relax SVN archive

Further cleaned up the code in NS CPMG 2site start.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Simplified model CPMG 2site 3D.

The expansion of matrixes to higher dimensionality is not neccessary.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Cleaned up the code in model NS CPMG 2site star.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Rearranged the dot code, for better view.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Moved the costly matrix_exponential of cR2 out of for loops.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Rearranged the code, to properly show the nested matrix exponentials in dot functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Moved the costly finding of matrix exponential out of for loops for eR_tcp.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Changes of values to systemtest test_hansen_cpmg_data_to_ns_cpmg_2site_star.

The values are changed, since chi2 is lower than before.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Started using the newly cR2 variable, extracted from higher dimensional data.

This should be okay, but systemtest test_hansen_cpmg_data_to_ns_cpmg_2site_star, now fails:

Optimised parameter values:
r2 (SQ CPMG - 500.00000000 MHz) 4.998935658499767
r2 (SQ CPMG - 800.00000000 MHz) 6.898256259440341
dw 2.092924953509931
pA 0.986716058519642
kex 2438.044235414625746

Optimised parameters:

Parameter Value (:70) Value (:71)
R2 (500 MHz) 6.95812598916492 4.99893565849977
R2 (800 MHz) 9.39656319607375 6.89825625944034
pA 0.989701272773474 0.986716058519642
dw 5.67316761415756 2.09292495350993
kex 1713.67781672744 2438.04423541463
chi2 52.510693756237 15.1644902423334

F
======================================================================
FAIL: test_hansen_cpmg_data_to_ns_cpmg_2site_star (test_suite.system_tests.relax_disp.Relax_disp)
Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site star' dispersion model.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/tlinnet/software/disp_spin_speed/test_suite/system_tests/relax_disp.py", line 3211, in test_hansen_cpmg_data_to_ns_cpmg_2site_star
self.assertAlmostEqual(spin71.pA, 0.992258541625787, 2)
AssertionError: 0.98671605851964195 != 0.992258541625787 within 2 places

---------------
Compared to systemtest:
It seems that there has been "problems" with residue 71 before.

# Checks for residue :70.
self.assertAlmostEqual(spin70.r2[r20_key1], 6.95543947938561, 1)
self.assertAlmostEqual(spin70.r2[r20_key2], 9.38991914134929, 1)
self.assertAlmostEqual(spin70.pA, 0.989702750971153, 3)
self.assertAlmostEqual(spin70.dw, 5.67527122494516, 1)
self.assertAlmostEqual(spin70.kex/1000, 1715.72032391817/1000, 1)
self.assertAlmostEqual(spin70.chi2, 52.5011991483842, 1)

# Checks for residue :71.
self.assertAlmostEqual(spin71.r2[r20_key1], 4.992594256544, 1)
self.assertAlmostEqual(spin71.pA, 0.992258541625787, 2)
self.assertAlmostEqual(spin71.dw/100, 2.75140650899058/100, 2)
self.assertAlmostEqual(spin71.kex/100000, 2106.60885247431/100000, 2)
self.assertAlmostEqual(spin71.chi2/100, 17.3293856656588/100, 1)

# Test the conversion to k_AB from kex and pA.
self.assertEqual(spin70.k_AB, spin70.kex * (1.0 - spin70.pA))
self.assertEqual(spin71.k_AB, spin71.kex * (1.0 - spin71.pA))

# Test the conversion to k_BA from kex and pA.
self.assertEqual(spin70.k_BA, spin70.kex * spin70.pA)
self.assertEqual(spin71.k_BA, spin71.kex * spin71.pA)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Added the systemtest: test_cpmg_synthetic_b14_to_ns_star_cluster, to check
for the model is still working after change.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.