svn+ssh://bugman@.../svn/relax/1.3
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r11269 | bugman | 2010-07-01 10:25:33 +0200 (Thu, 01 Jul 2010) | 3 lines
Inverted the x and y axes in the RDC and PCS correlation plots.
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r11270 | bugman | 2010-07-01 10:31:10 +0200 (Thu, 01 Jul 2010) | 3 lines
The errors in the correlation plots are now optional.
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r11271 | bugman | 2010-07-01 10:48:48 +0200 (Thu, 01 Jul 2010) | 3 lines
Better support for RDC and PCS correlation plots with and without errors.
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r11272 | bugman | 2010-07-02 10:40:23 +0200 (Fri, 02 Jul 2010) | 3 lines
Added a new system test for the direct optimisation of the paramagnetic centre.
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r11273 | bugman | 2010-07-02 10:41:41 +0200 (Fri, 02 Jul 2010) | 5 lines
Renamed the pcs.centre() user function to paramag.centre() in the system tests.
This is because in the future this paramagnetic centre position is shared with the PRE.
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r11274 | bugman | 2010-07-02 10:47:57 +0200 (Fri, 02 Jul 2010) | 6 lines
Renamed the pcs.centre() user function to paramag.centre() to abstract for the PRE.
The paramagnetic centre is shared between different NMR interactions, so this function has been
abstracted and is no longer PCS dependent.
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r11275 | bugman | 2010-07-02 10:53:18 +0200 (Fri, 02 Jul 2010) | 3 lines
The fix flag is now accepted by the paramag.centre() user function.
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r11276 | bugman | 2010-07-02 10:54:49 +0200 (Fri, 02 Jul 2010) | 3 lines
A few fixes for the paramag prompt code for the change from the PCS.
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r11277 | bugman | 2010-07-02 10:55:42 +0200 (Fri, 02 Jul 2010) | 3 lines
The paramag user function class is now accessible.
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r11278 | bugman | 2010-07-02 10:59:20 +0200 (Fri, 02 Jul 2010) | 3 lines
Fixes for the system tests for the pcs.centre() to paramag.centre() shift.
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r11279 | bugman | 2010-07-02 11:50:32 +0200 (Fri, 02 Jul 2010) | 5 lines
Activated the paramag centre finding system test.
This currently fails as the code to do this does not exist.
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r11280 | bugman | 2010-07-02 12:07:05 +0200 (Fri, 02 Jul 2010) | 3 lines
Fixes for solely specifying that the paramag centre will be optimised.
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r11281 | bugman | 2010-07-02 13:24:55 +0200 (Fri, 02 Jul 2010) | 5 lines
Fix for the RDC back_calc() function for when N=1 in the N-state model.
The bond vector structure was not correct.
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r11282 | bugman | 2010-07-02 13:31:52 +0200 (Fri, 02 Jul 2010) | 6 lines
Bug fix for the RDC back_calc() function - the align_id arg was being ignored.
The RDCs were being calculated for all tensors, and then assigned to the align_id key. The results
was that the back-calculated RDCs were for the last tensor, not for align_id.
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r11283 | bugman | 2010-07-02 17:39:21 +0200 (Fri, 02 Jul 2010) | 9 lines
Preparation for the optimisation of the paramagnetic centre in the N-state model.
The calculation of PCS unit vectors and distances has been shifted into the new
maths_fns.paramag_centre module and into the N-state model maths_fns code. The API of
maths_fns.n_state_model has been changed so that now atomic positions, the paramagnetic centre
position, the temperature, and frequency are passed in rather than the PCS vectors and constants.
The code is now more flexible making it easy to add PRE support.
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r11284 | bugman | 2010-07-02 17:50:23 +0200 (Fri, 02 Jul 2010) | 3 lines
The paramagnetic centre optimisation has been merged into the func_population() target function.
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r11285 | bugman | 2010-07-02 19:36:51 +0200 (Fri, 02 Jul 2010) | 5 lines
The paramagnetic centre is now part of the parameter vector for the N-state model.
Well, only when it is not fixed.
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r11286 | bugman | 2010-07-03 11:38:32 +0200 (Sat, 03 Jul 2010) | 5 lines
N-state models with no parameters are now caught prior to optimisation.
The minimise() method now simply throws a warning and returns without doing anything.
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r11287 | bugman | 2010-07-03 20:08:53 +0200 (Sat, 03 Jul 2010) | 3 lines
The N-state model calculate() method now stored the back-calculated RDCs and PCSs and Q factors.
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r11288 | bugman | 2010-07-03 21:56:40 +0200 (Sat, 03 Jul 2010) | 3 lines
The rdc.back_calc() user function without an ID arg will back-calculate RDCs for all alignments.
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r11289 | bugman | 2010-07-06 18:10:10 +0200 (Tue, 06 Jul 2010) | 3 lines
The N-state model now supports the paramagnetic centre in return_data_name().
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r11291 | bugman | 2010-07-08 11:45:21 +0200 (Thu, 08 Jul 2010) | 3 lines
Docstring improvements - the geometric info should be in Angstroms.
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r11292 | bugman | 2010-07-08 11:49:35 +0200 (Thu, 08 Jul 2010) | 9 lines
Better support for the optimisation and mapping of the Ln3+ position.
The position is now treated in Angstrom, and is properly scaled. A few additional API methods have
been added for the mapping of the optimisation space, and a few modified to support the Ln3+
position.
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r11293 | bugman | 2010-07-08 11:56:42 +0200 (Thu, 08 Jul 2010) | 3 lines
Fix for the Ln3+ position optimisation with no populations, the target function was overwritten.
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r11294 | bugman | 2010-07-08 13:03:13 +0200 (Thu, 08 Jul 2010) | 5 lines
Fix for the N-state model _assemble_scaling_matrix() method for the 2-domain model.
This is a recently introduced bug. For the 2-domain model, no alignment parameters are optimised.
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r11295 | bugman | 2010-07-08 13:49:04 +0200 (Thu, 08 Jul 2010) | 3 lines
Changed the alignment tensor parameter scaling back to 1 as this was slowing down the optimisation.
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r11296 | bugman | 2010-07-08 15:26:24 +0200 (Thu, 08 Jul 2010) | 3 lines
Created the n_state_model.elim_no_prob() to remove structures with zero probability.
