relax SVN archive

Reapplied the temporarily reverted r11578.

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r11582 | bugman | 2010-09-16 14:54:42 +0200 (Thu, 16 Sep 2010) | 23 lines
Changed paths:
M /branches/bieri_gui/relax

Temporarily reverted r11578.

The command used was:
svn merge -r11578:r11577 .

.....
r11578 | bugman | 2010-09-16 10:22:32 +0200 (Thu, 16 Sep 2010) | 12 lines
Changed paths:
M /branches/bieri_gui/relax

The Bieri GUI is now the default and only GUI for relax.

The options -b and --bieri have been removed. The -g and --gui options require no following 'bieri'
argument to launch the GUI. The GUI can now be started by typing:

$ relax -g

or:

$ relax --gui
.....
.....

Merged revisions 11688 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r11688 | bugman | 2010-11-19 14:46:34 +0100 (Fri, 19 Nov 2010) | 3 lines

Improved the diffusion tensor print out.
........

Improved the diffusion tensor print out.

Merged revisions 11661,11663-11685 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r11661 | bugman | 2010-10-25 10:10:42 +0200 (Mon, 25 Oct 2010) | 3 lines

Added 6 system tests for the spheroidal diffusion tensor.
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r11663 | bugman | 2010-11-16 18:07:43 +0100 (Tue, 16 Nov 2010) | 5 lines

Fix for the relatively unused calc_tensor_diag() for oblate tensors.

The eigenvalues were incorrectly ordered for oblate spheroids.
........
r11664 | bugman | 2010-11-17 15:04:52 +0100 (Wed, 17 Nov 2010) | 5 lines

Fix for a failing diffusion tensor unit test.

This was testing an unused element of the diffusion tensor data structure incorrectly.
........
r11665 | bugman | 2010-11-17 16:03:54 +0100 (Wed, 17 Nov 2010) | 5 lines

The rotation matrix for the spheroidal diffusion tensors is now correctly generated.

Again this is a fix for currently unused code (it will be used for BMRB support though).
........
r11666 | bugman | 2010-11-17 16:15:35 +0100 (Wed, 17 Nov 2010) | 5 lines

Fixes for the diffusion tensor system tests.

The spheroidal tensors are now correctly checked.
........
r11667 | bugman | 2010-11-17 16:15:57 +0100 (Wed, 17 Nov 2010) | 3 lines

Removed some debugging code.
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r11668 | bugman | 2010-11-17 16:45:32 +0100 (Wed, 17 Nov 2010) | 3 lines

Some rotation matrix check fixes for the diffusion tensor unit tests.
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r11669 | bugman | 2010-11-17 16:48:20 +0100 (Wed, 17 Nov 2010) | 3 lines

Dpar_unit is no longer passed into calc_rotation() for spheroidal diffusion, as it is not needed.
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r11670 | bugman | 2010-11-17 17:01:24 +0100 (Wed, 17 Nov 2010) | 5 lines

Fix for the updating of the rotation and tensor MC sim objects for the spheroidal diffusion.

This problem was only recently introduced.
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r11671 | bugman | 2010-11-17 17:05:46 +0100 (Wed, 17 Nov 2010) | 3 lines

Similar fix as in r11670, but for setting MC sim data.
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r11672 | bugman | 2010-11-17 17:18:29 +0100 (Wed, 17 Nov 2010) | 3 lines

Some more fixes for handling the diffusion tensor data structure 'spheroid_type' variable properly.
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r11673 | bugman | 2010-11-17 19:14:57 +0100 (Wed, 17 Nov 2010) | 5 lines

Fix for the creation of the oblate spheroid geometric object PDB file.

The x and z axes need to be swapped now for the oblate tensor.
........
r11674 | bugman | 2010-11-17 19:23:43 +0100 (Wed, 17 Nov 2010) | 6 lines

For some reason, the diffusion tensor PDB file for the oblate tensor now has a slight rotation.

This rotation is about the unique axis of the tensor, so this gives a different PDB file, but the
representation is the same.
........
r11675 | bugman | 2010-11-18 13:42:02 +0100 (Thu, 18 Nov 2010) | 3 lines

Some small cosmetic changes to the spheroid diffusion tensor system tests.
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r11676 | bugman | 2010-11-18 13:51:23 +0100 (Thu, 18 Nov 2010) | 3 lines

The hardcoded variables in get_spheroid() are now keyword args.
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r11677 | bugman | 2010-11-18 14:03:01 +0100 (Thu, 18 Nov 2010) | 3 lines

Added 6 system tests for the initialisation of the prolate spheroid diffusion tensor.
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r11678 | bugman | 2010-11-18 16:52:49 +0100 (Thu, 18 Nov 2010) | 6 lines

Fix for the spheroid diffusion tensors for a recently introduced bug.

