Re: r24024 - /trunk/test_suite/system_tests/relax_disp.py -- June 17, 2014 - 13:41

This test has the added benefit that the data used is not complete, so
it checks that the missing data handling is correct.  Obviously, as
can be seen with the Relax_disp.test_korzhnev_2005_all_data test
failure, this missing data testing is not comprehensive.

Regards,

Edward

On 17 June 2014 13:27, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Hi,
>
> There's no need to delete this - it's a useful test as it is on real
> data.  Once the Relax_disp.test_lm63_3site_synthetic system test is
> debugged and working, this
> Relax_disp.test_hansen_cpmg_data_to_lm63_3site test can be updated.
> There is no such thing as too much testing :)
>
> Regards,
>
> Edward
>
>
>
> On 17 June 2014 12:32,  <tlinnet@xxxxxxxxxxxxx> wrote:
> > Author: tlinnet
> > Date: Tue Jun 17 12:32:34 2014
> > New Revision: 24024
> >
> > URL: http://svn.gna.org/viewcvs/relax?rev=24024&view=rev
> > Log:
> > Removed systemtest test_hansen_cpmg_data_to_lm63_3site.
> >
> > This was a temporary implementation and has been replaced with systemtest:
> > Relax_disp.test_lm63_3site_synthetic
> >
> > 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=24024&r1=24023&r2=24024&view=diff
> > ==============================================================================
> > --- trunk/test_suite/system_tests/relax_disp.py (original)
> > +++ trunk/test_suite/system_tests/relax_disp.py Tue Jun 17 12:32:34 2014
> > @@ -2493,69 +2493,6 @@
> >          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
> > relax-commits@xxxxxxx
> >
> > 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