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r11298 | bugman | 2010-07-13 13:28:44 +0200 (Tue, 13 Jul 2010) | 14 lines
Major patch for integrating the GUI into the noe calculation.
This patch is from Michael Bieri (https://gna.org/users/michaelbieri) and is from file #9490
(https://gna.org/support/download.php?file_id=9490) attached to task #6847
(https://gna.org/task/?6847).
Changes include:
- output filename can be specified
- folder, where results files will be placed, can be specified
- label of hetero nucleus and proton of peak lists and pdb file can be selected
- sequence is read either by sequence file or pdb file
- removed white spaces and progress output.
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r11299 | bugman | 2010-07-15 13:19:11 +0200 (Thu, 15 Jul 2010) | 3 lines
Added a system test checking the conversion of alignment tensor to chi tensor.
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r11300 | bugman | 2010-07-15 13:39:35 +0200 (Thu, 15 Jul 2010) | 3 lines
Fix for the alignment tensor rotation matrix - it is now always in the right handed universe.
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r11301 | bugman | 2010-07-15 15:26:00 +0200 (Thu, 15 Jul 2010) | 3 lines
Initialising and alignment tensor now adds the ID to the alignment ID list.
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r11302 | bugman | 2010-07-15 15:26:35 +0200 (Thu, 15 Jul 2010) | 3 lines
Wrote the pcs.back_calc() user function back end.
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r11303 | bugman | 2010-07-15 15:29:46 +0200 (Thu, 15 Jul 2010) | 3 lines
Added a severely truncated PDB file for PCS back-calculation with ubiquitin.
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r11304 | bugman | 2010-07-15 15:46:30 +0200 (Thu, 15 Jul 2010) | 3 lines
Added a system test for the back-calculation of PCSs.
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r11305 | bugman | 2010-07-15 15:46:58 +0200 (Thu, 15 Jul 2010) | 3 lines
Added some unit tests for the pseudo-elliptic cosine function.
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r11306 | bugman | 2010-07-15 17:08:22 +0200 (Thu, 15 Jul 2010) | 5 lines
Fix for the alignment tensor initialisation for when the ID is added to cdp.align_ids.
This was introduced in r11301. cdp.align_ids was not being checked if the align ID already exists.
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r11307 | bugman | 2010-07-15 17:23:28 +0200 (Thu, 15 Jul 2010) | 3 lines
The Ln3+ position optimisation system test has been sped up by decreasing the accuracy.
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r11308 | bugman | 2010-07-15 18:32:33 +0200 (Thu, 15 Jul 2010) | 6 lines
Small fixes and improvements to the rdc.back_calc() user function.
Align IDs are being used instead of RDC IDs so RDCs can be back-calculated even if measured RDCs are
not present. And spin info is also being checked for better error reporting to the user.
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r11309 | bugman | 2010-07-15 18:34:04 +0200 (Thu, 15 Jul 2010) | 5 lines
The RDC and PCS back-calculation user fns now add the alignment ID to the RDC and PCS if absent.
Again this is to allow both data types to be back-calculated in the absence of measured data.
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r11310 | bugman | 2010-07-15 18:38:18 +0200 (Thu, 15 Jul 2010) | 3 lines
Added a system test to back-calculated RDCs from a PCS derived alignment tensor.
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r11311 | bugman | 2010-07-16 11:24:28 +0200 (Fri, 16 Jul 2010) | 3 lines
Made a RelaxError less stringent so that the paramagnetic centre can be unfixed.
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r11312 | bugman | 2010-07-16 11:28:33 +0200 (Fri, 16 Jul 2010) | 3 lines
The align_tensor.delete() user function can now be used to remove all tensors simultaneously.
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r11313 | bugman | 2010-07-16 19:12:36 +0200 (Fri, 16 Jul 2010) | 3 lines
Fixed the align_tensor.delete() arg unit test to accept None as an arg.
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r11314 | bugman | 2010-07-16 19:13:13 +0200 (Fri, 16 Jul 2010) | 3 lines
Pre-defined probabilities can now be used in the 'fixed' N-state model optimisation.
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r11315 | bugman | 2010-07-19 11:42:30 +0200 (Mon, 19 Jul 2010) | 5 lines
For for a bug introduced in the last revision (r11314).
The fixed probabilities were not being set for the Ln3+ optimisation case.
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r11316 | bugman | 2010-07-19 11:59:05 +0200 (Mon, 19 Jul 2010) | 3 lines
Large speed ups of the Ln3+ position finding system test.
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r11317 | bugman | 2010-07-19 15:35:24 +0200 (Mon, 19 Jul 2010) | 9 lines
Created compile_1st_matrix_pseudo_ellipse() for numerically making the 1st degree frame order matrix.
A number of new supplementary functions have been added for this numerical approximation:
part_int_daeg1_pseudo_ellipse_xx()
part_int_daeg1_pseudo_ellipse_yy()
part_int_daeg1_pseudo_ellipse_zz()
tmax_pseudo_ellipse()
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r11318 | bugman | 2010-07-19 17:36:43 +0200 (Mon, 19 Jul 2010) | 3 lines
Fix for the print_frame_order_2nd_degree() fn, sys.stdout overwriting now works.
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r11319 | bugman | 2010-07-19 18:04:13 +0200 (Mon, 19 Jul 2010) | 6 lines
Created compile_2nd_matrix_pseudo_ellipse() for numerically making the 2nd degree frame order matrix.
A series of part_int_daeg2_pseudo_ellipse_**() supplementary functions have been added for this
numerical approximation. The function is also unit tested.
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r11320 | bugman | 2010-07-19 18:39:18 +0200 (Mon, 19 Jul 2010) | 6 lines
Removal of the T23 transpose from compile_2nd_matrix_pseudo_ellipse() and an index shift of -1.
The removal of the transpose has changed all of the indices in part_int_daeg2_pseudo_ellipse_xx().
These indices now start at zero for easier debugging.
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r11321 | bugman | 2010-07-19 18:42:38 +0200 (Mon, 19 Jul 2010) | 3 lines
Reordering of the part_int_daeg2_pseudo_ellipse_xx() functions.
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r11322 | bugman | 2010-07-19 19:18:42 +0200 (Mon, 19 Jul 2010) | 3 lines
Added a debugging print out to test_compile_2nd_matrix_pseudo_ellipse().
