Author: bugman Date: Thu Jan 13 14:28:30 2011 New Revision: 12322 URL: http://svn.gna.org/viewcvs/relax?rev=12322&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. ........ 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. ........ 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. ........ 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. ........ 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. ........ r12234 | bugman | 2011-01-12 14:20:50 +0100 (Wed, 12 Jan 2011) | 3 lines Removed a duplicated chi2 test from value_test(). ........ 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. ........ 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. ........ r12237 | bugman | 2011-01-12 14:25:44 +0100 (Wed, 12 Jan 2011) | 3 lines Improved print out from mesg_opt_debug(). ........ r12238 | bugman | 2011-01-12 14:26:23 +0100 (Wed, 12 Jan 2011) | 3 lines Newline fix for the mesg_opt_debug() print out. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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/. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ r12250 | bugman | 2011-01-12 16:25:36 +0100 (Wed, 12 Jan 2011) | 3 lines Newline fix. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ r12259 | bugman | 2011-01-12 17:28:54 +0100 (Wed, 12 Jan 2011) | 3 lines This time really turn off the optimisation constraints! ........ 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! ..... ........ 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. ........ 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. ........ 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. ........ 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(). ........ r12265 | bugman | 2011-01-12 19:10:10 +0100 (Wed, 12 Jan 2011) | 3 lines Converted the rest of the S2 variables to s2. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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! ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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(). ........ 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. ........ 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! ........ 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. ........ 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. ........ r12286 | bugman | 2011-01-13 11:21:52 +0100 (Thu, 13 Jan 2011) | 3 lines Added a system test script for the tm1 grid. ........ r12287 | bugman | 2011-01-13 11:25:52 +0100 (Thu, 13 Jan 2011) | 3 lines Fixes for the tm3 and tm4 relaxation data grids. ........ 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. ........ 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! ........ 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! ........ 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(). ........ 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. ........ 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! ........ 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! ........ 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! ........ 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! ........ 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. ........ 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! ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ r12305 | bugman | 2011-01-13 12:14:00 +0100 (Thu, 13 Jan 2011) | 3 lines Loosened the S2f, S2s, ts, and tf checks. ........ 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. ........ 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. ........ 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. ........ 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. ........ 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. ........ r12311 | bugman | 2011-01-13 12:32:54 +0100 (Thu, 13 Jan 2011) | 3 lines Shortened the tm5 relaxation data grid. ........ r12312 | bugman | 2011-01-13 12:34:03 +0100 (Thu, 13 Jan 2011) | 3 lines Shortened the tm6 relaxation data grid. ........ 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. ........ 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. ........ 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. ........ 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. ........ r12317 | bugman | 2011-01-13 12:44:05 +0100 (Thu, 13 Jan 2011) | 3 lines Shortened the tm8 relaxation data grid. ........ 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. ........ 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. ........ 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/bmrb/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/bmrb/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/bmrb/test_suite/shared_data/model_free/tm0_grid/ - copied from r12320, 1.3/test_suite/shared_data/model_free/tm0_grid/ branches/bmrb/test_suite/shared_data/model_free/tm1_grid/ - copied from r12320, 1.3/test_suite/shared_data/model_free/tm1_grid/ branches/bmrb/test_suite/shared_data/model_free/tm2_grid/ - copied from r12320, 1.3/test_suite/shared_data/model_free/tm2_grid/ branches/bmrb/test_suite/shared_data/model_free/tm3_grid/ - copied from r12320, 1.3/test_suite/shared_data/model_free/tm3_grid/ branches/bmrb/test_suite/shared_data/model_free/tm4_grid/ - copied from r12320, 1.3/test_suite/shared_data/model_free/tm4_grid/ branches/bmrb/test_suite/shared_data/model_free/tm5_grid/ - copied from r12320, 1.3/test_suite/shared_data/model_free/tm5_grid/ branches/bmrb/test_suite/shared_data/model_free/tm6_grid/ - copied from r12320, 1.3/test_suite/shared_data/model_free/tm6_grid/ branches/bmrb/test_suite/shared_data/model_free/tm7_grid/ - copied from r12320, 1.3/test_suite/shared_data/model_free/tm7_grid/ branches/bmrb/test_suite/shared_data/model_free/tm8_grid/ - copied from r12320, 1.3/test_suite/shared_data/model_free/tm8_grid/ branches/bmrb/test_suite/shared_data/model_free/tm9_grid/ - copied from r12320, 1.3/test_suite/shared_data/model_free/tm9_grid/ branches/bmrb/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/bmrb/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/bmrb/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/bmrb/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/bmrb/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/bmrb/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 branches/bmrb/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py - copied unchanged from r12320, 1.3/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py branches/bmrb/test_suite/system_tests/scripts/model_free/opt_setup_S2_0_970_te_2048_Rex_0_149.py - copied unchanged [... 73 lines stripped ...]