relax SVN archive

The frame order analysis now uses the lib.compat.norm() replacement for numpy.linalg.norm().

This is to allow for the axis argument on numpy versions before version 1.8, though these older
versions will result in slower optimisation of the frame order models.

Created the lib.compat.norm() compatibility function for numpy.linalg.norm().

For numpy 1.8 and higher, the numpy.linalg.norm() function has introduced the 'axis' argument. This
is an incredibly fast way of determining the norm of an array of vectors. This is used by the frame
order analysis.

However for older numpy versions, this causes the frame order analysis, and many corresponding
system and GUI tests to fail. Therefore this new lib.compat.norm() function has been designed to
default to numpy.linalg.norm() if the axis argument is supported, or to switch to the much slower
numpy.apply_along_axis(numpy.linalg.norm, axis, x) call which is supported by older numpy.

Fix for an incorrect merger of the 'disp_speed' branch.

This branch was never used.

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/disp_speed

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/disp_speed

Merged revisions 23546,23548-23549,23563-23564,23566-23567,23569,23581-23588 via svnmerge from
svn+ssh://bugman@.../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.
........

Merged revisions 23465,23473,23483-23487,23502-23504,23526-23531 via svnmerge from
svn+ssh://bugman@.../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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........

Merged revisions 23425-23426,23431-23452,23455-23463 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_speed

........
r23425 | tlinnet | 2014-05-26 16:27:27 +0200 (Mon, 26 May 2014) | 1 line

Deleted unit test case for lm63 3site.
........
r23426 | tlinnet | 2014-05-26 16:27:30 +0200 (Mon, 26 May 2014) | 17 lines

Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'M61'.

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,
........
r23431 | tlinnet | 2014-05-26 20:13:46 +0200 (Mon, 26 May 2014) | 10 lines

Added the 8th 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:

- kex = 1e20,
........
r23432 | tlinnet | 2014-05-26 20:13:53 +0200 (Mon, 26 May 2014) | 1 line

Added "test_m61" to __init__.py in unit test directory.
........
r23433 | tlinnet | 2014-05-26 20:13:56 +0200 (Mon, 26 May 2014) | 17 lines

Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'M61b'.

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,
........
r23434 | tlinnet | 2014-05-26 20:14:01 +0200 (Mon, 26 May 2014) | 10 lines

Math-domain catching for model M61b.

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.
........
r23435 | tlinnet | 2014-05-26 20:14:03 +0200 (Mon, 26 May 2014) | 1 line

Modified script to be able to run systemtest Relax_disp.xxx_test_m61b_data_to_m61b.
........
r23436 | tlinnet | 2014-05-26 20:14:05 +0200 (Mon, 26 May 2014) | 1 line

Added "test_m61b" to __init__.py file in unit test directory.
........
r23437 | tlinnet | 2014-05-26 20:14:07 +0200 (Mon, 26 May 2014) | 17 lines

Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'IT99'.

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 = 1e19,
........
r23438 | tlinnet | 2014-05-26 23:09:40 +0200 (Mon, 26 May 2014) | 18 lines

Added 9 unit tests demonstrating edge case 'no Rex' failures of the model 'MMQ 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,
- dwH = 0.0,
........
r23439 | tlinnet | 2014-05-26 23:09:43 +0200 (Mon, 26 May 2014) | 8 lines

Critical fix for the math domain catching of model MMQ CR72.

This was discovered with the added 9 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.
........
r23440 | tlinnet | 2014-05-26 23:09:45 +0200 (Mon, 26 May 2014) | 17 lines

Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'MP05'.

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,
........
r23441 | tlinnet | 2014-05-26 23:09:47 +0200 (Mon, 26 May 2014) | 10 lines

Critical fix for the math domain catching of model IT99.

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.

The cathing of these occurences needed to be re-written.
........
r23442 | tlinnet | 2014-05-26 23:09:50 +0200 (Mon, 26 May 2014) | 17 lines

Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'TAP03'.

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,
........
r23443 | tlinnet | 2014-05-26 23:09:52 +0200 (Mon, 26 May 2014) | 8 lines

Critical fix for the math domain catching of model TAP03.

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.
........
r23444 | tlinnet | 2014-05-26 23:09:54 +0200 (Mon, 26 May 2014) | 17 lines

Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'TP02'.

