Ah, that is probably because of a bug you fixed (https://gna.org/bugs/?21954). The results were generated before this bug was fixed, so now they will be slightly different as the test_suite/shared_data/dispersion/Hansen/base_pipe.bz2 and test_suite/shared_data/dispersion/Hansen/r2eff_pipe.bz2 files have been updated. From the log file test_suite/shared_data/dispersion/Hansen/relax_results/relax_disp.log, you can see that the results are not too different. So just change the values at the start of the test to the final optimised values, and then change the values in the assertAlmostEqual() checks to the final values. I'll update the precision of these checks after running this on different OSes and 32-bit vs. 64-bit systems.
You can probably see that this is not ideal, but the only 2 other programs that support this 3-site model are Art Palmer's CPMGFit, and Michael Bieri's NESSY. But CPMGFit has the same R20 values for all fields, so we cannot compare. And the NESSY model number 4, which is this model, is not fully implemented and functional. So we have nothing to compare to. I have created synthetic data in test_suite/shared_data/dispersion/lm63_3site which was to be used for a system test, but I don't know why that is not in a test :S There is even a relax script at test_suite/shared_data/dispersion/lm63_3site/relax_results/relax_disp.py which can be converted into a single model optimisation. I must have been so busy with the paper drafting that I simply forgot to convert this to a system test. Regards, Edward On 17 June 2014 09:18, <[email protected]> wrote: > Author: tlinnet > Date: Tue Jun 17 09:18:24 2014 > New Revision: 24009 > > URL: http://svn.gna.org/viewcvs/relax?rev=24009&view=rev > Log: > Added systemtest for model LM63 3 site. > > According to results folder in: > test_suite/shared_data/dispersion/Hansen/relax_results/LM63 3-site > > This should pass. > > But i doesnt? > > Modified: > trunk/test_suite/system_tests/relax_disp.py > > Modified: trunk/test_suite/system_tests/relax_disp.py > URL: > http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=24009&r1=24008&r2=24009&view=diff > ============================================================================== > --- trunk/test_suite/system_tests/relax_disp.py (original) > +++ trunk/test_suite/system_tests/relax_disp.py Tue Jun 17 09:18:24 2014 > @@ -2492,6 +2492,70 @@ > self.assertAlmostEqual(spin71.phi_ex, 0.0553787828347638) > self.assertAlmostEqual(spin71.kex/1000, 2781.72293906248/1000) > self.assertAlmostEqual(spin71.chi2, 17.0776399916287) > + > + > + def test_hansen_cpmg_data_to_lm63_3site(self): > + """Optimisation of Dr. Flemming Hansen's CPMG data to the LM63 > dispersion model. > + > + This uses the data from Dr. Flemming Hansen's paper at > http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed > relaxation time period. > + """ > + > + # Base data setup. > + self.setup_hansen_cpmg_data(model='LM63 3-site') > + > + # Alias the spins. > + spin70 = return_spin(":70") > + spin71 = return_spin(":71") > + > + # The R20 keys. > + r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6) > + r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6) > + > + ## Set the initial parameter values. > + spin70.r2 = {r20_key1: 7.570370921220954, r20_key2: > 8.694446951909107} > + spin70.phi_ex_B = 0.14872003058250227 > + spin70.phi_ex_C = 0.1319419923472704 > + spin70.kB = 4103.672910444741 > + spin70.kC = 7029.001690726248 > + spin71.r2 = {r20_key1: 5.1347793381636, r20_key2: 7.156573986051575} > + spin71.phi_ex_B = 0.04013553485505605 > + spin71.phi_ex_C = 0.020050748406928887 > + spin71.kB = 4045.3007136121364 > + spin71.kC = 3586.38798270774 > + > + #self.interpreter.relax_disp.r20_from_min_r2eff(force=False) > + #self.interpreter.grid_search(lower=None, upper=None, inc=41, > constraints=True, verbosity=1) > + > + # Low precision optimisation. > + self.interpreter.minimise(min_algor='simplex', line_search=None, > hessian_mod=None, hessian_type=None, func_tol=1e-25, grad_tol=None, > max_iter=10000000, constraints=True, scaling=True, verbosity=1) > + > + # Printout. > + print("\n\nOptimised parameters:\n") > + print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value > (:71)")) > + print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", > spin70.r2[r20_key1], spin71.r2[r20_key1])) > + print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", > spin70.r2[r20_key2], spin71.r2[r20_key2])) > + print("%-20s %20.15g %20.15g" % ("phi_ex_B", spin70.phi_ex_B, > spin71.phi_ex_B)) > + print("%-20s %20.15g %20.15g" % ("phi_ex_C", spin70.phi_ex_C, > spin71.phi_ex_C)) > + print("%-20s %20.15g %20.15g" % ("kB", spin70.kB, spin71.kB)) > + print("%-20s %20.15g %20.15g" % ("kC", spin70.kC, spin71.kC)) > + print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2)) > + > + # Checks for residue :70. > + #self.assertAlmostEqual(spin70.r2[r20_key1], 6.74362294539099) > + #self.assertAlmostEqual(spin70.r2[r20_key2], 6.57406797067481, 6) > + self.assertAlmostEqual(spin70.phi_ex_B, 0.148720030582502) > + self.assertAlmostEqual(spin70.phi_ex_C, 0.13194199234727) > + self.assertAlmostEqual(spin70.kB/1000, 4103.67291044474/1000, 6) > + self.assertAlmostEqual(spin70.kC/1000, 7029.00169072625/1000, 6) > + #self.assertAlmostEqual(spin70.chi2, 363.534044873483) > + > + # Checks for residue :71. > + #self.assertAlmostEqual(spin71.r2[r20_key1], 5.00776657712558) > + self.assertAlmostEqual(spin71.phi_ex_B, 0.040135534855056) > + self.assertAlmostEqual(spin71.phi_ex_C, 0.0200507484069289) > + self.assertAlmostEqual(spin71.kB/1000, 4045.30071361214/1000) > + self.assertAlmostEqual(spin71.kC/1000, 3586.38798270774/1000) > + #self.assertAlmostEqual(spin71.chi2, 17.0776399916287) > > > def test_hansen_cpmg_data_to_ns_cpmg_2site_3D(self): > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
