Author: bugman
Date: Fri Sep 10 15:53:20 2010
New Revision: 11545
URL: http://svn.gna.org/viewcvs/relax?rev=11545&view=rev
Log:
Merged revisions 11334-11338,11340-11341,11366-11368,11381-11385,11388-11534
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r11334 | bugman | 2010-07-22 11:09:04 +0200 (Thu, 22 Jul 2010) | 6 lines
Bug fix for the func_pseudo_ellipse() target function.
The overwriting of the permanent storage data structures was killing the
optimisation of the average
domain position. Now temporary data structures are used for the functions
which return numpy arrays.
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r11335 | bugman | 2010-07-22 11:12:22 +0200 (Thu, 22 Jul 2010) | 5 lines
The same bug fix of r11334 has now been applied to the func_rigid() and
func_iso_cone() target fns.
The temporary data structures are no longer clobbering the permanent
storage structures.
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r11336 | bugman | 2010-07-22 11:38:26 +0200 (Thu, 22 Jul 2010) | 3 lines
Modified the test_compile_2nd_matrix_pseudo_ellipse() unit test to match
the new fn syntax.
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r11337 | bugman | 2010-07-22 15:57:03 +0200 (Thu, 22 Jul 2010) | 3 lines
Silenced the scipy.integrate.quad() warnings by setting the full_output arg
to 1.
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r11338 | bugman | 2010-07-22 18:26:42 +0200 (Thu, 22 Jul 2010) | 3 lines
Limit arrays are now sent into the minfx generic interface for limiting
simulated annealing.
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r11340 | bugman | 2010-07-23 10:56:51 +0200 (Fri, 23 Jul 2010) | 3 lines
Hardcoded the factorial() function using a dictionary to return support for
Python 2.4 and 2.5.
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r11341 | bugman | 2010-07-23 11:20:58 +0200 (Fri, 23 Jul 2010) | 3 lines
Converted the dictionary to a list in factorial() for speed.
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r11366 | bugman | 2010-07-27 10:14:12 +0200 (Tue, 27 Jul 2010) | 3 lines
The select.read() and deselect.read() user functions can now accept file
handles or dummy file objects.
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r11367 | bugman | 2010-07-27 14:00:43 +0200 (Tue, 27 Jul 2010) | 3 lines
When loading save states, data pipe names are always converted to a string
to avoid unicode problems.
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r11368 | bugman | 2010-07-27 15:13:12 +0200 (Tue, 27 Jul 2010) | 6 lines
The loading of RDCs and PCSs for non-existent spins now only throws a
RelaxWarning.
Rather than throwing a RelaxError, this allows for partial loading of
alignment data for certain
regions of the molecule.
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r11381 | bugman | 2010-07-28 11:13:46 +0200 (Wed, 28 Jul 2010) | 6 lines
Removed the docstring length check from the code validator script and
changed a printout.
The docstring length is only 100 characters in the user functions. For all
other functions, no
length is enforced.
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r11382 | bugman | 2010-07-28 11:38:32 +0200 (Wed, 28 Jul 2010) | 3 lines
The attached proton PDB name is no longer hardcoded to 'H' in the
dauvergne_protocol auto analysis.
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r11383 | bugman | 2010-07-29 14:18:18 +0200 (Thu, 29 Jul 2010) | 3 lines
The back-calculated alignments tensors are now being stored in the current
data pipe.
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r11384 | bugman | 2010-07-29 16:11:51 +0200 (Thu, 29 Jul 2010) | 3 lines
The align_tensor.display() user function now prints out the generalized
degree of order (GDO) value.
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r11385 | bugman | 2010-07-29 17:58:54 +0200 (Thu, 29 Jul 2010) | 3 lines
pipe.display() now places quotation marks around the pipe names and shows
which is the current data pipe.
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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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r11545 - in /branches/multi_processor_merge: ./ auto_analyses/ data/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ ...