relax SVN archive

Eliminated the analysis specific API _set_param_values() base method.

This is now in two parts, the _set_param_values_global() and _set_param_values_spin() methods. The
frame order analysis in the trunk had switched to _set_param_values_global(), and now this branch
does the same thing. Not sure why this change did not come across.

Fix for the frame_order.ref_domain call in the base script for the frame order CaM system tests.

Reimplementation of r15046 but within the auto-generated user function design.

The 'fix' flag of the frame_order.pivot user function was lost as the changes went into
prompt/frame_order.py.

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r15046 | bugman | 2011-12-07 18:04:11 +0100 (Wed, 07 Dec 2011) | 5 lines
Changed paths:
M /branches/frame_order_testing/prompt/frame_order.py
M /branches/frame_order_testing/specific_fns/frame_order.py

The frame_order.pivot user function now accepts the fix argument to allow the pivot to be fixed.

This is for optimisation.
.....

Reimplementation of r15044 but within the auto-generated user function design.

The merger of the redesigns from the trunk causes the user function front-end changes of r15044 in
prompt/align_tensor.py to be lost, as this file no longer exists. The align_tensor.init user
function arguments align_id and domain have been reintroduced.

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r15044 | bugman | 2011-12-07 16:32:01 +0100 (Wed, 07 Dec 2011) | 8 lines
Changed paths:
M /branches/frame_order_testing/generic_fns/align_tensor.py
M /branches/frame_order_testing/prompt/align_tensor.py

Converted the align_tensor.init user function to accept the align_id and domain arguments.

The domain argument complements the align_tensor.set_domain user function whereas the align_id arg
is new and is used to associate a tensor with an alignment. This is part of a redesign of how
alignment tensors are handled, as there can be multiple tensors per alignment if the molecule is
multi-domain.
.....

Converted the frame order system test base optimisation script to the interatomic data design.

Converted the domain user function to the new relax 2.x auto-generation design.

Converted the test suite CaM RDC data for the rotor frame order model to the interatomic design.

Merged revisions 17254-17255 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17254 | bugman | 2012-07-16 12:02:30 +0200 (Mon, 16 Jul 2012) | 6 lines

Bug fix for the RDC Q factor calculations for when the dipolar constants are not all the same.

Now instead of a RelaxError, a warning is given and the Q factor normalised by 2Da^2(4 + 3R)/5 is
skipped. This allows long range and mixed nuclear pairs to be supported.
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r17255 | bugman | 2012-07-16 15:26:11 +0200 (Mon, 16 Jul 2012) | 5 lines

Added the 'unit' argument to the dipole_pair.read_dist and dipole_pair.set_dist user functions.

This is to allow distances in Angstroms to be read into relax and converted to meters.
........

Converted the Frame order specific _minimise_setup_rdcs() to the interatomic data design.

The _check_rdcs() method was added by directly copying the N-state model method.

Added the 'unit' argument to the dipole_pair.read_dist and dipole_pair.set_dist user functions.

This is to allow distances in Angstroms to be read into relax and converted to meters.