Author: bugman
Date: Tue Jul 22 19:27:18 2014
New Revision: 24664
URL: http://svn.gna.org/viewcvs/relax?rev=24664&view=rev
Log:
Merged revisions 24362-24364,24510,24612-24615,24619-24637,24641-24648,24650
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_spin_speed
........
r24362 | bugman | 2014-06-30 10:41:27 +0200 (Mon, 30 Jun 2014) | 10 lines
Created a master profiling script for comparing the speed between different
dispersion models.
This is similar to the disp_profile_all.py script except it only operates
on a single relax version.
The output is then simply the timings, with statistics, of the calculation
time for 100 function
calls for 100 spins (either 10,000 function calls for single spins or 100
function calls for the
cluster of 100 spins).
The output of the script for the current disp_spin_speed branch code has
also been added.
........
r24363 | tlinnet | 2014-06-30 11:48:47 +0200 (Mon, 30 Jun 2014) | 5 lines
Critical fix for the recalculation of tau cpmg, when plotting for numerical
models.
The interpolated dispersion points with tau_cpgm was calculated with frq,
instead of cmpg_frq.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24364 | bugman | 2014-06-30 12:20:31 +0200 (Mon, 30 Jun 2014) | 7 lines
The new dispersion model profiling master script now includes links to the
relax wiki.
The models are no longer presented by name but rather by the relax wiki
links for each model (see
http://wiki.nmr-relax.com/Category:Relaxation_dispersion for all these
links). This is to improve
the Google rank of the relax wiki, as these links may appear in a number of
locations.
........
r24510 | bugman | 2014-07-10 12:04:53 +0200 (Thu, 10 Jul 2014) | 6 lines
Removal of many unused imports in the disp_spin_speed branch.
These were detected using the devel_scripts/find_unused_imports.py script
which uses pylint to find
all unused imports. The false positives also present in the trunk were
ignored.
........
r24612 | tlinnet | 2014-07-22 15:16:47 +0200 (Tue, 22 Jul 2014) | 13 lines
Reverted r24339 as relax dependency of numpy is now 1.6 where the "out"
argument is available.
The command used was:
svn merge -r24339:r24338 .
.....
r24339 | tlinnet | 2014-06-27 12:58:29 +0200 (Fri, 27 Jun 2014) | 3
lines
Added a list of systemtests to skip, if numpy "out" argument is not
available.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of
dispersion models for Clustered analysis.
.....
........
r24613 | tlinnet | 2014-07-22 15:23:47 +0200 (Tue, 22 Jul 2014) | 13 lines
Reverted r24336 as relax dependency of numpy is now 1.6 where the "einsum"
function is available.
The command used was:
svn merge -r24336:r24335 .
.....
r24336 | tlinnet | 2014-06-27 12:58:22 +0200 (Fri, 27 Jun 2014) | 3
lines
Added to target function that experiment_type_setup() should not be
initiated, if numpy.einsum is missing.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of
dispersion models for Clustered analysis.
.....
........
r24614 | tlinnet | 2014-07-22 15:27:44 +0200 (Tue, 22 Jul 2014) | 18 lines
Reverted r24337 as relax dependency of numpy is now 1.6 where the "out"
argument is available.
The command used was:
svn merge -r24337:r24336 .
.....
r24337 | tlinnet | 2014-06-27 12:58:24 +0200 (Fri, 27 Jun 2014) | 8
lines
Added a numpy "out" argument check to dep_check.py.
This is for checking the out argument of:
numpy.multiply
numpy.add
numpy.subtract
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of
dispersion models for Clustered analysis.
.....
........
r24615 | tlinnet | 2014-07-22 15:35:16 +0200 (Tue, 22 Jul 2014) | 13 lines
Reverted r24323 as relax dependency of numpy is now 1.6 where "einsum"
function is available.
The command used was:
svn merge -r24323:r24322 .
.....
r24323 | tlinnet | 2014-06-25 19:31:40 +0200 (Wed, 25 Jun 2014) | 3
lines
Implemented a dependency check for numpy einsum, so relax can still
start.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of
dispersion models for Clustered analysis.
.....
........
