Author: bugman
Date: Fri Mar 28 09:57:44 2008
New Revision: 5239
URL: http://svn.gna.org/viewcvs/relax?rev=5239&view=rev
Log:
Blocked revisions 5136-5233,5236,5238 via svnmerge
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r5136 | bugman | 2008-03-22 15:12:47 +0100 (Sat, 22 Mar 2008) | 3 lines
assemble_param_vector() now calls determine_param_set_type() to get the
model type.
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r5137 | bugman | 2008-03-22 15:22:52 +0100 (Sat, 22 Mar 2008) | 3 lines
Updated the model-free determine_param_set_type() method to the new relax
design.
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r5138 | bugman | 2008-03-22 15:25:06 +0100 (Sat, 22 Mar 2008) | 3 lines
Bug fix for determine_param_set_type(), the diff_data_exists() function is
properly called.
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r5139 | bugman | 2008-03-22 15:28:21 +0100 (Sat, 22 Mar 2008) | 6 lines
Another bug fix for determine_param_set_type().
The structure cdp.diff_tensor should have been accessed, not cdp.diff.
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r5140 | bugman | 2008-03-22 18:17:32 +0100 (Sat, 22 Mar 2008) | 3 lines
Created a new function count_selected_spins() for counting selected spins.
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r5141 | bugman | 2008-03-22 18:23:13 +0100 (Sat, 22 Mar 2008) | 3 lines
Converted the model-free minimise() method to the new relax design.
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r5142 | bugman | 2008-03-22 18:25:26 +0100 (Sat, 22 Mar 2008) | 3 lines
Bug fix in the minimise() method for the call to diff_data_exists().
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r5143 | bugman | 2008-03-22 18:26:10 +0100 (Sat, 22 Mar 2008) | 3 lines
Missing import of return_spin().
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r5144 | bugman | 2008-03-22 18:36:01 +0100 (Sat, 22 Mar 2008) | 3 lines
Created the new function generic_fns.selection.return_spin_from_index().
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r5145 | bugman | 2008-03-22 18:38:47 +0100 (Sat, 22 Mar 2008) | 3 lines
Modified the model-free minimise() method to use the new
return_spin_from_index() function.
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r5146 | bugman | 2008-03-22 18:41:24 +0100 (Sat, 22 Mar 2008) | 5 lines
Bug fix in the test_opt_constr_sd_back_S2_0_970_te_2048_Rex_0_149() system
test.
'spin.chi2' was being accessed as 'spin.chi'.
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r5147 | bugman | 2008-03-22 18:48:19 +0100 (Sat, 22 Mar 2008) | 3 lines
Changed 'unselected' to 'deselected'.
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r5148 | bugman | 2008-03-22 18:53:48 +0100 (Sat, 22 Mar 2008) | 3 lines
Modified all the model-free optimisation system tests to check if the spins
are properly selected.
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r5149 | bugman | 2008-03-22 19:03:06 +0100 (Sat, 22 Mar 2008) | 3 lines
Converted the model-free overfit_deselect() method to use booleans.
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r5150 | bugman | 2008-03-22 19:42:42 +0100 (Sat, 22 Mar 2008) | 3 lines
Modified all the model-free optimisation system tests to compare 'select'
to bools.
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r5151 | bugman | 2008-03-22 19:45:43 +0100 (Sat, 22 Mar 2008) | 5 lines
Bug fix for the model-free overfit_deselect() method.
The spin.xh_vect structure should only be checked for if structural info is
required.
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r5152 | bugman | 2008-03-22 22:08:39 +0100 (Sat, 22 Mar 2008) | 3 lines
Converted the copySign() docstring to epydoc format.
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r5153 | bugman | 2008-03-22 22:10:11 +0100 (Sat, 22 Mar 2008) | 3 lines
Fix for the copySign() docstring - incorrect parameter name.
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r5154 | bugman | 2008-03-22 22:14:07 +0100 (Sat, 22 Mar 2008) | 3 lines
Fixed the epytext '@raise' syntax in two docstrings.
