Author: bugman
Date: Mon Jun 16 11:05:28 2014
New Revision: 23970
URL: http://svn.gna.org/viewcvs/relax?rev=23970view=rev
Log:
Small speed ups for all of the frame order models in the quasi-random numerical
PCS integration.
These changes result in an ~10% speed up. Testing via the
Author: bugman
Date: Mon Jun 16 11:07:44 2014
New Revision: 23971
URL: http://svn.gna.org/viewcvs/relax?rev=23971view=rev
Log:
Attempt at speeding up the torsionless pseudo-ellipse frame order model.
The check if the Sobol' point is outside of an isotropic cone defined by the
largest angle
Author: bugman
Date: Mon Jun 16 11:11:13 2014
New Revision: 23972
URL: http://svn.gna.org/viewcvs/relax?rev=23972view=rev
Log:
Updated all of the CaM frame order system tests for the recent speed up
(r23970).
The speed up switched to the use of numpy.tensordot() for shifting each Sobol'
Author: bugman
Date: Mon Jun 16 11:40:37 2014
New Revision: 23973
URL: http://svn.gna.org/viewcvs/relax?rev=23973view=rev
Log:
The frame order target function calc_vectors() method arguments have all been
converted to keywords.
This is in preparation for handling a second pivot argument for the
Author: bugman
Date: Mon Jun 16 11:49:10 2014
New Revision: 23974
URL: http://svn.gna.org/viewcvs/relax?rev=23974view=rev
Log:
Updated the double rotor frame order model to be in a pseudo-functional state.
Bugs in the target function method have been removed, the calc_vectors() target
function
Author: bugman
Date: Mon Jun 16 12:05:39 2014
New Revision: 23975
URL: http://svn.gna.org/viewcvs/relax?rev=23975view=rev
Log:
The frame_order.pdb_model user function no longer tries to create a cone object
for the double rotor.
Modified:
Author: bugman
Date: Mon Jun 16 16:03:55 2014
New Revision: 23976
URL: http://svn.gna.org/viewcvs/relax?rev=23976view=rev
Log:
Added a timeit script and log file for different ways of checking a binary
numpy array.
Added:
Author: bugman
Date: Mon Jun 16 17:08:10 2014
New Revision: 23977
URL: http://svn.gna.org/viewcvs/relax?rev=23977view=rev
Log:
Modified the rigid_test.py system test script to really be the rigid case.
This is used in all of the Frame_order.test_rigid_data_to_*_model system tests.
Previously
Author: bugman
Date: Mon Jun 16 17:30:30 2014
New Revision: 23978
URL: http://svn.gna.org/viewcvs/relax?rev=23978view=rev
Log:
Fix for the frame order matrix calculation for a pseudo-elliptic cone with
angles of zero degrees.
The
Author: bugman
Date: Mon Jun 16 17:39:25 2014
New Revision: 23979
URL: http://svn.gna.org/viewcvs/relax?rev=23979view=rev
Log:
Fixes for all PCS numeric integration for all frame order models in the rigid
case.
The exact PCS values for the rigid state are now correctly calculated when no
Author: bugman
Date: Mon Jun 16 17:40:42 2014
New Revision: 23980
URL: http://svn.gna.org/viewcvs/relax?rev=23980view=rev
Log:
Updates for the chi-squared value in all the
Frame_order.test_rigid_data_to_*_model system tests.
This is now much reduced as the true rigid state is now being tested
Author: bugman
Date: Mon Jun 16 17:53:11 2014
New Revision: 23981
URL: http://svn.gna.org/viewcvs/relax?rev=23981view=rev
Log:
Fix for the fix of r23978, the theta_x angle should be checked for zero as it
is the smallest.
Modified:
Author: bugman
Date: Mon Jun 16 18:10:07 2014
New Revision: 23982
URL: http://svn.gna.org/viewcvs/relax?rev=23982view=rev
Log:
The rigid frame order matrix for the pseudo-ellipse models is now correctly
handled.
This allows the rigid case RDCs to be correctly calculated for both the
Author: bugman
Date: Mon Jun 16 18:28:49 2014
New Revision: 23983
URL: http://svn.gna.org/viewcvs/relax?rev=23983view=rev
Log:
Fix for the rigid frame order model broken at r23973.
Modified:
branches/frame_order_cleanup/target_functions/frame_order.py
Modified:
Author: bugman
Date: Mon Jun 16 18:32:49 2014
New Revision: 23984
URL: http://svn.gna.org/viewcvs/relax?rev=23984view=rev
Log:
Merged revisions 23945 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r23945 | bugman | 2014-06-13 17:54:50 +0200 (Fri, 13 Jun 2014) | 17
Author: bugman
Date: Mon Jun 16 18:47:49 2014
New Revision: 23985
URL: http://svn.gna.org/viewcvs/relax?rev=23985view=rev
Log:
Updates for the Frame_order.test_rigid_data_to_pseudo_ellipse*_model system
tests.
The chi-squared value now matches the rigid model.
Modified:
Author: tlinnet
Date: Mon Jun 16 19:01:34 2014
New Revision: 23988
URL: http://svn.gna.org/viewcvs/relax?rev=23988view=rev
Log:
Restructered all data structures into higher dimension in target function.
Fix for the input to the different models.
