Author: tlinnet
Date: Mon May 26 20:14:07 2014
New Revision: 23437
URL: http://svn.gna.org/viewcvs/relax?rev=23437&view=rev
Log:
Added 8 unit tests demonstrating edge case 'no Rex' failures of the model
'IT99'.
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 = 1e19,
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_it99.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=23437&r1=23436&r2=23437&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
Mon May 26 20:14:07 2014
@@ -29,5 +29,6 @@
'test_lm63',
'test_m61',
'test_m61b',
+ 'test_it99',
'test_ns_cpmg_2site_expanded'
]
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_it99.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_it99.py?rev=23437&r1=23436&r2=23437&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_it99.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_it99.py
Mon May 26 20:14:07 2014
@@ -24,18 +24,17 @@
from unittest import TestCase
# relax module imports.
-from lib.dispersion.b14 import r2eff_B14
+from lib.dispersion.it99 import r2eff_IT99
-class Test_b14(TestCase):
- """Unit tests for the lib.dispersion.b14 relax module."""
+class Test_it99(TestCase):
+ """Unit tests for the lib.dispersion.it99 relax module."""
def setUp(self):
"""Set up for all unit tests."""
# Default parameter values.
- self.r20a = 2.0
- self.r20b = 2.0
+ self.r20 = 2.0
self.pA = 0.99
self.dw = 2.0
self.kex = 1000.0
@@ -44,25 +43,28 @@
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.cpmg_frqs = self.ncyc / relax_times
# The spin Larmor frequencies.
self.sfrq = 200. * 1E6
+
def calc_r2eff(self):
"""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)
+ pB, dw_frq, tex = self.param_conversion(pA=self.pA, kex=self.kex,
dw=self.dw, sfrq=self.sfrq)
# 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 = r2eff_IT99(r20=self.r20, pA=self.pA, pB=pB, dw=dw_frq,
tex=tex, 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.r20a)
+ if self.kex > 1.e5:
+ for i in range(self.num_points):
+ self.assertAlmostEqual(R2eff[i], self.r20, 2)
+ else:
+ for i in range(self.num_points):
+ self.assertAlmostEqual(R2eff[i], self.r20)
def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None):
@@ -76,16 +78,12 @@
@type dw: float
@keyword sfrq: The spin Larmor frequencies in Hz.
@type sfrq: float
- @return: The parameters {k_AB, k_BA, pB, dw_frq}.
+ @return: The parameters {pB, dw_frq, tex}.
@rtype: tuple of float
"""
# Calculate pB.
pB = 1.0 - pA
-
- # Exchange rates.
- k_BA = pA * kex
- k_AB = pB * kex
# Calculate spin Larmor frequencies in 2pi.
frqs = sfrq * 2 * pi
@@ -93,12 +91,18 @@
# Convert dw from ppm to rad/s.
dw_frq = dw * frqs
+ # Time of exchange: 1/(2*kex)
+ if kex == 0.0:
+ tex = 0.0
+ else:
+ tex = 1 / (2*kex)
+
# Return all values.
- return k_AB, k_BA, pB, dw_frq
+ return pB, dw_frq, tex
- def test_b14_no_rex1(self):
- """Test the r2eff_b14() function for no exchange when dw = 0.0."""
+ def test_it99_no_rex1(self):
+ """Test the r2eff_it99() function for no exchange when dw = 0.0."""
# Parameter reset.
self.dw = 0.0
@@ -107,8 +111,8 @@
self.calc_r2eff()
- def test_b14_no_rex2(self):
- """Test the r2eff_b14() function for no exchange when pA = 1.0."""
+ def test_it99_no_rex2(self):
+ """Test the r2eff_it99() function for no exchange when pA = 1.0."""
# Parameter reset.
self.pA = 1.0
@@ -117,8 +121,8 @@
self.calc_r2eff()
- def test_b14_no_rex3(self):
- """Test the r2eff_b14() function for no exchange when kex = 0.0."""
+ def test_it99_no_rex3(self):
+ """Test the r2eff_it99() function for no exchange when kex = 0.0."""
# Parameter reset.
self.kex = 0.0
@@ -127,8 +131,8 @@
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_it99_no_rex4(self):
+ """Test the r2eff_it99() function for no exchange when dw = 0.0 and
pA = 1.0."""
# Parameter reset.
self.pA = 1.0
@@ -138,8 +142,8 @@
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_it99_no_rex5(self):
+ """Test the r2eff_it99() function for no exchange when dw = 0.0 and
kex = 0.0."""
# Parameter reset.
self.dw = 0.0
@@ -149,8 +153,8 @@
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_it99_no_rex6(self):
+ """Test the r2eff_it99() function for no exchange when pA = 1.0 and
kex = 0.0."""
# Parameter reset.
self.pA = 1.0
@@ -160,8 +164,8 @@
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_it99_no_rex7(self):
+ """Test the r2eff_it99() function for no exchange when dw = 0.0, pA
= 1.0, and kex = 0.0."""
# Parameter reset.
self.dw = 0.0
@@ -169,3 +173,13 @@
# Calculate and check the R2eff values.
self.calc_r2eff()
+
+
+ def test_it99_no_rex8(self):
+ """Test the r2eff_cr72() function for no exchange when kex = 1e19."""
+
+ # Parameter reset.
+ self.kex = 1e19
+
+ # Calculate and check the R2eff values.
+ self.calc_r2eff()
r23437 - in /branches/disp_speed/test_suite/unit_tests/_lib/_dispersion: __init__.py test_it99.py