Hi Troels, As I mentioned previously (http://article.gmane.org/gmane.science.nmr.relax.devel/5938), the R1rho value checking in these unit tests contains a bug.
Regards, Edward On 26 May 2014 23:09, <[email protected]> wrote: > Author: tlinnet > Date: Mon May 26 23:09:45 2014 > New Revision: 23440 > > URL: http://svn.gna.org/viewcvs/relax?rev=23440&view=rev > Log: > Added 8 unit tests demonstrating edge case 'no Rex' failures of the model > 'MP05'. > > 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. > - kex = 1e20, > > Modified: > branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mp05.py > > Modified: > branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mp05.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mp05.py?rev=23440&r1=23439&r2=23440&view=diff > ============================================================================== > --- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mp05.py > (original) > +++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mp05.py > Mon May 26 23:09:45 2014 > @@ -25,11 +25,11 @@ > from unittest import TestCase > > # relax module imports. > -from lib.dispersion.dpl94 import r1rho_DPL94 > +from lib.dispersion.mp05 import r1rho_MP05 > > > -class Test_dpl94(TestCase): > - """Unit tests for the lib.dispersion.dpl94 relax module.""" > +class Test_mp05(TestCase): > + """Unit tests for the lib.dispersion.mp05 relax module.""" > > def setUp(self): > """Set up for all unit tests.""" > @@ -38,7 +38,12 @@ > > > # The R1rho_prime parameter value (R1rho with no exchange). > - self.r1rho_prime = 2.5 > + self.r1rho_prime = 5.0 > + # The chemical shifts in rad/s. This is only used for off-resonance > R1rho models. > + self.omega = -35670.44192 > + # The structure of spin-lock or hard pulse offsets in rad/s. > + self.offset = -35040.3526693 > + > # Population of ground state. > self.pA = 0.9 > # The chemical exchange difference between states A and B in ppm. > @@ -48,8 +53,6 @@ > self.r1 = 1.0 > # The spin-lock field strengths in Hertz. > self.spin_lock_nu1 = array([ 1000., 1500., 2000., 2500., 3000., > 3500., 4000., 4500., 5000., 5500., 6000.]) > - # The rotating frame tilt angles for each dispersion point. > - self.theta = array([1.5707963267948966, 1.5707963267948966, > 1.5707963267948966, 1.5707963267948966, 1.5707963267948966, > 1.5707963267948966, 1.5707963267948966, 1.5707963267948966, > 1.5707963267948966, 1.5707963267948966, 1.5707963267948966]) > > # The spin Larmor frequencies. > self.sfrq = 599.8908617*1E6 > @@ -62,14 +65,19 @@ > """Calculate and check the R1rho values.""" > > # Parameter conversions. > - phi_ex_scaled, spin_lock_omega1_squared = > self.param_conversion(pA=self.pA, dw=self.dw, sfrq=self.sfrq, > spin_lock_nu1=self.spin_lock_nu1) > + pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared = > self.param_conversion(pA=self.pA, dw=self.dw, sfrq=self.sfrq, > spin_lock_nu1=self.spin_lock_nu1) > > # Calculate the R1rho values. > - R1rho = r1rho_DPL94(r1rho_prime=self.r1rho_prime, > phi_ex=phi_ex_scaled, kex=self.kex, theta=self.theta, R1=self.r1, > spin_lock_fields2=spin_lock_omega1_squared, num_points=self.num_points) > + R1rho = r1rho_MP05(r1rho_prime=self.r1rho_prime, omega=self.omega, > offset=self.offset, pA=self.pA, pB=pB, dw=dw_frq, kex=self.kex, R1=self.r1, > spin_lock_fields=spin_lock_omega1, > spin_lock_fields2=spin_lock_omega1_squared, num_points=self.num_points) > + > > # Check all R1rho values. > - for i in range(self.num_points): > - self.assertAlmostEqual(R1rho[i], self.r1rho_prime) > + if self.kex > 1.e5: > + for i in range(self.num_points): > + self.assertAlmostEqual(R1rho[i], self.r1, 6) > + else: > + for i in range(self.num_points): > + self.assertAlmostEqual(R1rho[i], self.r1rho_prime) > > > def param_conversion(self, pA=None, dw=None, sfrq=None, > spin_lock_nu1=None): > @@ -83,7 +91,7 @@ > @type sfrq: float > @keyword spin_lock_nu1: The spin-lock field strengths in Hertz. > @type spin_lock_nu1: float > - @return: The parameters {phi_ex_scaled, k_BA}. > + @return: The parameters {pB, dw_frq, > spin_lock_omega1, spin_lock_omega1_squared}. > @rtype: tuple of float > """ > > @@ -93,21 +101,21 @@ > # Calculate spin Larmor frequencies in 2pi. > frqs = sfrq * 2 * pi > > - # The phi_ex parameter value (pA * pB * delta_omega^2). > - phi_ex = pA * pB * dw**2 > + # Convert dw from ppm to rad/s. > + dw_frq = dw * frqs > > - # Convert phi_ex from ppm^2 to (rad/s)^2. > - phi_ex_scaled = phi_ex * frqs**2 > + # The R1rho spin-lock field strengths (in rad.s-1). > + spin_lock_omega1 = (2. * pi * spin_lock_nu1) > > # The R1rho spin-lock field strengths squared (in rad^2.s^-2). > - spin_lock_omega1_squared = (2. * pi * spin_lock_nu1)**2 > + spin_lock_omega1_squared = spin_lock_omega1**2 > > # Return all values. > - return phi_ex_scaled, spin_lock_omega1_squared > + return pB, dw_frq, spin_lock_omega1, spin_lock_omega1_squared > > > - def test_dpl94_no_rex1(self): > - """Test the r1rho_dpl94() function for no exchange when dw = 0.0.""" > + def test_mp05_no_rex1(self): > + """Test the r1rho_mp05() function for no exchange when dw = 0.0.""" > > # Parameter reset. > self.dw = 0.0 > @@ -116,8 +124,8 @@ > self.calc_r1rho() > > > - def test_dpl94_no_rex2(self): > - """Test the r1rho_dpl94() function for no exchange when pA = 1.0.""" > + def test_mp05_no_rex2(self): > + """Test the r1rho_mp05() function for no exchange when pA = 1.0.""" > > # Parameter reset. > self.pA = 1.0 > @@ -126,8 +134,8 @@ > self.calc_r1rho() > > > - def test_dpl94_no_rex3(self): > - """Test the r1rho_dpl94() function for no exchange when kex = 0.0.""" > + def test_mp05_no_rex3(self): > + """Test the r1rho_mp05() function for no exchange when kex = 0.0.""" > > # Parameter reset. > self.kex = 0.0 > @@ -136,8 +144,8 @@ > self.calc_r1rho() > > > - def test_dpl94_no_rex4(self): > - """Test the r1rho_dpl94() function for no exchange when dw = 0.0 and > pA = 1.0.""" > + def test_mp05_no_rex4(self): > + """Test the r1rho_mp05() function for no exchange when dw = 0.0 and > pA = 1.0.""" > > # Parameter reset. > self.pA = 1.0 > @@ -147,8 +155,8 @@ > self.calc_r1rho() > > > - def test_dpl94_no_rex5(self): > - """Test the r1rho_dpl94() function for no exchange when dw = 0.0 and > kex = 0.0.""" > + def test_mp05_no_rex5(self): > + """Test the r1rho_mp05() function for no exchange when dw = 0.0 and > kex = 0.0.""" > > # Parameter reset. > self.dw = 0.0 > @@ -158,8 +166,8 @@ > self.calc_r1rho() > > > - def test_dpl94_no_rex6(self): > - """Test the r1rho_dpl94() function for no exchange when pA = 1.0 and > kex = 0.0.""" > + def test_mp05_no_rex6(self): > + """Test the r1rho_mp05() function for no exchange when pA = 1.0 and > kex = 0.0.""" > > # Parameter reset. > self.pA = 1.0 > @@ -169,8 +177,8 @@ > self.calc_r1rho() > > > - def test_dpl94_no_rex7(self): > - """Test the r1rho_dpl94() function for no exchange when dw = 0.0, pA > = 1.0, and kex = 0.0.""" > + def test_mp05_no_rex7(self): > + """Test the r1rho_mp05() function for no exchange when dw = 0.0, pA > = 1.0, and kex = 0.0.""" > > # Parameter reset. > self.dw = 0.0 > @@ -178,3 +186,13 @@ > > # Calculate and check the R1rho values. > self.calc_r1rho() > + > + > + def test_mp05_no_rex8(self): > + """Test the r1rho_mp05() function for no exchange when kex = 1e20.""" > + > + # Parameter reset. > + self.kex = 1e20 > + > + # Calculate and check the R2eff values. > + self.calc_r1rho() > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > 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 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] 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-devel
