Author: bugman
Date: Wed Nov 19 19:28:11 2014
New Revision: 26640
URL: http://svn.gna.org/viewcvs/relax?rev=26640&view=rev
Log:
Merged revisions 26601-26609,26611-26639 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26601 | bugman | 2014-11-17 17:12:44 +0100 (Mon, 17 Nov 2014) | 5 lines
Implemented the lib.geometry.vectors.vector_angle_atan2() function.
This is for calculating the inter-vector angle using the more numerically
stable atan2() formula.
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r26602 | bugman | 2014-11-17 17:16:23 +0100 (Mon, 17 Nov 2014) | 6 lines
Implemented the lib.geometry.vectors.vector_angle_acos() function.
This is used to calculate the inter-vector angle using the arccos of the
dot product formula. The
function has been introduced into the relax library as the calculation is
repeated throughout relax.
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r26603 | bugman | 2014-11-17 17:16:36 +0100 (Mon, 17 Nov 2014) | 3 lines
Missing import.
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r26604 | bugman | 2014-11-17 17:23:30 +0100 (Mon, 17 Nov 2014) | 6 lines
Renamed vector_angle() to vector_angle_normal() in the lib.geometry.vectors
module.
This is to standardise the naming as there are now the standard vector
angle formula implemented as
the vector_angle_acos() and vector_angle_atan2() functions.
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r26605 | bugman | 2014-11-17 17:29:14 +0100 (Mon, 17 Nov 2014) | 6 lines
Added 6 unit tests for the lib.geometry.vectors.vector_angle_acos()
function.
These are similar to those of the vector_angle_normal() function but
unsigned angles are checked
for.
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r26606 | bugman | 2014-11-17 17:30:43 +0100 (Mon, 17 Nov 2014) | 3 lines
Created 6 unit tests for the lib.geometry.vectors.vector_angle_atan2()
function.
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r26607 | bugman | 2014-11-17 18:13:38 +0100 (Mon, 17 Nov 2014) | 5 lines
Created a script and log file to demonstrate differences between alignment
tensor basis sets.
This shows that the inter-tensor angles and condition numbers are dependent
on the basis set used.
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r26608 | bugman | 2014-11-17 18:20:05 +0100 (Mon, 17 Nov 2014) | 3 lines
Improved the printouts from the align_tensor.svd user function by including
the basis set text.
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r26609 | bugman | 2014-11-17 18:22:18 +0100 (Mon, 17 Nov 2014) | 3 lines
Updated the log file for comparing different alignment tensor basis sets
for align_tensor.svd changes.
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r26611 | bugman | 2014-11-18 11:54:21 +0100 (Tue, 18 Nov 2014) | 7 lines
Implemented a new default basis set for the align_tensor.matrix_angles user
function.
This is uses standard definition of the inter-matrix angle using the
Euclidean inner product of the
two matrices divided by the product of the Frobenius norm of each matrix.
As this is a linear map,
it should produce the most correct definition of inter-tensor angles.
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r26612 | bugman | 2014-11-18 13:46:26 +0100 (Tue, 18 Nov 2014) | 3 lines
Improvements to the description of the align_tensor.matrix_angles user
function.
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r26613 | bugman | 2014-11-18 14:08:58 +0100 (Tue, 18 Nov 2014) | 5 lines
Import fix for the frame order CaM system test base script.
The vector_angle() function of the lib.geometry.vectors module is now
called vector_angle_normal().
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r26614 | bugman | 2014-11-18 14:33:00 +0100 (Tue, 18 Nov 2014) | 7 lines
Updated the test_matrix_angles_identity() unit test for
pipe_control.align_tensor.matrix_angles().
This is the test in the _prompt.test_align_tensor.Test_align_tensor module.
The basis set has been
set back to the now non-default value of 0, and the value checks have been
converted from
assertEqual() to assertAlmostEqual() to allow for small truncation errors.
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r26615 | bugman | 2014-11-18 15:12:41 +0100 (Tue, 18 Nov 2014) | 7 lines
Conversion of the basis_set argument for the align_tensor.matrix_angles
user function.
The argument is now a string that accepts the values of 'matrix', 'unitary
5D', and 'geometric 5D'
to select between the different matrix angles techniques. This has been
updated in the test suite
as well.
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r26616 | bugman | 2014-11-18 15:14:45 +0100 (Tue, 18 Nov 2014) | 5 lines
Added a check for the values of the basis_set argument.
This is to the align_tensor.matrix_angles user function backend.
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r26617 | bugman | 2014-11-18 15:30:36 +0100 (Tue, 18 Nov 2014) | 3 lines
Printout improvements clarifying the align_tensor.matrix_angles user
function.
