Author: bugman
Date: Tue Jul 22 19:06:25 2014
New Revision: 24657
URL: http://svn.gna.org/viewcvs/relax?rev=24657&view=rev
Log:
Merged revisions 23949-23968,23986-24007,24010-24011,24013-24014 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_spin_speed
........
r23949 | tlinnet | 2014-06-15 08:53:31 +0200 (Sun, 15 Jun 2014) | 8 lines
Methods to replace math domain errors in model ns_cpmg_2site_3d, has been
replaced with numpy masks.
number of points has been removed, as the masks utility replaces this.
pB is now moved to be calculated inside. This makes the lib function
simpler.
k_AB and k_BA is also now calculated here.
Magnetization vector is also now filled in lib function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23950 | tlinnet | 2014-06-15 08:53:34 +0200 (Sun, 15 Jun 2014) | 3 lines
Fix for unit tests of model ns cpmg 2site 3d to the reduced input to the
lib function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23951 | tlinnet | 2014-06-15 08:53:36 +0200 (Sun, 15 Jun 2014) | 3 lines
Change to the target function to the model ns cpmg 2site 3d to use the
reduced input to the lib function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23952 | tlinnet | 2014-06-15 08:53:38 +0200 (Sun, 15 Jun 2014) | 3 lines
Changed linked matrix/vector inner products into chained dot expressions.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23953 | tlinnet | 2014-06-15 08:53:40 +0200 (Sun, 15 Jun 2014) | 3 lines
Wrote the essential dot matrix up to be initiated earlier.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23954 | tlinnet | 2014-06-15 08:53:42 +0200 (Sun, 15 Jun 2014) | 3 lines
Lowered the number of dot iterations, by pre-prepare the dot matrix another
round.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23955 | tlinnet | 2014-06-15 08:53:44 +0200 (Sun, 15 Jun 2014) | 3 lines
Turned Mint vector into a 7,1 matrix, so dimensions fit with evolution
matrix.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23956 | tlinnet | 2014-06-15 08:53:45 +0200 (Sun, 15 Jun 2014) | 7 lines
Lowered the number of dot operations, by pre-preparing the evolution matrix
another round.
The power is in system tests always even.
The trick to removing this for loop, would be to make a general multi dot
function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23957 | tlinnet | 2014-06-15 15:15:11 +0200 (Sun, 15 Jun 2014) | 5 lines
Moved the bulk operation of model CPMG 2site 3d into the lib file.
This is to keep the API clean.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23958 | tlinnet | 2014-06-15 15:15:14 +0200 (Sun, 15 Jun 2014) | 3 lines
Changed the unit test of NS CPMG 2site 3D, after the input to the function
has changed.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23959 | tlinnet | 2014-06-15 15:15:16 +0200 (Sun, 15 Jun 2014) | 5 lines
Changed the taget function for NS CPMG 2site 3D.
This reflects the new API layout.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23960 | tlinnet | 2014-06-15 15:15:18 +0200 (Sun, 15 Jun 2014) | 6 lines
Changed the lib function of NS CPMG 2site start, to get input of dw and
r20a+r20b of higher dimensional type.
This is to move the main operations from the target function to the lib
function, and
make the API code clean and consistent.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23961 | tlinnet | 2014-06-15 15:15:19 +0200 (Sun, 15 Jun 2014) | 3 lines
Changed the target function of NS CPMG 2site STAR, to reflect the input to
the function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23962 | tlinnet | 2014-06-15 15:15:21 +0200 (Sun, 15 Jun 2014) | 3 lines
Removal of temporary printout.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23963 | tlinnet | 2014-06-15 15:15:23 +0200 (Sun, 15 Jun 2014) | 3 lines
Made the dot evolution structure faster for NS CPMG 2site 3D.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23964 | tlinnet | 2014-06-15 15:57:33 +0200 (Sun, 15 Jun 2014) | 5 lines
Implemented the BLAS method of dot product, which should be faster.