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r11323 | bugman | 2010-07-19 19:19:18 +0200 (Mon, 19 Jul 2010) | 3 lines
Clean up of the maths functions in part_int_daeg2_pseudo_ellipse_xy().
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r11324 | bugman | 2010-07-21 11:24:16 +0200 (Wed, 21 Jul 2010) | 3 lines
Added support for the pseudo-elliptic cone model in the frame order user function and specific code.
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r11325 | bugman | 2010-07-21 11:46:03 +0200 (Wed, 21 Jul 2010) | 3 lines
Removed the docstring linewrapping in the frame order maths_fns module.
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r11326 | bugman | 2010-07-21 13:28:41 +0200 (Wed, 21 Jul 2010) | 3 lines
Alphabetical arrangement of the functions in the frame_order_matrix_ops module.
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r11327 | bugman | 2010-07-21 13:36:52 +0200 (Wed, 21 Jul 2010) | 3 lines
Modified compile_2nd_matrix_pseudo_ellipse() to rotate and return the frame order matrix.
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r11328 | bugman | 2010-07-21 13:38:29 +0200 (Wed, 21 Jul 2010) | 5 lines
Created the func_pseudo_ellipse() optimisation target fn. for the pseudo-elliptic cone model.
The structure of the Frame_order class has been simplified for handling multiple frame order models.
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r11329 | bugman | 2010-07-21 13:43:49 +0200 (Wed, 21 Jul 2010) | 3 lines
Fix for the frame order grid_search() method - the pseudo-elliptic parameters were incorrectly named.
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r11330 | bugman | 2010-07-21 13:54:01 +0200 (Wed, 21 Jul 2010) | 7 lines
Bug fix for the frame order grid search - the non-linear grid search is now performed.
Previously the minfx.grid.grid() function was being used, causing the custom grid to be ignored.
Now minfx.grid.grid_point_array() is being used allowing the non-regular grid to be used.
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r11331 | bugman | 2010-07-21 14:52:37 +0200 (Wed, 21 Jul 2010) | 3 lines
Bug fix for the frame order grid_search() method - the point grid is now properly constructed.
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r11332 | bugman | 2010-07-21 16:32:58 +0200 (Wed, 21 Jul 2010) | 3 lines
Fix for the _assemble_param_vector() method - the pseudo-ellipse parameter vector was not being created.
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r11334 | bugman | 2010-07-22 11:09:04 +0200 (Thu, 22 Jul 2010) | 6 lines
Bug fix for the func_pseudo_ellipse() target function.
The overwriting of the permanent storage data structures was killing the optimisation of the average
domain position. Now temporary data structures are used for the functions which return numpy arrays.
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r11335 | bugman | 2010-07-22 11:12:22 +0200 (Thu, 22 Jul 2010) | 5 lines
The same bug fix of r11334 has now been applied to the func_rigid() and func_iso_cone() target fns.
The temporary data structures are no longer clobbering the permanent storage structures.
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r11336 | bugman | 2010-07-22 11:38:26 +0200 (Thu, 22 Jul 2010) | 3 lines
Modified the test_compile_2nd_matrix_pseudo_ellipse() unit test to match the new fn syntax.
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r11337 | bugman | 2010-07-22 15:57:03 +0200 (Thu, 22 Jul 2010) | 3 lines
Silenced the scipy.integrate.quad() warnings by setting the full_output arg to 1.
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r11338 | bugman | 2010-07-22 18:26:42 +0200 (Thu, 22 Jul 2010) | 3 lines
Limit arrays are now sent into the minfx generic interface for limiting simulated annealing.
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r11340 | bugman | 2010-07-23 10:56:51 +0200 (Fri, 23 Jul 2010) | 3 lines
Hardcoded the factorial() function using a dictionary to return support for Python 2.4 and 2.5.
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r11341 | bugman | 2010-07-23 11:20:58 +0200 (Fri, 23 Jul 2010) | 3 lines
Converted the dictionary to a list in factorial() for speed.
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r11366 | bugman | 2010-07-27 10:14:12 +0200 (Tue, 27 Jul 2010) | 3 lines
The select.read() and deselect.read() user functions can now accept file handles or dummy file objects.
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r11367 | bugman | 2010-07-27 14:00:43 +0200 (Tue, 27 Jul 2010) | 3 lines
When loading save states, data pipe names are always converted to a string to avoid unicode problems.
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r11368 | bugman | 2010-07-27 15:13:12 +0200 (Tue, 27 Jul 2010) | 6 lines
The loading of RDCs and PCSs for non-existent spins now only throws a RelaxWarning.
Rather than throwing a RelaxError, this allows for partial loading of alignment data for certain
regions of the molecule.
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r11381 | bugman | 2010-07-28 11:13:46 +0200 (Wed, 28 Jul 2010) | 6 lines
Removed the docstring length check from the code validator script and changed a printout.
The docstring length is only 100 characters in the user functions. For all other functions, no
length is enforced.
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r11382 | bugman | 2010-07-28 11:38:32 +0200 (Wed, 28 Jul 2010) | 3 lines
The attached proton PDB name is no longer hardcoded to 'H' in the dauvergne_protocol auto analysis.
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r11383 | bugman | 2010-07-29 14:18:18 +0200 (Thu, 29 Jul 2010) | 3 lines
The back-calculated alignments tensors are now being stored in the current data pipe.
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r11384 | bugman | 2010-07-29 16:11:51 +0200 (Thu, 29 Jul 2010) | 3 lines
The align_tensor.display() user function now prints out the generalized degree of order (GDO) value.
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r11385 | bugman | 2010-07-29 17:58:54 +0200 (Thu, 29 Jul 2010) | 3 lines
pipe.display() now places quotation marks around the pipe names and shows which is the current data pipe.
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r11388 | bugman | 2010-08-03 11:22:53 +0200 (Tue, 03 Aug 2010) | 3 lines
Created the torsionless pseudo-ellipse cone model, where the torsion angle simga is zero.
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r11389 | bugman | 2010-08-03 14:44:56 +0200 (Tue, 03 Aug 2010) | 5 lines
Created the pseudo-ellipse, free rotor target function.
This model is not yet available.
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r11390 | bugman | 2010-08-03 15:16:23 +0200 (Tue, 03 Aug 2010) | 3 lines
Added the missing hyphen to 'pseudo ellipse' in the docstrings.
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r11391 | bugman | 2010-08-03 15:17:54 +0200 (Tue, 03 Aug 2010) | 3 lines
Added target function aliases for all 12 parameteric restriction models of the pseudo-ellipse.
