Merged revisions 25346-25391 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
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r25346 | tlinnet | 2014-08-27 20:06:21 +0200 (Wed, 27 Aug 2014) | 14 lines
Removed the user function to estimate the R2eff values and errors with scipy.optimize.leastsq.
With the newly implemented Jacobian and Hessian of the exponential decay function, the front-end to
scipy.optimize.leastsq does not serve a purpose.
This is because minfx is now as fast as scipy.optimize.leastsq, and can estimate the errors from the
Jacobian to the exact same numbers as scipy.optimize.leastsq.
In addition to that, the covariance can be calculated by QR decomposition.
This adds additional feature for checking for a singular matrix.
The back-end wilÃl still be kept in place for the coming tim, but could be removed later.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25347 | tlinnet | 2014-08-27 20:06:23 +0200 (Wed, 27 Aug 2014) | 12 lines
Added front-end to the new user function relax_disp.r2eff_err_estimate(), which will estimate the R2eff errors
from a pipe and spins with optimised values of R2eff and i0.
The co-variance matrix can be calculated from the optimised parameters, and the Jacobian.
Big care should be taken not to directly trust these results, since the errors are quite different compared to the Monte-Carlo simulations.
This implementation, will reach the exact same error estimation as scipy.optimize.leastsq.
But with much better control over the data, and insight into the calculations.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25348 | tlinnet | 2014-08-27 20:06:24 +0200 (Wed, 27 Aug 2014) | 3 lines
Added method to automatically perform error analysis on peak heights.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25349 | tlinnet | 2014-08-27 20:06:26 +0200 (Wed, 27 Aug 2014) | 3 lines
Modified systemtest Relax_disp.test_estimate_r2eff() to first do a Grid Search, then minimise and then estimate the errors for R2eff and i0.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25350 | tlinnet | 2014-08-27 20:06:28 +0200 (Wed, 27 Aug 2014) | 3 lines
Added back-end to estimate R2eff errors.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25351 | tlinnet | 2014-08-27 20:55:05 +0200 (Wed, 27 Aug 2014) | 3 lines
Fix to systemtest test_estimate_r2eff_error(), to first delete the old error estimations.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25352 | tlinnet | 2014-08-27 20:55:06 +0200 (Wed, 27 Aug 2014) | 3 lines
Added several tests to: test_estimate_r2eff_error, to compare different output from algorithms.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25353 | tlinnet | 2014-08-27 20:55:08 +0200 (Wed, 27 Aug 2014) | 3 lines
Cleaned up code in R2eff error module. Also removed a non working Hessian matrix.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25354 | tlinnet | 2014-08-27 21:02:30 +0200 (Wed, 27 Aug 2014) | 3 lines
Moved code around, and made function multifit_covar() independent of Class object.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25355 | tlinnet | 2014-08-27 21:08:45 +0200 (Wed, 27 Aug 2014) | 3 lines
Inserted checks for C module is available in module for estimateing R2eff error.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25356 | tlinnet | 2014-08-27 21:10:40 +0200 (Wed, 27 Aug 2014) | 3 lines
Removed unnessary call to eksperimental Exp class.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25357 | tlinnet | 2014-08-27 21:18:50 +0200 (Wed, 27 Aug 2014) | 6 lines
Renamed systemtest, that test the user function for estimating the R2eff error:
test_estimate_r2eff_err, test the user function.
test_estimate_r2eff_err_methods, test different methods for getting the error.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25358 | tlinnet | 2014-08-27 21:55:19 +0200 (Wed, 27 Aug 2014) | 7 lines
Added systemtest, Relax_disp.test_estimate_r2eff_err_auto and extended functionality to the auto analyses protocol.
If "exp_mc_sim_num" is set to "-1" and sent to the auto analyses, the errors of R2eff will be estimated from the Co-Variance matrix.
These errors is HIGHLY likely to be wrong, but can be used in an initial test fase, to rapidly produce data for plotting data.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25359 | tlinnet | 2014-08-27 23:45:19 +0200 (Wed, 27 Aug 2014) | 3 lines
Added script, to be used in GUI test.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25360 | tlinnet | 2014-08-27 23:45:22 +0200 (Wed, 27 Aug 2014) | 3 lines
Added gui test Relax_disp.test_r2eff_err_estimate, to test the setting of MC Sim to -1 for exponential R2eff error estimation.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25361 | tlinnet | 2014-08-27 23:45:26 +0200 (Wed, 27 Aug 2014) | 9 lines
Added keyword "exp_mc_sim_num", to the auto analyses in the GUI.