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r5155 | bugman | 2008-03-22 22:15:49 +0100 (Sat, 22 Mar 2008) | 3 lines
Updated the isNegInf() docstring.
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r5156 | bugman | 2008-03-22 22:48:29 +0100 (Sat, 22 Mar 2008) | 3 lines
Updated all the float function docstrings to epydoc format.
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r5157 | bugman | 2008-03-22 22:49:35 +0100 (Sat, 22 Mar 2008) | 3 lines
Renamed all 'nan' to 'NaN' in docstrings and comments.
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r5158 | bugman | 2008-03-22 23:03:16 +0100 (Sat, 22 Mar 2008) | 3 lines
Updated the float module docstring for epydoc.
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r5159 | bugman | 2008-03-22 23:08:49 +0100 (Sat, 22 Mar 2008) | 3 lines
Fixed the epydoc part of the getFloatClass() docstring.
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r5160 | bugman | 2008-03-22 23:12:10 +0100 (Sat, 22 Mar 2008) | 3 lines
Replaced all '@type return:' with '@rtype:' in the docstrings.
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r5161 | bugman | 2008-03-22 23:19:30 +0100 (Sat, 22 Mar 2008) | 3 lines
The Noe calculate() method maths in the docstring has been converted to
epydoc format.
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r5162 | bugman | 2008-03-22 23:22:43 +0100 (Sat, 22 Mar 2008) | 3 lines
Better epydoc support for the equations of the fold_angles() function.
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r5163 | bugman | 2008-03-22 23:23:33 +0100 (Sat, 22 Mar 2008) | 3 lines
Better epydoc support for the equations of the kappa() function.
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r5164 | bugman | 2008-03-22 23:24:11 +0100 (Sat, 22 Mar 2008) | 3 lines
Fix for the map_labels() docstring.
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r5165 | bugman | 2008-03-22 23:25:04 +0100 (Sat, 22 Mar 2008) | 3 lines
Better epydoc support for the equations of the svd() function.
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r5166 | bugman | 2008-03-22 23:27:00 +0100 (Sat, 22 Mar 2008) | 3 lines
Replaced all '@return type:' with '@rtype:'.
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r5167 | bugman | 2008-03-22 23:29:03 +0100 (Sat, 22 Mar 2008) | 3 lines
Better epydoc support for the equations of the fold_angles() function.
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r5168 | bugman | 2008-03-22 23:31:54 +0100 (Sat, 22 Mar 2008) | 3 lines
Better epydoc support for the equations and title of the unit_axes()
function.
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r5169 | bugman | 2008-03-23 01:18:50 +0100 (Sun, 23 Mar 2008) | 6 lines
Started the break up of the insanely complex model-free minimisation
methods in specific_fns.
The configuration of the spin specific part of the grid search has been
shifted into its own
function.
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r5170 | bugman | 2008-03-23 01:22:16 +0100 (Sun, 23 Mar 2008) | 3 lines
The diffusion tensor grid search configuration has been shifted into its
own function.
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r5171 | bugman | 2008-03-23 01:23:39 +0100 (Sun, 23 Mar 2008) | 3 lines
Whoops, removal of the old code which was shifted into a new function in
r5170.
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r5172 | bugman | 2008-03-23 01:42:29 +0100 (Sun, 23 Mar 2008) | 3 lines
Shifted the grid search limits, diagonal scaling, and grid size test into
new separate methods.
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r5173 | bugman | 2008-03-23 01:55:05 +0100 (Sun, 23 Mar 2008) | 3 lines
Shifted all the setting up of data for model-free minimisation into its own
function.
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r5174 | bugman | 2008-03-23 02:03:03 +0100 (Sun, 23 Mar 2008) | 3 lines
Split up the grid search function, reverting back to the structure as in
the 1.2 line.
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r5175 | bugman | 2008-03-23 13:07:49 +0100 (Sun, 23 Mar 2008) | 5 lines
The model-free grid search args are now passed into the minimise() method.
These will later be passed into the grid search configuration functions.
