Author: bugman
Date: Thu May 29 14:16:36 2014
New Revision: 23598
URL: http://svn.gna.org/viewcvs/relax?rev=23598&view=rev
Log:
Merged revisions 23465,23473,23483-23487,23502-23504,23526-23531 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_speed
........
r23465 | tlinnet | 2014-05-27 12:50:51 +0200 (Tue, 27 May 2014) | 6 lines
Various spacing fixes in unit test files _lib/_dispersion.
This is the preparation for merging back disp_speed branch into trunk.
This follows post
http://article.gmane.org/gmane.science.nmr.relax.devel/5948.
Usin the code validator script './devel_scripts/code_validator'.
........
r23473 | tlinnet | 2014-05-27 17:05:45 +0200 (Tue, 27 May 2014) | 4 lines
Modified that unit tests having different r20a and r20b values is checking
if the correct one is returned.
This is the preparation for merging back disp_speed branch into trunk.
This follows post
http://article.gmane.org/gmane.science.nmr.relax.devel/5948.
........
r23483 | tlinnet | 2014-05-27 19:11:26 +0200 (Tue, 27 May 2014) | 5 lines
Modified unit test to have standard population of pA=0.95, and a correctly
calculation of dw in ppm to rad/s.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
........
r23484 | tlinnet | 2014-05-27 19:29:56 +0200 (Tue, 27 May 2014) | 1 line
Small fix in parameter calculation in unit test
_dispersion/test_ns_cpmg_2site_expanded.
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r23485 | tlinnet | 2014-05-27 19:29:58 +0200 (Tue, 27 May 2014) | 1 line
Increased max kex to value 1e18 for unit test of
lin/ns_cpmg_2site_expanded.py.
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r23486 | tlinnet | 2014-05-27 19:30:00 +0200 (Tue, 27 May 2014) | 1 line
Increased max kex to value 1e20 for unit test of lib/ns_cpmg_2site_3d.py.
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r23487 | tlinnet | 2014-05-27 19:30:02 +0200 (Tue, 27 May 2014) | 6 lines
Fix for looking for negative values, when all values where converted to
positive in matrix in ns_cpmg_2site_3d.py.
This is to implement catching of math domain errors, before they occur.
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.
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r23502 | tlinnet | 2014-05-28 11:49:17 +0200 (Wed, 28 May 2014) | 1 line
Removed nested looping of returning back_calc in lib/ns_cpmg_2site_3d.
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r23503 | tlinnet | 2014-05-28 11:49:21 +0200 (Wed, 28 May 2014) | 5 lines
Removed the 8th unit test for model NS CPMG 2site 3D.
This was the catching of errors when kex=1e20.
The model cannot handle this situations, and we need to let it fail.
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r23504 | tlinnet | 2014-05-28 11:57:31 +0200 (Wed, 28 May 2014) | 5 lines
Removed the 8th unit test for model NS CPMG 2site extended.
This was the catching of errors when kex has high values.
The model cannot handle this situations, and we need to let it fail.
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r23526 | tlinnet | 2014-05-28 16:49:00 +0200 (Wed, 28 May 2014) | 13 lines
Added the default value lower grid value to be set for the pA parameter.
This is added in the collected table of
specific_analysis/relax_disp/parameter_object.py
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Discussed in post
http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.
In any function, these default values can get accessed by:
from specific_analyses.relax_disp.parameter_object import Relax_disp_params
PARAMS = Relax_disp_params()
PARAMS.default_value('pA')
PARAMS.grid_lower('pA')
........
r23527 | tlinnet | 2014-05-28 16:49:02 +0200 (Wed, 28 May 2014) | 4 lines
Added grid_lower to be handled in specific_analyses/parameter_object.py.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Discussed in post
http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.
........
r23528 | tlinnet | 2014-05-28 16:49:03 +0200 (Wed, 28 May 2014) | 13 lines
Added the default value upper grid value to be set for the pA parameter.
This is added in the collected table of
specific_analysis/relax_disp/parameter_object.py.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Discussed in post
http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.
In any function, these default values can get accessed by:
from specific_analyses.relax_disp.parameter_object import Relax_disp_params
PARAMS = Relax_disp_params()
PARAMS.default_value('pA')
PARAMS.grid_upper('pA')
........
r23529 | tlinnet | 2014-05-28 16:49:05 +0200 (Wed, 28 May 2014) | 4 lines
Added grid_upper to be handled in specific_analyses/parameter_object.py.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Discussed in post
http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.
........
r23530 | tlinnet | 2014-05-28 16:49:06 +0200 (Wed, 28 May 2014) | 16 lines
Added all the default values for the lower/upper bounds which is set for
the parameters in the grid search.
This is added in the collected table of
specific_analysis/relax_disp/parameter_object.py.
The values were extracted from:
specific_analysis/relax_disp/optimisation.py in grid_search_setup().
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Discussed in post
http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.
In any function, these default values can get accessed by:
from specific_analyses.relax_disp.parameter_object import Relax_disp_params
PARAMS = Relax_disp_params()
PARAMS.default_value('pA')
PARAMS.grid_upper('pA')
This provides a good look-up table, when stress testing the different
lib/dispersion/* functions.
........
r23531 | tlinnet | 2014-05-28 16:49:08 +0200 (Wed, 28 May 2014) | 15 lines
Added 9th and 10th unit test case for model B14.
These tests are setup, to check how the function behaves under conditions
of the grid-seach.
Two tests are setup, which either use the default lower or upper bound of
the parameters for the grid search.
The return of the values are not checked, but the behaving of the function
can be found when adding the --numpy-raise to run relax.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
These tests are implemented to show bug cases related to:
Bug #22032: (bug #22032: Minimisation explodes when using Grid_INC=None)
Minimisation explodes when using Grid_INC=None
The function can return nan or inf values, which are not handled by the
minimisation algorithm, causing it to stop.
There needs to be mechanism to catch these cases.
........
Modified:
trunk/ (props changed)
trunk/lib/dispersion/ns_cpmg_2site_3d.py
trunk/specific_analyses/parameter_object.py
trunk/specific_analyses/relax_disp/parameter_object.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_b14.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_it99.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_lm63.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_m61.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_m61b.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_mp05.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_tap03.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_tp02.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/dispersion/ns_cpmg_2site_3d.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_cpmg_2site_3d.py?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/specific_analyses/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/parameter_object.py?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/specific_analyses/relax_disp/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameter_object.py?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/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?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/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?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_it99.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_it99.py?rev=23598&r1=23597&r2=23598&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=23598&r1=23597&r2=23598&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_m61.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_m61.py?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_m61b.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_m61b.py?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_mp05.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_mp05.py?rev=23598&r1=23597&r2=23598&view=diff
Modified:
trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py?rev=23598&r1=23597&r2=23598&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=23598&r1=23597&r2=23598&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_tap03.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_tap03.py?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_tp02.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_tp02.py?rev=23598&r1=23597&r2=23598&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py?rev=23598&r1=23597&r2=23598&view=diff
r23598 - in /trunk: ./ lib/dispersion/ specific_analyses/ specific_analyses/relax_disp/ test_suite/unit_tests/_lib/_dispersion/