Author: bugman
Date: Fri Nov 27 12:11:06 2009
New Revision: 9993
URL: http://svn.gna.org/viewcvs/relax?rev=9993&view=rev
Log:
Merged revisions
9454,9457-9526,9528-9658,9696,9700,9706,9709,9747,9794,9799-9800,9829,9831,9834,9871-9875,9891-9986
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r9454 | bugman | 2009-09-03 15:23:45 +0200 (Thu, 03 Sep 2009) | 3 lines
Updated the non-dangerous Python3k update command.
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r9457 | bugman | 2009-09-03 17:53:41 +0200 (Thu, 03 Sep 2009) | 3 lines
Created a sub-directory for frame order test scripts.
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r9458 | bugman | 2009-09-03 18:18:51 +0200 (Thu, 03 Sep 2009) | 3 lines
Shifted the rigid frame order system test into the sub-directory.
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r9459 | bugman | 2009-09-03 18:31:23 +0200 (Thu, 03 Sep 2009) | 3 lines
Added another rigid frame order system test.
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r9460 | bugman | 2009-09-03 18:32:10 +0200 (Thu, 03 Sep 2009) | 3 lines
Renamed a frame order system test.
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r9461 | bugman | 2009-09-03 19:05:02 +0200 (Thu, 03 Sep 2009) | 3 lines
Specific architecture and optimisation details are now printed if the frame
order system tests fail.
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r9462 | bugman | 2009-09-03 19:17:08 +0200 (Thu, 03 Sep 2009) | 3 lines
Fix for the new frame order system test - the results file goes to devnull.
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r9463 | bugman | 2009-09-03 19:25:01 +0200 (Thu, 03 Sep 2009) | 3 lines
The beta angle for the tensor rotations is now folded to be between 0 and
pi.
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r9464 | bugman | 2009-09-04 10:24:52 +0200 (Fri, 04 Sep 2009) | 5 lines
Added a function for converting the frame order matrix to the rotational
superoperator.
The function is called daeg_to_rotational_superoperator().
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r9465 | bugman | 2009-09-04 11:21:28 +0200 (Fri, 04 Sep 2009) | 5 lines
Fix for the new daeg_to_rotational_superoperator() function.
The frame order matrix shape is now restored.
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r9466 | bugman | 2009-09-04 16:12:31 +0200 (Fri, 04 Sep 2009) | 5 lines
The print_frame_order_2nd_degree() function now accepts the epsilon arg.
This allows zero to be defined differently making the printout nicer.
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r9467 | bugman | 2009-09-07 19:28:57 +0200 (Mon, 07 Sep 2009) | 6 lines
Improved and expanded the output of the print_frame_order_2nd_degree()
function.
The print out can now be in integer form, dots can replace zeros, and
commas between elements are
now optional. Matrix forms are also converted to array forms.
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r9468 | bugman | 2009-09-07 19:31:49 +0200 (Mon, 07 Sep 2009) | 5 lines
Fix for the __update_model() method.
The theta_axis, phi_axis, and theta_cone params were not being added to the
parameter array!
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r9469 | bugman | 2009-09-08 11:14:08 +0200 (Tue, 08 Sep 2009) | 5 lines
Added some unit tests for the R_euler_zyz() function.
This tests some basic axis rotations.
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r9470 | bugman | 2009-09-08 11:26:37 +0200 (Tue, 08 Sep 2009) | 3 lines
Fixes for the R_euler_zyz() unit tests.
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r9471 | bugman | 2009-09-08 11:27:23 +0200 (Tue, 08 Sep 2009) | 5 lines
Fix for the R_euler_zyz() function.
The rotations were being performed in the opposite direction?!?
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r9472 | bugman | 2009-09-08 14:38:05 +0200 (Tue, 08 Sep 2009) | 3 lines
Removed the incorrect part of the R_euler_zyz() docstring.
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r9473 | bugman | 2009-09-08 14:40:37 +0200 (Tue, 08 Sep 2009) | 5 lines
Bug fix for the R_to_euler_zyz() function.
This matches the important bug fix in the R_euler_zyz() function.
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r9474 | bugman | 2009-09-08 14:43:47 +0200 (Tue, 08 Sep 2009) | 5 lines
Fixes for the test_func3() and test_func4() unit tests.
The rotations were backwards because of the R_euler_zyz() fix!
