Author: bugman
Date: Thu Sep 25 18:30:20 2008
New Revision: 7309
URL: http://svn.gna.org/viewcvs/relax?rev=7309&view=rev
Log:
Merged revisions
6837,6839,6841-6857,6859-6878,6880,6882-6938,6941-6945,6952,6957-6992,7021,7029,7076-7077,7080-7093,7106-7121,7130-7146,7148-7189,7191-7208,7226-7227,7230-7231,7307
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/rdc_analysis
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r6837 | bugman | 2008-07-08 16:23:35 +0200 (Tue, 08 Jul 2008) | 3 lines
Created the framework for a user function class for handling RDCs (by
copying the relax_data code).
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r6839 | bugman | 2008-07-08 20:30:14 +0200 (Tue, 08 Jul 2008) | 3 lines
Removed a test for the model setup in the set_non_spin_params() method.
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r6841 | bugman | 2008-07-08 21:02:19 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the return_data_name() method when no match occurs and the index
flag is True.
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r6842 | bugman | 2008-07-08 21:03:21 +0200 (Tue, 08 Jul 2008) | 5 lines
Added a number of new parameters to the return_data_name() method.
This include the bond length, and heteronucleus and proton types.
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r6843 | bugman | 2008-07-08 21:12:31 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the return_data_name() method when no match occurs and the index
flag is True.
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r6844 | bugman | 2008-07-08 21:17:05 +0200 (Tue, 08 Jul 2008) | 3 lines
Removed some debugging code.
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r6845 | bugman | 2008-07-08 21:24:29 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted the rdc.read() user function from the relax_data.read() code.
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r6846 | bugman | 2008-07-08 21:25:41 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted all instances of 'ri_label' to 'id'.
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r6847 | bugman | 2008-07-08 21:26:26 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted all instances of 'relax_data' to 'rdc'.
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r6848 | bugman | 2008-07-08 21:36:00 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted all of the rdc user functions from the relax_data code.
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r6849 | bugman | 2008-07-08 21:37:46 +0200 (Tue, 08 Jul 2008) | 3 lines
Created a generic_fns rdc module by copying the relax_data module.
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r6850 | bugman | 2008-07-08 21:54:07 +0200 (Tue, 08 Jul 2008) | 3 lines
Created 2 new error classes, RelaxNoRDCError and RelaxRDCError.
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r6851 | bugman | 2008-07-08 22:03:09 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted the read() function from the relax_data code.
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r6852 | bugman | 2008-07-08 22:20:28 +0200 (Tue, 08 Jul 2008) | 3 lines
Made the error column optional in the loading of RDCs.
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r6853 | bugman | 2008-07-08 22:25:44 +0200 (Tue, 08 Jul 2008) | 3 lines
Fixes for the read() function to allow the error column to be missing.
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r6854 | bugman | 2008-07-09 10:59:43 +0200 (Wed, 09 Jul 2008) | 8 lines
Split up the n_state_model.model() user function.
The new user functions are:
n_state_model.number_of_states()
n_state_model.ref_domain()
n_state_model.setup_model()
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r6855 | bugman | 2008-07-09 11:02:23 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the unit tests broken by the split up of n_state_model.model().
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r6856 | bugman | 2008-07-09 11:04:15 +0200 (Wed, 09 Jul 2008) | 3 lines
Wrote the model arg unit test for the n_state_model.setup_model() user
function.
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r6857 | bugman | 2008-07-09 11:06:51 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixes for the N-state model system test.
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r6859 | bugman | 2008-07-09 11:18:53 +0200 (Wed, 09 Jul 2008) | 3 lines
Split up the model_setup() method into number_of_states(), ref_domain(),
and setup_model().
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r6860 | bugman | 2008-07-09 11:20:29 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the new error class RelaxNoModelError.
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r6861 | bugman | 2008-07-09 11:21:18 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the n_state_model.select_model() user function.
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r6862 | bugman | 2008-07-09 11:23:36 +0200 (Wed, 09 Jul 2008) | 3 lines
Docstring and print out fixes for the n_state_model.select_model() user
function.
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r6863 | bugman | 2008-07-09 11:26:09 +0200 (Wed, 09 Jul 2008) | 5 lines
Renamed the n_state_model.setup_model() user function to
n_state_model.select_model().