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r11392 | bugman | 2010-08-03 16:22:39 +0200 (Tue, 03 Aug 2010) | 3 lines
The frame_order.select_model() user fn docstring now describes all 12 parametric restriction models.
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r11393 | bugman | 2010-08-03 22:18:07 +0200 (Tue, 03 Aug 2010) | 6 lines
Partial support for the 12 parametric restriction models of the pseudo-ellipse.
All of the specific frame order code can now support these models. The maths_fns code is still
missing, so not all models are available.
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r11394 | bugman | 2010-08-03 22:37:46 +0200 (Tue, 03 Aug 2010) | 5 lines
Shifted all of the shared code in the frame order target functions to reduce_and_rot().
This significantly simplifies the code base and removes a large source of bugs.
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r11395 | bugman | 2010-08-03 22:48:06 +0200 (Tue, 03 Aug 2010) | 5 lines
Abstracted the common code in compile_2nd_matrix_*() into rotate_daeg().
This will significantly simplify the addition of all of the 12 models.
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r11396 | bugman | 2010-08-03 23:02:21 +0200 (Tue, 03 Aug 2010) | 6 lines
Simplified compile_2nd_matrix_iso_cone() by using rotate_daeg().
The compile_2nd_matrix_*() functions now build the rotation matrix themselves as this is not shared
code.
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r11397 | bugman | 2010-08-03 23:09:43 +0200 (Tue, 03 Aug 2010) | 3 lines
Fix for the reduce_and_rot() method, the self arg was missing.
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r11398 | bugman | 2010-08-04 09:42:29 +0200 (Wed, 04 Aug 2010) | 3 lines
Ordering of the functions.
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r11399 | bugman | 2010-08-04 09:56:49 +0200 (Wed, 04 Aug 2010) | 6 lines
Simplified and sped up the torsionless pseudo ellipse.
6 functions, and hence 6 numerical integrations, have been deleted as they are repetitive of other
frame order matrix elements.
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r11400 | bugman | 2010-08-04 10:53:17 +0200 (Wed, 04 Aug 2010) | 5 lines
Renamed to isotropic cone functions to the free rotor isotropic cone.
The model name has changed, as the torsion angle was unrestricted in the earlier code.
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r11401 | bugman | 2010-08-04 11:26:58 +0200 (Wed, 04 Aug 2010) | 3 lines
Added support for the isotropic cone model, that is with a torsion angle restriction of sigma_max.
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r11402 | bugman | 2010-08-04 14:30:13 +0200 (Wed, 04 Aug 2010) | 5 lines
Removal of the reduce_alignment_tensor_reverse() frame order function.
This is not being used, and is of no use!
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r11403 | bugman | 2010-08-04 17:07:27 +0200 (Wed, 04 Aug 2010) | 3 lines
Modified reduce_alignment_tensor() to be in the Kronecker product notation.
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r11404 | bugman | 2010-08-04 17:13:47 +0200 (Wed, 04 Aug 2010) | 3 lines
Created the reduce_alignment_tensor_symmetric() function for computation efficiency.
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r11405 | bugman | 2010-08-04 17:14:34 +0200 (Wed, 04 Aug 2010) | 3 lines
The frame order target functions now use reduce_alignment_tensor_symmetric().
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r11406 | bugman | 2010-08-04 17:17:01 +0200 (Wed, 04 Aug 2010) | 3 lines
Modified rotate_daeg() to operate on the Kronecker product form of the frame order matrix.
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r11407 | bugman | 2010-08-04 17:33:49 +0200 (Wed, 04 Aug 2010) | 3 lines
Shifted populate_2nd_eigenframe_iso_cone_free_rotor() to be in the Kronecker product form.
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r11408 | bugman | 2010-08-04 18:44:25 +0200 (Wed, 04 Aug 2010) | 5 lines
Changed the frame order pseudo-ellipse equations.
These should be numerically more stable.
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r11409 | bugman | 2010-08-04 18:50:24 +0200 (Wed, 04 Aug 2010) | 5 lines
Fix for all the part_int_daeg2_pseudo_ellipse_*() functions.
The variable f should be phi!
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r11410 | bugman | 2010-08-04 18:53:40 +0200 (Wed, 04 Aug 2010) | 5 lines
Commented out unused frame order matrix elements in compile_2nd_matrix_pseudo_ellipse().
These elements are not part of the rotational superoperator.
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r11411 | bugman | 2010-08-04 19:04:53 +0200 (Wed, 04 Aug 2010) | 6 lines
Reverted r11410 as the change did not take into account the rotation of the frame order matrix.
The command used was:
svn merge -r11410:11409 .
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r11412 | bugman | 2010-08-04 19:08:38 +0200 (Wed, 04 Aug 2010) | 6 lines
Reverted r11405 as the eigenframe rotation of the frame order matrix breaks the symmetry.
The command used was:
svn merge -r11405:11404 .
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r11413 | bugman | 2010-08-04 19:17:44 +0200 (Wed, 04 Aug 2010) | 3 lines
Bug fix for reduce_alignment_tensor(), some subtractions should have been additions!
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r11414 | bugman | 2010-08-04 22:42:48 +0200 (Wed, 04 Aug 2010) | 5 lines
Fixes for the torsionless frame order matrix equations.
The previous equations were plain wrong!
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r11415 | bugman | 2010-08-04 22:47:56 +0200 (Wed, 04 Aug 2010) | 5 lines
Fix for the func_pseudo_ellipse_torsionless() frame order target function.
A variable was not fully typed out.
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r11416 | bugman | 2010-08-04 22:49:14 +0200 (Wed, 04 Aug 2010) | 3 lines
Fix for the pseudo-ellipse unit test as the matrix is now in Kronecker product form.
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r11417 | bugman | 2010-08-04 22:49:52 +0200 (Wed, 04 Aug 2010) | 5 lines
Another fix for func_pseudo_ellipse_torsionless().
The average position Euler angles were not correctly named.
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r11418 | bugman | 2010-08-05 11:12:07 +0200 (Thu, 05 Aug 2010) | 3 lines
Added 2 system tests for checking the pseudo-ellipse and torsionless pseudo-ellipse target fns.
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r11419 | bugman | 2010-08-05 12:36:42 +0200 (Thu, 05 Aug 2010) | 5 lines
Fixes for the free rotor pseudo-elliptic frame order matrix equations.
