Author: bugman
Date: Thu Mar 3 14:21:42 2011
New Revision: 12779
URL: http://svn.gna.org/viewcvs/relax?rev=12779&view=rev
Log:
Merged revisions 12647,12649-12767,12769-12777 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_data
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r12647 | bugman | 2011-03-01 15:36:46 +0100 (Tue, 01 Mar 2011) | 3 lines
Redesigned the relax_data.read() user function front end for handling data
ID strings.
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r12649 | bugman | 2011-03-01 17:04:07 +0100 (Tue, 01 Mar 2011) | 6 lines
Updated the relax_data.read() back end for the new ID string based design.
The update_data_structures_pipe() and data_init() functions have been
deleted and the pack_data()
function highly modified.
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r12650 | bugman | 2011-03-01 17:05:17 +0100 (Tue, 01 Mar 2011) | 3 lines
The model-free code no longer calls the deleted relax_data.data_init()
function.
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r12651 | bugman | 2011-03-01 17:19:26 +0100 (Tue, 01 Mar 2011) | 3 lines
Simplification of the return_value() function.
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r12652 | bugman | 2011-03-01 17:24:07 +0100 (Tue, 01 Mar 2011) | 3 lines
Updates for a number of model-free system tests for the changed
relax_data.read() user function.
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r12653 | bugman | 2011-03-01 17:24:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Simplified the return_data_desc() function.
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r12654 | bugman | 2011-03-01 17:25:20 +0100 (Tue, 01 Mar 2011) | 3 lines
Removal of the test_labels() function, as this was only needed with the old
design.
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r12655 | bugman | 2011-03-01 17:25:29 +0100 (Tue, 01 Mar 2011) | 3 lines
Spacing fix.
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r12656 | bugman | 2011-03-01 17:32:03 +0100 (Tue, 01 Mar 2011) | 3 lines
Deleted the now useless add_data_to_spin() function.
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r12657 | bugman | 2011-03-01 17:56:29 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the relax_data.back_calc() function for the new design.
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r12658 | bugman | 2011-03-01 18:05:03 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.bmrb_read() function to the new ID string design.
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r12659 | bugman | 2011-03-01 18:09:40 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the back and front ends of the relax_data.copy() user function to
the new design.
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r12660 | bugman | 2011-03-01 18:13:01 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted RelaxNoRiError and RelaxRiError to the new ID string design.
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r12661 | bugman | 2011-03-01 18:16:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.delete() user function back and front end to the
new design.
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r12662 | bugman | 2011-03-01 18:19:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.display() user function back and front end to the
new design.
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r12663 | bugman | 2011-03-01 18:20:25 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed the useless find_ri_index() function.
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r12664 | bugman | 2011-03-01 18:23:02 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.peak_intensity_type() user function back and front
end to the new design.
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r12665 | bugman | 2011-03-01 18:25:19 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.temp_calibration() user function back and front
end to the new design.
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r12666 | bugman | 2011-03-01 18:27:24 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.temp_calibration() user function back and front
end to the new design.
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r12667 | bugman | 2011-03-01 18:28:18 +0100 (Tue, 01 Mar 2011) | 3 lines
Fix for the last commit, which should have said relax_data.temp_control().
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r12668 | bugman | 2011-03-01 18:30:27 +0100 (Tue, 01 Mar 2011) | 3 lines
Deletion of the useless update_noe_r1_table() function.
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r12669 | bugman | 2011-03-01 18:33:40 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.write() user function back and front end to the
new design.
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r12670 | bugman | 2011-03-01 18:34:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed a non-existent import.
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r12671 | bugman | 2011-03-01 18:39:44 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the get_data_names() function for the new ID string design.
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r12672 | bugman | 2011-03-01 18:44:44 +0100 (Tue, 01 Mar 2011) | 3 lines
Fix for the relax_data.delete() user function.
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r12673 | bugman | 2011-03-01 18:48:41 +0100 (Tue, 01 Mar 2011) | 3 lines
Spacing fix.
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r12674 | bugman | 2011-03-01 18:51:54 +0100 (Tue, 01 Mar 2011) | 3 lines
Fixes for the pack_data() function.
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r12675 | bugman | 2011-03-01 19:19:47 +0100 (Tue, 01 Mar 2011) | 6 lines
Updated the _minimise_data_setup() method for the new relaxation data ID
string design.
The _relax_data_opt_structs() helper method has been created to convert the
new data structures into
the old ones used in the optimisation code of maths_fns.mf.