This is to match the convention of the other analyses.
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r6864 | bugman | 2008-07-09 11:26:58 +0200 (Wed, 09 Jul 2008) | 3 lines
System test fix for the renaming of n_state_model.setup_model().
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r6865 | bugman | 2008-07-09 11:29:10 +0200 (Wed, 09 Jul 2008) | 3 lines
Added some error checking for the validity of the selected model type.
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r6866 | bugman | 2008-07-09 11:41:10 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the model checking in the minimise() method.
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r6867 | bugman | 2008-07-09 11:51:05 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the setup_model() method so that the model parameters can be set up
by numerous methods.
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r6868 | bugman | 2008-07-09 11:52:45 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the model arg of the n_state_model.select_model() user function.
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r6869 | bugman | 2008-07-09 13:29:21 +0200 (Wed, 09 Jul 2008) | 3 lines
Spun out some of the minimisation code into the minimise_setup_tensors()
method.
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r6870 | bugman | 2008-07-09 13:33:29 +0200 (Wed, 09 Jul 2008) | 3 lines
Renamed setup_model() to the private __update_model() method.
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r6871 | bugman | 2008-07-09 13:34:46 +0200 (Wed, 09 Jul 2008) | 3 lines
Made a call to __update_model() from select_model().
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r6872 | bugman | 2008-07-09 13:37:45 +0200 (Wed, 09 Jul 2008) | 3 lines
Made the __update_model() method less fatal.
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r6873 | bugman | 2008-07-09 13:38:55 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the call to __update_model() from number_of_states().
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r6874 | bugman | 2008-07-09 13:39:18 +0200 (Wed, 09 Jul 2008) | 3 lines
Added a call to __update_model() from ref_domain().
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r6875 | bugman | 2008-07-09 13:40:26 +0200 (Wed, 09 Jul 2008) | 3 lines
Added an alias to the current data pipe in minimise_setup_tensors().
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r6876 | bugman | 2008-07-09 13:43:57 +0200 (Wed, 09 Jul 2008) | 3 lines
Passed the param_vector into minimise_setup_tensors() and fixed the
variable of the returned data.
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r6877 | bugman | 2008-07-09 13:53:23 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixes for the __update_model() to prevent the model data being overwritten
or too many params added.
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r6878 | bugman | 2008-07-09 14:40:41 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the minimise_setup_rdcs() method.
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r6880 | bugman | 2008-07-09 15:05:46 +0200 (Wed, 09 Jul 2008) | 3 lines
Modified minimise_setup_rdcs() to throw a warning if RDCs exist but XH bond
vectors are missing.
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r6882 | bugman | 2008-07-09 15:11:47 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for minimise_setup_rdcs(). The spin id is now generated for the
warning.
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r6883 | bugman | 2008-07-09 15:18:36 +0200 (Wed, 09 Jul 2008) | 3 lines
The N_state_opt class now accepts the model, rdcs, and xh_vect arguments.
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r6884 | bugman | 2008-07-09 15:35:23 +0200 (Wed, 09 Jul 2008) | 3 lines
Modified the N_state_opt class to handle both alignment tensor and RDC
optimisation.
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r6885 | bugman | 2008-07-09 15:40:54 +0200 (Wed, 09 Jul 2008) | 6 lines
Changed the N_state_opt functions to be model dependent.
The func_rdcs() method is now func_population(), and the func_tensors()
method is now
func_2domain().
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r6886 | bugman | 2008-07-09 15:42:16 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the N_state_opt class set up for the tensor optimisation.
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r6887 | bugman | 2008-07-09 15:49:39 +0200 (Wed, 09 Jul 2008) | 3 lines
Created an empty module to dump RDC related computational functions into.
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r6888 | bugman | 2008-07-09 16:13:45 +0200 (Wed, 09 Jul 2008) | 6 lines
Created the average_rdc_5D() function.
This calculates the average RDC for an ensemble set of XH bond vectors,
using the 5D alignment
tensor notation.
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r6889 | bugman | 2008-07-09 16:19:13 +0200 (Wed, 09 Jul 2008) | 6 lines
Created the average_rdc_tensor() function.