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r26618 | bugman | 2014-11-18 17:22:02 +0100 (Tue, 18 Nov 2014) | 6 lines
Conversion of the basis_set argument for the align_tensor.svd user function.
The argument is now a string that accepts the values of 'unitary 9D',
'unitary 5D', and 'geometric
5D' to select between the different SVD matrices. This has been updated in
the test suite as well.
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r26619 | bugman | 2014-11-18 17:23:53 +0100 (Tue, 18 Nov 2014) | 6 lines
Expanded the N_state_model.test_5_state_xz system test.
This now covers the new 'unitary 9D' basis set for the align_tensor.svd
user function and the new
'matrix' basis set for the align_tensor.matrix_angles user function.
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r26620 | bugman | 2014-11-18 17:50:23 +0100 (Tue, 18 Nov 2014) | 11 lines
Expansion of the align_tensor.matrix_angles user function.
The new basis set 'unitary 9D' has been introduced. This creates vectors
as {Sxx, Sxy, Sxz, Syx,
Syy, Syz, Szx, Szy, Szz} and computes the inter-vector angles. These match
the 'matrix' basis set
whereby the Euclidean inner product divided by the Frobenius norms is used
to calculate the
inter-tensor angles.
In addition, the user function documentation and printouts have been
improved. And the backend code
has been simplified.
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r26621 | bugman | 2014-11-18 18:05:29 +0100 (Tue, 18 Nov 2014) | 6 lines
Updated the script and log file for demonstrating differences between
alignment tensor basis sets.
This now handles the changes to the basis_set arguments used in the
align_tensor.matrix_angles and
align_tensor.svd user functions, and includes the new basis sets.
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r26622 | bugman | 2014-11-19 16:01:53 +0100 (Wed, 19 Nov 2014) | 14 lines
Added the irreducible tensor notation of {A-2, A-1, A0, A1, A2} to the
alignment tensor object.
This follows from the definition of Sass et al, J. Am. Chem. Soc. 1999,
121, 2047-2055,
http://dx.doi.org/10.1021/ja983887w.
The equations of (2) were converted using Gaussian elimination to obtain a
reduced row echelon form,
so that the equations in terms of {A-2, A-1, A0, A1, A2} were derived.
These have been coded into
the alignment tensor object calc_Am2, calc_Am1, calc_A0, calc_A1 and
calc_A2 methods respectively,
and the values can be obtained by accessing the Am2, Am1, A0, A1, and A2
objects.
To check that the implementation is correct, a unit test has been created
to compare the calculated
values with those determined using Pales.
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r26623 | bugman | 2014-11-19 16:03:39 +0100 (Wed, 19 Nov 2014) | 3 lines
Expanded the unit test of the alignment tensor {A-2, A-1, A0, A1, A2}
parameters to cover all values.
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r26624 | bugman | 2014-11-19 16:20:53 +0100 (Wed, 19 Nov 2014) | 7 lines
Created functions in the relax library for calculating the inter-vector
angle for complex vectors.
This is in the lib.geometry.vectors module. The function
vector_angle_complex_conjugate() has been
created to calculate the angle between two complex vectors. This uses the
new auxiliary function
complex_inner_product() to calculate <v1|v2>.
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r26625 | bugman | 2014-11-19 16:40:12 +0100 (Wed, 19 Nov 2014) | 6 lines
Added the 'irreducible 5D' basis set option to the
align_tensor.matrix_angles user function.
This is for the inter-tensor vector angle for the irreducible 5D basis set
{S-2, S-1, S0, S1, S2}.
Its results match that of the standard tensor angle as well as the 'unitary
9D' basis sets.
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r26626 | bugman | 2014-11-19 17:29:26 +0100 (Wed, 19 Nov 2014) | 6 lines
Added the 'irreducible 5D' basis set option to the align_tensor.svd user
function.
This is for the inter-tensor vector angle for the irreducible 5D basis set
{A-2, A-1, A0, A1, A2}.
Its results match that of the 'unitary 9D' basis set.
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r26627 | bugman | 2014-11-19 17:33:51 +0100 (Wed, 19 Nov 2014) | 6 lines
Editing of the description for the 'irreducible 5D' alignment tensor basis
set.
This is for the align_tensor.matrix_angles and align_tensor.svd user
functions. All Sm element have
been converted to Am.
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r26628 | bugman | 2014-11-19 17:44:46 +0100 (Wed, 19 Nov 2014) | 3 lines
Editing of the description for the align_tensor.matrix_angles user function.
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r26629 | bugman | 2014-11-19 17:50:42 +0100 (Wed, 19 Nov 2014) | 3 lines
Editing of the align_tensor.svd user function description.
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r26630 | bugman | 2014-11-19 18:01:26 +0100 (Wed, 19 Nov 2014) | 6 lines
Updated the script and log file for demonstrating differences between
alignment tensor basis sets.
