Author: bugman
Date: Mon Jun 3 12:06:06 2013
New Revision: 19850
URL: http://svn.gna.org/viewcvs/relax?rev=19850&view=rev
Log:
Better checking of optimisation in the Relax_disp system tests.
This affects the Relax_disp.test_hansen_cpmg_data_LM63 and
Relax_disp.test_hansen_cpmg_data_CR72
system tests. Instead of using the auto-analysis, these tests now set the
initial parameters close
to the minimum, skip the grid search, and perform a low precision
optimisation to reach the minimum.
This is important because the low quality grid search and optimisation can
not always find the real
minimum.
Modified:
branches/relax_disp/test_suite/system_tests/relax_disp.py
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=19850&r1=19849&r2=19850&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Mon Jun 3
12:06:06 2013
@@ -136,11 +136,43 @@
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.
"""
+ # Create the data pipe and load the base data.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'
+ self.interpreter.pipe.create(pipe_name='base pipe',
pipe_type='relax_disp')
+ self.interpreter.results.read(data_path+sep+'base_pipe')
+
+ # Set the nuclear isotope data.
+ self.interpreter.spin.isotope('15N')
+
+ # Create the R2eff data pipe and load the results.
+ self.interpreter.pipe.create(pipe_name='R2eff',
pipe_type='relax_disp')
+ self.interpreter.pipe.switch(pipe_name='R2eff')
+ self.interpreter.results.read(data_path+sep+'r2eff_pipe')
+
+ # The LM63 model data pipe.
+ self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to='LM63',
bundle_to='relax_disp')
+ self.interpreter.pipe.switch(pipe_name='LM63')
+
# Set the model.
- ds.models = ['LM63']
-
- # Execute the script.
- self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data.py')
+ self.interpreter.relax_disp.select_model(model='LM63')
+
+ # Copy the data.
+ self.interpreter.value.copy(pipe_from='R2eff', pipe_to='LM63',
param='r2eff')
+
+ # Alias the spins.
+ spin70 = cdp.mol[0].res[0].spin[0]
+ spin71 = cdp.mol[0].res[1].spin[0]
+
+ # Set the initial parameter values.
+ spin70.r2 = [7, 7]
+ spin70.phi_ex = 0.3
+ spin70.kex = 5000.0
+ spin71.r2 = [5, 9]
+ spin71.phi_ex = 0.1
+ spin71.kex = 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")
@@ -154,17 +186,17 @@
print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
# Checks for residue :70.
- self.assertAlmostEqual(spin70.r2[0], 6.8058772971170374)
- self.assertAlmostEqual(spin70.r2[1], 6.6790611414921477)
- self.assertAlmostEqual(spin70.phi_ex, 0.31009292384617337)
- self.assertAlmostEqual(spin70.kex, 4763.36556651067)
- self.assertAlmostEqual(spin70.chi2, 106.393365972649)
+ self.assertAlmostEqual(spin70.r2[0], 6.80566297338119)
+ self.assertAlmostEqual(spin70.r2[1], 6.67846669704843)
+ self.assertAlmostEqual(spin70.phi_ex, 0.31011906704072)
+ self.assertAlmostEqual(spin70.kex, 4763.71326098192)
+ self.assertAlmostEqual(spin70.chi2, 106.393365192324)
# Checks for residue :71.
- self.assertAlmostEqual(spin71.r2[0], 4.9264108615358406)
- self.assertAlmostEqual(spin71.phi_ex, 0.059254616846279792)
- self.assertAlmostEqual(spin71.kex, 2543.899105435682)
- self.assertAlmostEqual(spin71.chi2, 1.4423991744690439)
+ self.assertAlmostEqual(spin71.r2[0], 4.92610970714703)
+ self.assertAlmostEqual(spin71.phi_ex, 0.0592876975157063)
+ self.assertAlmostEqual(spin71.kex, 2544.61582323959)
+ self.assertAlmostEqual(spin71.chi2, 1.44240142554555)
def test_hansen_cpmg_data_CR72(self):
@@ -173,11 +205,70 @@
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.
"""
+ # Create the data pipe and load the base data.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'
+ self.interpreter.pipe.create(pipe_name='base pipe',
pipe_type='relax_disp')
+ self.interpreter.results.read(data_path+sep+'base_pipe')
+
+ # Set the nuclear isotope data.
+ self.interpreter.spin.isotope('15N')
+
+ # Create the R2eff data pipe and load the results.
+ self.interpreter.pipe.create(pipe_name='R2eff',
pipe_type='relax_disp')
+ self.interpreter.pipe.switch(pipe_name='R2eff')
+ self.interpreter.results.read(data_path+sep+'r2eff_pipe')
+
+ # The CR72 model data pipe.
+ self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to='CR72',
bundle_to='relax_disp')
+ self.interpreter.pipe.switch(pipe_name='CR72')
+
# Set the model.
- ds.models = ['CR72']
-
- # Execute the script.
- self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data.py')
+ self.interpreter.relax_disp.select_model(model='CR72')
+
+ # Copy the data.
+ self.interpreter.value.copy(pipe_from='R2eff', pipe_to='CR72',
param='r2eff')
+
+ # Alias the spins.
+ spin70 = cdp.mol[0].res[0].spin[0]
+ spin71 = cdp.mol[0].res[1].spin[0]
+
+ # Set the initial parameter values.
+ spin70.r2 = [7, 9]
+ spin70.pA = 0.9
+ spin70.dw = 6.0
+ spin70.kex = 1500.0
+ spin71.r2 = [5, 9]
+ spin71.pA = 0.9
+ spin71.dw = 4.0
+ spin71.kex = 1900.0
+
+ # 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 (:70)", "Value
(:71)"))
+ print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[0],
spin71.r2[0]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[1],
spin71.r2[1]))
+ print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA))
+ print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw))
+ print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex))
+ print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
+
+ # Checks for residue :70.
+ self.assertAlmostEqual(spin70.r2[0], 7.01155339809216)
+ self.assertAlmostEqual(spin70.r2[1], 9.46442835200306)
+ self.assertAlmostEqual(spin70.pA, 0.989902989352694)
+ self.assertAlmostEqual(spin70.dw, 5.57732933273956)
+ self.assertAlmostEqual(spin70.kex, 1765.90725820329)
+ self.assertAlmostEqual(spin70.chi2, 18.4500380435222)
+
+ # Checks for residue :71.
+ self.assertAlmostEqual(spin71.r2[0], 4.97810633804386)
+ self.assertAlmostEqual(spin71.pA, 0.996745738175374)
+ self.assertAlmostEqual(spin71.dw, 4.4520953297668)
+ self.assertAlmostEqual(spin71.kex, 1883.01233923508)
+ self.assertAlmostEqual(spin71.chi2, 1.37893904307118)
def test_hansen_cpmgfit_input(self):
r19850 - /branches/relax_disp/test_suite/system_tests/relax_disp.py