Author: bugman
Date: Fri Sep 10 15:27:15 2010
New Revision: 11540
URL: http://svn.gna.org/viewcvs/relax?rev=11540&view=rev
Log:
Merged revisions 11388-11534 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r11388 | bugman | 2010-08-03 11:22:53 +0200 (Tue, 03 Aug 2010) | 3 lines
Created the torsionless pseudo-ellipse cone model, where the torsion angle
simga is zero.
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r11389 | bugman | 2010-08-03 14:44:56 +0200 (Tue, 03 Aug 2010) | 5 lines
Created the pseudo-ellipse, free rotor target function.
This model is not yet available.
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r11390 | bugman | 2010-08-03 15:16:23 +0200 (Tue, 03 Aug 2010) | 3 lines
Added the missing hyphen to 'pseudo ellipse' in the docstrings.
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r11391 | bugman | 2010-08-03 15:17:54 +0200 (Tue, 03 Aug 2010) | 3 lines
Added target function aliases for all 12 parameteric restriction models of
the pseudo-ellipse.
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r11392 | bugman | 2010-08-03 16:22:39 +0200 (Tue, 03 Aug 2010) | 3 lines
The frame_order.select_model() user fn docstring now describes all 12
parametric restriction models.
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r11393 | bugman | 2010-08-03 22:18:07 +0200 (Tue, 03 Aug 2010) | 6 lines
Partial support for the 12 parametric restriction models of the
pseudo-ellipse.
All of the specific frame order code can now support these models. The
maths_fns code is still
missing, so not all models are available.
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r11394 | bugman | 2010-08-03 22:37:46 +0200 (Tue, 03 Aug 2010) | 5 lines
Shifted all of the shared code in the frame order target functions to
reduce_and_rot().
This significantly simplifies the code base and removes a large source of
bugs.
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r11395 | bugman | 2010-08-03 22:48:06 +0200 (Tue, 03 Aug 2010) | 5 lines
Abstracted the common code in compile_2nd_matrix_*() into rotate_daeg().
This will significantly simplify the addition of all of the 12 models.
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r11396 | bugman | 2010-08-03 23:02:21 +0200 (Tue, 03 Aug 2010) | 6 lines
Simplified compile_2nd_matrix_iso_cone() by using rotate_daeg().
The compile_2nd_matrix_*() functions now build the rotation matrix
themselves as this is not shared
code.
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r11397 | bugman | 2010-08-03 23:09:43 +0200 (Tue, 03 Aug 2010) | 3 lines
Fix for the reduce_and_rot() method, the self arg was missing.
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r11398 | bugman | 2010-08-04 09:42:29 +0200 (Wed, 04 Aug 2010) | 3 lines
Ordering of the functions.
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r11399 | bugman | 2010-08-04 09:56:49 +0200 (Wed, 04 Aug 2010) | 6 lines
Simplified and sped up the torsionless pseudo ellipse.
6 functions, and hence 6 numerical integrations, have been deleted as they
are repetitive of other
frame order matrix elements.
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r11400 | bugman | 2010-08-04 10:53:17 +0200 (Wed, 04 Aug 2010) | 5 lines
Renamed to isotropic cone functions to the free rotor isotropic cone.
The model name has changed, as the torsion angle was unrestricted in the
earlier code.
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r11401 | bugman | 2010-08-04 11:26:58 +0200 (Wed, 04 Aug 2010) | 3 lines
Added support for the isotropic cone model, that is with a torsion angle
restriction of sigma_max.
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r11402 | bugman | 2010-08-04 14:30:13 +0200 (Wed, 04 Aug 2010) | 5 lines
Removal of the reduce_alignment_tensor_reverse() frame order function.
This is not being used, and is of no use!
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r11403 | bugman | 2010-08-04 17:07:27 +0200 (Wed, 04 Aug 2010) | 3 lines
Modified reduce_alignment_tensor() to be in the Kronecker product notation.