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r12676 | bugman | 2011-03-01 19:22:25 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free overfit_deselect() method for the new relaxation
data structures.
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r12677 | bugman | 2011-03-01 19:28:43 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free sim_pack_data() method for the new relaxation data
structures.
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r12678 | bugman | 2011-03-01 19:30:28 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free create_mc_data() method for the new relaxation data
structures.
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r12679 | bugman | 2011-03-01 19:59:45 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed unused code from data_init().
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r12680 | bugman | 2011-03-01 20:12:48 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free model_statistics() method for the new relaxation
data structures.
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r12681 | bugman | 2011-03-01 20:31:50 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free calculate() method for the new relaxation data
structures.
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r12682 | bugman | 2011-03-01 20:33:42 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free minimise() method for the new relaxation data
structures.
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r12683 | bugman | 2011-03-01 21:04:02 +0100 (Tue, 01 Mar 2011) | 3 lines
Typo fix for _relax_data_opt_structs().
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r12684 | bugman | 2011-03-02 09:57:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed an incorrect arg to the relax_data.write() user function.
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r12685 | bugman | 2011-03-02 10:03:25 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated all of the unit tests relying on the relax_data user functions for
the new design.
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r12686 | bugman | 2011-03-02 10:08:41 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the front end to the relax_data.back_calc() user function for the
new design.
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r12687 | bugman | 2011-03-02 10:09:50 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for one of the relax_data unit tests - one of the obligatory args was
missing.
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r12688 | bugman | 2011-03-02 10:13:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the BMRB reading and writing system test script for the new relax
data ID string design.
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r12689 | bugman | 2011-03-02 10:18:43 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the Rx back calculation system test script for the new relax data
ID string design.
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r12690 | bugman | 2011-03-02 10:23:46 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated all of the model-free system test scripts for the new relax data ID
string design.
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r12691 | bugman | 2011-03-02 10:34:11 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2 system test to the new relax data ID
string design.
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r12692 | bugman | 2011-03-02 10:43:29 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2_pse4() system test to the new relax data
ID string design.
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r12693 | bugman | 2011-03-02 10:49:28 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2_tem1() system test to the new relax data
ID string design.
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r12694 | bugman | 2011-03-02 10:54:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the PDC reading system tests to the new relax data ID string design.
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r12695 | bugman | 2011-03-02 10:57:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the pdc.read() user function to the new relax data ID string design.
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r12696 | bugman | 2011-03-02 11:13:48 +0100 (Wed, 02 Mar 2011) | 3 lines
Simplified the setup_peak_intensity_type() data.exp_info method for the new
relax data ID string design.
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r12697 | bugman | 2011-03-02 11:15:48 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated temp_calibration_setup() for the new relax data ID string design.
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r12698 | bugman | 2011-03-02 11:17:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated temp_control_setup() for the new relax data ID string design.
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r12699 | bugman | 2011-03-02 11:18:19 +0100 (Wed, 02 Mar 2011) | 3 lines
Simple fixes for some of the methods.
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r12700 | bugman | 2011-03-02 11:29:47 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the relaxation data bmrb_write() method for the new relax data ID
string design.
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r12701 | bugman | 2011-03-02 11:30:26 +0100 (Wed, 02 Mar 2011) | 3 lines
Deleted the now useless get_peak_intensity_type(), get_temp_calibration(),
and get_temp_control().
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r12702 | bugman | 2011-03-02 11:35:05 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_aic_mod_sel_diff_tensor() system test for the new relax
data ID string design.
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r12703 | bugman | 2011-03-02 11:54:01 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the Modelfree4 generic_fns.palmer module for the new relax data ID
string design.
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r12704 | bugman | 2011-03-02 11:54:41 +0100 (Wed, 02 Mar 2011) | 3 lines
Syntax fix for the create_mfdata() function.
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r12705 | bugman | 2011-03-02 12:20:44 +0100 (Wed, 02 Mar 2011) | 7 lines
Added backwards compatibility for the old relaxation data structures in the
data pipe.
The methods _back_compat_hook() and _back_compat_hook_ri_data() have been
added to allow the base
data structures of the relax data pipe to be updated to the new structures.
The version
information is now being passed from the relax data store from_xml() method.
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r12706 | bugman | 2011-03-02 13:47:13 +0100 (Wed, 02 Mar 2011) | 7 lines
Added backwards compatibility for the old relaxation data structures in the
spin container.
The methods _back_compat_hook() and _back_compat_hook_ri_data() have been
added to allow the base
data structures of the spin container to be updated to the new structures.
The version information
is now being passed from the data pipe from_xml() method.