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r9475 | bugman | 2009-09-08 15:11:17 +0200 (Tue, 08 Sep 2009) | 6 lines
Fix to the frame order system tests.
This corresponds to the fixes in R_euler_zyz() where the rotation matrices
were in the left-handed
universe and hence the rotation was back to front.
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r9476 | bugman | 2009-09-08 16:40:16 +0200 (Tue, 08 Sep 2009) | 3 lines
Created 3 unit tests of the maths_fns.rotation_matrix.quaternion_to_R()
function.
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r9477 | bugman | 2009-09-08 17:07:06 +0200 (Tue, 08 Sep 2009) | 5 lines
Created 3 unit tests of the maths_fns.rotation_matrix.R_axis_angle()
function.
These are almost identical to those of quaternion_to_R().
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r9478 | bugman | 2009-09-08 17:42:48 +0200 (Tue, 08 Sep 2009) | 3 lines
Added a unit test for maths_fns.rotation_matrix.R_to_axis_angle() using R =
I.
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r9479 | bugman | 2009-09-08 17:43:36 +0200 (Tue, 08 Sep 2009) | 5 lines
Bug fix for R_to_axis_angle().
All vector elements were NaN when the angle is 0. Now the zero vector is
not normalised by zero.
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r9480 | bugman | 2009-09-08 17:47:59 +0200 (Tue, 08 Sep 2009) | 3 lines
Added another unit test for maths_fns.rotation_matrix.R_axis_angle().
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r9481 | bugman | 2009-09-08 18:20:08 +0200 (Tue, 08 Sep 2009) | 5 lines
Function renaming and argument order changes in the
maths_fns.rotation_matrix module.
The naming scheme is now more logical (as well as the argument order).
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r9482 | bugman | 2009-09-08 18:27:50 +0200 (Tue, 08 Sep 2009) | 3 lines
Alphabetical reordering of functions.
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r9483 | bugman | 2009-09-08 18:52:54 +0200 (Tue, 08 Sep 2009) | 3 lines
Huge simplifications to the unit tests for the maths_fns.rotation_matrix
package.
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r9484 | bugman | 2009-09-08 19:17:29 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.axis_angle_to_quaternion() function.
This is accompanied by 2 unit tests.
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r9485 | bugman | 2009-09-08 19:51:14 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.quaternion_to_axis_angle() function.
This is accompanied by 2 unit tests.
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r9486 | bugman | 2009-09-08 20:20:34 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.R_to_quaternion() function.
This is accompanied by 2 unit tests.
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r9487 | bugman | 2009-09-08 21:07:41 +0200 (Tue, 08 Sep 2009) | 13 lines
Added a unit test to bounce around all the conversion functions in
maths_fns.rotation_matrix.
This bounces through:
1) euler_zyz_to_R().
2) R_to_axis_angle().
3) axis_angle_to_quaternion().
4) quaternion_to_axis_angle().
5) axis_angle_to_R().
6) R_to_quaternion().
7) quaternion_to_R().
8) R_to_euler_zyz().
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r9488 | bugman | 2009-09-09 16:04:40 +0200 (Wed, 09 Sep 2009) | 5 lines
Added a unit test to check if all the
maths_fns.kronecker_product.transpose_*() functions revert.
Calling the function twice should return the matrix to the original state.
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r9489 | bugman | 2009-09-10 14:33:33 +0200 (Thu, 10 Sep 2009) | 3 lines
Renamed the data pipes system tests module.
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r9490 | bugman | 2009-09-10 16:51:39 +0200 (Thu, 10 Sep 2009) | 3 lines
Wrote a system test for the writing and re-reading of data pipes.
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r9491 | bugman | 2009-09-10 16:53:06 +0200 (Thu, 10 Sep 2009) | 3 lines
Shifted the valid types private function variable into a module variable.
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r9492 | bugman | 2009-09-10 16:54:55 +0200 (Thu, 10 Sep 2009) | 3 lines
The test_write_read_pipes() system test is now using the VALID_TYPES module
variable to get all pipes.
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r9493 | bugman | 2009-09-10 17:01:39 +0200 (Thu, 10 Sep 2009) | 3 lines
Deleted the __init__() class methods as these were empty, and shifted the
docstring to that of the class.
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r9494 | bugman | 2009-09-10 17:02:22 +0200 (Thu, 10 Sep 2009) | 3 lines
Removed an empty line.