The oblate and prolate check was failing as the 'spheroid_type' variable was set to None after a
call to diffusion_tensor.init(). 'spheroid_type' is now automatically updated if Da is changed.
........
r11679 | bugman | 2010-11-18 17:08:23 +0100 (Thu, 18 Nov 2010) | 5 lines

The tensor is first twisted before rotating to PDB frame in the spheroid diffusion tensor system tests.

The twisting rotation was not being correctly performed.
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r11680 | bugman | 2010-11-18 17:25:40 +0100 (Thu, 18 Nov 2010) | 5 lines

Renamed test_init_spheroid_as_ellipsoid() to test_init_prolate_spheroid_as_ellipsoid().

The print outs of the system test have been slightly improved.
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r11681 | bugman | 2010-11-18 17:38:09 +0100 (Thu, 18 Nov 2010) | 3 lines

Alphabetical ordering of methods, and shifting of the spheroid to ellipsoid checks into a separate method.
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r11682 | bugman | 2010-11-18 18:20:02 +0100 (Thu, 18 Nov 2010) | 3 lines

Added a new system test test_init_oblate_spheroid_as_ellipsoid().
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r11683 | bugman | 2010-11-18 18:25:51 +0100 (Thu, 18 Nov 2010) | 5 lines

Fix for the ellipsoid eigenvalue and rotation matrix reordering for when 2 eigenvalues are the same.

This only affects the (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) parameter input into diffusion_tensor.init().
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r11684 | bugman | 2010-11-18 18:29:29 +0100 (Thu, 18 Nov 2010) | 5 lines

Fix for the eigenvalue and rotation matrix sorting for (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).

The eigenvalues were being converted to ints!
........
r11685 | bugman | 2010-11-18 18:53:39 +0100 (Thu, 18 Nov 2010) | 6 lines

Final bug fix for the input of (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) ellipsoidal diffusion parameters.

The numpy eigenvalue decomposition has been replaced by SVD as the eigenvalue decomposition could
generate a proper rotation matrix when 2 eigenvalues are the same. The test suite now passes fully.
........

Merged revisions 11663-11685 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r11663 | bugman | 2010-11-16 18:07:43 +0100 (Tue, 16 Nov 2010) | 5 lines

Fix for the relatively unused calc_tensor_diag() for oblate tensors.

The eigenvalues were incorrectly ordered for oblate spheroids.
........
r11664 | bugman | 2010-11-17 15:04:52 +0100 (Wed, 17 Nov 2010) | 5 lines

Fix for a failing diffusion tensor unit test.

This was testing an unused element of the diffusion tensor data structure incorrectly.
........
r11665 | bugman | 2010-11-17 16:03:54 +0100 (Wed, 17 Nov 2010) | 5 lines

The rotation matrix for the spheroidal diffusion tensors is now correctly generated.

Again this is a fix for currently unused code (it will be used for BMRB support though).
........
r11666 | bugman | 2010-11-17 16:15:35 +0100 (Wed, 17 Nov 2010) | 5 lines

Fixes for the diffusion tensor system tests.

The spheroidal tensors are now correctly checked.
........
r11667 | bugman | 2010-11-17 16:15:57 +0100 (Wed, 17 Nov 2010) | 3 lines

Removed some debugging code.
........
r11668 | bugman | 2010-11-17 16:45:32 +0100 (Wed, 17 Nov 2010) | 3 lines

Some rotation matrix check fixes for the diffusion tensor unit tests.
........
r11669 | bugman | 2010-11-17 16:48:20 +0100 (Wed, 17 Nov 2010) | 3 lines

Dpar_unit is no longer passed into calc_rotation() for spheroidal diffusion, as it is not needed.
........
r11670 | bugman | 2010-11-17 17:01:24 +0100 (Wed, 17 Nov 2010) | 5 lines

Fix for the updating of the rotation and tensor MC sim objects for the spheroidal diffusion.