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r11404 | bugman | 2010-08-04 17:13:47 +0200 (Wed, 04 Aug 2010) | 3 lines
Created the reduce_alignment_tensor_symmetric() function for computation
efficiency.
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r11405 | bugman | 2010-08-04 17:14:34 +0200 (Wed, 04 Aug 2010) | 3 lines
The frame order target functions now use
reduce_alignment_tensor_symmetric().
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r11406 | bugman | 2010-08-04 17:17:01 +0200 (Wed, 04 Aug 2010) | 3 lines
Modified rotate_daeg() to operate on the Kronecker product form of the
frame order matrix.
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r11407 | bugman | 2010-08-04 17:33:49 +0200 (Wed, 04 Aug 2010) | 3 lines
Shifted populate_2nd_eigenframe_iso_cone_free_rotor() to be in the
Kronecker product form.
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r11408 | bugman | 2010-08-04 18:44:25 +0200 (Wed, 04 Aug 2010) | 5 lines
Changed the frame order pseudo-ellipse equations.
These should be numerically more stable.
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r11409 | bugman | 2010-08-04 18:50:24 +0200 (Wed, 04 Aug 2010) | 5 lines
Fix for all the part_int_daeg2_pseudo_ellipse_*() functions.
The variable f should be phi!
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r11410 | bugman | 2010-08-04 18:53:40 +0200 (Wed, 04 Aug 2010) | 5 lines
Commented out unused frame order matrix elements in
compile_2nd_matrix_pseudo_ellipse().
These elements are not part of the rotational superoperator.
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r11411 | bugman | 2010-08-04 19:04:53 +0200 (Wed, 04 Aug 2010) | 6 lines
Reverted r11410 as the change did not take into account the rotation of the
frame order matrix.
The command used was:
svn merge -r11410:11409 .
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r11412 | bugman | 2010-08-04 19:08:38 +0200 (Wed, 04 Aug 2010) | 6 lines
Reverted r11405 as the eigenframe rotation of the frame order matrix breaks
the symmetry.
The command used was:
svn merge -r11405:11404 .
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r11413 | bugman | 2010-08-04 19:17:44 +0200 (Wed, 04 Aug 2010) | 3 lines
Bug fix for reduce_alignment_tensor(), some subtractions should have been
additions!
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r11414 | bugman | 2010-08-04 22:42:48 +0200 (Wed, 04 Aug 2010) | 5 lines
Fixes for the torsionless frame order matrix equations.
The previous equations were plain wrong!
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r11415 | bugman | 2010-08-04 22:47:56 +0200 (Wed, 04 Aug 2010) | 5 lines
Fix for the func_pseudo_ellipse_torsionless() frame order target function.
A variable was not fully typed out.
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r11416 | bugman | 2010-08-04 22:49:14 +0200 (Wed, 04 Aug 2010) | 3 lines
Fix for the pseudo-ellipse unit test as the matrix is now in Kronecker
product form.
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r11417 | bugman | 2010-08-04 22:49:52 +0200 (Wed, 04 Aug 2010) | 5 lines
Another fix for func_pseudo_ellipse_torsionless().
The average position Euler angles were not correctly named.
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r11418 | bugman | 2010-08-05 11:12:07 +0200 (Thu, 05 Aug 2010) | 3 lines
Added 2 system tests for checking the pseudo-ellipse and torsionless
pseudo-ellipse target fns.
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r11419 | bugman | 2010-08-05 12:36:42 +0200 (Thu, 05 Aug 2010) | 5 lines
Fixes for the free rotor pseudo-elliptic frame order matrix equations.
The previous equations were plain wrong!
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r11420 | bugman | 2010-08-05 12:50:23 +0200 (Thu, 05 Aug 2010) | 3 lines
Fix for compile_2nd_matrix_pseudo_ellipse(), the pseudo-ellipse has slight
asymmetry in daeg.
