Author: bugman
Date: Thu Jan 13 14:28:39 2011
New Revision: 12324
URL: http://svn.gna.org/viewcvs/relax?rev=12324&view=rev
Log:
Merged revisions 12229-12274,12276-12320 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r12229 | bugman | 2011-01-12 11:52:40 +0100 (Wed, 12 Jan 2011) | 3 lines
Created a module to aid in the back-calculation of relaxation data from
model-free parameters.
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r12230 | bugman | 2011-01-12 12:00:34 +0100 (Wed, 12 Jan 2011) | 3 lines
Added a new model-free test set, calculated using the new back_calc.py
module.
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r12231 | bugman | 2011-01-12 12:18:50 +0100 (Wed, 12 Jan 2011) | 3 lines
Created the test_local_tm_10_S2_0_8_te_40 system test for testing
model-free optimisation.
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r12232 | bugman | 2011-01-12 14:17:11 +0100 (Wed, 12 Jan 2011) | 5 lines
Improved the model-free system test value_test() method to handle all types
of model-free data.
This includes not checking certain values or statistic unless specifically
asked for.
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r12233 | bugman | 2011-01-12 14:20:18 +0100 (Wed, 12 Jan 2011) | 3 lines
The test_local_tm_10_S2_0_8_te_40 model-free system test is now checking
the parameter values.
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r12234 | bugman | 2011-01-12 14:20:50 +0100 (Wed, 12 Jan 2011) | 3 lines
Removed a duplicated chi2 test from value_test().
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r12235 | bugman | 2011-01-12 14:23:16 +0100 (Wed, 12 Jan 2011) | 3 lines
Modified the model-free system test method mesg_opt_debug() to handle all
model-free models.
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r12236 | bugman | 2011-01-12 14:24:33 +0100 (Wed, 12 Jan 2011) | 3 lines
Added the local_tm parameter to the model-free mesg_opt_debug() system test
method.
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r12237 | bugman | 2011-01-12 14:25:44 +0100 (Wed, 12 Jan 2011) | 3 lines
Improved print out from mesg_opt_debug().
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r12238 | bugman | 2011-01-12 14:26:23 +0100 (Wed, 12 Jan 2011) | 3 lines
Newline fix for the mesg_opt_debug() print out.
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r12239 | bugman | 2011-01-12 14:27:54 +0100 (Wed, 12 Jan 2011) | 3 lines
More improvements to the mesg_opt_debug() print out - the correlation times
are better reported.
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r12240 | bugman | 2011-01-12 14:29:54 +0100 (Wed, 12 Jan 2011) | 5 lines
Fix for the test_local_tm_10_S2_0_8_te_40() system test.
The te value should be sent in a ps units.
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r12241 | bugman | 2011-01-12 14:31:27 +0100 (Wed, 12 Jan 2011) | 3 lines
Added a directory for holding relaxation data from a grid of model-free
values.
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r12242 | bugman | 2011-01-12 14:50:34 +0100 (Wed, 12 Jan 2011) | 3 lines
Created all the relaxation data for the tm2 model-free grid.
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r12243 | bugman | 2011-01-12 15:06:28 +0100 (Wed, 12 Jan 2011) | 3 lines
Shifted all the model-free system test scripts into
test_suite/system_tests/scripts/model_free/.
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r12244 | bugman | 2011-01-12 15:20:56 +0100 (Wed, 12 Jan 2011) | 3 lines
Added some more local_tm_10_S2_0_8_te_40 system tests, but this time
randomising the Ri data loading.
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r12245 | bugman | 2011-01-12 15:39:41 +0100 (Wed, 12 Jan 2011) | 3 lines
Created the system test for checking the tm2 grid of model-free parameters.
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r12246 | bugman | 2011-01-12 15:42:54 +0100 (Wed, 12 Jan 2011) | 3 lines
The model-free system test value_test() method is now checking the local tm
value from a number of tests.
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r12247 | bugman | 2011-01-12 15:44:19 +0100 (Wed, 12 Jan 2011) | 3 lines
Set the initial param values of the test_tm2_grid() system test to the real
ones.
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r12248 | bugman | 2011-01-12 15:48:04 +0100 (Wed, 12 Jan 2011) | 6 lines
Bug fix for the module for back-calculating relaxation data from model-free
parameters.
