[r23596]
by
bugman
Merged revisions 23348-23351,23356-23359,23364,23413-23420 via svnmerge from
svn+ssh://bugman@.../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.
........
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2014-05-29 12:12:42
|
Tree
|
[r23595]
by
bugman
Merged revisions 23333-23334,23338,23342 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_speed
........
r23333 | tlinnet | 2014-05-22 15:19:30 +0200 (Thu, 22 May 2014) | 7 lines
Align math-domain catching for model NS CPMG 2-site expanded with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23334 | tlinnet | 2014-05-22 15:19:32 +0200 (Thu, 22 May 2014) | 18 lines
Modified unit tests demonstrating edge case 'no Rex' failures of the model 'NS CPMG 2-site expanded'.
This is to align with the current return of data in the disp_speed branch.
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.
........
r23338 | tlinnet | 2014-05-22 16:56:32 +0200 (Thu, 22 May 2014) | 16 lines
Added 7 unit tests demonstrating edge case 'no Rex' failures of the model 'DPL94'.
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.
........
r23342 | tlinnet | 2014-05-22 17:46:50 +0200 (Thu, 22 May 2014) | 5 lines
Unit test _lib/test_ns_cpmg_2site_expanded.py copied to _/test_lm63.py.
They are both of CPMG type.
........
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2014-05-29 12:09:47
|
Tree
|
[r23594]
by
bugman
Merged revisions 23246-23250,23259,23268-23278,23295-23304 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_speed
........
r23246 | tlinnet | 2014-05-20 01:47:30 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model: 'NS CPMG 2-site expanded'.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23247 | tlinnet | 2014-05-20 01:47:32 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model CR72.
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 can be found via the --numpy-raise function to the systemtests.
The skipping of test when num_points > 0, is a bad implementation.
If such a case should show, it is best to catch the wrong input for the
calculations. This is best done with a check before running the calculations.
........
r23248 | tlinnet | 2014-05-20 01:47:34 +0200 (Tue, 20 May 2014) | 11 lines
Turned of processor.run_queue() when using calc().
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
A weird behaviour was found when running the test-suite.
Somehow, queued jobs from the last test suite was not flushed and done.
Running the test-suite gave errors on almost all tests.
Inspecting systemtest which only used calc() for the dispersion API, showed that no jobs was queued
in the calculate() method, and the call to processor.run_queue(), was turned off, solving the problem.
........
r23249 | tlinnet | 2014-05-20 01:47:37 +0200 (Tue, 20 May 2014) | 4 lines
An attempt to fix the pipe_control/minimisy.py minimise() call to processor.run_queue().
It was thought that I was modifying the address of array class(back_calc).
But this does not seem to be the problem.
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r23250 | tlinnet | 2014-05-20 02:02:19 +0200 (Tue, 20 May 2014) | 1 line
Fix for variable num_points not set.
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r23259 | tlinnet | 2014-05-20 14:55:11 +0200 (Tue, 20 May 2014) | 34 lines
Reverted r23250-23248 as the correct fix was done in fixing bug 22055.
bug #22055 (https://gna.org/bugs/?22055) The processor.run_queue() does not clean up in uni_processor - chain-reaction failures in the test suite.
The command used was:
svn merge -r23250:r23247 .
.....
r23250 | tlinnet | 2014-05-20 02:02:19 +0200 (Tue, 20 May 2014) | 1 line
Fix for variable num_points not set.
------------------------------------------------------------------------
r23249 | tlinnet | 2014-05-20 01:47:37 +0200 (Tue, 20 May 2014) | 4 lines
An attempt to fix the pipe_control/minimisy.py minimise() call to processor.run_queue().
It was thought that I was modifying the address of array class(back_calc).
But this does not seem to be the problem.
------------------------------------------------------------------------
r23248 | tlinnet | 2014-05-20 01:47:34 +0200 (Tue, 20 May 2014) | 11 lines
Turned of processor.run_queue() when using calc().
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
A weird behaviour was found when running the test-suite.
Somehow, queued jobs from the last test suite was not flushed and done.
Running the test-suite gave errors on almost all tests.
Inspecting systemtest which only used calc() for the dispersion API, showed that no jobs was queued
in the calculate() method, and the call to processor.run_queue(), was turned off, solving the problem.
.....
........
r23268 | tlinnet | 2014-05-20 22:29:35 +0200 (Tue, 20 May 2014) | 8 lines
Fix for commit 23246.
http://svn.gna.org/viewcvs/relax?view=revision&revision=23246
The testing taking a value to a power was performed wrong.
This made systemtest Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric
not working.