The previous equations were plain wrong!
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r11420 | bugman | 2010-08-05 12:50:23 +0200 (Thu, 05 Aug 2010) | 3 lines
Fix for compile_2nd_matrix_pseudo_ellipse(), the pseudo-ellipse has slight asymmetry in daeg.
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r11421 | bugman | 2010-08-05 13:04:57 +0200 (Thu, 05 Aug 2010) | 6 lines
Simplification of compile_2nd_matrix_pseudo_ellipse() by removal of identical numerical integrations.
A number of the frame order matrix diagonal elements are equal to each other, so the repetitive
calculations were removed for speed.
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r11422 | bugman | 2010-08-05 13:10:23 +0200 (Thu, 05 Aug 2010) | 5 lines
Fix for the pseudo-ellipse frame order system test.
The chi2 is different with the corrected equations.
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r11423 | bugman | 2010-08-05 15:04:08 +0200 (Thu, 05 Aug 2010) | 5 lines
Bug fix for compile_2nd_matrix_pseudo_ellipse_free_rotor() - element 04 was incorrectly set.
It was set to 11 rather than 00.
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r11424 | bugman | 2010-08-06 10:42:19 +0200 (Fri, 06 Aug 2010) | 3 lines
Bug fixes for populate_2nd_eigenframe_iso_cone() as the frame order equations were incorrect.
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r11425 | bugman | 2010-08-06 11:08:01 +0200 (Fri, 06 Aug 2010) | 3 lines
Fixed a typo in populate_2nd_eigenframe_iso_cone().
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r11426 | bugman | 2010-08-06 11:09:09 +0200 (Fri, 06 Aug 2010) | 3 lines
Fixed another typo in populate_2nd_eigenframe_iso_cone().
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r11427 | bugman | 2010-08-06 11:29:23 +0200 (Fri, 06 Aug 2010) | 5 lines
Created a new module for performing coordinate transformations.
The new function cartesian_to_spherical() has been added as the first conversion.
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r11428 | bugman | 2010-08-06 13:47:54 +0200 (Fri, 06 Aug 2010) | 3 lines
Switched the theta and phi angles in cartesian_to_spherical() to match the rest of relax.
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r11429 | bugman | 2010-08-06 14:00:26 +0200 (Fri, 06 Aug 2010) | 5 lines
Shifted frame_order_matrix_ops.generate_vector() to coord_transform.spherical_to_cartesian().
The function input has been modified to accept a spherical coordinate vector.
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r11430 | bugman | 2010-08-06 14:03:28 +0200 (Fri, 06 Aug 2010) | 3 lines
The frame order specific module now uses spherical_to_cartesian().
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r11431 | bugman | 2010-08-06 15:12:56 +0200 (Fri, 06 Aug 2010) | 5 lines
The isotropic cone frame order model now uses the full eigenframe.
This is necessary to define the torsion angle restriction.
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r11432 | bugman | 2010-08-06 15:26:13 +0200 (Fri, 06 Aug 2010) | 5 lines
Bug fix for the frame order _update_model() method for the isotropic cone.
The cone angle parameter cone_theta was incorrectly referenced.
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r11433 | bugman | 2010-08-06 15:29:00 +0200 (Fri, 06 Aug 2010) | 3 lines
The isotropic cone parameter cone_theta is now being unpacked and stored after optimisation.
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r11434 | bugman | 2010-08-07 21:31:05 +0200 (Sat, 07 Aug 2010) | 3 lines
Created maths_fns.order_parameters.iso_cone_theta_to_S() function for angle to order param conversion.
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r11435 | bugman | 2010-08-08 17:14:48 +0200 (Sun, 08 Aug 2010) | 5 lines
Fixed a bug in populate_2nd_eigenframe_iso_cone().
One of the many trig functions were incorrectly typed out.
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r11436 | bugman | 2010-08-08 17:21:18 +0200 (Sun, 08 Aug 2010) | 5 lines
Fixed another 2 trig typo bugs in populate_2nd_eigenframe_iso_cone().
These are the same issue, sin(2.0*tmax)**2 should have been sin(tmax)**2.
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r11437 | bugman | 2010-08-09 10:00:36 +0200 (Mon, 09 Aug 2010) | 3 lines
Added the maths_fns.coord_transform module to the package __all__ list.
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r11438 | bugman | 2010-08-09 10:28:53 +0200 (Mon, 09 Aug 2010) | 3 lines
Wrote 4 unit tests for the compile_2nd_matrix_iso_cone*() frame order functions.
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r11439 | bugman | 2010-08-09 10:39:16 +0200 (Mon, 09 Aug 2010) | 3 lines
Implemented the sinc() function.
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r11440 | bugman | 2010-08-09 11:52:09 +0200 (Mon, 09 Aug 2010) | 6 lines
Added a second unit test for perfect order in compile_2nd_matrix_iso_cone().
This checks values at and close to zero, as the sinc() function is differently defined at this
position.
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r11441 | bugman | 2010-08-09 11:56:38 +0200 (Mon, 09 Aug 2010) | 5 lines
Converted the isotropic cone frame order model to use the sinc() function.
This removes much round off error and significantly simplifies the equations.
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r11442 | bugman | 2010-08-09 12:21:07 +0200 (Mon, 09 Aug 2010) | 3 lines
Added 4 more unit tests for the compile_2nd_matrix_*() functions, and modified one of the others.
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r11443 | bugman | 2010-08-09 13:59:55 +0200 (Mon, 09 Aug 2010) | 3 lines
Shifted to using numpy.sinc() for the frame order equations.
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r11444 | bugman | 2010-08-09 14:02:15 +0200 (Mon, 09 Aug 2010) | 14 lines
Reverted r11439 as the sinc function is implemented in numpy.
The command used was:
svn merge -r11439:11438 .
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r11439 | bugman | 2010-08-09 10:39:16 +0200 (Mon, 09 Aug 2010) | 3 lines
Changed paths:
M /1.3/maths_fns/pseudo_ellipse.py
Implemented the sinc() function.
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r11445 | bugman | 2010-08-09 14:09:47 +0200 (Mon, 09 Aug 2010) | 5 lines
Properly implemented order_parameters.iso_cone_S_to_theta().
The previous order_parameters.iso_cone_S_to_cos_theta() function did nothing.
