relax SVN archive

Merged revisions 23509 via svnmerge from
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r23509 | bugman | 2014-05-28 12:15:10 +0200 (Wed, 28 May 2014) | 8 lines

Partial fix for bug #22100.

This is the bug report at https://gna.org/bugs/?22100, the rotation argument for the
structure.rotate user function cannot be changed in the GUI, as an AttributeError is raised.

The append_row() method call has been replaced by the correct add_element() call.
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Merged revisions 23506-23508 via svnmerge from
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r23506 | bugman | 2014-05-28 12:04:15 +0200 (Wed, 28 May 2014) | 5 lines

Expanded the User_functions.test_structure_rotate GUI test.

This is to more extensively check the 'float_matrix' user function argument type in the GUI.
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r23507 | tlinnet | 2014-05-28 12:04:27 +0200 (Wed, 28 May 2014) | 3 lines

Modified the dim dimensions to (None, 3) to allow the user to change number of points in the GUI.

This is for the user function dx.map.
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r23508 | tlinnet | 2014-05-28 12:09:37 +0200 (Wed, 28 May 2014) | 5 lines

Modified the dim dimensions to (None, 4) to allow the user to change number of points in the GUI.

THe first dimension was used as a counter, the last 3 dimensions is for x,y,z position.

This is for the user function dx.map.
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Merged revisions 23505 via svnmerge from
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r23505 | bugman | 2014-05-28 11:58:29 +0200 (Wed, 28 May 2014) | 6 lines

Some more fixes for the User_functions.test_structure_rotate GUI test.

The open_dialog() method cannot be used, as it deletes the window at the end. Instead the
selection_win_show() and selection_win_data() method combination is used.
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Merged revisions 23500 via svnmerge from
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r23500 | bugman | 2014-05-28 11:31:19 +0200 (Wed, 28 May 2014) | 3 lines

Fixes for some big mistakes in the previous commit.
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Merged revisions 23499 via svnmerge from
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r23499 | bugman | 2014-05-28 11:29:57 +0200 (Wed, 28 May 2014) | 3 lines

Modified the User_functions.test_structure_rotate GUI test to change and check the rotation matrix.
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Modified the User_functions.test_dx_map GUI test to catch another problem with the Sequence_2D element.

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.

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.

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.

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')