........
r23269 | tlinnet | 2014-05-20 22:29:38 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model TSMFK01.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23270 | tlinnet | 2014-05-20 22:29:40 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model TP02.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23271 | tlinnet | 2014-05-20 22:29:41 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model TAP03.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23272 | tlinnet | 2014-05-20 22:29:43 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model DPL94.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23273 | tlinnet | 2014-05-20 22:29:45 +0200 (Tue, 20 May 2014) | 3 lines
Math-domain catching for model TAP03.
Another check for division with 0 inserted.
........
r23274 | tlinnet | 2014-05-20 22:29:47 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model MP05.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23275 | tlinnet | 2014-05-20 22:29:49 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model IT99.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23276 | tlinnet | 2014-05-20 22:29:50 +0200 (Tue, 20 May 2014) | 7 lines
Removed class object "back_calc" being updated per time point for model LM63.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23277 | tlinnet | 2014-05-20 22:29:52 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model M61.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23278 | tlinnet | 2014-05-20 22:29:54 +0200 (Tue, 20 May 2014) | 10 lines
Math-domain catching for model MMQ CR72.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23295 | tlinnet | 2014-05-21 13:02:55 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model CR72 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23296 | tlinnet | 2014-05-21 13:02:56 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model DPL94 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23297 | tlinnet | 2014-05-21 13:02:58 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model IT99 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23298 | tlinnet | 2014-05-21 13:02:59 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model LM63 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23299 | tlinnet | 2014-05-21 13:03:01 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model M61 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23300 | tlinnet | 2014-05-21 13:03:02 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model MP05 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23301 | tlinnet | 2014-05-21 13:03:04 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model TAP03 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23302 | tlinnet | 2014-05-21 13:03:06 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model TP02 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23303 | tlinnet | 2014-05-21 13:03:07 +0200 (Wed, 21 May 2014) | 7 lines
Align math-domain catching for model TSMFK01 with trunk implementation.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is to implement catching of math domain errors, before they occur.
The catching of errors have to be more careful.
........
r23304 | tlinnet | 2014-05-21 13:03:09 +0200 (Wed, 21 May 2014) | 5 lines
Removing unnecessary math-domain catching for model IT99.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models..
The denominator is always positive.
........
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2014-05-29 11:59:18
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Tree
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[r23593]
by
bugman
Merged revisions 23240 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_speed
........
r23240 | tlinnet | 2014-05-19 14:44:12 +0200 (Mon, 19 May 2014) | 10 lines
Math-domain catching for model CR72.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
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2014-05-29 11:56:16
|
Tree
|
[r23592]
by
bugman
Merged revisions 23239 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_speed
........
r23239 | tlinnet | 2014-05-19 14:44:10 +0200 (Mon, 19 May 2014) | 10 lines
Math-domain catching for model B14.
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 can be found via the --numpy-raise function to the systemtests.
To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
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2014-05-29 11:55:17
|
Tree
|
[r23591]
by
bugman
Merged revisions 23216-23229 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_speed
........
r23216 | tlinnet | 2014-05-18 23:36:14 +0200 (Sun, 18 May 2014) | 13 lines
Huge speed-up for model CR72.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Systemtest Relax_disp.test_cpmg_synthetic_cr72_full_noise_cluster
changes from 7 seconds to 4.5 seconds.
This is won by not checking single values in the R2eff array for math domain
errors, but calculating all steps, and in one single round check for finite values.
If just one non-finite value is found, the whole array is returned with a large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23217 | tlinnet | 2014-05-18 23:36:17 +0200 (Sun, 18 May 2014) | 12 lines
Fix for systemtest test_cpmg_synthetic_dx_map_points.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is after commit 23216:
The systemtest uses: GRID_INC = None, which have found to be catastrophic: https://gna.org/bugs/?22032.
Commit 23216 fixed this, and now the found minimization point is much much better.
Start:
0.8 3.92 0.39964
End:
0.76982 3.9169 0.41353
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r23218 | tlinnet | 2014-05-19 00:51:15 +0200 (Mon, 19 May 2014) | 9 lines
Critical fixes for systemtest: Relax_disp.test_hansen_cpmg_data_missing_auto_analysis.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This was found necessary after commit 23216.
It is suspected that when relax have touched boundary values which made
math domain errors, the error cathing have created local minima or
interfered with the simplex search algorithm.
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r23219 | tlinnet | 2014-05-19 00:51:18 +0200 (Mon, 19 May 2014) | 10 lines
Speed-up of model TSMFK01.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is won by not checking single values in the R2eff array for math domain
errors, but calculating all steps, and in one single round check for finite values.