This is equivalent to the average_rdc_5D() function but takes the full
tensor in numpy matrix form
rather than the elements of the 5D vector.
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r6890 | bugman | 2008-07-09 16:20:01 +0200 (Wed, 09 Jul 2008) | 3 lines
Docstring fix for average_rdc_5D(). The XH vectors must be unit vectors!
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r6891 | bugman | 2008-07-09 16:25:57 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the to_tensor() function to convert from 5D vector to 3D matrix.
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r6892 | bugman | 2008-07-09 16:28:49 +0200 (Wed, 09 Jul 2008) | 3 lines
Some fixes for the to_tensor() function. The elements Ayx, Azx, and Azy
were being referenced!
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r6893 | bugman | 2008-07-09 16:36:25 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the to_5D() function for converting from matrix form to 5D vector
form.
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r6894 | bugman | 2008-07-09 16:39:11 +0200 (Wed, 09 Jul 2008) | 3 lines
Modified the to_tensor() to be more efficient by working only with numpy
arrays.
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r6895 | bugman | 2008-07-09 16:42:14 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixes for the to_tensor() function. The tensor was completely wrong.
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r6896 | bugman | 2008-07-09 16:49:43 +0200 (Wed, 09 Jul 2008) | 3 lines
Created maxA() for finding the maximal alignment or the Azz component in
the alignment frame.
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r6897 | bugman | 2008-07-09 16:50:31 +0200 (Wed, 09 Jul 2008) | 3 lines
Imported some of the RDC functions.
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r6898 | bugman | 2008-07-09 16:54:09 +0200 (Wed, 09 Jul 2008) | 3 lines
Renamed the invalid variable name 5D_vector to vector_5D.
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r6899 | bugman | 2008-07-09 17:28:28 +0200 (Wed, 09 Jul 2008) | 3 lines
Implemented the core of the func_population() method.
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r6900 | bugman | 2008-07-09 17:35:01 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the average_rdc_5D() function. The unit XH bond vector indecies
were still in Mathematica format.
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r6901 | bugman | 2008-07-09 17:40:12 +0200 (Wed, 09 Jul 2008) | 6 lines
Fix for the func_population() method.
The RDC errors are now set to 1.0 if no errors are supplied, converting the
chi2 value to a SSE
value.
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r6902 | bugman | 2008-07-09 18:03:07 +0200 (Wed, 09 Jul 2008) | 5 lines
Fixes for the __update_model() method.
The probabilities and Euler angle parameter arrays are only created for the
relevant N-state model.
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r6903 | bugman | 2008-07-09 18:09:14 +0200 (Wed, 09 Jul 2008) | 3 lines
Spun out some of the minimise() code to create the __determine_data_type()
method.
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r6904 | bugman | 2008-07-09 18:22:10 +0200 (Wed, 09 Jul 2008) | 3 lines
Updated the assemble_param_vector() method to return the correct parameter
vector.
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r6905 | bugman | 2008-07-09 18:23:04 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for a missing cdp alias.
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r6906 | bugman | 2008-07-09 18:26:09 +0200 (Wed, 09 Jul 2008) | 5 lines
Complete change of the __determine_data_type() method.
The alignment tensors should be present when RDCs are loaded - they are
part of the optimised model!
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r6907 | bugman | 2008-07-09 18:33:20 +0200 (Wed, 09 Jul 2008) | 5 lines
Modified the __update_model() method to create empty alignment tensors as
necessary.
This is for the RDC based analysis were the tensors are optimised.
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r6908 | bugman | 2008-07-09 18:35:38 +0200 (Wed, 09 Jul 2008) | 5 lines
Fix for the __determine_data_type() method.
The flags were not correctly checked.
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r6909 | bugman | 2008-07-09 18:41:40 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the tensor_5D automatically generated object to AlignTensorData.
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r6910 | bugman | 2008-07-09 18:43:34 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the addition of alignment tensor parameters in
assemble_param_vector().
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r6911 | bugman | 2008-07-09 18:55:11 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixes for the func_population() method.
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r6912 | bugman | 2008-07-09 19:04:20 +0200 (Wed, 09 Jul 2008) | 6 lines
Changed the initialisation of the N_state_opt class.
