Author: tlinnet
Date: Wed Jun 25 02:14:22 2014
New Revision: 24290
URL: http://svn.gna.org/viewcvs/relax?rev=24290&view=rev
Log:
Split systemtest test_tp02_data_to_ns_r1rho_2site into a setup and test part.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24290&r1=24289&r2=24290&view=diff
==============================================================================
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py Wed
Jun 25 02:14:22 2014
@@ -689,6 +689,60 @@
self.interpreter.relax_disp.select_model(model=MODEL)
# Calculate R2eff values
self.interpreter.calc(verbosity=1)
+
+
+ def setup_tp02_data_to_ns_r1rho_2site(self, clustering=False):
+ """Setup data for the test of relaxation dispersion 'NS R1rho
2-site' model fitting against the 'TP02' test data."""
+
+ # Reset.
+ self.interpreter.reset()
+
+ # Create the data pipe and load the base data.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_off_res_tp02'
+ self.interpreter.state.load(data_path+sep+'r2eff_values')
+
+ # The model data pipe.
+ model = 'NS R1rho 2-site'
+ pipe_name = "%s - relax_disp" % model
+ self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to=pipe_name,
bundle_to='relax_disp')
+ self.interpreter.pipe.switch(pipe_name=pipe_name)
+
+ # Set the model.
+ self.interpreter.relax_disp.select_model(model=model)
+
+ # Copy the data.
+ self.interpreter.value.copy(pipe_from='R2eff', pipe_to=pipe_name,
param='r2eff')
+
+ # Alias the spins.
+ spin1 = cdp.mol[0].res[0].spin[0]
+ spin2 = cdp.mol[0].res[1].spin[0]
+
+ # The R20 keys.
+ r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6)
+ r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)
+
+ # Set the initial parameter values.
+ spin1.r2 = {r20_key1: 9.9963793866185, r20_key2: 15.0056724422684}
+ spin1.pA = 0.779782428085762
+ spin1.dw = 7.57855284496424
+ spin1.kex = 1116.7911285203
+ spin2.r2 = {r20_key1: 11.9983346935434, r20_key2: 18.0076097513337}
+ spin2.pA = 0.826666229688602
+ spin2.dw = 9.5732624231366
+ spin2.kex = 1380.46162655657
+
+ # 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" % ("pA", spin1.pA, spin2.pA))
+ print("%-20s %20.15g %20.15g" % ("dw", spin1.dw, spin2.dw))
+ print("%-20s %20.15g %20.15g" % ("kex", spin1.kex, spin2.kex))
+ print("%-20s %20.15g %20.15g\n" % ("chi2", spin1.chi2, spin2.chi2))
def test_baldwin_synthetic(self):
@@ -6013,24 +6067,8 @@
def test_tp02_data_to_ns_r1rho_2site(self, model=None):
"""Test the relaxation dispersion 'NS R1rho 2-site' model fitting
against the 'TP02' test data."""
- # Reset.
- self.interpreter.reset()
-
- # Create the data pipe and load the base data.
- data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_off_res_tp02'
- self.interpreter.state.load(data_path+sep+'r2eff_values')
-
- # The model data pipe.
- model = 'NS R1rho 2-site'
- pipe_name = "%s - relax_disp" % model
- self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to=pipe_name,
bundle_to='relax_disp')
- self.interpreter.pipe.switch(pipe_name=pipe_name)
-
- # Set the model.
- self.interpreter.relax_disp.select_model(model=model)
-
- # Copy the data.
- self.interpreter.value.copy(pipe_from='R2eff', pipe_to=pipe_name,
param='r2eff')
+ # Setup the data.
+ self.setup_tp02_data_to_ns_r1rho_2site()
# Alias the spins.
spin1 = cdp.mol[0].res[0].spin[0]
@@ -6039,29 +6077,6 @@
# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)
-
- # Set the initial parameter values.
- spin1.r2 = {r20_key1: 9.9963793866185, r20_key2: 15.0056724422684}
- spin1.pA = 0.779782428085762
- spin1.dw = 7.57855284496424
- spin1.kex = 1116.7911285203
- spin2.r2 = {r20_key1: 11.9983346935434, r20_key2: 18.0076097513337}
- spin2.pA = 0.826666229688602
- spin2.dw = 9.5732624231366
- spin2.kex = 1380.46162655657
-
- # 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" % ("pA", spin1.pA, spin2.pA))
- print("%-20s %20.15g %20.15g" % ("dw", spin1.dw, spin2.dw))
- print("%-20s %20.15g %20.15g" % ("kex", spin1.kex, spin2.kex))
- print("%-20s %20.15g %20.15g\n" % ("chi2", spin1.chi2, spin2.chi2))
# Checks for residue :1.
self.assertAlmostEqual(spin1.r2[r20_key1], 8.50207717367548, 4)
r24290 - /branches/disp_spin_speed/test_suite/system_tests/relax_disp.py