Author: tlinnet
Date: Wed May 28 19:17:08 2014
New Revision: 23563
URL: http://svn.gna.org/viewcvs/relax?rev=23563&view=rev
Log:
Converting back to having back_calc as a function argument to model B14.
This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.
The problem is, that many numerical models can't be optimised further, since
they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put
into
a larger numpy array.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Modified:
branches/disp_speed/lib/dispersion/b14.py
branches/disp_speed/target_functions/relax_disp.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_b14.py
Modified: branches/disp_speed/lib/dispersion/b14.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/b14.py?rev=23563&r1=23562&r2=23563&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/b14.py (original)
+++ branches/disp_speed/lib/dispersion/b14.py Wed May 28 19:17:08 2014
@@ -115,7 +115,7 @@
# Repetitive calculations (to speed up calculations).
g_fact = 1/sqrt(2)
-def r2eff_B14(r20a=None, r20b=None, pA=None, pB=None, dw=None, kex=None,
k_AB=None, k_BA=None, ncyc=None, inv_tcpmg=None, tcp=None, num_points=None):
+def r2eff_B14(r20a=None, r20b=None, pA=None, pB=None, dw=None, kex=None,
k_AB=None, k_BA=None, ncyc=None, inv_tcpmg=None, tcp=None, back_calc=None,
num_points=None):
"""Calculate the R2eff values for the CR72 model.
See the module docstring for details.
@@ -143,13 +143,16 @@
@type inv_tcpmg: float
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
@type tcp: numpy rank-1 float array
- @keyword num_points: The number of points on the dispersion curve,
equal to the length of the cpmg_frqs.
+ @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 rank-1 float array
+ @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: int
"""
# Catch parameter values that will result in no exchange, returning flat
R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
if dw == 0.0 or pA == 1.0 or k_AB == 0.0:
- return array([r20a]*num_points)
+ back_calc[:] = array([r20a]*num_points)
+ return
# Repetitive calculations (to speed up calculations).
deltaR2 = r20a - r20b
@@ -200,7 +203,8 @@
# Catch math domain error of sinh(val > 710).
# This is when E0 > 710.
if max(E0) > 700:
- return array([r20a]*num_points)
+ back_calc[:] = array([r20a]*num_points)
+ return
# Derived from chemical shifts #E2 = complex(0,-2.0 * tcp * (F00I -
f11I)).
E2 = two_tcp * g4
@@ -248,4 +252,4 @@
if not isfinite(sum(R2eff)):
R2eff = array([1e100]*num_points)
- return R2eff
+ back_calc[:] = R2eff
Modified: branches/disp_speed/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/target_functions/relax_disp.py?rev=23563&r1=23562&r2=23563&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Wed May 28 19:17:08
2014
@@ -439,7 +439,7 @@
aliased_dw = dw_frq
# Back calculate the R2eff values.
- self.back_calc[ei][si][mi][0] =
r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, pB=pB,
dw=aliased_dw, kex=kex, k_AB=k_AB, k_BA=k_BA, ncyc=self.power[ei][mi],
inv_tcpmg=self.inv_relax_times[ei][mi], tcp=self.tau_cpmg[ei][mi],
num_points=self.num_disp_points[ei][si][mi][0])
+ r2eff_B14(r20a=R20A[r20_index], r20b=R20B[r20_index],
pA=pA, pB=pB, dw=aliased_dw, kex=kex, k_AB=k_AB, k_BA=k_BA,
ncyc=self.power[ei][mi], inv_tcpmg=self.inv_relax_times[ei][mi],
tcp=self.tau_cpmg[ei][mi], back_calc=self.back_calc[ei][si][mi][0],
num_points=self.num_disp_points[ei][si][mi][0])
# For all missing data points, set the back-calculated
value to the measured values so that it has no effect on the chi-squared
value.
for di in range(self.num_disp_points[ei][si][mi][0]):
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=23563&r1=23562&r2=23563&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
Wed May 28 19:17:08 2014
@@ -47,6 +47,7 @@
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
@@ -59,11 +60,11 @@
k_AB, k_BA, pB, dw_frq = 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_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, back_calc=self.R2eff,
num_points=self.num_points)
# 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):
r23563 - in /branches/disp_speed: lib/dispersion/ target_functions/ test_suite/unit_tests/_lib/_dispersion/