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r9495 | bugman | 2009-09-10 17:20:21 +0200 (Thu, 10 Sep 2009) | 5 lines
Added a very basic, and completely empty module and class for SRLS analysis.
This is to allow the data pipe to be created.
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r9496 | bugman | 2009-09-10 17:37:16 +0200 (Thu, 10 Sep 2009) | 3 lines
Updated the specific_fns module __all__ list for the SRLS module.
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r9497 | bugman | 2009-09-10 17:38:20 +0200 (Thu, 10 Sep 2009) | 5 lines
Shifted the test_write_read_pipes() system test to the 'state' test module.
The program state is now being saved as the results file is for just one
data pipe.
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r9498 | bugman | 2009-09-10 18:07:22 +0200 (Thu, 10 Sep 2009) | 3 lines
A few fixes for the test_write_read_pipes() system test.
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r9499 | bugman | 2009-09-10 18:32:31 +0200 (Thu, 10 Sep 2009) | 7 lines
Redesign of the relax state loading for adding support for a XML formatted
state file.
Half of the load_state() is now in load_pickle(), and a new function
load_xml() added.
The determine_format() function will tell if the file is a pickle or XML
file, and then
load_pickle() will run the appropriate loading function.
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r9500 | bugman | 2009-09-10 18:36:40 +0200 (Thu, 10 Sep 2009) | 5 lines
Added the pickle flag to save_state().
This defaults to True to prevent relax failures during the XML file
implementation.
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r9501 | bugman | 2009-09-10 19:01:25 +0200 (Thu, 10 Sep 2009) | 5 lines
The save_state() function now calls the relax data store to_xml() method.
This method is currently only for one data pipe, and is used by the results
writing user function.
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r9502 | bugman | 2009-09-10 19:24:30 +0200 (Thu, 10 Sep 2009) | 6 lines
The relax data store to_xml() method now can add all data pipes to the XML
file (or a subset).
The results.write() method now asks to_xml() for just the current pipe to
be stored, whereas
state.save() supplies no 'pipes' argument to have all pipes stored.
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r9503 | bugman | 2009-09-10 19:26:22 +0200 (Thu, 10 Sep 2009) | 5 lines
Shifted the results.write() force arg to the end.
Bool args should be last!
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r9504 | bugman | 2009-09-10 19:37:33 +0200 (Thu, 10 Sep 2009) | 3 lines
Removed trailing whitespace.
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r9505 | bugman | 2009-09-10 19:56:32 +0200 (Thu, 10 Sep 2009) | 3 lines
Updates to the load_xml() function. This now does something!
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r9506 | bugman | 2009-09-10 20:04:05 +0200 (Thu, 10 Sep 2009) | 3 lines
Created the relax data store is_empty() method.
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r9507 | bugman | 2009-09-11 10:06:05 +0200 (Fri, 11 Sep 2009) | 6 lines
Added the pickle arg to state.save().
This allows the relax state - the contents of the relax data store - to
either be saved as XML or as
a pickled object.
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r9508 | bugman | 2009-09-11 10:07:11 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a warning to the state.save() user function about the pickle format
compatibility.
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r9509 | bugman | 2009-09-11 10:16:04 +0200 (Fri, 11 Sep 2009) | 6 lines
Absorbed the load_xml() function into load_state().
After shifting the data store check to load_state() for all formats, the
function only had one
statement.
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r9510 | bugman | 2009-09-11 10:29:08 +0200 (Fri, 11 Sep 2009) | 3 lines
Docstring clarification of the dir arg.
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r9511 | bugman | 2009-09-11 11:12:30 +0200 (Fri, 11 Sep 2009) | 3 lines
Updated the relax data store from_xml() method for support of the loading
of the XML state file.
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r9512 | bugman | 2009-09-11 11:31:44 +0200 (Fri, 11 Sep 2009) | 5 lines
Added the force flag to the state.load() user function.
When True, this causes the relax data store to be reset prior to state
loading.
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r9513 | bugman | 2009-09-11 11:36:02 +0200 (Fri, 11 Sep 2009) | 5 lines
Duplicated the test_state() system test into test_state_pickle() and
test_state_xml().
This tests both formats.
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r9514 | bugman | 2009-09-11 11:39:53 +0200 (Fri, 11 Sep 2009) | 6 lines
Fixes for load_pickle().
The ds.__reset__() call has been removed because of redundancy and the new
ds.is_empty() has been
blacklisted.