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r5176 | bugman | 2008-03-23 13:14:52 +0100 (Sun, 23 Mar 2008) | 3 lines
Updated the model-free assemble_param_vector() to accept spin containers.
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r5177 | bugman | 2008-03-23 13:18:50 +0100 (Sun, 23 Mar 2008) | 3 lines
Changed all epydoc '@param' to '@keyword' for all keyword args in the
mf_minimise module.
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r5178 | bugman | 2008-03-23 13:31:02 +0100 (Sun, 23 Mar 2008) | 3 lines
Updated the model-free assemble_scaling_matrix() method to the new relax
design.
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r5179 | bugman | 2008-03-23 13:42:32 +0100 (Sun, 23 Mar 2008) | 3 lines
Converted the num_params keyword arg in assemble_scaling_matrix() to a
normal arg.
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r5180 | bugman | 2008-03-23 13:43:43 +0100 (Sun, 23 Mar 2008) | 3 lines
Passed the number of params into the assemble_scaling_matrix() method.
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r5181 | bugman | 2008-03-23 13:46:58 +0100 (Sun, 23 Mar 2008) | 3 lines
The param_set variable is now passed into assemble_scaling_matrix().
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r5182 | bugman | 2008-03-23 14:36:11 +0100 (Sun, 23 Mar 2008) | 3 lines
Bug fix, 'if scaling_matrix:' cannot be used on a numpy object.
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r5183 | bugman | 2008-03-23 14:44:00 +0100 (Sun, 23 Mar 2008) | 3 lines
A number of modifications to get the grid_search_config() method to work.
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r5184 | bugman | 2008-03-23 14:46:28 +0100 (Sun, 23 Mar 2008) | 3 lines
Passed the lower, upper, and inc variables into grid_search_config().
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r5185 | bugman | 2008-03-23 14:47:10 +0100 (Sun, 23 Mar 2008) | 3 lines
Added the missing self arg to a number of grid search methods.
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r5186 | bugman | 2008-03-23 14:47:42 +0100 (Sun, 23 Mar 2008) | 3 lines
Added the missing self arg to test_grid_size().
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r5187 | bugman | 2008-03-23 14:51:05 +0100 (Sun, 23 Mar 2008) | 3 lines
Passed the scaling matrix into the grid_search_config() method.
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r5188 | bugman | 2008-03-23 14:51:59 +0100 (Sun, 23 Mar 2008) | 3 lines
Fix in the assemble_scaling_matrix() docstring.
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r5189 | bugman | 2008-03-23 15:05:06 +0100 (Sun, 23 Mar 2008) | 3 lines
Converted the model-free linear_constraints() method to the new relax
design.
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r5190 | bugman | 2008-03-23 15:16:39 +0100 (Sun, 23 Mar 2008) | 3 lines
Updated the return_spin_from_index() function to return the spin_id string
if asked.
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r5191 | bugman | 2008-03-23 15:18:37 +0100 (Sun, 23 Mar 2008) | 3 lines
Modified the model-free minimise() function to print out the spin_id rather
than res name and num.
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r5192 | bugman | 2008-03-23 15:27:16 +0100 (Sun, 23 Mar 2008) | 3 lines
Modified generate_spin_id() to handle None and int entries in the data
array.
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r5193 | bugman | 2008-03-23 15:33:19 +0100 (Sun, 23 Mar 2008) | 3 lines
Shifted the grid size print out to the test_grid_size() method.
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r5194 | bugman | 2008-03-23 15:35:21 +0100 (Sun, 23 Mar 2008) | 5 lines
minimise_data_setup() is now called and the data stored.
The self arg has also been added.
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r5195 | bugman | 2008-03-23 15:43:52 +0100 (Sun, 23 Mar 2008) | 3 lines
Passed all the necessary data into minimise_data_setup().
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r5196 | bugman | 2008-03-23 15:52:53 +0100 (Sun, 23 Mar 2008) | 3 lines
Started some code to get minimise_data_setup() to return the gyromagnetic
ratios.