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r11446 | bugman | 2010-08-09 14:10:16 +0200 (Mon, 09 Aug 2010) | 3 lines
populate_2nd_eigenframe_iso_cone_free_rotor() now uses the iso_cone_S_to_theta() function.
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r11447 | bugman | 2010-08-09 14:17:43 +0200 (Mon, 09 Aug 2010) | 3 lines
Clean up of the frame order unit tests.
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r11448 | bugman | 2010-08-09 14:28:45 +0200 (Mon, 09 Aug 2010) | 3 lines
Added 4 frame order unit tests checking the half cone frame order matrix.
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r11449 | bugman | 2010-08-09 14:29:14 +0200 (Mon, 09 Aug 2010) | 3 lines
Reactivated test_compile_2nd_matrix_pseudo_ellipse().
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r11450 | bugman | 2010-08-09 14:29:45 +0200 (Mon, 09 Aug 2010) | 3 lines
Removed an unused data structure.
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r11451 | bugman | 2010-08-09 14:35:14 +0200 (Mon, 09 Aug 2010) | 3 lines
Added a eigenframe rotation to test_compile_2nd_matrix_pseudo_ellipse_free_rotor_half_cone().
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r11452 | bugman | 2010-08-09 14:43:51 +0200 (Mon, 09 Aug 2010) | 3 lines
Added 4 frame order unit tests for half cones rotated 90 deg about y.
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r11453 | bugman | 2010-08-09 14:59:43 +0200 (Mon, 09 Aug 2010) | 3 lines
Deactivated 2 frame order unit tests as these cannot be satisfied with numerical integration.
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r11454 | bugman | 2010-08-09 15:58:25 +0200 (Mon, 09 Aug 2010) | 3 lines
Added 2 more unit tests of compile_2nd_matrix_pseudo_ellipse().
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r11455 | bugman | 2010-08-10 10:28:52 +0200 (Tue, 10 Aug 2010) | 3 lines
Added 2 unit tests for the free rotor pseudo-ellipse frame order model.
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r11456 | bugman | 2010-08-10 10:33:21 +0200 (Tue, 10 Aug 2010) | 3 lines
Created a unit test for the collapse of the isotropic cone to the free rotor iso cone.
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r11457 | bugman | 2010-08-10 10:37:00 +0200 (Tue, 10 Aug 2010) | 5 lines
Bug fix for the iso cone frame order model fn populate_2nd_eigenframe_iso_cone().
A few signs were wrong in the {0,4} and {4,0} element.
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r11458 | bugman | 2010-08-10 11:15:47 +0200 (Tue, 10 Aug 2010) | 3 lines
Added 9 unit tests for the parametric restriction collapse of all frame order model compile_2nd_matrix*() fns.
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r11459 | bugman | 2010-08-10 11:57:02 +0200 (Tue, 10 Aug 2010) | 5 lines
Simplified populate_2nd_eigenframe_iso_cone() even further.
This should bring some numerical stability.
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r11460 | bugman | 2010-08-10 13:59:48 +0200 (Tue, 10 Aug 2010) | 3 lines
Fix for the test_compile_2nd_matrix_pseudo_ellipse_restriction_test3() frame order unit test.
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r11461 | bugman | 2010-08-11 00:27:59 +0200 (Wed, 11 Aug 2010) | 5 lines
Large simplifications to the equations of the pseudo-ellipse frame order model.
This significantly increases the numerical stability and allows parameters to be close to zero.
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r11462 | bugman | 2010-08-11 00:48:26 +0200 (Wed, 11 Aug 2010) | 3 lines
The tmax_pseudo_ellipse() fn now handles the zero points correctly.
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r11463 | bugman | 2010-08-11 00:59:36 +0200 (Wed, 11 Aug 2010) | 3 lines
Reactivated the test_compile_2nd_matrix_pseudo_ellipse_order() frame order unit test.
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r11464 | bugman | 2010-08-11 01:07:12 +0200 (Wed, 11 Aug 2010) | 3 lines
Modified the pseudo-ellipse frame order matrix point unit tests.
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r11465 | bugman | 2010-08-11 11:36:40 +0200 (Wed, 11 Aug 2010) | 3 lines
daeg_to_rotational_superoperator() now operates on the Kronecker product form.
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r11466 | bugman | 2010-08-11 12:01:10 +0200 (Wed, 11 Aug 2010) | 3 lines
Added 3 unit tests for reduce_alignment_tensor().
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r11467 | bugman | 2010-08-11 12:31:29 +0200 (Wed, 11 Aug 2010) | 3 lines
Another numerical simplification to tmax_pseudo_ellipse().
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r11468 | bugman | 2010-08-11 14:31:11 +0200 (Wed, 11 Aug 2010) | 5 lines
Big bug fix for the reduce_alignment_tensor() function - the frame order matrix was transposed!!!
The indices were back to front, so the non-symmetric frame order models were failing.
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r11469 | bugman | 2010-08-11 16:30:13 +0200 (Wed, 11 Aug 2010) | 11 lines
Added system tests for 5 of the frame order models.
These use synthetic alignment data (tensors) to test the model via the calc() user function. The
tests models include:
iso cone, free rotor
iso cone, free rotor (in the eigenframe)
iso cone
pseudo-ellipse, free rotor (out of frame and in the eigenframe)
pseudo-ellipse.
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r11470 | bugman | 2010-08-11 16:32:04 +0200 (Wed, 11 Aug 2010) | 3 lines
Fix for the test_pseudo_ellipse() system test.
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r11471 | bugman | 2010-08-11 17:54:04 +0200 (Wed, 11 Aug 2010) | 3 lines
Added 5 system tests checking the parametric restriction of frame order models.
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r11472 | bugman | 2010-08-11 18:37:11 +0200 (Wed, 11 Aug 2010) | 5 lines
Fixes for the calls to compile_2nd_matrix_iso_cone_torsionless() in the unit tests.
More debugging printouts have been included throughout.
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r11473 | bugman | 2010-08-11 18:37:35 +0200 (Wed, 11 Aug 2010) | 3 lines
Implemented the torsionless isotropic cone frame order model.
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r11474 | bugman | 2010-08-11 23:03:37 +0200 (Wed, 11 Aug 2010) | 5 lines
Implemented the rotor frame order matrix model.
This includes the addition of the target function and a unit test.