This sets the number of Monte Carlo simulations for R2eff error estimation in exponential curve fitting.
When setting to -1, the errors are estimated from the Covariance Matrix.
These errors are highly likely to be wrong, but can be used in Rapid testing of data and plotting.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25362 | tlinnet | 2014-08-27 23:45:28 +0200 (Wed, 27 Aug 2014) | 12 lines
Tried to click the "fit_r1" button in the GUI test, but receives an error.
relax --gui-tests Relax_disp.test_r2eff_err_estimate
----
File "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/api.py", line 463, in get_param_values
values.append(get_value(spins=spins, sim_index=sim_index, param_name=param_name, spin_index=si, r20_key=r20_key))
File "/Users/tlinnet/software/relax_trunk/specific_analyses/relax_disp/parameters.py", line 393, in get_value
obj = getattr(spins[spin_index], param_name)
AttributeError: 'SpinContainer' object has no attribute 'r1'
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25363 | tlinnet | 2014-08-28 09:40:09 +0200 (Thu, 28 Aug 2014) | 5 lines
Moved the mc_sim_num GUI element in the analysis tab ip, as it is executed first.
Also modified the tooltip.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25364 | tlinnet | 2014-08-28 09:46:45 +0200 (Thu, 28 Aug 2014) | 3 lines
Added a warning to the auto analyses about error estimation from the Co-variance.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25365 | tlinnet | 2014-08-28 09:49:32 +0200 (Thu, 28 Aug 2014) | 3 lines
Removed yet another comma from GUI tooltip.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25366 | bugman | 2014-08-28 09:53:32 +0200 (Thu, 28 Aug 2014) | 5 lines
Formatting changes for the lib.periodic_table module.
This is in preparation for extending the information content of this module.
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r25367 | tlinnet | 2014-08-28 10:18:40 +0200 (Thu, 28 Aug 2014) | 8 lines
Modified systemtest 'test_estimate_r2eff_err_auto', to use the GUI script.
It seems to work Ãperfect.
This is to test against GUI script:
test_r2eff_err_estimate
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25368 | tlinnet | 2014-08-28 10:18:43 +0200 (Thu, 28 Aug 2014) | 7 lines
Modified test_estimate_r2eff_err_auto, to set r1_fit to False.
This still make the systemtest pass, and fit R1.
So this means R1 fit button is not functioning properly.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25369 | tlinnet | 2014-08-28 10:20:15 +0200 (Thu, 28 Aug 2014) | 3 lines
Fix for warning message in the auto analyses in the GUI.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25370 | tlinnet | 2014-08-28 10:31:22 +0200 (Thu, 28 Aug 2014) | 3 lines
Tried to improve docstring for API documentation.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25371 | bugman | 2014-08-28 11:08:50 +0200 (Thu, 28 Aug 2014) | 5 lines
Added all of the IUPAC 2011 atomic weights to the lib.periodic_table module.
These will be useful for correctly calculating the centre of mass of a molecule.
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r25372 | bugman | 2014-08-28 11:09:38 +0200 (Thu, 28 Aug 2014) | 3 lines
The lib.periodic_table method for adding elements is now private.
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r25373 | bugman | 2014-08-28 11:21:46 +0200 (Thu, 28 Aug 2014) | 3 lines
Fix for an accidental mistake in the lib.periodic_table module.
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r25374 | bugman | 2014-08-28 11:24:49 +0200 (Thu, 28 Aug 2014) | 6 lines
Created the unit test infrastructure for the lib.periodic_table module.
This includes one unit test of the lib.periodic_table.periodic_table.atomic_weight() function which
has not been implemented yet.
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r25375 | bugman | 2014-08-28 11:35:37 +0200 (Thu, 28 Aug 2014) | 5 lines
Implemented the lib.periodic_table.periodic_table.atomic_weight() method.
This returns the standard atomic weight of the atom as a float.
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r25376 | tlinnet | 2014-08-28 12:34:25 +0200 (Thu, 28 Aug 2014) | 3 lines
Yet another try to make the API documentation working.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25377 | tlinnet | 2014-08-28 12:34:29 +0200 (Thu, 28 Aug 2014) | 39 lines
Implemented system test Relax_disp.verify_estimate_r2eff_err_compare_mc for testing R2eff error as function of Monte Carlo simulation.
Note, since the name does not start with "test", but with "verify", this test will not be issued in the system test suite.