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r5197 | bugman | 2008-03-23 15:57:11 +0100 (Sun, 23 Mar 2008) | 3 lines
Converted many physical constant comments to docstrings.
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r5198 | bugman | 2008-03-23 16:24:16 +0100 (Sun, 23 Mar 2008) | 3 lines
Shifted the variable docstrings to the correct position below the variable.
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r5199 | bugman | 2008-03-23 16:30:08 +0100 (Sun, 23 Mar 2008) | 3 lines
Wrote the return_gyromagnetic_ratio() for returning the desired value.
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r5200 | bugman | 2008-03-23 16:34:45 +0100 (Sun, 23 Mar 2008) | 3 lines
Wrote the return_atomic_mass() function for returning the desired atomic
mass.
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r5201 | bugman | 2008-03-23 16:38:34 +0100 (Sun, 23 Mar 2008) | 3 lines
Modified generic_fns.align_tensor.kappa() to use the new
return_gyromagnetic_ratio() function.
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r5202 | bugman | 2008-03-23 16:44:37 +0100 (Sun, 23 Mar 2008) | 3 lines
Completed the gyromagnetic ratio part of the model-free
minimise_data_setup() method.
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r5203 | bugman | 2008-03-23 16:49:00 +0100 (Sun, 23 Mar 2008) | 3 lines
Added a module docstring.
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r5204 | bugman | 2008-03-23 16:53:05 +0100 (Sun, 23 Mar 2008) | 3 lines
Added a package docstring for the OpenDX code.
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r5205 | bugman | 2008-03-23 16:55:34 +0100 (Sun, 23 Mar 2008) | 3 lines
Added a package docstring for the maths_fns package.
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r5206 | bugman | 2008-03-23 17:00:20 +0100 (Sun, 23 Mar 2008) | 3 lines
Added a package docstring for the docs/ directory.
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r5207 | bugman | 2008-03-23 17:00:45 +0100 (Sun, 23 Mar 2008) | 3 lines
Shifted the module docstring to the correct location (the very start).
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r5208 | bugman | 2008-03-23 17:03:05 +0100 (Sun, 23 Mar 2008) | 3 lines
Added module docstrings for the RelaxErrors and RelaxWarnings.
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r5209 | bugman | 2008-03-23 17:12:16 +0100 (Sun, 23 Mar 2008) | 5 lines
Updated the specific_fns.model_free package __init__ module.
A module docstring has been added, as well as the __all__ list.
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r5210 | bugman | 2008-03-23 17:14:23 +0100 (Sun, 23 Mar 2008) | 3 lines
The specific_fns.model_free package is now being included in the API
documentation.
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r5211 | bugman | 2008-03-23 17:17:43 +0100 (Sun, 23 Mar 2008) | 3 lines
All packages in the specific_fns and test_suite directories are now being
included in the API docs.
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r5212 | bugman | 2008-03-23 18:02:43 +0100 (Sun, 23 Mar 2008) | 3 lines
Fixed indentation in the Unit_test_runner.__init__ docstring to allow the
API docs to be compiled.
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r5213 | bugman | 2008-03-23 18:08:08 +0100 (Sun, 23 Mar 2008) | 3 lines
Removed all the subdirectories of test_suite and model_free from the API
docs.
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r5214 | bugman | 2008-03-23 18:10:32 +0100 (Sun, 23 Mar 2008) | 5 lines
Updated the test_suite package __init__ module.
A package docstring was added, and the __all__ list completed.
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r5215 | bugman | 2008-03-23 18:13:42 +0100 (Sun, 23 Mar 2008) | 5 lines
Updated the test_suite.system_tests package __init__ module.
A package docstring was added, and the __all__ list completed.
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r5216 | bugman | 2008-03-23 18:17:28 +0100 (Sun, 23 Mar 2008) | 5 lines
Updated the test_suite.unit_tests package __init__ module.
A package docstring was added, and the __all__ list completed.
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r5217 | bugman | 2008-03-23 18:20:08 +0100 (Sun, 23 Mar 2008) | 3 lines
Removed a duplicated entry in __all__.