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r11475 | bugman | 2010-08-11 23:05:10 +0200 (Wed, 11 Aug 2010) | 5 lines
Fixes for a number of the frame order model unit tests.
The frame order matrix comparison was not correct.
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r11476 | bugman | 2010-08-11 23:06:23 +0200 (Wed, 11 Aug 2010) | 3 lines
Fix for a typo in the previous r11475 revision.
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r11477 | bugman | 2010-08-11 23:14:14 +0200 (Wed, 11 Aug 2010) | 5 lines
Made the test_compile_2nd_matrix_pseudo_ellipse_free_rotor_point2() unit test less stringent.
The matrix is not very precise.
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r11478 | bugman | 2010-08-11 23:17:42 +0200 (Wed, 11 Aug 2010) | 5 lines
Fixes for the test_compile_2nd_matrix_pseudo_ellipse_order() unit test.
The pec() function is not precise when the theta_x or theta_y cone angles are close to zero.
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r11479 | bugman | 2010-08-11 23:31:39 +0200 (Wed, 11 Aug 2010) | 3 lines
Added a system test for the torsionless pseudo-ellipse frame order model.
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r11480 | bugman | 2010-08-11 23:56:45 +0200 (Wed, 11 Aug 2010) | 3 lines
Created the free rotor frame order model.
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r11481 | bugman | 2010-08-12 00:01:48 +0200 (Thu, 12 Aug 2010) | 3 lines
Added a higher precision simulated matrix to test_compile_2nd_matrix_rotor().
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r11482 | bugman | 2010-08-12 08:57:04 +0200 (Thu, 12 Aug 2010) | 3 lines
Increased the precision of the test_model_iso_cone_free_rotor() frame order system test.
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r11483 | bugman | 2010-08-12 09:19:37 +0200 (Thu, 12 Aug 2010) | 3 lines
Fixes for all frame order system tests of the parametric restriction to the free rotor iso cone.
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r11484 | bugman | 2010-08-12 10:01:43 +0200 (Thu, 12 Aug 2010) | 3 lines
Renamed one frame order unit test and updated comments to better explain the embedded data.
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r11485 | bugman | 2010-08-12 10:46:20 +0200 (Thu, 12 Aug 2010) | 3 lines
The test_model_iso_cone_free_rotor_eigenframe() frame order system test is now functional.
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r11486 | bugman | 2010-08-12 11:10:33 +0200 (Thu, 12 Aug 2010) | 3 lines
Added 2 unit tests for the compile_2nd_matrix_free_rotor() frame order function.
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r11487 | bugman | 2010-08-12 11:32:54 +0200 (Thu, 12 Aug 2010) | 3 lines
Better support for the free rotor frame order model.
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r11488 | bugman | 2010-08-12 11:57:04 +0200 (Thu, 12 Aug 2010) | 3 lines
Added 2 system tests for the free rotor frame order model.
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r11489 | bugman | 2010-08-12 13:32:31 +0200 (Thu, 12 Aug 2010) | 3 lines
Better support for the rotor frame order model.
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r11490 | bugman | 2010-08-12 13:35:48 +0200 (Thu, 12 Aug 2010) | 3 lines
The rotor frame order model is now functional.
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r11491 | bugman | 2010-08-12 14:54:16 +0200 (Thu, 12 Aug 2010) | 3 lines
Added 2 system tests for the rotor frame order model.
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r11492 | bugman | 2010-08-12 15:20:53 +0200 (Thu, 12 Aug 2010) | 5 lines
Fix for the test_compile_2nd_matrix_rotor_point1() unit test.
The compile_2nd_matrix_rotor() function was being incorrectly called.
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r11493 | bugman | 2010-08-12 15:51:09 +0200 (Thu, 12 Aug 2010) | 3 lines
Removed the model check from frame_order.ref_domain().
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r11494 | bugman | 2010-08-12 15:52:20 +0200 (Thu, 12 Aug 2010) | 3 lines
frame_order.ref_domain() now only updates the model info if the model is set.
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r11495 | bugman | 2010-08-12 16:05:44 +0200 (Thu, 12 Aug 2010) | 3 lines
Missing relax error import.
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r11496 | bugman | 2010-08-12 16:09:24 +0200 (Thu, 12 Aug 2010) | 3 lines
The model can be overwritten by frame_order.select_model().
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r11497 | bugman | 2010-08-12 16:37:16 +0200 (Thu, 12 Aug 2010) | 3 lines
arg_check.is_int_or_int_list() can now allow for None list elements.
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r11498 | bugman | 2010-08-12 16:38:24 +0200 (Thu, 12 Aug 2010) | 5 lines
The grid_search() user function argument incs can now be a list with None elements to fix parameters.
This will only be used in the frame order optimisation for now.
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r11499 | bugman | 2010-08-12 17:00:01 +0200 (Thu, 12 Aug 2010) | 3 lines
Parameters can be fixed to the original values during the frame order grid search.
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r11500 | bugman | 2010-08-12 17:02:55 +0200 (Thu, 12 Aug 2010) | 3 lines
Added a check in the frame order grid search so that the inc list size matches the number of parameters.
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r11501 | bugman | 2010-08-12 18:11:09 +0200 (Thu, 12 Aug 2010) | 3 lines
Fix for the grid search with the isotropic cone frame order models having the 'cone_theta' parameter.
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r11502 | bugman | 2010-08-12 18:13:15 +0200 (Thu, 12 Aug 2010) | 6 lines
Fix for the free rotor isotropic grid search - the 'cone_s1' parameter has a minimum of -0.125.
The previous minimum of -0.5 was no in line with Woessner's diffusion in a cone order parameter and
was causing the grid search to fail.
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r11503 | bugman | 2010-08-12 18:14:54 +0200 (Thu, 12 Aug 2010) | 5 lines
Fixed some calls to maths_fns.order_parameters.iso_cone_S_to_theta().
The wrong function was being called by the free rotor isotropic cone model.
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r11504 | bugman | 2010-08-12 18:19:53 +0200 (Thu, 12 Aug 2010) | 5 lines
Added a catch in iso_cone_S_to_theta() for bad order parameters > 1.
Now the function will return a cone angle of zero. Simplex optimisation will set S > 1.
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r11505 | bugman | 2010-08-12 19:27:53 +0200 (Thu, 12 Aug 2010) | 5 lines
Objects placed into the relax data store structure are now stored in the XML save file.