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r11421 | bugman | 2010-08-05 13:04:57 +0200 (Thu, 05 Aug 2010) | 6 lines
Simplification of compile_2nd_matrix_pseudo_ellipse() by removal of
identical numerical integrations.
A number of the frame order matrix diagonal elements are equal to each
other, so the repetitive
calculations were removed for speed.
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r11422 | bugman | 2010-08-05 13:10:23 +0200 (Thu, 05 Aug 2010) | 5 lines
Fix for the pseudo-ellipse frame order system test.
The chi2 is different with the corrected equations.
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r11423 | bugman | 2010-08-05 15:04:08 +0200 (Thu, 05 Aug 2010) | 5 lines
Bug fix for compile_2nd_matrix_pseudo_ellipse_free_rotor() - element 04 was
incorrectly set.
It was set to 11 rather than 00.
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r11424 | bugman | 2010-08-06 10:42:19 +0200 (Fri, 06 Aug 2010) | 3 lines
Bug fixes for populate_2nd_eigenframe_iso_cone() as the frame order
equations were incorrect.
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r11425 | bugman | 2010-08-06 11:08:01 +0200 (Fri, 06 Aug 2010) | 3 lines
Fixed a typo in populate_2nd_eigenframe_iso_cone().
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r11426 | bugman | 2010-08-06 11:09:09 +0200 (Fri, 06 Aug 2010) | 3 lines
Fixed another typo in populate_2nd_eigenframe_iso_cone().
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r11427 | bugman | 2010-08-06 11:29:23 +0200 (Fri, 06 Aug 2010) | 5 lines
Created a new module for performing coordinate transformations.
The new function cartesian_to_spherical() has been added as the first
conversion.
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r11428 | bugman | 2010-08-06 13:47:54 +0200 (Fri, 06 Aug 2010) | 3 lines
Switched the theta and phi angles in cartesian_to_spherical() to match the
rest of relax.
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r11429 | bugman | 2010-08-06 14:00:26 +0200 (Fri, 06 Aug 2010) | 5 lines
Shifted frame_order_matrix_ops.generate_vector() to
coord_transform.spherical_to_cartesian().
The function input has been modified to accept a spherical coordinate
vector.
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r11430 | bugman | 2010-08-06 14:03:28 +0200 (Fri, 06 Aug 2010) | 3 lines
The frame order specific module now uses spherical_to_cartesian().
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r11431 | bugman | 2010-08-06 15:12:56 +0200 (Fri, 06 Aug 2010) | 5 lines
The isotropic cone frame order model now uses the full eigenframe.
This is necessary to define the torsion angle restriction.
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r11432 | bugman | 2010-08-06 15:26:13 +0200 (Fri, 06 Aug 2010) | 5 lines
Bug fix for the frame order _update_model() method for the isotropic cone.
The cone angle parameter cone_theta was incorrectly referenced.
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r11433 | bugman | 2010-08-06 15:29:00 +0200 (Fri, 06 Aug 2010) | 3 lines
The isotropic cone parameter cone_theta is now being unpacked and stored
after optimisation.
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r11434 | bugman | 2010-08-07 21:31:05 +0200 (Sat, 07 Aug 2010) | 3 lines
Created maths_fns.order_parameters.iso_cone_theta_to_S() function for angle
to order param conversion.
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r11435 | bugman | 2010-08-08 17:14:48 +0200 (Sun, 08 Aug 2010) | 5 lines
Fixed a bug in populate_2nd_eigenframe_iso_cone().
One of the many trig functions were incorrectly typed out.
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r11436 | bugman | 2010-08-08 17:21:18 +0200 (Sun, 08 Aug 2010) | 5 lines
Fixed another 2 trig typo bugs in populate_2nd_eigenframe_iso_cone().
These are the same issue, sin(2.0*tmax)**2 should have been sin(tmax)**2.
