Author: tlinnet
Date: Tue May 27 00:08:06 2014
New Revision: 23450
URL: http://svn.gna.org/viewcvs/relax?rev=23450&view=rev
Log:
Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'NS
CPMG 2site 3D'.
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 = 1e7,
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py?rev=23450&r1=23449&r2=23450&view=diff
==============================================================================
---
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py
(original)
+++
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py
Tue May 27 00:08:06 2014
@@ -24,29 +24,38 @@
from unittest import TestCase
# relax module imports.
-from lib.dispersion.b14 import r2eff_B14
+from lib.dispersion.ns_cpmg_2site_3d import r2eff_ns_cpmg_2site_3D
+from lib.dispersion.ns_matrices import r180x_3d
-class Test_b14(TestCase):
- """Unit tests for the lib.dispersion.b14 relax module."""
+class Test_ns_cpmg_2site_3d(TestCase):
+ """Unit tests for the lib.dispersion.ns_cpmg_2site_3D relax module."""
def setUp(self):
"""Set up for all unit tests."""
# Default parameter values.
self.r20a = 2.0
- self.r20b = 2.0
+ self.r20b = 3.0
self.pA = 0.99
self.dw = 2.0
self.kex = 1000.0
# Required data structures.
+ # The 3D rotation matrix for an imperfect X-axis pi-pulse.
+ self.r180x = r180x_3d()
+
+ # This is a vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
+ self.M0 = zeros(7, float64)
+ self.M0[0] = 0.5
+
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
+ self.R2eff = zeros(self.num_points, float64)
# The spin Larmor frequencies.
self.sfrq = 200. * 1E6
@@ -55,17 +64,17 @@
"""Calculate and check the R2eff values."""
# Parameter conversions.
- k_AB, k_BA, pB, dw_frq = self.param_conversion(pA=self.pA,
kex=self.kex, dw=self.dw, sfrq=self.sfrq)
+ k_AB, k_BA, pB, dw_frq, M0 = self.param_conversion(pA=self.pA,
kex=self.kex, dw=self.dw, sfrq=self.sfrq, M0=self.M0)
# Calculate the R2eff values.
- 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)
-
+ r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=M0, r20a=self.r20a,
r20b=self.r20b, pA=self.pA, pB=pB, dw=dw_frq, k_AB=k_AB, k_BA=k_BA,
inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg, back_calc=self.R2eff,
num_points=self.num_points, power=self.ncyc)
+
# Check all R2eff values.
for i in range(self.num_points):
- self.assertAlmostEqual(R2eff[i], self.r20a)
+ self.assertAlmostEqual(self.R2eff[i], self.r20a)
- def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None):
+ def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None,
M0=None):
"""Convert the parameters.
@keyword pA: The population of state A.
@@ -76,12 +85,18 @@
@type dw: float
@keyword sfrq: The spin Larmor frequencies in Hz.
@type sfrq: float
- @return: The parameters {k_AB, k_BA, pB, dw_frq}.
+ @keyword M0: Vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
+ @type M0: numpy float64, rank-1, 7D array
+ @return: The parameters {k_AB, k_BA, pB, dw_frq, M0}.
@rtype: tuple of float
"""
# Calculate pB.
pB = 1.0 - pA
+
+ # This is a vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
+ M0[1] = pA
+ M0[4] = pB
# Exchange rates.
k_BA = pA * kex
@@ -94,11 +109,11 @@
dw_frq = dw * frqs
# Return all values.
- return k_AB, k_BA, pB, dw_frq
+ return k_AB, k_BA, pB, dw_frq, M0
- def test_b14_no_rex1(self):
- """Test the r2eff_b14() function for no exchange when dw = 0.0."""
+ def test_ns_cpmg_2site_3D_no_rex1(self):
+ """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when
dw = 0.0."""
# Parameter reset.
self.dw = 0.0
@@ -107,8 +122,8 @@
self.calc_r2eff()
- def test_b14_no_rex2(self):
- """Test the r2eff_b14() function for no exchange when pA = 1.0."""
+ def test_ns_cpmg_2site_3D_no_rex2(self):
+ """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when
pA = 1.0."""
# Parameter reset.
self.pA = 1.0
@@ -117,8 +132,8 @@
self.calc_r2eff()
- def test_b14_no_rex3(self):
- """Test the r2eff_b14() function for no exchange when kex = 0.0."""
+ def test_ns_cpmg_2site_3D_no_rex3(self):
+ """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when
kex = 0.0."""
# Parameter reset.
self.kex = 0.0
@@ -127,8 +142,8 @@
self.calc_r2eff()
- def test_b14_no_rex4(self):
- """Test the r2eff_b14() function for no exchange when dw = 0.0 and
pA = 1.0."""
+ def test_ns_cpmg_2site_3D_no_rex4(self):
+ """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when
dw = 0.0 and pA = 1.0."""
# Parameter reset.
self.pA = 1.0
@@ -138,8 +153,8 @@
self.calc_r2eff()
- def test_b14_no_rex5(self):
- """Test the r2eff_b14() function for no exchange when dw = 0.0 and
kex = 0.0."""
+ def test_ns_cpmg_2site_3D_no_rex5(self):
+ """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when
dw = 0.0 and kex = 0.0."""
# Parameter reset.
self.dw = 0.0
@@ -149,8 +164,8 @@
self.calc_r2eff()
- def test_b14_no_rex6(self):
- """Test the r2eff_b14() function for no exchange when pA = 1.0 and
kex = 0.0."""
+ def test_ns_cpmg_2site_3D_no_rex6(self):
+ """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when
pA = 1.0 and kex = 0.0."""
# Parameter reset.
self.pA = 1.0
@@ -160,8 +175,8 @@
self.calc_r2eff()
- 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."""
+ def test_ns_cpmg_2site_3D_no_rex7(self):
+ """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when
dw = 0.0, pA = 1.0, and kex = 0.0."""
# Parameter reset.
self.dw = 0.0
@@ -171,11 +186,11 @@
self.calc_r2eff()
- def test_b14_no_rex8(self):
- """Test the r2eff_b14() function for no exchange when kex = 1e5."""
+ def test_ns_cpmg_2site_3D_no_rex8(self):
+ """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when
kex = 1e7."""
# Parameter reset.
- self.kex = 1e5
+ self.kex = 1e7
# Calculate and check the R2eff values.
self.calc_r2eff()
r23450 - /branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py