Author: tlinnet
Date: Tue May 27 19:11:26 2014
New Revision: 23483
URL: http://svn.gna.org/viewcvs/relax?rev=23483&view=rev
Log:
Modified unit test to have standard population of pA=0.95, and a correctly
calculation of dw in ppm to rad/s.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_it99.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_lm63.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61b.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mp05.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tap03.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tp02.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py?rev=23483&r1=23482&r2=23483&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py
Tue May 27 19:11:26 2014
@@ -36,7 +36,7 @@
# Default parameter values.
self.r20a = 2.0
self.r20b = 4.0
- self.pA = 0.99
+ self.pA = 0.95
self.dw = 2.0
self.kex = 1000.0
@@ -92,7 +92,7 @@
frqs = sfrq * 2 * pi
# Convert dw from ppm to rad/s.
- dw_frq = dw * frqs
+ dw_frq = dw * frqs / 1.e6
# Return all values.
return k_AB, k_BA, pB, dw_frq
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py?rev=23483&r1=23482&r2=23483&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_cr72.py
Tue May 27 19:11:26 2014
@@ -36,7 +36,7 @@
# Default parameter values.
self.r20a = 2.0
self.r20b = 4.0
- self.pA = 0.99
+ self.pA = 0.95
self.dw = 2.0
self.kex = 1000.0
@@ -90,7 +90,7 @@
frqs = sfrq * 2 * pi
# Convert dw from ppm to rad/s.
- dw_frq = dw * frqs
+ dw_frq = dw * frqs / 1.e6
# Return all values.
return k_AB, k_BA, pB, dw_frq
Modified:
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=23483&r1=23482&r2=23483&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
Tue May 27 19:11:26 2014
@@ -40,7 +40,7 @@
# The R1rho_prime parameter value (R1rho with no exchange).
self.r1rho_prime = 2.5
# Population of ground state.
- self.pA = 0.9
+ self.pA = 0.95
# The chemical exchange difference between states A and B in ppm.
self.dw = 0.5
self.kex = 1000.0
@@ -101,7 +101,7 @@
frqs = sfrq * 2 * pi
# The phi_ex parameter value (pA * pB * delta_omega^2).
- phi_ex = pA * pB * dw**2
+ phi_ex = pA * pB * (dw / 1.e6)**2
# Convert phi_ex from ppm^2 to (rad/s)^2.
phi_ex_scaled = phi_ex * frqs**2
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=23483&r1=23482&r2=23483&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
Tue May 27 19:11:26 2014
@@ -35,7 +35,7 @@
# Default parameter values.
self.r20 = 2.0
- self.pA = 0.99
+ self.pA = 0.95
self.dw = 2.0
self.kex = 1000.0
@@ -89,7 +89,7 @@
frqs = sfrq * 2 * pi
# Convert dw from ppm to rad/s.
- dw_frq = dw * frqs
+ dw_frq = dw * frqs / 1.e6
# Time of exchange: 1/(2*kex)
if kex == 0.0:
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_lm63.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_lm63.py?rev=23483&r1=23482&r2=23483&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_lm63.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_lm63.py
Tue May 27 19:11:26 2014
@@ -36,7 +36,7 @@
# Default parameter values.
self.r20 = 2.0
- self.pA = 0.9
+ self.pA = 0.95
self.dw = 0.5
self.kex = 100.0
@@ -86,7 +86,7 @@
frqs = sfrq * 2 * pi
# The phi_ex parameter value (pA * pB * delta_omega^2).
- phi_ex = pA * pB * dw**2
+ phi_ex = pA * pB * (dw / 1.e6)**2
# Convert phi_ex from ppm^2 to (rad/s)^2.
phi_ex_scaled = phi_ex * frqs**2
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61.py?rev=23483&r1=23482&r2=23483&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61.py