The 'irreducible 5D' basis set in now used for both the
align_tensor.matrix_angles and
align_tensor.svd user functions.
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r26631 | bugman | 2014-11-19 18:08:18 +0100 (Wed, 19 Nov 2014) | 3 lines
Fix for a spelling mistake in the align_tensor.matrix_angles user function
printouts.
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r26632 | bugman | 2014-11-19 18:21:50 +0100 (Wed, 19 Nov 2014) | 3 lines
Small fix for the align_tensor.matrix_angles user function documentation.
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r26633 | bugman | 2014-11-19 18:27:28 +0100 (Wed, 19 Nov 2014) | 6 lines
Expanded the N_state_model.test_5_state_xz system test for more alignment
tensor basis sets.
The align_tensor.matrix_angles and align_tensor.svd user functions are now
being called with the
additional 'irreducible 5D', and 'unitary 9D' basis sets, to make sure
these work correctly.
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r26634 | bugman | 2014-11-19 18:30:28 +0100 (Wed, 19 Nov 2014) | 3 lines
Trailing whitespace removal.
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r26635 | bugman | 2014-11-19 18:40:28 +0100 (Wed, 19 Nov 2014) | 7 lines
Created the Align_tensor.test_align_tensor_matrix_angles system test.
This is to check the angles calculated by the align_tensor.matrix_angles
user function. As there
are no external references, this essentially fixes the angles to the
currently calculated values to
catch any accidental changes in the future.
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r26636 | bugman | 2014-11-19 18:46:44 +0100 (Wed, 19 Nov 2014) | 7 lines
Created the Align_tensor.test_align_tensor_svd system test.
This is to check the angles calculated by the align_tensor.svd user
function. As there are no
external references, this essentially fixes the singular values and
condition numbers to the
currently calculated values to catch any accidental changes in the future.
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r26637 | bugman | 2014-11-19 18:57:53 +0100 (Wed, 19 Nov 2014) | 5 lines
Added the angle_units and precision arguments to the
align_tensor.matrix_angles user function.
This allows either degrees or radians to be output, and the number of
decimal points to be specified.
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r26638 | bugman | 2014-11-19 18:59:46 +0100 (Wed, 19 Nov 2014) | 3 lines
Fixes for the proportions of the align_tensor.matrix_angle user function
GUI wizard.
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r26639 | bugman | 2014-11-19 19:04:35 +0100 (Wed, 19 Nov 2014) | 6 lines
Added the precision argument to the align_tensor.matrix_angles user
function.
This allows the number of decimal points for the singular values and
condition number to be
specified.
........
Added:
branches/frame_order_cleanup/test_suite/shared_data/align_data/basis_sets/
- copied from r26639,
trunk/test_suite/shared_data/align_data/basis_sets/
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/data_store/align_tensor.py
branches/frame_order_cleanup/lib/geometry/vectors.py
branches/frame_order_cleanup/pipe_control/align_tensor.py
branches/frame_order_cleanup/test_suite/system_tests/align_tensor.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/5_state_xz.py
branches/frame_order_cleanup/test_suite/unit_tests/_data_store/test_align_tensor.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_geometry/test_vectors.py
branches/frame_order_cleanup/test_suite/unit_tests/_prompt/test_align_tensor.py
branches/frame_order_cleanup/test_suite/unit_tests/align_tensor_testing_base.py
branches/frame_order_cleanup/user_functions/align_tensor.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/data_store/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/data_store/align_tensor.py?rev=26640&r1=26639&r2=26640&view=diff
Modified: branches/frame_order_cleanup/lib/geometry/vectors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/geometry/vectors.py?rev=26640&r1=26639&r2=26640&view=diff
Modified: branches/frame_order_cleanup/pipe_control/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/align_tensor.py?rev=26640&r1=26639&r2=26640&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/align_tensor.py?rev=26640&r1=26639&r2=26640&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=26640&r1=26639&r2=26640&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/5_state_xz.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/5_state_xz.py?rev=26640&r1=26639&r2=26640&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_data_store/test_align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_data_store/test_align_tensor.py?rev=26640&r1=26639&r2=26640&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_geometry/test_vectors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_lib/_geometry/test_vectors.py?rev=26640&r1=26639&r2=26640&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_prompt/test_align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_prompt/test_align_tensor.py?rev=26640&r1=26639&r2=26640&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/align_tensor_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/align_tensor_testing_base.py?rev=26640&r1=26639&r2=26640&view=diff
Modified: branches/frame_order_cleanup/user_functions/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/align_tensor.py?rev=26640&r1=26639&r2=26640&view=diff
r26640 - in /branches/frame_order_cleanup: ./ data_store/ lib/geometry/ pipe_control/ test_suite/shared_data/align_data/basi...