I cannot get the "out" argument to work.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23965 | tlinnet | 2014-06-15 16:22:42 +0200 (Sun, 15 Jun 2014) | 5 lines
Small fix for the dot method.
But the out argument does not work.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23966 | tlinnet | 2014-06-15 16:27:07 +0200 (Sun, 15 Jun 2014) | 5 lines
Implemented the dot method via blas.
This needs a array with one more axis.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23967 | tlinnet | 2014-06-15 16:41:00 +0200 (Sun, 15 Jun 2014) | 5 lines
Last try to use the out argument.
In the last dotting loop, the out argument wont work, no matter what I do.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23968 | tlinnet | 2014-06-15 22:59:15 +0200 (Sun, 15 Jun 2014) | 10 lines
Inner product fix in model NS CPMG 2site 3D.
Fix for system tests:
F 1.34 s for Relax_disp.test_cpmg_synthetic_ns3d_to_b14
F 0.78 s for Relax_disp.test_cpmg_synthetic_ns3d_to_cr72
F 3.74 s for Relax_disp.test_cpmg_synthetic_ns3d_to_cr72_noise_cluster
The number of dotting with Mint, should corespond to the power.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23986 | tlinnet | 2014-06-16 19:01:30 +0200 (Mon, 16 Jun 2014) | 3 lines
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 dispersion
models for Clustered analysis.
........
r23987 | tlinnet | 2014-06-16 19:01:32 +0200 (Mon, 16 Jun 2014) | 3 lines
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 dispersion
models for Clustered analysis.
........
r23988 | tlinnet | 2014-06-16 19:01:34 +0200 (Mon, 16 Jun 2014) | 6 lines
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 and dispersion points.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23989 | tlinnet | 2014-06-16 19:01:36 +0200 (Mon, 16 Jun 2014) | 3 lines
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 analysis.
........
r23990 | tlinnet | 2014-06-16 19:01:39 +0200 (Mon, 16 Jun 2014) | 3 lines
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 analysis.
........
r23991 | tlinnet | 2014-06-16 19:01:41 +0200 (Mon, 16 Jun 2014) | 5 lines
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
points.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23992 | tlinnet | 2014-06-16 19:05:38 +0200 (Mon, 16 Jun 2014) | 5 lines
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 of dispersion
models for Clustered analysis.
........
r23993 | tlinnet | 2014-06-16 19:58:10 +0200 (Mon, 16 Jun 2014) | 3 lines
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.
........
r23994 | tlinnet | 2014-06-16 19:58:12 +0200 (Mon, 16 Jun 2014) | 3 lines
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.
........
r23995 | tlinnet | 2014-06-16 19:58:14 +0200 (Mon, 16 Jun 2014) | 3 lines
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 analysis.
........
r23996 | tlinnet | 2014-06-16 19:58:17 +0200 (Mon, 16 Jun 2014) | 3 lines
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.
........
r23997 | tlinnet | 2014-06-16 19:58:19 +0200 (Mon, 16 Jun 2014) | 3 lines
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.
........
r23998 | tlinnet | 2014-06-16 20:23:34 +0200 (Mon, 16 Jun 2014) | 3 lines
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.
........
r23999 | tlinnet | 2014-06-16 20:23:36 +0200 (Mon, 16 Jun 2014) | 3 lines
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.
........
r24000 | tlinnet | 2014-06-16 20:23:38 +0200 (Mon, 16 Jun 2014) | 3 lines
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.
........
r24001 | tlinnet | 2014-06-16 22:11:33 +0200 (Mon, 16 Jun 2014) | 5 lines
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 Clustered analysis.
........
r24002 | tlinnet | 2014-06-16 22:11:36 +0200 (Mon, 16 Jun 2014) | 3 lines
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 analysis.
........
r24003 | tlinnet | 2014-06-16 22:11:38 +0200 (Mon, 16 Jun 2014) | 3 lines
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 dispersion
models for Clustered analysis.
