Author: bugman
Date: Thu May 29 14:19:21 2014
New Revision: 23599
URL: http://svn.gna.org/viewcvs/relax?rev=23599&view=rev
Log:
Merged revisions 23546,23548-23549,23563-23564,23566-23567,23569,23581-23588
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_speed
........
r23546 | tlinnet | 2014-05-28 17:55:10 +0200 (Wed, 28 May 2014) | 96 lines
Reverted r23531-23526 as this would prevent a clean merge back into the
trunk.
The parameter_object changes should be perfomed in its own branch.
And there was not a clean separation with the unit tests.
The command used was:
svn merge -r23531:23526 .
.....
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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')
------------------------------------------------------------------------
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.
------------------------------------------------------------------------
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')
------------------------------------------------------------------------
.....
........
r23548 | tlinnet | 2014-05-28 18:03:15 +0200 (Wed, 28 May 2014) | 4 lines
Fix for differences in systemtests which are different from trunk.
These were found with the command:
diff -bur disp_speed/test_suite/ relax_trunk/test_suite/ | grep -v "Binary
files" > diff.txt
........
r23549 | tlinnet | 2014-05-28 18:08:27 +0200 (Wed, 28 May 2014) | 29 lines
FIx for incorrectly svnmerge command.
To complete the full reverse, I should have gone one reversion number down.
The command used was:
svn merge -r23526:23504 .
.....
------------------------------------------------------------------------
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')
------------------------------------------------------------------------
.....
........
r23563 | tlinnet | 2014-05-28 19:17:08 +0200 (Wed, 28 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model B14.
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.
........
r23564 | tlinnet | 2014-05-28 19:17:11 +0200 (Wed, 28 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model CR72:
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.
........
r23566 | tlinnet | 2014-05-28 19:17:19 +0200 (Wed, 28 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model DPL94:
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.
........
r23567 | tlinnet | 2014-05-28 19:17:27 +0200 (Wed, 28 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model IT99:
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.
........
r23569 | tlinnet | 2014-05-28 19:22:17 +0200 (Wed, 28 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model LM63:
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.
........
r23581 | tlinnet | 2014-05-29 11:29:25 +0200 (Thu, 29 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model M61:
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.
........
r23582 | tlinnet | 2014-05-29 11:35:35 +0200 (Thu, 29 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model M61b:
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.
........
r23583 | tlinnet | 2014-05-29 11:52:37 +0200 (Thu, 29 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model MMQ
CR72:
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.
........
r23584 | tlinnet | 2014-05-29 11:52:39 +0200 (Thu, 29 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model MP05:
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.
........
r23585 | tlinnet | 2014-05-29 12:24:23 +0200 (Thu, 29 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model NS CPMG
2site expanded.
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.
........
r23586 | tlinnet | 2014-05-29 12:24:25 +0200 (Thu, 29 May 2014) | 10 lines
Converting back to having back_calc as a function argument to model TAP03.
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.
........
r23587 | tlinnet | 2014-05-29 12:33:34 +0200 (Thu, 29 May 2014) | 10 lines
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.
........
r23588 | tlinnet | 2014-05-29 12:33:36 +0200 (Thu, 29 May 2014) | 10 lines
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.
........
Modified:
trunk/ (props changed)
trunk/lib/dispersion/b14.py
trunk/lib/dispersion/cr72.py
trunk/lib/dispersion/dpl94.py
trunk/lib/dispersion/it99.py
trunk/lib/dispersion/lm63.py
trunk/lib/dispersion/m61.py
trunk/lib/dispersion/m61b.py
trunk/lib/dispersion/mmq_cr72.py
trunk/lib/dispersion/mp05.py
trunk/lib/dispersion/ns_cpmg_2site_expanded.py
trunk/lib/dispersion/tap03.py
trunk/lib/dispersion/tp02.py
trunk/lib/dispersion/tsmfk01.py
trunk/specific_analyses/parameter_object.py
trunk/specific_analyses/relax_disp/parameter_object.py
trunk/target_functions/relax_disp.py
trunk/test_suite/system_tests/relax_disp.py
trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.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_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/b14.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/cr72.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/dpl94.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/it99.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/it99.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/lm63.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/lm63.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/m61.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/m61.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/m61b.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/m61b.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/mmq_cr72.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/mp05.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/mp05.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_cpmg_2site_expanded.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/tap03.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tap03.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/tp02.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tp02.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/lib/dispersion/tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tsmfk01.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/specific_analyses/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/parameter_object.py?rev=23599&r1=23598&r2=23599&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=23599&r1=23598&r2=23599&view=diff
Modified: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=23599&r1=23598&r2=23599&view=diff
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=23599&r1=23598&r2=23599&view=diff
Modified:
trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py?rev=23599&r1=23598&r2=23599&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=23599&r1=23598&r2=23599&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=23599&r1=23598&r2=23599&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=23599&r1=23598&r2=23599&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=23599&r1=23598&r2=23599&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=23599&r1=23598&r2=23599&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=23599&r1=23598&r2=23599&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_m61b.py
[... 20 lines stripped ...]
r23599 - in /trunk: ./ lib/dispersion/ specific_analyses/ specific_analyses/relax_disp/ target_functions/ test_suite/system_...