The heteronucleus was being ignored when calculating the 5 frequencies of
the spectral density
function.
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r12249 | bugman | 2011-01-12 15:50:33 +0100 (Wed, 12 Jan 2011) | 3 lines
Fix for the test_tm2_grid() system test - the correct values of the
correlations times are being checked.
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r12250 | bugman | 2011-01-12 16:25:36 +0100 (Wed, 12 Jan 2011) | 3 lines
Newline fix.
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r12251 | bugman | 2011-01-12 16:31:07 +0100 (Wed, 12 Jan 2011) | 3 lines
Created a system test for checking model-free model m2 against the tm2 grid.
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r12252 | bugman | 2011-01-12 16:39:03 +0100 (Wed, 12 Jan 2011) | 3 lines
The same setup script is now used for all of the system tests using the tm2
grid data.
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r12253 | bugman | 2011-01-12 16:40:22 +0100 (Wed, 12 Jan 2011) | 3 lines
Created a system test for checking model-free model m3 against the tm2 grid
data.
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r12254 | bugman | 2011-01-12 17:03:09 +0100 (Wed, 12 Jan 2011) | 3 lines
Simplified the 3 system tests based on the model-free tm2 grid by shifting
all the code to the script.
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r12255 | bugman | 2011-01-12 17:04:43 +0100 (Wed, 12 Jan 2011) | 3 lines
Fix for the test_tm2_grid system test, the diffusion tensor should not be
initialised.
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r12256 | bugman | 2011-01-12 17:08:01 +0100 (Wed, 12 Jan 2011) | 5 lines
The test_m2_grid_vs_m3() system test should really have been against model
m4!
Model m3 has no te parameter, so the model does not fit perfectly.
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r12257 | bugman | 2011-01-12 17:09:17 +0100 (Wed, 12 Jan 2011) | 5 lines
Turned constraints off in the tm2 grid system tests to speed up the tests.
Constrained optimisation is not required in these simple models to find the
exact solution.
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r12258 | bugman | 2011-01-12 17:27:53 +0100 (Wed, 12 Jan 2011) | 3 lines
The tm2 model parameters are now properly initialised in the tm2 grid
system test script.
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r12259 | bugman | 2011-01-12 17:28:54 +0100 (Wed, 12 Jan 2011) | 3 lines
This time really turn off the optimisation constraints!
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r12260 | bugman | 2011-01-12 17:41:01 +0100 (Wed, 12 Jan 2011) | 14 lines
Reverted revision r12259 as this was completely false - it actually undid
the previous commit.
The command used was:
svn merge -r12259:12258 .
.....
r12259 | bugman | 2011-01-12 17:28:54 +0100 (Wed, 12 Jan 2011) | 3 lines
Changed paths:
M /1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py
This time really turn off the optimisation constraints!
.....
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r12261 | bugman | 2011-01-12 17:42:37 +0100 (Wed, 12 Jan 2011) | 5 lines
The initial parameters are now slightly perturbed in the 3 tm2 grid system
tests.
This allows the optimisation to be a bit challenged.
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r12262 | bugman | 2011-01-12 17:46:57 +0100 (Wed, 12 Jan 2011) | 3 lines
Te values of zero can now be handled by the spectral_density_mf_orig()
model-free method.
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r12263 | bugman | 2011-01-12 18:49:18 +0100 (Wed, 12 Jan 2011) | 5 lines
Chemical exchange relaxation is now handled properly in the
relaxation_data() function.
The back-calculated relaxation data is now correct for model-free models
with Rex.
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r12264 | bugman | 2011-01-12 18:49:41 +0100 (Wed, 12 Jan 2011) | 3 lines
Changed the S2 parameter to lower case in spectral_density_mf_orig().
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r12265 | bugman | 2011-01-12 19:10:10 +0100 (Wed, 12 Jan 2011) | 3 lines
Converted the rest of the S2 variables to s2.
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r12266 | bugman | 2011-01-12 19:15:25 +0100 (Wed, 12 Jan 2011) | 5 lines
Created the spectral_density_mf_ext() function for the extended model-free
theory.
This calculates the spectral density values at the given model-free
parameter values.