If just one non-finite value is found, the whole array is returned with a large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
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r23220 | tlinnet | 2014-05-19 00:51:20 +0200 (Mon, 19 May 2014) | 18 lines
Huge speed-up of model B14.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Time test for systemtests:
test_baldwin_synthetic
2.626s -> 1.990s
test_baldwin_synthetic_full
18.326s -> 13.742s
This is won by not checking single values in the R2eff array for math domain
errors, but calculating all steps, and in one single round check for finite values.
If just one non-finite value is found, the whole array is returned with a large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23221 | tlinnet | 2014-05-19 01:19:02 +0200 (Mon, 19 May 2014) | 20 lines
Speed-up of model TP02.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
The change for running systemtest is:
test_curve_type_r1rho_fixed_time
0.057s -> 0.049s
test_tp02_data_to_ns_r1rho_2site
10.539s -> 10.456s
test_tp02_data_to_tp02
8.608s -> 5.727s
This is won by not checking single values in the R1rho array for math domain
errors, but calculating all steps, and in one single round check for finite values.
If just one non-finite value is found, the whole array is returned with a large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23222 | tlinnet | 2014-05-19 03:20:43 +0200 (Mon, 19 May 2014) | 14 lines
Huge speed-up for model TAP03.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
The change for running systemtest is:
test_tp02_data_to_tap03
13.869s -> 7.263s
This is won by not checking single values in the R1rho array for math domain
errors, but calculating all steps, and in one single round check for finite values.
If just one non-finite value is found, the whole array is returned with a large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23223 | tlinnet | 2014-05-19 03:20:46 +0200 (Mon, 19 May 2014) | 8 lines
Speed-up of model MP05.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
The change in systemtest is:
test_tp02_data_to_mp05
10.750s -> 6.644s
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r23224 | tlinnet | 2014-05-19 03:20:47 +0200 (Mon, 19 May 2014) | 7 lines
Speed-up of model MMQ CR72.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in systemtest:
test_sprangers_data_to_mmq_cr72
9.892s -> 4.121s
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r23225 | tlinnet | 2014-05-19 03:20:49 +0200 (Mon, 19 May 2014) | 7 lines
Speed-up for model M61.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in speed is:
test_m61_data_to_m61
6.692s -> 3.480s
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r23226 | tlinnet | 2014-05-19 03:20:51 +0200 (Mon, 19 May 2014) | 13 lines
Speed-up of model LM63.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in systemtest was:
test_hansen_cpmg_data_auto_analysis
13.731s -> 9.971s
test_hansen_cpmg_data_auto_analysis_r2eff
13.370s -> 9.510s
test_hansen_cpmg_data_to_lm63
3.254s -> 2.080s
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r23227 | tlinnet | 2014-05-19 03:20:53 +0200 (Mon, 19 May 2014) | 10 lines
Speed-up of model IT99.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in speed is:
test_hansen_cpmg_data_auto_analysis
9.74s -> 8.330s
test_hansen_cpmg_data_to_it99
4.928s -> 3.138s
........
r23228 | tlinnet | 2014-05-19 03:20:54 +0200 (Mon, 19 May 2014) | 3 lines
Added missing imports of "numpy.array".
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
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r23229 | tlinnet | 2014-05-19 03:20:56 +0200 (Mon, 19 May 2014) | 8 lines
Speed-up of model DPL94.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in speed is:
test_dpl94_data_to_dpl94
19.412s -> 4.427s
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2014-05-29 11:46:48
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[r23590]
by
bugman
Initialized merge tracking via "svnmerge" with revisions "1-23214" from
svn+ssh://bugman@.../svn/relax/branches/disp_speed
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2014-05-29 11:22:39
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Tree
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[r23589]
by
tlinnet
Merged revisions 23551,23554-23562,23568,23571-23572,23574,23577-23579 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk
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r23551 | bugman | 2014-05-28 18:11:40 +0200 (Wed, 28 May 2014) | 11 lines
Fix for bug #22102, the point argument of the dx.map user function failing in the GUI.
This is reported at https://gna.org/bugs/?22102.
The Sequence_2D GUI element used for all list of lists arguments in the user function GUI windows
now correctly handles variable length lists. The first column which shows a count of the elements
is now properly taken into account in the SetValue(), GetValue() and add_item() methods, via a new
self.offset variable. The self.variable_length variable has also been fixed so it is not
overwritten by the parent Sequence GUI element.
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r23554 | bugman | 2014-05-28 18:24:57 +0200 (Wed, 28 May 2014) | 5 lines
Increased the width of the first column of the Sequence_2D GUI element for variable lists.
This is so the column title "Number" will fit.
