Author: tlinnet
Date: Thu May 29 12:24:25 2014
New Revision: 23586
URL: http://svn.gna.org/viewcvs/relax?rev=23586&view=rev
Log:
Converting back to having back_calc as a function argument to model TAP03.
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/tap03.py
branches/disp_speed/target_functions/relax_disp.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_tap03.py
Modified: branches/disp_speed/lib/dispersion/tap03.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/tap03.py?rev=23586&r1=23585&r2=23586&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/tap03.py (original)
+++ branches/disp_speed/lib/dispersion/tap03.py Thu May 29 12:24:25 2014
@@ -63,7 +63,7 @@
from numpy import arctan2, array, isfinite, min, sin, sqrt, sum
-def r1rho_TAP03(r1rho_prime=None, omega=None, offset=None, pA=None, pB=None,
dw=None, kex=None, R1=0.0, spin_lock_fields=None, spin_lock_fields2=None,
num_points=None):
+def r1rho_TAP03(r1rho_prime=None, omega=None, offset=None, pA=None, pB=None,
dw=None, kex=None, R1=0.0, spin_lock_fields=None, spin_lock_fields2=None,
back_calc=None, num_points=None):
"""Calculate the R1rho' values for the TP02 model.
See the module docstring for details. This is the Trott, Abergel and
Palmer (2003) equation.
@@ -89,7 +89,9 @@
@type spin_lock_fields: numpy rank-1 float array
@keyword spin_lock_fields2: The R1rho spin-lock field strengths squared
(in rad^2.s^-2). This is for speed.
@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 offset and 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
"""
@@ -116,7 +118,8 @@
# Bad gamma.
if min(gamma) < 0.0:
- return array([1e100]*num_points)
+ back_calc[:] = array([1e100]*num_points)
+ return
# Special omega values.
waeff2 = gamma*spin_lock_fields2 + da**2 # Effective field at A.
@@ -136,7 +139,8 @@
# Catch zeros (to avoid pointless mathematical operations).
# This will result in no exchange, returning flat lines.
if numer == 0.0:
- return R1_cos_theta2 + R1rho_prime_sin_theta2
+ back_calc[:] = R1_cos_theta2 + R1rho_prime_sin_theta2
+ return
# Denominator.
denom = waeff2*wbeff2/weff2 + kex2 - 2.0*hat_sin_theta2*phi_ex + (1.0 -
gamma)*spin_lock_fields2
@@ -149,4 +153,4 @@
if not isfinite(sum(R1rho)):
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=23586&r1=23585&r2=23586&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Thu May 29 12:24:25
2014
@@ -1823,7 +1823,7 @@
# Loop over the offsets.
for oi in range(self.num_offsets[0][si][mi]):
# Back calculate the R1rho values.
- self.back_calc[0][si][mi][oi] =
r1rho_TAP03(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[0][si][mi], offset=self.offset[0][si][mi][oi],
pA=pA, pB=pB, dw=dw_frq, kex=kex, R1=self.r1[si, mi],
spin_lock_fields=self.spin_lock_omega1[0][mi][oi],
spin_lock_fields2=self.spin_lock_omega1_squared[0][mi][oi],
num_points=self.num_disp_points[0][si][mi][oi])
+ r1rho_TAP03(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[0][si][mi], offset=self.offset[0][si][mi][oi],
pA=pA, pB=pB, dw=dw_frq, kex=kex, R1=self.r1[si, mi],
spin_lock_fields=self.spin_lock_omega1[0][mi][oi],
spin_lock_fields2=self.spin_lock_omega1_squared[0][mi][oi],
back_calc=self.back_calc[0][si][mi][oi],
num_points=self.num_disp_points[0][si][mi][oi])
# 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][oi]):
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=23586&r1=23585&r2=23586&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
Thu May 29 12:24:25 2014
@@ -59,6 +59,7 @@
# Required data structures.
self.num_points = 11
+ self.R1rho = zeros(self.num_points, float64)
def calc_r1rho(self):
@@ -68,7 +69,7 @@
pB, dw_frq, spin_lock_omega1, 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_TAP03(r1rho_prime=self.r1rho_prime, omega=self.omega,
offset=self.offset, pA=self.pA, pB=pB, dw=dw_frq, kex=self.kex, R1=self.r1,
spin_lock_fields=spin_lock_omega1,
spin_lock_fields2=spin_lock_omega1_squared, num_points=self.num_points)
+ r1rho_TAP03(r1rho_prime=self.r1rho_prime, omega=self.omega,
offset=self.offset, pA=self.pA, pB=pB, dw=dw_frq, kex=self.kex, R1=self.r1,
spin_lock_fields=spin_lock_omega1,
spin_lock_fields2=spin_lock_omega1_squared, back_calc=self.R1rho,
num_points=self.num_points)
# Compare to function value.
# Larmor frequency [s^-1].
@@ -89,7 +90,7 @@
# Check all R1rho values.
for i in range(self.num_points):
- self.assertAlmostEqual(R1rho[i], r1rho_no_rex[i])
+ self.assertAlmostEqual(self.R1rho[i], r1rho_no_rex[i])
def param_conversion(self, pA=None, dw=None, sfrq=None,
spin_lock_nu1=None):
r23586 - in /branches/disp_speed: lib/dispersion/ target_functions/ test_suite/unit_tests/_lib/_dispersion/