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r5218 | bugman | 2008-03-23 18:26:53 +0100 (Sun, 23 Mar 2008) | 3 lines
Updated the epydoc compilation of the API docs to include all unit tests.
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r5219 | bugman | 2008-03-23 18:34:07 +0100 (Sun, 23 Mar 2008) | 3 lines
Added some missing imports of physical constants.
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r5220 | bugman | 2008-03-23 18:47:06 +0100 (Sun, 23 Mar 2008) | 6 lines
Modified the model-free default_value() and return_data_name() methods.
The heteronucleus type is now stored in 'spin.heteronuc_type'. The proton
type has also been added,
and is located in 'spin.proton_type'.
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r5221 | bugman | 2008-03-23 18:56:10 +0100 (Sun, 23 Mar 2008) | 3 lines
Modified the unit tests due to the changed of r5220.
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r5222 | bugman | 2008-03-23 18:57:30 +0100 (Sun, 23 Mar 2008) | 3 lines
Typo fix.
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r5223 | bugman | 2008-03-23 19:02:28 +0100 (Sun, 23 Mar 2008) | 3 lines
Changes to the J(w) mapping code to reflect the model-free changes of r5220.
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r5224 | bugman | 2008-03-23 19:05:14 +0100 (Sun, 23 Mar 2008) | 3 lines
Modified the model-free optimisation test suite script for the new
value.set() behaviour.
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r5225 | bugman | 2008-03-23 19:07:45 +0100 (Sun, 23 Mar 2008) | 3 lines
Fixed the initialisation of the model-free maths_fns code.
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r5226 | bugman | 2008-03-23 19:18:37 +0100 (Sun, 23 Mar 2008) | 3 lines
Renamed all 'num_res' to 'num_spins'.
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r5227 | bugman | 2008-03-23 19:19:28 +0100 (Sun, 23 Mar 2008) | 3 lines
The gyromagnetic ratios are now properly handled.
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r5228 | bugman | 2008-03-23 19:20:41 +0100 (Sun, 23 Mar 2008) | 5 lines
Fix for the testing of the presence of the scaling matrix.
Again a numpy problem.
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r5229 | bugman | 2008-03-23 19:24:11 +0100 (Sun, 23 Mar 2008) | 3 lines
Updated copyright statement.
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r5230 | bugman | 2008-03-23 19:42:31 +0100 (Sun, 23 Mar 2008) | 5 lines
Updated the model-free disassemble_param_vector() method to the new relax
design.
Many model-free optimisation system tests now pass!!!
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r5231 | bugman | 2008-03-23 19:43:30 +0100 (Sun, 23 Mar 2008) | 3 lines
Added missing epydoc entries in the assemble_param_vector() method
docstring.
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r5232 | bugman | 2008-03-23 19:49:26 +0100 (Sun, 23 Mar 2008) | 3 lines
The min_options object is now returned by the grid_search_config() method.
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r5233 | bugman | 2008-03-26 11:28:53 +0100 (Wed, 26 Mar 2008) | 3 lines
Comment fixes in the N-state model maths fns.
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r5236 | bugman | 2008-03-27 11:32:40 +0100 (Thu, 27 Mar 2008) | 9 lines
Fix for bug #11378 (https://gna.org/bugs/?11378).
This bug was reported by Ryan Hoffman (https://gna.org/users/rydog).
The fix for the 1.3 line is very different to that for the 1.2 line. These
functions have changed
significantly, and the pdb() user function doesn't exist any more! The
concept is similar though.
The xh_vect variable is now set to None rather than being non-existant, and
the spin is deselected.
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r5238 | bugman | 2008-03-28 09:44:20 +0100 (Fri, 28 Mar 2008) | 5 lines
Partially reverted r5236, the 'xh_vect' structure does not exist rather
than being set to None.
See the post by Seb at
https://mail.gna.org/public/relax-devel/2008-03/msg00008.html.
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Modified:
1.2/ (props changed)
Propchange: 1.2/
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Binary property 'svnmerge-blocked' - no diff available.
r5239 - /1.2/