relax SVN archive

Fix for the Test_periodic_table.test_get_atomic_mass unit test - the method calls were incorrect.

Changed the method call in the new Test_periodic_table.test_get_atomic_mass unit test.

Created a unit test for the Periodic_table.atomic_mass() method.

This method is not implemented yet.

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.

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.

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.

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.

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.

Implemented the lib.periodic_table.periodic_table.atomic_weight() method.

This returns the standard atomic weight of the atom as a float.

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.