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r11437 | bugman | 2010-08-09 10:00:36 +0200 (Mon, 09 Aug 2010) | 3 lines
Added the maths_fns.coord_transform module to the package __all__ list.
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r11438 | bugman | 2010-08-09 10:28:53 +0200 (Mon, 09 Aug 2010) | 3 lines
Wrote 4 unit tests for the compile_2nd_matrix_iso_cone*() frame order
functions.
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r11439 | bugman | 2010-08-09 10:39:16 +0200 (Mon, 09 Aug 2010) | 3 lines
Implemented the sinc() function.
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r11440 | bugman | 2010-08-09 11:52:09 +0200 (Mon, 09 Aug 2010) | 6 lines
Added a second unit test for perfect order in compile_2nd_matrix_iso_cone().
This checks values at and close to zero, as the sinc() function is
differently defined at this
position.
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r11441 | bugman | 2010-08-09 11:56:38 +0200 (Mon, 09 Aug 2010) | 5 lines
Converted the isotropic cone frame order model to use the sinc() function.
This removes much round off error and significantly simplifies the
equations.
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r11442 | bugman | 2010-08-09 12:21:07 +0200 (Mon, 09 Aug 2010) | 3 lines
Added 4 more unit tests for the compile_2nd_matrix_*() functions, and
modified one of the others.
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r11443 | bugman | 2010-08-09 13:59:55 +0200 (Mon, 09 Aug 2010) | 3 lines
Shifted to using numpy.sinc() for the frame order equations.
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r11444 | bugman | 2010-08-09 14:02:15 +0200 (Mon, 09 Aug 2010) | 14 lines
Reverted r11439 as the sinc function is implemented in numpy.
The command used was:
svn merge -r11439:11438 .
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r11439 | bugman | 2010-08-09 10:39:16 +0200 (Mon, 09 Aug 2010) | 3 lines
Changed paths:
M /1.3/maths_fns/pseudo_ellipse.py
Implemented the sinc() function.
.....
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r11445 | bugman | 2010-08-09 14:09:47 +0200 (Mon, 09 Aug 2010) | 5 lines
Properly implemented order_parameters.iso_cone_S_to_theta().
The previous order_parameters.iso_cone_S_to_cos_theta() function did
nothing.
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r11446 | bugman | 2010-08-09 14:10:16 +0200 (Mon, 09 Aug 2010) | 3 lines
populate_2nd_eigenframe_iso_cone_free_rotor() now uses the
iso_cone_S_to_theta() function.
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r11447 | bugman | 2010-08-09 14:17:43 +0200 (Mon, 09 Aug 2010) | 3 lines
Clean up of the frame order unit tests.
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r11448 | bugman | 2010-08-09 14:28:45 +0200 (Mon, 09 Aug 2010) | 3 lines
Added 4 frame order unit tests checking the half cone frame order matrix.
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r11449 | bugman | 2010-08-09 14:29:14 +0200 (Mon, 09 Aug 2010) | 3 lines
Reactivated test_compile_2nd_matrix_pseudo_ellipse().
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r11450 | bugman | 2010-08-09 14:29:45 +0200 (Mon, 09 Aug 2010) | 3 lines
Removed an unused data structure.
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r11451 | bugman | 2010-08-09 14:35:14 +0200 (Mon, 09 Aug 2010) | 3 lines
Added a eigenframe rotation to
test_compile_2nd_matrix_pseudo_ellipse_free_rotor_half_cone().
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r11452 | bugman | 2010-08-09 14:43:51 +0200 (Mon, 09 Aug 2010) | 3 lines
Added 4 frame order unit tests for half cones rotated 90 deg about y.
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r11453 | bugman | 2010-08-09 14:59:43 +0200 (Mon, 09 Aug 2010) | 3 lines
Deactivated 2 frame order unit tests as these cannot be satisfied with
numerical integration.