r24619 | tlinnet | 2014-07-22 16:51:26 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/b14.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24620 | tlinnet | 2014-07-22 16:51:28 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/cr72.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24621 | tlinnet | 2014-07-22 16:51:30 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/dpl94.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24622 | tlinnet | 2014-07-22 16:51:32 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/lm63_3site.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24623 | tlinnet | 2014-07-22 16:51:33 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/lm63.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24624 | tlinnet | 2014-07-22 16:51:35 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/m61b.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24625 | tlinnet | 2014-07-22 16:51:37 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/m61.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24626 | tlinnet | 2014-07-22 16:51:38 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/matrix_exponential.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24627 | tlinnet | 2014-07-22 16:51:40 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/mp05.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24628 | tlinnet | 2014-07-22 16:51:42 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/ns_cpmg_2site_expanded.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24629 | tlinnet | 2014-07-22 16:51:44 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/ns_cpmg_2site_star.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24630 | tlinnet | 2014-07-22 16:51:46 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/ns_mmq_2site.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24631 | tlinnet | 2014-07-22 16:51:48 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/ns_mmq_3site.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24632 | tlinnet | 2014-07-22 16:51:50 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/ns_r1rho_2site.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24633 | tlinnet | 2014-07-22 16:51:51 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/ns_r1rho_3site.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24634 | tlinnet | 2014-07-22 16:51:53 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/tap03.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24635 | tlinnet | 2014-07-22 16:51:55 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/tp02.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24636 | tlinnet | 2014-07-22 16:51:57 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of lib/dispersion/two_point.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24637 | tlinnet | 2014-07-22 16:51:59 +0200 (Tue, 22 Jul 2014) | 3 lines
Code validation of target_functions/relax_disp.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24641 | tlinnet | 2014-07-22 17:53:38 +0200 (Tue, 22 Jul 2014) | 3 lines
Removal of space after for loop in target_functions/relax_disp.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24642 | tlinnet | 2014-07-22 17:53:40 +0200 (Tue, 22 Jul 2014) | 3 lines
Copyright time extension for lib/dispersion/tsmfk01.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24643 | tlinnet | 2014-07-22 17:53:42 +0200 (Tue, 22 Jul 2014) | 3 lines
More removal of space after for loop in target_functions/relax_disp.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24644 | tlinnet | 2014-07-22 17:53:43 +0200 (Tue, 22 Jul 2014) | 3 lines
For model ns mmq 3site, moved the parameter conversion of dw_AB from target
function to lib function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24645 | tlinnet | 2014-07-22 17:53:45 +0200 (Tue, 22 Jul 2014) | 3 lines
Removed chi sum initialisation in func_ns_mmq_2site() as this is not used.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24646 | tlinnet | 2014-07-22 17:53:47 +0200 (Tue, 22 Jul 2014) | 3 lines
Documentation fix for the get_back_calc() function in
target_function/relax_disp.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24647 | tlinnet | 2014-07-22 17:56:23 +0200 (Tue, 22 Jul 2014) | 3 lines
Removed unnecessary repetitive calculation of kex**2 in model DPL94.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24648 | tlinnet | 2014-07-22 18:08:22 +0200 (Tue, 22 Jul 2014) | 3 lines
API documentation fixes, where a "\" is the last character on the line.
There should be a space " ", ending this characater.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r24650 | tlinnet | 2014-07-22 18:21:20 +0200 (Tue, 22 Jul 2014) | 3 lines
Comment space fixing in target_functions/relax_disp.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
Added:
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_single.log
- copied unchanged from r24364,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_single.log
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_single.py
- copied, changed from r24364,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_single.py
Modified:
trunk/ (props changed)
trunk/dep_check.py
trunk/lib/dispersion/b14.py
trunk/lib/dispersion/cr72.py
trunk/lib/dispersion/dpl94.py
trunk/lib/dispersion/lm63.py
trunk/lib/dispersion/lm63_3site.py
trunk/lib/dispersion/m61.py
trunk/lib/dispersion/m61b.py
trunk/lib/dispersion/matrix_exponential.py
trunk/lib/dispersion/mp05.py
trunk/lib/dispersion/ns_cpmg_2site_expanded.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/lib/dispersion/tap03.py
trunk/lib/dispersion/tp02.py
trunk/lib/dispersion/tsmfk01.py
trunk/target_functions/relax_disp.py
trunk/test_suite/shared_data/dispersion/bug_22146_unpacking_r2a_r2b_cluster/cpmg_synthetic.py
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_b14.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_it99.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_lm63.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_lm63_3site.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_m61.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_matrix_power.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_mmq_cr72.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_mp05.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_norex.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D_full.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star_full.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_2site.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site_linear.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_2site.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site_linear.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_tap03.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_tp02.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py
trunk/test_suite/system_tests/relax_disp.py
trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_cr72_full_cluster_one_field.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_cr72_full_cluster_three_fields.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_matrix_exponential.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/dep_check.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/dep_check.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/b14.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/cr72.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/dpl94.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/lm63.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/lm63.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/lm63_3site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/lm63_3site.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/m61.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/m61.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/m61b.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/m61b.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/matrix_exponential.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/matrix_exponential.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/mp05.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/mp05.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_cpmg_2site_expanded.py?rev=24664&r1=24663&r2=24664&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=24664&r1=24663&r2=24664&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=24664&r1=24663&r2=24664&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=24664&r1=24663&r2=24664&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=24664&r1=24663&r2=24664&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=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/tap03.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tap03.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/tp02.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tp02.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/lib/dispersion/tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tsmfk01.py?rev=24664&r1=24663&r2=24664&view=diff
Modified: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=24664&r1=24663&r2=24664&view=diff
Modified:
trunk/test_suite/shared_data/dispersion/bug_22146_unpacking_r2a_r2b_cluster/cpmg_synthetic.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/bug_22146_unpacking_r2a_r2b_cluster/cpmg_synthetic.py?rev=24664&r1=24663&r2=24664&view=diff
Modified:
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all.py?rev=24664&r1=24663&r2=24664&view=diff
Copied:
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_single.py
(from r24364,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_single.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/profiling/disp_profile_single.py?p2=trunk/test_suite/shared_data/dispersion/profiling/disp_profile_single.py&p1=branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_single.py&r1=24364&r2=24664&rev=24664&view=diff
Modified: trunk/test_suite/shared_data/dispersion/profiling/profiling_b14.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/profiling/profiling_b14.py?rev=24664&r1=24663&r2=24664&view=diff
Modified:
trunk/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py
[... 92 lines stripped ...]
r24664 - in /trunk: ./ lib/dispersion/ target_functions/ test_suite/shared_data/dispersion/bug_22146_unpacking_r2a_r2b_clust...