-1 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
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
50 0.038 0.037 0.048 0.041 0.048 0.036 0.041 0.036 0.030 0.035 0.014 0.018 0.010 0.007 sum= 0.438
100 0.036 0.039 0.040 0.044 0.043 0.039 0.041 0.040 0.033 0.037 0.013 0.018 0.008 0.007 sum= 0.440
150 0.035 0.040 0.045 0.046 0.043 0.041 0.041 0.035 0.034 0.035 0.013 0.017 0.008 0.008 sum= 0.442
200 0.034 0.040 0.046 0.047 0.042 0.037 0.039 0.035 0.033 0.039 0.012 0.019 0.009 0.008 sum= 0.440
250 0.036 0.039 0.042 0.042 0.043 0.039 0.043 0.035 0.033 0.037 0.013 0.016 0.009 0.007 sum= 0.436
300 0.034 0.040 0.047 0.047 0.043 0.037 0.042 0.036 0.033 0.039 0.013 0.018 0.009 0.008 sum= 0.446
350 0.034 0.041 0.045 0.046 0.043 0.037 0.038 0.036 0.036 0.037 0.013 0.018 0.009 0.008 sum= 0.441
400 0.036 0.037 0.043 0.047 0.044 0.038 0.043 0.038 0.035 0.037 0.014 0.018 0.009 0.008 sum= 0.448
450 0.034 0.040 0.044 0.045 0.044 0.038 0.041 0.035 0.034 0.039 0.012 0.018 0.009 0.008 sum= 0.442
0.9 ++-----+------+------+------+------+-----+------+------+------+-----++
+ A + + R2eff error as function of MC number **A*** +
0.8 ++ * ++
| * |
0.7 ++ * ++
| * |
0.6 ++ * ++
| * |
0.5 ++ * ++
| * |
| * A******A******A******A*****A******A******A******A******A
0.4 ++ * * ++
| * * |
0.3 ++ * * ++
| * * |
0.2 ++ * * ++
| * * |
0.1 ++ * * ++
+ ** + + + + + + + + +
0 ++-----A------+------+------+------+-----+------+------+------+-----++
-50 0 50 100 150 200 250 300 350 400 450
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25378 | bugman | 2014-08-28 13:52:33 +0200 (Thu, 28 Aug 2014) | 6 lines
Converted the periodic table in lib.periodic_table into a dictionary type object.
The new Element container has been added for storing the information about each element in the
table. The Periodic_table object used the atomic symbol as a key for each Element instance.
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r25379 | tlinnet | 2014-08-28 15:14:16 +0200 (Thu, 28 Aug 2014) | 94 lines
Modified systemtest test Relax_disp.test_estimate_r2eff_err_methods() to show the difference between using the direct function Jacobian, or the chi2 function Jacobian.
Added also the functionality to the estimate R2eff module, to switch between using the different Jacobians.
The results show, that R2eff can be estimated better.
----------------------
The results are:
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0.
r2eff=8.646/8.646 r2eff_err=0.0348/0.0692 i0=202664.191/202664.191 i0_err=699.6443/712.4201
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2.
r2eff=10.377/10.377 r2eff_err=0.0403/0.0810 i0=206049.558/206049.558 i0_err=776.4215/782.1833
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5.
r2eff=10.506/10.506 r2eff_err=0.0440/0.0853 i0=202586.332/202586.332 i0_err=763.9678/758.7052
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0.
r2eff=10.903/10.903 r2eff_err=0.0476/0.0922 i0=203455.021/203455.021 i0_err=837.8779/828.7280
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1.
r2eff=10.684/10.684 r2eff_err=0.0446/0.0853 i0=218670.412/218670.412 i0_err=850.0210/830.9558
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5.
r2eff=10.501/10.501 r2eff_err=0.0371/0.0742 i0=206502.512/206502.512 i0_err=794.0523/772.9843
R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1.
r2eff=11.118/11.118 r2eff_err=0.0413/0.0827 i0=216447.241/216447.241 i0_err=784.6562/788.0384
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5.
r2eff=7.866/7.866 r2eff_err=0.0347/0.0695 i0=211869.715/211869.715 i0_err=749.2776/763.6930
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1.
r2eff=9.259/9.259 r2eff_err=0.0331/0.0661 i0=217703.151/217703.151 i0_err=682.2137/685.5838
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5.
r2eff=9.565/9.565 r2eff_err=0.0373/0.0745 i0=211988.939/211988.939 i0_err=839.0313/827.0373
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5.
r2eff=3.240/3.240 r2eff_err=0.0127/0.0253 i0=214417.382/214417.382 i0_err=595.8865/613.4378
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1.