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r12707 | bugman | 2011-03-02 13:49:51 +0100 (Wed, 02 Mar 2011) | 3 lines
All objects starting with '_' are now considered special and skipped,
instead of just starting with '__'.
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r12708 | bugman | 2011-03-02 14:05:57 +0100 (Wed, 02 Mar 2011) | 3 lines
Bug fixes for the new _back_compat_hook_ri_data() methods.
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r12709 | bugman | 2011-03-02 14:10:58 +0100 (Wed, 02 Mar 2011) | 3 lines
Some changes to the consistency testing specific code for the new relax
data ID string design.
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r12710 | bugman | 2011-03-02 14:21:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the relax_data.copy() back end.
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r12711 | bugman | 2011-03-02 14:23:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the spin container _back_compat_hook_ri_data() method.
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r12712 | bugman | 2011-03-02 14:23:40 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed a debugging print statement.
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r12713 | bugman | 2011-03-02 14:31:06 +0100 (Wed, 02 Mar 2011) | 3 lines
More fixes for the relax_data.copy() user function back end.
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r12714 | bugman | 2011-03-02 14:31:30 +0100 (Wed, 02 Mar 2011) | 3 lines
Epydoc docstring fixes.
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r12715 | bugman | 2011-03-02 14:39:38 +0100 (Wed, 02 Mar 2011) | 3 lines
Converted all spin.frq[0] to cdp.frq[cdp.ri_ids[0]] as the spin object
'frq' no longer exists.
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r12716 | bugman | 2011-03-02 15:01:58 +0100 (Wed, 02 Mar 2011) | 3 lines
Update of the palmer.py Modelfree4 system test script for the new relax
data ID string design.
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r12717 | bugman | 2011-03-02 15:11:06 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the model-free back_calc_ri() method for the new relax data ID
string design.
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r12718 | bugman | 2011-03-02 15:11:50 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the back_calc_ri() method.
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r12719 | bugman | 2011-03-02 15:29:00 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the setting up of model-free optimisation.
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r12720 | bugman | 2011-03-02 15:33:19 +0100 (Wed, 02 Mar 2011) | 3 lines
The relax_data return_value() function can now handle missing data.
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r12721 | bugman | 2011-03-02 15:49:37 +0100 (Wed, 02 Mar 2011) | 3 lines
Simplifications for all of the diffusion tensor system tests.
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r12722 | bugman | 2011-03-02 15:56:10 +0100 (Wed, 02 Mar 2011) | 6 lines
Fixes for the back end of the relax_data.back_calc() user function.
The missing ri_id arg situation was not being handled and spin container
ri_data_bc structure was
being constantly overwritten.
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r12723 | bugman | 2011-03-02 16:20:05 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated many system test scripts for the new relax_data.read() user
function interface.
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r12724 | bugman | 2011-03-02 16:29:59 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for SpinContainer._back_compat_hook_ri_data(), the MC sim object is
only deleted if it exists.
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r12725 | bugman | 2011-03-02 16:34:01 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the opt_tm_fns system test module for the local_tm model-free
model tests.
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r12726 | bugman | 2011-03-02 16:38:56 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the test_read_relax_data() model-free system test.
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r12727 | bugman | 2011-03-02 16:51:53 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed the relaxation data data structure names from the model-free
data_names() method.
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r12728 | bugman | 2011-03-02 17:11:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for a typo in the model-free test_read_results_1_2 system test.
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r12729 | bugman | 2011-03-02 17:13:54 +0100 (Wed, 02 Mar 2011) | 3 lines
Another fix for the test_read_results_1_2 system test - the relaxation data
was incorrectly checked.
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r12730 | bugman | 2011-03-02 17:18:12 +0100 (Wed, 02 Mar 2011) | 3 lines
The previous fix from r12729 used the wrong index!!
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r12731 | bugman | 2011-03-02 17:19:37 +0100 (Wed, 02 Mar 2011) | 6 lines
Fix for the model-free _load_relax_data() method.
The method now generates the relaxation data structures itself rather than
calling a function which
was deleted from generic_fns.relax_data.
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r12732 | bugman | 2011-03-02 17:31:35 +0100 (Wed, 02 Mar 2011) | 3 lines
Renamed a script so it can be executed as a module.
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r12733 | bugman | 2011-03-02 17:38:00 +0100 (Wed, 02 Mar 2011) | 14 lines
Reverted revision r12727, as this is used in the XML file generation.
The command used was:
svn merge -r12727:12726 .
