Author: tlinnet
Date: Fri Jun 13 11:47:38 2014
New Revision: 23919
URL: http://svn.gna.org/viewcvs/relax?rev=23919&view=rev
Log:
Removed number of points, pB, k_AB, k_BA to be send to lib function of model
B14.
Number of points are not used anymore.
pB is calculated in lib function insted.
k_AB, and k_BA are calculated in lib functions instead.
Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/lib/dispersion/b14.py
branches/disp_spin_speed/target_functions/relax_disp.py
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py
Modified: branches/disp_spin_speed/lib/dispersion/b14.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/b14.py?rev=23919&r1=23918&r2=23919&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/b14.py (original)
+++ branches/disp_spin_speed/lib/dispersion/b14.py Fri Jun 13 11:47:38
2014
@@ -116,7 +116,7 @@
# Repetitive calculations (to speed up calculations).
g_fact = 1/sqrt(2)
-def r2eff_B14(r20a=None, r20b=None, pA=None, pB=None, dw=None, dw_orig=None,
kex=None, k_AB=None, k_BA=None, ncyc=None, inv_tcpmg=None, tcp=None,
back_calc=None, num_points=None):
+def r2eff_B14(r20a=None, r20b=None, pA=None, dw=None, dw_orig=None,
kex=None, ncyc=None, inv_tcpmg=None, tcp=None, back_calc=None):
"""Calculate the R2eff values for the CR72 model.
See the module docstring for details.
@@ -128,18 +128,12 @@
@type r20b: numpy float array of rank [NE][NS][[NM][NO][ND]
@keyword pA: The population of state A.
@type pA: float
- @keyword pB: The population of state B.
- @type pB: float
@keyword dw: The chemical exchange difference between states
A and B in rad/s.
@type dw: numpy float array of rank [NE][NS][[NM][NO][ND]
@keyword dw_orig: The chemical exchange difference between states
A and B in ppm. This is only for faster checking of zero value, which result
in no exchange.
@type dw_orig: numpy float array of rank-1
@keyword kex: The kex parameter value (the exchange rate in
rad/s).
@type kex: float
- @keyword k_AB: The rate of exchange from site A to B (rad/s).
- @type k_AB: float
- @keyword k_BA: The rate of exchange from site B to A (rad/s).
- @type k_BA: float
@keyword ncyc: The matrix exponential power array. The number
of CPMG blocks.
@type ncyc: numpy int16 array of rank [NE][NS][[NM][NO][ND]
@keyword inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
@@ -148,8 +142,6 @@
@type tcp: numpy float array of rank [NE][NS][[NM][NO][ND]
@keyword back_calc: The array for holding the back calculated R2eff
values. Each element corresponds to one of the CPMG nu1 frequencies.
@type back_calc: numpy float array of rank [NE][NS][[NM][NO][ND]
- @keyword num_points: The number of points on the dispersion curve,
equal to the length of the cpmg_frqs and back_calc arguments.
- @type num_points: numpy int array of rank [NE][NS][[NM][NO][ND]
"""
# Flag to tell if values should be replaced if math function is violated.
@@ -168,6 +160,11 @@
if min(fabs(dw_orig)) == 0.0:
t_dw_zero = True
mask_dw_zero = masked_where(dw == 0.0, dw)
+
+ # Parameter conversions.
+ pB = 1.0 - pA
+ k_BA = pA * kex
+ k_AB = pB * kex
# Repetitive calculations (to speed up calculations).
deltaR2 = r20a - r20b
Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=23919&r1=23918&r2=23919&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Fri Jun 13
11:47:38 2014
@@ -542,11 +542,6 @@
@rtype: float
"""
- # Once off parameter conversions.
- pB = 1.0 - pA
- k_BA = pA * kex
- k_AB = pB * kex
-
# Convert dw from ppm to rad/s. Use the out argument, to pass
directly to structure.
multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs_a, out=self.dw_struct )
@@ -555,7 +550,7 @@
self.r20b_struct[:] = multiply.outer( R20B.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
# Back calculate the R2eff values.
- r2eff_B14(r20a=self.r20a_struct, r20b=self.r20b_struct, pA=pA,
pB=pB, dw=self.dw_struct, dw_orig=dw, kex=kex, k_AB=k_AB, k_BA=k_BA,
ncyc=self.power_a, inv_tcpmg=self.inv_relax_times_a, tcp=self.tau_cpmg_a,
back_calc=self.back_calc_a, num_points=self.num_disp_points_a)
+ r2eff_B14(r20a=self.r20a_struct, r20b=self.r20b_struct, pA=pA,
dw=self.dw_struct, dw_orig=dw, kex=kex, ncyc=self.power_a,
inv_tcpmg=self.inv_relax_times_a, tcp=self.tau_cpmg_a,
back_calc=self.back_calc_a)
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc_a = self.back_calc_a*self.disp_struct
Modified:
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py?rev=23919&r1=23918&r2=23919&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py
(original)
+++
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py
Fri Jun 13 11:47:38 2014
@@ -63,7 +63,7 @@
a = ones([self.num_points])
# Calculate the R2eff values.
- r2eff_B14(r20a=self.r20a*a, r20b=self.r20b*a, pA=self.pA, pB=pB,
dw=dw_frq*a, dw_orig=dw_frq*a, kex=self.kex, k_AB=k_AB, k_BA=k_BA,
ncyc=self.ncyc, inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg,
back_calc=self.R2eff, num_points=self.num_points)
+ r2eff_B14(r20a=self.r20a*a, r20b=self.r20b*a, pA=self.pA,
dw=dw_frq*a, dw_orig=dw_frq*a, kex=self.kex, ncyc=self.ncyc,
inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg, back_calc=self.R2eff)
# Check all R2eff values.
for i in range(self.num_points):
r23919 - in /branches/disp_spin_speed: lib/dispersion/ target_functions/ test_suite/unit_tests/_lib/_dispersion/