Tue May 27 19:11:26 2014
@@ -37,7 +37,7 @@
# The R1rho_prime parameter value (R1rho with no exchange).
self.r1rho_prime = 2.5
# Population of ground state.
- self.pA = 0.9
+ self.pA = 0.95
# The chemical exchange difference between states A and B in ppm.
self.dw = 0.5
self.kex = 1000.0
@@ -96,7 +96,7 @@
frqs = sfrq * 2 * pi
# The phi_ex parameter value (pA * pB * delta_omega^2).
- phi_ex = pA * pB * dw**2
+ phi_ex = pA * pB * (dw / 1.e6)**2
# Convert phi_ex from ppm^2 to (rad/s)^2.
phi_ex_scaled = phi_ex * frqs**2
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=23483&r1=23482&r2=23483&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
Tue May 27 19:11:26 2014
@@ -37,7 +37,7 @@
# The R1rho_prime parameter value (R1rho with no exchange).
self.r1rho_prime = 2.5
# Population of ground state.
- self.pA = 0.9
+ self.pA = 0.95
# The chemical exchange difference between states A and B in ppm.
self.dw = 0.5
self.kex = 1000.0
@@ -96,10 +96,10 @@
frqs = sfrq * 2 * pi
# Convert dw from ppm to rad/s.
- dw_frq = dw * frqs
+ dw_frq = dw * frqs / 1.e6
# The phi_ex parameter value (pA * pB * delta_omega^2).
- phi_ex = pA * pB * dw**2
+ phi_ex = pA * pB * (dw / 1.e6)**2
# Convert phi_ex from ppm^2 to (rad/s)^2.
phi_ex_scaled = phi_ex * frqs**2
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py?rev=23483&r1=23482&r2=23483&view=diff
==============================================================================
---
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
(original)
+++
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
Tue May 27 19:11:26 2014
@@ -35,7 +35,7 @@
# Default parameter values.
self.r20 = 2.0
- self.pA = 0.99
+ self.pA = 0.95
self.dw = 2.0
self.dwH = 0.5
self.kex = 1000.0
@@ -94,10 +94,10 @@
frqs = sfrq * 2 * pi
# Convert dw from ppm to rad/s.
- dw_frq = dw * frqs
+ dw_frq = dw * frqs / 1.e6
# Convert dwH from ppm to rad/s.
- dwH_frq = dwH * frqs
+ dwH_frq = dwH * frqs / 1.e6
# Return all values.
return k_AB, k_BA, pB, dw_frq, dwH_frq
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=23483&r1=23482&r2=23483&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
Tue May 27 19:11:26 2014
@@ -42,7 +42,7 @@
self.offset = -35040.3526693
# Population of ground state.
- self.pA = 0.9
+ self.pA = 0.95
# The chemical exchange difference between states A and B in ppm.
self.dw = 0.5
self.kex = 1000.0
@@ -111,7 +111,7 @@
frqs = sfrq * 2 * pi
# Convert dw from ppm to rad/s.
- dw_frq = dw * frqs
+ dw_frq = dw * frqs / 1.e6
# The R1rho spin-lock field strengths (in rad.s-1).
spin_lock_omega1 = (2. * pi * spin_lock_nu1)
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=23483&r1=23482&r2=23483&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 19:11:26 2014
@@ -37,7 +37,7 @@
# Default parameter values.
self.r20a = 2.0
self.r20b = 3.0
- self.pA = 0.99
+ self.pA = 0.95
self.dw = 2.0
self.kex = 1000.0
@@ -107,7 +107,7 @@
frqs = sfrq * 2 * pi
# Convert dw from ppm to rad/s.
- dw_frq = dw * frqs
+ dw_frq = dw * frqs / 1.e6
# Return all values.
return k_AB, k_BA, pB, dw_frq, M0
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py?rev=23483&r1=23482&r2=23483&view=diff
==============================================================================
---
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
(original)
+++
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
Tue May 27 19:11:26 2014
@@ -35,7 +35,7 @@
# Default parameter values.
self.r20 = 2.0
- self.pA = 0.9
+ self.pA = 0.95
self.dw = 0.5
self.kex = 100.0
@@ -44,15 +44,18 @@
self.tcp = array([0.1, 0.2, 0.3], float64)
self.num_cpmg = array([1, 2, 3], int16)
+ # The spin Larmor frequencies.
+ self.sfrq = 200. * 1E6
+
def calc_r2eff(self):
"""Calculate and check the R2eff values."""