The rdcs, rdc_errors, and xh_vect args are now all expected to be numpy
matricies. The rdcs and
rdc_errors matricies have also been transposed!
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r6913 | bugman | 2008-07-09 19:13:45 +0200 (Wed, 09 Jul 2008) | 3 lines
Converted the RDC and unit vector lists in minimise_setup_rdcs() to numpy
matrices.
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r6914 | bugman | 2008-07-09 19:15:11 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the incorrect testing for the presence of RDC errors.
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r6915 | bugman | 2008-07-09 19:15:33 +0200 (Wed, 09 Jul 2008) | 3 lines
Missing import.
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r6916 | bugman | 2008-07-09 19:16:32 +0200 (Wed, 09 Jul 2008) | 3 lines
Initialised the back calculated RDC array.
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r6917 | bugman | 2008-07-09 19:18:04 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed all the broken references to self.rdcs_back_calc.
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r6918 | bugman | 2008-07-09 19:21:47 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the calculation of the total number of spins and alignments.
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r6919 | bugman | 2008-07-09 19:23:48 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the setting up of RDC errors when missing. These should be 1.0, not
0.0!
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r6920 | bugman | 2008-07-09 19:35:48 +0200 (Wed, 09 Jul 2008) | 5 lines
Fixed the setting up of self.rdc_errors when no errors are present.
Retard, 1.0 times another matrix does not make a matrix of ones!
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r6921 | bugman | 2008-07-09 19:40:11 +0200 (Wed, 09 Jul 2008) | 3 lines
The population weights are now taken into account in the func_population()
target function.
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r6922 | bugman | 2008-07-09 19:40:53 +0200 (Wed, 09 Jul 2008) | 3 lines
Added some more comments.
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r6923 | bugman | 2008-07-09 19:41:54 +0200 (Wed, 09 Jul 2008) | 3 lines
The weights are passed into average_rdc_5D() as a keyword to make them
optional.
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r6924 | bugman | 2008-07-09 19:44:35 +0200 (Wed, 09 Jul 2008) | 3 lines
Converted average_rdc_5D() to expect a numpy array for the 5D tensor.
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r6925 | bugman | 2008-07-09 19:45:05 +0200 (Wed, 09 Jul 2008) | 3 lines
The 5D tensor is passed directly into average_rdc_5D() from
func_population().
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r6926 | bugman | 2008-07-09 19:52:22 +0200 (Wed, 09 Jul 2008) | 3 lines
Added weights to the average_rdc_5D() function.
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r6927 | bugman | 2008-07-09 19:53:41 +0200 (Wed, 09 Jul 2008) | 3 lines
Added weights to the average_rdc_tensor() function.
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r6928 | bugman | 2008-07-09 19:54:24 +0200 (Wed, 09 Jul 2008) | 3 lines
Docstring fixes.
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r6929 | bugman | 2008-07-10 09:43:16 +0200 (Thu, 10 Jul 2008) | 3 lines
Redesigned the disassemble_param_vector() method for the multiple N-state
model types.
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r6930 | bugman | 2008-07-10 10:06:29 +0200 (Thu, 10 Jul 2008) | 3 lines
Updated the param_num() method to take the various models into account.
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r6931 | bugman | 2008-07-10 10:54:29 +0200 (Thu, 10 Jul 2008) | 3 lines
Fix for the counting of header lines. The residue or spin number need not
be supplied.
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r6932 | bugman | 2008-07-10 13:26:51 +0200 (Thu, 10 Jul 2008) | 3 lines
Wrote the __assemble_scaling_matrix() method for creating a scaling matrix
for the N-state model.
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r6933 | bugman | 2008-07-10 13:30:26 +0200 (Thu, 10 Jul 2008) | 3 lines
Made diagonal scaling optional.
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r6934 | bugman | 2008-07-10 13:42:41 +0200 (Thu, 10 Jul 2008) | 3 lines
Made some more use of the scaling matrix.
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r6935 | bugman | 2008-07-10 13:43:36 +0200 (Thu, 10 Jul 2008) | 3 lines
Unscaled the parameter vector after optimisation.
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r6936 | bugman | 2008-07-10 13:44:25 +0200 (Thu, 10 Jul 2008) | 3 lines
Missing import fix.