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r12727 | bugman | 2011-03-02 16:51:53 +0100 (Wed, 02 Mar 2011) | 3 lines
Changed paths:
M /branches/relax_data/specific_fns/model_free/main.py
Removed the relaxation data data structure names from the model-free
data_names() method.
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r12734 | bugman | 2011-03-02 17:41:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Regenerated the relax 1.3 save file of the OMP model-free results.
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r12735 | bugman | 2011-03-02 17:45:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the frq list of the test_read_results_1_2_pse4 model-free system
test.
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r12736 | bugman | 2011-03-02 17:47:20 +0100 (Wed, 02 Mar 2011) | 5 lines
Fix for the relax 1.2 model-free result file _load_relax_data() method.
The relaxation values and errors are only set if they exist.
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r12737 | bugman | 2011-03-02 17:56:40 +0100 (Wed, 02 Mar 2011) | 3 lines
Many fixes for the test_read_results_1_2_tem1 model-free system test.
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r12738 | bugman | 2011-03-02 18:02:21 +0100 (Wed, 02 Mar 2011) | 3 lines
The model-free data_init() method now skips the relaxation data data
structures.
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r12739 | bugman | 2011-03-02 18:27:39 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the create_mc_data() model-free method - the ri_type is now being
passed into back_calc_ri().
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r12740 | bugman | 2011-03-02 18:32:12 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the _return_data_relax_data() and _return_error_relax_data() common
API methods for the new design.
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r12741 | bugman | 2011-03-02 18:37:03 +0100 (Wed, 02 Mar 2011) | 3 lines
User function echoing is now turned on for the interpreter embedded in the
SystemTestCase base class.
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r12742 | bugman | 2011-03-02 20:03:10 +0100 (Wed, 02 Mar 2011) | 3 lines
Replaced all instances of cdp.frq[0] with cdp.frq[cdp.ri_ids[0]].
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r12743 | bugman | 2011-03-02 20:21:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Created the new function generic_fns.relax_data.frq_loop() for looping over
unique frequencies.
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r12744 | bugman | 2011-03-02 20:29:14 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the model-free calculate() method - spin.relax_error no longer
exists.
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r12745 | bugman | 2011-03-02 20:29:52 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the model-free minimise() method when using Levenberg-Marquardt
optimisation.
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r12746 | bugman | 2011-03-02 20:37:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the generate_ri.py sample script for the new relax data ID string
design.
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r12747 | bugman | 2011-03-02 21:09:36 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the generate_ri.py model-free system test script.
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r12748 | bugman | 2011-03-02 21:10:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Another fix for the generate_ri.py model-free system test script.
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r12749 | bugman | 2011-03-02 21:13:26 +0100 (Wed, 02 Mar 2011) | 5 lines
Simplifications to the generate_ri.py model-free system test script.
The error calculation function is not required and all functions have been
eliminated.
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r12750 | bugman | 2011-03-03 07:57:47 +0100 (Thu, 03 Mar 2011) | 3 lines
Added checks for the relax_data user functions for the ri_type being one of
'R1', 'R2', or 'NOE'.
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r12751 | bugman | 2011-03-03 07:58:21 +0100 (Thu, 03 Mar 2011) | 3 lines
The echoing of user functions on() method no longer shows a print out.
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r12752 | bugman | 2011-03-03 08:28:59 +0100 (Thu, 03 Mar 2011) | 5 lines
Fix for the call to _relax_data_opt_structs() from _minimise_data_setup().
This was being performed for each relaxation data set, but it should be
done only once per spin!
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r12753 | bugman | 2011-03-03 09:37:22 +0100 (Thu, 03 Mar 2011) | 3 lines
The _relax_data_opt_structs() model-free method now handles MC sim data.
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r12754 | bugman | 2011-03-03 09:49:38 +0100 (Thu, 03 Mar 2011) | 3 lines
The model-free sim_pack_data() now converts the sim_data structure into a
dictionary with Rx IDs.
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r12755 | bugman | 2011-03-03 10:20:24 +0100 (Thu, 03 Mar 2011) | 3 lines
Alphabetical ordering of functions in the relax_data module.
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r12756 | bugman | 2011-03-03 10:22:52 +0100 (Thu, 03 Mar 2011) | 3 lines
Created a new function called num_frq() for determining the number of
frequencies.
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r12757 | bugman | 2011-03-03 10:44:30 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated all of the Dasha module for the new relax data ID string design.
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r12779 - in /1.3: ./ data/ generic_fns/ prompt/ sample_scripts/ specific_fns/ specific_fns/model_free/ test_suite/shared_dat...