# Parameter conversions.
- k_AB, k_BA = self.param_conversion(pA=self.pA, kex=self.kex)
+ k_AB, k_BA, dw_frq = self.param_conversion(pA=self.pA, kex=self.kex,
dw=self.dw, sfrq=self.sfrq)
# Calculate the R2eff values.
- R2eff = r2eff_ns_cpmg_2site_expanded(r20=self.r20, pA=self.pA,
dw=self.dw, k_AB=k_AB, k_BA=k_BA, relax_time=0.3, inv_relax_time=1/0.3,
tcp=self.tcp, num_points=self.num_points, num_cpmg=self.num_cpmg)
+ R2eff = r2eff_ns_cpmg_2site_expanded(r20=self.r20, pA=self.pA,
dw=dw_frq, k_AB=k_AB, k_BA=k_BA, relax_time=0.3, inv_relax_time=1/0.3,
tcp=self.tcp, num_points=self.num_points, num_cpmg=self.num_cpmg)
if self.kex >= 1.e5:
for i in range(self.num_points):
@@ -62,14 +65,18 @@
self.assertAlmostEqual(R2eff[i], self.r20)
- def param_conversion(self, pA=None, kex=None):
+ def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None):
"""Convert the parameters.
@keyword pA: The population of state A.
@type pA: float
@keyword kex: The rate of exchange.
@type kex: float
- @return: The parameters {k_AB, k_BA}.
+ @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 {k_AB, k_BA, dw_frq}.
@rtype: tuple of float
"""
@@ -80,8 +87,11 @@
k_BA = pA * kex
k_AB = pB * kex
+ # Convert dw from ppm to rad/s.
+ dw_frq = dw * frqs / 1.e6
+
# Return all values.
- return k_AB, k_BA
+ return k_AB, k_BA, dw_frq
def test_ns_cpmg_2site_expanded_no_rex1(self):
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tap03.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tap03.py?rev=23483&r1=23482&r2=23483&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tap03.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tap03.py
Tue May 27 19:11:26 2014
@@ -45,7 +45,7 @@
self.offset = -35040.3526693
# Population of ground state.
- self.pA = 0.9
+ self.pA = 0.95
# The chemical exchange difference between states A and B in ppm.
self.dw = 0.5
self.kex = 1000.0
@@ -114,7 +114,7 @@
frqs = sfrq * 2 * pi
# Convert dw from ppm to rad/s.
- dw_frq = dw * frqs
+ dw_frq = dw * frqs / 1.e6
# The R1rho spin-lock field strengths (in rad.s-1).
spin_lock_omega1 = (2. * pi * spin_lock_nu1)
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tp02.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tp02.py?rev=23483&r1=23482&r2=23483&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tp02.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tp02.py
Tue May 27 19:11:26 2014
@@ -45,7 +45,7 @@
self.offset = -35040.3526693
# Population of ground state.
- self.pA = 0.9
+ self.pA = 0.95
# The chemical exchange difference between states A and B in ppm.
self.dw = 0.5
self.kex = 1000.0
@@ -114,7 +114,7 @@
frqs = sfrq * 2 * pi
# Convert dw from ppm to rad/s.
- dw_frq = dw * frqs
+ dw_frq = dw * frqs / 1.e6
# The R1rho spin-lock field strengths (in rad.s-1).
spin_lock_omega1 = (2. * pi * spin_lock_nu1)
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py?rev=23483&r1=23482&r2=23483&view=diff
==============================================================================
---
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
(original)
+++
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tsmfk01.py
Tue May 27 19:11:26 2014
@@ -35,7 +35,7 @@
# Default parameter values.
self.r20a = 2.0
- self.pA = 0.99
+ self.pA = 0.95
self.dw = 2.0
self.kex = 1000.0
@@ -90,7 +90,7 @@
frqs = sfrq * 2 * pi
# Convert dw from ppm to rad/s.
- dw_frq = dw * frqs
+ dw_frq = dw * frqs / 1.e6
# Return all values.
return k_AB, k_BA, pB, dw_frq
r23483 - /branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/