relax SVN archive

svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23985 | bugman | 2014-06-16 18:47:49 +0200 (Mon, 16 Jun 2014) | 5 lines

Updates for the Frame_order.test_rigid_data_to_pseudo_ellipse*_model system tests.

The chi-squared value now matches the rigid model.
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r24015 | bugman | 2014-06-17 09:52:10 +0200 (Tue, 17 Jun 2014) | 13 lines

Large increase in precision for the CaM frame order torsionless pseudo-ellipse model test data set.

In addition, the theta_x and theta_y angles have also been swapped so that the new constraint of
0 <= theta_x <= theta_y <= pi built into the analysis is satisfied.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used. The algorithm for finding
suitable random domain positions within the motional limits has been changed as well by extracting
the theta and phi tilt angles from the random rotation, dropping the torsion angle sigma, and
reconstructing the rotation from just the tilt angles. This increases the speed of the data
generation script by minimally 5 orders of magnitude.
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r24016 | bugman | 2014-06-17 09:54:01 +0200 (Tue, 17 Jun 2014) | 6 lines

Changed the parameter values for the Frame_order.test_cam_pseudo_ellipse_torsionless* system tests.

The theta_x and theta_y angles are now swapped. The chi-squared values are now also lower in the
3 system tests as the data is now of much higher precision.
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r24017 | bugman | 2014-06-17 11:30:47 +0200 (Tue, 17 Jun 2014) | 7 lines

Speed up for the frame order analyses when only one domain is aligned.

When only one domain is aligned, the reverse Ln3+ to spin vectors for the PCS are no longer
calculated. For most analyses, this should significantly reduce the number of mathematical
operations required for the quasi-random Sobol' point numerical integration.
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r24090 | bugman | 2014-06-18 15:38:33 +0200 (Wed, 18 Jun 2014) | 12 lines

Support for the 3 vector system for double motions has been added to the frame order analysis.

This is used for the quasi-random Sobol' numeric integration of the PCS. The lanthanide to atom
vector is the sum of three parts: the 1st pivot to atom vector rotated by the 1st mode of motion;
the 2nd pivot to 1st pivot vector rotated by the 2nd mode of motion (together with the rotated 1st
pivot to atom vectors); and the lanthanide to second pivot vector.

All these vectors are passed into the lib.frame_order.double_rotor.pcs_numeric_int_double_rotor()
function, which passes them to the pcs_pivot_motion_double_rotor() function where they are rotated
and reconstructed into the Ln3+ to atom vectors.
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r24279 | bugman | 2014-06-24 14:52:58 +0200 (Tue, 24 Jun 2014) | 18 lines

Fully implemented the double rotor frame order model for PCS data.

Sobol' quasi-random points for the numerical integration are now generated separately for both
torsion angles, and two separate sets of rotation matrices for both angles for each Sobol' point are
now pre-calculated in the create_sobol_data() target function method. The calc_vectors() target
function method has also been modified as the lanthanide to pivot vector is to the second pivot in
the double rotor model rather than the first. The target function itself has been fixed as the two
pivots were mixed up - the 2nd pivot is optimised and the inter-pivot distance along the z-axis
gives the position of the 1st pivot.

For the lib.frame_order.double_rotor module, the second set of Sobol' point rotation matrices
corresponding to sigma2, the rotation about the second pivot, is now passed into the
pcs_numeric_int_double_rotor() function. These rotations are frame shifted into the eigenframe of
the motion, and then correctly passed into pcs_pivot_motion_double_rotor(). The elimination of
Sobol' points outside of the distribution has been fixed in the base pcs_numeric_int_double_rotor()
function and now both torsion angles are being checked.
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r24284 | bugman | 2014-06-24 16:10:00 +0200 (Tue, 24 Jun 2014) | 5 lines

Fix for the unpacking of the double rotor frame order parameters in the target function.

This is for when the pivot point is being optimised.
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r24309 | bugman | 2014-06-25 09:35:40 +0200 (Wed, 25 Jun 2014) | 8 lines

Created a new synthetic CaM data set for the double rotor frame order model.

This is the same as the test_suite/shared_data/frame_order/cam/double_rotor data except that the
angles have been increased from 11.5 and 10.5 degrees to 85.0 and 55.0 for the two torsion angles.
This is to help in debugging the double rotor model as the original test data is too close to the
rigid state to notice certain issues.
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r24310 | bugman | 2014-06-25 09:37:14 +0200 (Wed, 25 Jun 2014) | 6 lines

Corrected the printout from the CaM frame order data generation base script.

The number of states used in the distribution of domain positions is now correctly reported for the
models with multiple modes of motion.
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r24311 | bugman | 2014-06-25 09:47:33 +0200 (Wed, 25 Jun 2014) | 5 lines

Created a frame order optimisation script for the CaM double rotor test suite data.

This is the script used for testing the implementation, it will not be used in the test suite.
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r24312 | bugman | 2014-06-25 10:27:03 +0200 (Wed, 25 Jun 2014) | 6 lines

The pivot to atom vectors, and the reverse vectors, are no longer set up in the __init__() method.

This is for the frame order target functions. The structures are generated in the calc_vectors()
method via a dot product, and hence do not need to be initialised.
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r24313 | bugman | 2014-06-25 10:32:07 +0200 (Wed, 25 Jun 2014) | 17 lines

Reverted r24312 as the reverse vector data structure must exist in all cases.

The command used was:
svn merge -r24312:r24311 .

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r24312 | bugman | 2014-06-25 10:27:03 +0200 (Wed, 25 Jun 2014) | 6 lines
Changed paths:
M /branches/frame_order_cleanup/target_functions/frame_order.py

The pivot to atom vectors, and the reverse vectors, are no longer set up in the __init__() method.

This is for the frame order target functions. The structures are generated in the calc_vectors()
method via a dot product, and hence do not need to be initialised.
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r24314 | bugman | 2014-06-25 10:56:37 +0200 (Wed, 25 Jun 2014) | 5 lines

Created the Frame_order.test_rigid_data_to_double_rotor_model system test.

This shows that the double rotor model works perfectly when the domains of the molecule are rigid.
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r24316 | bugman | 2014-06-25 16:41:20 +0200 (Wed, 25 Jun 2014) | 7 lines

Fix for the frame order target functions for when no PCS data is present.

In this case, the self.pivot structure was being created as an empty array rather than a rank-2
array with dimensions 1 and 3. This was causing the rotor models to fail, as this pivot is used to
recreate the rotation axis.
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r24317 | bugman | 2014-06-25 16:48:54 +0200 (Wed, 25 Jun 2014) | 6 lines

Fix for the CaM double rotor frame order system tests.

The torsion angle cone_sigma_max is a half angle, therefore the full angles from the data generation
script are now halved in the system test script.
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r24318 | bugman | 2014-06-25 16:53:16 +0200 (Wed, 25 Jun 2014) | 7 lines

Created 3 frame order system tests for the new large angle double rotor CaM synthetic data.

These are the Frame_order.test_cam_double_rotor_large_angle,
Frame_order.test_cam_double_rotor_large_angle_rdc, and
Frame_order.test_cam_double_rotor_large_angle_pcs system tests.
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r24321 | bugman | 2014-06-25 17:19:02 +0200 (Wed, 25 Jun 2014) | 5 lines

Added the full optimisation results for the torsionless pseudo-ellipse frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.
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r24322 | bugman | 2014-06-25 17:21:13 +0200 (Wed, 25 Jun 2014) | 5 lines

Added the full optimisation results for the 2nd free rotor isotropic cone frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.
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