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,
........
r23445 | tlinnet | 2014-05-26 23:09:56 +0200 (Mon, 26 May 2014) | 8 lines

Critical fix for the math domain catching of model TP02.

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.
........
r23446 | tlinnet | 2014-05-26 23:09:58 +0200 (Mon, 26 May 2014) | 16 lines

Added 7 unit tests demonstrating edge case 'no Rex' failures of the model 'TSMFK01'.

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.
........
r23447 | tlinnet | 2014-05-26 23:10:00 +0200 (Mon, 26 May 2014) | 10 lines

Critical fix for the math domain catching of model TSMFK01.

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.

The cathing of these occurences needed to be re-written.
........
r23448 | tlinnet | 2014-05-26 23:10:03 +0200 (Mon, 26 May 2014) | 1 line

Added missing files to __init__.py in unit_tests/_lib/_dispersion.
........
r23449 | tlinnet | 2014-05-26 23:23:16 +0200 (Mon, 26 May 2014) | 3 lines

Copied unit test test_b14.py to test_ns_cpmg_2site_3d.py
........
r23450 | tlinnet | 2014-05-27 00:08:06 +0200 (Tue, 27 May 2014) | 17 lines

Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'NS CPMG 2site 3D'.

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 = 1e7,
........
r23451 | tlinnet | 2014-05-27 00:08:08 +0200 (Tue, 27 May 2014) | 8 lines

Critical fix for the math domain catching of model NS CPMG 2site 3D.

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.
........
r23452 | tlinnet | 2014-05-27 00:08:09 +0200 (Tue, 27 May 2014) | 1 line

Added missing files to __init__.py in unit_tests/_lib/_dispersion.
........
r23455 | tlinnet | 2014-05-27 12:24:56 +0200 (Tue, 27 May 2014) | 20 lines

Modified unit tests demonstrating edge cases 'no Rex' failures of the model 'TP02'.

The cathing of errors for off-resonance R1rho models was implemented wrong.

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 was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.

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,
........
r23456 | tlinnet | 2014-05-27 12:26:20 +0200 (Tue, 27 May 2014) | 5 lines

Critical fix for the math domain catching of model TP02.

The cathing of errors for off-resonance R1rho models was implemented wrong.

This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.
........
r23457 | tlinnet | 2014-05-27 12:26:22 +0200 (Tue, 27 May 2014) | 3 lines

Modified unit tests demonstrating edge cases 'no Rex' failures of the model 'DPL94'.

This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.
........
r23458 | tlinnet | 2014-05-27 12:26:23 +0200 (Tue, 27 May 2014) | 10 lines

Modified unit tests demonstrating edge cases 'no Rex' failures of the model 'MP05'.

The cathing of errors for off-resonance R1rho models was implemented wrong.

This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.

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.
........
r23459 | tlinnet | 2014-05-27 12:26:25 +0200 (Tue, 27 May 2014) | 5 lines

Critical fix for the math domain catching of model MP05.

The cathing of errors for off-resonance R1rho models was implemented wrong.

This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.
........
r23460 | tlinnet | 2014-05-27 12:26:26 +0200 (Tue, 27 May 2014) | 9 lines

Modified unit tests demonstrating edge cases 'no Rex' failures of the model 'TAP03'.

The cathing of errors for off-resonance R1rho models was implemented wrong.

This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.
And post http://article.gmane.org/gmane.science.nmr.relax.devel/5944.

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.
........
r23461 | tlinnet | 2014-05-27 12:26:28 +0200 (Tue, 27 May 2014) | 6 lines

Critical fix for the math domain catching of model TAP03.

The cathing of errors for off-resonance R1rho models was implemented wrong.

This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.
And post http://article.gmane.org/gmane.science.nmr.relax.devel/5944.
........
r23462 | tlinnet | 2014-05-27 12:26:30 +0200 (Tue, 27 May 2014) | 7 lines

Modified unit tests demonstrating edge cases 'no Rex' failures of the model 'MMQ CR72'.

This was pointed out in post http://article.gmane.org/gmane.science.nmr.relax.devel/5940.
And in post http://article.gmane.org/gmane.science.nmr.relax.devel/5946.

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.
........
r23463 | tlinnet | 2014-05-27 12:26:32 +0200 (Tue, 27 May 2014) | 4 lines

Small fix for the math domain catching of model MMQ CR72.

This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5940.
And in post http://article.gmane.org/gmane.science.nmr.relax.devel/5946.
........

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.
........