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r12267 | bugman | 2011-01-12 21:47:04 +0100 (Wed, 12 Jan 2011) | 5 lines
Generated relaxation data for model-free parameters for all of the local tm
models.
This can be used for testing both the 10 local tm models and the normal 10
model-free models.
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r12268 | bugman | 2011-01-12 21:55:48 +0100 (Wed, 12 Jan 2011) | 3 lines
Added a system test for the optimisation of the tm0 model-free parameter
grid.
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r12269 | bugman | 2011-01-12 21:57:33 +0100 (Wed, 12 Jan 2011) | 3 lines
Added a system test for the optimisation of the m0 model-free model against
the tm0 parameter grid.
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r12270 | bugman | 2011-01-12 22:06:00 +0100 (Wed, 12 Jan 2011) | 3 lines
Added system tests of models m1-m4 optimised against the tm0 grid.
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r12271 | bugman | 2011-01-13 09:28:55 +0100 (Thu, 13 Jan 2011) | 5 lines
Split out most of the code from the tm0 grid system test script into a
separate module.
This opt_tm_fns will be used for all of the model-free parameter grid
system tests.
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r12272 | bugman | 2011-01-13 09:35:42 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the opt_and_check() function - the interpreter is in the module
namespace.
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r12273 | bugman | 2011-01-13 09:38:47 +0100 (Thu, 13 Jan 2011) | 3 lines
The interpreter now has echoing turned on in the model-free grid system
tests.
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r12274 | bugman | 2011-01-13 09:39:47 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for opt_and_check(), the diffusion tensor object is called
cdp.diff_tensor!
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r12276 | bugman | 2011-01-13 10:53:03 +0100 (Thu, 13 Jan 2011) | 3 lines
Modified the value_test() model-free system test method to skip certain
parameters if not a float or None.
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r12277 | bugman | 2011-01-13 10:53:38 +0100 (Thu, 13 Jan 2011) | 3 lines
Abstracted opt_and_check() to handle all model-free models and parameter
combinations.
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r12278 | bugman | 2011-01-13 10:54:09 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the opt_tm0_grid.py script, the parameter values now should be sent
in.
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r12279 | bugman | 2011-01-13 11:06:59 +0100 (Thu, 13 Jan 2011) | 5 lines
Converted all the local tm model grids to use 13C.
This is to make the testing easier.
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r12280 | bugman | 2011-01-13 11:07:44 +0100 (Thu, 13 Jan 2011) | 3 lines
Abstracted the 'tm._grid' directory to a function arg and converted the
tests to 13C.
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r12281 | bugman | 2011-01-13 11:08:16 +0100 (Thu, 13 Jan 2011) | 3 lines
Modified the module docstring, and passed in the 'tm0_grid' directory to
setup_data().
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r12282 | bugman | 2011-01-13 11:08:47 +0100 (Thu, 13 Jan 2011) | 3 lines
Modified the opt_tm2_grid.py model-free system test script to use the
abstracted opt_tm_fns.py fns.
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r12283 | bugman | 2011-01-13 11:11:40 +0100 (Thu, 13 Jan 2011) | 5 lines
Fix for the tm0 and tm9 relaxation data grids.
The data was a mixture of 15N spectral densities and 13C relaxation values!
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r12284 | bugman | 2011-01-13 11:15:43 +0100 (Thu, 13 Jan 2011) | 3 lines
Added system tests for the optimisation of all the local tm model-free
parameter grids.
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r12285 | bugman | 2011-01-13 11:17:55 +0100 (Thu, 13 Jan 2011) | 3 lines
Added system tests for the optimisation of the normal model-free models
against the all the tm parameter grids.
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r12286 | bugman | 2011-01-13 11:21:52 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the tm1 grid.
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r12287 | bugman | 2011-01-13 11:25:52 +0100 (Thu, 13 Jan 2011) | 3 lines
Fixes for the tm3 and tm4 relaxation data grids.
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r12288 | bugman | 2011-01-13 11:30:01 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm3 relaxation data
grid.
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r12289 | bugman | 2011-01-13 11:34:08 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm3 relaxation data grid - Rex should be scaled by the 1st frq
in all cases!
