Author: tlinnet
Date: Thu May 29 11:35:35 2014
New Revision: 23582
URL: http://svn.gna.org/viewcvs/relax?rev=23582&view=rev
Log:
Converting back to having back_calc as a function argument to model M61b:
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/m61b.py
branches/disp_speed/target_functions/relax_disp.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_m61b.py
Modified: branches/disp_speed/lib/dispersion/m61b.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/m61b.py?rev=23582&r1=23581&r2=23582&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/m61b.py (original)
+++ branches/disp_speed/lib/dispersion/m61b.py Thu May 29 11:35:35 2014
@@ -62,7 +62,7 @@
# Python module imports.
from numpy import abs, array, isfinite, min, sum
-def r1rho_M61b(r1rho_prime=None, pA=None, dw=None, kex=None,
spin_lock_fields2=None, num_points=None):
+def r1rho_M61b(r1rho_prime=None, pA=None, dw=None, kex=None,
spin_lock_fields2=None, back_calc=None, num_points=None):
"""Calculate the R1rho values for the M61 skew model.
See the module docstring for details.
@@ -78,7 +78,9 @@
@type kex: float
@keyword spin_lock_fields2: The R1rho spin-lock field strengths squared
(in rad^2.s^-2).
@type spin_lock_fields2: numpy rank-1 float array
- @keyword num_points: The number of points on the dispersion
curve, equal to the length of the spin_lock_fields.
+ @keyword back_calc: The array for holding the back calculated
R1rho values. Each element corresponds to the combination of spin lock field.
+ @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 spin_lock_fields and back_calc arguments.
@type num_points: int
"""
@@ -95,7 +97,8 @@
# Catch zeros (to avoid pointless mathematical operations).
# This will result in no exchange, returning flat lines.
if numer == 0.0:
- return array([r1rho_prime]*num_points)
+ back_calc[:] = array([r1rho_prime]*num_points)
+ return
# Denominator.
denom = kex2_pA2dw2 + spin_lock_fields2
@@ -103,7 +106,8 @@
# Catch math domain error of dividing with 0.
# This is when denom=0.
if min(abs(denom)) == 0:
- return array([1e100]*num_points)
+ back_calc[:] = array([1e100]*num_points)
+ return
# R1rho calculation.
@@ -112,6 +116,6 @@
# Catch errors, taking a sum over array is the fastest way to check for
# +/- inf (infinity) and nan (not a number).
if not isfinite(sum(R1rho)):
- return array([1e100]*num_points)
+ R1rho = array([1e100]*num_points)
- return R1rho
+ back_calc[:] = R1rho
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=23582&r1=23581&r2=23582&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Thu May 29 11:35:35
2014
@@ -1210,7 +1210,7 @@
dw_frq = dw[si] * self.frqs[0][si][mi]
# Back calculate the R1rho values.
- self.back_calc[0][si][mi][0] =
r1rho_M61b(r1rho_prime=R20[r20_index], pA=pA, dw=dw_frq, kex=kex,
spin_lock_fields2=self.spin_lock_omega1_squared[0][mi][0],
num_points=self.num_disp_points[0][si][mi][0])
+ r1rho_M61b(r1rho_prime=R20[r20_index], pA=pA, dw=dw_frq,
kex=kex, spin_lock_fields2=self.spin_lock_omega1_squared[0][mi][0],
back_calc=self.back_calc[0][si][mi][0],
num_points=self.num_disp_points[0][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[0][si][mi][0]):
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=23582&r1=23581&r2=23582&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
Thu May 29 11:35:35 2014
@@ -53,6 +53,7 @@
# Required data structures.
self.num_points = 11
+ self.R1rho = zeros(self.num_points, float64)
def calc_r1rho(self):
@@ -62,16 +63,16 @@
phi_ex_scaled, dw_frq, spin_lock_omega1_squared =
self.param_conversion(pA=self.pA, dw=self.dw, sfrq=self.sfrq,
spin_lock_nu1=self.spin_lock_nu1)
# Calculate the R1rho values.
- R1rho = r1rho_M61b(r1rho_prime=self.r1rho_prime, pA=self.pA,
dw=dw_frq, kex=self.kex, spin_lock_fields2=spin_lock_omega1_squared,
num_points=self.num_points)
+ R1rho = r1rho_M61b(r1rho_prime=self.r1rho_prime, pA=self.pA,
dw=dw_frq, kex=self.kex, spin_lock_fields2=spin_lock_omega1_squared,
back_calc=self.R1rho, num_points=self.num_points)
# Check all R1rho values.
if self.kex > 1.e5:
for i in range(self.num_points):
- self.assertAlmostEqual(R1rho[i], self.r1rho_prime, 2)
+ self.assertAlmostEqual(self.R1rho[i], self.r1rho_prime, 2)
else:
for i in range(self.num_points):
- self.assertAlmostEqual(R1rho[i], self.r1rho_prime)
+ self.assertAlmostEqual(self.R1rho[i], self.r1rho_prime)
def param_conversion(self, pA=None, dw=None, sfrq=None,
spin_lock_nu1=None):
r23582 - in /branches/disp_speed: lib/dispersion/ target_functions/ test_suite/unit_tests/_lib/_dispersion/