Author: tlinnet
Date: Fri Jun 20 08:11:55 2014
New Revision: 24179
URL: http://svn.gna.org/viewcvs/relax?rev=24179&view=rev
Log:
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.
Modified:
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py?rev=24179&r1=24178&r2=24179&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
(original)
+++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py Fri
Jun 20 08:11:55 2014
@@ -203,7 +203,7 @@
eR_tcp = matrix_exponential(R_mat_i)
# This is the propagator for an element of [delay tcp; 180
deg pulse; 2 times delay tcp; 180 deg pulse; delay tau], i.e. for 2 times
tau-180-tau.
- prop_2 = dot(dot(eR_tcp,
matrix_exponential(cR2*tcp_si_mi_di)), eR_tcp)
+ prop_2 = dot(dot(eR_tcp, matrix_exponential(cR2_mat_i)),
eR_tcp)
# Now create the total propagator that will evolve the
magnetization under the CPMG train, i.e. it applies the above
tau-180-tau-tau-180-tau so many times as required for the CPMG frequency
under consideration.
prop_total = square_matrix_power(prop_2, power_si_mi_di)
r24179 - /branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py