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r11454 | bugman | 2010-08-09 15:58:25 +0200 (Mon, 09 Aug 2010) | 3 lines
Added 2 more unit tests of compile_2nd_matrix_pseudo_ellipse().
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r11455 | bugman | 2010-08-10 10:28:52 +0200 (Tue, 10 Aug 2010) | 3 lines
Added 2 unit tests for the free rotor pseudo-ellipse frame order model.
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r11456 | bugman | 2010-08-10 10:33:21 +0200 (Tue, 10 Aug 2010) | 3 lines
Created a unit test for the collapse of the isotropic cone to the free
rotor iso cone.
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r11457 | bugman | 2010-08-10 10:37:00 +0200 (Tue, 10 Aug 2010) | 5 lines
Bug fix for the iso cone frame order model fn
populate_2nd_eigenframe_iso_cone().
A few signs were wrong in the {0,4} and {4,0} element.
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r11458 | bugman | 2010-08-10 11:15:47 +0200 (Tue, 10 Aug 2010) | 3 lines
Added 9 unit tests for the parametric restriction collapse of all frame
order model compile_2nd_matrix*() fns.
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r11459 | bugman | 2010-08-10 11:57:02 +0200 (Tue, 10 Aug 2010) | 5 lines
Simplified populate_2nd_eigenframe_iso_cone() even further.
This should bring some numerical stability.
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r11460 | bugman | 2010-08-10 13:59:48 +0200 (Tue, 10 Aug 2010) | 3 lines
Fix for the test_compile_2nd_matrix_pseudo_ellipse_restriction_test3()
frame order unit test.
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r11461 | bugman | 2010-08-11 00:27:59 +0200 (Wed, 11 Aug 2010) | 5 lines
Large simplifications to the equations of the pseudo-ellipse frame order
model.
This significantly increases the numerical stability and allows parameters
to be close to zero.
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r11462 | bugman | 2010-08-11 00:48:26 +0200 (Wed, 11 Aug 2010) | 3 lines
The tmax_pseudo_ellipse() fn now handles the zero points correctly.
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r11463 | bugman | 2010-08-11 00:59:36 +0200 (Wed, 11 Aug 2010) | 3 lines
Reactivated the test_compile_2nd_matrix_pseudo_ellipse_order() frame order
unit test.
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r11464 | bugman | 2010-08-11 01:07:12 +0200 (Wed, 11 Aug 2010) | 3 lines
Modified the pseudo-ellipse frame order matrix point unit tests.
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r11465 | bugman | 2010-08-11 11:36:40 +0200 (Wed, 11 Aug 2010) | 3 lines
daeg_to_rotational_superoperator() now operates on the Kronecker product
form.
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r11466 | bugman | 2010-08-11 12:01:10 +0200 (Wed, 11 Aug 2010) | 3 lines
Added 3 unit tests for reduce_alignment_tensor().
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r11467 | bugman | 2010-08-11 12:31:29 +0200 (Wed, 11 Aug 2010) | 3 lines
Another numerical simplification to tmax_pseudo_ellipse().
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r11468 | bugman | 2010-08-11 14:31:11 +0200 (Wed, 11 Aug 2010) | 5 lines
Big bug fix for the reduce_alignment_tensor() function - the frame order
matrix was transposed!!!
The indices were back to front, so the non-symmetric frame order models
were failing.
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r11469 | bugman | 2010-08-11 16:30:13 +0200 (Wed, 11 Aug 2010) | 11 lines
Added system tests for 5 of the frame order models.
These use synthetic alignment data (tensors) to test the model via the
calc() user function. The
tests models include:
iso cone, free rotor
iso cone, free rotor (in the eigenframe)
iso cone
pseudo-ellipse, free rotor (out of frame and in the eigenframe)
pseudo-ellipse.
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r11470 | bugman | 2010-08-11 16:32:04 +0200 (Wed, 11 Aug 2010) | 3 lines
Fix for the test_pseudo_ellipse() system test.