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r9515 | bugman | 2009-09-11 11:48:17 +0200 (Fri, 11 Sep 2009) | 3 lines
Changed the default save state to XML.
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r9516 | bugman | 2009-09-11 13:43:34 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a dir arg to a state.save() call in test_state_pickle().
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r9517 | bugman | 2009-09-11 13:52:36 +0200 (Fri, 11 Sep 2009) | 5 lines
Renamed the state.load() and state.save() directory argument from dir_name
to dir.
This is to bring it in line with the rest of relax.
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r9518 | bugman | 2009-09-11 14:44:41 +0200 (Fri, 11 Sep 2009) | 3 lines
Fixes for print_frame_order_2nd_degree() for when NaN is encountered.
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r9519 | bugman | 2009-09-11 14:46:04 +0200 (Fri, 11 Sep 2009) | 5 lines
Fix for the print_frame_order_2nd_degree().
The NaN fix was partly incorrect.
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r9520 | bugman | 2009-09-11 15:04:15 +0200 (Fri, 11 Sep 2009) | 3 lines
Made the integer printout 4 char wide.
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r9521 | bugman | 2009-09-11 15:31:42 +0200 (Fri, 11 Sep 2009) | 5 lines
Bug fix for the compile_2nd_matrix_iso_cone() function.
The T23 and not T14 transpose should be performed!
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r9522 | bugman | 2009-09-11 15:59:04 +0200 (Fri, 11 Sep 2009) | 2 lines
Reordered the relax debugging save state so that the format is
yyyymmdd_hhmmss rather than yyyyddmm_hhmmss.
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r9523 | bugman | 2009-09-11 17:55:23 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a check for the setting of the domain the tensor corresponds to.
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r9524 | bugman | 2009-09-14 13:59:44 +0200 (Mon, 14 Sep 2009) | 3 lines
Renamed the frame order target function module.
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r9525 | bugman | 2009-09-14 14:07:40 +0200 (Mon, 14 Sep 2009) | 3 lines
Bug fix, the func_iso_cone_elements() method was been replaced with
func_iso_cone().
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r9526 | bugman | 2009-09-14 14:23:10 +0200 (Mon, 14 Sep 2009) | 5 lines
Fix for r9525.
The func_iso_cone() was now not being set up.
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r9528 | bugman | 2009-09-18 14:04:52 +0200 (Fri, 18 Sep 2009) | 3 lines
Created the euler_zyz_to_axis_angle() conversion function.
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r9529 | bugman | 2009-09-18 14:28:37 +0200 (Fri, 18 Sep 2009) | 6 lines
Created axis_angle_to_euler_zyz().
The test_euler_zyz_to_euler_zyz() unit test now checks both
euler_zyz_to_axis_angle() and
axis_angle_to_euler_zyz().
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r9530 | bugman | 2009-09-18 17:38:27 +0200 (Fri, 18 Sep 2009) | 12 lines
Final 1.3 line redesigns of the relax_io module.
The log() and tee() functions have been renamed to io_streams_log() and
io_streams_tee(), and the
old IO.logging_off() class method has been converted to the
io_streams_restore() function. The
io_streams_restore() function is also differently designed, using the true
original IO streams
(sys.__stdin__, sys.__stdout__, and sys.__stderr__).
The IO.delete() method has been converted to a module function.
The IO class has been eliminated.
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r9531 | bugman | 2009-09-18 18:19:26 +0200 (Fri, 18 Sep 2009) | 6 lines
Created a module for alignment tensor related system tests.
Only the single test test_to_and_from_xml() has been created so far. This
checks the dumping and
reloading of alignment tensors into an XML file.
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r9532 | bugman | 2009-09-18 18:26:40 +0200 (Fri, 18 Sep 2009) | 5 lines
Bug fix for the delete function.
The function was failing if the file was missing!
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r9533 | bugman | 2009-09-18 18:28:05 +0200 (Fri, 18 Sep 2009) | 6 lines
Bug fix for the test suite.
The temporary files were not always deleted if a .bz2 extension was added!
Now relax_io.delete() is
being called to fix this.
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r9534 | bugman | 2009-09-18 18:28:56 +0200 (Fri, 18 Sep 2009) | 3 lines
Reactivated the system tests turned off in r9533.
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r9535 | bugman | 2009-09-18 18:32:41 +0200 (Fri, 18 Sep 2009) | 5 lines
Fix for the data_names() method for when no model has been setup.