........
r24004 | tlinnet | 2014-06-16 22:11:40 +0200 (Mon, 16 Jun 2014) | 3 lines
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.
........
r24005 | tlinnet | 2014-06-16 22:11:41 +0200 (Mon, 16 Jun 2014) | 5 lines
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 dispersion
models for Clustered analysis.
........
r24006 | tlinnet | 2014-06-16 22:11:49 +0200 (Mon, 16 Jun 2014) | 3 lines
Changed the reshaping of dw and dwH, since it is not dependent on
experiment.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24007 | tlinnet | 2014-06-16 22:11:56 +0200 (Mon, 16 Jun 2014) | 5 lines
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 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24010 | tlinnet | 2014-06-17 09:18:39 +0200 (Tue, 17 Jun 2014) | 3 lines
Added missing instances of cleaning the data.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24011 | tlinnet | 2014-06-17 09:18:41 +0200 (Tue, 17 Jun 2014) | 3 lines
Bug fix for model LM63 3site. The index si has to be used to extract data
to lib function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24013 | tlinnet | 2014-06-17 09:33:32 +0200 (Tue, 17 Jun 2014) | 8 lines
Temporary added systemtest: test_korzhnev_2005_all_data_disp_speed_bug.
This makes a minimisation with 1 iteration, and so will give the chi2 value
at the preset
parameter values.
This is chi2 value should give 162.5, but gives 74.7104.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24014 | tlinnet | 2014-06-17 09:47:09 +0200 (Tue, 17 Jun 2014) | 6 lines
Updated documentation on dimensionality of numpy array num_points.
They are in dimension [NE][NS][[NM][NO], where oi gives the number of
dispersion points at that offset.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
Modified:
trunk/ (props changed)
trunk/lib/dispersion/mmq_cr72.py
trunk/lib/dispersion/ns_cpmg_2site_3d.py
trunk/lib/dispersion/ns_cpmg_2site_star.py
trunk/lib/dispersion/ns_mmq_2site.py
trunk/lib/dispersion/ns_mmq_3site.py
trunk/lib/dispersion/ns_r1rho_2site.py
trunk/lib/dispersion/ns_r1rho_3site.py
trunk/specific_analyses/relax_disp/data.py
trunk/target_functions/relax_disp.py
trunk/test_suite/system_tests/relax_disp.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/dispersion/mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/mmq_cr72.py?rev=24657&r1=24656&r2=24657&view=diff
Modified: trunk/lib/dispersion/ns_cpmg_2site_3d.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_cpmg_2site_3d.py?rev=24657&r1=24656&r2=24657&view=diff
Modified: trunk/lib/dispersion/ns_cpmg_2site_star.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_cpmg_2site_star.py?rev=24657&r1=24656&r2=24657&view=diff
Modified: trunk/lib/dispersion/ns_mmq_2site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_mmq_2site.py?rev=24657&r1=24656&r2=24657&view=diff
Modified: trunk/lib/dispersion/ns_mmq_3site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_mmq_3site.py?rev=24657&r1=24656&r2=24657&view=diff
Modified: trunk/lib/dispersion/ns_r1rho_2site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_r1rho_2site.py?rev=24657&r1=24656&r2=24657&view=diff
Modified: trunk/lib/dispersion/ns_r1rho_3site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_r1rho_3site.py?rev=24657&r1=24656&r2=24657&view=diff
Modified: trunk/specific_analyses/relax_disp/data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/data.py?rev=24657&r1=24656&r2=24657&view=diff
Modified: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=24657&r1=24656&r2=24657&view=diff
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=24657&r1=24656&r2=24657&view=diff
Modified: trunk/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py?rev=24657&r1=24656&r2=24657&view=diff
Modified:
trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py?rev=24657&r1=24656&r2=24657&view=diff
r24657 - in /trunk: ./ lib/dispersion/ specific_analyses/relax_disp/ target_functions/ test_suite/system_tests/ test_suite/u...