r2eff=5.084/5.084 r2eff_err=0.0177/0.0352 i0=226358.691/226358.691 i0_err=660.5314/655.7670
R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1.
r2eff=2.208/2.208 r2eff_err=0.0091/0.0178 i0=228620.553/228620.553 i0_err=564.8353/560.0873
R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1.
r2eff=1.711/1.711 r2eff_err=0.0077/0.0155 i0=224087.486/224087.486 i0_err=539.4300/546.4217
Fitting with minfx to: 52V @N
-----------------------------
min_algor='Newton', c_code=True, constraints=False, chi2_jacobian?=False
------------------------------------------------------------------------
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0, with 4 time points. r2eff=8.646 r2eff_err=0.0692, i0=202664.2, i0_err=712.4201, chi2=3.758.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2, with 5 time points. r2eff=10.377 r2eff_err=0.0810, i0=206049.6, i0_err=782.1833, chi2=27.291.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5, with 5 time points. r2eff=10.506 r2eff_err=0.0853, i0=202586.3, i0_err=758.7052, chi2=13.357.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0, with 5 time points. r2eff=10.903 r2eff_err=0.0922, i0=203455.0, i0_err=828.7280, chi2=33.632.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1, with 5 time points. r2eff=10.684 r2eff_err=0.0853, i0=218670.4, i0_err=830.9558, chi2=35.818.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5, with 5 time points. r2eff=10.501 r2eff_err=0.0742, i0=206502.5, i0_err=772.9843, chi2=7.356.
R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1, with 5 time points. r2eff=11.118 r2eff_err=0.0827, i0=216447.2, i0_err=788.0384, chi2=15.587.
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5, with 5 time points. r2eff=7.866 r2eff_err=0.0695, i0=211869.7, i0_err=763.6930, chi2=14.585.
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1, with 5 time points. r2eff=9.259 r2eff_err=0.0661, i0=217703.2, i0_err=685.5838, chi2=79.498.
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5, with 5 time points. r2eff=9.565 r2eff_err=0.0745, i0=211988.9, i0_err=827.0373, chi2=0.447.
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5, with 5 time points. r2eff=3.240 r2eff_err=0.0253, i0=214417.4, i0_err=613.4378, chi2=1.681.
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1, with 5 time points. r2eff=5.084 r2eff_err=0.0352, i0=226358.7, i0_err=655.7670, chi2=23.170.
R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1, with 5 time points. r2eff=2.208 r2eff_err=0.0178, i0=228620.6, i0_err=560.0873, chi2=7.794.
R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1, with 5 time points. r2eff=1.711 r2eff_err=0.0155, i0=224087.5, i0_err=546.4217, chi2=21.230.
Fitting with minfx to: 52V @N
-----------------------------
min_algor='BFGS', c_code=False, constraints=False, chi2_jacobian?=True
----------------------------------------------------------------------
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0, with 4 time points. r2eff=8.646 r2eff_err=0.0524, i0=202664.2, i0_err=1239.0827, chi2=3.758.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2, with 5 time points. r2eff=10.377 r2eff_err=0.0228, i0=206049.6, i0_err=178.1907, chi2=27.291.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5, with 5 time points. r2eff=10.506 r2eff_err=0.0345, i0=202586.3, i0_err=705.7630, chi2=13.357.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0, with 5 time points. r2eff=10.903 r2eff_err=0.0206, i0=203455.0, i0_err=186.0857, chi2=33.632.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1, with 5 time points. r2eff=10.684 r2eff_err=0.0198, i0=218670.4, i0_err=165.0420, chi2=35.818.
R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5, with 5 time points. r2eff=10.501 r2eff_err=0.0407, i0=206502.5, i0_err=321.3685, chi2=7.356.
R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1, with 5 time points. r2eff=11.118 r2eff_err=0.0301, i0=216447.2, i0_err=248.9394, chi2=15.587.
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5, with 5 time points. r2eff=7.866 r2eff_err=0.0280, i0=211869.7, i0_err=259.8845, chi2=14.585.
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1, with 5 time points. r2eff=9.259 r2eff_err=0.0108, i0=217703.2, i0_err=88.1514, chi2=79.498.
R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5, with 5 time points. r2eff=9.565 r2eff_err=0.1630, i0=211988.9, i0_err=2054.6615, chi2=0.447.
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5, with 5 time points. r2eff=3.240 r2eff_err=0.0485, i0=214417.4, i0_err=611.7573, chi2=1.681.
R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1, with 5 time points. r2eff=5.084 r2eff_err=0.0124, i0=226358.7, i0_err=122.7341, chi2=23.170.
