Author: tlinnet
Date: Thu May 22 16:56:32 2014
New Revision: 23338
URL: http://svn.gna.org/viewcvs/relax?rev=23338&view=rev
Log:
Added 7 unit tests demonstrating edge case 'no Rex' failures of the model
'DPL94'.
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.
Added:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.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=23338&r1=23337&r2=23338&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 16:56:32 2014
@@ -22,5 +22,6 @@
__all__ = [
'test___init__',
+ 'test_ns_dpl94',
'test_ns_cpmg_2site_expanded'
]
Added:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py?rev=23338&view=auto
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
(added)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
Thu May 22 16:56:32 2014
@@ -0,0 +1,180 @@
+###############################################################################
+#
#
+# Copyright (C) 2014 Edward d'Auvergne
#
+# Copyright (C) 2014 Troels E. Linnet
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Python module imports.
+from numpy import array, float64, int16, pi, zeros
+from unittest import TestCase
+
+# relax module imports.
+from lib.dispersion.dpl94 import r1rho_DPL94
+
+
+class Test_dpl94(TestCase):
+ """Unit tests for the lib.dispersion.dpl94 relax module."""
+
+ def setUp(self):
+ """Set up for all unit tests."""
+
+ # Default parameter values.
+
+
+ # The R1rho_prime parameter value (R1rho with no exchange).
+ self.r1rho_prime = 2.5
+ # Population of ground state.
+ self.pA = 0.9
+ # The chemical exchange difference between states A and B in ppm.
+ self.dw = 0.5
+ self.kex = 1000.0
+ # The R1 relaxation rates.
+ 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
+
+ # Required data structures.
+ self.num_points = 11
+
+
+ def calc_r1rho(self):
+ """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)
+
+ # 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)
+
+ # Check all R1rho values.
+ 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):
+ """Convert the parameters.
+
+ @keyword pA: The population of state A.
+ @type pA: float
+ @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
+ @keyword spin_lock_nu1: The spin-lock field strengths in Hertz.
+ @type spin_lock_nu1: float
+ @return: The parameters {phi_ex_scaled, k_BA}.
+ @rtype: tuple of float
+ """
+
+ # Calculate pB.
+ pB = 1.0 - pA
+
+ # 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 phi_ex from ppm^2 to (rad/s)^2.
+ phi_ex_scaled = phi_ex * frqs**2
+
+ # The R1rho spin-lock field strengths squared (in rad^2.s^-2).
+ spin_lock_omega1_squared = (2. * pi * spin_lock_nu1)**2
+
+ # Return all values.
+ return phi_ex_scaled, spin_lock_omega1_squared
+
+
+ def test_dpl94_no_rex1(self):
+ """Test the r1rho_dpl94() function for no exchange when dw = 0.0."""
+
+ # Parameter reset.
+ self.dw = 0.0
+
+ # Calculate and check the R1rho values.
+ self.calc_r1rho()
+
+
+ def test_dpl94_no_rex2(self):
+ """Test the r1rho_dpl94() function for no exchange when pA = 1.0."""
+
+ # Parameter reset.
+ self.pA = 1.0
+
+ # Calculate and check the R1rho values.
+ self.calc_r1rho()
+
+
+ def test_dpl94_no_rex3(self):
+ """Test the r1rho_dpl94() function for no exchange when kex = 0.0."""
+
+ # Parameter reset.
+ self.kex = 0.0
+
+ # Calculate and check the R1rho values.
+ 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."""
+
+ # Parameter reset.
+ self.pA = 1.0
+ self.dw = 0.0
+
+ # Calculate and check the R1rho values.
+ 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."""
+
+ # Parameter reset.
+ self.dw = 0.0
+ self.kex = 0.0
+
+ # Calculate and check the R1rho values.
+ 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."""
+
+ # Parameter reset.
+ self.pA = 1.0
+ self.kex = 0.0
+
+ # Calculate and check the R1rho values.
+ 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."""
+
+ # Parameter reset.
+ self.dw = 0.0
+ self.kex = 0.0
+
+ # Calculate and check the R1rho values.
+ self.calc_r1rho()
r23338 - in /branches/disp_speed/test_suite/unit_tests/_lib/_dispersion: __init__.py test_dpl94.py