlinnet | 2014-05-22 18:27:40 +0200 (Thu, 22 May 2014) | 1 line
Fix for wrong file name in __init__.py.
........
r23349 | tlinnet | 2014-05-22 18:27:42 +0200 (Thu, 22 May 2014) | 16 lines
Added 7 unit tests demonstrating edge case 'no Rex' failures of the model
'LM63'.
This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
This is to implement catching of math domain errors, before they occur.
These tests cover all parameter value combinations which result in no
exchange:
- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.
........
r23350 | tlinnet | 2014-05-22 18:27:43 +0200 (Thu, 22 May 2014) | 8 lines
Critical fix for the math domain catching of model LM63.
This was discovered with the added 7 unit tests demonstrating edge case 'no
Rex' failures.
This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
This is to implement catching of math domain errors, before they occur.
........
r23351 | tlinnet | 2014-05-22 18:30:53 +0200 (Thu, 22 May 2014) | 4 lines
Unit test _lib/_dispersion/test_ns_cpmg_2site_expanded.py copied to
_lib/_dispersion/b14.py.
They are both of CPMG type, and can be re-used.
........
r23356 | tlinnet | 2014-05-22 19:15:32 +0200 (Thu, 22 May 2014) | 16 lines
Added 7 unit tests demonstrating edge case 'no Rex' failures of the model
'B14'.
This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
This is to implement catching of math domain errors, before they occur.
These tests cover all parameter value combinations which result in no
exchange:
- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.
........
r23357 | tlinnet | 2014-05-22 19:15:34 +0200 (Thu, 22 May 2014) | 8 lines
Critical fix for the math domain catching of model B14.
This was discovered with the added 7 unit tests demonstrating edge case 'no
Rex' failures.
This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
This is to implement catching of math domain errors, before they occur.
........
r23358 | tlinnet | 2014-05-22 19:15:36 +0200 (Thu, 22 May 2014) | 7 lines
Removed unnecessary math domain checking in model B14.
They are slowing down the code.
There is now protection for edge cases, and a last final check, before
returning values.
That should be sufficient.
........
r23359 | tlinnet | 2014-05-22 19:27:31 +0200 (Thu, 22 May 2014) | 5 lines
Unit test _lib/_dispersion/test_b14.py copied to
_lib/_dispersion/test_cr72.py.
They are both of CPMG type, and can be re-used.
........
r23364 | tlinnet | 2014-05-22 22:26:56 +0200 (Thu, 22 May 2014) | 3 lines
Copied unit test _lib/_dispersion/* to be reused for other models.
........
r23413 | tlinnet | 2014-05-26 13:38:07 +0200 (Mon, 26 May 2014) | 17 lines
Added 8 unit tests demonstrating edge case 'no Rex' failures of the model
'CR72'.
This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
This is to implement catching of math domain errors, before they occur.
These tests cover all parameter value combinations which result in no
exchange:
- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.
- kex = 1e5,
........
r23414 | tlinnet | 2014-05-26 13:38:09 +0200 (Mon, 26 May 2014) | 15 lines
Critical fix for the math domain catching of model CR72.
This was discovered with the added 8 unit tests demonstrating edge case 'no
Rex' failures.
This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
This is to implement catching of math domain errors, before they occur.
When kex is large, ex: kex = 1e5, the values of:
etapos = eta_scale * sqrt(Psi + sqrt_psi2_zeta2) / cpmg_frqs
will exceed possible numerical representation.
The cathing of these occurences needed to be re-written.
........
r23415 | tlinnet | 2014-05-26 13:38:11 +0200 (Mon, 26 May 2014) | 17 lines
Added the 8th unit tests demonstrating edge case 'no Rex' failures of the
model 'B14'.
This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
This is to implement catching of math domain errors, before they occur.
These tests cover all parameter value combinations which result in no
exchange:
- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.
