Author: tlinnet Date: Thu May 22 19:15:32 2014 New Revision: 23356 URL: http://svn.gna.org/viewcvs/relax?rev=23356&view=rev Log: Added 7 unit tests demonstrating edge case 'no Rex' failures of the model 'B14'. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models. This is to implement catching of math domain errors, before they occur. These tests cover all parameter value combinations which result in no exchange: - dw = 0.0, - pA = 1.0, - kex = 0.0, - dw = 0.0 and pA = 1.0, - dw = 0.0 and kex = 0.0, - pA = 1.0 and kex = 0.0, - dw = 0.0, pA = 1.0, and kex = 0.0. Modified: branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py Modified: branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py URL: http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py?rev=23356&r1=23355&r2=23356&view=diff ============================================================================== --- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py (original) +++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py Thu May 22 19:15:32 2014 @@ -23,6 +23,7 @@ __all__ = [ 'test___init__', + 'test_b14', 'test_dpl94', 'test_lm63', 'test_ns_cpmg_2site_expanded' Modified: branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py URL: http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py?rev=23356&r1=23355&r2=23356&view=diff ============================================================================== --- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py (original) +++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py Thu May 22 19:15:32 2014 @@ -20,54 +20,63 @@ ############################################################################### # Python module imports. -from numpy import array, float64, int16, zeros +from numpy import array, float64, int16, pi, zeros from unittest import TestCase # relax module imports. -from lib.dispersion.ns_cpmg_2site_expanded import r2eff_ns_cpmg_2site_expanded +from lib.dispersion.b14 import r2eff_B14 -class Test_ns_cpmg_2site_expanded(TestCase): - """Unit tests for the lib.dispersion.ns_cpmg_2site_expanded relax module.""" +class Test_b14(TestCase): + """Unit tests for the lib.dispersion.b14 relax module.""" def setUp(self): """Set up for all unit tests.""" # Default parameter values. - self.r20 = 2.0 - self.pA = 0.9 - self.dw = 0.5 - self.kex = 100.0 + self.r20a = 2.0 + self.r20b = 2.0 + self.pA = 0.99 + self.dw = 2.0 + self.kex = 1000.0 # Required data structures. - self.num_points = 3 - self.tcp = array([0.1, 0.2, 0.3], float64) - self.R2eff = zeros(3, float64) - self.num_cpmg = array([1, 2, 3], int16) + self.num_points = 7 + self.ncyc = array([2, 4, 8, 10, 20, 40, 500]) + relax_times = 0.04 + cpmg_frqs = self.ncyc / relax_times + self.inv_relax_times = 1.0 / relax_times + self.tau_cpmg = 0.25 / cpmg_frqs + # The spin Larmor frequencies. + self.sfrq = 200. * 1E6 def calc_r2eff(self): """Calculate and check the R2eff values.""" # Parameter conversions. - k_AB, k_BA = self.param_conversion(pA=self.pA, kex=self.kex) + k_AB, k_BA, pB, dw_frq = self.param_conversion(pA=self.pA, kex=self.kex, dw=self.dw, sfrq=self.sfrq) # Calculate the R2eff values. - R2eff = r2eff_ns_cpmg_2site_expanded(r20=self.r20, pA=self.pA, dw=self.dw, k_AB=k_AB, k_BA=k_BA, relax_time=0.3, inv_relax_time=1/0.3, tcp=self.tcp, num_points=self.num_points, num_cpmg=self.num_cpmg) + R2eff = r2eff_B14(r20a=self.r20a, r20b=self.r20b, pA=self.pA, pB=pB, dw=dw_frq, kex=self.kex, k_AB=k_AB, k_BA=k_BA, ncyc=self.ncyc, inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg, num_points=self.num_points) # Check all R2eff values. for i in range(self.num_points): - self.assertAlmostEqual(R2eff[i], self.r20) + self.assertAlmostEqual(R2eff[i], self.r20a) - def param_conversion(self, pA=None, kex=None): + def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None): """Convert the parameters. @keyword pA: The population of state A. @type pA: float @keyword kex: The rate of exchange. @type kex: float - @return: The parameters {k_AB, k_BA}. + @keyword dw: The chemical exchange difference between states A and B in ppm. + @type dw: float + @keyword sfrq: The spin Larmor frequencies in Hz. + @type sfrq: float + @return: The parameters {k_AB, k_BA, pB, dw_frq}. @rtype: tuple of float """ @@ -78,12 +87,18 @@ k_BA = pA * kex k_AB = pB * kex + # Calculate spin Larmor frequencies in 2pi. + frqs = sfrq * 2 * pi + + # Convert dw from ppm to rad/s. + dw_frq = dw * frqs + # Return all values. - return k_AB, k_BA + return k_AB, k_BA, pB, dw_frq - def test_ns_cpmg_2site_expanded_no_rex1(self): - """Test the r2eff_ns_cpmg_2site_expanded() function for no exchange when dw = 0.0.""" + def test_b14_no_rex1(self): + """Test the r2eff_b14() function for no exchange when dw = 0.0.""" # Parameter reset. self.dw = 0.0 @@ -92,8 +107,8 @@ self.calc_r2eff() - def test_ns_cpmg_2site_expanded_no_rex2(self): - """Test the r2eff_ns_cpmg_2site_expanded() function for no exchange when pA = 1.0.""" + def test_b14_no_rex2(self): + """Test the r2eff_b14() function for no exchange when pA = 1.0.""" # Parameter reset. self.pA = 1.0 @@ -102,8 +117,8 @@ self.calc_r2eff() - def test_ns_cpmg_2site_expanded_no_rex3(self): - """Test the r2eff_ns_cpmg_2site_expanded() function for no exchange when kex = 0.0.""" + def test_b14_no_rex3(self): + """Test the r2eff_b14() function for no exchange when kex = 0.0.""" # Parameter reset. self.kex = 0.0 @@ -112,8 +127,8 @@ self.calc_r2eff() - def test_ns_cpmg_2site_expanded_no_rex4(self): - """Test the r2eff_ns_cpmg_2site_expanded() function for no exchange when dw = 0.0 and pA = 1.0.""" + def test_b14_no_rex4(self): + """Test the r2eff_b14() function for no exchange when dw = 0.0 and pA = 1.0.""" # Parameter reset. self.pA = 1.0 @@ -123,8 +138,8 @@ self.calc_r2eff() - def test_ns_cpmg_2site_expanded_no_rex5(self): - """Test the r2eff_ns_cpmg_2site_expanded() function for no exchange when dw = 0.0 and kex = 0.0.""" + def test_b14_no_rex5(self): + """Test the r2eff_b14() function for no exchange when dw = 0.0 and kex = 0.0.""" # Parameter reset. self.dw = 0.0 @@ -134,8 +149,8 @@ self.calc_r2eff() - def test_ns_cpmg_2site_expanded_no_rex6(self): - """Test the r2eff_ns_cpmg_2site_expanded() function for no exchange when pA = 1.0 and kex = 0.0.""" + def test_b14_no_rex6(self): + """Test the r2eff_b14() function for no exchange when pA = 1.0 and kex = 0.0.""" # Parameter reset. self.pA = 1.0 @@ -145,8 +160,8 @@ self.calc_r2eff() - def test_ns_cpmg_2site_expanded_no_rex7(self): - """Test the r2eff_ns_cpmg_2site_expanded() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" + def test_b14_no_rex7(self): + """Test the r2eff_b14() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" # Parameter reset. self.dw = 0.0