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r12290 | bugman | 2011-01-13 11:34:47 +0100 (Thu, 13 Jan 2011) | 3 lines
The Rex scaling was (2pi)^2 too much - the frequency was already in rad/s!
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r12291 | bugman | 2011-01-13 11:37:47 +0100 (Thu, 13 Jan 2011) | 3 lines
Rex was being scaled the wrong way in opt_and_check().
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r12292 | bugman | 2011-01-13 11:38:19 +0100 (Thu, 13 Jan 2011) | 3 lines
Both Rex values need to be scaled in the model-free value_test() system
test method.
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r12293 | bugman | 2011-01-13 11:39:52 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm4 relaxation data grid - Rex should be scaled by the 1st frq
in all cases!
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r12294 | bugman | 2011-01-13 11:40:13 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm7 relaxation data grid - Rex should be scaled by the 1st frq
in all cases!
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r12295 | bugman | 2011-01-13 11:40:31 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm8 relaxation data grid - Rex should be scaled by the 1st frq
in all cases!
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r12296 | bugman | 2011-01-13 11:40:49 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm9 relaxation data grid - Rex should be scaled by the 1st frq
in all cases!
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r12297 | bugman | 2011-01-13 11:42:53 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm4 relaxation data
grid.
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r12298 | bugman | 2011-01-13 11:50:30 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the opt_tm4_grid.py model-free system test script - the tm4 grid
should be used!
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r12299 | bugman | 2011-01-13 11:51:50 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the opt_tm4_grid.py model-free system test script - the correct
number of residues is needed.
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r12300 | bugman | 2011-01-13 11:56:32 +0100 (Thu, 13 Jan 2011) | 3 lines
The te, tf, and ts parameters are now being compared on the picosecond
scale.
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r12301 | bugman | 2011-01-13 11:57:10 +0100 (Thu, 13 Jan 2011) | 3 lines
The te, tf, and ts parameters are being scaled to ps in opt_and_check() now.
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r12302 | bugman | 2011-01-13 11:58:57 +0100 (Thu, 13 Jan 2011) | 3 lines
The perturbation to the initial parameter values is an order of magnitude
less in opt_and_check() now.
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r12303 | bugman | 2011-01-13 12:03:17 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm5 relaxation data grid - the parameter is ts, not tf.
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r12304 | bugman | 2011-01-13 12:05:30 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm5 relaxation data
grid.
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r12305 | bugman | 2011-01-13 12:14:00 +0100 (Thu, 13 Jan 2011) | 3 lines
Loosened the S2f, S2s, ts, and tf checks.
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r12306 | bugman | 2011-01-13 12:14:19 +0100 (Thu, 13 Jan 2011) | 3 lines
The S2s parameter is being calculated from S2 and S2f.
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r12307 | bugman | 2011-01-13 12:22:33 +0100 (Thu, 13 Jan 2011) | 3 lines
Loosened the ts check even further to only 4 significant figs.
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r12308 | bugman | 2011-01-13 12:22:58 +0100 (Thu, 13 Jan 2011) | 3 lines
The initial model-free parameters are no longer perturbed at all - that
costs too much time.
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r12309 | bugman | 2011-01-13 12:26:03 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the comments, s2 and s2f were being mixed up.
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r12310 | bugman | 2011-01-13 12:28:06 +0100 (Thu, 13 Jan 2011) | 5 lines
Fix for the tm5 relaxation data grid - some of the relaxation data was
negative.
The s2 values are now all smaller than s2f to prevent s2s from being > 1.
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r12311 | bugman | 2011-01-13 12:32:54 +0100 (Thu, 13 Jan 2011) | 3 lines
Shortened the tm5 relaxation data grid.
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r12312 | bugman | 2011-01-13 12:34:03 +0100 (Thu, 13 Jan 2011) | 3 lines
Shortened the tm6 relaxation data grid.
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r12313 | bugman | 2011-01-13 12:36:32 +0100 (Thu, 13 Jan 2011) | 5 lines
Loosened the tf check even further to only 4 significant figs.
This now matches the ts check.
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r12314 | bugman | 2011-01-13 12:36:51 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm6 relaxation data
grid.
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r12315 | bugman | 2011-01-13 12:38:01 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm7 relaxation data grid - the parameter is ts, not tf.
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r12316 | bugman | 2011-01-13 12:42:57 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm7 relaxation data
grid.