R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1, with 5 time points. r2eff=2.208 r2eff_err=0.0086, i0=228620.6, i0_err=219.4208, chi2=7.794.
R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1, with 5 time points. r2eff=1.711 r2eff_err=0.0101, i0=224087.5, i0_err=166.9081, chi2=21.230.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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r25380 | bugman | 2014-08-28 15:17:35 +0200 (Thu, 28 Aug 2014) | 8 lines
Added isotope information to the lib.periodic_table module including mass number and atomic mass.
A new Isotope data container has been added to store this information. The Periodic_table._add()
method now returns the initialised Element container. This container has the _add_isotope() method
which is used to initialise Isotope data containers with the mass number and atomic mass and append
it to the list.
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r25381 | bugman | 2014-08-28 15:24:39 +0200 (Thu, 28 Aug 2014) | 5 lines
Created a unit test for the Periodic_table.atomic_mass() method.
This method is not implemented yet.
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r25382 | bugman | 2014-08-28 15:34:20 +0200 (Thu, 28 Aug 2014) | 3 lines
Changed the method call in the new Test_periodic_table.test_get_atomic_mass unit test.
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r25383 | bugman | 2014-08-28 15:42:34 +0200 (Thu, 28 Aug 2014) | 3 lines
Fix for the Test_periodic_table.test_get_atomic_mass unit test - the method calls were incorrect.
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r25384 | bugman | 2014-08-28 15:57:42 +0200 (Thu, 28 Aug 2014) | 5 lines
Implemented the lib.periodic_table module Periodic_table.atomic_mass() method.
This method will return either the atomic mass of an isotope or the standard atomic weight.
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r25385 | bugman | 2014-08-28 16:19:12 +0200 (Thu, 28 Aug 2014) | 7 lines
Changed the operation of the lib.structure.mass.centre_of_mass() function.
Instead of using the lib.physical_constants.return_atomic_mass() function, the centre_of_mass()
function instead uses the lib.periodic_table.periodic_table.atomic_mass() method. This is a huge
improvement in that the exact mass of absolutely all elements are taken into account.
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r25386 | bugman | 2014-08-28 16:21:39 +0200 (Thu, 28 Aug 2014) | 7 lines
Deletion of the lib.physical_constants.return_atomic_mass() function and all relative atomic masses.
These were inaccurate and only included a tiny subset of all standard atomic weight and isotope
masses. The functionality has been replaced by the complete and 100% accurate complete
Periodic_table object in the lib.periodic_table module.
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r25387 | bugman | 2014-08-28 16:29:09 +0200 (Thu, 28 Aug 2014) | 6 lines
Fix for the MolContainer.fill_object_from_gaussian() method.
This is in the lib.structure.internal.molecules module. The Periodic_table.lookup_z_to_symbol()
method in the lib.periodic_table module has been renamed to lookup_symbol().
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r25388 | bugman | 2014-08-28 16:33:37 +0200 (Thu, 28 Aug 2014) | 7 lines
Fix for the Periodic_table.lookup_symbol() method.
The __init__() method of the Periodic_table has been reintroduced to initialise a fast atomic symbol
lookup table. The _add() method then updates this table. And the lookup_symbol() method now uses
this lookup table to correctly return the symbol.
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r25389 | bugman | 2014-08-28 16:37:16 +0200 (Thu, 28 Aug 2014) | 7 lines
Tiny fix for the Diffusion_tensor.test_create_diff_tensor_pdb_ellipsoid system test.
The switch to using the lib.periodic_table module for atomic masses has caused the centre of mass of
the ellipsoid to shift just enough that one ATOM coordinate in the PDB file has changed its last
significant digit.
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r25390 | bugman | 2014-08-28 16:46:23 +0200 (Thu, 28 Aug 2014) | 8 lines
Created the lib.periodic_table.process_symbol() function.
This will take an atomic symbol and return a copy of it with an uppercase first letter and lowercase
second letter. This is used by the Periodic_table methods atomic_mass() and atomic_weight() to
allow for non-standard symbol input, for example if the element name comes directly from the all
uppercase PDB file format without translation.
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r25391 | tlinnet | 2014-08-28 16:49:43 +0200 (Thu, 28 Aug 2014) | 7 lines
Tried to scale the Covariance matrix, as explained here: http://www.orbitals.com/self/least/least.htm.
This does not work better.
Also replaced "errors" to "weights" to the multifit_covar(), to better determine control calculations.
task #7822(https://gna.org/task/index.php?7822): Implement user function to estimate R2eff and associated errors for exponential curve fitting.
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