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[r24349] by tlinnet

Replaced all self.spins with self.NS in target function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

2014-06-27 15:12:25 Tree
[r24348] by tlinnet

Made the validation check in profiling of marix_power check all values.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

2014-06-27 15:09:45 Tree
[r24347] by tlinnet

Initial try to write up a 2x2 matrix by closed form.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

2014-06-27 15:09:42 Tree
[r24346] by bugman

Created an auxiliary function for automatically generating the pivots of the frame order analysis.

This is the new specific_analyses.frame_order.data.generate_pivot() function. It will generate the
1st or 2nd pivot, hence supporting both the single motion models and the double motion double rotor
model.

2014-06-27 14:31:45 Tree
[r24345] by bugman

The frame order geometric representation functions are no longer PDB specific.

Instead the format argument is accepted. This will allow different formats to be supported in the
future. Because of this change, all specific_analyses.frame_order.geometric.pdb_*() functions has
been renamed to create_*().

2014-06-27 14:07:16 Tree
[r24344] by bugman

Shifted the frame order geometric representation functions into their own module.

This is the new specific_analyses.frame_order.geometric module.

2014-06-27 13:57:39 Tree
[r24343] by bugman

Slight speed up of the 'B14' and 'B14 full' dispersion models by minimising repetitive maths.

Using the disp_profile_all.py script, the speed ups for these two models are:

100 single spins analysis:
B14: 3.944+/-0.032 -> 3.888+/-0.038, 1.014x faster.
B14 full: 4.037+/-0.040 -> 3.940+/-0.025, 1.025x faster.

Cluster of 100 spins analysis:
B14: 0.522+/-0.003 -> 0.507+/-0.008, 1.031x faster.
B14 full: 0.507+/-0.008 -> 0.487+/-0.007, 1.042x faster.

2014-06-27 12:52:08 Tree
[r24342] by bugman

Added Ti and NT to the dispersion target function class documentation.

2014-06-27 12:27:27 Tree
[r24341] by bugman

Expanded the dispersion target function class documentation.

The NE, NS, NM, NO, and ND notation is now explained.

2014-06-27 12:24:23 Tree
[r24340] by tlinnet

Fix for unit test passing on old numpy systems.

The error was:
ValueError: setting an array element with a sequence.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

2014-06-27 11:35:32 Tree
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