Author: tlinnet
Date: Mon May 26 20:13:56 2014
New Revision: 23433
URL: http://svn.gna.org/viewcvs/relax?rev=23433&view=rev
Log:
Added 8 unit tests demonstrating edge case 'no Rex' failures of the model
'M61b'.
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_m61b.py
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61b.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61b.py?rev=23433&r1=23432&r2=23433&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61b.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61b.py
Mon May 26 20:13:56 2014
@@ -25,54 +25,71 @@
from unittest import TestCase
# relax module imports.
-from lib.dispersion.lm63 import r2eff_LM63
+from lib.dispersion.m61b import r1rho_M61b
-class Test_lm63(TestCase):
- """Unit tests for the lib.dispersion.lm63 relax module."""
+class Test_m61b(TestCase):
+ """Unit tests for the lib.dispersion.m61b relax module."""
def setUp(self):
"""Set up for all unit tests."""
# Default parameter values.
- self.r20 = 2.0
+
+
+ # 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 = 100.0
+ 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 = 3
- self.cpmg_frqs = array([[2.5, 1.25, 0.83]], float64)
- self.R2eff = zeros(3, float64)
+ self.num_points = 11
- def calc_r2eff(self):
- """Calculate and check the R2eff values."""
+ def calc_r1rho(self):
+ """Calculate and check the R1rho values."""
# Parameter conversions.
- phi_ex_scaled = self.param_conversion(pA=self.pA, dw=self.dw,
sfrq=self.sfrq)
+ phi_ex_scaled, dw_frq, 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 R2eff values.
- R2eff = r2eff_LM63(r20=self.r20, phi_ex=phi_ex_scaled, kex=self.kex,
cpmg_frqs=self.cpmg_frqs, num_points=self.num_points)
- # Check all R2eff values.
- for i in range(self.num_points):
- self.assertAlmostEqual(R2eff[i], self.r20)
+ # Calculate the R1rho values.
+ R1rho = r1rho_M61b(r1rho_prime=self.r1rho_prime, pA=self.pA,
dw=dw_frq, kex=self.kex, spin_lock_fields2=spin_lock_omega1_squared,
num_points=self.num_points)
- def param_conversion(self, pA=None, dw=None, sfrq=None):
+ # Check all R1rho values.
+ if self.kex > 1.e5:
+ for i in range(self.num_points):
+ self.assertAlmostEqual(R1rho[i], self.r1rho_prime, 2)
+ 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):
"""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
- @return: The parameters phi_ex_scaled
- @rtype: float
+ @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, dw_frq,
spin_lock_omega1_squared}.
+ @rtype: tuple of float
"""
# Calculate pB.
@@ -81,85 +98,101 @@
# Calculate spin Larmor frequencies in 2pi.
frqs = sfrq * 2 * pi
+ # Convert dw from ppm to rad/s.
+ dw_frq = dw * frqs
+
# 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
+ return phi_ex_scaled, dw_frq, spin_lock_omega1_squared
- def test_lm63_no_rex1(self):
- """Test the r2eff_lm63() function for no exchange when dw = 0.0."""
+ def test_m61b_no_rex1(self):
+ """Test the r1rho_m61b() function for no exchange when dw = 0.0."""
# Parameter reset.
self.dw = 0.0
- # Calculate and check the R2eff values.
- self.calc_r2eff()
+ # Calculate and check the R1rho values.
+ self.calc_r1rho()
- def test_lm63_no_rex2(self):
- """Test the r2eff_lm63() function for no exchange when pA = 1.0."""
+ def test_m61b_no_rex2(self):
+ """Test the r1rho_m61b() function for no exchange when pA = 1.0."""
# Parameter reset.
self.pA = 1.0
- # Calculate and check the R2eff values.
- self.calc_r2eff()
+ # Calculate and check the R1rho values.
+ self.calc_r1rho()
- def test_lm63_no_rex3(self):
- """Test the r2eff_lm63() function for no exchange when kex = 0.0."""
+ def test_m61b_no_rex3(self):
+ """Test the r1rho_m61b() function for no exchange when kex = 0.0."""
# Parameter reset.
self.kex = 0.0
- # Calculate and check the R2eff values.
- self.calc_r2eff()
+ # Calculate and check the R1rho values.
+ self.calc_r1rho()
- def test_lm63_no_rex4(self):
- """Test the r2eff_lm63() function for no exchange when dw = 0.0 and
pA = 1.0."""
+ def test_m61b_no_rex4(self):
+ """Test the r1rho_m61b() 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 R2eff values.
- self.calc_r2eff()
+ # Calculate and check the R1rho values.
+ self.calc_r1rho()
- def test_lm63_no_rex5(self):
- """Test the r2eff_lm63() function for no exchange when dw = 0.0 and
kex = 0.0."""
+ def test_m61b_no_rex5(self):
+ """Test the r1rho_m61b() 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 R2eff values.
- self.calc_r2eff()
+ # Calculate and check the R1rho values.
+ self.calc_r1rho()
- def test_lm63_no_rex6(self):
- """Test the r2eff_lm63() function for no exchange when pA = 1.0 and
kex = 0.0."""
+ def test_m61b_no_rex6(self):
+ """Test the r1rho_m61b() 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 R2eff values.
- self.calc_r2eff()
+ # Calculate and check the R1rho values.
+ self.calc_r1rho()
- def test_lm63_no_rex7(self):
- """Test the r2eff_lm63() function for no exchange when dw = 0.0, pA
= 1.0, and kex = 0.0."""
+ def test_m61b_no_rex7(self):
+ """Test the r1rho_m61b() 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()
+
+
+ def test_m61b_no_rex8(self):
+ """Test the r1rho_m61b() function for no exchange when kex = 1e20."""
+
+ # Parameter reset.
+ self.kex = 1e20
+
# Calculate and check the R2eff values.
- self.calc_r2eff()
+ self.calc_r1rho()
r23433 - /branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61b.py