This problem was only recently introduced.
........
r11671 | bugman | 2010-11-17 17:05:46 +0100 (Wed, 17 Nov 2010) | 3 lines

Similar fix as in r11670, but for setting MC sim data.
........
r11672 | bugman | 2010-11-17 17:18:29 +0100 (Wed, 17 Nov 2010) | 3 lines

Some more fixes for handling the diffusion tensor data structure 'spheroid_type' variable properly.
........
r11673 | bugman | 2010-11-17 19:14:57 +0100 (Wed, 17 Nov 2010) | 5 lines

Fix for the creation of the oblate spheroid geometric object PDB file.

The x and z axes need to be swapped now for the oblate tensor.
........
r11674 | bugman | 2010-11-17 19:23:43 +0100 (Wed, 17 Nov 2010) | 6 lines

For some reason, the diffusion tensor PDB file for the oblate tensor now has a slight rotation.

This rotation is about the unique axis of the tensor, so this gives a different PDB file, but the
representation is the same.
........
r11675 | bugman | 2010-11-18 13:42:02 +0100 (Thu, 18 Nov 2010) | 3 lines

Some small cosmetic changes to the spheroid diffusion tensor system tests.
........
r11676 | bugman | 2010-11-18 13:51:23 +0100 (Thu, 18 Nov 2010) | 3 lines

The hardcoded variables in get_spheroid() are now keyword args.
........
r11677 | bugman | 2010-11-18 14:03:01 +0100 (Thu, 18 Nov 2010) | 3 lines

Added 6 system tests for the initialisation of the prolate spheroid diffusion tensor.
........
r11678 | bugman | 2010-11-18 16:52:49 +0100 (Thu, 18 Nov 2010) | 6 lines

Fix for the spheroid diffusion tensors for a recently introduced bug.

The oblate and prolate check was failing as the 'spheroid_type' variable was set to None after a
call to diffusion_tensor.init(). 'spheroid_type' is now automatically updated if Da is changed.
........
r11679 | bugman | 2010-11-18 17:08:23 +0100 (Thu, 18 Nov 2010) | 5 lines

The tensor is first twisted before rotating to PDB frame in the spheroid diffusion tensor system tests.

The twisting rotation was not being correctly performed.
........
r11680 | bugman | 2010-11-18 17:25:40 +0100 (Thu, 18 Nov 2010) | 5 lines

Renamed test_init_spheroid_as_ellipsoid() to test_init_prolate_spheroid_as_ellipsoid().

The print outs of the system test have been slightly improved.
........
r11681 | bugman | 2010-11-18 17:38:09 +0100 (Thu, 18 Nov 2010) | 3 lines

Alphabetical ordering of methods, and shifting of the spheroid to ellipsoid checks into a separate method.
........
r11682 | bugman | 2010-11-18 18:20:02 +0100 (Thu, 18 Nov 2010) | 3 lines

Added a new system test test_init_oblate_spheroid_as_ellipsoid().
........
r11683 | bugman | 2010-11-18 18:25:51 +0100 (Thu, 18 Nov 2010) | 5 lines

Fix for the ellipsoid eigenvalue and rotation matrix reordering for when 2 eigenvalues are the same.

This only affects the (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) parameter input into diffusion_tensor.init().
........
r11684 | bugman | 2010-11-18 18:29:29 +0100 (Thu, 18 Nov 2010) | 5 lines

Fix for the eigenvalue and rotation matrix sorting for (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).

The eigenvalues were being converted to ints!
........
r11685 | bugman | 2010-11-18 18:53:39 +0100 (Thu, 18 Nov 2010) | 6 lines

Final bug fix for the input of (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) ellipsoidal diffusion parameters.

The numpy eigenvalue decomposition has been replaced by SVD as the eigenvalue decomposition could
generate a proper rotation matrix when 2 eigenvalues are the same. The test suite now passes fully.
........

Final bug fix for the input of (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) ellipsoidal diffusion parameters.

The numpy eigenvalue decomposition has been replaced by SVD as the eigenvalue decomposition could
generate a proper rotation matrix when 2 eigenvalues are the same. The test suite now passes fully.

Fix for the eigenvalue and rotation matrix sorting for (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).

The eigenvalues were being converted to ints!

Fix for the ellipsoid eigenvalue and rotation matrix reordering for when 2 eigenvalues are the same.

This only affects the (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) parameter input into diffusion_tensor.init().

Added a new system test test_init_oblate_spheroid_as_ellipsoid().

Alphabetical ordering of methods, and shifting of the spheroid to ellipsoid checks into a separate method.