Author: bugman
Date: Thu Aug 28 18:19:08 2014
New Revision: 25401
URL: http://svn.gna.org/viewcvs/relax?rev=25401&view=rev
Log:
Merged revisions 25393-25400 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r25393 | bugman | 2014-08-28 17:12:57 +0200 (Thu, 28 Aug 2014) | 6 lines
Added all gyromagnetic ratio information from lib.physical_constants to
lib.periodic_table.
The Periodic_table.gyromagnetic_ratio() method has been added to allow this
value to be easily
returned.
........
r25394 | tlinnet | 2014-08-28 17:31:56 +0200 (Thu, 28 Aug 2014) | 3 lines
Added to back-end of R2eff estimate module, to be able to switch between
the function Jacobian or the chi2 Jacobian.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25395 | tlinnet | 2014-08-28 17:31:59 +0200 (Thu, 28 Aug 2014) | 3 lines
Modified user function 'relax_disp.r2eff_err_estimate', to be able switch
between the Jacobians.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25396 | tlinnet | 2014-08-28 17:32:01 +0200 (Thu, 28 Aug 2014) | 36 lines
Modified systemtest Relax_disp.verify_estimate_r2eff_err_compare_mc, to try
the difference between the Jacobian.
The results are:
Printing the estimated R2eff error as function of estimation from
Co-variance and number of Monte-Carlo simulations.
-2 0.069 0.081 0.085 0.092 0.085 0.074 0.083 0.069 0.066 0.074 0.025
0.035 0.018 0.016 sum= 0.874
-1 0.052 0.023 0.034 0.021 0.020 0.041 0.030 0.028 0.011 0.163 0.048
0.012 0.009 0.010 sum= 0.502
0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000 sum= 0.000
10 0.044 0.043 0.044 0.049 0.053 0.027 0.048 0.043 0.032 0.038 0.016
0.014 0.013 0.009 sum= 0.473
20 0.038 0.044 0.051 0.050 0.049 0.040 0.046 0.035 0.037 0.034 0.015
0.020 0.009 0.008 sum= 0.475
30 0.029 0.050 0.050 0.054 0.041 0.040 0.030 0.041 0.024 0.038 0.015
0.012 0.009 0.008 sum= 0.441
40 0.031 0.041 0.043 0.044 0.046 0.039 0.040 0.036 0.032 0.036 0.014
0.020 0.008 0.009 sum= 0.439
0.9 ++------+------+-------+-------+------+-------+-------+------+------++
+ A + + + R2eff error as function of MC number+**A*** +
0.8 ++ * ++
| * |
0.7 ++ * ++
| * |
0.6 ++ * ++
| * |
0.5 ++ A ++
| * A**************A*************** |
| * ** A**************A
0.4 ++ * * ++
| * ** |
0.3 ++ * * ++
| * ** |
0.2 ++ * * ++
| * ** |
0.1 ++ * * ++
+ *** + + + + + + + +
0 ++------A------+-------+-------+------+-------+-------+------+------++
-5 0 5 10 15 20 25 30 35
40
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
........
r25397 | bugman | 2014-08-28 17:35:28 +0200 (Thu, 28 Aug 2014) | 3 lines
Fix for the recently introduced lib.periodic_table.isotope_to_mass_symbol()
function.
........
r25398 | bugman | 2014-08-28 17:39:08 +0200 (Thu, 28 Aug 2014) | 3 lines
Bug fix for the Periodic_table.gyromagnetic_ratio() method - the self
argument was missing.
........
r25399 | bugman | 2014-08-28 18:15:38 +0200 (Thu, 28 Aug 2014) | 3 lines
Deleted the gyromagnetic ratio values and return_gyromagnetic_ratio()
function from lib.physical_constants.
........
r25400 | bugman | 2014-08-28 18:17:20 +0200 (Thu, 28 Aug 2014) | 6 lines
Shifted all of relax to use the lib.periodic_table module for gyromagnetic
ratios.
The values and value returning function have been removed from
lib.physical_constants and replaced
by the Periodic_table.gyromagnetic_ratio() method in the lib.periodic_table
module.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/stereochem_analysis.py
branches/frame_order_cleanup/lib/alignment/alignment_tensor.py
branches/frame_order_cleanup/lib/nmr.py
branches/frame_order_cleanup/lib/periodic_table.py
branches/frame_order_cleanup/lib/physical_constants.py
branches/frame_order_cleanup/pipe_control/palmer.py
branches/frame_order_cleanup/pipe_control/pcs.py
branches/frame_order_cleanup/pipe_control/rdc.py
branches/frame_order_cleanup/pipe_control/spectrometer.py
branches/frame_order_cleanup/specific_analyses/consistency_tests/api.py
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
branches/frame_order_cleanup/specific_analyses/jw_mapping/api.py
branches/frame_order_cleanup/specific_analyses/model_free/api.py
branches/frame_order_cleanup/specific_analyses/model_free/optimisation.py
branches/frame_order_cleanup/specific_analyses/relax_disp/cpmgfit.py
branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py
branches/frame_order_cleanup/specific_analyses/relax_disp/nessy.py
branches/frame_order_cleanup/specific_analyses/relax_disp/sherekhan.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/A_to_chi.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/pcs_back_calc.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
branches/frame_order_cleanup/user_functions/relax_disp.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/stereochem_analysis.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/lib/alignment/alignment_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/alignment/alignment_tensor.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/lib/nmr.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/nmr.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/lib/periodic_table.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/periodic_table.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/lib/physical_constants.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/physical_constants.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/pipe_control/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/palmer.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pcs.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/rdc.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/pipe_control/spectrometer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/spectrometer.py?rev=25401&r1=25400&r2=25401&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/consistency_tests/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/consistency_tests/api.py?rev=25401&r1=25400&r2=25401&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/jw_mapping/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/jw_mapping/api.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/model_free/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/model_free/api.py?rev=25401&r1=25400&r2=25401&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/model_free/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/model_free/optimisation.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/cpmgfit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/cpmgfit.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/data.py?rev=25401&r1=25400&r2=25401&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/estimate_r2eff.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/nessy.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/nessy.py?rev=25401&r1=25400&r2=25401&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/sherekhan.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/sherekhan.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=25401&r1=25400&r2=25401&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/A_to_chi.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/A_to_chi.py?rev=25401&r1=25400&r2=25401&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/pcs_back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/pcs_back_calc.py?rev=25401&r1=25400&r2=25401&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py?rev=25401&r1=25400&r2=25401&view=diff
Modified: branches/frame_order_cleanup/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/relax_disp.py?rev=25401&r1=25400&r2=25401&view=diff
r25401 - in /branches/frame_order_cleanup: ./ auto_analyses/ lib/ lib/alignment/ pipe_control/ specific_analyses/consistency...