- kex = 1e5,
........
r23416 | tlinnet | 2014-05-26 13:38:13 +0200 (Mon, 26 May 2014) | 13 lines
Critical fix for the math domain catching of model B14.
This was discovered with the added 8 unit tests demonstrating edge case 'no
Rex' failures.
This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
This is to implement catching of math domain errors, before they occur.
When kex is large, ex: kex = 1e5, "nan" values where produced,
which was replaced with 1e100.
The cathing of these occurences needed to be re-written.
........
r23417 | tlinnet | 2014-05-26 13:50:02 +0200 (Mon, 26 May 2014) | 5 lines
Critical fix for the math domain catching of model CR72.
Removed the test for kex >= 1.e5.
This catching should rather be performed on the math functions instead.
........
r23418 | tlinnet | 2014-05-26 13:50:05 +0200 (Mon, 26 May 2014) | 7 lines
Critical fix for the math domain catching of model B14.
Removed the test for kex >= 1.e5.
This catching should rather be performed on the math functions instead.
In this case, it is the cathing of sinh(), not evaluating values above 710.
........
r23419 | tlinnet | 2014-05-26 14:37:50 +0200 (Mon, 26 May 2014) | 17 lines
Added the 8th unit tests demonstrating edge case 'no Rex' failures of the
model 'LM63'.
This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
This is to implement catching of math domain errors, before they occur.
These tests cover all parameter value combinations which result in no
exchange:
- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.
- kex = 1e20,
........
r23420 | tlinnet | 2014-05-26 14:41:52 +0200 (Mon, 26 May 2014) | 3 lines
Small fix for 8 unit tests demonstrating edge case 'no Rex' failures of the
model 'ns cpmg_2site_expanded'.
The comparison of R2eff is now divided into a special case for kex having
large values.
........
Added:
trunk/test_suite/unit_tests/_lib/_dispersion/test_b14.py
- copied, changed from r23359,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
- copied, changed from r23359,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_it99.py
- copied unchanged from r23364,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_it99.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_lm63_3site.py
- copied unchanged from r23364,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_lm63_3site.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_m61.py
- copied unchanged from r23364,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_m61b.py
- copied unchanged from r23364,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61b.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
- copied unchanged from r23364,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_mp05.py
- copied unchanged from r23364,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mp05.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_tap03.py
- copied unchanged from r23364,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tap03.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_tp02.py
- copied unchanged from r23364,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tp02.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
- copied unchanged from r23364,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
Modified:
trunk/ (props changed)
trunk/lib/dispersion/b14.py
trunk/lib/dispersion/cr72.py
trunk/lib/dispersion/lm63.py
trunk/test_suite/unit_tests/_lib/_dispersion/__init__.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_lm63.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/dispersion/b14.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=23596&r1=23595&r2=23596&view=diff
Modified: trunk/lib/dispersion/cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/cr72.py?rev=23596&r1=23595&r2=23596&view=diff
Modified: trunk/lib/dispersion/lm63.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/lm63.py?rev=23596&r1=23595&r2=23596&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/__init__.py?rev=23596&r1=23595&r2=23596&view=diff
Copied: trunk/test_suite/unit_tests/_lib/_dispersion/test_b14.py (from
r23359,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_b14.py?p2=trunk/test_suite/unit_tests/_lib/_dispersion/test_b14.py&p1=branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py&r1=23359&r2=23596&rev=23596&view=diff
Copied: trunk/test_suite/unit_tests/_lib/_dispersion/test_cr72.py (from
r23359,
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_cr72.py?p2=trunk/test_suite/unit_tests/_lib/_dispersion/test_cr72.py&p1=branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py&r1=23359&r2=23596&rev=23596&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_lm63.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_lm63.py?rev=23596&r1=23595&r2=23596&view=diff
Modified:
trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py?rev=23596&r1=23595&r2=23596&view=diff
r23596 - in /trunk: ./ lib/dispersion/ test_suite/unit_tests/_lib/_dispersion/