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r12317 | bugman | 2011-01-13 12:44:05 +0100 (Thu, 13 Jan 2011) | 3 lines
Shortened the tm8 relaxation data grid.
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r12318 | bugman | 2011-01-13 12:50:15 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm8 relaxation data
grid.
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r12319 | bugman | 2011-01-13 12:51:45 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm9 relaxation data
grid.
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r12320 | bugman | 2011-01-13 14:18:52 +0100 (Thu, 13 Jan 2011) | 3 lines
The Rex parameters have been made independent of field strength prior to
running value_test().
........
Added:
branches/multi_processor_merge/test_suite/shared_data/model_free/back_calc.py
- copied unchanged from r12320,
1.3/test_suite/shared_data/model_free/back_calc.py
branches/multi_processor_merge/test_suite/shared_data/model_free/local_tm_10_S2_0.8_te_40/
- copied from r12320,
1.3/test_suite/shared_data/model_free/local_tm_10_S2_0.8_te_40/
branches/multi_processor_merge/test_suite/shared_data/model_free/tm0_grid/
- copied from r12320, 1.3/test_suite/shared_data/model_free/tm0_grid/
branches/multi_processor_merge/test_suite/shared_data/model_free/tm1_grid/
- copied from r12320, 1.3/test_suite/shared_data/model_free/tm1_grid/
branches/multi_processor_merge/test_suite/shared_data/model_free/tm2_grid/
- copied from r12320, 1.3/test_suite/shared_data/model_free/tm2_grid/
branches/multi_processor_merge/test_suite/shared_data/model_free/tm3_grid/
- copied from r12320, 1.3/test_suite/shared_data/model_free/tm3_grid/
branches/multi_processor_merge/test_suite/shared_data/model_free/tm4_grid/
- copied from r12320, 1.3/test_suite/shared_data/model_free/tm4_grid/
branches/multi_processor_merge/test_suite/shared_data/model_free/tm5_grid/
- copied from r12320, 1.3/test_suite/shared_data/model_free/tm5_grid/
branches/multi_processor_merge/test_suite/shared_data/model_free/tm6_grid/
- copied from r12320, 1.3/test_suite/shared_data/model_free/tm6_grid/
branches/multi_processor_merge/test_suite/shared_data/model_free/tm7_grid/
- copied from r12320, 1.3/test_suite/shared_data/model_free/tm7_grid/
branches/multi_processor_merge/test_suite/shared_data/model_free/tm8_grid/
- copied from r12320, 1.3/test_suite/shared_data/model_free/tm8_grid/
branches/multi_processor_merge/test_suite/shared_data/model_free/tm9_grid/
- copied from r12320, 1.3/test_suite/shared_data/model_free/tm9_grid/
branches/multi_processor_merge/test_suite/system_tests/scripts/model_free/bug_14872_unicode_selection.py
- copied unchanged from r12320,
1.3/test_suite/system_tests/scripts/model_free/bug_14872_unicode_selection.py
branches/multi_processor_merge/test_suite/system_tests/scripts/model_free/bugs_12582_12591_12607.py
- copied unchanged from r12320,
1.3/test_suite/system_tests/scripts/model_free/bugs_12582_12591_12607.py
branches/multi_processor_merge/test_suite/system_tests/scripts/model_free/create_m4.py
- copied unchanged from r12320,
1.3/test_suite/system_tests/scripts/model_free/create_m4.py
branches/multi_processor_merge/test_suite/system_tests/scripts/model_free/generate_ri.py
- copied unchanged from r12320,
1.3/test_suite/system_tests/scripts/model_free/generate_ri.py
branches/multi_processor_merge/test_suite/system_tests/scripts/model_free/latex_mf_table.py
- copied unchanged from r12320,
1.3/test_suite/system_tests/scripts/model_free/latex_mf_table.py
branches/multi_processor_merge/test_suite/system_tests/scripts/model_free/omp_model_free.py
- copied unchanged from r12320,
1.3/test_suite/system_tests/scripts/model_free/omp_model_free.py
[... 76 lines stripped ...]
r12324 - in /branches/multi_processor_merge: ./ test_suite/shared_data/model_free/ test_suite/shared_data/model_free/local_t...