Author: bugman
Date: Tue Jun 17 12:07:35 2014
New Revision: 24020
URL: http://svn.gna.org/viewcvs/relax?rev=24020&view=rev
Log:
Created an initial Relax_disp.test_lm63_3site_synthetic system test.
This should have been set up a long time ago. It uses the synthetic
noise-free data in the
test_suite/shared_data/dispersion/lm63_3site directory which was created for
a system test but never
converted into one. The test still needs modifications to allow it to pass.
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=24020&r1=24019&r2=24020&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Tue Jun 17 12:07:35 2014
@@ -3765,6 +3765,70 @@
self.assertAlmostEqual(res61L.k_AB, 10.55, 0)
+ def test_lm63_3site_synthetic(self):
+ """Test the 'LM63 3-site' dispersion model using the pure noise-free
synthetic data."""
+
+ # The path to the data files.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'lm63_3site'
+
+ # Load the state file.
+ self.interpreter.reset()
+ self.interpreter.state.load(data_path+sep+'r2eff_values')
+
+ # A new data pipe.
+ self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to='LM63
3-site', bundle_to='relax_disp')
+ self.interpreter.pipe.switch(pipe_name='LM63 3-site')
+
+ # Set up the model data.
+ self.interpreter.relax_disp.select_model(model='LM63 3-site')
+ self.interpreter.value.copy(pipe_from='R2eff', pipe_to='LM63
3-site', param='r2eff')
+ self.interpreter.spin.isotope('15N')
+
+ # Alias the spins.
+ spin1 = return_spin(":1")
+ spin2 = return_spin(":2")
+
+ # 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)
+
+ # Manually set the parameter values.
+ spin1.r2 = {r20_key1: 12.0, r20_key2: 12.0}
+ spin1.phi_ex_B = 0.1
+ spin1.phi_ex_C = 0.5
+ spin1.kB = 1500.0
+ spin1.kC = 2500.0
+ spin2.r2 = {r20_key1: 15.0, r20_key2: 15.0}
+ spin2.phi_ex_B = 0.1
+ spin2.phi_ex_C = 0.5
+ spin2.kB = 1500.0
+ spin2.kC = 2500.0
+
+ # Low precision optimisation.
+ self.interpreter.minimise(min_algor='simplex', line_search=None,
hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None,
max_iter=1000, constraints=True, scaling=True, verbosity=1)
+
+ # Printout.
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s %-20s" % ("Parameter", "Value (:1)", "Value
(:2)"))
+ print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin1.r2[r20_key1],
spin2.r2[r20_key1]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin1.r2[r20_key2],
spin2.r2[r20_key2]))
+ print("%-20s %20.15g %20.15g" % ("phi_ex_B", spin1.phi_ex_B,
spin2.phi_ex_B))
+ print("%-20s %20.15g %20.15g" % ("phi_ex_C", spin1.phi_ex_C,
spin2.phi_ex_C))
+ print("%-20s %20.15g %20.15g" % ("kB", spin1.kB, spin2.kB))
+ print("%-20s %20.15g %20.15g" % ("kC", spin1.kC, spin2.kC))
+ print("%-20s %20.15g %20.15g\n" % ("chi2", spin1.chi2, spin2.chi2))
+
+ # Monte Carlo simulations.
+ self.interpreter.monte_carlo.setup(number=3)
+
self.interpreter.self.interpreter.monte_carlo.create_data(method='back_calc')
+ self.interpreter.monte_carlo.initial_values()
+ self.interpreter.minimise(min_algor='simplex', line_search=None,
hessian_mod=None, hessian_type=None, func_tol=1e-2, grad_tol=None,
max_iter=10, constraints=True, scaling=True, verbosity=1)
+ self.interpreter.monte_carlo.error_analysis()
+
+ # Save the results.
+ self.interpreter.results.write(file='devnull', compress_type=1,
force=True)
+
+
def test_m61_data_to_m61(self):
"""Test the relaxation dispersion 'M61' model curve fitting to fixed
time synthetic data."""
r24020 - /trunk/test_suite/system_tests/relax_disp.py