They are also restored again with state.load().
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r11506 | bugman | 2010-08-12 19:48:38 +0200 (Thu, 12 Aug 2010) | 3 lines
Fix for the test_grid_search_argfail_inc() unit test as the inc arg can be a list of None.
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r11507 | bugman | 2010-08-12 22:58:09 +0200 (Thu, 12 Aug 2010) | 7 lines
Fix for bug #13259, the failure of model elimination in the full analysis script.
The problem was that model elimination is only performed on the current data pipe, so it should be
performed in the multi_model() method just after the optimisation of the individual model-free
models.
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r11508 | bugman | 2010-08-13 09:43:27 +0200 (Fri, 13 Aug 2010) | 5 lines
Created a common specific code model_loop() method for a single global model.
The method is stored as _model_loop_single_global().
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r11509 | bugman | 2010-08-13 09:49:18 +0200 (Fri, 13 Aug 2010) | 6 lines
Created a API common set_selected_sim() method for a single global model.
The method is called _set_selected_sim_global() and simply puts the select_sim bool list into the
cdp.
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r11510 | bugman | 2010-08-13 12:06:14 +0200 (Fri, 13 Aug 2010) | 3 lines
Implemented Monte Carlo simulations for the N-state model.
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r11511 | bugman | 2010-08-13 21:21:29 +0200 (Fri, 13 Aug 2010) | 5 lines
Added another check to iso_cone_S_to_theta() for bad order parameters.
This time the check is for order parameters less than -0.125.
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r11512 | bugman | 2010-08-13 21:29:15 +0200 (Fri, 13 Aug 2010) | 3 lines
Missing import!
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r11513 | bugman | 2010-08-15 10:54:32 +0200 (Sun, 15 Aug 2010) | 3 lines
The sign of the RDC can be inverted to correct for the negative 15N gyromagnetic ratio.
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r11514 | bugman | 2010-08-15 13:12:02 +0200 (Sun, 15 Aug 2010) | 5 lines
Better identification of the molecule end in the internal PDB reader.
HETATMs after a TER are now considered part of the same molecule, as they should be.
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r11515 | bugman | 2010-08-15 13:19:06 +0200 (Sun, 15 Aug 2010) | 3 lines
The negative gyromagnetic ratio correction flag neg_g_corr is now available in the rdc.read() user fn.
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r11516 | bugman | 2010-08-15 16:07:28 +0200 (Sun, 15 Aug 2010) | 3 lines
Fix for rdc.read() when neg_g_corr is set to True and the RDC list contains entries with None.
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r11517 | bugman | 2010-08-16 15:34:03 +0200 (Mon, 16 Aug 2010) | 3 lines
Fix for the pcs.back_calc() user function for when multiple structures are loaded.
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r11518 | bugman | 2010-08-16 18:21:20 +0200 (Mon, 16 Aug 2010) | 5 lines
Bug fix for the unpacking of results from the torsionless isotropic cone frame order model.
The optimised cone angle was being set to the order parameter in cone_s1.
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r11519 | bugman | 2010-08-16 18:26:31 +0200 (Mon, 16 Aug 2010) | 3 lines
More fixes for the torsionless isotropic cone frame order model.
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r11520 | bugman | 2010-08-16 22:10:56 +0200 (Mon, 16 Aug 2010) | 3 lines
The base contents of the relax data store are no longer saved with a call to results.write().
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r11521 | bugman | 2010-08-17 14:02:27 +0200 (Tue, 17 Aug 2010) | 3 lines
Bug fix for the frame_order.pivot() user function - it is now functional.
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r11522 | bugman | 2010-08-17 16:18:19 +0200 (Tue, 17 Aug 2010) | 3 lines
Switched the names of the Pseudo_elliptic and Pseudo_elliptic2 classes.
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r11523 | bugman | 2010-08-17 16:54:55 +0200 (Tue, 17 Aug 2010) | 3 lines
Modified create_cone_pdb() to accept a pre-made structural object and to create a file only when asked.
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r11524 | bugman | 2010-08-17 16:55:48 +0200 (Tue, 17 Aug 2010) | 3 lines
Modified the pymol.cone_pdb() user function to handle x, y, and z-axes.
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r11525 | bugman | 2010-08-17 17:21:49 +0200 (Tue, 17 Aug 2010) | 3 lines
The start_res arg to create_cone_pdb() is now actually the number of the starting residue of the cone.
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r11526 | bugman | 2010-08-17 17:22:21 +0200 (Tue, 17 Aug 2010) | 3 lines
Rewrote frame_order.cone_pdb() to handle all of the frame order models.
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r11527 | bugman | 2010-08-17 17:45:08 +0200 (Tue, 17 Aug 2010) | 5 lines
Created the frame_order.domain_to_pdb() user function to associated PDB files with domains.
This will be used to rotated the moving domain to the average position within pymol.
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r11528 | bugman | 2010-08-17 17:56:50 +0200 (Tue, 17 Aug 2010) | 5 lines
Modified frame_order.domain_to_pdb() to remove the file ending if given.
This allows the structure to be rotated in pymol.
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r11529 | bugman | 2010-08-17 18:40:03 +0200 (Tue, 17 Aug 2010) | 3 lines
pymol.cone_pdb() is now rotating the moving domain to the average position for the frame order theory.
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r11530 | bugman | 2010-08-18 08:38:35 +0200 (Wed, 18 Aug 2010) | 5 lines
Fix for the average domain rotation in pymol.cone_pdb().
The pymol angle should be degrees, and the rotation is passive not active.
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r11531 | bugman | 2010-08-18 08:45:45 +0200 (Wed, 18 Aug 2010) | 3 lines
Fix for the frame_order.cone_pdb() user function - the cone is already in the PDB frame, no rotation required.
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r11532 | bugman | 2010-08-18 16:00:01 +0200 (Wed, 18 Aug 2010) | 3 lines
Added some transparency to the cone in pymol.cone_pdb().
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r11533 | bugman | 2010-08-18 16:01:10 +0200 (Wed, 18 Aug 2010) | 3 lines
The negative cones and z-axes are now not created for the pseudo-ellipses in frame_order.cone_pdb().
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r11534 | bugman | 2010-09-06 11:04:48 +0200 (Mon, 06 Sep 2010) | 3 lines
The structure.load_spins() user function now gives a RelaxWarning if no data could be found.
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