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r11471 | bugman | 2010-08-11 17:54:04 +0200 (Wed, 11 Aug 2010) | 3 lines
Added 5 system tests checking the parametric restriction of frame order
models.
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r11472 | bugman | 2010-08-11 18:37:11 +0200 (Wed, 11 Aug 2010) | 5 lines
Fixes for the calls to compile_2nd_matrix_iso_cone_torsionless() in the
unit tests.
More debugging printouts have been included throughout.
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r11473 | bugman | 2010-08-11 18:37:35 +0200 (Wed, 11 Aug 2010) | 3 lines
Implemented the torsionless isotropic cone frame order model.
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r11474 | bugman | 2010-08-11 23:03:37 +0200 (Wed, 11 Aug 2010) | 5 lines
Implemented the rotor frame order matrix model.
This includes the addition of the target function and a unit test.
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r11475 | bugman | 2010-08-11 23:05:10 +0200 (Wed, 11 Aug 2010) | 5 lines
Fixes for a number of the frame order model unit tests.
The frame order matrix comparison was not correct.
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r11476 | bugman | 2010-08-11 23:06:23 +0200 (Wed, 11 Aug 2010) | 3 lines
Fix for a typo in the previous r11475 revision.
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r11477 | bugman | 2010-08-11 23:14:14 +0200 (Wed, 11 Aug 2010) | 5 lines
Made the test_compile_2nd_matrix_pseudo_ellipse_free_rotor_point2() unit
test less stringent.
The matrix is not very precise.
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r11478 | bugman | 2010-08-11 23:17:42 +0200 (Wed, 11 Aug 2010) | 5 lines
Fixes for the test_compile_2nd_matrix_pseudo_ellipse_order() unit test.
The pec() function is not precise when the theta_x or theta_y cone angles
are close to zero.
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r11479 | bugman | 2010-08-11 23:31:39 +0200 (Wed, 11 Aug 2010) | 3 lines
Added a system test for the torsionless pseudo-ellipse frame order model.
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r11480 | bugman | 2010-08-11 23:56:45 +0200 (Wed, 11 Aug 2010) | 3 lines
Created the free rotor frame order model.
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r11481 | bugman | 2010-08-12 00:01:48 +0200 (Thu, 12 Aug 2010) | 3 lines
Added a higher precision simulated matrix to
test_compile_2nd_matrix_rotor().
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r11482 | bugman | 2010-08-12 08:57:04 +0200 (Thu, 12 Aug 2010) | 3 lines
Increased the precision of the test_model_iso_cone_free_rotor() frame order
system test.
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r11483 | bugman | 2010-08-12 09:19:37 +0200 (Thu, 12 Aug 2010) | 3 lines
Fixes for all frame order system tests of the parametric restriction to the
free rotor iso cone.
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r11484 | bugman | 2010-08-12 10:01:43 +0200 (Thu, 12 Aug 2010) | 3 lines
Renamed one frame order unit test and updated comments to better explain
the embedded data.
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r11485 | bugman | 2010-08-12 10:46:20 +0200 (Thu, 12 Aug 2010) | 3 lines
The test_model_iso_cone_free_rotor_eigenframe() frame order system test is
now functional.
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r11486 | bugman | 2010-08-12 11:10:33 +0200 (Thu, 12 Aug 2010) | 3 lines
Added 2 unit tests for the compile_2nd_matrix_free_rotor() frame order
function.
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r11487 | bugman | 2010-08-12 11:32:54 +0200 (Thu, 12 Aug 2010) | 3 lines
Better support for the free rotor frame order model.
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r11488 | bugman | 2010-08-12 11:57:04 +0200 (Thu, 12 Aug 2010) | 3 lines
[... 351 lines stripped ...]
r11540 - in /branches/bieri_gui: ./ auto_analyses/ data/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ specific_fns...