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r23555 | bugman | 2014-05-28 18:26:19 +0200 (Wed, 28 May 2014) | 6 lines
Added list titles for the dx.map user function point argument.
This is so that the Sequence_2D GUI element will have column titles of 'X coordinate',
'Y coordinate', and 'Z coordinate'.
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r23556 | bugman | 2014-05-28 18:35:34 +0200 (Wed, 28 May 2014) | 3 lines
The self.variable_length flag is now used throughout the Sequence GUI element.
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r23557 | bugman | 2014-05-28 18:38:29 +0200 (Wed, 28 May 2014) | 3 lines
The self.variable_length flag is used in one more spot in the Sequence_2D GUI element.
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r23558 | bugman | 2014-05-28 18:59:17 +0200 (Wed, 28 May 2014) | 6 lines
Created the User_functions.test_structure_add_atom GUI test.
This is used to check the operation of the Sequence GUI element via the 'pos' argument of the
structure.add_atom user function. This is a list fixed to 3 elements.
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r23559 | bugman | 2014-05-28 19:01:14 +0200 (Wed, 28 May 2014) | 5 lines
Titles are now handled and set in the Sequence GUI element.
The titles will replace the numbering of 1 onwards in the first column of the GUI element.
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r23560 | bugman | 2014-05-28 19:07:38 +0200 (Wed, 28 May 2014) | 3 lines
Small fix for switched indices in the new User_functions.test_structure_add_atom GUI test.
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r23561 | bugman | 2014-05-28 19:10:00 +0200 (Wed, 28 May 2014) | 6 lines
Modified the 'pos' argument of the structure.add_atom user function.
The argument is now a list of fixed length of 3, and it has the titles 'X coordinate',
'Y coordinate', and 'Z coordinate' which are shown in the GUI.
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r23562 | bugman | 2014-05-28 19:12:21 +0200 (Wed, 28 May 2014) | 7 lines
Bug fixes for the Sequence GUI element used for lists in the user function windows.
Invalid values input into the Sequence GUI window are now ignored rather than raising different
types of error. And invalid input lists for fixed dimension arguments are also ignored. This
allows the User_functions.test_structure_add_atom GUI test to pass.
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r23568 | bugman | 2014-05-28 19:21:59 +0200 (Wed, 28 May 2014) | 6 lines
Bug fix for the lib.arg_check.is_float_object() function.
The dim argument can sometimes be an integer rather than a tuple, but this was not handled by the
function. Now integer dim arguments are pre-converted to lists before performing all the checks.
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r23571 | bugman | 2014-05-28 20:25:54 +0200 (Wed, 28 May 2014) | 8 lines
Created the User_functions.test_spectrum_read_intensities GUI test to catch bug #22105.
This is reported at https://gna.org/bugs/?22105.
The problem is that a single file name is split up into many files when the file selection button
is clicked, one for each character of the file name.
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r23572 | bugman | 2014-05-28 20:31:19 +0200 (Wed, 28 May 2014) | 5 lines
Fix for the User_functions.test_spectrum_read_intensities GUI test.
A valid value was being checked as invalid.
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r23574 | bugman | 2014-05-28 20:33:22 +0200 (Wed, 28 May 2014) | 7 lines
Fix for bug #22105 (https://gna.org/bugs/?22105).
This is the failure spectrum.read_intensities GUI user function whereby a file name is turned into
lists of characters. A few changes were made to allow the Selector_file_multiple GUI element to
operate correctly.
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r23577 | bugman | 2014-05-28 22:22:24 +0200 (Wed, 28 May 2014) | 6 lines
Shifted all wildcards used in GUI file selection dialogs into the new user_functions.wildcard module.
These have now all been standardised, and expanded to include more capitalisation combinations and
to include more *.* options.
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r23578 | bugman | 2014-05-28 22:39:51 +0200 (Wed, 28 May 2014) | 5 lines
Created a file selection wildcard for use in the GUI for selecting peak lists.
This is used in the four user functions which read peak lists.
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r23579 | bugman | 2014-05-28 22:42:43 +0200 (Wed, 28 May 2014) | 3 lines
Changed all *.* GUI file selection wildcards to *.
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2014-05-29 11:05:53
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Tree
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[r23588]
by
tlinnet
Converting back to having back_calc as a function argument to model TSMFK01.
This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.
The problem is, that many numerical models can't be optimised further, since they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put into
a larger numpy array.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
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2014-05-29 10:33:36
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Tree
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[r23587]
by
tlinnet
Converting back to having back_calc as a function argument to model TP02.
This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.
The problem is, that many numerical models can't be optimised further, since they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put into
a larger numpy array.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
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2014-05-29 10:33:34
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Tree
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