Restructured how to detect the number of offset
Author: tlinnet
Date: Mon Jun 16 19:01:32 2014
New Revision: 23987
URL: http://svn.gna.org/viewcvs/relax?rev=23987view=rev
Log:
Replaced the temporary structure self.cpmg_frqs_a to self.cpmg_frqs, which
works for all target functions
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of
Author: tlinnet
Date: Mon Jun 16 19:01:30 2014
New Revision: 23986
URL: http://svn.gna.org/viewcvs/relax?rev=23986view=rev
Log:
Replaced the temporary structure self.frqs_a to self.frqs, which works for all
target functions.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of
Author: tlinnet
Date: Mon Jun 16 19:01:36 2014
New Revision: 23989
URL: http://svn.gna.org/viewcvs/relax?rev=23989view=rev
Log:
Various index fixes, after the data structures have been reordered.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered
Author: tlinnet
Date: Mon Jun 16 19:01:41 2014
New Revision: 23991
URL: http://svn.gna.org/viewcvs/relax?rev=23991view=rev
Log:
Fix for plotting, since the back_calc now can hold more datapoints that cpmg
frequencies.
This is because the numpy array has been expanded to the maximum number of
Author: tlinnet
Date: Mon Jun 16 19:01:39 2014
New Revision: 23990
URL: http://svn.gna.org/viewcvs/relax?rev=23990view=rev
Log:
Fix for unit test, where the dimension of points has to be one lower.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered
Author: tlinnet
Date: Mon Jun 16 19:05:38 2014
New Revision: 23992
URL: http://svn.gna.org/viewcvs/relax?rev=23992view=rev
Log:
Implemented a frqs_squared calculation in the init of target function.
This is to speed up the calculations.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up
Author: tlinnet
Date: Mon Jun 16 19:58:14 2014
New Revision: 23995
URL: http://svn.gna.org/viewcvs/relax?rev=23995view=rev
Log:
Moved the calculation of dw and dwH out of for loops for model MMQ CR72.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered
Author: tlinnet
Date: Mon Jun 16 19:58:12 2014
New Revision: 23994
URL: http://svn.gna.org/viewcvs/relax?rev=23994view=rev
Log:
Removed fatal print for python 3 in unit tests.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered analysis.
Modified:
Author: tlinnet
Date: Mon Jun 16 19:58:10 2014
New Revision: 23993
URL: http://svn.gna.org/viewcvs/relax?rev=23993view=rev
Log:
Restructured frqs_H to higher dimension in target function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered analysis.
Author: tlinnet
Date: Mon Jun 16 19:58:17 2014
New Revision: 23996
URL: http://svn.gna.org/viewcvs/relax?rev=23996view=rev
Log:
Removed looping over spin and frequencies for model MMD CR72.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered analysis.
Author: tlinnet
Date: Mon Jun 16 19:58:19 2014
New Revision: 23997
URL: http://svn.gna.org/viewcvs/relax?rev=23997view=rev
Log:
Temporary removed check for dw = 0.0 in MMQ CR72.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered analysis.
Modified:
Author: tlinnet
Date: Mon Jun 16 20:23:34 2014
New Revision: 23998
URL: http://svn.gna.org/viewcvs/relax?rev=23998view=rev
Log:
Removed number of points to be parsed to model MMQ CR72.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered analysis.
Author: tlinnet
Date: Mon Jun 16 20:23:36 2014
New Revision: 23999
URL: http://svn.gna.org/viewcvs/relax?rev=23999view=rev
Log:
Removed power to be parsed to MMQ CR72, since it is not used.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered analysis.
Author: tlinnet
Date: Mon Jun 16 20:23:38 2014
New Revision: 24000
URL: http://svn.gna.org/viewcvs/relax?rev=24000view=rev
Log:
Changed MMQ CR72 to use multi dimensional data.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered analysis.
Modified:
Author: tlinnet
Date: Mon Jun 16 22:11:36 2014
New Revision: 24002
URL: http://svn.gna.org/viewcvs/relax?rev=24002view=rev
Log:
Moved the calculation of dw out of for loops for model ns mmq 2site.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered
Author: tlinnet
Date: Mon Jun 16 22:11:40 2014
New Revision: 24004
URL: http://svn.gna.org/viewcvs/relax?rev=24004view=rev
Log:
Fixed the use of higher dimensional data in mmq 2site sq dq zq.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for Clustered analysis.
Author: tlinnet
Date: Mon Jun 16 22:11:41 2014
New Revision: 24005
URL: http://svn.gna.org/viewcvs/relax?rev=24005view=rev
Log:
Fix for documentation in ns mmq 2site/sq/dq/zq/mq.
Now explains which dimension data should be in.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of
Author: tlinnet
Date: Mon Jun 16 22:11:33 2014
New Revision: 24001
URL: http://svn.gna.org/viewcvs/relax?rev=24001view=rev
Log:
Changed unit test of MMQ CR72 to pass.
dw needs to be of numpy structure.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models
for
Author: tlinnet
Date: Mon Jun 16 22:11:38 2014
New Revision: 24003
URL: http://svn.gna.org/viewcvs/relax?rev=24003view=rev
Log:
Modified lib function for NS MMQ 2site, to have looping over spins and
frequencies inside lib function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of
Author: tlinnet
Date: Mon Jun 16 22:11:56 2014
New Revision: 24007
URL: http://svn.gna.org/viewcvs/relax?rev=24007view=rev
Log:
Changed the calculation of inner product in model ns cpmg 2site 3d.
The out argument of numpy.dot is buggy, and should not be used.
Task #7807
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