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r6937 | bugman | 2008-07-10 13:51:21 +0200 (Thu, 10 Jul 2008) | 3 lines
The minimisation code now uses the scaling matrix.
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r6938 | bugman | 2008-07-10 14:46:35 +0200 (Thu, 10 Jul 2008) | 3 lines
Inverted the population scaling factor in __assemble_scaling_matrix().
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r6941 | bugman | 2008-07-23 11:27:38 +0200 (Wed, 23 Jul 2008) | 3 lines
Started to add the framework for the addition of gradients and Hessians.
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r6942 | bugman | 2008-07-23 11:47:41 +0200 (Wed, 23 Jul 2008) | 3 lines
Split the rdc module in half, shifting the alignment tensor components into
their own module.
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r6943 | bugman | 2008-07-23 11:48:36 +0200 (Wed, 23 Jul 2008) | 3 lines
Import fixes.
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r6944 | bugman | 2008-07-23 13:33:22 +0200 (Wed, 23 Jul 2008) | 3 lines
Wrote functions for all the alignment tensor gradients.
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r6945 | bugman | 2008-07-23 13:36:31 +0200 (Wed, 23 Jul 2008) | 3 lines
Fixes for the alignment tensor gradient function code.
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r6952 | bugman | 2008-07-24 14:49:13 +0200 (Thu, 24 Jul 2008) | 3 lines
A lot of modifications to the population N-state model optimisation code.
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r6957 | bugman | 2008-07-24 15:22:13 +0200 (Thu, 24 Jul 2008) | 3 lines
Spelling fix for the word 'indices'.
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r6958 | bugman | 2008-07-24 16:54:46 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixed the setting up of optimisation of the population N-state model.
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r6959 | bugman | 2008-07-24 16:55:09 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixed the call to to_tensor().
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r6960 | bugman | 2008-07-24 17:00:43 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixes for the func_population() target function.
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r6961 | bugman | 2008-07-24 17:02:21 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixes for the setup of the N-state model optimisation code.
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r6962 | bugman | 2008-07-24 17:03:06 +0200 (Thu, 24 Jul 2008) | 3 lines
Missing import.
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r6963 | bugman | 2008-07-24 17:07:34 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixed a call to the non-existant chi2_element() function (should be to
chi2()).
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r6964 | bugman | 2008-07-24 17:07:59 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixed some index names.
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r6965 | bugman | 2008-07-24 17:31:20 +0200 (Thu, 24 Jul 2008) | 3 lines
Large expansion of the dfunc_population() docstring.
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r6966 | bugman | 2008-07-25 10:04:15 +0200 (Fri, 25 Jul 2008) | 3 lines
More rewriting of the population N-state model optimisation code.
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r6967 | bugman | 2008-07-25 11:19:15 +0200 (Fri, 25 Jul 2008) | 5 lines
Wrote the average_rdc_tensor_dDij_dAmn() function.
This calculates the ensemble averaged RDC gradient element for the Amn
partial derivative.
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r6968 | bugman | 2008-07-25 11:21:34 +0200 (Fri, 25 Jul 2008) | 3 lines
Fixed the N-state model code to use the renamed averaged RDC functions.
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r6969 | bugman | 2008-07-25 11:27:44 +0200 (Fri, 25 Jul 2008) | 3 lines
Added a missing import.
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r6970 | bugman | 2008-07-25 11:47:49 +0200 (Fri, 25 Jul 2008) | 9 lines
Wrote the dipolar_constant() function for calculating the dipolar constant.
The constant is defined as:
mu0 gI.gS.h_bar
d = - --- -----------
4pi r**3
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r6971 | bugman | 2008-07-25 11:49:58 +0200 (Fri, 25 Jul 2008) | 3 lines
Pre-calculated the dipolar constants prior to optimisation.
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r6972 | bugman | 2008-07-25 11:51:42 +0200 (Fri, 25 Jul 2008) | 3 lines
Updated a comment describing why the dipolar constant is multiplied by
3/(2pi).
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r6973 | bugman | 2008-07-25 12:03:53 +0200 (Fri, 25 Jul 2008) | 3 lines
[... 738 lines stripped ...]
r7309 - in /1.3: ./ data/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ specific_fns/ test_suite/system_tests/scrip...