This allows the frame order data pipe to be written out prior to the model
setup.
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r9536 | bugman | 2009-09-18 18:43:02 +0200 (Fri, 18 Sep 2009) | 3 lines
Expansion of the test_to_and_from_xml() system test to check more data
structures.
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r9537 | bugman | 2009-09-18 18:47:49 +0200 (Fri, 18 Sep 2009) | 3 lines
The data structures of the AlignTensorList class are now packed into the
XML file.
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r9538 | bugman | 2009-09-18 19:11:30 +0200 (Fri, 18 Sep 2009) | 3 lines
Added the blacklist arg to xml_to_object().
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r9539 | bugman | 2009-09-18 19:15:06 +0200 (Fri, 18 Sep 2009) | 6 lines
Reverted r9538. The wrong file was committed!
The command used was:
svn merge -r9538:9537 .
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r9540 | bugman | 2009-09-18 19:15:40 +0200 (Fri, 18 Sep 2009) | 3 lines
Try again: Added the blacklist arg to xml_to_object().
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r9541 | bugman | 2009-09-18 19:18:14 +0200 (Fri, 18 Sep 2009) | 3 lines
Bug fix, the blacklist args now default to [].
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r9542 | bugman | 2009-09-18 19:19:39 +0200 (Fri, 18 Sep 2009) | 3 lines
Fix for the test_to_and_from_xml() check of the 'reduction' data structure.
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r9543 | bugman | 2009-09-18 19:20:15 +0200 (Fri, 18 Sep 2009) | 3 lines
The 'reduction' data structure is now properly created from the XML file.
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r9544 | bugman | 2009-09-21 13:25:14 +0200 (Mon, 21 Sep 2009) | 6 lines
Modified the frame order grid search.
The angle end points are now avoided (as they are the same as the start
points) and the beta Euler
angle increments are halved, as the search is half of that of alpha and
gamma (0 to pi).
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r9545 | bugman | 2009-09-21 13:53:39 +0200 (Mon, 21 Sep 2009) | 5 lines
Removed the end point of the cone angle from the grid search.
This is unrestricted motion, so is physically not possible.
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r9546 | bugman | 2009-09-21 14:03:55 +0200 (Mon, 21 Sep 2009) | 5 lines
Also halved the number of theta polar angle increments in the frame order
grid search.
This is to match the cone axis azimuthal angle phi.
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r9547 | bugman | 2009-09-21 16:20:58 +0200 (Mon, 21 Sep 2009) | 6 lines
Fix for the missing PDB file error.
The extension '.pdb' was being added to the end so if the missing file
'1F3Y.pdb' was specified,
the RelaxError would say that '1F3Y.pdb.pdb' was missing.
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r9548 | bugman | 2009-09-21 18:44:14 +0200 (Mon, 21 Sep 2009) | 7 lines
Complete redesign of the grid_search() method.
The grid ops structure is no longer created, rather the grid is directly
created to be passed to the
grid search algorithm. The __grid_row() method has been added to create
the row of the grid
corresponding to a certain parameter.
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r9549 | bugman | 2009-09-21 19:37:50 +0200 (Mon, 21 Sep 2009) | 3 lines
Implemented the acos grid search for angular parameters of the frame order
theories.
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r9550 | bugman | 2009-09-21 19:39:41 +0200 (Mon, 21 Sep 2009) | 3 lines
Fixed the call to the grid search.
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r9551 | bugman | 2009-09-21 20:25:52 +0200 (Mon, 21 Sep 2009) | 5 lines
Fix for the __unpack_opt_results() for the new direct calling of the grid
search.
The returned results are different.
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r9552 | bugman | 2009-09-22 11:50:31 +0200 (Tue, 22 Sep 2009) | 3 lines
Added a false, deliberately broken Xplor line to test the parsing of Xplor
NOE files.
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r9553 | bugman | 2009-09-22 12:04:37 +0200 (Tue, 22 Sep 2009) | 3 lines
Bug fix for the reading of Xplor NOE data when a line starts with '#'.
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r9554 | bugman | 2009-09-22 13:15:40 +0200 (Tue, 22 Sep 2009) | 5 lines
Fix for the test_opt_rigid_rand_rot() system test.
The changes to the frame order grid search broke this test.
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[... 1695 lines stripped ...]
r9993 - in /branches/cst: ./ data/ docs/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ sample_scripts/ ...